Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

PubMed Central

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

2017-01-01

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems. PMID:28262753

Patterns and drivers of soil microbial communities in temperate grasslands on the Mongolian plateau

NASA Astrophysics Data System (ADS)

Yang, Y.; Hu, H.; Hao, B.; Liu, Y.; Chen, Y.; Ma, W.

2016-12-01

Soil microorganisms play key roles in regulating many important ecosystem processes. However, our understanding of the patterns and drivers of soil microbial communities at the regional scale remains limited. In this study, on the basis of phospholipid fatty acid (PLFA) analysis, we investigated large-scale patterns and drivers of soil microbial communities using data from 78 sites between two depths (0-10 cm and 10-20 cm) within three major grassland types (desert steppe, typical steppe, and meadow steppe) on the Mongolian Plateau. Our findings demonstrated that, at the regional scale, the total soil microbial biomass, fungal biomass, bacterial biomass, and actinomycete biomass in Inner Mongolian temperate grasslands were all positively associated with mean annual precipitation (MAP), soil organic carbon (SOC), soil total nitrogen (TN), C:N ratio, plant aboveground biomass (AGB), and plant species richness (SR), but negatively correlated with mean annual temperature (MAT), soil bulk density (BD), and soil pH in both depths, except actinomycete biomass with MAP and BD in 10-20 cm. A stepwise regression analysis revealed that soil microbial community variations in Inner Mongolian temperate grasslands were mainly explained by C : N ratio in 0-10 cm, but by SR (total soil microbial biomass, fungal biomass, and actinomycete biomass) and MAT (bacterial biomass) in 10-20 cm. Our findings strongly indicate that the dominant drivers of spatial variations in soil microbial communities between 0-10 cm and 10-20 cm in the Inner Mongolia grasslands are significantly different, with edaphic factors (e.g., C: N ratio) in 0-10 cm but climatic (e.g, MAT) and/or biotic (e.g, SR) in 10-20 cm.

Effects of application of corn straw on soil microbial community structure during the maize growing season.

PubMed

Lu, Ping; Lin, Yin-Hua; Yang, Zhong-Qi; Xu, Yan-Peng; Tan, Fei; Jia, Xu-Dong; Wang, Miao; Xu, De-Rong; Wang, Xi-Zhuo

2015-01-01

This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p < 0.05). We also found a high ratio of fungal-to-bacterial PLFAs in black soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p < 0.05). These results indicated that the application of corn straw positively influences soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Petroleum-degrading microbial numbers in rhizosphere and non-rhizosphere crude oil-contaminated soil.

PubMed

Kirkpatrick, W D; White, P M; Wolf, D C; Thoma, G J; Reynolds, C M

2008-01-01

Phytoremediation can be a cost-effective and environmentally acceptable method to clean up crude oil-contaminated soils in situ. Our research objective was to determine the effects of nitrogen (N) additions and plant growth on the number of total hydrocarbon (TH)-, alkane-, and polycyclic aromatic hydrocarbon (PAH)-degrading microorganisms in weathered crude oil-contaminated soil. A warm-season grass, sudangrass (Sorghum sudanense (Piper) Stapf), was grown for 7 wk in soil with a total petroleum hydrocarbon (TPH) level of 16.6 g TPH/kg soil. Nitrogen was added based upon TPH-C:added total N (TPH-C:TN) ratios ranging from 44:1 to 11:1. Unvegetated and unamended controls were also evaluated. The TH-, alkane-, and PAH-degrading microbial numbers per gram of dry soil were enumerated from rhizosphere and non-rhizosphere soil for vegetated pots and non-rhizosphere soil populations were enumerated from non-vegetated pots. Total petroleum-degrading microbial numbers were also calculated for each pot. The TH-, alkane-, and PAH-degrading microbial numbers per gram of dry soil in the sudangrass rhizosphere were 3.4, 2.6, and 4.8 times larger, respectively, than those in non-rhizosphere soil across all N rates. The presence of sudangrass resulted in significantly more TH-degrading microorganisms per pot when grown in soil with a TPH-C:TN ratio of 11:1 as compared to the control. Increased plant root growth in a crude oil-contaminated soil and a concomitant increase in petroleum-degrading microbial numbers in the rhizosphere have the potential to enhance phytoremediation.

Influence of different forms of acidities on soil microbiological properties and enzyme activities at an acid mine drainage contaminated site.

PubMed

Sahoo, Prafulla Kumar; Bhattacharyya, Pradip; Tripathy, Subhasish; Equeenuddin, Sk Md; Panigrahi, M K

2010-07-15

Assessment of microbial parameters, viz. microbial biomass, fluorescence diacetate, microbial respiration, acid phosphatase, beta-glucosidase and urease with respect to acidity helps in evaluating the quality of soils. This study was conducted to investigate the effects of different forms of acidities on soil microbial parameters in an acid mine drainage contaminated site around coal deposits in Jainta Hills of India. Total potential and exchangeable acidity, extractable and exchangeable aluminium were significantly higher in contaminated soil compared to the baseline (p<0.01). Different forms of acidity were significantly and positively correlated with each other (p<0.05). Further, all microbial properties were positively and significantly correlated with organic carbon and clay (p<0.05). The ratios of microbial parameters with organic carbon were negatively correlated with different forms of acidity. Principal component analysis and cluster analyses showed that the microbial activities are not directly influenced by the total potential acidity and extractable aluminium. Though acid mine drainage affected soils had higher microbial biomass and activities due to higher organic matter content than those of the baseline soils, the ratios of microbial parameters/organic carbon indicated suppression of microbial growth and activities due to acidity stress. 2010 Elsevier B.V. All rights reserved.

Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

NASA Astrophysics Data System (ADS)

Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

2014-05-01

Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community development which was soil horizon specific and its effects on soil microbial activity may impact on nutrient cycling.

Soil mineral assemblage influences on microbial communities and carbon cycling under fresh organic matter input

NASA Astrophysics Data System (ADS)

Finley, B. K.; Schwartz, E.; Koch, B.; Dijkstra, P.; Hungate, B. A.

2017-12-01

The interactions between soil mineral assemblages and microbial communities are important drivers of soil organic carbon (SOC) cycling and storage, although the mechanisms driving these interactions remain unclear. There is increasing evidence supporting the importance of associations with poorly crystalline, short-range order (SRO) minerals in protection of SOC from microbial utilization. However, how the microbial processing of SRO-associated SOC may be influenced by fresh organic matter inputs (priming) remains poorly understood. The influence on SRO minerals on soil microbial community dynamics is uncertain as well. Therefore, we conducted a priming incubation by adding either a simulated root exudate mixture or conifer needle litter to three soils from a mixed-conifer ecosystem. The parent material of the soils were andesite, basalt, and granite and decreased in SRO mineral content, respectively. We also conducted a parallel quantitative stable isotope probing incubation by adding 18O-labelled water to the soils to isotopically label microbial DNA in situ. This allowed us to characterize and identify the active bacterial and archaeal community and taxon-specific growth under fresh organic matter input. While the granite soil (lowest SRO content), had the largest total mineralization, the least priming occurred. The andesite and basalt soils (greater SRO content) had lower total respiration, but greater priming. Across all treatments, the granite soil, while having the lowest species richness of the entire community (249 taxa, both active and inactive), had a larger active community (90%) in response to new SOC input. The andesite and basalt soils, while having greater total species richness of the entire community at 333 and 325 taxa, respectively, had fewer active taxa in response to new C compared to the granite soil (30% and 49% taxa, respectively). These findings suggest that the soil mineral assemblage is an important driver on SOC cycling under fresh organic matter inputs, as well as on the activity and diversity of the microbial community. Often, microbial diversity is associated with function. Our results suggest that the soil environment, in this case SRO mineral content, may be more important on SOC cycling and storage than microbial diversity alone.

Stability of soil organic carbon changes in successive rotations of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) plantations.

PubMed

Zhang, Jian; Wang, Silong; Feng, Zongwei; Wang, Qingkui

2009-01-01

The importance of soil organic carbon (SOC) under forests in the global carbon cycle depends on the stability of the soil carbon and its availability to soil microbial biomass. We investigated the effects of successive rotations of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) plantations on the stability of SOC and its availability to microbes by adopting the two-step hydrolysis with H2SO4 and density fractionation. The results showed that successive rotations of Chinese fir decreased the quantity of total SOC, recalcitrant fraction, and carbohydrates in Labile Pool I (LP I), and microbial properties evidently, especially at 0-10 cm horizon. However, cellulose included in Labile Pool II (LP II) and the cellulose/total carbohydrates ratio increased in successive rotations of Chinese fir. The non-cellulose of carbohydrates included in LP I maybe highly available to soil microbial biomass. Hence the availability of SOC to microbial biomass declined over the successive rotations. Although there was no significant change in recalcitrance of SOC over the successive rotations of Chinese fir, the percentage of heavy fraction to total SOC increased, suggesting that the degree of physical protection for SOC increased and SOC became more stable over the successive rotations. The degradation of SOC quality in successive rotation soils may be attributed to worse environmental conditions resulted from disturbance that related to "slash and burn" site preparation. Being highly correlated with soil microbial properties, the cellulose/total carbohydrates ratio as an effective indicator of changes in availability of SOC to microbial biomass brought by management practices in forest soils.

Status of microbial diversity in agroforestry systems in Tamil Nadu, India.

PubMed

Radhakrishnan, Srinivasan; Varadharajan, Mohan

2016-06-01

Soil is a complex and dynamic biological system. Agroforestry systems are considered to be an alternative land use option to help and prevent soil degradation, improve soil fertility, microbial diversity, and organic matter status. An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The present study deals with the status of microbial diversity in agroforestry systems in Tamil Nadu. Eight soil samples were collected from different fields in agroforestry systems in Cuddalore, Villupuram, Tiruvanamalai, and Erode districts, Tamil Nadu. The number of microorganisms and physico-chemical parameters of soils were quantified. Among different microbial population, the bacterial population was recorded maximum (64%), followed by actinomycetes (23%) and fungi (13%) in different samples screened. It is interesting to note that the microbial population was positively correlated with the physico-chemical properties of different soil samples screened. Total bacterial count had positive correlation with soil organic carbon (C), moisture content, pH, nitrogen (N), and micronutrients such as Iron (Fe), copper (Cu), and zinc (Zn). Similarly, the total actinomycete count also showed positive correlations with bulk density, moisture content, pH, C, N, phosphorus (P), potassium (K), calcium (Ca), copper (Cu), magnesium (Mg), manganese (Mn), and zinc (Zn). It was also noticed that the soil organic matter, vegetation, and soil nutrients altered the microbial community under agroforestry systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Influence of Different Straws Returning with Landfill on Soil Microbial Community Structure Under Dry and Water Farming].

PubMed

Lan, Mu-ling; Gao, Ming

2015-11-01

Based on rice, wheat, corn straw and rape, broad bean green stalk as the research object, using phospholipid fatty acid (PLFA) method, combining principal component analysis method to study the soil microbial quantity, distribution of flora, community structure characteristics under dry and water farming as two different cultivated land use types. The PLFA analysis results showed that: under dry farming, total PLFA quantity ranged 8.35-25.15 nmol x g(-1), showed rape > broad bean > corn > rice > wheat, rape and broad bean significantly increased total PLFA quantity by 1.18 and 1.08 times compared to the treatment without straw; PLFA quantity of bacterial flora in treatments with straws was higher than that without straw, and fungal biomass was significantly increased, so was the species richness of microbial community. Under water faming, the treatments of different straws returning with landfill have improved the PLFA quantity of total soil microbial and flora comparing with the treatment without straw, fungi significantly increased, and species richness of microbial communities value also increased significantly. Total PLFA quantity ranged 4.04-22.19 nmol x g(-1), showed rice > corn > wheat > broad bean > rape, which in rape and broad bean treatments were lower than the treatment without straw; fungal PLFA amount in 5 kinds of straw except broad bean treatment was significantly higher than that of the treatment without straw, bacteria and total PLFA quantity in broad bean processing were significantly lower than those of other treatments, actinomycetes, G+, G- had no significant difference between all treatments; rice, wheat, corn, rape could significantly increase the soil microbial species richness index and dominance index under water faming. The results of principal component analysis showed that broad bean green stalk had the greatest impact on the microbial community structure in the dry soil, rape green stalk and wheat straw had the biggest influence on soil microbial community structure in water soil.

Soil fertility and plant diversity enhance microbial performance in metal-polluted soils.

PubMed

Stefanowicz, Anna M; Kapusta, Paweł; Szarek-Łukaszewska, Grażyna; Grodzińska, Krystyna; Niklińska, Maria; Vogt, Rolf D

2012-11-15

This study examined the effects of soil physicochemical properties (including heavy metal pollution) and vegetation parameters on soil basal respiration, microbial biomass, and the activity and functional richness of culturable soil bacteria and fungi. In a zinc and lead mining area (S Poland), 49 sites were selected to represent all common plant communities and comprise the area's diverse soil types. Numerous variables describing habitat properties were reduced by PCA to 7 independent factors, mainly representing subsoil type (metal-rich mining waste vs. sand), soil fertility (exchangeable Ca, Mg and K, total C and N, organic C), plant species richness, phosphorus content, water-soluble heavy metals (Zn, Cd and Pb), clay content and plant functional diversity (based on graminoids, legumes and non-leguminous forbs). Multiple regression analysis including these factors explained much of the variation in most microbial parameters; in the case of microbial respiration and biomass, it was 86% and 71%, respectively. The activity of soil microbes was positively affected mainly by soil fertility and, apparently, by the presence of mining waste in the subsoil. The mining waste contained vast amounts of trace metals (total Zn, Cd and Pb), but it promoted microbial performance due to its inherently high content of macronutrients (total Ca, Mg, K and C). Plant species richness had a relatively strong positive effect on all microbial parameters, except for the fungal component. In contrast, plant functional diversity was practically negligible in its effect on microbes. Other explanatory variables had only a minor positive effect (clay content) or no significant influence (phosphorus content) on microbial communities. The main conclusion from this study is that high nutrient availability and plant species richness positively affected the soil microbes and that this apparently counteracted the toxic effects of metal contamination. Copyright © 2012 Elsevier B.V. All rights reserved.

Soil microbial community response to land use change in an agricultural landscape of western Kenya.

PubMed

Bossio, D A; Girvan, M S; Verchot, L; Bullimore, J; Borelli, T; Albrecht, A; Scow, K M; Ball, A S; Pretty, J N; Osborn, A M

2005-01-01

Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.

Respiration-to-DNA ratio reflects physiological state of microorganisms in root-free and rhizosphere soil

NASA Astrophysics Data System (ADS)

Blagodatskaya, E.; Blagodatsky, S.; Kuzyakov, Y.

2009-04-01

The double-stranded DNA (dsDNA) content in soil can serve as a measure of microbial biomass under near steady-state conditions and quantitatively reflect the exponential microbial growth initiated by substrate addition. The yield of respired CO2 per microbial biomass unit (expressed as DNA content) could be a valuable physiological indicator reflecting state of soil microbial community. Therefore, investigations combining both analyses of DNA content and respiration of soil microorganisms under steady-state and during periods of rapid growth are needed. We studied the relationship between CO2 evolution and microbial dsDNA content in native and glucose-amended samples of root-free and rhizosphere soil under Beta vulgaris (Cambisol, loamy sand from the field experiment of the Institute of Agroecology FAL, Braunschweig, Germany). Quantity of dsDNA was determined by direct DNA isolation from soil with mechanic and enzymatic disruption of microbial cell walls with following spectrofluorimetric detection with PicoGreen (Blagodatskaya et al., 2003). Microbial biomass and the kinetic parameters of microbial growth were estimated by dynamics of the CO2 emission from soil amended with glucose and nutrients (Blagodatsky et al., 2000). The CO2 production rate was measured hourly at 22оС using an automated infrared-gas analyzer system. The overall increase in microbial biomass, DNA content, maximal specific growth rate and therefore, in the fraction of microorganisms with r-strategy were observed in rhizosphere as compared to bulk soil. The rhizosphere effect for microbial respiration, biomass and specific growth rate was more pronounced for plots with half-rate of N fertilizer compared to full N addition. The DNA content was significantly lower in bulk compared to rhizosphere soil both before and during microbial growth initiated by glucose amendment. Addition of glucose to the soil strongly increased the amount of CO2 respired per DNA unit. Without substrate addition the VCO2-to-total DNA ratios were lower than 0.1 µg CO2-C µg-1 total DNA h-1 whereas during exponential microbial growth these values increased consistently and exceeded 1 µg CO2-C µg-1 DNA h-1. Thus, the VCO2-to-total DNA ratio strongly changes along with the physiological state of soil microorganisms and can be used as valuable physiological parameter. In growing microorganisms the quantity of CO2 evolved per unit of newly formed DNA was identical in rhizosphere and root free soil and averaged for 13.5 ± 1.1 µg CO2-C µg-1 newly formed DNA. The CO2 yield per unit of newly formed DNA allows the estimation of microbial growth efficiency and validation of specific growth rates obtained during kinetic analysis of respiration curves. The study was supported by European Commission (Marie Curie IIF program, project MICROSOM) and by Alexander von Humboldt Foundation. References: Blagodatskaya EV, Blagodatskii SA, Anderson TH. 2003. Quantitative Isolation of Microbial DNA from Different Types of Soils of Natural and Agricultural Ecosystems. Microbiology 72(6):744-749. Blagodatsky SA, Heinemeyer O, Richter J. 2000. Estimating the active and total soil microbial biomass by kinetic respiration analysis. Biology and Fertility of Soils 32(1):73-81.

Extractable nitrogen and microbial community structure respond to grassland restoration regardless of historical context and soil composition

PubMed Central

Dickens, Sara Jo M.; Allen, Edith B.; Santiago, Louis S.; Crowley, David

2015-01-01

Grasslands have a long history of invasion by exotic annuals, which may alter microbial communities and nutrient cycling through changes in litter quality and biomass turnover rates. We compared plant community composition, soil chemical and microbial community composition, potential soil respiration and nitrogen (N) turnover rates between invaded and restored plots in inland and coastal grasslands. Restoration increased microbial biomass and fungal : bacterial (F : B) ratios, but sampling season had a greater influence on the F : B ratio than did restoration. Microbial community composition assessed by phospholipid fatty acid was altered by restoration, but also varied by season and by site. Total soil carbon (C) and N and potential soil respiration did not differ between treatments, but N mineralization decreased while extractable nitrate and nitrification and N immobilization rate increased in restored compared with unrestored sites. The differences in soil chemistry and microbial community composition between unrestored and restored sites indicate that these soils are responsive, and therefore not resistant to feedbacks caused by changes in vegetation type. The resilience, or recovery, of these soils is difficult to assess in the absence of uninvaded control grasslands. However, the rapid changes in microbial and N cycling characteristics following removal of invasives in both grassland sites suggest that the soils are resilient to invasion. The lack of change in total C and N pools may provide a buffer that promotes resilience of labile pools and microbial community structure. PMID:25555522

Effects of Praxelis clematidea invasion on soil nitrogen fractions and transformation rates in a tropical savanna.

PubMed

Wei, Hui; Xu, Jialin; Quan, Guoming; Zhang, Jiaen; Qin, Zhong

2017-02-01

Plant invasion has been reported to affect a mass of soil ecological processes and functions, although invasion effects are often context-, species- and ecosystem- specific. This study was conducted to explore potential impacts of Praxelis clematidea invasion on contents of total and available soil nitrogen (N) and microbial N transformations in a tropical savanna. Soil samples were collected from the surface and sub-surface layers in plots with non-, slight, or severe P. clematidea invasion in Hainan Province of southern China, which remains less studied, and analyzed for contents of the total and available N fractions and microbial N transformations. Results showed that total N content significantly increased in the surface soil but trended to decrease in the sub-surface soil in the invaded plots relative to the non-invaded control. Slight invasion significantly increased soil alkali-hydrolysable N content in the two soil layers. Soil net N mineralization rate was not significantly changed in both the soil layers, although soil microbial biomass N was significantly higher in plots with severe invasion than the control. There was no significant difference in content of soil N fractions between plots with slight and severe invasion. Our results suggest that invasion of P. clematidea promotes soil N accumulation in the surface soil layer, which is associated with increased microbial biomass N. However, the invasion-induced ecological impacts did not increase with further invasion. Significantly higher microbial biomass N was maintained in plots with severe invasion, implying that severe P. clematidea invasion may accelerate nutrient cycling in invaded ecosystems.

Differential sensitivity of total and active soil microbial communities to drought and forest management.

PubMed

Bastida, Felipe; Torres, Irene F; Andrés-Abellán, Manuela; Baldrian, Petr; López-Mondéjar, Rubén; Větrovský, Tomáš; Richnow, Hans H; Starke, Robert; Ondoño, Sara; García, Carlos; López-Serrano, Francisco R; Jehmlich, Nico

2017-10-01

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change. © 2017 John Wiley & Sons Ltd.

The influence of e-waste recycling on the molecular ecological network of soil microbial communities in Pakistan and China.

PubMed

Jiang, Longfei; Cheng, Zhineng; Zhang, Dayi; Song, Mengke; Wang, Yujie; Luo, Chunling; Yin, Hua; Li, Jun; Zhang, Gan

2017-12-01

Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e.g., Cu, Zn, and Pb). The geographical distance showed limited impacts on microbial communities compared with geochemical factors. The constructed ecological network of soil microbial communities illustrated microbial co-occurrence, competition and antagonism across soils, revealing the response of microbes to soil properties and pollutants. Two of the three main modules constructed with core operational taxonomic units (OTUs) were sensitive to nutrition (total organic carbon and total nitrogen) and pollutants. Five key OTUs assigned to Acidobacteria, Proteobacteria, and Nitrospirae in ecological network were identified. This is the first study to report the effects of e-waste pollutants on soil microbial network, providing a deeper understanding of the ecological influence of crude e-waste recycling activities on soil ecological functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Repeated application of composted tannery sludge affects differently soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms.

PubMed

Araújo, Ademir Sérgio Ferreira; Lima, Luciano Moura; Santos, Vilma Maria; Schmidt, Radomir

2016-10-01

Repeated application of composted tannery sludge (CTS) changes the soil chemical properties and, consequently, can affect the soil microbial properties. The aim of this study was to evaluate the responses of soil microbial biomass and ammonia-oxidizing organisms to repeated application of CTS. CTS was applied repeatedly during 6 years, and, at the sixth year, the soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms were determined in the soil. The treatments consisted of 0 (without CTS application), 2.5, 5, 10, and 20 t ha(-1) of CTS (dry basis). Soil pH, EC, SOC, total N, and Cr concentration increased with the increase in CTS rate. Soil microbial biomass did not change significantly with the amendment of 2.5 Mg ha(-1), while it decreased at the higher rates. Total and specific enzymes activity responded differently after CTS application. The abundance of bacteria did not change with the 2.5-Mg ha(-1) CTS treatment and decreased after this rate, while the abundance of archaea increased significantly with the 2.5-Mg ha(-1) CTS treatment. Repeated application of different CTS rates for 6 years had different effects on the soil microbial biomass and ammonia-oxidizing organisms as a response to changes in soil chemical properties.

Response of microbial activities and diversity to PAHs contamination at coal tar contaminated land

NASA Astrophysics Data System (ADS)

Zhao, Xiaohui; Sun, Yujiao; Ding, Aizhong; Zhang, Dan; Zhang, Dayi

2015-04-01

Coal tar is one of the most hazardous and concerned organic pollutants and the main hazards are polycyclic aromatic hydrocarbons (PAHs). The indigenous microorganisms in soils are capable to degrade PAHs, with essential roles in biochemical process for PAHs natural attenuation. This study investigated 48 soil samples (from 8 depths of 6 boreholes) in Beijing coking and chemistry plant (China) and revealed the correlation between PAHs contamination, soil enzyme activities and microbial community structure, by 16S rRNA denaturing gradient gel electrophoresis (DGGE). At the site, the key contaminants were identified as naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene and anthracene, and the total PAHs concentration ranged from 0.1 to 923.9 mg/kg dry soil. The total PAHs contamination level was positively correlated (p<0.05) with the bacteria count (0.9×107-14.2×107 CFU/mL), catalase activities (0.554-6.230 mL 0.02 M KMnO4/g•h) and dehydrogenase activities (1.9-30.4 TF μg/g•h soil), showing the significant response of microbial population and degrading functions to the organic contamination in soils. The PAHs contamination stimulated the PAHs degrading microbes and promoted their biochemical roles in situ. The positive relationship between bacteria count and dehydrogenase activities (p<0.05) suggested the dominancy of PAHs degrading bacteria in the microbial community. More interestingly, the microbial community deterioration was uncovered via the decline of microbial biodiversity (richness from 16S rRNA DGGE) against total PAHs concentration (p<0.05). Our research described the spatial profiles of PAHs contamination and soil microbial functions at the PAHs heavily contaminated sites, offering deeper understanding on the roles of indigenous microbial community in natural attenuation process.

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh.

PubMed

Chaudhary, Doongar R; Kim, Jinhyun; Kang, Hojeong

2018-04-01

Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages.

PubMed

Yang, Miao; Yang, Dan; Yu, Xuan

2018-01-01

The aim of this study was to assess the impact of forest age and season on the soil microbial community and enzyme activities in sea-buckthorn plantation system and to determine the relative contributions to soil microbial properties. Soil sampling was carried out in the dry season (April) and wet season (September) in four areas, including: abandoned farmland (NH), an 8-year- old plantation (young plantation, 8Y), a 13-year-old plantation (middle-aged plantation, 13Y), and an 18-year-old plantation (mature plantation, 18Y). The results showed that forest age and season have a significant effect on soil microbial community structure and enzyme activities. The total, bacterial, fungal, Gram-negative (G+), and Gram-positive (G-) PLFAs increased gradually with forest age, with the highest values detected in 18Y. All the detected enzyme activities showed the trend as a consequence of forest age. The microbial PLFAs and soil enzyme activities were higher in the wet season than the dry season. However, there were no significant interactions between forest age and season. A Correlation analysis suggested that soil microbial communities and enzyme activities were significantly and positively correlated with pH, total nitrogen (TN) and available phosphorus (AP). Season had a stronger influence on soil microbial communities than forest age. In general, sea-buckthorn plantations establishment might be a potential tool for maintaining and increasing soil fertility in arid and semi-arid regions.

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages

PubMed Central

Yang, Miao; Yang, Dan

2018-01-01

The aim of this study was to assess the impact of forest age and season on the soil microbial community and enzyme activities in sea-buckthorn plantation system and to determine the relative contributions to soil microbial properties. Soil sampling was carried out in the dry season (April) and wet season (September) in four areas, including: abandoned farmland (NH), an 8-year- old plantation (young plantation, 8Y), a 13-year-old plantation (middle-aged plantation, 13Y), and an 18-year-old plantation (mature plantation, 18Y). The results showed that forest age and season have a significant effect on soil microbial community structure and enzyme activities. The total, bacterial, fungal, Gram-negative (G+), and Gram-positive (G-) PLFAs increased gradually with forest age, with the highest values detected in 18Y. All the detected enzyme activities showed the trend as a consequence of forest age. The microbial PLFAs and soil enzyme activities were higher in the wet season than the dry season. However, there were no significant interactions between forest age and season. A Correlation analysis suggested that soil microbial communities and enzyme activities were significantly and positively correlated with pH, total nitrogen (TN) and available phosphorus (AP). Season had a stronger influence on soil microbial communities than forest age. In general, sea-buckthorn plantations establishment might be a potential tool for maintaining and increasing soil fertility in arid and semi-arid regions. PMID:29324845

[Effects of re-vegetation on soil microbial functional diversity in purple soils at different re-vegetation stages on sloping-land in Hengyang, Hunan Province, China.

PubMed

Wen, Dong Xin; Yang, Ning; Yang, Man Yuan

2016-08-01

The aim of the study was to explore the effects of re-vegetation on soil microbial functio-nal diversity in purple soils at different re-vegetation stages on sloping-land in Hengyang, Hunan Province, China. By using the spatial series to replace time series, four typical sampling plots, grass (Setaria viridi, GS), frutex and grass (Lagerstroemia indica-Setaria viridi, FG), frutex (Vitex negundo var. cannabifolia+Robinia pseudoacacia, FX), as well as arbor and frutex (Liquidamdar formosana+Melia azedarach-Vitex negundo var. cannabifolia, AF) community were selected to study the soil microbial functional diversity by using the Biolog-ECO micro-plate technique. The four communities in purple soils on sloping-land were similar and denoted four different re-vegetation stages. The results showed that the soil microbial metabolic activity increased after re-vegetation significantly, and the average well color development (AWCD) which represented soil microbial activity and functional diversity followed the order of AF community＞FX community＞FG community＞GS community at different re-vegetation stages, and followed the order of 0-10 cm ＞10-20 cm in different soil layers. Principal component analysis (PCA) identified that FG and FX community had similar C sources utilization mode and metabolic function, and GS and AF community were diffe-rent. The carbohydrates, amino acids, intermediate metabolites, and secondary metabolites were the main carbon sources separating the two principal component factors. The Shannon species richness index (H), Shannon evenness index (E), Simpson dominance index (D), McIntosh index (U) at four re-vegetation stages were the highest in AF community, the second in FG and FX community, and the lowest in GS community. The results of correlation analysis indicated that the content of soil water content (SWC), soil total organic carbon (STOC), total nitrogen (TN), total phospho-rus (TP) and available phosphorus (AP) had important influence on the soil microbial metabolic function and functional diversity indices. There existed significant correlation between the activities of urease (URE), alk-phosphatase (APE), invertase (INV), catalase (CAT) and the soil microbial metabolic function and functional diversity indices. All the results indicated that re-vegetation could enhance the soil microbial metabolic function, which was beneficial to the reproduction of soil micro-organisms, thereby promoting an increase of soil carbon source utilization intensity.

The resistance of the active microbiome as a fundamental compartment of soil quality in the face of climate change

NASA Astrophysics Data System (ADS)

Bastida, Felipe; Andrés, Manuela; Torres, Irene; García, Carlos; Ruiz Navarro, Antonio; Moreno, Francisco R.; López Serrano, Francisco R.

2017-04-01

Arid and semiarid ecosystems will be severely affected by drought derived from climate change. Forest management can promote the adaptations of plant and microbial communities to drought. For instance, thinning reduces competition for resources through a decrease in tree density and the promotion of plant survival. The resistance of soil microbial communities must be strongly related to the soil quality. However, in order to evaluate these properties, the active (and not only the total) microbial community should be carefully assessed. Here, we studied the functional and phylogenetic responses of the microbial community to six years of drought induced by rainfall exclusion and how thinning shapes its resistance to drought, in a semiarid ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel strategies against drought. The diversity and the composition of the total and active soil microbial communities were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially-mediated ecosystem multifunctionality was studied by the evaluation of enzyme activities related to C, N, and P dynamics. The microbial biomass and ecosystem multifunctionality decreased in plots subjected to drought, but this decrease was greater in unthinned plots. The diversity of the total bacterial and fungal communities were resistant to drought but were shaped by seasonal dynamics. However, the active community was more sensitive to drought and related to multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of multifunctionality to drought by changes in the active microbiome. Protein-based phylogeny was a better predictor of the impacts of drought and the adaptations of microbial communities. We highlight that the resistance of the microbial community and the active microbial community are ecological concepts strongly related to the concept of soil quality in the face of climate change.

Effects of vegetation type on microbial biomass carbon and nitrogen in subalpine mountain forest soils.

PubMed

Ravindran, Anita; Yang, Shang-Shyng

2015-08-01

Microbial biomass plays an important role in nutrient transformation and conservation of forest and grassland ecosystems. The objective of this study was to determine the microbial biomass among three vegetation types in subalpine mountain forest soils of Taiwan. Tatachia is a typical high-altitude subalpine temperate forest ecosystem in Taiwan with an elevation of 1800-3952 m and consists of three vegetation types: spruce, hemlock, and grassland. Three plots were selected in each vegetation type. Soil samples were collected from the organic layer, topsoil, and subsoil. Microbial biomass carbon (Cmic) was determined by the chloroform fumigation-extraction method, and microbial biomass nitrogen (Nmic) was determined from the total nitrogen (Ntot) released during fumigation-extraction. Bacteria, actinomycetes, fungi, cellulolytic microbes, phosphate-solubilizing microbes, and nitrogen-fixing microbes were also counted. The Cmic and Nmic were highest in the surface soil and declined with the soil depth. These were also highest in spruce soils, followed by in hemlock soils, and were lowest in grassland soils. Cmic and Nmic had the highest values in the spring season and the lowest values in the winter season. Cmic and Nmic had significantly positive correlations with total organic carbon (Corg) and Ntot. Contributions of Cmic and Nmic, respectively, to Corg and Ntot indicated that the microbial biomass was immobilized more in spruce and hemlock soils than in grassland soils. Microbial populations of the tested vegetation types decreased with increasing soil depth. Cmic and Nmic were high in the organic layer and decreased with the depth of layers. These values were higher for spruce and hemlock soils than for grassland soils. Positive correlations were observed between Cmic and Nmic and between Corg and Ntot. Copyright © 2014. Published by Elsevier B.V.

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

PubMed Central

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-01-01

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition. PMID:27256545

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition.

PubMed

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-06-03

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

NASA Astrophysics Data System (ADS)

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-06-01

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Linking Toluene Degradation with Specific Microbial Populations in Soil

PubMed Central

Hanson, Jessica R.; Macalady, Jennifer L.; Harris, David; Scow, Kate M.

1999-01-01

Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated 13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling 13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil. PMID:10583996

Microbial dynamics and enzyme activities in tropical Andosols depending on land use and nutrient inputs

NASA Astrophysics Data System (ADS)

Mganga, Kevin; Razavi, Bahar; Kuzyakov, Yakov

2015-04-01

Microbial decomposition of soil organic matter is mediated by enzymes and is a key source of terrestrial CO2 emissions. Microbial and enzyme activities are necessary to understand soil biochemical functioning and identify changes in soil quality. However, little is known about land use and nutrients availability effects on enzyme activities and microbial processes, especially in tropical soils of Africa. This study was conducted to examine how microbial and enzyme activities differ between different land uses and nutrient availability. As Andosols of Mt. Kilimanjaro are limited by nutrient concentrations, we hypothesize that N and P additions will stimulate enzyme activity. N and P were added to soil samples (0-20 cm) representing common land use types in East Africa: (1) savannah, (2) maize fields, (3) lower montane forest, (4) coffee plantation, (5) grasslands and (6) traditional Chagga homegardens. Total CO2 efflux from soil, microbial biomass and activities of β-glucosidase, cellobiohydrolase, chitinase and phosphatase involved in C, N and P cycling, respectively was monitored for 60 days. Total CO2 production, microbial biomass and enzyme activities varied in the order forest soils > grassland soils > arable soils. Increased β-glucosidase and cellobiohydrolase activities after N addition of grassland soils suggest that microorganisms increased N uptake and utilization to produce C-acquiring enzymes. Low N concentration in all soils inhibited chitinase activity. Depending on land use, N and P addition had an inhibitory or neutral effect on phosphatase activity. We attribute this to the high P retention of Andosols and low impact of N and P on the labile P fractions. Enhanced CO2 production after P addition suggests that increased P availability could stimulate soil organic matter biodegradation in Andosols. In conclusion, land use and nutrients influenced soil enzyme activities and microbial dynamics and demonstrated the decline in soil quality after landuse change. Key words: Andosols, β-glucosidase, Cellobiohydrolase, Chitinase, Phosphatase, Mt. Kilimanjaro

Effects of myclobutanil on soil microbial biomass, respiration, and soil nitrogen transformations.

PubMed

Ju, Chao; Xu, Jun; Wu, Xiaohu; Dong, Fengshou; Liu, Xingang; Zheng, Yongquan

2016-01-01

A 3-month-long experiment was conducted to ascertain the effects of different concentrations of myclobutanil (0.4 mg kg(-1) soil [T1]; 1.2 mg kg(-1) soil [T3]; and 4 mg kg(-1) soil [T10]) on soil microbial biomass, respiration, and soil nitrogen transformations using two typical agricultural soils (Henan fluvo-aquic soil and Shanxi cinnamon soil). Soil was sampled after 7, 15, 30, 60, and 90 days of incubation to determine myclobutanil concentration and microbial parameters: soil basal respiration (RB), microbial biomass carbon (MBC) and nitrogen (MBN), NO(-)3-N and NH(+)4-N concentrations, and gene abundance of total bacteria, N2-fixing bacteria, fungi, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB). The half-lives of the different doses of myclobutanil varied from 20.3 to 69.3 d in the Henan soil and from 99 to 138.6 d in the Shanxi soil. In the Henan soil, the three treatments caused different degrees of short-term inhibition of RB and MBC, NH(+)4-N, and gene abundance of total bacteria, fungi, N2-fixing bacteria, AOA, and AOB, with the exception of a brief increase in NO(-)3-N content during the T10 treatment. The MBN (immobilized nitrogen) was not affected. In the Shanxi soil, MBC, the populations of total bacteria, fungi, and N2-fixing bacteria, and NH(+)4-N concentration were not significantly affected by myclobutanil. The RB and MBN were decreased transitorily in the T10 treatment. The NO(-)3-N concentrations and the abundance of both AOA and AOB were erratically stimulated by myclobutanil. Regardless of whether stimulation or suppression occurred, the effects of myclobutanil on the two soil types were short term. In summary, myclobutanil had no long-term negative effects on the soil microbial biomass, respiration, and soil nitrogen transformations in the two types of soil, even at 10-fold the recommended dosage. Copyright © 2015 Elsevier Ltd. All rights reserved.

Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only.

PubMed

Pan, Yao; Abell, Guy C J; Bodelier, Paul L E; Meima-Franke, Marion; Sessitsch, Angela; Bodrossy, Levente

2014-08-01

Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.

[Nutrient contents and microbial populations of aeolian sandy soil in Sanjiangyuan region of Qinghai Province].

PubMed

Lin, Chao-feng; Chen, Zhan-quan; Xue, Quan-hong; Lai, Hang-xian; Chen, Lai-sheng; Zhang, Deng-shan

2007-01-01

Sanjiangyuan region (the headstream of three rivers) in Qinghai Province of China is the highest and largest inland alpine wetland in the world. The study on the nutrient contents and microbial populations of aeolian sandy soils in this region showed that soil organic matter content increased with the evolution of aeolian sand dunes from un-stabilized to stabilized state, being 5.9 and 3.8 times higher in stabilized sand dune than in mobile and semi-stabilized sand dunes, respectively. Soil nitrogen and phosphorus contents increased in line with the amount of organic matter, while potassium content and pH value varied slightly. The microbial populations changed markedly with the development of vegetation, fixing of mobile sand, and increase of soil nutrients. The quantities of soil bacteria, fungi and actinomycetes were 4.0 and 2.8 times, 19.6 and 6.3 times, and 12.4 and 2.6 times higher in stabilized and semi-stabilized sand dunes than in mobile sand dune, respectively, indicating that soil microbial bio-diversity was increased with the evolution of aeolian sand dunes from mobile to stabilized state. In addition, the quantities of soil microbes were closely correlated with the contents of soil organic matter, total nitrogen, and available nitrogen and phosphorus, but not correlated with soil total phosphorus, total and available potassium, or pH value.

Microbial Community Dynamics from Permafrost Across the Pleistocene-Holocene Boundary and Response to Abrupt Climate Change

NASA Astrophysics Data System (ADS)

Hammad, A.; Mahony, M.; Froese, D. G.; Lanoil, B. D.

2014-12-01

Earth is currently undergoing rapid warming similar to that observed about 10,000 years ago at the end of the Pleistocene. We know a considerable amount about the adaptations and extinctions of mammals and plants at the Pleistocene/Holocene (P/H) boundary, but relatively little about changes at the microbial level. Due to permafrost soils' freezing anoxic conditions, they act as microbial diversity archives allowing us to determine how microbial communities adapted to the abrupt warming at the end of P. Since microbial community composition only helps differentiate viable and extant microorganisms in frozen permafrost, microbial activity in thawing permafrost must be investigated to provide a clear understanding of microbial response to climate change. Current increased temperatures will result in warming and potential thaw of permafrost and release of stored organic carbon, freeing it for microbial utilization; turning permafrost into a carbon source. Studying permafrost viable microbial communities' diversity and activity will provide a better understanding of how these microorganisms respond to soil edaphic variability due to climate change across the P/H boundary, providing insight into the changes that the soil community is currently undergoing in this modern era of rapid climate change. Modern soil, H and P permafrost cores were collected from Lucky Lady II site outside Dawson City, Yukon. 16S rRNA high throughput sequencing of permafrost DNA showed the same trends for total and viable community richness and diversity with both decreasing with permafrost depth and only the richness increasing in mid and early P. The modern, H and P soils had 50.9, 33.9, and 27.3% unique viable species and only 14% of the total number of viable species were shared by all soils. Gas flux measurements of thawed permafrost showed metabolic activity in modern and permafrost soils, aerobic CH­­4 consumption in modern, some H and P soils, and anaerobic CH­­4 production in one H sample. Soil chemistry analysis showed that older permafrost, P, had higher pH, lower total nitrogen, ammonium, and organic carbon than younger permafrost, H.

Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics.

PubMed

Ren, Chengjie; Zhang, Wei; Zhong, ZeKun; Han, Xinhui; Yang, Gaihe; Feng, Yongzhong; Ren, Guangxin

2018-01-01

Alt'itudinal gradients strongly affect plant biodiversity, but the effects on microbial patterns remain unclear, especially in the large scale. We therefore designed an altitudinal gradient experiment that covered three climate zones to monitor soil microbial community dynamics and to compare those with plant and soil characteristics. Illumina sequencing of the 16S rRNA gene and ITS gene was used to analyze soil microbial (bacterial and fungal) diversity and composition, and fumigation-extraction was used to determine microbial biomass; the plant community metrics (i.e., percent cover, Shannon-Wiener, grass biomass, and carbon/nitrogen in leaf and biomass) and soil properties (i.e., soil moisture, soil temperature, bulk density, organic carbon, total nitrogen, and available nitrogen) were determined. The results showed that carbon/nitrogen in microbial biomass was higher at medium altitude and was positively related to carbon and nitrogen in both soil and grass biomass along the altitudinal gradients. Soil bacterial alpha diversity was significantly higher at medium altitude but fungal alpha diversity did not affected by altitudinal gradients; the effect of altitudinal gradients on bacterial beta diversity was larger than that on fungal beta diversity, although both groups were significantly affected by altitudinal gradients. Moreover, Alpha-proteobacteria, Beta-proteobacteria, and Gemmatimonadetes were significantly more abundant in higher altitude than in lower altitude, both Acidobacteria and Actinobacteria significantly declined with increasing altitude; other bacterial taxa such as Chloroflexi, Nitrospirae, Gamma-proteobacteria, and Delta-proteobacteria were significantly higher at medium altitudes. For fungal taxa, Basidiomycota and Ascomycota were the dominant phyla and responded insignificantly to the altitudinal gradients. The responses of microbial alpha diversity were mostly associated with plant Shannon index, organic carbon, and total nitrogen, whereas microbial beta diversity and composition mainly depended on soil moisture and temperature. Overall, these results suggest that soil bacteria rather than fungi can reflect changes in plant and soil characteristics along altitudinal gradients. Copyright © 2017 Elsevier B.V. All rights reserved.

Short-term contributions of cover crop surface residue return to soil carbon and nitrogen contents in temperate Australia.

PubMed

Zhou, Xiaoqi; Wu, Hanwen; Li, Guangdi; Chen, Chengrong

2016-11-01

Cover crop species are usually grown to control weeds. After cover crop harvest, crop residue is applied on the ground to improve soil fertility and crop productivity. Little information is available about quantifying the contributions of cover crop application to soil total carbon (C) and nitrogen (N) contents in temperate Australia. Here, we selected eight cover crop treatments, including two legume crops (vetch and field pea), four non-legume crops (rye, wheat, Saia oat, and Indian mustard), a mixture of rye and vetch, and a nil-crop control in temperate Australia to calculate the contributions of cover crops (crop growth + residue decomposition) to soil C and N contents. Cover crops were sown in May 2009 (autumn). After harvest, the crop residue was placed on the soil surface in October 2009. Soil and crop samples were collected in October 2009 after harvest and in May 2010 after 8 months of residue decomposition. We examined cover crop residue biomass, soil and crop total C and N contents, and soil microbial biomass C and N contents. The results showed that cover crop application increased the mean soil total C by 187-253 kg ha -1 and the mean soil total N by 16.3-19.1 kg ha -1 relative to the nil-crop treatment, except for the mixture treatment, which had similar total C and N contents to the nil-crop control. Cover crop application increased the mean soil microbial biomass C by 15.5-20.9 kg ha -1 and the mean soil microbial biomass N by 4.5-10.2 kg ha -1 . We calculated the apparent percentage of soil total C derived from cover crop residue C losses and found that legume crops accounted for 10.6-13.9 %, whereas non-legume crops accounted for 16.4-18.4 % except for the mixture treatment (0.2 %). Overall, short-term cover crop application increased soil total C and N contents and microbial biomass C and N contents, which might help reduce N fertilizer use and improve sustainable agricultural development.

Impact of land-use and long-term (>150 years) charcoal accumulation on microbial activity, biomass and community structure in temperate soils (Belgium).

NASA Astrophysics Data System (ADS)

Hardy, Brieuc; Cornelis, Jean-Thomas; Dufey, Joseph E.

2015-04-01

In the last decade, biochar has been increasingly investigated as a soil amendment for long-term soil carbon sequestration while improving soil fertility. On the short term, biochar application to soil generally increases soil respiration as well as microbial biomass and activity and affects significantly the microbial community structure. However, such effects are relatively short-term and tend to vanish over time. In our study, we investigated the long-term impact of charcoal accumulation and land-use on soil biota in temperate haplic Luvisols developed in the loess belt of Wallonia (Belgium). Charcoal-enriched soils were collected in the topsoil of pre-industrial (>150 years old) charcoal kilns in forest (4 sites) and cropland (5 sites). The topsoil of the adjacent charcoal-unaffected soils was sampled in a comparable way. Soils were characterized (pH, total, organic and inorganic C, total N, exchangeable Ca, Mg, K, Na, cation exchange capacity and available P) and natural soil organic matter (SOM) and black carbon (BC) contents were determined by differential scanning calorimetry. After rewetting at pF 2.5, soils were incubated during 140 days at 20 °C. At 70 days of incubation, 10 g of each soil were freeze dried in order to measure total microbial biomass and community structure by PLFA analysis. The PLFA dataset was analyzed by principal component analysis (PCA) while soil parameters were used as supplementary variables. For both agricultural and forest soils, the respiration rate is highly related to the total microbial biomass (R²=0.90). Both soil respiration and microbial biomass greatly depend on the SOM content, which indicates that the BC pool is relatively inert microbiologically. Land-use explains most of the variance in the PLFA dataset, largely governing the first principal component of the ACP. In forest soils, we observe a larger proportion of gram + bacteria, actinomycetes and an increased bacteria:fungi ratio compared to cropland, where gram - bacteria, arbuscular mycorrhizal fungi and 18:2 and 18:3 fungi are more present. BC is quite well represented (R=-0.765) by the third principal component of the PCA, representing 12.2 % of the total variance. It has limited impact on the community structure, particularly in cropland. However, in forest BC is negatively correlated (R=-0.785) with 18:1 fungi. The more pronounced effect of BC on community structure under forest could result from modified trophic conditions at kiln site (e.g. higher pH, lower available P content, …) while cultivation practices attenuated such differences over time in cropland. In conclusion, our survey tends to confirm that the influence of BC on the soil microbiological parameters is governed by indirect effects on trophic conditions. On the other hand, land-use affects dramatically soil microbial community structure.

Interactive Effects of Nitrogen and Phosphorus on Soil Microbial Communities in a Tropical Forest

PubMed Central

Liu, Lei; Zhang, Tao; Gilliam, Frank S.; Gundersen, Per; Zhang, Wei; Chen, Hao; Mo, Jiangming

2013-01-01

Elevated nitrogen (N) deposition in humid tropical regions may exacerbate phosphorus (P) deficiency in forests on highly weathered soils. However, it is not clear how P availability affects soil microbes and soil carbon (C), or how P processes interact with N deposition in tropical forests. We examined the effects of N and P additions on soil microbes and soil C pools in a N-saturated old-growth tropical forest in southern China to test the hypotheses that (1) N and P addition will have opposing effects on soil microbial biomass and activity, (2) N and P addition will alter the composition of the microbial community, (3) the addition of N and P will have interactive effects on soil microbes and (4) addition-mediated changes in microbial communities would feed back on soil C pools. Phospholipid fatty acid (PLFA) analysis was used to quantify the soil microbial community following four treatments: Control, N addition (15 g N m−2 yr−1), P addition (15 g P m−2 yr−1), and N&P addition (15 g N m−2 yr−1 plus 15 g P m−2 yr−1). These were applied from 2007 to 2011. Whereas additions of P increased soil microbial biomass, additions of N reduced soil microbial biomass. These effects, however, were transient, disappearing over longer periods. Moreover, N additions significantly increased relative abundance of fungal PLFAs and P additions significantly increased relative abundance of arbuscular mycorrhizal (AM) fungi PLFAs. Nitrogen addition had a negative effect on light fraction C, but no effect on heavy fraction C and total soil C. In contrast, P addition significantly decreased both light fraction C and total soil C. However, there were no interactions between N addition and P addition on soil microbes. Our results suggest that these nutrients are not co-limiting, and that P rather than N is limiting in this tropical forest. PMID:23593427

Effect of dry mycelium of Penicillium chrysogenum fertilizer on soil microbial community composition, enzyme activities and snap bean growth.

PubMed

Wang, Bing; Liu, Huiling; Cai, Chen; Thabit, Mohamed; Wang, Pu; Li, Guomin; Duan, Ziheng

2016-10-01

The dry mycelium fertilizer (DMF) was produced from penicillin fermentation fungi mycelium (PFFM) following an acid-heating pretreatment to degrade the residual penicillin. In this study, it was applied into soil as fertilizer to investigate its effects on soil properties, phytotoxicity, microbial community composition, enzyme activities, and growth of snap bean in greenhouse. As the results show, pH, total nitrogen, total phosphorus, total potassium, and organic matter of soil with DMF treatments were generally higher than CON treatment. In addition, the applied DMF did not cause heavy metal and residual drug pollution of the modified soil. The lowest GI values (<0.3) were recorded at DMF8 (36 kg DMF/plat) on the first days after applying the fertilizer, indicating that severe phytotoxicity appeared in the DMF8-modified soil. Results of microbial population and enzyme activities illustrated that DMF was rapidly decomposed and the decomposition process significantly affected microbial growth and enzyme activities. The DMF-modified soil phytotoxicity decreased at the late fertilization time. DMF1 was considered as the optimum amount of DMF dose based on principal component analysis scores. Plant height and plant yield of snap bean were remarkably enhanced with the optimum DMF dose.

The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem.

PubMed

Lee, Seung-Hoon; Kang, Hojeong

2016-02-01

The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to biogeochemical factors, the study of the microbial community even in surface soil should be performed in detail by considering the soil depth.

Water regime history drives responses of soil Namib Desert microbial communities to wetting events

NASA Astrophysics Data System (ADS)

Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

2015-07-01

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

Water regime history drives responses of soil Namib Desert microbial communities to wetting events.

PubMed

Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A

2015-07-21

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

Mapping and determinism of soil microbial community distribution across an agricultural landscape

PubMed Central

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-01-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

Impact of ecosystem management on microbial community level physiological profiles of postmining forest rehabilitation.

PubMed

Cookson, W R; O'Donnell, A J; Grant, C D; Grierson, P F; Murphy, D V

2008-02-01

We investigated the impacts of forest thinning, prescribed fire, and contour ripping on community level physiological profiles (CLPP) of the soil microbial population in postmining forest rehabilitation. We hypothesized that these management practices would affect CLPP via an influence on the quality and quantity of soil organic matter. The study site was an area of Jarrah (Eucalyptus marginata Donn ex Sm.) forest rehabilitation that had been mined for bauxite 12 years previously. Three replicate plots (20 x 20 m) were established in nontreated forest and in forest thinned from 3,000-8,000 stems ha(-1) to 600-800 stems ha(-1) in April (autumn) of 2003, followed either by a prescribed fire in September (spring) of 2003 or left nonburned. Soil samples were collected in August 2004 from two soil depths (0-5 cm and 5-10 cm) and from within mounds and furrows caused by postmining contour ripping. CLPP were not affected by prescribed fire, although the soil pH and organic carbon (C), total C and total nitrogen (N) contents were greater in burned compared with nonburned plots, and the coarse and fine litter mass lower. However, CLPP were affected by forest thinning, as were fine litter mass, soil C/N ratio, and soil pH, which were all higher in thinned than nonthinned plots. Furrow soil had greater coarse and fine litter mass, and inorganic phosphorous (P), organic P, organic C, total C, total N, ammonium, microbial biomass C contents, but lower soil pH and soil C/N ratio than mound soil. Soil pH, inorganic P, organic P, organic C, total C and N, ammonium, and microbial biomass C contents also decreased with depth, whereas soil C/N ratio increased. Differences in CLPP were largely (94%) associated with the relative utilization of gluconic, malic (greater in nonthinned than thinned soil and mound than furrow soil), L-tartaric, succinic, and uric acids (greater in thinned than nonthinned, mound than furrow, and 5-10 cm than 0-5 cm soil). The relative utilization of amino acids also tended to increase with increasing soil total C and organic C contents but decreased with increasing nitrate content, whereas the opposite was true for carboxylic acids. Only 45% of the variance in CLPP was explained using a multivariate multiple regression model, but soil C and N pools and litter mass were significant predictors of CLPP. Differences in soil textural components between treatments were also correlated with CLPP; likely causes of these differences are discussed. Our results suggest that 1 year after treatment, CLPP from this mined forest ecosystem are resilient to a spring prescribed fire but not forest thinning. We conclude that differences in CLPP are likely to result from complex interactions among soil properties that mediate substrate availability, microbial nutrient demand, and microbial community composition.

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil.

PubMed

Yang, Wenhao; Zhang, Taoxiang; Lin, Sen; Ni, Wuzhong

2017-06-01

The recovery of microbial community and activities is crucial to the remediation of contaminated soils. Distance-dependent variations of microbial community composition and metabolic characteristics in the rhizospheric soil of hyperaccumulator during phytoextraction are poorly understood. A 12-month phytoextraction experiment with Sedum alfredii in a Cd-contaminated soil was conducted. A pre-stratified rhizobox was used for separating sub-layer rhizospheric (0-2, 2-4, 4-6, 6-8, 8-10 mm from the root mat)/bulk soils. Soil microbial structure and function were analyzed by phospholipid fatty acid (PLFA) and MicroResp™ methods. The concentrations of total and specified PLFA biomarkers and the utilization rates for the 14 substrates (organic carbon) in the 0-2-mm sub-layer rhizospheric soil were significantly increased, as well as decreased with the increase in the distance from the root mat. Microbial structure measured by the ratios of different groups of PLFAs such as fungal/bacterial, monounsaturated/saturated, ratios of Gram-positive to Gram-negative (GP/GN) bacterial, and cyclopropyl/monoenoic precursors and 19:0 cyclo/18:1ω7c were significantly changed in the 0-2-mm soil. The PLFA contents and substrate utilization rates were negatively correlated with pH and total, acid-soluble, and reducible fractions of Cd, while positively correlated with labile carbon. The dynamics of microbial community were likely due to root exudates and Cd uptake by S. alfredii. This study revealed the stimulations and gradient changes of rhizosphere microbial community through phytoextraction, as reduced Cd concentration, pH, and increased labile carbons are due to the microbial community responses.

Soil microbiological properties and enzymatic activities of long-term post-fire recovery in dry and semiarid Aleppo pine (Pinus halepensis M.) forest stands

NASA Astrophysics Data System (ADS)

Hedo, J.; Lucas-Borja, M. E.; Wic, C.; Andrés-Abellán, M.; de Las Heras, J.

2015-02-01

Wildfires affecting forest ecosystems and post-fire silvicultural treatments may cause considerable changes in soil properties. The capacity of different microbial groups to recolonise soil after disturbances is crucial for proper soil functioning. The aim of this work was to investigate some microbial soil properties and enzyme activities in semiarid and dry Aleppo pine (Pinus halepensis M.) forest stands. Different plots affected by a wildfire event 17 years ago without or with post-fire silvicultural treatments 5 years after the fire event were selected. A mature Aleppo pine stand, unaffected by wildfire and not thinned was used as a control. Physicochemical soil properties (soil texture, pH, carbonates, organic matter, electrical conductivity, total N and P), soil enzymes (urease, phosphatase, β-glucosidase and dehydrogenase activities), soil respiration and soil microbial biomass carbon were analysed in the selected forests areas and plots. The main finding was that long time after this fire event produces no differences in the microbiological soil properties and enzyme activities of soil after comparing burned and thinned, burned and not thinned, and mature plots. Moreover, significant site variation was generally seen in soil enzyme activities and microbiological parameters. We conclude that total vegetation recovery normalises post-fire soil microbial parameters, and that wildfire and post-fire silvicultural treatments are not significant factors affecting soil properties after 17 years.

Mineralogical impact on long-term patterns of soil nitrogen and phosphorus enzyme activities

NASA Astrophysics Data System (ADS)

Mikutta, Robert; Turner, Stephanie; Meyer-Stüve, Sandra; Guggenberger, Georg; Dohrmann, Reiner; Schippers, Axel

2014-05-01

Soil chronosequences provide a unique opportunity to study microbial activity over time in mineralogical diverse soils of different ages. The main objective of this study was to test the effect of mineralogical properties, nutrient and organic matter availability over whole soil pro-files on the abundance and activity of the microbial communities. We focused on microbio-logical processes involved in nitrogen and phosphorus cycling at the 120,000-year Franz Josef soil chronosequence. Microbial abundances (microbial biomass and total cell counts) and enzyme activities (protease, urease, aminopeptidase, and phosphatase) were determined and related to nutrient contents and mineralogical soil properties. Both, microbial abundances and enzyme activities decreased with soil depth at all sites. In the organic layers, microbial biomass and the activities of N-hydrolyzing enzymes showed their maximum at the intermediate-aged sites, corresponding to a high aboveground biomass. In contrast, the phosphatase activity increased with site age. The activities of N-hydrolyzing enzymes were positively correlated with total carbon and nitrogen contents, whereas the phosphatase activity was negatively correlated with the phosphorus content. In the mineral soil, the enzyme activities were generally low, thus reflecting the presence of strongly sorbing minerals. Sub-strate-normalized enzyme activities correlated negatively to clay content as well as poorly crystalline Al and Fe oxyhydroxides, supporting the view that the evolution of reactive sec-ondary mineral phases alters the activity of the microbial communities by constraining sub-strate availability. Our data suggest a strong mineralogical influence on nutrient cycling par-ticularly in subsoil environments.

Transformation of ecofunctional parameters of soil microbial cenoses in clearings for power transmission lines in Central Siberia

NASA Astrophysics Data System (ADS)

Bogorodskaya, A. V.; Ponomareva, T. V.; Efimov, D. Yu.; Shishikin, A. S.

2017-06-01

Changes in soil microbial processes and phytocenotic parameters were studied in clearings made for power transmission lines in the subtaiga and southern taiga of Central Siberia. In these clearings, secondary meadow communities play the main environmental role. The substitution of meadow vegetation for forest vegetation, the increase in the phytomass by 40-120%, and the transformation of the hydrothermic regime in the clearings led to the intensification of the humus-accumulative process, growth of the humus content, reduction in acidity and oligotrophy of the upper horizons in the gray soils of the meadow communities, and more active microbial mineralization of organic matter. In the humus horizon of the soils under meadows, the microbial biomass (Cmicr) increased by 20-90%, and the intensity of basal respiration became higher by 60-90%. The values of the microbial metabolic quotient were also higher in these soils than in the soils under the native forests. In the 0- to 50-cm layer of the gray soils under the meadows, the total Cmicr reserves were 35-45% greater and amounted to 230-320 g/m3; the total microbial production of CO2 was 1.5-2 times higher than that in the soil of the adjacent forest and reached 770-840 mg CO2-C/m3 h. The predominance of mineralization processes in the soils under meadows in the clearings reflected changes in edaphic and trophic conditions of the soils and testified to an active inclusion of the herb falloff into the biological cycle.

[Effects of altitudes on soil microbial biomass and enzyme activity in alpine-gorge regions.

PubMed

Cao, Rui; Wu, Fu Zhong; Yang, Wan Qin; Xu, Zhen Feng; Tani, Bo; Wang, Bin; Li, Jun; Chang, Chen Hui

2016-04-22

In order to understand the variations of soil microbial biomass and soil enzyme activities with the change of altitude, a field incubation was conducted in dry valley, ecotone between dry valley and mountain forest, subalpine coniferous forest, alpine forest and alpine meadow from 1563 m to 3994 m of altitude in the alpine-gorge region of western Sichuan. The microbial biomass carbon and nitrogen, and the activities of invertase, urease and acid phosphorus were measured in both soil organic layer and mineral soil layer. Both the soil microbial biomass and soil enzyme activities showed the similar tendency in soil organic layer. They increased from 2158 m to 3028 m, then decreased to the lowest value at 3593 m, and thereafter increased until 3994 m in the alpine-gorge region. In contrast, the soil microbial biomass and soil enzyme activities in mineral soil layer showed the trends as, the subalpine forest at 3028 m > alpine meadow at 3994 m > montane forest ecotone at 2158 m > alpine forest at 3593 m > dry valley at 1563 m. Regardless of altitudes, soil microbial biomass and soil enzyme activities were significantly higher in soil organic layer than in mineral soil layer. The soil microbial biomass was significantly positively correlated with the activities of the measured soil enzymes. Moreover, both the soil microbial biomass and soil enzyme activities were significantly positively correlated with soil water content, organic carbon, and total nitrogen. The activity of soil invertase was significantly positively correlated with soil phosphorus content, and the soil acid phosphatase was so with soil phosphorus content and soil temperature. In brief, changes in vegetation and other environmental factors resulting from altitude change might have strong effects on soil biochemical properties in the alpine-gorge region.

Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses

PubMed Central

Narendrula-Kotha, Ramya; Nkongolo, Kabwe K.

2017-01-01

Aims To assess the effects of dolomitic limestone applications on soil microbial communities’ dynamics and bacterial and fungal biomass, relative abundance, and diversity in metal reclaimed regions. Methods and Results The study was conducted in reclaimed mining sites and metal uncontaminated areas. The limestone applications were performed over 35 years ago. Total microbial biomass was determined by Phospholipid fatty acids. Bacterial and fungal relative abundance and diversity were assessed using 454 pyrosequencing. There was a significant increase of total microbial biomass in limed sites (342 ng/g) compared to unlimed areas (149 ng/g). Chao1 estimates followed the same trend. But the total number of OTUs (Operational Taxonomic Units) in limed (463 OTUs) and unlimed (473 OTUs) soil samples for bacteria were similar. For fungi, OTUs were 96 and 81 for limed and unlimed soil samples, respectively. Likewise, Simpson and Shannon diversity indices revealed no significant differences between limed and unlimed sites. Bacterial and fungal groups specific to either limed or unlimed sites were identified. Five major bacterial phyla including Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, and Proteobacteria were found. The latter was the most prevalent phylum in all the samples with a relative abundance of 50%. Bradyrhizobiaceae family with 12 genera including the nitrogen fixing Bradirhizobium genus was more abundant in limed sites compared to unlimed areas. For fungi, Ascomycota was the most predominant phylum in unlimed soils (46%) while Basidiomycota phylum represented 86% of all fungi in the limed areas. Conclusion Detailed analysis of the data revealed that although soil liming increases significantly the amount of microbial biomass, the level of species diversity remain statistically unchanged even though the microbial compositions of the damaged and restored sites are different. Significance and Impact of the study Soil liming still have a significant beneficial effects on soil microbial abundance and composition > 35 years after dolomitic limestone applications. PMID:28052072

Soil water availability and microsite mediate fungal and bacterial phospholipid fatty acid biomarker abundances in Mojave Desert soils exposed to elevated atmospheric CO2

NASA Astrophysics Data System (ADS)

Jin, V. L.; Schaeffer, S. M.; Ziegler, S. E.; Evans, R. D.

2011-06-01

Changes in the rates of nitrogen (N) cycling, microbial carbon (C) substrate use, and extracellular enzyme activities in a Mojave Desert ecosystem exposed to elevated atmospheric CO2 suggest shifts in the size and/or functional characteristics of microbial assemblages in two dominant soil microsites: plant interspaces and under the dominant shrub Larrea tridentata. We used ester-linked phospholipid fatty acid (PLFA) biomarkers as a proxy for microbial biomass to quantify spatial and temporal differences in soil microbial communities from February 2003 to May 2005. Further, we used the 13C signature of the fossil CO2 source for elevated CO2 plots to trace recent plant C inputs into soil organic matter (SOM) and broad microbial groups using δ13C (‰). Differences between individual δ13CPLFA and δ13CSOM for fungal biomarkers indicated active metabolism of newer C in elevated CO2 soils. Total PLFA-C was greater in shrub microsites compared to plant interspaces, and CO2 treatment differences within microsites increased under higher soil water availability. Total, fungal, and bacterial PLFA-C increased with decreasing soil volumetric water content (VWC) in both microsites, suggesting general adaptations to xeric desert conditions. Increases in fungal-to-bacterial PLFA-C ratio with decreasing VWC reflected functional group-specific responses to changing soil water availability. While temporal and spatial extremes in resource availability in desert ecosystems contribute to the difficulty in identifying common trends or mechanisms driving microbial responses in less extreme environments, we found that soil water availability and soil microsite interacted with elevated CO2 to shift fungal and bacterial biomarker abundances in Mojave Desert soils.

Effects of poultry manure on soil biochemical properties in phthalic acid esters contaminated soil.

PubMed

Gao, Jun; Qin, Xiaojian; Ren, Xuqin; Zhou, Haifeng

2015-12-01

This study aimed to evaluate the effects of poultry manure (PM) on soil biological properties in DBP- and DEHP-contaminated soils. An indoor incubation experiment was conducted. Soil microbial biomass C (Cmic), soil enzymatic activities, and microbial phospholipid fatty acid (PLFA) concentrations were measured during incubation period. The results indicated that except alkaline phosphatase activity, DBP and DEHP had negative effects on Cmic, dehydrogenase, urease, protease activities, and contents of total PLFA. However, 5 % PM treatment alleviated the negative effects of PAEs on the above biochemical parameters. In DBP-contaminated soil, 5 % PM amendment even resulted in dehydroenase activity and Cmic content increasing by 17.8 and 11.8 % on the day 15 of incubation, respectively. During the incubation periods, the total PLFA contents decreased maximumly by 17.2 and 11.6 % in DBP- and DEHP-contaminated soils without PM amendments, respectively. Compared with those in uncontaminated soil, the total PLFA contents increased slightly and the value of bacPLFA/fugalPLFA increased significantly in PAE-contaminated soils with 5 % PM amendment. Nevertheless, in both contaminated soils, the effects of 5 % PM amendment on the biochemical parameters were not observed with 10 % PM amendment. In 10 % PM-amended soils, DBP and DEHP had little effect on Cmic, soil enzymatic activities, and microbial community composition. At the end of incubation, the effects of PAEs on these parameters disappeared, irrespective of PM amendment. The application of PM ameliorated the negative effect of PAEs on soil biological environment. However, further work is needed to study the effect of PM on soil microbial gene expression in order to explain the change mechanisms of soil biological properties.

Organic farming enhances soil microbial abundance and activity—A meta-analysis and meta-regression

PubMed Central

Symnaczik, Sarah; Mäder, Paul; De Deyn, Gerlinde; Gattinger, Andreas

2017-01-01

Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation. Several studies have reported a positive effect of organic farming on soil health and quality including microbial community traits. However, so far no systematic quantification of whether organic farming systems comprise larger and more active soil microbial communities compared to conventional farming systems was performed on a global scale. Therefore, we conducted a meta-analysis on current literature to quantify possible differences in key indicators for soil microbial abundance and activity in organic and conventional cropping systems. All together we integrated data from 56 mainly peer-reviewed papers into our analysis, including 149 pairwise comparisons originating from different climatic zones and experimental duration ranging from 3 to more than 100 years. Overall, we found that organic systems had 32% to 84% greater microbial biomass carbon, microbial biomass nitrogen, total phospholipid fatty-acids, and dehydrogenase, urease and protease activities than conventional systems. Exclusively the metabolic quotient as an indicator for stresses on microbial communities remained unaffected by the farming systems. Categorical subgroup analysis revealed that crop rotation, the inclusion of legumes in the crop rotation and organic inputs are important farming practices affecting soil microbial community size and activity. Furthermore, we show that differences in microbial size and activity between organic and conventional farming systems vary as a function of land use (arable, orchards, and grassland), plant life cycle (annual and perennial) and climatic zone. In summary, this study shows that overall organic farming enhances total microbial abundance and activity in agricultural soils on a global scale. PMID:28700609

Abundance and activity of soil microorganisms in Cedrus atlantica forests are more related to land use than to altitude or latitude

NASA Astrophysics Data System (ADS)

Ramírez Rojas, Irene; Perez Fernandez, María; Moreno Gallardo, Laura; Lechuga Ordoñez, Victor; Linares, Juan Carlos

2016-04-01

Several environmental traits might change the abundance and the function of soil microorganisms in forest soils by plant-mediated reactions. Few studies have related the landscape-scale forest structural diversity with the micro-scale distribution of microorganism and their activities. High mountain environments harbor ecosystems that are very sensitive to global change and hence highly vulnerable, as those of Atlantic cedar. Altitudinal gradients in mountains are orrelated with changes in vegetation. We propose that altitudinal gradients drive shifts in microbial communities and are correlated with land uses. Thus, the latitudinal and longitudinal pattern of abundance and activity of soil micro-organisms was studied in an intercontinental comparison. We investigate soil extractable organic carbon (EOC) and nitrogen and carbon, microbial biomass and microbial metabolic activities at eight different sites along the latitudinal range of Cedrus atlantica, covering different altitudes and soils characteristics both in Southern Spain and Northern Morocco. Analyses of the abundances of total bacteria, (16S rRNA gene), was conducted using the Ilumina metagenomics technique. Results show that the stands at the highest altitudes had distinct microbial and biochemical characteristics compared with other areas. Overall, microbial activity, as measured by soil respiration, is higher in forests subjected to lower human pressure than in stands highly degraded, probably reflecting the quality of litter input that results of the influence of local assemblage of different tree, shrub and annual species, though changes in the soil N and C contents. Indeed, total soil C and N contents explained the microbial properties at every scale. Our results suggest that in contrast to the observed pronounced altitudinal changes, the kind of human-mediate land management has a stronger role in defining changes in microbial composition and activities in the investigated forest systems.

Effects of soil depth and plant-soil interaction on microbial community in temperate grasslands of northern China.

PubMed

Yao, Xiaodong; Zhang, Naili; Zeng, Hui; Wang, Wei

2018-07-15

Although the patterns and drivers of soil microbial community composition are well studied, little is known about the effects of plant-soil interactions and soil depth on soil microbial distribution at a regional scale. We examined 195 soil samples from 13 sites along a climatic transect in the temperate grasslands of northern China to measure the composition of and factors influencing soil microbial communities within a 1-m soil profile. Soil microbial community composition was measured using phospholipid fatty acids (PLFA) analysis. Fungi predominated in topsoil (0-10 cm) and bacteria and actinomycetes in deep soils (40-100 cm), independent of steppe types. This variation was explained by contemporary environmental factors (including above- and below-ground plant biomass, soil physicochemical and climatic factors) >58% in the 0-40 cm of soil depth, but <45% in deep soils. Interestingly, when we considered the interactive effects between plant traits (above ground biomass and root biomass) and soil factors (pH, clay content, and soil total carbon, nitrogen, phosphorous), we observed a significant interaction effect occurring at depths of 10-20 cm soil layer, due to different internal and external factors of the plant-soil system along the soil profile. These results improve understanding of the drivers of soil microbial community composition at regional scales. Copyright © 2018 Elsevier B.V. All rights reserved.

Assessment of microbial biomass carbon and nitrogen of native and non-native perennial pasture soils using hyperspectral data

USDA-ARS?s Scientific Manuscript database

Soil microbial biomass carbon (MBC) and nitrogen (MBN) are integral parts to soil organic matter. Increased production costs and chemical runoff can result from excessive application of fertilizer if these measurements are not used in total nutrient calculations. More timely and cost-effective me...

[Effects and Biological Response on Bioremediation of Petroleum Contaminated Soil].

PubMed

Yang, Qian; Wu, Man-li; Nie, Mai-qian; Wang, Ting-ting; Zhang, Ming-hui

2015-05-01

Bioaugmentation and biostimulation were used to remediate petroleum-contaminated soil which were collected from Zichang city in North of Shaanxi. The optimal bioremediation method was obtained by determining the total petroleum hydrocarbon(TPH) using the infrared spectroscopy. During the bioremediation, number of degrading strains, TPH catabolic genes, and soil microbial community diversity were determined by Most Probable Number (MPN), polymerase chain reaction (PCR) combined agarose electrophoresis, and PCR-denaturing gradient electrophoresis (DGGE). The results in different treatments showed different biodegradation effects towards total petroleum hydrocarbon (TPH). Biostimulation by adding N and P to soils achieved the best degradation effects towards TPH, and the bioaugmentation was achieved by inoculating strain SZ-1 to soils. Further analysis indicated the positive correlation between catabolic genes and TPH removal efficiency. During the bioremediation, the number of TPH and alkanes degrading strains was higher than the number of aromatic degrading strains. The results of PCR-DGGE showed microbial inoculums could enhance microbial community functional diversity. These results contribute to understand the ecologically microbial effects during the bioremediation of petroleum-polluted soil.

Time-dependent effect of composted tannery sludge on the chemical and microbial properties of soil.

PubMed

de Sousa, Ricardo Silva; Santos, Vilma Maria; de Melo, Wanderley Jose; Nunes, Luis Alfredo Pinheiro Leal; van den Brink, Paul J; Araújo, Ademir Sérgio Ferreira

2017-12-01

Composting has been suggested as an efficient method for tannery sludge recycling before its application to the soil. However, the application of composted tannery sludge (CTS) should be monitored to evaluate its effect on the chemical and microbial properties of soil. This study evaluated the time-dependent effect of CTS on the chemical and microbial properties of soil. CTS was applied at 0, 2.5, 5, 10, and 20 Mg ha -1 and the soil chemical and microbial properties were evaluated at 0, 45, 75, 150, and 180 days. Increased CTS rates increased the levels of Ca, Cr, and Mg. While Soil pH, organic C, and P increased with the CTS rates initially, this effect decreased over time. Soil microbial biomass, respiration, metabolic quotient, and dehydrogenase increased with the application of CTS, but decreased over time. Analysis of the Principal Response Curve showed a significant effect of CTS rate on the chemical and microbial properties of the soil over time. The weight of each variable indicated that all soil properties, except β-glucosidase, dehydrogenase and microbial quotient, increased due to the CTS application. However, the highest weights were found for Cr, pH, Ca, P, phosphatase and total organic C. The application of CTS in the soil changed the chemical and microbial properties over time, indicating Cr, pH, Ca, phosphatase, and soil respiration as the more responsive chemical and microbial variables by CTS application.

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

PubMed Central

Yrjälä, Kim; Alakukku, Laura; Palojärvi, Ansa

2012-01-01

The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy. PMID:22983972

[Effect of afforestation modes on soil microbial community and nitrogen functional genes in Hippophae rhamnoides plantation].

PubMed

Yang, Dan; Yu, Xuan; Liu, Xu; Liu, Jin-liana; Zhang, Shun-xiang; Yu, Ze-qun

2015-12-01

The study aimed to assess the effect of different afforestation modes on microbial composition and nitrogen functional genes in soil. Soil samples from a pure Hippophae rhamnoides stand (SS) and three mixed stands, namely, H. rhamnoides and Pinus tabuliformis (SY), H. rhamnoides and Platycladus orientalis (SB), H. rhamnoides and Robinia pseucdoacacia (SC) were selected. The results showed that the total PLFA (TPLFA), bacterial PLFA, gram positive bacterial PLFA (G⁺PLFA) were significantly higher in soil samples from other three stands than those of the pure one. However, no significant difference was found for fungal PLFA among them. The abundance of nifH, amoA, nirK and narG genes were higher in SY and SC than in SS. The TPLFA, G⁺PLFA, gram negative bacterial PLFA (G⁻PLFA), and all of the detected gene abundance were significantly and positively correlated with soil pH, total organic carbon, total nitrogen, ammonium nitrogen and available potassium. Afforestation modes affected indirectly soil microbial composition and functional genes through soil properties. Mixing P. tabuliformis or P. orientalis with H. rhamnoides might be suitable afforestation modes, which might improve soil quality.

Divergent Responses of Forest Soil Microbial Communities under Elevated CO 2 in Different Depths of Upper Soil Layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Hao; He, Zhili; Wang, Aijie

Numerous studies have shown that the continuous increase of atmosphere CO 2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO 2 (eCO 2) at different soil depth profiles in forest ecosystems. In this paper, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO 2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO 2 significantly shifted the compositions, including phylogenetic and functional genemore » structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO 2 at both soil depths, although the stimulation effect of eCO 2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO 3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO 2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO 2 increases. The concentration of atmospheric carbon dioxide (CO 2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO 2 (eCO 2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO 2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO 2 at both soil depths. Finally, more functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO 2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.« less

Divergent Responses of Forest Soil Microbial Communities under Elevated CO 2 in Different Depths of Upper Soil Layers

DOE PAGES

Yu, Hao; He, Zhili; Wang, Aijie; ...

2017-10-27

Numerous studies have shown that the continuous increase of atmosphere CO 2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO 2 (eCO 2) at different soil depth profiles in forest ecosystems. In this paper, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO 2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO 2 significantly shifted the compositions, including phylogenetic and functional genemore » structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO 2 at both soil depths, although the stimulation effect of eCO 2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO 3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO 2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO 2 increases. The concentration of atmospheric carbon dioxide (CO 2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO 2 (eCO 2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO 2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO 2 at both soil depths. Finally, more functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO 2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.« less

Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers.

PubMed

Yu, Hao; He, Zhili; Wang, Aijie; Xie, Jianping; Wu, Liyou; Van Nostrand, Joy D; Jin, Decai; Shao, Zhimin; Schadt, Christopher W; Zhou, Jizhong; Deng, Ye

2018-01-01

Numerous studies have shown that the continuous increase of atmosphere CO 2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO 2 (eCO 2 ) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO 2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO 2 significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO 2 at both soil depths, although the stimulation effect of eCO 2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO 3 -N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO 2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO 2 increases. IMPORTANCE The concentration of atmospheric carbon dioxide (CO 2 ) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO 2 (eCO 2 ) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO 2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO 2 at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO 2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm. Copyright © 2017 American Society for Microbiology.

The effect of biochar amendment on the soil microbial community - PLFA analyses and 13C labeling results

NASA Astrophysics Data System (ADS)

Watzinger, A.; Feichtmair, S.; Rempt, F.; Anders, E.; Wimmer, B.; Kitzler, B.; Zechmeister-Boltenstern, S.; Horacek, M.; Zehetner, F.; Kloss, S.; Richoz, S.; Soja, G.

2012-04-01

The effects of biochar amendment on plant growth and on the chemical / physical soil characteristics are well explored but only few studies have investigated the impact on soil microorganisms. The response of the soil microbial community to biochar amendment was investigated by phospholipid fatty acid (PLFA) analysis in (i) a large scale pot experiment, (ii) a small scale pot experiment using 13C labeled biochar and (iii) an incubation study using 13C labeled biochar. In the large scale pot experiment, three different agricultural soils from Austria (Planosol, Cambisol, Chernozem) and four different types of biochar were investigated. In total, 25 treatments with 5 replicates each were set up and monitored over a year. The results from the pot experiments showed no significant influence of biochar amendment on the total microbial biomass in the first 100 days after biochar addition. However, discriminant analysis showed a distinction of biochar and control soils as well as a strong effect of the pyrolysis temperature on the microbial composition. The effect of biochar was dependent on the type of soil. In the Planosol, some PLFAs were affected positively, especially when adding biochar with a low pyrolysis temperature, in the first month. In the long term, microbial community composition altered. Growth of fungi and gram negative bacteria was enhanced. In the Chernozem, PLFAs from various microbial groups decreased in the long term. Variability in the incubation study was low. Consequently, many PLFAs were significantly affected by biochar amendment. Again, in the Planosol, gram negative bacteria, actinomycetes and, after 2 weeks, gram positive bacteria increased under biochar amendment whereas in the chernozem total microbial biomass and gram positive bacteria were negatively affected in the long term. The 13C labeling studies confirmed the low degradability of the biochar, i.e. no alteration of the content and the δ13C in the soil organic matter within 100 days, decreased CO2 emission after biochar addition and little 13C signature from the biochar in the respired CO2. The uptake of the labeled biochar into the microbial PLFAs was analysed and will provide an evidence if biochar was used as a carbon source. In addition, the long term effect of biochar amendment (beyond 100 days) on the soil microbial community is currently investigated. These results will be also presented in the oncoming meeting.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE PAGES

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; ...

2017-09-28

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

NASA Astrophysics Data System (ADS)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; Zhou, Xiaolu; Wang, Meng; Zhang, Kerou; Wang, Gangsheng

2017-10-01

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195 Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated by Xu et al. (2014). We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC), and mineral-associated organic carbon (MOC). However, our work represents the first step toward a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles.

PubMed

Li, Yang; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

2017-03-01

Native soil amendment has been widely used to stabilize mine tailings and speed up the development of soil biogeochemical functions before revegetation; however, it remains poorly understood about the response of microbial communities to ecological restoration of mine tailings with soil-covered strategy. In this study, microbial communities along a 60-cm profile were investigated in mine tailings during ecological restoration of two revegetation strategies (directly revegetation and native soil covered) with different plant species. The mine tailings were covered by native soils as thick as 40 cm for more than 10 years, and the total nitrogen, total organic carbon, water content, and heavy metal (Fe, Cu, and Zn) contents in the 0-40 cm intervals of profiles were changed. In addition, increased microbial diversity and changed microbial community structure were also found in the 10-40 cm intervals of profiles in soil-covered area. Soil-covered strategy rather than plant species and soil depth was the main factor influencing the bacterial community, which explained the largest portion (29.96%) of the observed variation. Compared directly to revegetation, soil-covered strategy exhibited the higher relative abundance of Acidobacteria and Deltaproteobacteria and the lower relative abundance of Bacteroidetes, Gemmatimonadetes, Betaproteobacteria, and Gammaproteobacteria. PICRUSt analysis further demonstrated that soil-covered caused energy metabolic functional changes in carbon, nitrogen, and sulfur metabolism. Given all these, the soil-covered strategy may be used to fast-track the establishment of native microbial communities and is conducive to the rehabilitation of biogeochemical processes for establishing native plant species.

Mapping and determinism of soil microbial community distribution across an agricultural landscape.

PubMed

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-06-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Impact of understory vegetation on soil carbon and nitrogen dynamic in aerially seeded Pinus massoniana plantations.

PubMed

Pan, Ping; Zhao, Fang; Ning, Jinkui; Zhang, Ling; Ouyang, Xunzhi; Zang, Hao

2018-01-01

Understory vegetation plays a vital role in regulating soil carbon (C) and nitrogen (N) characteristics due to differences in plant functional traits. Different understory vegetation types have been reported following aerial seeding. While aerial seeding is common in areas with serious soil erosion, few studies have been conducted to investigate changes in soil C and N cycling as affected by understory vegetation in aerially seeded plantations. Here, we studied soil C and N characteristics under two naturally formed understory vegetation types (Dicranopteris and graminoid) in aerially seeded Pinus massoniana Lamb plantations. Across the two studied understory vegetation types, soil organic C was significantly correlated with all measured soil N variables, including total N, available N, microbial biomass N and water-soluble organic N, while microbial biomass C was correlated with all measured variables except soil organic C. Dicranopteris and graminoid differed in their effects on soil C and N process. Except water-soluble organic C, all the other C and N variables were higher in soils with graminoids. The higher levels of soil organic C, microbial biomass C, total N, available N, microbial biomass N and water-soluble organic N were consistent with the higher litter and root quality (C/N) of graminoid vegetation compared to Dicranopteris. Changes in soil C and N cycles might be impacted by understory vegetation types via differences in litter or root quality.

Impact of understory vegetation on soil carbon and nitrogen dynamic in aerially seeded Pinus massoniana plantations

PubMed Central

Pan, Ping; Zhao, Fang; Ning, Jinkui; Ouyang, Xunzhi; Zang, Hao

2018-01-01

Understory vegetation plays a vital role in regulating soil carbon (C) and nitrogen (N) characteristics due to differences in plant functional traits. Different understory vegetation types have been reported following aerial seeding. While aerial seeding is common in areas with serious soil erosion, few studies have been conducted to investigate changes in soil C and N cycling as affected by understory vegetation in aerially seeded plantations. Here, we studied soil C and N characteristics under two naturally formed understory vegetation types (Dicranopteris and graminoid) in aerially seeded Pinus massoniana Lamb plantations. Across the two studied understory vegetation types, soil organic C was significantly correlated with all measured soil N variables, including total N, available N, microbial biomass N and water-soluble organic N, while microbial biomass C was correlated with all measured variables except soil organic C. Dicranopteris and graminoid differed in their effects on soil C and N process. Except water-soluble organic C, all the other C and N variables were higher in soils with graminoids. The higher levels of soil organic C, microbial biomass C, total N, available N, microbial biomass N and water-soluble organic N were consistent with the higher litter and root quality (C/N) of graminoid vegetation compared to Dicranopteris. Changes in soil C and N cycles might be impacted by understory vegetation types via differences in litter or root quality. PMID:29377926

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

PubMed Central

Oates, Lawrence G.; Read, Harry W.; Gutknecht, Jessica L. M.; Duncan, David S.; Balser, Teri B.; Jackson, Randall D.

2017-01-01

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition. An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step. PMID:28745639

Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development

PubMed Central

Gui, Heng; Hyde, Kevin; Xu, Jianchu; Mortimer, Peter

2017-01-01

Although there is a growing amount of evidence that arbuscular mycorrhizal fungi (AMF) influence the decomposition process, the extent of their involvement remains unclear. Therefore, given this knowledge gap, our aim was to test how AMF influence the soil decomposer communities. Dual compartment microcosms, where AMF (Glomus mosseae) were either allowed access (AM+) to or excluded (AM−) from forest soil compartments containing litterbags (leaf litter from Calophyllum polyanthum) were used. The experiment ran for six months, with destructive harvests at 0, 90, 120, 150, and 180 days. For each harvest we measured AMF colonization, soil nutrients, litter mass loss, and microbial biomass (using phospholipid fatty acid analysis (PLFA)). AMF significantly enhanced litter decomposition in the first 5 months, whilst delaying the development of total microbial biomass (represented by total PLFA) from T150 to T180. A significant decline in soil available N was observed through the course of the experiment for both treatments. This study shows that AMF have the capacity to interact with soil microbial communities and inhibit the development of fungal and bacterial groups in the soil at the later stage of the litter decomposition (180 days), whilst enhancing the rates of decomposition. PMID:28176855

[Variations of soil microbial community composition and enzyme activities with different salinities on Yuyao coast, Zhejiang, China].

PubMed

Sun, Hui; Zhang, Jian Feng; Xu, Hua Sen; Chen, Guang Cai; Wang, Li Ping

2016-10-01

In October 2015, soil samples with different salinity were collected in a coast area in Yuyao, Zhejiang, and soil microbial community composition, soil catalase, urease activities, as well as soil physical and chemical properties were studied. The results showed that Nitrospira took absolute advantage in the bacterial community, and showed good correlations to total potassium. Cladosporium and Fusarium were predominant in the fungal community. Meanwhile, Cladosporium was related to soil urease and total nitrogen, and same correlation was found between Fusarium and soil urease. Catalase activity ranged from 3.52 to 4.56 mL·g -1 , 3.08 to 4.61 mL·g -1 and 5.81 to 6.91 mL·g -1 for soils with heavy, medium and weak salinity, respectively. Catalase activity increased with the soil layer deepening, which was directly related to soil total potassium, and indirectly related to pH, organic matter, total nitrogen and total phosphorus through total potassium. Soil urease activity ranged among 0.04 to 0.52 mg·g -1 , 0.08 to 1.07 mg·g -1 and 0.27 to 8.21 mg·g -1 for each saline soil, respectively. Urease activity decreased with soil layer deepening which was directly related to soil total nitrogen, and was indirectly related to pH, organic matter and total potassium through total nitrogen. The total phosphorus was the largest effect factor on the bacterial community CCA ordination, and the urease was on fungal community.

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.

PubMed

Gill, Aman S; Lee, Angela; McGuire, Krista L

2017-08-15

New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation ( cbbL-R [ cbbL gene, red-like subunit] and apsA ), nitrogen cycling ( noxZ and amoA ), and contaminant degradation ( bphA ); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered. Copyright © 2017 American Society for Microbiology.

Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils

PubMed Central

Lee, Angela; McGuire, Krista L.

2017-01-01

ABSTRACT New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered. PMID:28576763

Comparative effects of sulfuric and nitric acid rain on litter decomposition and soil microbial community in subtropical plantation of Yangtze River Delta region.

PubMed

Liu, Xin; Zhang, Bo; Zhao, Wenrui; Wang, Ling; Xie, Dejin; Huo, Wentong; Wu, Yanwen; Zhang, Jinchi

2017-12-01

Acid rain is mainly caused by dissolution of sulfur dioxide and nitrogen oxides in the atmosphere, and has a significant negative effect on ecosystems. The relative composition of acid rain is changing gradually from sulfuric acid rain (SAR) to nitric acid rain (NAR) with the rapidly growing amount of nitrogen deposition. In this study, we investigated the impact of simulated SAR and NAR on litter decomposition and the soil microbial community over four seasons since March 2015. Results first showed that the effects of acid rain on litter decomposition and soil microbial were positive in the early period of the experiment, except for SAR on soil microbes. Second, soil pH with NAR decreased more rapidly with the amount of acid rain increased in summer than with SAR treatments. Only strongly acid rain (both SAR and NAR) was capable of depressing litter decomposition and its inhibitory effect was stronger on leaf than on fine root litter. Meanwhile, NAR had a higher inhibitory effect on litter decomposition than SAR. Third, in summer, autumn and winter, PLFAs were negatively impacted by the increased acidity level resulting from both SAR and NAR. However, higher acidity level of NAR (pH=2.5) had the strongest inhibitory impact on soil microbial activity, especially in summer. In addition, Gram-negative bacteria (cy19:0) and fungi (18:1ω9) were more sensitive to both SAR and NAR, and actinomycetes was more sensitive to SAR intensity. Finally, soil total carbon, total nitrogen and pH were the most important soil property factors affecting soil microbial activity, and high microbial indices (fungi/bacteria) with high soil pH. Our results suggest that the ratio of SO 4 2- to NO 3 - in acid rain is an important factor which could affect litter decomposition and soil microbial in subtropical forest of China. Copyright © 2017. Published by Elsevier B.V.

Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils.

PubMed

Cao, Qing; Steinman, Alan D; Su, Xiaomei; Xie, Liqiang

2017-12-01

A 30-day indoor incubation experiment was conducted to investigate the effects of different concentrations of microcystin (1, 10, 100 and 1000 μg eq. MC-LR L -1 ) on soil enzyme activity, soil respiration, physiological profiles, potential nitrification, and microbial abundance (total bacteria, total fungi, ammonia-oxidizing bacteria and archaea) in two lakeside soils in China (Soil A from the lakeside of Lake Poyanghu at Jiujiang; Soil B from the lakeside of Lake Taihu at Suzhou). Of the enzymes tested, only phenol oxidase activity was negatively affected by microcystin application. In contrast, dehydrogenase activity was stimulated in the 1000 μg treatment, and a stimulatory effect also occurred with soil respiration in contaminated soil. The metabolic profiles of the microbial communities indicated that overall carbon metabolic activity in the soils treated with high microcystin concentrations was inhibited, and high concentrations of microcystin also led to different patterns of potential carbon utilization. High microcystin concentrations (100, 1000 μg eq. MC-LR L -1 in Soil A; 10, 100 1000 μg eq. MC-LR L -1 in Soil B) significantly decreased soil potential nitrification rate. Furthermore, the decrease in soil potential nitrification rate was positively correlated with the decrease of the amoA gene abundance, which corresponds to the ammonia-oxidizing bacterial community. We conclude that application of microcystin-enriched irrigation water can significantly impact soil microbial community structure and function. Copyright © 2017 Elsevier Ltd. All rights reserved.

Soil microbial responses to warming and increased precipitation and their implications for ecosystem C cycling.

PubMed

Zhang, Naili; Liu, Weixing; Yang, Haijun; Yu, Xingjun; Gutknecht, Jessica L M; Zhang, Zhe; Wan, Shiqiang; Ma, Keping

2013-11-01

A better understanding of soil microbial ecology is critical to gaining an understanding of terrestrial carbon (C) cycle-climate change feedbacks. However, current knowledge limits our ability to predict microbial community dynamics in the face of multiple global change drivers and their implications for respiratory loss of soil carbon. Whether microorganisms will acclimate to climate warming and ameliorate predicted respiratory C losses is still debated. It also remains unclear how precipitation, another important climate change driver, will interact with warming to affect microorganisms and their regulation of respiratory C loss. We explore the dynamics of microorganisms and their contributions to respiratory C loss using a 4-year (2006-2009) field experiment in a semi-arid grassland with increased temperature and precipitation in a full factorial design. We found no response of mass-specific (per unit microbial biomass C) heterotrophic respiration to warming, suggesting that respiratory C loss is directly from microbial growth rather than total physiological respiratory responses to warming. Increased precipitation did stimulate both microbial biomass and mass-specific respiration, both of which make large contributions to respiratory loss of soil carbon. Taken together, these results suggest that, in semi-arid grasslands, soil moisture and related substrate availability may inhibit physiological respiratory responses to warming (where soil moisture was significantly lower), while they are not inhibited under elevated precipitation. Although we found no total physiological response to warming, warming increased bacterial C utilization (measured by BIOLOG EcoPlates) and increased bacterial oxidation of carbohydrates and phenols. Non-metric multidimensional scaling analysis as well as ANOVA testing showed that warming or increased precipitation did not change microbial community structure, which could suggest that microbial communities in semi-arid grasslands are already adapted to fluctuating climatic conditions. In summary, our results support the idea that microbial responses to climate change are multifaceted and, even with no large shifts in community structure, microbial mediation of soil carbon loss could still occur under future climate scenarios.

Effects of Different Regeneration Scenarios and Fertilizer Treatments on Soil Microbial Ecology in Reclaimed Opencast Mining Areas on the Loess Plateau, China

PubMed Central

Li, Junjian; Zheng, Yuanming; Yan, Junxia; Li, Hongjian; Wang, Xiang; He, Jizheng; Ding, Guangwei

2013-01-01

The soil microbial community in reclaimed mining areas is fundamental to vegetative establishment. However, how this community responds to different regeneration scenarios and fertilizer treatments is poorly understood. This research evaluated plant and soil microbial communities from different regeneration scenarios and different fertilizer treatments. Regeneration scenarios significantly influenced soil bacterial, archaeal, and fungal rDNA abundance. The ratios of fungi to bacteria or archaea were increased with fertilizer application. The diversity of both plants and microbes was lowest in Lotus corniculatus grasslands. Regeneration scenario, fertilizer treatment, and their interaction influenced soil microbial richness, diversity and evenness indices. Labile carbon pool 2 was a significant factor affected plant and microbe communities in July, suggesting that plants and microbes may be competing for nutrients. The higher ratios of positive to negative association were found in soil bacteria and total microbe than in archaea and fungi. Stronger clustering of microbial communities from the same regeneration scenario indicated that the vegetative composition of regeneration site may have a greater influence on soil microbial communities than fertilizer treatment. PMID:23658819

Microbial activity in the profiles of gray forest soil and chernozems

NASA Astrophysics Data System (ADS)

Susyan, E. A.; Rybyanets, D. S.; Ananyeva, N. D.

2006-08-01

Soil samples were taken from the profiles of a gray forest soil (under a forest) and southern chernozems of different textures under meadow vegetation. The microbial biomass (MB) was determined by the method of substrate-induced respiration; the basal respiration (BR) and the population density of microorganisms on nutrient media of different composition were also determined in the samples. The microbial metabolic quotient ( qCO2 = BR/MB) and the portion of microbial carbon (C mic) in C org were calculated. The MB and BR values were shown to decrease down the soil profiles. About 57% of the total MB in the entire soil profile was concentrated in the layer of 0-24 cm of the gray forest soil. The MB in the C horizon of chernozems was approximately two times lower than the MB in the A horizon of these soils. The correlation was found between the MB and the C org ( r = 0.99) and between the MB and the clay content ( r = 0.89) in the profile of the gray forest soil. The C mic/C org ratio in the gray forest soil and in the chernozems comprised 2.3-6.6 and 1.2-9.6%, respectively. The qCO2 value increased with the depth. The microbial community in the lower layers of the gray forest soil was dominated (88-96%) by oligotrophic microorganisms (grown on soil agar); in the upper 5 cm, these microorganisms comprised only 50% of the total amount of microorganisms grown on three media.

Similar soil microbial community structure across different environments after long-term succession: evidence from volcanoes of different ages.

PubMed

Xu, Shangqi; Zhang, Jianfeng; Luo, Shasha; Zhou, Xue; Shi, Shaohua; Tian, Chunjie

2018-06-08

Soil microbes play critical roles in global biogeochemical cycles, but their succession patterns across long temporal scales have rarely been studied. In this study, soil samples were collected from three volcanoes in Wudalianchi, northeastern China: Laoheishan (LH, approximately 240 years old), Dongjiaodebushan (DJ, 0.45-0.6 million years old), and Nangelaqiushan (NG, 0.8-1.3 million years old). For each volcano, both southern (S) and northern (N) slope aspects were sampled. Soil microbial communities were analyzed using phospholipid fatty acid analysis (PLFA). The results showed that soil properties and microbial biomass changed perceptibly among different volcanoes and different slope aspects. Almost all of the detected soil nutrient contents of LH were lowest, and total microbial biomass of LH was 40 and 36% lower than those of NG and DJ, respectively. LH was significantly different from NG and DJ in soil microbial community structure with a higher relative abundance of fungi and a lower relative abundance of actinomycetes and bacteria. However, for the two ancient volcanoes (NG and DJ), soil microbial community structures were highly similar among different ages and different slope aspects. No difference was detected in any of the measured microbial indices, including richness, evenness, Shannon's diversity, Simpson's diversity and the relative abundance of different microbial groups. The results indicated that while soil microbial biomass may change across different soil environments after long-term succession, soil microbial community structure can remain relatively stable. The results further indicated that soil microbes may show different successional patterns in different stages of succession. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial Indicators of Soil Quality under Different Land Use Systems in Subtropical Soils

NASA Astrophysics Data System (ADS)

Maharjan, M.

2016-12-01

Land-use change from native forest to intensive agricultural systems can negatively impact numerous soil parameters. Understanding the effects of forest ecosystem transformations on markers of long-term soil health is particularly important in rapidly developing regions such as Nepal, where unprecedented levels of agriculturally-driven deforestation have occurred in recent decades. However, the effects of widespread land use changes on soil quality in this region have yet to be properly characterized. Microbial indicators (soil microbial biomass, metabolic quotient and enzymes activities) are particularly suited to assessing the consequences of such ecosystem disturbances, as microbial communities are especially sensitive to environmental change. Thus, the aim of this study was to assess the effect of land use system; i.e. forest, organic and conventional farming, on soil quality in Chitwan, Nepal using markers of microbial community size and activity. Total organic C and N contents were higher in organic farming compared with conventional farming and forest, suggesting higher nutrient retention and soil preservation with organic farming practices compared to conventional. These differences in soil composition were reflected in the health of the soil microbial communities: Organic farm soil exhibited higher microbial biomass C, elevated β-glucosidase and chitinase activities, and a lower metabolic quotient relative to other soils, indicating a larger, more active, and less stressed microbial community, respectively. These results collectively demonstrate that application of organic fertilizers and organic residues positively influence nutrient availability, with subsequent improvements in soil quality and productivity. Furthermore, the sensitivity of microbial indicators to different management practices demonstrated in this study supports their use as effective markers of ecosystem disturbance in subtropical soils.

Effects of Jet Fuel Spills on the Microbial Community of Soil †

PubMed Central

Song, Hong-Gyu; Bartha, Richard

1990-01-01

Hydrocarbon residues, microbial numbers, and microbial activity were measured and correlated in loam soil contaminated by jet fuel spills resulting in 50 and 135 mg of hydrocarbon g of soil−1. Contaminated soil was incubated at 27°C either as well-aerated surface soil or as poorly aerated subsurface soil. In the former case, the effects of bioremediation treatment on residues, microbial numbers, and microbial activity were also assessed. Hydrocarbon residues were measured by quantitative gas chromatography. Enumerations included direct counts of metabolically active bacteria, measurement of mycelial length, plate counts of aerobic heterotrophs, and most probable numbers of hydrocarbon degraders. Activity was assessed by fluorescein diacetate (FDA) hydrolysis. Jet fuel disappeared much more rapidly from surface soil than it did from subsurface soil. In surface soil, microbial numbers and mycelial length were increased by 2 to 2.5 orders of magnitude as a result of jet fuel contamination alone and by 3 to 4 orders of magnitude as a result of the combination of jet fuel contamination and bioremediation. FDA hydrolysis was stimulated by jet fuel and bioremediation, but was inhibited by jet fuel alone. The latter was traced to an inhibition of the FDA assay by jet fuel biodegradation products. In subsurface soil, oxygen limitation strongly attenuated microbial responses to jet fuel. An increase in the most probable numbers of hydrocarbon degraders was accompanied by a decline in other aerobic heterotrophs, so that total plate counts changed little. The correlations between hydrocarbon residues, microbial numbers, and microbial activity help in elucidating microbial contributions to jet fuel elimination from soil. PMID:16348138

Elevated CO2 benefits the soil microenvironment in the rhizosphere of Robinia pseudoacacia L. seedlings in Cd- and Pb-contaminated soils.

PubMed

Huang, Shuping; Jia, Xia; Zhao, Yonghua; Bai, Bo; Chang, Yafei

2017-02-01

Soil contamination by heavy metals in combination with elevated atmospheric CO 2 has important effects on the rhizosphere microenvironment by influencing plant growth. Here, we investigated the response of the R. pseudoacacia rhizosphere microenvironment to elevated CO 2 in combination with cadmium (Cd)- and lead (Pb)-contamination. Organic compounds (total soluble sugars, soluble phenolic acids, free amino acids, and organic acids), microbial abundance and activity, and enzyme activity (urease, dehydrogenase, invertase, and β-glucosidase) in rhizosphere soils increased significantly (p < 0.05) under elevated CO 2 relative to ambient CO 2 ; however, l-asparaginase activity decreased. Addionally, elevated CO 2 alone affected soil microbial community in the rhizosphere. Heavy metals alone resulted in an increase in total soluble sugars, free amino acids, and organic acids, a decrease in phenolic acids, microbial populations and biomass, and enzyme activity, and a change in microbial community in rhizosphere soils. Elevated CO 2 led to an increase in organic compounds, microbial populations, biomass, and activity, and enzyme activity (except for l-asparaginase), and changes in microbial community under Cd, Pb, or Cd + Pb treatments relative to ambient CO 2 . In addition, elevated CO 2 significantly (p < 0.05) enhanced the removal ratio of Cd and Pb in rhizosphere soils. Overall, elevated CO 2 benefited the rhizosphere microenvironment of R. pseudoacacia seedlings under heavy metal stress, which suggests that increased atmospheric CO 2 concentrations could have positive effects on soil fertility and rhizosphere microenvironment under heavy metals. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of enhanced UV-B radiation on the diversity and activity of soil microorganism of alpine meadow ecosystem in Qinghai-Tibet Plateau.

PubMed

Niu, Fujun; He, Junxia; Zhang, Gaosen; Liu, Xiaomei; Liu, Wei; Dong, Maoxing; Wu, Fasi; Liu, Yongjun; Ma, Xiaojun; An, Lizhe; Feng, Huyuan

2014-12-01

The effects of enhanced UV-B radiation on abundance, community composition and the total microbial activity of soil bacteria in alpine meadow ecosystem of Qinghai-Tibet Plateau were investigated. Traditional counting and 16S rRNA gene sequencing were used to investigate the culturable bacteria and their composition in soil, meanwhile the total microbial activity was measured by microcalorimetry. The population of soil culturable bacteria was slightly reduced with the enhanced UV-B radiation in both of the two depths, 2.46 × 10(6) CFU/g in upper layer (0-10 cm), 1.44 × 10(6) CFU/g in under layer (10-20 cm), comparing with the control (2.94 × 10(6) CFU/g in upper layer, 1.65 × 10(6) CFU/g in under layer), although the difference was not statistically significant (P > 0.05). However, the bacteria diversity decreased obviously due to enhanced UV-B, the number of species for upper layer was decreased from 20 to 13, and from 16 to 13 for the lower layer. The distribution of species was also quite different between the two layers. Another obvious decrease induced by enhanced UV-B radiation was in the total soil microbial activities, which was represented by the microbial growth rate constant (k) in this study. The results indicated that the culturable bacteria community composition and the total activity of soil microbes have been considerably changed by the enhanced UV-B radiation.

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity.

PubMed

Sun, Bingjie; Jia, Shuxia; Zhang, Shixiu; McLaughlin, Neil B; Liang, Aizhen; Chen, Xuewen; Liu, Siyi; Zhang, Xiaoping

2016-04-01

Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

PubMed Central

Li, Xiaofang; Bond, Philip L.; Van Nostrand, Joy D.; Zhou, Jizhong; Huang, Longbin

2015-01-01

Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes. PMID:26268667

Microbial communities and soil fertility in flood irrigated orchards under different management systems in eastern spain

NASA Astrophysics Data System (ADS)

Morugán-Coronado, Alicia; García-Orenes, Fuensanta; Caravaca, Fuensanta; Roldán, Antonio

2016-04-01

Unsuitable land management such as the excessive use of herbicides can lead to a loss of soil fertility and a drastic reduction in the abundance of microbial populations and their functions related to nutrient cycling. Microbial communities are the most sensitive and rapid indicators of perturbations in agroecosystems. A field experiment was performed in an orange-trees orchard (Citrus sinensis) to assess the long-term effect of three different management systems on the soil microbial community biomass, structure and composition (phospholipid fatty acids (PLFAs) total, pattern, and abundance). The three agricultural systems assayed were established 30 years ago: herbicides (Glyphosate (N-(phosphonomethyl)glycine) with inorganic fertilizers (H), intensive ploughing and inorganic fertilizers (NPK 15%) (P) and organic farming (chipped pruned branches and weeds, manure from sheep and goats) (O). Nine soil samples were taken from each system. The results showed that the management practices including herbicides and intensive ploughing had similar results on soil microbial properties, while organic fertilization significantly increased microbial biomass, shifted the structure and composition of the soil microbial community, and stimulated microbial activity, when compared to inorganic fertilization systems; thus, enhancing the sustainability of this agroecosystem under semiarid conditions.

The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

NASA Astrophysics Data System (ADS)

Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

2011-12-01

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial communities, while the quality of available organic matter may have played a significant role in supporting high performing microbial communities.

Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

NASA Astrophysics Data System (ADS)

He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

2014-12-01

Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

Abiotic factors shape microbial diversity in Sonoran Desert soils.

PubMed

Andrew, David R; Fitak, Robert R; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G; Dontsova, Katerina

2012-11-01

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

PubMed Central

Fitak, Robert R.; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G.; Dontsova, Katerina

2012-01-01

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments. PMID:22885757

Effect of rice straw application on microbial community and activity in paddy soil under different water status.

PubMed

Pan, Fuxia; Li, Yaying; Chapman, Stephen James; Yao, Huaiying

2016-03-01

Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10 g kg(-1) soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp(™) method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7 %, while soil water status explained 7.5 and 29.1 %, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity.

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition.

PubMed

Ma, Xingyu; Zhao, Cancan; Gao, Ying; Liu, Bin; Wang, Tengxu; Yuan, Tong; Hale, Lauren; Nostrand, Joy D Van; Wan, Shiqiang; Zhou, Jizhong; Yang, Yunfeng

2017-08-01

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling. © 2017 John Wiley & Sons Ltd.

Biodegradation of spilled diesel fuel in agricultural soil: effect of humates, zeolite, and bioaugmentation.

PubMed

Kuráň, Pavel; Trögl, Josef; Nováková, Jana; Pilařová, Věra; Dáňová, Petra; Pavlorková, Jana; Kozler, Josef; Novák, František; Popelka, Jan

2014-01-01

Possible enhancement of biodegradation of petroleum hydrocarbons in agricultural soil after tank truck accident (~5000 mg/kg dry soil initial concentration) by bioaugmentation of diesel degrading Pseudomonas fluorescens strain and addition of abiotic additives (humates, zeolite) was studied in a 9-month pot experiment. The biodegradation process was followed by means of analytical parameters (hydrocarbon index expressed as content of C10-C40 aliphatic hydrocarbons, ratio pristane/C17, and total organic carbon content) and characterization of soil microbial community (content of phospholipid fatty acids (PLFA) as an indicator of living microbial biomass, respiration, and dehydrogenase activity). The concentration of petroleum hydrocarbons (C10-C40) was successfully reduced by ~60% in all 15 experiment variants. The bioaugmentation resulted in faster hydrocarbon elimination. On the contrary, the addition of humates and zeolite caused only a negligible increase in the degradation rate. These factors, however, affected significantly the amount of PLFA. The humates caused significantly faster increase of the total PLFA suggesting improvement of the soil microenvironment. Zeolite caused significantly slower increase of the total PLFA; nevertheless it aided in homogenization of the soil. Comparison of microbial activities and total PLFA revealed that only a small fraction of autochthonous microbes took part in the biodegradation which confirms that bioaugmentation was the most important treatment.

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

PubMed

Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich

2017-05-01

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe.

PubMed

Delgado-Baquerizo, Manuel; Eldridge, David J; Ochoa, Victoria; Gozalo, Beatriz; Singh, Brajesh K; Maestre, Fernando T

2017-10-01

The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N and P cycling (multifunctionality resistance) to global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide to investigate the importance of microbial communities as predictor of multifunctionality resistance to climate change and nitrogen fertilisation. Multifunctionality had a lower resistance to wetting-drying cycles than to warming or N deposition. Multifunctionality resistance was regulated by changes in microbial composition (relative abundance of phylotypes) but not by richness, total abundance of fungi and bacteria or the fungal: bacterial ratio. Our results suggest that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH. Together, our work demonstrates strong links between microbial community composition and multifunctionality resistance in dryland soils from six continents, and provides insights into the importance of microbial community composition for buffering effects of global change in drylands worldwide. © 2017 John Wiley & Sons Ltd/CNRS.

Effects and risk assessment of linear alkylbenzene sulfonates in agricultural soil. 1. Short-term effects on soil microbiology.

PubMed

Elsgaard, L; Petersen, S O; Debosz, K

2001-08-01

Linear alkylbenzene sulfonates (LAS) may occur in sewage sludge that is applied to agricultural soil, in which LAS can be inhibitory to biological activity. As a part of a broader risk assessment of LAS in the terrestrial environment, we tested the short-term effects of aqueous LAS on microbial parameters in a sandy agricultural soil that was incubated for up to 11 d. The assays included 10 microbial soil parameters; ethylene degradation; potential ammonium oxidation; potential dehydrogenase activity; beta-glucosidase activity; iron reduction; the populations of cellulolytic bacteria, fungi and actinomycetes; the basal soil respiration; and the phospholipid fatty acid (PLFA) content. Except for beta-glucosidase activity, basal respiration, and total PLFA content, all soil parameters were sensitive to LAS, with EC10 values in the range of less than 8 to 22 mg/kg dry weight. This probably reflected a similar mode of LAS toxicity, ascribed to cell membrane interactions, and showed that sensitivity to LAS was common for various soil microorganisms. The extracellular beta-glucosidase activity was rather insensitive to LAS (ECI10, 47 mg/kg dry wt), whereas the basal soil respiration was not inhibited even at 793 mg/kg dry weight. This was interpreted as a combined response of inhibited and stimulated compartments of the microbial community. The PLFA content, surprisingly, showed no decrease even at 488 mg/kg. In conclusion, LAS inhibited specific microbial activities, although this could not be deduced from the basal respiration or the total PLFA content. The lowest EC10 values for microbial soil parameters were slightly higher than the predicted no-effect concentrations recently derived for plants and soil fauna (approximately 5 mg/kg dry wt).

Estimating phosphorus availability for microbial growth in an emerging landscape

USGS Publications Warehouse

Schmidt, S.K.; Cleveland, C.C.; Nemergut, D.R.; Reed, S.C.; King, A.J.; Sowell, P.

2011-01-01

Estimating phosphorus (P) availability is difficult—particularly in infertile soils such as those exposed after glacial recession—because standard P extraction methods may not mimic biological acquisition pathways. We developed an approach, based on microbial CO2 production kinetics and conserved carbon:phosphorus (C:P) ratios, to estimate the amount of P available for microbial growth in soils and compared this method to traditional, operationally-defined indicators of P availability. Along a primary succession gradient in the High Andes of Perú, P additions stimulated the growth-related (logistic) kinetics of glutamate mineralization in soils that had been deglaciated from 0 to 5 years suggesting that microbial growth was limited by soil P availability. We then used a logistic model to estimate the amount of C incorporated into biomass in P-limited soils, allowing us to estimate total microbial P uptake based on a conservative C:P ratio of 28:1 (mass:mass). Using this approach, we estimated that there was < 1 μg/g of microbial-available P in recently de-glaciated soils in both years of this study. These estimates fell well below estimates of available soil P obtained using traditional extraction procedures. Our results give both theoretical and practical insights into the kinetics of C and P utilization in young soils, as well as show changes in microbial P availability during early stages of soil development.

The Influence of Ecological and Conventional Plant Production Systems on Soil Microbial Quality under Hops (Humulus lupulus)

PubMed Central

Oszust, Karolina; Frąc, Magdalena; Gryta, Agata; Bilińska, Nina

2014-01-01

The knowledge about microorganisms—activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions) significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential). Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a) ecological based on the use of probiotic preparations and organic fertilization (b) conventional—with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA) was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP) of PCR ammonia monooxygenase α-subunit (amoA) gene products. Conventional and ecological systems of hop production were able to affect soil microbial state in different seasonal manner. Favorable effect on soil microbial activity met under ecological, was more probably due to livestock-based manure and fermented plant extracts application. No negative influence on conventional hopyard soil was revealed. Both type of production fulfilled fertilizing demands. Under ecological production it was due to livestock-based manure fertilizers and fermented plant extracts application. PMID:24897025

The Microbiome Structure of Oklahoma Cropland and Prairie Soils and its Response to Seasonal Forcing and Management Practices

NASA Astrophysics Data System (ADS)

Cornell, C. R.; Peterson, B.; Zhou, J.; Xiao, X.; Wawrik, B.

2017-12-01

Greenhouse gases (GHG) emissions from soils are primarily the consequence of microbial processes. Agricultural management of soils is known to affect the structure of microbial communities, and it is likely that dominant GHG emitting microbial activities are impacted via requisite practices. To gain better insight into the impact of seasonal forcing and management practices on the microbiome structure in Oklahoma agricultural soils, a seasonal study was conducted. Over a year period, samples were collected bi-weekly during wet months, and monthly during dry months from two grassland and two managed agricultural sites in El Reno, Oklahoma. Microbial community structure was determined in quadruplicate for each site and time point via 16S rRNA gene sequencing. Measures of soil water content, subsoil nitrate, ammonium, organic matter, total nitrogen, and biomass were also taken for each time point. Data analysis revealed several important trends, indicating greater microbial diversity in native grassland and distinct microbial community changes in response to management practices. The native grassland soils also contained greater microbial biomass than managed soils and both varied in response to rainfall events. Native grassland soils harbor more diverse microbial communities, with the diversity and biomass decreasing along a gradient of agricultural management intensity. These data indicate that microbial community structure in El Reno soils occurs along a continuum in which native grasslands and highly managed agricultural soils (tilling and manure application) form end members. Integration with measurements from eddy flux towers into modelling efforts using the DeNitrification-DeComposition (DNDC) model is currently being explored to improve predictions of GHG emissions from grassland soils.

Responses of soil microbial and nematode communities to aluminum toxicity in vegetated oil-shale-waste lands.

PubMed

Shao, Yuanhu; Zhang, Weixin; Liu, Zhanfeng; Sun, Yuxin; Chen, Dima; Wu, Jianping; Zhou, Lixia; Xia, Hanping; Neher, Deborah A; Fu, Shenglei

2012-11-01

Both soil nematodes and microorganisms have been shown to be sensitive bioindicators of soil recovery in metal-contaminated habitats; however, the underlying processes are poorly understood. We investigated the relationship among soil microbial community composition, nematode community structure and soil aluminum (Al) content in different vegetated aluminum-rich ecosystems. Our results demonstrated that there were greater soil bacterial, fungal and arbuscular mycorrhizal fungal biomass in Syzygium cumini plantation, greater abundance of soil nematodes in Acacia auriculiformis plantation, and greater abundance of soil predatory and herbivorous nematodes in Schima wallichii plantation. The concentration of water-soluble Al was normally greater in vegetated than non-vegetated soil. The residual Al and total Al concentrations showed a significant decrease after planting S. cumini plantation onto the shale dump. Acid extractable, reducible and oxidisable Al concentrations were greater in S. wallichii plantation. Stepwise linear regression analysis suggests the concentrations of water-soluble Al and total Al content explain the most variance associated with nematode assembly; whereas, the abundance of early-successional nematode taxa was explained mostly by soil moisture, soil organic C and total N rather than the concentrations of different forms of Al. In contrast, no significant main effects of either Al or soil physico-chemical characteristics on soil microbial biomass were observed. Our study suggests that vegetation was the primary driver on soil nematodes and microorganisms and it also could regulate the sensitivity of bio-indicator role mainly through the alteration of soil Al and physico-chemical characteristics, and S. cumini is effective for amending the Al contaminated soils.

Soil microbiological properties and enzymatic activities of long-term post-fire recovery in dry and semiarid Aleppo pine (Pinus halepensis M.) forest stands

NASA Astrophysics Data System (ADS)

Hedo, J.; Lucas-Borja, M. E.; Wic, C.; Andrés Abellán, M.; de Las Heras, J.

2014-10-01

Wildfires affecting forest ecosystems and post-fire silvicultural treatments may cause considerable changes in soil properties. The capacity of different microbial groups to recolonize soil after disturbances is crucial for proper soil functioning. The aim of this work was to investigate some microbial soil properties and enzyme activities in semiarid and dry Aleppo pine (Pinus halepensis M.) forest stands. Different plots affected by a wildfire event 17 years ago without or with post-fire silvicultural treatments five years after the fire event were selected. A mature Aleppo pine stand unaffected by wildfire and not thinned was used as a control. Physicochemical soil properties (soil texture, pH, carbonates, organic matter, electrical conductivity, total N and P), soil enzymes (urease, phosphatase, β-glucosidase and dehydrogenase activities), soil respiration and soil microbial biomass carbon were analysed in the selected forests areas and plots. The main finding was that long time after this fire event produces no differences in the microbiological soil properties and enzyme activities of soil after comparing burned and thinned, burned and not thinned, and mature plots. Thus, the long-term consequences and post-fire silvicultural management in the form of thinning have a significant effect on the site recovery after fire. Moreover, significant site variation was generally seen in soil enzyme activities and microbiological parameters. We conclude that total vegetation restoration normalises microbial parameters, and that wildfire and post-fire silvicultural treatments are not significant factors of soil properties after 17 years.

Soil-borne microbial functional structure across different land uses.

PubMed

Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

Responses of Soil CO2 Emissions to Extreme Precipitation Regimes: a Simulation on Loess Soil in Semi-arid Regions

NASA Astrophysics Data System (ADS)

Wang, R.; Zhao, M.; Hu, Y.; Guo, S.

2016-12-01

Responses of soil CO2 emission to natural precipitation play an essential role in regulating regional C cycling. With more erratic precipitation regimes, mostly likely of more frequent heavy rainstorms, projected into the future, extreme precipitation would potentially affect local soil moisture, plant growth, microbial communities, and further soil CO2 emissions. However, responses of soil CO2 emissions to extreme precipitation have not yet been systematically investigated. Such performances could be of particular importance for rainfed arable soil in semi-arid regions where soil microbial respiration stress is highly sensitive to temporal distribution of natural precipitation.In this study, a simulated experiment was conducted on bare loess soil from the semi-arid Chinese Loess Plateau. Three precipitation regimes with total precipitation amounts of 150 mm, 300 mm and 600 mm were carried out to simulate the extremely dry, business as usual, and extremely wet summer. The three regimes were individually materialized by wetting soils in a series of sub-events (10 mm or 150 mm). Co2 emissions from surface soil were continuously measured in-situ for one month. The results show that: 1) Evident CO2 emission pulses were observed immediately after applying sub-events, and cumulative CO2 emissions from events of total amount of 600 mm were greater than that from 150 mm. 3) In particular, for the same total amount of 600 mm, wetting regimes by applying four times of 150 mm sub-events resulted in 20% less CO2 emissions than by applying 60 times of 10 mm sub-events. This is mostly because its harsh 150 mm storms introduced more over-wet soil microbial respiration stress days (moisture > 28%). As opposed, for the same total amount of 150 mm, CO2 emissions from wetting regimes by applying 15 times of 10 mm sub-events were 22% lower than by wetting at once with 150 mm water, probably because its deficiency of soil moisture resulted in more over-dry soil microbial respiration stress days (moisture < 15%). Overall, soil CO2 emissions not only responded to total precipitation amount, but was also sensitive to precipitation regimes. Such differentiated responses of CO2 emissions highlight the necessity to properly account for relative contributions from CO2 emissions when projecting global carbon cycling into future climate scenarios.

Bioremediation and phytoremediation of total petroleum hydrocarbons (TPH) under various conditions.

PubMed

McIntosh, Patrick; Schulthess, Cristian P; Kuzovkina, Yulia A; Guillard, Karl

2017-08-03

Remediation of contaminated soils is often studied using fine-textured soils rather than low-fertility sandy soils, and few studies focus on recontamination events. This study compared aerobic and anaerobic treatments for remediation of freshly introduced used motor oil on a sandy soil previously phytoremediated and bioacclimated (microorganisms already adapted in the soil environment) with some residual total petroleum hydrocarbon (TPH) contamination. Vegetated and unvegetated conditions to remediate anthropogenic fill containing residual TPH that was spiked with nonaqueous phase liquids (NAPLs) were evaluated in a 90-day greenhouse pot study. Vegetated treatments used switchgrass (Panicum virgatum). The concentration of aerobic bacteria were orders of magnitude higher in vegetated treatments compared to unvegetated. Nevertheless, final TPH concentrations were low in all saturated soil treatments, and high in the presence of switchgrass. Concentrations were also low in unvegetated pots with fertilizer. Acclimated indigenous microbial communities were shown to be more effective in breaking down hydrocarbons than introducing microbes from the addition of plant treatments in sandy soils. Remediation of fresh introduced NAPLs on pre-phytoremediated and bioacclimated soil was most efficient in saturated, anaerobic environments, probably due to the already pre-established microbial associations, easily bioavailable contaminants, and optimized soil conditions for microbial establishment and survival.

Long-term rice cultivation stabilizes soil organic carbon and promotes soil microbial activity in a salt marsh derived soil chronosequence

PubMed Central

Wang, Ping; Liu, Yalong; Li, Lianqing; Cheng, Kun; Zheng, Jufeng; Zhang, Xuhui; Zheng, Jinwei; Joseph, Stephen; Pan, Genxing

2015-01-01

Soil organic carbon (SOC) sequestration with enhanced stable carbon storage has been widely accepted as a very important ecosystem property. Yet, the link between carbon stability and bio-activity for ecosystem functioning with OC accumulation in field soils has not been characterized. We assessed the changes in microbial activity versus carbon stability along a paddy soil chronosequence shifting from salt marsh in East China. We used mean weight diameter, normalized enzyme activity (NEA) and carbon gain from straw amendment for addressing soil aggregation, microbial biochemical activity and potential C sequestration, respectively. In addition, a response ratio was employed to infer the changes in all analyzed parameters with prolonged rice cultivation. While stable carbon pools varied with total SOC accumulation, soil respiration and both bacterial and fungal diversity were relatively constant in the rice soils. Bacterial abundance and NEA were positively but highly correlated to total SOC accumulation, indicating an enhanced bio-activity with carbon stabilization. This could be linked to an enhancement of particulate organic carbon pool due to physical protection with enhanced soil aggregation in the rice soils under long-term rice cultivation. However, the mechanism underpinning these changes should be explored in future studies in rice soils where dynamic redox conditions exist. PMID:26503629

Long-term rice cultivation stabilizes soil organic carbon and promotes soil microbial activity in a salt marsh derived soil chronosequence

NASA Astrophysics Data System (ADS)

Wang, Ping; Liu, Yalong; Li, Lianqing; Cheng, Kun; Zheng, Jufeng; Zhang, Xuhui; Zheng, Jinwei; Joseph, Stephen; Pan, Genxing

2015-10-01

Soil organic carbon (SOC) sequestration with enhanced stable carbon storage has been widely accepted as a very important ecosystem property. Yet, the link between carbon stability and bio-activity for ecosystem functioning with OC accumulation in field soils has not been characterized. We assessed the changes in microbial activity versus carbon stability along a paddy soil chronosequence shifting from salt marsh in East China. We used mean weight diameter, normalized enzyme activity (NEA) and carbon gain from straw amendment for addressing soil aggregation, microbial biochemical activity and potential C sequestration, respectively. In addition, a response ratio was employed to infer the changes in all analyzed parameters with prolonged rice cultivation. While stable carbon pools varied with total SOC accumulation, soil respiration and both bacterial and fungal diversity were relatively constant in the rice soils. Bacterial abundance and NEA were positively but highly correlated to total SOC accumulation, indicating an enhanced bio-activity with carbon stabilization. This could be linked to an enhancement of particulate organic carbon pool due to physical protection with enhanced soil aggregation in the rice soils under long-term rice cultivation. However, the mechanism underpinning these changes should be explored in future studies in rice soils where dynamic redox conditions exist.

Long-term rice cultivation stabilizes soil organic carbon and promotes soil microbial activity in a salt marsh derived soil chronosequence.

PubMed

Wang, Ping; Liu, Yalong; Li, Lianqing; Cheng, Kun; Zheng, Jufeng; Zhang, Xuhui; Zheng, Jinwei; Joseph, Stephen; Pan, Genxing

2015-10-27

Soil organic carbon (SOC) sequestration with enhanced stable carbon storage has been widely accepted as a very important ecosystem property. Yet, the link between carbon stability and bio-activity for ecosystem functioning with OC accumulation in field soils has not been characterized. We assessed the changes in microbial activity versus carbon stability along a paddy soil chronosequence shifting from salt marsh in East China. We used mean weight diameter, normalized enzyme activity (NEA) and carbon gain from straw amendment for addressing soil aggregation, microbial biochemical activity and potential C sequestration, respectively. In addition, a response ratio was employed to infer the changes in all analyzed parameters with prolonged rice cultivation. While stable carbon pools varied with total SOC accumulation, soil respiration and both bacterial and fungal diversity were relatively constant in the rice soils. Bacterial abundance and NEA were positively but highly correlated to total SOC accumulation, indicating an enhanced bio-activity with carbon stabilization. This could be linked to an enhancement of particulate organic carbon pool due to physical protection with enhanced soil aggregation in the rice soils under long-term rice cultivation. However, the mechanism underpinning these changes should be explored in future studies in rice soils where dynamic redox conditions exist.

Effect of addition of organic materials and irrigation conditions on soil quality in olive groves in the region of Messinia, Greece.

NASA Astrophysics Data System (ADS)

Kavvadias, Victor; Papadopoulou, Maria; Vavoulidou, Evangelia; Theocharopoulos, Sideris; Repas, Spiros; Koubouris, Georgos; Psaras, Georgios

2017-04-01

Intensive cultivation practices are associated to soil degradation mainly due to low soil organic matter content. The application of organic materials to land is a common practice in sustainable agriculture in the last years. However, its implementation in olive groves under different irrigation regimes has not been systematically tested under the prevailing Mediterranean conditions. The aim of this work was to study the effect of alternative carbon input techniques (i.e. wood shredded, pruning residues, returning of olive mill wastes the field with compost) and irrigation conditions (irrigated and rainfed olive orchards) on spatial distribution of soil chemical (pH, EC, total organic carbon, total nitrogen, inorganic nitrogen, humic and fulvic acids, available P, and exchangeable K) and microbial properties (soil basal microbial respiration and microbial biomass carbon) in two soil depths (0-10 cm and 10-40 cm). The study took place in the region of Messinia, South western Peloponnese, Greece during three year soil campaigns. Forty soil plots of olive groves were selected (20 rainfed and 20 irrigated) and carbon input practices were applied on the half of the irrigated and rainfed soil parcels (10 rainfed and 10 irrigated), while the remaining ones were used as controls. The results showed significant changes of chemical and biological properties of soil in olive orchards due to carbon treatments. However, these changes were depended on irrigation conditions. Microbial parameters appeared to be reliable indicators of changes in soil management. Proper management of alternative soil carbon inputs in olive orchards can positively affect soil fertility.

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

PubMed

Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

2017-12-01

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

[Effects of Different Reclaimed Scenarios on Soil Microbe and Enzyme Activities in Mining Areas].

PubMed

Li, Jun-jian; Liu, Feng; Zhou, Xiao-mei

2015-05-01

Abstract: Ecological degradation in the mining areas is greatly aggravated in recent several decades, and ecological restoration has become the primary measure for the sustainable development. Soil microbe and enzyme activity are sensitive indices to evaluate soil quality. Ecological reconstruction was initiated in Antaibao mining area, and we tested soil physicochemical properties, microbial populations of azotobacteria, nitrifying-bacteria and denitrifying-bacteria, and enzyme activities (including sucrose, polyphenol oxidase, dehydrogenase and urease) under different regeneration scenarios. Regeneration scenarios had significant effects on soil physicochemical properties, microbial population and enzyme activities. Total nitrogen was strongly correlated with azotobacteria and nitrifying-bacteria, however, total nitrogen was not correlated with denitrifying-bacteria. Phenol oxidase activity was negatively correlated with soil organic carbon and total nitrogen, but other enzyme activities were positively correlated with soil organic carbon and total nitrogen. Principal Component Analysis ( PCA) was applied to analyze the integrated fertility index (IFI). The highest and lowest IFIs were in Robinia pseudoacacia-Pinus tabuliformis mixed forests and un-reclaimed area, respectively. R. pseudoacacia-P. tabuliformis mixed forests were feasible for reclaimed mining areas in semi-arid region Northwest Shanxi.

Microbial biomass and basal respiration in Sub-Antarctic and Antarctic soils in the areas of some Russian polar stations

NASA Astrophysics Data System (ADS)

Abakumov, E.; Mukhametova, N.

2014-03-01

Antarctica is the unique place for pedological investigations. Soils of Antarctica have been studied intensively during the last century. Antarctic logistic provides the possibility to scientists access the terrestrial landscapes mainly in the places of polar stations. That is why the main and most detailed pedological investigations were conducted in Mc Murdo Valleys, Transantarctic Mountains, South Shetland Islands, Larsemann hills and Schirmacher Oasis. Investigations were conducted during the 53rd and 55th Russian Antarctic expeditions on the base of soil pits and samples collected in Sub-Antarctic and Antarctic regions. Soils of diverse Antarctic landscapes were studied with aim to assess the microbial biomass level, basal respiration rates and metabolic activity of microbial communities. The investigation conducted shows that soils of Antarctic are quite different in profile organization and carbon content. In general, Sub-Antarctic soils are characterized by more developed humus (sod) organo-mineral horizons as well as the upper organic layer. The most developed organic layers were revealed in peat soils of King-George Island, where its thickness reach even 80 cm. These soils as well as soils under guano are characterized by the highest amount of total organic carbon (TOC) 7.22-33.70%. Coastal and continental soils of Antarctic are presented by less developed Leptosols, Gleysols, Regolith and rare Ornhitosol with TOC levels about 0.37-4.67%. The metabolic ratios and basal respiration were higher in Sub-Antarctic soils than in Antarctic ones which can be interpreted as result of higher amounts of fresh organic remnants in organic and organo-mineral horizons. Also the soils of King-George island have higher portion of microbial biomass (max 1.54 mg g-1) than coastal (max 0.26 mg g-1) and continental (max 0.22 mg g-1) Antarctic soils. Sub-Antarctic soils mainly differ from Antarctic ones in increased organic layers thickness and total organic carbon content, higher microbial biomass carbon content, basal respiration and metabolic activity levels.

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem.

PubMed

Ma, Zhiliang; Zhao, Wenqiang; Zhao, Chunzhang; Wang, Dong; Liu, Mei; Li, Dandan; Liu, Qing

2018-01-01

Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai-Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems.

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem

PubMed Central

Ma, Zhiliang; Zhao, Wenqiang; Zhao, Chunzhang; Wang, Dong; Liu, Mei; Li, Dandan

2018-01-01

Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai–Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems. PMID:29668711

Determination of microbial carbon sources and cycling during remediation of petroleum hydrocarbon impacted soil using natural abundance (14)C analysis of PLFA.

PubMed

Cowie, Benjamin R; Greenberg, Bruce M; Slater, Gregory F

2010-04-01

In a petroleum impacted land-farm soil in Sarnia, Ontario, compound-specific natural abundance radiocarbon analysis identified biodegradation by the soil microbial community as a major pathway for hydrocarbon removal in a novel remediation system. During remediation of contaminated soils by a plant growth promoting rhizobacteria enhanced phytoremediation system (PEPS), the measured Delta(14)C of phospholipid fatty acid (PLFA) biomarkers ranged from -793 per thousand to -897 per thousand, directly demonstrating microbial uptake and utilization of petroleum hydrocarbons (Delta(14)C(PHC) = -1000 per thousand). Isotopic mass balance indicated that more than 80% of microbial PLFA carbon was derived from petroleum hydrocarbons (PHC) and a maximum of 20% was obtained from metabolism of more modern carbon sources. These PLFA from the contaminated soils were the most (14)C-depleted biomarkers ever measured for an in situ environmental system, and this study demonstrated that the microbial community in this soil was subsisting primarily on petroleum hydrocarbons. In contrast, the microbial community in a nearby uncontaminated control soil maintained a more modern Delta(14)C signature than total organic carbon (Delta(14)C(PLFA) = +36 per thousand to -147 per thousand, Delta(14)C(TOC) = -148 per thousand), indicating preferential consumption of the most modern plant-derived fraction of soil organic carbon. Measurements of delta(13)C and Delta(14)C of soil CO(2) additionally demonstrated that mineralization of PHC contributed to soil CO(2) at the contaminated site. The CO(2) in the uncontaminated control soil exhibited substantially more modern Delta(14)C values, and lower soil CO(2) concentrations than the contaminated soils, suggesting increased rates of soil respiration in the contaminated soils. In combination, these results demonstrated that biodegradation in the soil microbial community was a primary pathway of petroleum hydrocarbon removal in the PEPS system. This study highlights the power of natural abundance radiocarbon for determining microbial carbon sources and identifying biodegradation pathways in complex remediation systems.

Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil.

PubMed

Lynn, Tin Mar; Liu, Qiong; Hu, Yajun; Yuan, Hongzhao; Wu, Xiaohong; Khai, Aye Aye; Wu, Jinshui; Ge, Tida

2017-07-01

Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected archaeal community composition. Pearson correlation analysis showed that bacterial and archaeal 16S rRNA gene abundance had the highest correlation with clay content (r > 0.905, P < 0.01), followed by total-P, CEC, pH, and silt (%). These results will lead to more comprehensive understanding of how land use affects microbial distribution.

Biodegradation of Spilled Diesel Fuel in Agricultural Soil: Effect of Humates, Zeolite, and Bioaugmentation

PubMed Central

Kuráň, Pavel; Nováková, Jana; Pilařová, Věra; Dáňová, Petra; Pavlorková, Jana; Kozler, Josef; Novák, František

2014-01-01

Possible enhancement of biodegradation of petroleum hydrocarbons in agricultural soil after tank truck accident (~5000 mg/kg dry soil initial concentration) by bioaugmentation of diesel degrading Pseudomonas fluorescens strain and addition of abiotic additives (humates, zeolite) was studied in a 9-month pot experiment. The biodegradation process was followed by means of analytical parameters (hydrocarbon index expressed as content of C10–C40 aliphatic hydrocarbons, ratio pristane/C17, and total organic carbon content) and characterization of soil microbial community (content of phospholipid fatty acids (PLFA) as an indicator of living microbial biomass, respiration, and dehydrogenase activity). The concentration of petroleum hydrocarbons (C10–C40) was successfully reduced by ~60% in all 15 experiment variants. The bioaugmentation resulted in faster hydrocarbon elimination. On the contrary, the addition of humates and zeolite caused only a negligible increase in the degradation rate. These factors, however, affected significantly the amount of PLFA. The humates caused significantly faster increase of the total PLFA suggesting improvement of the soil microenvironment. Zeolite caused significantly slower increase of the total PLFA; nevertheless it aided in homogenization of the soil. Comparison of microbial activities and total PLFA revealed that only a small fraction of autochthonous microbes took part in the biodegradation which confirms that bioaugmentation was the most important treatment. PMID:24672346

Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

NASA Astrophysics Data System (ADS)

Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

2016-04-01

Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3- concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

Divergence of dominant factors in soil microbial communities and functions in forest ecosystems along a climatic gradient

NASA Astrophysics Data System (ADS)

Xu, Zhiwei; Yu, Guirui; Zhang, Xinyu; He, Nianpeng; Wang, Qiufeng; Wang, Shengzhong; Xu, Xiaofeng; Wang, Ruili; Zhao, Ning

2018-03-01

Soil microorganisms play an important role in regulating nutrient cycling in terrestrial ecosystems. Most of the studies conducted thus far have been confined to a single forest biome or have focused on one or two controlling factors, and few have dealt with the integrated effects of climate, vegetation, and soil substrate availability on soil microbial communities and functions among different forests. In this study, we used phospholipid-derived fatty acid (PLFA) analysis to investigate soil microbial community structure and extracellular enzymatic activities to evaluate the functional potential of soil microbes of different types of forests in three different climatic zones along the north-south transect in eastern China (NSTEC). Both climate and forest type had significant effects on soil enzyme activities and microbial communities with considerable interactive effects. Except for soil acid phosphatase (AP), the other three enzyme activities were much higher in the warm temperate zone than in the temperate and the subtropical climate zones. The soil total PLFAs and bacteria were much higher in the temperate zone than in the warm temperate and the subtropical zones. The soil β-glucosidase (BG) and N-acetylglucosaminidase (NAG) activities were highest in the coniferous forest. Except for the soil fungi and fungi-bacteria (F/B), the different groups of microbial PLFAs were much higher in the conifer broad-leaved mixed forests than in the coniferous forests and the broad-leaved forests. In general, soil enzyme activities and microbial PLFAs were higher in primary forests than in secondary forests in temperate and warm temperate regions. In the subtropical region, soil enzyme activities were lower in the primary forests than in the secondary forests and microbial PLFAs did not differ significantly between primary and secondary forests. Different compositions of the tree species may cause variations in soil microbial communities and enzyme activities. Our results showed that the main controls on soil microbes and functions vary in different climatic zones and that the effects of soil moisture content, soil temperature, clay content, and the soil N / P ratio were considerable. This information will add value to the modeling of microbial processes and will contribute to carbon cycling in large-scale carbon models.

[Effects of tree species transition on soil microbial community composition and functions in subtropical China].

PubMed

Ding, Guo Chang; Wang, Xiao Hua; Yang, Qi Fan; Lin, Qun Xing; Huang, Zhi Qun

2017-11-01

We employed a comparative study to examine the effects of tree species transition on soil microbial biomass, community composition and enzymes activities under Cunninghamia lanceolata (Lamb.) Hook, Eucalyptus grandis and a N-fixing species, Acacia melanoxylon in subtropical China. Results showed that the effect of tree species on soil microbial community and enzymes activities was significant only in the 0-10 cm soil layer. Reforestation with N-fixing species A. melanoxylon on the C. lanceolata harvest site significantly increased the total phospholipid fatty acid (PLFA), fungal PLFAs, Gram-positive bacterial PLFAs, Gram-negative bacterial PLFAs and actinomycetes biomasses in the 0-10 cm soil layer. The principal component analysis (PCA) showed that the soil microbial community composition in A. melanoxylon soil differed significantly from that in C. lanceolata and E. grandis soils. N-fixing species (A. melanoxylon) significantly enhanced the percent abundance of Gram-positive bacteria, Gram-negative bacteria and actinomycetes. Activities of cellobiohydrolase, N-acetyl-β-d-glucosaminidase and acid phosphatase were significantly higher under A. melanoxylon than under C. lanceolata and E. grandis plantations. Our results suggested that reforestation with N-fixing species, A. melanoxylon on C. lanceolata harvest site could increase soil microbial biomass, enzyme activities and soil organic matter content.

Use of Bacillus thuringiensis supernatant from a fermentation process to improve bioremediation of chlorpyrifos in contaminated soils.

PubMed

Aceves-Diez, Angel E; Estrada-Castañeda, Kelly J; Castañeda-Sandoval, Laura M

2015-07-01

The aim of this research was to investigate the potential of a nutrient-rich organic waste, namely the cell-free supernatant of Bacillus thuringiensis (BtS) gathered from fermentation, as a biostimulating agent to improve and sustain microbial populations and their enzymatic activities, thereby assisting in the bioremediation of chlorpyrifos-contaminated soil at a high dose (70 mg kg(-1)). Experiments were performed for up to 80 d. Chlorpyrifos degradation and its major metabolic product, 3,5,6-trichloro-2-pyridinol (TCP), were quantified by high-performance liquid chromatography (HPLC); total microbial populations were enumerated by direct counts in specific medium; and fluorescein diacetate (FDA) hydrolysis was measured as an index of soil microbial activity. Throughout the experiment, there was higher chlorpyrifos degradation in soil supplemented with BtS (83.1%) as compared to non-supplemented soil. TCP formation and degradation occurred in all soils, but the greatest degradation (30.34%) was observed in soil supplemented with BtS. The total microbial populations were significantly improved by supplementation with BtS. The application of chlorpyrifos to soil inhibited the enzymatic activity; however, this negative effect was counteracted by BtS, inducing an increase of approximately 16% in FDA hydrolysis. These results demonstrate the potential of B. thuringiensis supernatant as a suitable biostimulation agent for enhancing chlorpyrifos and TCP biodegradation in chlorpyrifos-contaminated soils. Copyright © 2015 Elsevier Ltd. All rights reserved.

Shift in soil microbial communities with shrub encroachment in Inner Mongolia grasslands, China

NASA Astrophysics Data System (ADS)

Shen, H.; Li, H.; Zhang, J.; Hu, H.; Chen, L.; Zhu, Y.; Fang, J.

2017-12-01

The ongoing expansion of shrub encroachment into grasslands represents a unique form of land cover change. How this process affects soil microbial communities is poorly understood. In this study, we aim to assess the effects of shrub encroachment on soil microbial biomass, abundance and composition by comparing data between shrub patches and neighboring herb patches in shrub-encroached grasslands (SEGs) in Inner Mongolia, China. Fourteen SEG sites from two ecosystem types (typical and desert grasslands) were investigated. The phospholipid fatty acid (PLFA) method was used to analyze the composition and biomass of the soil microbial community. Our results showed that the top-soil microbial biomass and abundances of gram-negative bacteria, arbuscular mycorrhizal fungi, and actinomycetes were significantly higher in shrub patches than in herb patches in both typical and desert grasslands (P < 0.05). The fungi to bacteria ratio was significantly higher in shrub patches than in herb patches in desert grassland (P < 0.05). The microbial biomass was positively associated with mean annual precipitation, total nitrogen and available phosphorus, and negatively associated with mean annual temperature. Our results also indicated that the variation in microbial composition was largely explained by edaphic factors, followed by climate factors. In conclusion, shrub encroachment in Inner Mongolia grasslands has significantly influenced the structure and abundance of soil microbial communities, which makes the microbial communities toward a fresh organic carbon-based structure. This study highlights the importance of edaphic and climate factors in microbial community shifts in SEGs.

Soil Nitrogen-Cycling Responses to Conversion of Lowland Forests to Oil Palm and Rubber Plantations in Sumatra, Indonesia

PubMed Central

Tjoa, Aiyen; Veldkamp, Edzo

2015-01-01

Rapid deforestation in Sumatra, Indonesia is presently occurring due to the expansion of palm oil and rubber production, fueled by an increasing global demand. Our study aimed to assess changes in soil-N cycling rates with conversion of forest to oil palm (Elaeis guineensis) and rubber (Hevea brasiliensis) plantations. In Jambi Province, Sumatra, Indonesia, we selected two soil landscapes – loam and clay Acrisol soils – each with four land-use types: lowland forest and forest with regenerating rubber (hereafter, “jungle rubber”) as reference land uses, and rubber and oil palm as converted land uses. Gross soil-N cycling rates were measured using the 15N pool dilution technique with in-situ incubation of soil cores. In the loam Acrisol soil, where fertility was low, microbial biomass, gross N mineralization and NH4 + immobilization were also low and no significant changes were detected with land-use conversion. The clay Acrisol soil which had higher initial fertility based on the reference land uses (i.e. higher pH, organic C, total N, effective cation exchange capacity (ECEC) and base saturation) (P≤0.05–0.09) had larger microbial biomass and NH4 + transformation rates (P≤0.05) compared to the loam Acrisol soil. Conversion of forest and jungle rubber to rubber and oil palm in the clay Acrisol soil decreased soil fertility which, in turn, reduced microbial biomass and consequently decreased NH4 + transformation rates (P≤0.05–0.09). This was further attested by the correlation of gross N mineralization and microbial biomass N with ECEC, organic C, total N (R=0.51–0. 76; P≤0.05) and C:N ratio (R=-0.71 – -0.75, P≤0.05). Our findings suggest that the larger the initial soil fertility and N availability, the larger the reductions upon land-use conversion. Because soil N availability was dependent on microbial biomass, management practices in converted oil palm and rubber plantations should focus on enriching microbial biomass. PMID:26222690

Humic fractions of forest, pasture and maize crop soils resulting from microbial activity

PubMed Central

Tavares, Rose Luiza Moraes; Nahas, Ely

2014-01-01

Humic substances result from the degradation of biopolymers of organic residues in the soil due to microbial activity. The objective of this study was to evaluate the influence of three different ecosystems: forest, pasture and maize crop on the formation of soil humic substances relating to their biological and chemical attributes. Microbial biomass carbon (MBC), microbial respiratory activity, nitrification potential, total organic carbon, soluble carbon, humic and fulvic acid fractions and the rate and degree of humification were determined. Organic carbon and soluble carbon contents decreased in the order: forest > pasture > maize; humic and fulvic acids decreased in the order forest > pasture=maize. The MBC and respiratory activity were not influenced by the ecosystems; however, the nitrification potential was higher in the forest than in other soils. The rate and degree of humification were higher in maize soil indicating greater humification of organic matter in this system. All attributes studied decreased significantly with increasing soil depth, with the exception of the rate and degree of humification. Significant and positive correlations were found between humic and fulvic acids contents with MBC, microbial respiration and nitrification potential, suggesting the microbial influence on the differential formation of humic substances of the different ecosystems. PMID:25477932

A simple evaluation of soil quality of waterlogged purple paddy soils with different productivities.

PubMed

Liu, Zhanjun; Zhou, Wei; Lv, Jialong; He, Ping; Liang, Guoqing; Jin, Hui

2015-01-01

Evaluation of soil quality can be crucial for designing efficient farming systems and ensuring sustainable agriculture. The present study aimed at evaluating the quality of waterlogged purple paddy soils with different productivities in Sichuan Basin. The approach involved comprehensive analyses of soil physical and chemical properties, as well as enzyme activities and microbial community structure measured by phospholipid fatty acid analysis (PLFA). A total of 36 soil samples were collected from four typical locations, with 12 samples representing high productivity purple paddy soil (HPPS), medium productivity purple paddy soil (MPPS) and low productivity purple paddy soil (LPPS), respectively. Most measured soil properties showed significant differences (P ≤ 0.05) among HPPS, MPPS and LPPS. Pearson correlation analysis and principal component analysis were used to identify appropriate soil quality indicators. A minimum data set (MDS) including total nitrogen (TN), available phosphorus (AP), acid phosphatase (ACP), total bacteria (TB) and arbuscular mycorrhizal fungi was established and accounted for 82.1% of the quality variation among soils. A soil quality index (SQI) was developed based on the MDS method, whilst HPPS, MPPS and LPPS received mean SQI scores of 0.725, 0.536 and 0.425, respectively, with a ranking of HPPS > MPPS > LPPS. HPPS showed relatively good soil quality characterized by optimal nutrient availability, enzymatic and microbial activities, but the opposite was true of LPPS. Low levels of TN, AP and soil microbial activities were considered to be the major constraints limiting the productivity in LPPS. All soil samples collected were rich in available N, K, Si and Zn, but deficient in available P, which may be the major constraint for the studied regions. Managers in our study area should employ more appropriate management in the LPPS to improve its rice productivity, and particularly to any potential limiting factor.

[Effect of long-term fertilizing regime on soil microbial diversity and soil property].

PubMed

Li, Chenhua; Zhang, Caixia; Tang, Lisong; Xiong, Zhengqin; Wang, Baozhan; Jia, Zhongjun; Li, Yan

2014-03-04

To evaluate the effect of long-term fertilization on soil microbial community and soil chemical and physical properties. Using a high-throughput pyrosequencing technique, we studied microbial community in the 0-300 cm soil samples covering a 20-year field-experiment with different fertilization applications including inorganic fertilizer alone (N 300 kg/hm2, P2O5 150 kg/hm2 and K2O 60 kg/hm2) and inorganic fertilizer combined with straw (same application rate of N and P fertilizer combined with 5.4 t straw). Actinobacteria and alpha-proteobacteria were the predominant groups in the topsoil (0-20 cm). As the soil depth increased, the relative abundance of actinobacteria decreased whereas that of proteobacteria, especially gamma-proteobacteria and beta-proteobacteria increased and gradually became the dominant groups in the subsoil (20-300 cm). Long-term fertilizing applications significantly affected soil microbial communities throughout the soil profile, and increased the relative abundance of ammonia-oxidizing archaea at 0-40 cm depth. In addition, agriculture management, e. g. irrigation may be an important driving factor for the distribution of ammonia-oxidizing bacteria in soil profile. Total nitrogen and organic carbon contents were the most influential factors on microbial community in the topsoil and in the subsoil, respectively. Long-term fertilizer applications altered soil nutrient availability within the soil profile, which was likely to result in the different microbial community structure between the fertilizer treatments, especially for the subsoil.

Changes in Soil Organic Matter Abundance, Molecular Composition, and Diversity in an Arid Ecosystem in Response to Long-term Elevated CO2 Manipulation.

NASA Astrophysics Data System (ADS)

Hess, N. J.; Tfaily, M.; Evans, R. D.; Koyama, A.

2017-12-01

Little is known about how soils in arid ecosystems will respond to rising atmospheric CO2 concentration yet arid and semi-arid ecosystems cover more than 40% of Earth's land surface. Previous work in the Mojave Desert (Evans et al., 2014 Nature Climate Change) reported higher soil organic carbon (SOC) and total nitrogen (N) concentrations following 10 years exposure to elevated atmospheric CO2 at the Nevada Desert Free-Air-Carbon dioxide-Enrichment (FACE) Facility (NDFF). In this study, we investigated potential mechanisms that resulted in increased SOC and total N accumulation and stabilization using high resolution mass spectrometry at the NDFF site. Samples were collected from soil profiles to 1 m in depth with a 0.2 m a increment under the dominant evergreen shrub Larrea tridentata. The differences in the molecular composition and diversity of soil organic matter (SOM) were more evident in surface soils and declined with depth, and were consistent with higher SOC and total N concentrations under elevated than ambient CO2. Our molecular analysis also suggested increased root exudation and/or microbial necromass from stabilization of labile C and N contributed to SOM and N stocks. Increased microbial activity and metabolism under elevated CO2 compared to ambient plots suggested that elevated CO2 altered microbial carbon (C) use patterns, reflecting changes in the quality and quantity of SOC inputs. We found that plant-derived compounds were primary substrates for microbial activity under elevated CO2 and microbial products were the main constituents of stabilized SOM. Our results suggest that arid ecosystems are a potential large C sink under elevated CO2, give the extensive coverage of the land surface, and that labile compounds are transformed to stable SOM via microbial processes. Arid systems are limited by water, and thus may have a different C storage potential under changing climates than other ecosystems that are limited by nitrogen or phosphorus.

Changes in Soil Carbon and Moisture over the Six Year after Thinning of a Natural Oak Forest

NASA Astrophysics Data System (ADS)

Kim, S.; Han, S. H.; Li, G.; Chang, H.; Kim, H. J.; Son, Y.

2017-12-01

The objective of this study was to assess the effects of thinning on soil carbon (C) in a natural oak forest in central Korea. The study forest received three different thinning treatments consisting of un-thinned control (UTC) and two thinning intensities (15% and 30% basal area reductions) in March in 2010. Precipitation near the study forest maintained the normal level from 2010 to 2013 (average 1,400 mm year-1), but abnormally decreased from 2014 to 2016 (average 800 mm year-1). To measure total soil C stock and soil moisture conditions, soils were collected from 0-10, 10-20, and 20-30 cm depths in June, 2010, 2013, and 2016, respectively. Soil microbial biomass C and C-cycling enzymes (β-glucosidase, cellobiohydrolase, β-xylosidase, phenol oxidase, and peroxidase) at 0-10 cm depth were determined in June, 2016. Total soil C stock at 0-30 cm depth increased throughout the study period, whereas soil moisture decreased at all depths from 2013 to 2016. Both thinning treatments had higher total soil C stock at 0-30 cm depth and moisture at 10-20 and 20-30 cm depths than the UTC in 2013 and 2016, whereas the treatments showed no effects in 2010. Microbial biomass C at 0-10 cm depth in 2016 also increased because of the thinning treatments, which was positively correlated to total soil C stock. However, any effects of thinning on C-cycling enzymes were not significant. Our results indicate that thinning could contribute to relieving the impacts of decreasing precipitation by enhancing the storage of soil moisture. Furthermore, the change in total soil C stock under thinning might result from the stimulation of microbial potential for retaining organic C as a form of biomass. This study was supported by the Ministry of Environment (2014001810002) and the National Institute of Forest Science of Korea (FM0101-2009-01).

Short-term effects of natural and NH4+-enriched chabazite zeolitite amendments to soil microbial biomass

NASA Astrophysics Data System (ADS)

Ferretti, Giacomo; Keiblinger, Katharina Maria; Di Giuseppe, Dario; Faccini, Barbara; Colombani, Nicolò; Zechmeister-Boltenstern, Sophie; Coltorti, Massimo; Mastrocicco, Micòl

2017-04-01

Natural zeolite-bearing rocks (zeolitites) are known to be a suitable material for agricultural purposes by improving soil physicochemical properties and nitrogen use efficiency (NUE). However, little is known about their effects on soil microbial biomass. Aim of this work is to evaluate short-term effects of different chabazite-zeolitite amendments on soil microbial biomass (and activity). To this purpose a silty-clay agricultural soil was amended in three different ways, by the addition of 5 and 15 wt% of natural chabazite zeolitites (NZ) and 10 wt% of NH4+-enriched chabazite zeolitites (CZ). Soil pH, water content, dissolved organic carbon (C), total dissolved N, NH4+, NO3-, NO2-, microbial biomass C and N and ergosterol were periodically measured over a time course of 16 days in a laboratory incubation experiment. In order to verify the immobilization of N derived from CZ into microbial biomass, the δ15N signature of microorganisms was evaluated by the Extraction-Fumigation-Extraction method followed by EA-IRMS analysis. This latter investigation was possible because zeolitites were enriched with NH4+ derived from pig-slurry, which have a very high 15N natural abundance that allow to trace microbial incorporation. Soil amended with 5 wt% of NZ showed increased ergosterol content as well as microbial C/N ratio starting from day 9 of incubation, suggesting that fungal biomass was probably favored, although the same behavior was not found in the soil amended with 15 wt% of the same material. On the other hand, the NH4+-enriched CZ showed strong interactions with soil microbial biomass N. Isotopic measurements supported microbial assimilation of the N introduced with CZ since the second day of incubation. The high dissolved organic C and microbial biomass N suggested an increase of mineralization and immobilization processes. In addition, in CZ amended soil, microbial biomass N was related to NO3- production over time and inversely related to NH4+, suggesting high nitrification processes especially from day 7 of incubation. Low microbial C/N ratio support bacterial prevalence in the soil amended with CZ for N-assimilation and ammonia oxidation. This confirm that CZ is an efficient soil amendment providing an immediately available N pool to soil microbial biomass.

Soil temperature and water content drive microbial carbon fixation in grassland of permafrost area on the Tibetan plateau

NASA Astrophysics Data System (ADS)

Kong, W.; Guo, G.; Liu, J.

2014-12-01

Soil microbial communities underpin terrestrial biogeochemical cycles and are greatly influenced by global warming and global-warming-induced dryness. However, the response of soil microbial community function to global change remains largely uncertain, particularly in the ecologically vulnerable Tibetan plateau permafrost area with large carbon storage. With the concept of space for time substitution, we investigated the responses of soil CO2-fixing microbial community and its enzyme activity to climate change along an elevation gradient (4400-5100 m) of alpine grassland on the central Tibetan plateau. The elevation gradient in a south-facing hill slope leads to variation in climate and soil physicochemical parameters. The autotrophic microbial communities were characterized by quantitative PCR (qPCR), terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning/sequencing targeting the CO2-fixing gene (RubisCO). The results demonstrated that the autotrophic microbial community abundance, structure and its enzyme activity were mainly driven by soil temperature and water content. Soil temperature increase and water decrease dramatically reduced the abundance of the outnumbered form IC RubisCO-containing microbes, and significantly changed the structure of form IC, IAB and ID RubisCO-containing microbial community. Structural equation model revealed that the RubisCO enzyme was directly derived from RubisCO-containing microbes and its activity was significantly reduced by soil temperature increase and water content decrease. Thus our results provide a novel positive feedback loop of climate warming and warming-induced dryness by that soil microbial carbon fixing potential will reduce by 3.77%-8.86% with the soil temperature increase of 1.94oC and water content decrease of 60%-70%. This positive feedback could be capable of amplifying the climate change given the significant contribution of soil microbial CO2-fixing up to 4.9% of total soil organic carbon.

Effect of land management on soil properties in flood irrigated citrus orchards in Eastern Spain

NASA Astrophysics Data System (ADS)

Morugán-Coronado, A.; García-Orenes, F.; Cerdà, A.

2015-01-01

Agricultural land management greatly affects soil properties. Microbial soil communities are the most sensitive and rapid indicators of perturbations in land use and soil enzyme activities are sensitive biological indicators of the effects of soil management practices. Citrus orchards frequently have degraded soils and this paper evaluates how land management in citrus orchards can improve soil quality. A field experiment was performed in an orchard of orange trees (Citrus Sinensis) in the Alcoleja Experimental Station (Eastern Spain) with clay-loam agricultural soils to assess the long-term effects of herbicides with inorganic fertilizers (H), intensive ploughing and inorganic fertilizers (P) and organic farming (O) on the soil microbial properties, and to study the relationship between them. Nine soil samples were taken from each agricultural management plot. In all the samples the basal soil respiration, soil microbial biomass carbon, water holding capacity, electrical conductivity, soil organic matter, total nitrogen, available phosphorus, available potassium, aggregate stability, cation exchange capacity, pH, texture, macronutrients (Na, Ca and Mg), micronutrients (Fe, Mn, Zn and Cu), calcium carbonate equivalent, calcium carbonate content of limestone and enzimatic activities (urease, dehydrogenase, β-glucosidase and acid phosphatase) were determined. The results showed a substantial level of differentiation in the microbial properties, which were highly associated with soil organic matter content. The management practices including herbicides and intensive ploughing had similar results on microbial soil properties. O management contributed to an increase in the soil biology quality, aggregate stability and organic matter content.

[Carbon Source Utilization Characteristics of Soil Microbial Community for Apple Orchard with Interplanting Herbage].

PubMed

Du, Yi-fei; Fang, Kai-kai; Wang, Zhi-kang; Li, Hui-ke; Mao, Peng-juan; Zhang, Xiang-xu; Wang, Jing

2015-11-01

As soil fertility in apple orchard with clean tillage is declined continuously, interplanting herbage in orchard, which is a new orchard management model, plays an important role in improving orchard soil conditions. By using biolog micro-plate technique, this paper studied the functional diversity of soil microbial community under four species of management model in apple orchards, including clear tillage model, interplanting white clover model, interplanting small crown flower model and interplanting cocksfoot model, and the carbon source utilization characteristics of microbial community were explored, which could provide a reference for revealing driving mechanism of ecological process of orchard soil. The results showed that the functional diversity of microbial community had a significant difference among different treatments and in the order of white clover > small crown flower > cocksfoot > clear tillage. The correlation analysis showed that the average well color development (AWCD), Shannon index, Richness index and McIntosh index were all highly significantly positively correlated with soil organic carbon, total nitrogen, microbial biomass carbon, and Shannon index was significantly positively correlated with soil pH. The principal component analysis and the fingerprints of the physiological carbon metabolism of the microbial community demonstrated that grass treatments improved carbon source metabolic ability of soil microbial community, and the soil microbes with perennial legumes (White Clover and small crown flower) had a significantly higher utilization rate in carbohydrates (N-Acetyl-D-Glucosamine, D-Mannitol, β-Methyl-D-Glucoside), amino acids (Glycyl-L-Glutamic acid, L-Serine, L-Threonine) and polymers (Tween 40, Glycogen) than the soil microbes with clear tillage. It was considered that different treatments had the unique microbial community structure and peculiar carbon source utilization characteristics.

Short-term effect of aniline on soil microbial activity: a combined study by isothermal microcalorimetry, glucose analysis, and enzyme assay techniques.

PubMed

Chen, Huilun; Zhuang, Rensheng; Yao, Jun; Wang, Fei; Qian, Yiguang; Masakorala, Kanaji; Cai, Minmin; Liu, Haijun

2014-01-01

The accidents of aniline spill and explosion happened almost every year in China, whereas the toxic effect of aniline on soil microbial activity remained largely unexplored. In this study, isothermal microcalorimetric technique, glucose analysis, and soil enzyme assay techniques were employed to investigate the toxic effect of aniline on microbial activity in Chinese soil for the first time. Soil samples were treated with aniline from 0 to 2.5 mg/g soil to tie in with the fact of aniline spill. Results from microcalorimetric analysis showed that the introduction of aniline had a significant adverse effect on soil microbial activity at the exposure concentrations ≥0.4 mg/g soil (p < 0.05) and ≥0.8 mg/g soil (p < 0.01), and the activity was totally inhibited when the concentration increased to 2.5 mg/g soil. The glucose analysis indicated that aniline significantly decreased the soil microbial respiratory activity at the concentrations ≥0.8 mg/g soil (p < 0.05) and ≥1.5 mg/g soil (p < 0.01). Soil enzyme activities for β-glucosidase, urease, acid-phosphatase, and dehydrogenase revealed that aniline had a significant effect (p < 0.05) on the nutrient cycling of C, N, and P as well as the oxidative capacity of soil microorganisms, respectively. All of these results showed an intensively toxic effect of aniline on soil microbial activity. The proposed methods can provide toxicological information of aniline to soil microbes from the metabolic and biochemical point of views which are consistent with and correlated to each other.

Long-term carbon exclusion alters soil microbial function but not community structure across forests of contrasting productivity

NASA Astrophysics Data System (ADS)

Hart, S. C.; Dove, N. C.; Stark, J.

2017-12-01

While it is well-documented that distinct heterotrophic microbial communities emerge under different conditions of carbon (C) availability, the response of soil microbial communities and their function to long-term conditions of C exclusion in situ has yet to be investigated. We evaluated the role of C in controlling soil microbial communities and function by experimentally excluding plant C inputs for nine years at four forest sites along a productivity gradient in Oregon, USA. Carbon exclusion treatments were implemented by root trenching to a depth of 30 cm using 25-cm diameter steel pipe, and minimizing aboveground inputs as plant litter by covering the pipe with a 1-mm mesh screen. After nine years, we measured rates of gross and net nitrogen (N) transformations and microbial respiration in situ in the upper 15-cm of mineral soil in both C excluded plots and undisturbed control soils. We measured the soil total C and N concentration and potential extracellular enzyme activities. We used phospholipid fatty acid (PLFA) analysis to determine potential changes in the microbial community structure. Nine years of C exclusion reduced soil total C by about 20%, except at the highest productivity site where no statistically significant change was observed. Although PLFA community structure and microbial C were unchanged, microbial respiration was reduced by 15-45% at all sites. Similarly, specific extracellular enzyme activities for all enzymes increased at these sites with C exclusion, suggesting that the microbial communities were substrate-limited. Although gross N mineralization decreased under C exclusion, decreases in gross N immobilization were greater, resulting in increased net N mineralization rates in all but the lowest productivity site. Furthermore, C exclusion only increased net nitrification in the highest productivity site. Although these field-based results are largely consistent with previous laboratory studies indicating a strong coupling between C and N biogeochemical cycles, they build upon this earlier research by suggesting that the "C connection" to the N cycle depends on the rate of C cycling within the ecosystem.

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska.

PubMed

Deng, Jie; Gu, Yunfu; Zhang, Jin; Xue, Kai; Qin, Yujia; Yuan, Mengting; Yin, Huaqun; He, Zhili; Wu, Liyou; Schuur, Edward A G; Tiedje, James M; Zhou, Jizhong

2015-01-01

Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical-chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw. © 2014 John Wiley & Sons Ltd.

Effects of nitrogen addition on soil microbes and their implications for soil C emission in the Gurbantunggut Desert, center of the Eurasian Continent.

PubMed

Huang, Gang; Cao, Yan Feng; Wang, Bin; Li, Yan

2015-05-15

Nitrogen (N) deposition can influence carbon cycling of terrestrial ecosystems. However, a general recognition of how soil microorganisms respond to increasing N deposition is not yet reached. We explored soil microbial responses to two levels of N addition (2.5 and 5 gN m(-2) yr(-1)) in interplant soil and beneath shrubs of Haloxylon ammodendron and their consequences to soil respiration in the Gurbantunggut Desert, northwestern China from 2011 to 2013. Microbial biomass and respiration were significantly higher beneath H. ammodendron than in interplant soil. The responses of microbial biomass carbon (MBC) and microbial respiration (MR) showed opposite responses to N addition in interplant and beneath H. ammodendron. N addition slightly increased MBC and MR in interplant soil and decreased them beneath H. ammodendron, with a significant inhibition only in 2012. N addition had no impacts on the total microbial physiological activity, but N addition decreased the labile carbon substrate utilization beneath H. ammodendron when N addition level was high. Phospholipid fatty acid (PLFA) analysis showed that N addition did not alter the soil microbial community structure as evidenced by the similar ratios of fungal to bacterial PLFAs and gram-negative to gram-positive bacterial PLFAs. Microbial biomass and respiration showed close correlations with soil water content and dissolved carbon, and they were independent of soil inorganic nitrogen across three years. Our study suggests that N addition effects on soil microorganisms and carbon emission are dependent on the respiratory substrates and water availability in the desert ecosystem. Copyright © 2015 Elsevier B.V. All rights reserved.

Combination of microbial oxidation and biogenic schwertmannite immobilization: A potential remediation for highly arsenic-contaminated soil.

PubMed

Yang, Zhihui; Wu, Zijian; Liao, Yingping; Liao, Qi; Yang, Weichun; Chai, Liyuan

2017-08-01

Here, a novel strategy that combines microbial oxidation by As(III)-oxidizing bacterium and biogenic schwertmannite (Bio-SCH) immobilization was first proposed and applied for treating the highly arsenic-contaminated soil. Brevibacterium sp. YZ-1 isolated from a highly As-contaminated soil was used to oxidize As(III) in contaminated soils. Under optimum culture condition for microbial oxidation, 92.3% of water-soluble As(III) and 84.4% of NaHCO 3 -extractable As(III) in soils were removed. Bio-SCH synthesized through the oxidation of ferrous sulfate by Acidithiobacillus ferrooxidans immobilize As(V) in the contaminated soil effectively. Consequently, the combination of microbial oxidation and Bio-SCH immobilization performed better in treating the highly As-contaminated soil with immobilization efficiencies of 99.3% and 82.6% for water-soluble and NaHCO 3 -extractable total As, respectively. Thus, the combination can be considered as a green remediation strategy for developing a novel and valuable solution for As-contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Effects of adding straw carbon source to root knot nematode diseased soil on soil microbial biomass and protozoa abundance].

PubMed

Zhang, Si-Hui; Lian, Jian-Hong; Cao, Zhi-Ping; Zhao, Li

2013-06-01

A field experiment with successive planting of tomato was conducted to study the effects of adding different amounts of winter wheat straw (2.08 g x kg(-1), 1N; 4.16 g x kg(-1), 2N; and 8.32 g x kg(-1), 4N) to the soil seriously suffered from root knot nematode disease on the soil microbial biomass and protozoa abundance. Adding straw carbon source had significant effects on the contents of soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) and the abundance of soil protozoa, which all decreased in the order of 4N > 2N > 1N > CK. The community structure of soil protozoa also changed significantly under straw addition. In the treatments with straw addition, the average proportion of fagellate, amoeba, and ciliates accounted for 36.0%, 59.5%, and 4.5% of the total protozoa, respectively. Under the same adding amounts of wheat straw, there was an increase in the soil MBC and MBN contents, MBC/MBN ratio, and protozoa abundance with increasing cultivation period.

Retention of potentially mobile radiocesium in forest surface soils affected by the Fukushima nuclear accident

PubMed Central

Koarashi, Jun; Moriya, Koichi; Atarashi-Andoh, Mariko; Matsunaga, Takeshi; Fujita, Hiroki; Nagaoka, Mika

2012-01-01

The fate of 137Cs derived from the Fukushima nuclear accident fallout and associated radiological hazards are largely dependent on its mobility in the surface soils of forest ecosystems. Thus, we quantified microbial and adsorptive retentions of 137Cs in forest surface (0–3 cm) soils. The K2SO4 extraction process liberated 2.1%–12.8% of the total 137Cs from the soils. Two soils with a higher content of clay- and silt-sized particles, organic carbon content, and cation exchange capacity showed higher 137Cs extractability. Microbial biomass was observed in all of the soils. However, the 137Cs extractability did not increase after destruction of the microbial biomass by chloroform fumigation, providing no evidence for microbial retention of the Fukushima-fallout 137Cs. The results indicate that uptake of 137Cs by soil microorganisms is less important for retention of potentially mobile 137Cs in the forest surface soils compared to ion-exchange adsorption on non-specific sites provided by abiotic components. PMID:23256039

Impact of diverse soil microbial communities on crop residues decomposition

NASA Astrophysics Data System (ADS)

Mrad, Fida; Bennegadi-Laurent, Nadia; Ailhas, Jérôme; Leblanc, Nathalie; Trinsoutrot-Gattin, Isabelle; Laval, Karine; Gattin, Richard

2017-04-01

Soils provide many basic ecosystem services for our society and most of these services are carried out by the soil communities, thus influencing soils quality. Soil organic matter (SOM) can be considered as one of the most important soil quality indices for it plays a determinant role in many physical, chemical and biological processes, such as soil structure and erosion resistance, cation exchange capacity, nutrient cycling and biological activity (Andrews et al., 2004). Since a long time, exogenous organic inputs are largely used for improving agricultural soils, affecting highly soil fertility and productivity. The use of organic amendments such as crop residues influences the soil microbial populations' diversity and abundance. In the meantime, soil microbial communities play a major role in the organic matter degradation, and the effect of different microbial communities on the decomposition of crop residues is not well documented. In this context, studying the impact of crop residues on soil microbial ecology and the processes controlling the fate of plant residues in different management practices is essential for understanding the long-term environmental and agronomic effects on soil and organic matters. Our purpose in the present work was to investigate the decomposition by two contrasting microbial communities of three crop residues, and compare the effect of different residues amendments on the abundance and function of each soil microbial communities. Among the main crops which produce large amounts of residues, we focused on three different plants: wheat (Triticum aestivum L.), rape (Brassica napus) and sunflower (Helianthus annuus). The residues degradation in two soils of different management practices and the microbial activity were evaluated by: microbial abundance (microbial carbon, culturable bacteria, total DNA, qPCR), in combination with functional indicators (enzymatic assays and Biolog substrate utilization), kinetics of C and N mineralization, and chemical measures. Physicochemical composition of crop residues was assessed by Fourier transform infrared spectroscopy FTIR technique at 0 and 83 days. The experiment was conducted in microcosms over 83 days for the biological measurements and 175 days for the C mineralization. The first results showed variations in the C & N rates, and the microbial abundances and functions over time, with a peak at 5 days and a decrease at 83 days for most of the measurements. The soil microbial communities' composition (different management practices) highly impacted the crop residues decomposition. The biochemical composition of crop residues influenced less the microbial communities of each soil. Further studies on the valorization of these residues into agro materials will be carried out. References: Andrews SS., Karlen DL., and Cambardella CA. (2004) The soil management assessment framework: a quantitative soil quality evaluation method. Soil Science Society of America, 68: 1945-1962

Responses of Bacterial Communities in Arable Soils in a Rice-Wheat Cropping System to Different Fertilizer Regimes and Sampling Times

PubMed Central

Zhao, Jun; Ni, Tian; Li, Yong; Xiong, Wu; Ran, Wei; Shen, Biao; Shen, Qirong; Zhang, Ruifu

2014-01-01

Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production. PMID:24465530

Changes in microbial community structure following herbicide (glyphosate) additions to forest soils

Treesearch

Alice W. Ratcliff; Matt D. Busse; Carol J. Shestak

2006-01-01

Glyphosate applied at the recommended field rate to a clay loam and a sandy loam forest soil resulted in few changes in microbial community structure. Total and culturable bacteria, fungal hyphal length, bacterial:fungal biomass, carbon utilization profiles (BIOLOG), and bacterial and fungal phospholipid fatty acids (PLFA) were unaffected 1, 3, 7, or 30 days...

Microbial models with data-driven parameters predict stronger soil carbon responses to climate change.

PubMed

Hararuk, Oleksandra; Smith, Matthew J; Luo, Yiqi

2015-06-01

Long-term carbon (C) cycle feedbacks to climate depend on the future dynamics of soil organic carbon (SOC). Current models show low predictive accuracy at simulating contemporary SOC pools, which can be improved through parameter estimation. However, major uncertainty remains in global soil responses to climate change, particularly uncertainty in how the activity of soil microbial communities will respond. To date, the role of microbes in SOC dynamics has been implicitly described by decay rate constants in most conventional global carbon cycle models. Explicitly including microbial biomass dynamics into C cycle model formulations has shown potential to improve model predictive performance when assessed against global SOC databases. This study aimed to data-constrained parameters of two soil microbial models, evaluate the improvements in performance of those calibrated models in predicting contemporary carbon stocks, and compare the SOC responses to climate change and their uncertainties between microbial and conventional models. Microbial models with calibrated parameters explained 51% of variability in the observed total SOC, whereas a calibrated conventional model explained 41%. The microbial models, when forced with climate and soil carbon input predictions from the 5th Coupled Model Intercomparison Project (CMIP5), produced stronger soil C responses to 95 years of climate change than any of the 11 CMIP5 models. The calibrated microbial models predicted between 8% (2-pool model) and 11% (4-pool model) soil C losses compared with CMIP5 model projections which ranged from a 7% loss to a 22.6% gain. Lastly, we observed unrealistic oscillatory SOC dynamics in the 2-pool microbial model. The 4-pool model also produced oscillations, but they were less prominent and could be avoided, depending on the parameter values. © 2014 John Wiley & Sons Ltd.

Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling.

PubMed

Berthrong, Sean T; Buckley, Daniel H; Drinkwater, Laurie E

2013-07-01

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.

Effects of subsurface aeration and trinexapac-ethyl application on soil microbial communities in a creeping bentgrass putting green

USGS Publications Warehouse

Feng, Y.; Stoeckel, D.M.; Van Santen, E.; Walker, R.H.

2002-01-01

The sensitivity of creeping bentgrass (Agrostis palustris Huds.) to the extreme heat found in the southeastern United States has led to the development of new greens-management methods. The purpose of this study was to examine the effects of subsurface aeration and growth regulator applications on soil microbial communities and mycorrhizal colonization rates in a creeping bentgrass putting green. Two cultivars (Crenshaw and Penncross), a growth regulator (trinexapacethyl), and subsurface aeration were evaluated in cool and warm seasons. Total bacterial counts were higher in whole (unsieved) soils than in sieved soils, indicating a richer rhizosphere soil environment. Mycorrhizal infection rates were higher in trinexapac-ethyl (TE) treated plants. High levels of hyphal colonization and relatively low arbuscule and vesicle occurrence were observed. Principal components analysis of whole-soil fatty acid methyl ester (FAME) profiles indicated that warm-season microbial populations in whole and sieved soils had similar constituents, but the populations differed in the cool season. FAME profiles did not indicate that subsurface aeration and TE application affected soil microbial community structure. This is the first reported study investigating the influences of subsurface aeration and TE application on soil microorganisms in a turfgrass putting green soil.

Microbial Activity in Organic Soils as Affected by Soil Depth and Crop †

PubMed Central

Tate, Robert L.

1979-01-01

The microbial activity of Pahokee muck, a lithic medisaprist, and the effect of various environmental factors, such as position in the profile and type of plant cover, were examined. Catabolic activity for [7-14C]salicylic acid, [1,4-14C]succinate, and [1,2-14C]acetate remained reasonably constant in surface (0 to 10 cm) soil samples from a fallow (bare) field from late in the wet season (May to September) through January. Late in January, the microbial activity toward all three compounds decreased approximately 50%. The microbial activity of the soil decreased with increasing depth of soil. Salicylate catabolism was the most sensitive to increasing moisture deep in the soil profile. At the end of the wet season, a 90% decrease in activity between the surface and the 60- to 70-cm depth occurred. Catabolism of acetate and succinate decreased approximately 75% in the same samples. Little effect of crop was observed. Variation in the microbial activity, as measured by the catabolism of labeled acetate, salicylate, or succinate, was not significant between a sugarcane (Saccharum officinarum L.) field and a fallow field. The activity with acetate was insignificantly different in a St. Augustine grass [Stenotaphrum secundatum (Walt) Kuntz] field, whereas the catabolism of the remaining substrates was elevated in the grass field. These results indicate that the total carbon evolved from the different levels of the soil profile by the microbial community oxidizing the soil organic matter decreased as the depth of the soil column increased. However, correction of the amount of carbon yielded at each level for the bulk density of that level reveals that the microbial contribution to the soil subsidence is approximately equivalent throughout the soil profile above the water table. PMID:16345393

Microbial activity in organic soils as affected by soil depth and crop.

PubMed

Tate, R L

1979-06-01

The microbial activity of Pahokee muck, a lithic medisaprist, and the effect of various environmental factors, such as position in the profile and type of plant cover, were examined. Catabolic activity for [7-C]salicylic acid, [1,4-C]succinate, and [1,2-C]acetate remained reasonably constant in surface (0 to 10 cm) soil samples from a fallow (bare) field from late in the wet season (May to September) through January. Late in January, the microbial activity toward all three compounds decreased approximately 50%. The microbial activity of the soil decreased with increasing depth of soil. Salicylate catabolism was the most sensitive to increasing moisture deep in the soil profile. At the end of the wet season, a 90% decrease in activity between the surface and the 60- to 70-cm depth occurred. Catabolism of acetate and succinate decreased approximately 75% in the same samples. Little effect of crop was observed. Variation in the microbial activity, as measured by the catabolism of labeled acetate, salicylate, or succinate, was not significant between a sugarcane (Saccharum officinarum L.) field and a fallow field. The activity with acetate was insignificantly different in a St. Augustine grass [Stenotaphrum secundatum (Walt) Kuntz] field, whereas the catabolism of the remaining substrates was elevated in the grass field. These results indicate that the total carbon evolved from the different levels of the soil profile by the microbial community oxidizing the soil organic matter decreased as the depth of the soil column increased. However, correction of the amount of carbon yielded at each level for the bulk density of that level reveals that the microbial contribution to the soil subsidence is approximately equivalent throughout the soil profile above the water table.

Tracking Water, C, N, and P by Linking Local Scale Soil Hydrologic and Biogeochemical Features to Watershed Scale

NASA Astrophysics Data System (ADS)

Sedaghatdoost, A.; Mohanty, B.; Huang, Y.

2017-12-01

The biogeochemical cycles of carbon (C), nitrogen (N), and phosphorus (P) have many contemporary significance due to their critical roles in determining the structure and function of ecosystems. The objectives of our study is to find out temporal dynamics and spatial distribution of soil physical, chemical, and biological properties and their interaction with C, N, and P cycles in the soil for different land covers and weather conditions. The study is being conducted at three locations within Texas Water Observatory (TWO), including Riesel (USDA-ARS experimental watersheds), Texas A&M Agrilife Research Farm, and Danciger forest in Texas. Soil physical, hydraulic, chemical (total C, total N, total P, pH, EC, redox potential, N-NO3-, N-NH4+, PO42-, K, Ca, Mg, Na, Mn, and Alox and Feox), and microbiological (Microbial biomass C, N, and P, PLFA analysis, enzymatic activity) properties are being measured in the top 30 cm of the soil profile. Our preliminary data shows that biogeochemical processes would be more profound in the areas with higher temperature and precipitation as these factors stimulate microbial activity and thus influence C, N, and P cycles. Also concentrations of C and N are greater in woodlands relative to remnant grasslands as a consequence of the greater above- and below-ground productivity of woodlands relative to remnant grasslands. We hypothesize that finer soil textures have more organic matter, microbial population, and reactive surfaces for chemicals than coarse soils, as described in some recent literature. However, the microbial activity may not be active in fine textured soils as organic materials may be sorbed to clay surfaces or protected from decomposing organisms. We also expect reduced condition in saturated soils which will decrease carbon mineralization while increase denitrification and alkalinity in the soil. Spatio-temporal data with initial evaluation of biogeochemical factors/processes for different land covers will be presented.

Nutrient Limitation of Microbial Mediated Decomposition and Arctic Soil Chronology

NASA Astrophysics Data System (ADS)

Melle, C. J.; Darrouzet-Nardi, A.; Wallenstein, M. D.

2012-12-01

Soils of northern permafrost regions currently contain twice as much carbon as the entire Earth's atmosphere. Traditionally, environmental constraints have limited microbial activity resulting in restricted decomposition of soil organic matter in these systems and accumulation of massive amounts of soil organic carbon (SOC), however climate change is reducing the constraints of decomposition in arctic permafrost regions. Carbon cycling in nutrient poor, arctic ecosystems is tightly coupled to other biogeochemical cycles. Several studies have suggested strong nitrogen limitations of primary productivity and potentially warm-season microbial activity in these nutrient deficient soils. Nitrogen is required for microbial extracellular enzyme production which drives the decomposition of soil organic matter (SOM). Nitrogen limited arctic soils may also experience limitation via labile carbon availability despite the SOM rich environment due to low extracellular enzyme production. Few studies have directly addressed nutrient induced microbial limitation in SOC rich arctic tundra soils, and even less is known about the potential for nutrient co-limitation. Additionally, through the process of becoming deglaciated, sites within close proximity to one another may have experienced drastic differences in their effective soil ages due to the varied length of their active histories. Many soil properties and nutrient deficiencies are directly related to soil age, however this chronology has not previously been a focus of research on nutrient limitation of arctic soil microbial activity. Understanding of nutrient limitations, as well as potential co-limitation, on arctic soil microbial activity has important implications for carbon cycling and the ultimate fate of the current arctic SOC reservoir. Analyses of nutrient limitation on soils of a single site are not adequate for fully understanding the controls on soil microbial activity across a vast land mass with large variation in effective soil age. My research is focused on addressing the questions of the extent of microbial N limitation in arctic tundra soils, the potential for co-limitation of labile C despite a high SOC environment, and the dependence, if any, nutrient limitation may have on the effective age of the soil. I have addressed these questions by conducting a laboratory soil incubation of factorial design with treatments of amended glucose, amended ammonium nitrate, and a control consisting of an addition of an equivalent volume of deionized water. Moist acid tundra soils possessing similar soil properties from two arctic sites of close proximity yet with varying deglaciation chronologies were utilized in my study. Soil properties of C-mineralization via respiration, microbial biomass, and nitrogen content in the forms of ammonium, nitrate, and total free amino acids and microbial extra-cellular enzyme production were assayed to determine the microbial response to the experimental treatments. Through the results of this work, I hope to better our understanding of biogeochemical cycling within arctic tundra ecosystems and the response to climate change by contributing to existing knowledge of nutrient limitation on microbial mediated decomposition of SOC in the arctic and how this may differ in soils of varying effective age.

[Effect of soil phenolic acids on soil microbe of coal-mining depressed land after afforestation restoration by different tree species].

PubMed

Ji, Li; Yang, Li Xue

2017-12-01

Phenolic acids are one of the most important factors that influence microbial community structure. Investigating the dynamic changes of phenolic acids and their relationship with the microbial community structure in plantation soils with different tree species could contribute to better understanding and revealing the mechanisms of microbial community changes under afforestation restoration in coal-mining subsidence areas. In this study, plantations of three conifer and one deciduous species (Pinus koraiensis, Larix gmelinii, Pinus sylvestris var. mongolica, and Populus ussuriensis) were established on abandoned coal-mining subsidence areas in Baoshan District, Shuangyashan City. The contents of soil phenols, 11 types of phenolic acids, and microbial communities in all plots were determined. The results showed that the contents of soil complex phenol in plantations were significantly higher than that of abandoned land overall. Specifically, soils in larch and poplar plantations had higher contents of complex phenol, while soils in larch and Korean pine plantations had greater contents of total phenol. Moreover, soil in the P. koraiensis plantation had a higher content of water-soluble phenol compared with abandoned lands. The determination of 11 phenolic acids indicated that the contents of ferulic acid, abietic acid, β-sitosterol, oleanolic acid, shikimic acid, linoleic acid, and stearic acid were higher in plantation soils. Although soil phenol contents were not related with soil microbial biomass, the individual phenolic acids showed a significant relationship with soil microbes. Ferulic acid, abietic acid, and β-sitosterol showed significant promoting effects on soil microbial biomass, and they showed positive correlations with fungi and fungi/bacteria ratio. These three phenolic acids had higher contents in the poplar plantation, suggesting that poplar affo-restation had a beneficial effect on soil quality in coal-mining subsidence areas.

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

PubMed

Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan

2015-06-16

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

Forms of organic phosphorus in wetland soils

NASA Astrophysics Data System (ADS)

Cheesman, A. W.; Turner, B. L.; Reddy, K. R.

2014-12-01

Phosphorus (P) cycling in freshwater wetlands is dominated by biological mechanisms, yet there has been no comprehensive examination of the forms of biogenic P (i.e., forms derived from biological activity) in wetland soils. We used solution 31P NMR spectroscopy to identify and quantify P forms in surface soils of 28 palustrine wetlands spanning a range of climatic, hydrogeomorphic, and vegetation types. Total P concentrations ranged between 51 and 3516 μg P g-1, of which an average of 58% was extracted in a single-step NaOH-EDTA procedure. The extracts contained a broad range of P forms, including phosphomonoesters (averaging 24% of the total soil P), phosphodiesters (averaging 10% of total P), phosphonates (up to 4% of total P), and both pyrophosphate and long-chain polyphosphates (together averaging 6% of total P). Soil P composition was found to be dependant upon two key biogeochemical properties: organic matter content and pH. For example, stereoisomers of inositol hexakisphosphate were detected exclusively in acidic soils with high mineral content, while phosphonates were detected in soils from a broad range of vegetation and hydrogeomorphic types but only under acidic conditions. Conversely inorganic polyphosphates occurred in a broad range of wetland soils, and their abundance appears to reflect more broadly that of a "substantial" and presumably active microbial community with a significant relationship between total inorganic polyphosphates and microbial biomass P. We conclude that soil P composition varies markedly among freshwater wetlands but can be predicted by fundamental soil properties.

Forms of organic phosphorus in wetland soils

NASA Astrophysics Data System (ADS)

Cheesman, A. W.; Turner, B. L.; Reddy, K. R.

2014-06-01

Phosphorus (P) cycling in freshwater wetlands is dominated by biological mechanisms, yet there has been no comprehensive examination of the forms of biogenic P (i.e. forms derived from biological activity) in wetland soils. We used solution 31P NMR spectroscopy to identify and quantify P forms in surface soils of 28 palustrine wetlands spanning a range of climatic, hydro-geomorphic and vegetation types. Total P concentrations ranged between 51 and 3516 μg P g

[Changes in soil organic carbon and soil microbial functional diversity of Carya cathayensis plantations under intensive managements].

PubMed

Wu, Jia-Sen; Qian, Jin-Fang; Tong, Zhi-Peng; Huang, Jian-Qin; Zhao, Ke-Li

2014-09-01

The change characteristics of soil organic carbon and microbial function diversity in Chinese hickory Carya cathayensis stands with different intensive-management durations (5, 10, 15 and 20 years) were studied. The results showed that soil total organic carbon (TOC), microbial biomass carbon (MBC), water-soluble organic carbon (WSOC) decreased significantly, while the stability of soil C pool increased significantly after the conversion from evergreen and deciduous broadleaf forest to intensively-managed forest (IMF). TOC, MBC and WSOC in the hickory forest soil decreased by 28.4%, 34.1% and 53.3% with 5-year intensive management, and by 38.6%, 48.9% and 64.1% with 20-year intensive management, respectively. The proportions of carboxyl C, phenolic C and aromatic C in the hickory forest soil all increased significantly, and the aromaticity of soil organic C increased by 23.0%. Soil microbial functional diversity decreased greatly af- ter intensive management of Chinese hickory forest. Significant differences in average well color development (AWCD) were found between the 0- and 5-year treatments and the 10-, 15- and 20- year treatments. The microbial diversity indexes (H) and evenness indexes (E) in the 0- and 5-year treatments were much greater than in the 10- and 20-year treatments. Correlation analysis showed that there were significant correlations among soil TOC, WSOC, MBC, AWCD, H and E.

Responses of soil microbial activity to cadmium pollution and elevated CO2.

PubMed

Chen, Yi Ping; Liu, Qiang; Liu, Yong Jun; Jia, Feng An; He, Xin Hua

2014-03-06

To address the combined effects of cadmium (Cd) and elevated CO2 on soil microbial communities, DGGE (denaturing gradient gel electrophoresis) profiles, respiration, carbon (C) and nitrogen (N) concentrations, loessial soils were exposed to four levels of Cd, i.e., 0 (Cd0), 1.5 (Cd1.5), 3.0 (Cd3.0) and 6.0 (Cd6.0) mg Cd kg(-1) soil, and two levels of CO2, i.e., 360 (aCO2) and 480 (eCO2) ppm. Compared to Cd0, Cd1.5 increased fungal abundance but decreased bacterial abundance under both CO2 levels, whilst Cd3.0 and Cd6.0 decreased both fungal and bacterial abundance. Profiles of DGGE revealed alteration of soil microbial communities under eCO2. Soil respiration decreased with Cd concentrations and was greater under eCO2 than under aCO2. Soil total C and N were greater under higher Cd. These results suggest eCO2 could stimulate, while Cd pollution could restrain microbial reproduction and C decomposition with the restraint effect alleviated by eCO2.

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil.

PubMed

Jing, Da-Wei; Liu, Fang-Chun; Wang, Ming-You; Ma, Hai-Lin; Du, Zhen-Yu; Ma, Bing-Yao; Dong, Yu-Feng

2017-01-01

This study aimed to determine the effects of root pruning on the physicochemical characteristics and microbial activities of poplar rhizosphere soil. The root systems of 5-year-old poplar (Populus×euramericana cv. 'Neva') trees were manually pruned at 6, 8, or 10 times diameter at breast height (DBH) from the trunk (severe, moderate, and light, respectively) along both inter-row sides. Moderate root pruning significantly increased the concentrations of amino acids, organic acids, and total sugars in the root exudates and decreased the pH of rhizosphere soil. This treatment also increased the contents of available nitrogen, phosphorus, potassium, and total organic carbon as well as high-, medium-, and low-activity organic carbon in rhizosphere soil. Moreover, moderate pruning increased the contents of microbial biomass carbon and nitrogen, and enhanced basal respiration, in addition to decreasing the metabolic quotients in rhizosphere soil by 8.9%, 5.0%, and 11.4% compared with control, light, and severe root pruning treatments, respectively. Moderate pruning increased the growth rates of DBH, tree height, and volume to the highest levels. Furthermore, these indices were not significantly different between the light root pruning and control groups, but varied significantly between severe and moderate root-pruning treatments. Thus, root pruning, depending on the distance from the trunk, significantly influences the physicochemical properties and microbial activities in poplar rhizosphere soil.

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil

PubMed Central

Jing, Da-Wei; Liu, Fang-Chun; Wang, Ming-You; Ma, Hai-Lin; Du, Zhen-Yu; Ma, Bing-Yao; Dong, Yu-Feng

2017-01-01

This study aimed to determine the effects of root pruning on the physicochemical characteristics and microbial activities of poplar rhizosphere soil. The root systems of 5-year-old poplar (Populus×euramericana cv. ‘Neva’) trees were manually pruned at 6, 8, or 10 times diameter at breast height (DBH) from the trunk (severe, moderate, and light, respectively) along both inter-row sides. Moderate root pruning significantly increased the concentrations of amino acids, organic acids, and total sugars in the root exudates and decreased the pH of rhizosphere soil. This treatment also increased the contents of available nitrogen, phosphorus, potassium, and total organic carbon as well as high-, medium-, and low-activity organic carbon in rhizosphere soil. Moreover, moderate pruning increased the contents of microbial biomass carbon and nitrogen, and enhanced basal respiration, in addition to decreasing the metabolic quotients in rhizosphere soil by 8.9%, 5.0%, and 11.4% compared with control, light, and severe root pruning treatments, respectively. Moderate pruning increased the growth rates of DBH, tree height, and volume to the highest levels. Furthermore, these indices were not significantly different between the light root pruning and control groups, but varied significantly between severe and moderate root-pruning treatments. Thus, root pruning, depending on the distance from the trunk, significantly influences the physicochemical properties and microbial activities in poplar rhizosphere soil. PMID:29117215

Metals other than uranium affected microbial community composition in a historical uranium-mining site.

PubMed

Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

2015-12-01

To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

Disentangling residence time and temperature sensitivity of microbial decomposition in a global soil carbon model

NASA Astrophysics Data System (ADS)

Exbrayat, J.-F.; Pitman, A. J.; Abramowitz, G.

2014-03-01

Recent studies have identified the first-order parameterization of microbial decomposition as a major source of uncertainty in simulations and projections of the terrestrial carbon balance. Here, we use a reduced complexity model representative of the current state-of-the-art parameterization of soil organic carbon decomposition. We undertake a systematic sensitivity analysis to disentangle the effect of the time-invariant baseline residence time (k) and the sensitvity of microbial decomposition to temperature (Q10) on soil carbon dynamics at regional and global scales. Our simulations produce a range in total soil carbon at equilibrium of ~ 592 to 2745 Pg C which is similar to the ~ 561 to 2938 Pg C range in pre-industrial soil carbon in models used in the fifth phase of the Coupled Model Intercomparison Project. This range depends primarily on the value of k, although the impact of Q10 is not trivial at regional scales. As climate changes through the historical period, and into the future, k is primarily responsible for the magnitude of the response in soil carbon, whereas Q10 determines whether the soil remains a sink, or becomes a source in the future mostly by its effect on mid-latitudes carbon balance. If we restrict our simulations to those simulating total soil carbon stocks consistent with observations of current stocks, the projected range in total soil carbon change is reduced by 42% for the historical simulations and 45% for the future projections. However, while this observation-based selection dismisses outliers it does not increase confidence in the future sign of the soil carbon feedback. We conclude that despite this result, future estimates of soil carbon, and how soil carbon responds to climate change should be constrained by available observational data sets.

Disentangling residence time and temperature sensitivity of microbial decomposition in a global soil carbon model

NASA Astrophysics Data System (ADS)

Exbrayat, J.-F.; Pitman, A. J.; Abramowitz, G.

2014-12-01

Recent studies have identified the first-order representation of microbial decomposition as a major source of uncertainty in simulations and projections of the terrestrial carbon balance. Here, we use a reduced complexity model representative of current state-of-the-art models of soil organic carbon decomposition. We undertake a systematic sensitivity analysis to disentangle the effect of the time-invariant baseline residence time (k) and the sensitivity of microbial decomposition to temperature (Q10) on soil carbon dynamics at regional and global scales. Our simulations produce a range in total soil carbon at equilibrium of ~ 592 to 2745 Pg C, which is similar to the ~ 561 to 2938 Pg C range in pre-industrial soil carbon in models used in the fifth phase of the Coupled Model Intercomparison Project (CMIP5). This range depends primarily on the value of k, although the impact of Q10 is not trivial at regional scales. As climate changes through the historical period, and into the future, k is primarily responsible for the magnitude of the response in soil carbon, whereas Q10 determines whether the soil remains a sink, or becomes a source in the future mostly by its effect on mid-latitude carbon balance. If we restrict our simulations to those simulating total soil carbon stocks consistent with observations of current stocks, the projected range in total soil carbon change is reduced by 42% for the historical simulations and 45% for the future projections. However, while this observation-based selection dismisses outliers, it does not increase confidence in the future sign of the soil carbon feedback. We conclude that despite this result, future estimates of soil carbon and how soil carbon responds to climate change should be more constrained by available data sets of carbon stocks.

Long lasting effects of the conversion from natural forest to poplar plantation on soil microbial communities.

PubMed

Vitali, Francesco; Mastromei, Giorgio; Senatore, Giuliana; Caroppo, Cesarea; Casalone, Enrico

2016-01-01

In this study, we evaluate the long-lasting effects on soil microbial communities of a change within a single land-use category, specifically the conversion from natural forest to forest plantation. To minimize the effects of impacts other than land-use (i.e., climatic and anthropogenic), we chose three sites within a Natural Park, with homogeneous orographic and soil texture characteristics. We compared microbial diversity in a total of 156 soil samples from two natural mixed forests and a similar forest converted to poplar plantation about thirty years ago. The diversity and structure of bacterial and fungal communities were investigated by terminal restriction fragments length polymorphism (T-RFLP) analysis of the 16S-rRNA gene and the ITS-rDNA regions, respectively. Bacterial and fungal communities from the forest plantation, compared to those from natural forest soils, showed different community structure and lower α-diversity values, consistently with the significantly higher pH values and lower organic matter content of those soils. β-diversity values, the number of measured and estimated dominant OTUs, and their distribution among the three sites showed that microbial communities from the two natural forests were much more similar to each other than they were to communities from the poplar plantation, suggesting an effect of the forest conversion on the composition and diversity of soil microbial communities. α-diversity in cultivated forest soils had narrower temporal fluctuations than in natural forest soils, suggesting higher temporal stability of microbial communities. Overall, we demonstrated that the conversion from natural forest to forest plantation altered soil microbial communities, changing their structure, lowering their diversity, and causing a spatial and temporal homogenization. Copyright © 2015 Elsevier GmbH. All rights reserved.

Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils.

PubMed

Lee, Seung-Hoon; Jang, Inyoung; Chae, Namyi; Choi, Taejin; Kang, Hojeong

2013-02-01

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.

Plant- versus microbial signature in densimetric fractions of mediterranean forest soils: a study by thermochemolysis gas chromatography mass spectrometry

NASA Astrophysics Data System (ADS)

Rovira, Pere; Grasset, Laurent

2015-04-01

Plant- versus microbial signature in densimetric fractions of mediterranean forest soils: a study by thermochemolysis gas chromatography mass spectrometry The ageing of a given organic substrate decomposing in soil is strongly dependant of its microbial utilization and transformation (reworking) by the soil microflora. How far a given substrate or soil fraction has gone in this evolution is usually measured by means of molecular signatures, ratios between organic compounds which enlighten us about the origin and/or the degree of microbial reworking of a specific group of compounds: lipids, proteins, lignin, carbohydrates, etc. Owing to the biochemical heterogeneity of decomposing substrates it is unlikely that the degree of microbial reworking can be approached with a single signature. Applying a couple of them is much better, but obtaining a wide collection of molecular signatures can be time consuming. Here, instead of applying specific methods to obtain a collection of specific signatures, we apply TMAH-thermochemolysis to obtain a panoramic view of the biochemical composition of a series of densimetric fractions of soils. From the compounds identified after TMAH-thermochemolysis, a collection of indicators was obtained: (a) ratio between short and long-chained linear alkanoic acids; (b) ratio between branched and long-chained linear alkanoic acids; (c) ratio between C16 and total alpha-omega-alkanedioic acids; (d) ratio microbial to plant-derived 1-methoxyalkanes; (e) ratio syringyl to total lignin-derived phenolic compounds; (f) vanillic acid to vanillin ratio; (g) fucose/glucose ratio; and (h) xylose/glucose ratio. From these indicators a single numerical value is distilled, allowing to order a couple of densimetric fractions of soil organic matter according to its degree of microbial reworking. This approach was applied to the comparison of a couple of densimetric fractions of soil organic matter of three organic H horizons from mediterranean forest soils. Fractions were obtained by a sequential extraction with sodium polytungstate (NaPT) at density 1.6, 1.8 and 2.0, after ultrasonic disintegration of the sample. Before ultrasonic treatment, a previous extraction was done with NaPT d = 1.6, to isolate the free light fraction. Results were overall consistent in the sense that occluded fractions of density <1.8, and particularly those of density < 1.6, appear as the most microbially evolved. The free light fraction was overall the most fresh-, least evolved fraction. The dense fraction (d > 2.0), made of organomineral complexes with fine silt plus clay, was overall fresh and poorly microbially reworked. Our future work will be the application of this approach to the study of complete soil profiles and soil fractions, thus allowing to obtain a panoramic view of the stabilization of soil organic matter at different depths.

Biodegradable Plastic Mulch Films: Impacts on Soil Microbial Communities and Ecosystem Functions.

PubMed

Bandopadhyay, Sreejata; Martin-Closas, Lluis; Pelacho, Ana M; DeBruyn, Jennifer M

2018-01-01

Agricultural plastic mulch films are widely used in specialty crop production systems because of their agronomic benefits. Biodegradable plastic mulches (BDMs) offer an environmentally sustainable alternative to conventional polyethylene (PE) mulch. Unlike PE films, which need to be removed after use, BDMs are tilled into soil where they are expected to biodegrade. However, there remains considerable uncertainty about long-term impacts of BDM incorporation on soil ecosystems. BDMs potentially influence soil microbial communities in two ways: first, as a surface barrier prior to soil incorporation, indirectly affecting soil microclimate and atmosphere (similar to PE films) and second, after soil incorporation, as a direct input of physical fragments, which add carbon, microorganisms, additives, and adherent chemicals. This review summarizes the current literature on impacts of plastic mulches on soil biological and biogeochemical processes, with a special emphasis on BDMs. The combined findings indicated that when used as a surface barrier, plastic mulches altered soil microbial community composition and functioning via microclimate modification, though the nature of these alterations varied between studies. In addition, BDM incorporation into soil can result in enhanced microbial activity and enrichment of fungal taxa. This suggests that despite the fact that total carbon input from BDMs is minuscule, a stimulatory effect on microbial activity may ultimately affect soil organic matter dynamics. To address the current knowledge gaps, long term studies and a better understanding of impacts of BDMs on nutrient biogeochemistry are needed. These are critical to evaluating BDMs as they relate to soil health and agroecosystem sustainability.

Potential microbial risk factors related to soil amendments and irrigation water of potato crops.

PubMed

Selma, M V; Allende, A; López-Gálvez, F; Elizaquível, P; Aznar, R; Gil, M I

2007-12-01

This study assesses the potential microbial risk factors related to the use of soil amendments and irrigation water on potato crops, cultivated in one traditional and two intensive farms during two harvest seasons. The natural microbiota and potentially pathogenic micro-organisms were evaluated in the soil amendment, irrigation water, soil and produce. Uncomposted amendments and residual and creek water samples showed the highest microbial counts. The microbial load of potatoes harvested in spring was similar among the tested farms despite the diverse microbial levels of Listeria spp. and faecal coliforms in the potential risk sources. However, differences in total coliform load of potato were found between farms cultivated in the autumn. Immunochromatographic rapid tests and the BAM's reference method (Bacteriological Analytical Manual; AOAC International) were used to detect Escherichia coli O157:H7 from the potential risk sources and produce. Confirmation of the positive results by polymerase chain reaction procedures showed that the immunochromatographic assay was not reliable as it led to false-positive results. The potentially pathogenic micro-organisms of soil amendment, irrigation water and soil samples changed with the harvest seasons and the use of different agricultural practices. However, the microbial load of the produce was not always influenced by these risk sources. Improvements in environmental sample preparation are needed to avoid interferences in the use of immunochromatographic rapid tests. The potential microbial risk sources of fresh produce should be regularly controlled using reliable detection methods to guarantee their microbial safety.

Predicting effects of climate change on the composition and function of soil microbial communities

NASA Astrophysics Data System (ADS)

Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

2008-12-01

Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences of these predictable changes in community composition were measured with functional arrays that detect genes involved in the metabolism of carbon, nitrogen and other elements. The response of soil microbial communities to altered precipitation can be predicted from the distribution of microbial taxa across moisture gradients.

Microbial secondary succession in soil microcosms of a desert oasis in the Cuatro Cienegas Basin, Mexico.

PubMed

López-Lozano, Nguyen E; Heidelberg, Karla B; Nelson, William C; García-Oliva, Felipe; Eguiarte, Luis E; Souza, Valeria

2013-01-01

Ecological succession is one of the most important concepts in ecology. However for microbial community succession, there is a lack of a solid theoretical framework regarding succession in microorganisms. This is in part due to microbial community complexity and plasticity but also because little is known about temporal patterns of microbial community shifts in different kinds of ecosystems, including arid soils. The Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, is an arid zone with high diversity and endemisms that has recently been threatened by aquifer overexploitation. The gypsum-based soil system of the CCB is one of the most oligotrophic places in the world. We undertook a comparative 16S rRNA 454 pyrosequencing study to evaluate microbial community succession and recovery over a year after disturbance at two sites. Results were related to concurrent measurements of humidity, organic matter and total C and N content. While each site differed in both biogeochemistry and biodiversity, both present similar pattern of change at the beginning of the succession that diverged in later stages. After one year, experimentally disturbed soil was not similar to established and undisturbed adjacent soil communities indicating recovery and succession in disturbed soils is a long process.

Post-fire drought effects and their legacy on soil functionality and microbial community structure in a Mediterranean shrubland

NASA Astrophysics Data System (ADS)

Belen Hinojosa, M.; Parra, Antonio; Laudicina, V. Armando; Moreno, José M.

2017-04-01

Climate change in subtropical areas, like the Mediterranean, is projected to decrease precipitation and to lengthen the seasonal drought period. Fire danger is also projected to increase under the most severe conditions. Little is known about the effects of increasing drought and, particularly, its legacy when precipitation resumes to normal, on the recovery of burned ecosystems. Here we studied the effects of post-fire drought and its legacy two years after it stopped on soil microbial community structure and functionality of a Cistus-Erica shrubland. To do this, a manipulative experiment was setup in which rainfall total patterns were modified by means of a rain-out shelters and irrigation system in a fully replicated set of previously burned plots. The treatments were: environmental control (natural rainfall), historical control (average rainfall, 2 months drought), moderate drought (25% reduction of historical control, 5 months drought) and severe drought (45% reduction, 7 months drought). One set of unburned plots under natural rainfall served as an additional control. Availability of the main soil nutrients and microbial community composition and functionality were monitored over 4 years under these rainfall manipulation treatments. Thereafter, treatments were discontinued and plots were subjected to ambient rainfall for two additional years. Post-fire drought had not effect on total C or N. Fire increased soil P and N availability. However, post-fire drought reduced available soil P and increased nitrate in the short term. Post- fire reduction of available K was accentuated by continued drought. Fire significantly reduced soil organic matter, enzyme activities and carbon mineralization, mainly in drought treated soils. Fire also decreased soil microbial biomass and the proportion of fungi, while that of actinomycetes increased in the short term. Post-fire drought accentuated the decrease of soil total microbial biomass and fungi, with bacteria becoming more abundant. After discontinuing the drought treatments, the effect of the previous drought was significant for available P and enzyme activities. Although the microbial biomass did not show a drought legacy effect of the previous drought period, the proportion of fungi was still lower in post-fire drought treatments and the proportion of bacteria (mainly Gram+) higher. Our results show that post-fire drought had an effect on soil functionality and microbial community structure, and that once the drought ceased its effects on some biogeochemical constituents and microbial groups were still visible two years thereafter. The fact that in a lapse of two years some variables had resume to normal while others still differed among drought treatment signifies that the legacies will last for some additional years, impairing during this time the normal functioning of the soil. However, these legacy was related to the magnitude of drought and, although not tested in our study, on the time since the occurrence of the phenomenon, and the sensitivity of the ecological system.

Changes in Soil Microbial Community and Its Effect on Carbon Sequestration Following Afforestation on the Loess Plateau, China.

PubMed

Xiang, Yun; Cheng, Man; Huang, Yimei; An, Shaoshan; Darboux, Frédéric

2017-08-22

Afforestation plays an important role in soil protection and ecological restoration. The objective of this study is to understand the effect of afforestation on soil carbon and soil microbial communities in the Loess Plateau of China. We measured two chemically-separated carbon fractions (i.e., humic acid, HA, and fulvic acid, FA) and soil microbial communities within shrublands (18-year-old Caragana korshinskii Kom (shrubland I) and 28-year-old Caragana korshinskii Kom (shrubland II)) and cropland. The size and structure of the soil microbial community was measured by phospholipid fatty acid (PLFA) analysis. The analysis of C-fractions indicated that at a depth of 0-20 cm, FA-C concentration in shrubland I and shrubland II were 1.7 times that of cropland, while HA-C had similar values across all three sites. Total PLFAs, G⁺ (Gram positive) bacterial, G - (Gram negative) bacterial, and actinobacterial PLFAs were highest in shrubland II, followed by shrubland I and finally cropland. Fungal PLFAs were significantly higher in shrubland II compared to the other sites. Additionally, we found a high degree of synergy between main microbial groups (apart from fungi) with FA-C. We concluded that planting C. korshinskii in abandoned cropland could alter the size and structure of soil microbial community, with these changes being closely related to carbon sequestration and humus formation.

Changes in Soil Microbial Community and Its Effect on Carbon Sequestration Following Afforestation on the Loess Plateau, China

PubMed Central

Xiang, Yun; Huang, Yimei; An, Shaoshan; Darboux, Frédéric

2017-01-01

Afforestation plays an important role in soil protection and ecological restoration. The objective of this study is to understand the effect of afforestation on soil carbon and soil microbial communities in the Loess Plateau of China. We measured two chemically-separated carbon fractions (i.e., humic acid, HA, and fulvic acid, FA) and soil microbial communities within shrublands (18-year-old Caragana korshinskii Kom (shrubland I) and 28-year-old Caragana korshinskii Kom (shrubland II)) and cropland. The size and structure of the soil microbial community was measured by phospholipid fatty acid (PLFA) analysis. The analysis of C-fractions indicated that at a depth of 0–20 cm, FA-C concentration in shrubland I and shrubland II were 1.7 times that of cropland, while HA-C had similar values across all three sites. Total PLFAs, G+ (Gram positive) bacterial, G− (Gram negative) bacterial, and actinobacterial PLFAs were highest in shrubland II, followed by shrubland I and finally cropland. Fungal PLFAs were significantly higher in shrubland II compared to the other sites. Additionally, we found a high degree of synergy between main microbial groups (apart from fungi) with FA-C. We concluded that planting C. korshinskii in abandoned cropland could alter the size and structure of soil microbial community, with these changes being closely related to carbon sequestration and humus formation. PMID:28829374

Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil.

PubMed

Chen, Junhui; He, Feng; Zhang, Xuhui; Sun, Xuan; Zheng, Jufeng; Zheng, Jinwei

2014-01-01

Chemical and microbial characterisations of particle-size fractions (PSFs) from a rice paddy soil subjected to long-term heavy metal pollution (P) and nonpolluted (NP) soil were performed to investigate whether the distribution of heavy metals (Cd, Cu, Pb and Zn) regulates microbial community activity, abundance and diversity at the microenvironment scale. The soils were physically fractionated into coarse sand, fine sand, silt and clay fractions. Long-term heavy metal pollution notably decreased soil basal respiration (a measurement of the total activity of the soil microbial community) and microbial biomass carbon (MBC) across the fractions by 3-45% and 21-53%, respectively. The coarse sand fraction was more affected by pollution than the clay fraction and displayed a significantly lower MBC content and respiration and dehydrogenase activity compared with the nonpolluted soils. The abundances and diversities of bacteria were less affected within the PSFs under pollution. However, significant decreases in the abundances and diversities of fungi were noted, which may have strongly contributed to the decrease in MBC. Sequencing of denaturing gradient gel electrophoresis bands revealed that the groups Acidobacteria, Ascomycota and Chytridiomycota were clearly inhibited under pollution. Our findings suggest that long-term heavy metal pollution decreased the microbial biomass, activity and diversity in PSFs, particularly in the large-size fractions. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Specific features of the structure of microbial biomass in soils of annular mesodepressions in Lipetsk and Volgograd oblasts

NASA Astrophysics Data System (ADS)

Polyanskaya, L. V.; Sukhanova, N. I.; Chakmazyan, K. V.; Zvyagintsev, D. G.

2014-09-01

In the studied mesodepressions, the total microbial biomass in the gray forest and chernozemic soils decreases by two-three times under the impact of hydrogen flux from the subsoil horizons and soil waterlogging. The biomass decrease is especially pronounced in the lower soil horizons. The population density of bacteria in the soil samples subjected to the impact of hydrogen fluxes and temporary waterlogging decreases by two-three times in the upper horizons and by ten times in the lower horizons in comparison with that in the control samples. These factors also affect the length of fungal mycelium: it decreases by three-four times in the upper horizons and may completely disappear in the lower horizons. The reduction of the microbial biomass can be explained by the fact that hydrogen and waterlogging sharply decrease the soil redox potential, which retards the development of most microbes, except for methanogens and some other specialized groups of microorganisms. The domination of bacteria with diameter ≥0.23 and ≥0.38 μm and the decrease in the total number of bacteria have been found with the use of the cascade filtration method.

Comparison of whole-cell fatty acid (MIDI) or phospholipid fatty acid (PLFA) extractants as biomarkers to profile soil microbial communities.

PubMed

Fernandes, Marcelo F; Saxena, Jyotisna; Dick, Richard P

2013-07-01

The whole-cell lipid extraction to profile microbial communities on soils using fatty acid (FA) biomarkers is commonly done with the two extractants associated with the phospholipid fatty acid (PLFA) or Microbial IDentification Inc. (MIDI) methods. These extractants have very different chemistry and lipid separation procedures, but often shown a similar ability to discriminate soils from various management and vegetation systems. However, the mechanism and the chemistry of the exact suite of FAs extracted by these two methods are poorly understood. Therefore, the objective was to qualitatively and quantitatively compare the MIDI and PLFA microbial profiling methods for detecting microbial community shifts due to soil type or management. Twenty-nine soil samples were collected from a wide range of soil types across Oregon and extracted FAs by each method were analyzed by gas chromatography (GC) and GC-mass spectrometry. Unlike PLFA profiles, which were highly related to microbial FAs, the overall MIDI-FA profiles were highly related to the plant-derived FAs. Plant-associated compounds were quantitatively related to particulate organic matter (POM) and qualitatively related to the standing vegetation at sampling. These FAs were negatively correlated to respiration rate normalized to POM (RespPOM), which increased in systems under more intensive management. A strong negative correlation was found between MIDI-FA to PLFA ratios and total organic carbon (TOC). When the reagents used in MIDI procedure were tested for the limited recovery of MIDI-FAs from soil with high organic matter, the recovery of MIDI-FA microbial signatures sharply decreased with increasing ratios of soil to extractant. Hence, the MIDI method should be used with great caution for interpreting changes in FA profiles due to shifts in microbial communities.

Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture

PubMed Central

Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S.

2016-01-01

Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (tlag) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h−1 of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced tlag, indicating that favorable abiotic conditions activated soil microorganisms. We conclude that soil respiratory responses to short-term changes in environmental conditions are better explained by changes in AMB than in TMB. These results suggest that decomposition models that explicitly represent microbial carbon pools should take into account the active microbial pool, and researchers should be cautious in comparing modeled microbial pool sizes with measurements of TMB. PMID:27148213

Remediation of soil co-contaminated with petroleum and heavy metals by the integration of electrokinetics and biostimulation.

PubMed

Dong, Zhi-Yong; Huang, Wen-Hui; Xing, Ding-Feng; Zhang, Hong-Feng

2013-09-15

Successful remediation of soil co-contaminated with high levels of organics and heavy metals is a challenging task, because that metal pollutants in soil can partially or completely suppress normal heterotrophic microbial activity and thus hamper biodegradation of organics. In this study, the benefits of integrating electrokinetic (EK) remediation with biodegradation for decontaminating soil co-contaminated with crude oil and Pb were evaluated in laboratory-scale experiments lasting for 30 days. The treated soil contained 12,500 mg/kg of total petroleum hydrocarbons (TPH) and 450 mg/kg Pb. The amendments of EDTA and Tween 80, together with a regular refreshing of electrolyte showed the best performance to remediate this contaminated soil. An important function of EDTA-enhanced EK treatment was to eliminate heavy metal toxicity from the soil, thus activating microbial degradation of oil. Although Tween 80 reduced current, it could serve as a second substrate for enhancing microbial growth and biodegradation. It was found that oil biodegradation degree and microbial numbers increased toward the anode and cathode. Microbial metabolism was found to be beneficial to metal release from the soil matrix. Under the optimum conditions, the soil Pb and TPH removal percentages after 30 days of running reached 81.7% and 88.3%, respectively. After treatment, both the residual soil Pb and TPH concentrations met the requirement of the Chinese soil environmental quality standards. Copyright © 2013 Elsevier B.V. All rights reserved.

Contrasting influence of soil nutrients and microbial community on differently sized basal consumers

NASA Astrophysics Data System (ADS)

Vonk, J. Arie; Mulder, Christian

2013-07-01

There is increasing evidence of the coexistence of trophic and environmental constraints belowground. While too often ignored in current literature, the extent to which phosphorus is relevant for soil biota was demonstrated in this study by positive correlations of soil C/P and N/P ratios with all the measured microbial parameters (biomass, density and activity), with the numerical abundance of roundworms (Nematoda) and potworms (Enchytraeidae) from lower trophic levels and with the roundworm biomass. Total worm biomass seems dependent on land use, being in rangelands about twice as high as in croplands, although the relative contribution of potworms remains comparable for both land use types (49 ± 20 % SD versus 45 ± 27 % SD). Besides soil [P], soil type plays an important role in the relative biomass of potworms compared to roundworms. Soil parameters (here pH, C/P and N/P ratios) are better predictors for the abundance and biomass of roundworms than microbial parameters. We also propose a graphical way to visualize the major responses of basal consumers to their microbial drivers.

[Effects of different tillage methods on phospholipid fatty acids and enzyme activities in calcareous cinnamon soil].

PubMed

Pei, Xue-Xia; Dang, Jian-You; Zhang, Ding-Yi; Wang, Jiao-Ai; Zhang, Jing

2014-08-01

In order to study changes of physical and chemical characteristics and microbial activities in soil under different tillage methods, effects of four tillage methods, rotary tillage (RT), subsoil tillage (ST), conventional tillage (CT) with corn straw returned to soil, and rotary tillage with no corn straw returned to soil (CK), on phospholipid fatty acids (PLFA) characteristics and hydrolase enzymes activities in calcareous cinnamon soil were investigated. The results showed that soil hydrolase enzymes activities, nutrient contents, microbial diversity varied greatly with the different tillage methods. Returning corn straw to soil increased the kinds, amount of soil total PLFAs, bacteria PLFAs and actonomycetes PLFAs, while decreased the fungi PLFAs, indicating that fungi was more adaptable than bacteria to an infertile environment. ST and CT resulted in higher amounts of total PLFAs, which were 74.7% and 53.3% higher than that of CK, indicating they were more beneficial to the growth of plants. They could also improve soil physical and chemical properties, increase alk-phosphatase, protease and urease activities, which would provide a favorable soil condition for high and stable crop yields.

Effects of carbon amendment on in situ atrazine degradation and total microbial biomass.

PubMed

Ngigi, Anastasiah N; Getenga, Zachary M; Dörfler, Ulrike; Boga, Hamadi I; Kuria, Benson; Ndalut, Paul; Schroll, Reiner

2013-01-01

This study elucidates the effects of carbon amendment on metabolic degradation of atrazine (6-chloro-N(2)-ethyl-N(4)-isopropyl-1,3,5-triazine-2,4-diamine) and total microbial biomass in soil. Degradation of (14)C-ring-labelled atrazine was monitored in laboratory incubations of soils supplemented with 0, 10, 100 and 1000 μg g(-1) sucrose concentrations. An experiment to determine the effect of carbon amendment on total microbial biomass and soil respiration was carried out with different concentrations of sucrose and non-labelled atrazine. The soils were incubated at a constant temperature and constant soil moisture at water potential of -15 kPa and a soil density of 1.3 g cm(-3). Mineralization of (14)C-ring-labelled atrazine was monitored continuously over a period of 59 d in the first experiment. The CO(2) production was monitored for 62 d in the second experiment and microbial biomass determined at the end of the incubation period. The addition of 1000 μg g(-1) sucrose reduced atrazine mineralization to 43.5% compared to 51.7% of the applied amount for the treatment without sucrose. The addition of 1000 μg g(-1) sucrose modified the transformation products to 1.08 μg g(-1) deisopropylatrazine (DIA), 0.32 μg g(-1) desethylatrazine (DEA) and 0.18 μg g(-1) deisopropyl-2-hydroxyatrazine (OH-DIA). Treatment without sucrose resulted in formation of 0.64 μg g(-1) hydroxyatrazine (HA), 0.28 μg g(-1) DIA and 0.20 μg g(-1) OH-DIA. Atrazine dealkylation was enhanced in treatments with 100 and 1000 μg g(-1) of sucrose added. HA metabolite was formed in the control (no sucrose) and in the presence of 10 μg g(-1) of sucrose, whereas DEA was only detected in treatment with 1000 μg g(-1) sucrose. Results indicate that total microbial biomass increased significantly (P < 0.001) with the addition of 1000 μg g(-1) sucrose.

Combinational effects of sulfomethoxazole and copper on soil microbial community and function.

PubMed

Liu, Aiju; Cao, Huansheng; Yang, Yan; Ma, Xiaoxuan; Liu, Xiao

2016-03-01

Sulfonamides and Cu are largely used feed additives in poultry farm. Subsequently, they are spread onto agricultural soils together with contaminated manure used as fertilizer. Both sulfonamides and Cu affect the soil microbial community. However, an interactive effect of sulfonamides and Cu on soil microorganisms is not well understood. Therefore, a short-time microcosm experiment was conducted to investigate the interaction of veterinary antibiotic sulfomethoxazole (SMX) and Cu on soil microbial structure composition and functions. To this end, selected concentrations of SMX (0, 5, and 50 mg kg(-1)) and Cu (0, 300, and 500 mg kg(-1)) were combined, respectively. Clear dose-dependent effects of SMX on microbial biomass and basal respiration were determined, and these effects were amplified in the presence of additional Cu. For activities of soil enzymes including β-glucosidase, urease, and protease, clear reducing effects were determined in soil samples containing 5 or 50 mg kg(-1) of SMX, and the interaction of SMX and Cu was significant, particularly in soil samples containing 50 mg kg(-1) SMX or 500 mg kg(-1) Cu. SMX amendments, particularly in combination with Cu, significantly reduced amounts of the total, bacterial, and fungal phospholipid fatty acids (PLFAs) in soil. Moreover, the derived ratio of bacteria to fungi decreased significantly with incremental SMX and Cu, and principal component analysis of the PLFAs showed that soil microbial composition was significantly affected by SMX interacted with Cu at 500 mg kg(-1). All of these results indicated that the interaction of SMX and Cu was synergistic to amplify the negative effect of SMX on soil microbial biomass, structural composition, and even the enzymatic function.

Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils.

PubMed

Cébron, Aurélie; Beguiristain, Thierry; Bongoua-Devisme, Jeanne; Denonfoux, Jérémie; Faure, Pierre; Lorgeoux, Catherine; Ouvrard, Stéphanie; Parisot, Nicolas; Peyret, Pierre; Leyval, Corinne

2015-09-01

The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the development of PAH-degrading bacteria holding Gram-negative PAH-ring hydroxylating dioxygenase, catechol-1,2-dioxygenase and catechol-2,3-dioxygenase genes. Regarding the total community structure, bacteria closely related to Thiobacillus (β-Proteobacteria) and Steroidobacter (γ-Proteobacteria) genera were favoured by wood sawdust amendment. In both soils, plant rhizospheres induced the development of fungi belonging to Ascomycota and related to Alternaria and Fusarium genera. Bacteria closely related to Luteolibacter (Verrucomicrobia) and Microbacterium (Actinobacteria) were favoured in alfalfa and ryegrass rhizosphere.

Integrated metagenomics and network analysis of soil microbial community of the forest timberline

PubMed Central

Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; Van Nostrand, Joy D.; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

2015-01-01

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4+-N, NO3−-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift. PMID:25613225

Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area.

PubMed

Han, Xue-Mei; Liu, Yu-Rong; Zheng, Yuan-Ming; Zhang, Xiao-Xia; He, Ji-Zheng

2014-01-01

Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by real-time quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.

[The relationship between abiotic factors and microbial activities of microbial eco-system in contaminated soil with petroleum hydrocarbons].

PubMed

Jia, Jian-li; Li, Guang-he; Zhong, Yi

2004-05-01

By means of the biostimulation and bioaugmentation in the micro-ecological environment of contaminated soil with petrochemical hydrocarbons, the biodegradation rates and mode of the contaminants were significantly improved. Based on the investigations carried out in some oilfields and petrochemical industrial area of Northern China, the relationship between the abiotic factors such as nutrient, pH, contaminants, water content, alkalinity, etc., and microbial activities was interpreted and identified in this paper. The results from the investigations and indoor and in-situ experiments conducted recent years indicated that the soils in the areas, to the extent, have been polluted by the different kinds of organic compounds composed of monoaromatic benzene, PAHs, chlorinated solvent, and alkanes, and the concentrations of the compounds mostly were elevated as compared to the background, with the highest 34,000 mg/kg dry soil. The column chromatography analysis results showed that the alkyl and aromatic compounds were accounted for more than 50% of the total hydrocarbon contents, which was readily degraded by degrading bacteria and improved the degrading microbe activities. The effective nitrogen and phosphorus encountered in the soil was less than 30 mg/kg dry soil and 10 mg/kg dry soil, only about 5% of total contents of them respectively. Based on the stoichiometric calculation and reasonable ratio of carbon to nutrient content regarding the biodegradation of organic compounds, the nutrient levels mainly composed of nitrogen and phosphorus in polluted soil as importantly limiting factors to degrading bacterial growth and activity were insufficient to the biodegradation of petrochemicals, and it is needed to add the nutrient for the bioremediation of contaminated soil. It is undoubted that the optimization of abiotic factors play significant role in increasing the microbial activity and improving the biodegradation rates.

Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

PubMed

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.

Soil Mineral Composition Matters: Response of Microbial Communities to Phenanthrene and Plant Litter Addition in Long-Term Matured Artificial Soils

PubMed Central

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications. PMID:25222697

Quantification of Microbial Osmolytes in a Drought Impacted California Grassland

NASA Astrophysics Data System (ADS)

Boot, C. M.; Schaeffer, S. M.; Doyle, A. P.; Schimel, J. P.

2008-12-01

With drought frequency and severity likely increasing in the future, understanding its effect on terrestrial carbon (C) and nitrogen (N) cycling has become essential for accurately modeling ecosystem responses to climate change. Microbes respond to drought stress by accumulating internal solutes, or osmolytes, such as amino acids, betaines and polyols, to balance cell membrane water potential as the soil dries. However, when seasonal rains arrive, internal solutes are released and rapidly mineralized. We have been studying these processes in a California grassland. Beginning in summer 2007, we made monthly measurements of soil moisture, individual amino acid concentration in total soil and in microbial biomass, total dissolved organic carbon and nitrogen (DOC and DON), and microbial biomass carbon and nitrogen (MBC and MBN). We expected microbial concentrations of the known amino acid osmolytes glutamate (glu) and proline (pro) to fluctuate inversely with soil moisture. However, pro was only recovered in Mar 2008 (0.30 μg C g-1 dry soil) and the glu concentration varied proportionally with soil moisture: lowest during summer (0.06 g H2O g-1 dry soil, 2.22 μg glutamate-C g-1 dry soil) and highest in winter (0.27 g H2O g-1 dry soil, 4.43 μg glutamate-C g-1 dry soil). The trend from DOC, MBC, and DON measurements was opposite, however, with all concentrations decreasing as soil moisture shifted from dry to wet, (DOC: 64.61 to 32.49 μg C g-1 dry soil respectively). MBN was the exception to this trend, with concentrations staying nearly constant across seasons. These patterns suggest that the expected amino acids glu and pro are not being used for microbial osmoregulation in the CA grassland, and given the summer to winter decrease in MBC, the primary osmolyte source is likely to be either polyol-type compounds such as mannitol or betaines. The implications for terrestrial carbon cycle are considerable because as the frequency of drought increases, the accumulation and release of osmolytes in response to drought has potential to pump carbon out of the grassland ecosystem.

Microbial dormancy improves development and experimental validation of ecosystem model

DOE PAGES

Wang, Gangsheng; Jagadamma, Sindhu; Mayes, Melanie; ...

2014-07-11

Climate feedbacks from soils can result from environmental change followed by response of plant and microbial communities, and/or associated changes in nutrient cycling. Explicit consideration of microbial life history traits and functions may be necessary to predict climate feedbacks due to changes in the physiology and community composition of microbes and their associated effect on carbon cycling. Here, we enhanced the Microbial-Enzyme-mediated Decomposition (MEND) model by incorporating microbial dormancy and the ability to track multiple isotopes of carbon. We tested two versions of MEND, i.e., MEND with dormancy and MEND without dormancy, against long-term (270 d) lab incubations of fourmore » soils with isotopically-labeled substrates. MEND without dormancy adequately fitted multiple observations (total and 14C respiration, and dissolved organic carbon), but at the cost of significantly underestimating the total microbial biomass. The MEND with dormancy improved estimates of microbial biomass by 20 71% over the MEND without dormancy. We observed large differences for two fitted model parameters, the specific maintenance and growth rates for active microbes, depending on whether dormancy was considered. Together our model extrapolations of the incubation study show that long-term soil incubations with observations in multiple carbon pools are necessary to estimate both decomposition and microbial parameters. These efforts should provide essential support to future field- and global-scale simulations and enable more confident predictions of feedbacks between environmental change and carbon cycling.« less

Controls upon microbial accessibility to soil organic matter following woody plant encroachment into grasslands

NASA Astrophysics Data System (ADS)

Creamer, C. A.; Boutton, T. W.; Filley, T. R.

2009-12-01

Woody plant encroachment (WPE) into savannas and grasslands is a global phenomenon that alters soil organic matter (SOM) dynamics through changes in litter quality and quantity, soil structure, microbial ecology, and soil hydrology. To elucidate the controls upon microbial accessibility to SOM, bulk soils from a chronosequence of progressive WPE into native grasslands at the Texas A&M Agricultural Experimental Station La Copita Research Area were incubated for one year. The quantity and stable carbon isotope composition of respired CO2, plant biopolymer chemistry in SOM, and microbial community structure were tracked. Respiration rates declined steadily over the course of the experiment with 15-25% of the total CO2 respired released in the first month of incubation. Between 8 and 18% of the total carbon was mineralized to CO2 throughout the incubation. After day 84 a significantly (p < 0.05) greater portion of carbon was mineralized from soils of older woody clusters (34-86 years) than from soils of younger clusters (14-23 years) and the native grassland. Approximately 80% of patterns seen in cumulative CO2 loss could be explained by the proportions of macro- and micro-aggregates within each soil, suggesting soil structure is a major controlling factor of respiration rates. Despite documented carbon accrual within La Copita soils due to WPE, we observed no evidence of enhanced carbon stabilization in these respiration experiments. In fact, a greater proportion of total carbon was lost from the soil of mature woody stands than from young stands, suggesting carbon accumulation observed with WPE may be due to greater input rates or microbial dynamics not captured in the laboratory incubation. A cluster approximately 34 years in age represents a transition point in WPE where respiration dynamics become distinct between grassland and wooded elements. By day 84 of the incubation CO2 respired from all soils was depleted with respect to bulk SOM (1.5 to 5‰) and this pattern remained for the rest of the incubation. As the depletion of CO2 relative to bulk SOM was observed in grassland and cluster soils, we hypothesized the depleted signature resulted from the utilization of depleted biopolymers, specifically lignin, cutin and suberin, as hypothesized by others. Quantitative and isotopic comparisons of these monomers prior to and following the incubation will determine if selective compound utilization is a reason for this depletion. The results discussed herein provide important insights into the dynamics of SOM accrual with WPE as well as respiration dynamics during laboratory incubations.

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica.

PubMed

Goordial, Jacqueline; Davila, Alfonso; Lacelle, Denis; Pollard, Wayne; Marinova, Margarita M; Greer, Charles W; DiRuggiero, Jocelyn; McKay, Christopher P; Whyte, Lyle G

2016-07-01

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature -23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival.

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica

PubMed Central

Goordial, Jacqueline; Davila, Alfonso; Lacelle, Denis; Pollard, Wayne; Marinova, Margarita M; Greer, Charles W; DiRuggiero, Jocelyn; McKay, Christopher P; Whyte, Lyle G

2016-01-01

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature −23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival. PMID:27323892

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil

PubMed Central

Mitchell, Jeffrey; Scow, Kate

2018-01-01

Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California’s Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0–5, 5–15 and 15–30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0–5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals–organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how agricultural practices shift microbial abundance, diversity and life strategies, such as presented here, can assist with designing farming systems that can support high yields, while enhancing C sequestration and increasing resilience to climate change. PMID:29447262

Biodegradable Plastic Mulch Films: Impacts on Soil Microbial Communities and Ecosystem Functions

PubMed Central

Bandopadhyay, Sreejata; Martin-Closas, Lluis; Pelacho, Ana M.; DeBruyn, Jennifer M.

2018-01-01

Agricultural plastic mulch films are widely used in specialty crop production systems because of their agronomic benefits. Biodegradable plastic mulches (BDMs) offer an environmentally sustainable alternative to conventional polyethylene (PE) mulch. Unlike PE films, which need to be removed after use, BDMs are tilled into soil where they are expected to biodegrade. However, there remains considerable uncertainty about long-term impacts of BDM incorporation on soil ecosystems. BDMs potentially influence soil microbial communities in two ways: first, as a surface barrier prior to soil incorporation, indirectly affecting soil microclimate and atmosphere (similar to PE films) and second, after soil incorporation, as a direct input of physical fragments, which add carbon, microorganisms, additives, and adherent chemicals. This review summarizes the current literature on impacts of plastic mulches on soil biological and biogeochemical processes, with a special emphasis on BDMs. The combined findings indicated that when used as a surface barrier, plastic mulches altered soil microbial community composition and functioning via microclimate modification, though the nature of these alterations varied between studies. In addition, BDM incorporation into soil can result in enhanced microbial activity and enrichment of fungal taxa. This suggests that despite the fact that total carbon input from BDMs is minuscule, a stimulatory effect on microbial activity may ultimately affect soil organic matter dynamics. To address the current knowledge gaps, long term studies and a better understanding of impacts of BDMs on nutrient biogeochemistry are needed. These are critical to evaluating BDMs as they relate to soil health and agroecosystem sustainability. PMID:29755440

Influence of petroleum hydrocarbon contamination on microalgae and microbial activities in a long-term contaminated soil.

PubMed

Megharaj, M; Singleton, I; McClure, N C; Naidu, R

2000-05-01

Petroleum hydrocarbons are widespread environmental pollutants. Although biodegradation of petroleum hydrocarbons has been the subject of numerous investigations, information on their toxicity to microorganisms in soil is limited, with virtually no work conducted on soil algae. We carried out a screening experiment for total petroleum hydrocarbons (TPH) and their toxicity to soil algal populations, microbial biomass, and soil enzymes (dehydrogenase and urease) in a long-term TPH-polluted site with reference to an adjacent unpolluted site. Microbial biomass, soil enzyme activity, and microalgae declined in medium to high-level (5,200-21,430 mg kg(-1) soil) TPH-polluted soils, whereas low-level (<2,120 mg kg(-1) soil) pollution stimulated the algal populations and showed no effect on microbial biomass and enzymes. However, inhibition of all the tested parameters was more severe in soil considered to have medium-level pollution than in soils that were highly polluted. This result could not be explained by chemical analysis alone. Of particular interest was an observed shift in the species composition of algae in polluted soils with elimination of sensitive species in the medium to high polluted soils. Also, an algal growth inhibition test carried out using aqueous eluates prepared from polluted soils supported these results. Given the sensitivity of algae to synthetic pollutants, alteration in the algal species composition can serve as a useful bioindicator of pollution. The results of this experiment suggest that chemical analysis alone is not adequate for toxicological estimations and should be used in conjunction with bioassays. Furthermore, changes in species composition of algae proved to be more sensitive than microbial biomass and soil enzyme activity measurements.

Microbial quality and bioactive constituents of sweet peppers from sustainable production systems.

PubMed

Marín, Alicia; Gil, María I; Flores, Pilar; Hellín, Pilar; Selma, María V

2008-12-10

Integrated, organic, and soil-less production systems are the principal production practices that have emerged to encourage more sustainable agricultural practices and safer edible plants, reducing inputs of plaguicides, pesticides, and fertilizers. Sweet peppers grown commercially under integrated, organic, and soil-less production systems were compared to study the influence of these sustainable production systems on the microbial quality and bioactive constituents (vitamin C, individual and total carotenoids, hydroxycinnamic acids, and flavonoids). The antioxidant composition of peppers was analyzed at green and red maturity stages and at three harvest times (initial, middle, and late season). Irrigation water, manure, and soil were shown to be potential transmission sources of pathogens to the produce. Coliform counts of soil-less peppers were up to 2.9 log units lower than those of organic and integrated peppers. Soil-less green and red peppers showed maximum vitamin C contents of 52 and 80 mg 100 g(-1) fresh weight (fw), respectively, similar to those grown in the organic production system. Moreover, the highest content of total carotenoids was found in the soil-less red peppers, which reached a maximum of 148 mg 100 g(-1) fw, while slightly lower contents were found in integrated and organic red peppers. Hydroxycinnamic acids and flavonoids represented 15 and 85% of the total phenolic content, respectively. Total phenolic content, which ranged from 1.2 to 4.1 mg 100 g(-1) fw, was significantly affected by the harvest time but not by the production system assayed. Soil-less peppers showed similar or even higher concentrations of bioactive compounds (vitamin C, provitamin A, total carotenoid, hydroxycinnamic acids, and flavonoids) than peppers grown under organic and integrated practices. Therefore, in the commercial conditions studied, soil-less culture was a more suitable alternative than organic or integrated practices, because it improved the microbial safety of sweet peppers without detrimental effects on the bioactive compound content.

Effect of rhizosphere on soil microbial community and in-situ pyrene biodegradation

USGS Publications Warehouse

Su, Y.; Yang, X.; Chiou, C.T.

2008-01-01

To access the influence of a vegetation on soil microorganisms toward organic pollutant biogegration, this study examined the rhizospheric effects of four plant species (sudan grass, white clover, alfalfa, and fescue) on the soil microbial community and in-situ pyrene (PYR) biodegradation. The results indicated that the spiked PYR levels in soils decreased substantially compared to the control soil without planting. With equal planted densities, the efficiencies of PYR degradation in rhizosphere with sudan grass, white clover, alfalfa and fescue were 34.0%, 28.4%, 27.7%, and 9.9%, respectively. However, on the basis of equal root biomass the efficiencies were in order of white clover >> alfalfa > sudan > fescue. The increased PYR biodegradation was attributed to the enhanced bacterial population and activity induced by plant roots in the rhizosphere. Soil microbial species and biomasses were elucidated in terms of microbial phospholipid ester-linked fatty acid (PLFA) biomarkers. The principal component analysis (PCA) revealed significant changes in PLFA pattern in planted and non-planted soils spiked with PYR. Total PLFAs in planted soils were all higher than those in non-planted soils. PLFA assemblages indicated that bacteria were the primary PYR degrading microorganisms, and that Gram-positive bacteria exhibited higher tolerance to PYR than Gram-negative bacteria did. ?? 2008 Higher Education Press and Springer-Verlag GmbH.

Microbial properties explain temporal variation in soil respiration in a grassland subjected to nitrogen addition

PubMed Central

Li, Yue; Liu, Yinghui; Wu, Shanmei; Niu, Lei; Tian, Yuqiang

2015-01-01

The role of soil microbial variables in shaping the temporal variability of soil respiration has been well acknowledged but is poorly understood, particularly under elevated nitrogen (N) deposition conditions. We measured soil respiration along with soil microbial properties during the early, middle, and late growing seasons in temperate grassland plots that had been treated with N additions of 0, 2, 4, 8, 16, or 32 g N m−2 yr−1 for 10 years. Representing the averages over three observation periods, total (Rs) and heterotrophic (Rh) respiration were highest with 4 g N m−2 yr−1, but autotrophic respiration (Ra) was highest with 8 to 16 g N m−2 yr−1. Also, the responses of Rh and Ra were unsynchronized considering the periods separately. N addition had no significant impact on the temperature sensitivity (Q10) for Rs but inhibited the Q10 for Rh. Significant interactions between observation period and N level occurred in soil respiration components, and the temporal variations in soil respiration components were mostly associated with changes in microbial biomass carbon (MBC) and phospholipid fatty acids (PLFAs). Further observation on soil organic carbon and root biomass is needed to reveal the long-term effect of N deposition on soil C sequestration. PMID:26678303

Soil microbial respiration and PICT responses to an industrial and historic lead pollution: a field study.

PubMed

Bérard, Annette; Capowiez, Line; Mombo, Stéphane; Schreck, Eva; Dumat, Camille; Deola, Frédéric; Capowiez, Yvan

2016-03-01

We performed a field investigation to study the long-term impacts of Pb soil contamination on soil microbial communities and their catabolic structure in the context of an industrial site consisting of a plot of land surrounding a secondary lead smelter. Microbial biomass, catabolic profiles, and ecotoxicological responses (PICT) were monitored on soils sampled at selected locations along 110-m transects established on the site. We confirmed the high toxicity of Pb on respirations and microbial and fungal biomasses by measuring positive correlations with distance from the wall factory and negative correlation with total Pb concentrations. Pb contamination also induced changes in microbial and fungal catabolic structure (from carbohydrates to amino acids through carboxylic malic acid). Moreover, PICT measurement allowed to establish causal linkages between lead and its effect on biological communities taking into account the contamination history of the ecosystem at community level. The positive correlation between qCO2 (based on respiration and substrate use) and PICT suggested that the Pb stress-induced acquisition of tolerance came at a greater energy cost for microbial communities in order to cope with the toxicity of the metal. In this industrial context of long-term polymetallic contamination dominated by Pb in a field experiment, we confirmed impacts of this metal on soil functioning through microbial communities, as previously observed for earthworm communities.

Microbial biomass and basal respiration of selected Sub-Antarctic and Antarctic soils in the areas of some Russian polar stations

NASA Astrophysics Data System (ADS)

Abakumov, E.; Mukhametova, N.

2014-07-01

Antarctica is a unique place for soil, biological, and ecological investigations. Soils of Antarctica have been studied intensively during the last century, when different national Antarctic expeditions visited the sixth continent with the aim of investigating nature and the environment. Antarctic investigations are comprised of field surveys mainly in the terrestrial landscapes, where the polar stations of different countries are situated. That is why the main and most detailed soil surveys were conducted in the McMurdo Valleys, Transantarctic Mountains, South Shetland Islands, Larsemann Hills and the Schirmacher Oasis. Our investigations were conducted during the 53rd and 55th Russian Antarctic expeditions in the base of soil pits, and samples were collected in Sub-Antarctic and Antarctic regions. Sub-Antarctic or maritime landscapes are considered to be very different from Antarctic landscapes due to differing climatic and geogenic conditions. Soils of diverse zonal landscapes were studied with the aim of assessing the microbial biomass level, basal respiration rates and metabolic activity of microbial communities. This investigation shows that Antarctic soils are quite diverse in profile organization and carbon content. In general, Sub-Antarctic soils are characterized by more developed humus (sod) organo-mineral horizons as well as by an upper organic layer. The most developed organic layers were revealed in peat soils of King George Island, where its thickness reach, in some cases, was 80 cm. These soils as well as soils formed under guano are characterized by the highest amount of total organic carbon (TOC), between 7.22 and 33.70%. Coastal and continental Antarctic soils exhibit less developed Leptosols, Gleysols, Regolith and rare Ornhitosol, with TOC levels between 0.37 and 4.67%. The metabolic ratios and basal respiration were higher in Sub-Antarctic soils than in Antarctic ones, which can be interpreted as a result of higher amounts of fresh organic remnants in organic and organo-mineral horizons. The soils of King George Island also have higher portions of microbial biomass (max 1.54 mg g-1) compared to coastal (max 0.26 mg g-1) and continental (max 0.22 mg g-1) Antarctic soils. Sub-Antarctic soils differ from Antarctic ones mainly by having increased organic layer thickness and total organic carbon content, higher microbial biomass carbon content, basal respiration, and metabolic activity levels.

Microbial carbon turnover in the plant-rhizosphere-soil continuum

NASA Astrophysics Data System (ADS)

Malik, Ashish; Dannert, Helena; Griffiths, Robert; Thomson, Bruce; Gleixner, Gerd

2014-05-01

Soil microbial biomass contributes significantly to maintenance of soil organic matter (SOM). It is well known that biochemical fractions of soil microorganisms have varying turnover and therefore contribute differentially to soil C storage. Here we compare the turnover rates of different microbial biochemical fractions using a pulse chase 13CO2 plant labelling experiment. The isotope signal was temporally traced into rhizosphere soil microorganisms using the following biomarkers: DNA, RNA, fatty acids and chloroform fumigation extraction derived microbial biomass size classes. C flow into soil microbial functional groups was assessed through phospholipid and neutral lipid fatty acid (PLFA/NLFA) analyses. Highest 13C enrichment was seen in the low molecular weight (LMW) size class of microbial biomass (Δδ13C =151) and in nucleic acids (DNA: 38o RNA: 66) immediately after the pulse followed by a sharp drop. The amount of 13C in the high molecular weight (HMW) microbial biomass (17-81) and total fatty acids (32-54) was lower initially and stayed relatively steady over the 4 weeks experimental period. We found significant differences in turnover rates of different microbial biochemical and size fractions. We infer that LMW cytosolic soluble compounds are rapidly metabolized and linked to respiratory C fluxes, whereas mid-sized products of microbial degradation and HMW polymeric compounds have lower renewal rate in that order. The turnover of cell wall fatty acids was also very slow. DNA and RNA showed faster turnover rate; and as expected RNA renewal was the fastest due to its rapid production by active microorganisms independent of cell replication. 13C incorporation into different functional groups confirmed that mutualistic arbuscular mycorrhizal fungi rely on root C and are important in the initial plant C flux. We substantiated through measurements of isotope incorporation into bacterial RNA that rhizosphere bacteria are also important in the initial C conduit from plants. Other saprophytic fungi and bacteria show a delayed 13C incorporation pattern which could suggest secondary 13C assimilation often indicative of trophic interactions. Thus, different soil microbial biochemical fractions as well as functional groups show differential C turnover which could have implications on soil C storage.

Vertical and horizontal distributions of microbial abundances and enzymatic activities in propylene-glycol-affected soils.

PubMed

Biró, Borbála; Toscano, Giuseppe; Horváth, Nikoletta; Matics, Heléna; Domonkos, Mónika; Scotti, Riccardo; Rao, Maria A; Wejden, Bente; French, Helen K

2014-01-01

The natural microbial activity in the unsaturated soil is vital for protecting groundwater in areas where high loads of biodegradable contaminants are supplied to the surface, which usually is the case for airports using aircraft de-icing fluids (ADF) in the cold season. Horizontal and vertical distributions of microbial abundance were assessed along the western runway of Oslo Airport (Gardermoen, Norway) to monitor the effect of ADF dispersion with special reference to the component with the highest chemical oxygen demand (COD), propylene glycol (PG). Microbial abundance was evaluated by several biondicators: colony-forming units (CFU) of some physiological groups (aerobic and anaerobic heterotrophs and microscopic fungi), most probable numbers (MPN) of PG degraders, selected catabolic enzymatic activities (fluorescein diacetate (FDA) hydrolase, dehydrogenase, and β-glucosidase). High correlations were found between the enzymatic activities and microbial counts in vertical soil profiles. All microbial abundance indicators showed a steep drop in the first meter of soil depth. The vertical distribution of microbial abundance can be correlated by a decreasing exponential function of depth. The horizontal trend of microbial abundance (evaluated as total aerobic CFU, MPN of PG-degraders, and FDA hydrolase activity) assessed in the surface soil at an increasing distance from the runway is correlated negatively with the PG and COD loads, suggesting the relevance of other chemicals in the modulation of microbial growth. The possible role of potassium formate, component of runway de-icers, has been tested in the laboratory by using mixed cultures of Pseudomonas spp., obtained by enrichment with a selective PG medium from soil samples taken at the most contaminated area near the runway. The inhibitory effect of formate on the growth of PG degraders is proven by the reduction of biomass yield on PG in the presence of formate.

Microbial communities in riparian soils of a settling pond for mine drainage treatment.

PubMed

Fan, Miaochun; Lin, Yanbing; Huo, Haibo; Liu, Yang; Zhao, Liang; Wang, Entao; Chen, Weimin; Wei, Gehong

2016-06-01

Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Denaturing gradient gel electrophoresis fingerprinting of soil bacteria in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica.

PubMed

Pan, Qi; Wang, Feng; Zhang, Yang; Cai, Minghong; He, Jianfeng; Yang, Haizhen

2013-08-01

Bacterial diversity was investigated in soil samples collected from 13 sites around the Great Wall Station, Fildes Peninsula, King George Island, Antarctica, using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes. The classes alpha-, beta-, and gamma-Proteobacteria, as well as the phylum Actinobacteria, were found to be the dominant bacteria in the soils around the Great Wall Station. Although the selected samples were not contaminated by oil, a relationship between soil parameters, microbial biodiversity, and human impact was still seen. Sample sites in human impacted areas showed lower bacterial biodiversity (average H' = 2.65) when compared to non-impacted sites (average H' = 3.05). There was no statistically significant correlation between soil bacterial diversity and total organic carbon (TOC), total nitrogen, or total phosphorus contents of the soil. Canonical correlation analysis showed that TOC content was the most important factor determining bacterial community profiles among the measured soil parameters. In conclusion, microbial biodiversity and community characteristics within relatively small scales (1.5 km) were determined as a function of local environment parameters and anthropogenic impact.

Microbial and geochemical assessment of bauxitic un-mined and post-mined chronosequence soils from Mocho Mountains, Jamaica.

PubMed

Lewis, Dawn E; Chauhan, Ashvini; White, John R; Overholt, Will; Green, Stefan J; Jasrotia, Puja; Wafula, Denis; Jagoe, Charles

2012-10-01

Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20 years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.

Characterization of Early Microbial Communities on Volcanic Deposits along a Vegetation Gradient on the Island of Miyake, Japan

PubMed Central

Guo, Yong; Fujimura, Reiko; Sato, Yoshinori; Suda, Wataru; Kim, Seok-won; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Narisawa, Kazuhiko; Ohta, Hiroyuki

2014-01-01

The 2000 eruption of Mount Oyama on the island of Miyake (Miyake-jima) created a unique opportunity to study the early ecosystem development on newly exposed terrestrial substrates. In this study, bacterial and fungal communities on 9- and 11-year-old volcanic deposits at poorly to fully vegetation-recovered sites in Miyake-jima, Japan, were characterized by conventional culture-based methods and pyrosequencing of 16S rRNA and 18S rRNA genes. Despite the differences in the vegetation cover, the upper volcanic deposit layer samples displayed low among-site variation for chemical properties (pH, total organic carbon, and total nitrogen) and microbial population densities (total direct count and culturable count). Statistical analyses of pyrosequencing data revealed that the microbial communities of volcanic deposit samples were phylogenetically diverse, in spite of very low-carbon environmental conditions, and their diversity was comparable to that in the lower soil layer (buried soil) samples. Comparing with the microbial communities in buried soil, the volcanic deposit communities were characterized by the presence of Betaproteobacteria and Gammaproteobacteria as the main bacterial class, Deinococcus- Thermus as the minor bacterial phyla, and Ascomycota as the major fungal phyla. Multivariate analysis revealed that several bacterial families and fungal classes correlated positively or negatively with plant species. PMID:24463576

Nitrogen Deposition Reduces Decomposition Rates Through Shifts in Microbial Community Composition and Function

NASA Astrophysics Data System (ADS)

Waldrop, M.; Zak, D.; Sinsabaugh, R.

2002-12-01

Atmospheric nitrogen (N) deposition may alter soil biological activity in northern hardwood forests by repressing phenol oxidase enzyme activity and altering microbial community composition, thereby slowing decomposition and increasing the export of phenolic compounds. We tested this hypothesis by adding 13C-labelled cellobiose, vanillin, and catechol to control and N fertilized soils (30 and 80 kg ha-1) collected from three forests; two dominated by Acer Saccharum and one dominated by Quercus Alba and Quercus Velutina. While N deposition increased total microbial respiration, it decreased soil oxidative enzyme activities, resulting in slower degradation rates of all compounds, and larger DOC pools. This effect was larger in the oak forest, where fungi dominate C-cycling processes. DNA and 13C-phospolipid analyses showed that N addition altered the fungal community and reduced the activity of fungal and bacterial populations in soil, potentially explaining reduced soil enzyme activities and incomplete decomposition.

Microbial secondary succession in soil microcosms of a desert oasis in the Cuatro Cienegas Basin, Mexico

PubMed Central

López-Lozano, Nguyen E.; Heidelberg, Karla B.; Nelson, William C.; García-Oliva, Felipe; Eguiarte, Luis E.

2013-01-01

Ecological succession is one of the most important concepts in ecology. However for microbial community succession, there is a lack of a solid theoretical framework regarding succession in microorganisms. This is in part due to microbial community complexity and plasticity but also because little is known about temporal patterns of microbial community shifts in different kinds of ecosystems, including arid soils. The Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, is an arid zone with high diversity and endemisms that has recently been threatened by aquifer overexploitation. The gypsum-based soil system of the CCB is one of the most oligotrophic places in the world. We undertook a comparative 16S rRNA 454 pyrosequencing study to evaluate microbial community succession and recovery over a year after disturbance at two sites. Results were related to concurrent measurements of humidity, organic matter and total C and N content. While each site differed in both biogeochemistry and biodiversity, both present similar pattern of change at the beginning of the succession that diverged in later stages. After one year, experimentally disturbed soil was not similar to established and undisturbed adjacent soil communities indicating recovery and succession in disturbed soils is a long process. PMID:23638384

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil

PubMed Central

Wang, Lei; Yang, Fang; E, Yaoyao; Yuan, Jun; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2016-01-01

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009–2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0–20 cm, 20–40 cm, and 40–60 cm), e.g., the relative abundance of bio-control bacteria (Xanthomonadales, Lysobacter, Pseudomonas, and Bacillus), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria, and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter, and Ohtaekwangia. These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity. PMID:27965631

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil.

PubMed

Wang, Lei; Yang, Fang; E, Yaoyao; Yuan, Jun; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2016-01-01

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009-2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0-20 cm, 20-40 cm, and 40-60 cm), e.g., the relative abundance of bio-control bacteria ( Xanthomonadales, Lysobacter, Pseudomonas , and Bacillus ), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria , and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter , and Ohtaekwangia . These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity.

Limits to soil carbon stability; Deep, ancient soil carbon decomposition stimulated by new labile organic inputs

USDA-ARS?s Scientific Manuscript database

Soil carbon (C) pools store about one-third of the total terrestrial organic carbon. Deep soil C pools (below 1 m) are thought to be stable due to their low biodegradability, but little is known about soil microbial processes and carbon dynamics below the soil surface, or how global change might aff...

Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

PubMed

Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2016-06-15

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Phosphorus status and microbial community of paddy soil with the growth of annual ryegrass (Lolium multiflorum Lam.) under different phosphorus fertilizer treatments*

PubMed Central

Guo, Hai-chao; Wang, Guang-huo

2009-01-01

Annual ryegrass (Lolium multiflorum Lam.) was grown in paddy soil in pots under different phosphorus (P) fertilizer treatments to investigate changes of P fractions and microbial community of the soil. The treatments included Kunyang phosphate rock (KPR) applications at 50 mg P/kg (KPR50) and 250 mg P/kg (KPR250), mono-calcium phosphate (MCP) application at 50 mg P/kg (MCP50), and the control without P application. The results showed that KPR50, KPR250, and MCP50 applications significantly increased the dry weight of the ryegrass by 13%, 38%, and 55%, and increased P uptake by 19%, 135%, and 324%, respectively. Compared with MCP50, the relative effectiveness of KPR50 and KPR250 treatments in ryegrass production was about 23% and 68%, respectively. After one season of ryegrass growth, the KPR50, KPR250, and MCP50 applications increased soil-available P by 13.4%, 26.8%, and 55.2%, respectively. More than 80% of the applied KPR-P remained as HCl-P fraction in the soil. Phospholipid fatty acid (PLFA) analysis showed that the total and bacterial PLFAs were significantly higher in the soils with KPR250 and MCP50 treatments compared with KPR50 and control. The latter had no significant difference in the total or bacterial PLFAs. The KPR50, KPR250, and MCP50 treatments increased fungal PLFA by 69%, 103%, and 69%, respectively. Both the principal component analysis and the cluster analysis of the PLFA data suggest that P treatments altered the microbial community composition of the soils, and that P availability might be an important contributor to the changes in the microbial community structure during the ryegrass growth in the paddy soils. PMID:19817001

Effect of simulated tillage on microbial autotrophic CO2 fixation in paddy and upland soils

PubMed Central

Ge, Tida; Wu, Xiaohong; Liu, Qiong; Zhu, Zhenke; Yuan, Hongzhao; Wang, Wei; Whiteley, A. S.; Wu, Jinshui

2016-01-01

Tillage is a common agricultural practice affecting soil structure and biogeochemistry. To evaluate how tillage affects soil microbial CO2 fixation, we incubated and continuously labelled samples from two paddy soils and two upland soils subjected to simulated conventional tillage (CT) and no-tillage (NT) treatments. Results showed that CO2 fixation (14C-SOC) in CT soils was significantly higher than in NT soils. We also observed a significant, soil type- and depth-dependent effect of tillage on the incorporation rates of labelled C to the labile carbon pool. Concentrations of labelled C in the carbon pool significantly decreased with soil depth, irrespective of tillage. Additionally, quantitative PCR assays revealed that for most soils, total bacteria and cbbL-carrying bacteria were less abundant in CT versus NT treatments, and tended to decrease in abundance with increasing depth. However, specific CO2 fixation activity was significantly higher in CT than in NT soils, suggesting that the abundance of cbbL-containing bacteria may not always reflect their functional activity. This study highlights the positive effect of tillage on soil microbial CO2 fixation, and the results can be readily applied to the development of sustainable agricultural management. PMID:26795428

Direct and indirect effects of metal contamination on soil biota in a Zn-Pb post-mining and smelting area (S Poland).

PubMed

Kapusta, Paweł; Szarek-Łukaszewska, Grażyna; Stefanowicz, Anna M

2011-06-01

Effects of metal contamination on soil biota activity were investigated at 43 sites in 5 different habitats (defined by substratum and vegetation type) in a post-mining area. Sites were characterised in terms of soil pH and texture, nutrient status, total and exchangeable metal concentrations, as well as plant species richness and cover, abundances of enchytraeids, nematodes and tardigrades, and microbial respiration and biomass. The concentrations of total trace metals were highest in soils developed on mining waste (metal-rich dolomite), but these habitats were more attractive than sandy sites for plants and soil biota because of their higher content of organic matter, clay and nutrients. Soil mesofauna and microbes were strongly dependent on natural habitat properties. Pollution (exchangeable Zn and Cd) negatively affected only enchytraeid density; due to a positive relationship between enchytraeids and microbes it indirectly reduced microbial activity. Copyright © 2011 Elsevier Ltd. All rights reserved.

Key factors controlling microbial community response after a fire: importance of severity and recurrence

NASA Astrophysics Data System (ADS)

Lombao, Alba; Barreiro, Ana; Martín, Ángela; Díaz-Raviña, Montserrat

2015-04-01

Microorganisms play an important role in forest ecosystems, especially after fire when vegetation is destroyed and soil is bared. Fire severity and recurrence might be one of main factors controlling the microbial response after a wildfire but information about this topic is scarce. The aim of this study is to evaluate the influence of fire regimen (recurrence and severity) on soil microbial community structure by means of the analysis of phospholipid fatty acid (PLFA). The study was performed with unburned and burned samples collected from the top layer of a soil affected by a high severity fire (Laza, NW Spain) heated under laboratory conditions at different temperatures (50°C, 75°C, 100°C, 125°C, 150°C, 175°C, 200°C, 300°C) to simulate different fire intensities; the process was repeated after further soil recovery (1 month incubation) to simulate fire recurrence. The soil temperature was measured with thermocouples and used to calculate the degree-hours as estimation of the amount of heat supplied to the samples (fire severity). The PLFA analysis was used to estimate total biomass and the biomass of specific groups (bacteria, fungi, gram-positive bacteria and gram-negative bacteria) as well as microbial community structure (PLFA pattern) and PLFA data were analyzed by means of principal component analysis (PCA) in order to identify main factors determining microbial community structure. The results of PCA, performed with the whole PLFA data set, showed that first component explained 35% of variation and clearly allow us to differentiate unburned samples from the corresponding burned samples, while the second component, explaining 16% of variation, separated samples according the heating temperature. A marked impact of fire regimen on soil microorganisms was detected; the microbial community response varied depending on previous history of soil heating and the magnitude of changes in the PLFA pattern was related to the amount of heat supplied to the samples. Thus, wildfire was the main factor determining the microbial community structure followed, in less extent, by fire severity. The total biomass and the biomass of specifics microbial groups decreased notably as consequence of wildfire and minor changes were detected due to soil heating under laboratory conditions. The results clearly showed the usefulness of PLFA pattern combined with PCA to study the relationships between fire regimen (recurrence and severity) and associated direct and indirect changes in soil microorganisms. The data also indicated that degree-hours methodology rather than temperature is adequate for evaluating the impact of soil heating on microbial communities. Keywords: wildfire, heating temperature, degree-hours, PLFA pattern, microbial biomass Acknowledgements. This study was supported by the Ministerio Español de Economía y Competitividad (AGL2012-39688-C02-01). A Lombao is recipient of FPU grant from Ministerio Español de Educación.

Soil microbial toxicity assessment of a copper-based fungicide in two contrasting soils

NASA Astrophysics Data System (ADS)

Dober, Melanie; Deltedesco, Evi; Jöchlinger, Lisa; Schneider, Martin; Gorfer, Markus; Bruckner, Alexander; Zechmeister-Boltenstern, Sophie; Soja, Gerhard; Zehetner, Franz; Keiblinger, Katharina Maria

2016-04-01

The infestation with the fungus downy mildew (Plasmopara viticola) causes dramatic losses in wine production. Copper (Cu) based fungicides have been used in viticulture since the end of the 19th century, and until today both conventional and organic viticulture strongly rely on Cu to prevent and reduce fungal diseases. Consequently, Cu has built up in many vineyard soils and it is still unclear how this affects soil functioning. The aim of the present study is the evaluation of the soil microbial toxicity of Cu contamination. Two contrasting agricultural soils, an acidic sandy soil and a calcareous loamy soil, were sampled to conduct an eco-toxicological greenhouse pot experiment. The soils were spiked with a commonly used fungicide based on copper hydroxid in seven concentrations (0, 50, 100, 200, 500, 1500 and 5000 mg Cu kg-1 soil) and Lucerne (Medicago sativa L. cultivar. Plato) was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test copper's soil microbial toxicity in total microbial biomass and basal respiration, as well as enzyme activities, such as exoglucanase, β-glucosidase, exochitinase, phosphatase, protease, phenol-, peroxidase and urease. Additionally, DOC, TN, Cmic, Nmic, NO3 and NH4 were determined to provide further insight into the carbon and nitrogen cycle. Microbial community structure was analysed by phospholipid fatty acids (PLFAs), and ergosterol as a fungal biomarker. In addition, molecular tools were applied by extracting soil DNA and performing real time quantitative polymerase chain reaction (qPCR) and a metagenomic approach using 16S and ITS amplification and sequencing with MiSeq platform for the second sampling. Hydrolytic extracellular enzymes were not clearly affected by rising Cu concentrations, while a trend of increasing activity of oxidative enzymes (phenol- and peroxidase) was observed. Microbial respiration rate as well as the amount of Cmic and Nmic decreased with increasing Cu concentrations. Ergosterol was especially sensitive to Cu and started to decline at even lower concentrations. A shift in the microbial community structure with rising Cu was observed using PLFA. The metagenomics approach enables us to investigate these changes at even finer taxonomic resolution and possible effects on the soil nutrient cycles will be discussed. In summary, our results showed distinct Cu toxicity effects on soil microbial biomass with a larger sensitivity of the loamy soil.

Influence of Pig Slurry on Microbial and Biochemical Characteristics of Soil in Albacete Region, SE Spain

NASA Astrophysics Data System (ADS)

Halil Yanardaǧ, Ibrahim

2013-04-01

Soil quality is very important in terms of agricultural sustainability, ecosystem and terrestrial carbon (C) cycle. In turn, soil microbial and biochemical characteristics are indicative of nutrient cycling and soil organic matter dynamics. We investigated the effects of the pig slurries (raw pig slurry (RPS) and treated pig slurry (TPS) from liquid and solid feeding diets) on microbial and biochemical characteristics of soil under barley cropping system. Application doses of slurries are identified with legal doses of Castilla La Mancha Region, which is 210 kg N ha-1 year-1. Microbial biomass C, soluble C, black C and three soil enzymes (β-Glucosidase, β-galactosidase and Arylesterase enzymes) are studied to determine effect slurry on soil biochemical characteristics, which are very important in terms of C cycle in soil. Black carbon content and β-Glucosidase enzyme activities are increased with all pig slurry applications from liquid and traditional feeding diet, as well as microbial biomass and organic carbon content and β-galactosidase enzyme activities are increased with slurry from liquid feeding diet doses. However, pig slurry application from liquid feeding diet doses have increased yield, quality, length and total biomass content of barley. Bioavailable metal contents are increased with all slurry application and with using high doses of slurry can be caused soil pollution. Pig slurries from liquid feeding diet had positive impacts on microbial and biochemical characteristics in terms of soil quality in comparison to the different feeding diets. PS addition to soil had a very significant stimulating effect on the enzyme activities, microbial biomass, soluble and black C compared with different kind of PS and control plots on Mediterranean soil in barley monoculture. This effect may originate from the organic C, N, P and S compounds added with PS. The highest enzyme activity and microbial biomass were observed on the soil samples from the RPS treatment, whereas, black and soluble C was decreased with PS addition. There may have been a transient positive effect of the RPS treatments on the soil biochemical parameters. However, the effect could not be detected because of less labile C content during the experiment. The beneficial effects of the PS additions were less pronounced in the 0-30 cm. soil layer. In this monoculture barley production system and under these Mediterranean climate conditions, applications of TPS should be avoided, so they were associated with a decline in microbial counts and a leveling of almost all the enzymatic activities and microbial biomass C. Keywords: Pig slurry, Microbial biomass C, soluble C, black C, β-Glucosidase, β-galactosidase and Arylesterase enzyme activities.

Bacterial community shift and hydrocarbon transformation during bioremediation of short-term petroleum-contaminated soil.

PubMed

Wu, Manli; Ye, Xiqiong; Chen, Kaili; Li, Wei; Yuan, Jing; Jiang, Xin

2017-04-01

A laboratory study was conducted to evaluate the impact of bioaugmentation plus biostimulation (BR, added both nutrients and bacterial consortia), and natural attenuation (NA) on hydrocarbon degradation efficiency and microflora characterization during remediation of a freshly contaminated soil. After 112 days of remediation, the initial level of total petroleum hydrocarbon (TPH) (61,000 mg/kg soil) was reduced by 4.5% and 5.0% in the NA and BR treatments, respectively. Bioremediation did not significantly enhance TPH biodegradation compared to natural attenuation. The degradation of the aliphatic fraction was the most active with the degradation rate of 30.3 and 28.7 mg/kg/day by the NA and BR treatments, respectively. Soil microbial activities and counts in soil were generally greater for bioremediation than for natural attenuation. MiSeq sequencing indicated that the diversity and structure of microbial communities were affected greatly by bioremediation. In response to bioremediation treatment, Promicromonospora, Pseudomonas, Microcella, Mycobacterium, Alkanibacter, and Altererythrobacter became dominant genera in the soil. The result indicated that combining bioaugmentation with biostimulation did not improve TPH degradation, but soil microbial activities and structure of microbial communities are sensitive to bioremediation in short-term and heavily oil-contaminated soil. Copyright © 2017 Elsevier Ltd. All rights reserved.

The impact of biofumigation and chemical fumigation methods on the structure and function of the soil microbial community.

PubMed

Omirou, Michalis; Rousidou, Constantina; Bekris, Fotios; Papadopoulou, Kalliope K; Menkissoglou-Spiroudi, Urania; Ehaliotis, Constantinos; Karpouzas, Dimitrios G

2011-01-01

Biofumigation (BIOF) is carried out mainly by the incorporation of brassica plant parts into the soil, and this fumigation activity has been linked to their high glucosinolate (GSL) content. GSLs are hydrolyzed by the endogenous enzyme myrosinase to release isothiocyanates (ITCs). A microcosm study was conducted to investigate the effects induced on the soil microbial community by the incorporation of broccoli residues into soil either with (BM) or without (B) added myrosinase and of chemical fumigation, either as soil application of 2-phenylethyl ITC (PITC) or metham sodium (MS). Soil microbial activity was evaluated by measuring fluorescein diacetate hydrolysis and soil respiration. Effects on the structure of the total microbial community were assessed by phospholipid fatty acid analysis, while the impact on important fungal (ascomycetes (ASC)) and bacterial (ammonia-oxidizing bacteria (AOB)) guilds was evaluated by denaturating gradient gel electrophoresis (DGGE). Overall, B, and to a lesser extent BM, stimulated microbial activity and biomass. The diminished effect of BM compared to B was particularly evident in fungi and Gram-negative bacteria and was attributed to rapid ITC release following the myrosinase treatment. PITC did not have a significant effect, whereas an inhibitory effect was observed in the MS-treated soil. DGGE analysis showed that the ASC community was temporarily altered by BIOF treatments and more persistently by the MS treatment, while the structure of the AOB community was not affected by the treatments. Cloning of the ASC community showed that MS application had a deleterious effect on potential plant pathogens like Fusarium, Nectria, and Cladosporium compared to BIOF treatments which did not appear to inhibit them. Our findings indicate that BIOF induces changes on the structure and function of the soil microbial community that are mostly related to microbial substrate availability changes derived from the soil amendment with fresh organic materials.

[Effects of Different Residue Part Inputs of Corn Straws on CO2 Efflux and Microbial Biomass in Clay Loam and Sandy Loam Black Soils].

PubMed

Liu, Si-yi; Liang, Ai-zhen; Yang, Xue-ming; Zhang, Xiao-ping; Jia, Shu-xia; Chen, Xue-wen; Zhang, Shi-xiu; Sun, Bing-jie; Chen, Sheng-long

2015-07-01

The decomposed rate of crop residues is a major determinant for carbon balance and nutrient cycling in agroecosystem. In this study, a constant temperature incubation study was conducted to evaluate CO2 emission and microbial biomass based on four different parts of corn straw (roots, lower stem, upper stem and leaves) and two soils with different textures (sandy loam and clay loam) from the black soil region. The relationships between soil CO2 emission, microbial biomass and the ratio of carbon (C) to nitrogen (N) and lignin of corn residues were analyzed by the linear regression. Results showed that the production of CO2 was increased with the addition of different parts of corn straw to soil, with the value of priming effect (PE) ranged from 215. 53 µmol . g-1 to 335. 17 µmol . g -1. Except for corn leaves, the cumulative CO2 production and PE of clay loam soil were significantly higher than those in sandy loam soil. The correlation of PE with lignin/N was obviously more significant than that with lignin concentration, nitrogen concentration and C/N of corn residue. The addition of corn straw to soil increased the contents of MBC and MBN and decreased MBC/MBN, which suggested that more nitrogen rather than carbon was conserved in microbial community. The augmenter of microbial biomass in sandy loam soil was greater than that in clay loam soil, but the total dissolved nitrogen was lower. Our results indicated that the differences in CO2 emission with the addition of residues to soils were primarily ascribe to the different lignin/N ratio in different corn parts; and the corn residues added into the sandy loam soil could enhance carbon sequestration, microbial biomass and nitrogen holding ability relative to clay loam soil.

Nitrogen Addition Altered the Effect of Belowground C Allocation on Soil Respiration in a Subtropical Forest

PubMed Central

He, Tongxin; Wang, Qingkui; Wang, Silong; Zhang, Fangyue

2016-01-01

The availabilities of carbon (C) and nitrogen (N) in soil play an important role in soil carbon dioxide (CO2) emission. However, the variation in the soil respiration (Rs) and response of microbial community to the combined changes in belowground C and N inputs in forest ecosystems are not yet fully understood. Stem girdling and N addition were performed in this study to evaluate the effects of C supply and N availability on Rs and soil microbial community in a subtropical forest. The trees were girdled on 1 July 2012. Rs was monitored from July 2012 to November 2013, and soil microbial community composition was also examined by phospholipid fatty acids (PLFAs) 1 year after girdling. Results showed that Rs decreased by 40.5% with girdling alone, but N addition only did not change Rs. Interestingly, Rs decreased by 62.7% under the girdling with N addition treatment. The reducing effect of girdling and N addition on Rs differed between dormant and growing seasons. Girdling alone reduced Rs by 33.9% in the dormant season and 54.8% in the growing season compared with the control. By contrast, girdling with N addition decreased Rs by 59.5% in the dormant season and 65.4% in the growing season. Girdling and N addition significantly decreased the total and bacterial PLFAs. Moreover, the effect of N addition was greater than girdling. Both girdling and N addition treatments separated the microbial groups on the basis of the first principal component through principal component analysis compared with control. This indicated that girdling and N addition changed the soil microbial community composition. However, the effect of girdling with N addition treatment separated the microbial groups on the basis of the second principal component compared to N addition treatment, which suggested N addition altered the effect of girdling on soil microbial community composition. These results suggest that the increase in soil N availability by N deposition alters the effect of belowground C allocation on the decomposition of soil organic matter by altering the composition of the soil microbial community. PMID:27213934

Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analyses.

PubMed Central

Frostegård, A; Petersen, S O; Bååth, E; Nielsen, T H

1997-01-01

Microbial community dynamics associated with manure hot spots were studied by using a model system consisting of a gel-stabilized mixture of soil and manure, placed between layers of soil, during a 3-week incubation period. The microbial biomass, measured as the total amount of phospholipid fatty acids (PLFA), had doubled within a 2-mm distance from the soil-manure interface after 3 days. Principal-component analyses demonstrated that this increase was accompanied by reproducible changes in the composition of PLFA, indicating changes in the microbial community structure. The effect of the manure was strongest in the 2-mm-thick soil layer closest to the interface, in which the PLFA composition was statistically significantly different (P < 0.05) from that of the unaffected soil layers throughout the incubation period. An effect was also observed in the soil layer 2 to 4 mm from the interface. The changes in microbial biomass and community structure were mainly attributed to the diffusion of dissolved organic carbon from the manure. During the initial period of microbial growth, PLFA, which were already more abundant in the manure than in the soil, increased in the manure core and in the 2-mm soil layer closest to the interface. After day 3, the PLFA composition of these layers gradually became more similar to that of the soil. The dynamics of individual PLFA suggested that both taxonomic and physiological changes occurred during growth. Examples of the latter were decreases in the ratios of 16:1 omega 7t to 16:1 omega 7c and of cyclopropyl fatty acids to their respective precursors, indicating a more active bacterial community. An inverse relationship between bacterial PLFA and the eucaryotic 20:4 PLFA (arachidonic acid) suggested that grazing was important. PMID:9172342

Biological activity of soddy-calcareous soils and cultural layers in Alanian settlements of the Kislovodsk basin

NASA Astrophysics Data System (ADS)

Chernysheva, E. V.; Kashirskaya, N. N.; Korobov, D. S.; Borisov, A. V.

2014-09-01

Microbiological investigations of cultural layers were performed in a settlement of the Alanian culture—Podkumskoe-2 (the 2nd-4th centuries AD). The present-day soddy-calcareous soils (rendzinas) used for different purposes were also studied near this settlement. The most significant changes in the initial characteristics of the soil microbial communities occurred under the residential influence more than 1500 years ago; these changes have been preserved until the present time. In the areas subjected to the anthropogenic impact, the total microbial biomass (the weighted average of 3720 μg C/g soil) was lower than that in the background soil. The minimal values of the microbial biomass were found in the soil of the pasture—2.5 times less than in the background soil. The urease activity of the cultural layer was higher than that of the soils nearby the settlement. Elevated values of the cellulose activity were also recorded only in the cultural layers. The current plowing has led to a significant decrease in the mycelium biomass of the microscopic fungi. In the soil of the fallow, the weighted average value of the fungal hyphae biomass along the profile was twice lower than that in the background soil and cultural layers of the settlement. The pasture first affected the active microbial biomass and, to a lesser extent, the amount of microscopic fungi.

Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene.

PubMed

Babin, Doreen; Ding, Guo-Chun; Pronk, Geertje Johanna; Heister, Katja; Kögel-Knabner, Ingrid; Smalla, Kornelia

2013-10-01

Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Effect of Inoculation of Acacia senegal mature trees with Mycorrhiza and Rhizobia on soil properties and microbial community structure

NASA Astrophysics Data System (ADS)

Assigbetsé, K.; Ciss, I.; Bakhoum, N.; Dieng, L.

2012-04-01

Inoculation of legume plants with symbiotic microorganisms is widely used to improve their development and productivity. The objective of this study was to investigate the effect of inoculation of Acacia senegal mature trees with rhizobium (Sinorhizobium) and arbuscular mycorrhizal fungus (G. mosseae, G. fasciculatum, G. intraradices) either singly or in combination, on soil properties, activity and the genetic structure of soil microbial communities. The experiment set up in Southern Senegal consisted of 4 randomized blocks of A. senegal mature trees with 4 treatments including inoculated trees with Rhizobium (R), mycorrhizal fungus (M) and with Rhizobium+mycorhizal fungus (RM) and non-inoculated control (CON). Soil were sampled 2 years after the inoculation. Soil pH, C and N and available P contents were measured. The microbial abundance and activity were measured in terms of microbial biomass C (MBC) and basal soil respiration. The community structure of the total bacterial, diazotrophic and denitrifying communities was assessed by denaturing gradient gel electrophoresis of 16S rDNA, nifH and nirK genes respectively. Inoculations with symbiont under field conditions have increased soil pH. The C and N contents were enhanced in the dual-inoculated treatments (RM). The mycorrhized treatment have displayed the lowest available P contents while RM and R treatments exhibited higher contents rates. The microbial biomass C rates were higher in treatments co-inoculated with AM fungi and Rhizobium than in those inoculated singly with AM fungi or Rhizobium strains. The basal soil respiration were positively correlated to MBC, and the highest rates were found in the co-inoculated treatments. Fingerprints of 16S rDNA gene exhibited similar patterns between inoculated treatments and the control showing that the inoculation of mature trees have not impacted the total bacterial community structure. In contrast, the inoculated treatments have displayed individually different diazotrophic and denitrifying communities fingerprints, indicating that the inoculation with microsymbionts have modified the genetic structure of the two functional communities in soil. Further, the diazotrophic community richness was reduced over the control indicating the impact of the addition of symbionts on the free-living N2-fixing bacterial (nifH) diversity. This study shows that inoculation of A. senegal mature trees with rhizobium and arbuscular mycorrhizal fungus has enhanced soil biofunctioning and modified the genetic structure of microbial community involved in N-cycling. Combined inoculation of AM fungi and Rhizobium have improved these effects on chemical characteristics, microbial community abundance and activity demonstrating synergism between the two microsymbionts.

Microbial community structure across a wastewater-impacted riparian buffer zone in the southeastern coastal plain.

PubMed

Ducey, T F; Johnson, P R; Shriner, A D; Matheny, T A; Hunt, P G

2013-01-01

Riparian buffer zones are important for both natural and developed ecosystems throughout the world because of their ability to retain nutrients, prevent soil erosion, protect aquatic environments from excessive sedimentation, and filter pollutants. Despite their importance, the microbial community structures of riparian buffer zones remains poorly defined. Our objectives for this study were twofold: first, to characterize the microbial populations found in riparian buffer zone soils; and second, to determine if microbial community structure could be linked to denitrification enzyme activity (DEA). To achieve these objectives, we investigated the microbial populations of a riparian buffer zone located downslope of a pasture irrigated with swine lagoon effluent, utilizing DNA sequencing of the 16S rDNA, DEA, and quantitative PCR (qPCR) of the denitrification genes nirK, nirS, and nosZ. Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs). The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs). Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.

A Novel Method for Analyzing Microbially Affiliated Volatile Organic Compounds in Soil Environments

NASA Astrophysics Data System (ADS)

Ruhs, C. V.; McNeal, K. S.

2010-12-01

A concerted, international effort by citizens, governments, industries and educational systems is necessary to address the myriad environmental issues that face us today. The authors of this paper concentrate on soil environments and, specifically, the methods currently used to characterize them. The ability to efficiently and effectively monitor and characterize various soils is desired, allows for the study, supervision, and protection of natural and cultivated ecosystems, and may assist stakeholders in meeting governmentally-imposed environmental standards. This research addresses soil characterization by a comparison of four methods that emphasize a combination of microbial community and metabolic measures: BIOLOG, fatty acid methyl-ester analysis (FAME), descriptive physical and chemical analysis (moisture content, pH, carbon content, nutrient content, and grain size), and the novel soil-microbe volatile organic compound analysis (SMVOC) presented in this work. In order to achieve the method comparison, soils were collected from three climatic regions (Bahamas, Michigan, and Mississippi), with three samples taken from niche ecosystems found at each climatic region (a total of nine sites). Of interest to the authors is whether or not an investigation of microbial communities and the volatile organic compounds (VOCs) produced by microbial communities from nine separate soil ecosystems provides useful information about soil dynamics. In essence, is analysis of soil-derived VOCs using gas chromatography-mass spectrometry (GC-MS) an effective method for characterizing microbial communities and their metabolic activity of soils rapidly and accurately compared with the other three traditional characterization methods? Preliminary results suggest that VOCs in each of these locales differ with changes in soil types, soil moisture, and bacterial community. Each niche site shows distinct patterns in both VOCs and BIOLOG readings. Results will be presented to show the efficacy of the SMVOC approach and the statistical alignment of the VOC and community measures.

Changes of soil organic matter and microbial activity in irrigated and non irrigated olive groves

NASA Astrophysics Data System (ADS)

Kavvadias, Victor; Papadopoulou, Maria; Theocharopoulos, Sideris; Vavoulidou, Evagelia; Doula, Maria; Reppas, Spiros

2014-05-01

The implementation of olive cultivation techniques in Greece has not been systematically tested under the prevailing Mediterranean conditions. A LIFE+ project was initiated (oLIVE-CLIMA; LIFE 11/ENV/000942) aiming to introduce new management practices in olive tree crops that lead to increased carbon dioxide uptake by plants as well as carbon sequestration from the atmosphere and reverse the trend of soil organic matter decline, erosion and desertification. This paper presents data on soil organic matter and microbial activity from a soil campaign in a pilot region in Greece, and particularly in the area of Chora, prefecture of Messinia, South west Peloponnese. The soil campaign took place during the period December 2012-February 2013. Twelve soil parcels of olive groves were selected (6 irrigated and 6 rainfed) and in each soil parcel six composite soil samples were taken from 0-10 cm depth at equal intervals along a straight line of the trunk of the tree to the middle of the distance from the nearest tree of the next tree series. The first three samples were under olive tree canopy. An additional composite sample was taken at depth of 10-40 cm. Soil samples were analyzed for soil physicochemical and biological properties. In this study results for total organic carbon (TOC), soil basal microbial respiration (BR), microbial biomass C (MB-C) from the region of Messinia, are presented. Organic matter was determined by dichromate oxidation. The microbial activity was measured by the amount of CO2 evolution, while microbial biomass C was determined by substrate-induced respiration, after the addition of glucose. The results showed considerable differences in TOC, BR and MB-C associated with the sampling position and soil depth. The higher TOC, BR and MB-C values, in most cases, were determined in samples taken from points under the canopy, but not close to the tree trunk compared to the sampling points outside the canopy. This indicates the positive effect of rhizosphere and the favorable soil moisture conditions under tree canopy on soil microbial activities. TOC, BR and MB-C values were considerably lower in soil depth of 10-40cm compared with 0-10 cm in both irrigated and rainfed soil parcels. Moreover BR and MB-C was higher in irrigated soil parcels compared with rainfed ones suggesting that the periodic irrigation significantly enhances the soil microbial activity. There were no considerable differences in TOC. For this the TOC and potential activity of microbial community can contribute in the soil nutrient and irrigation management guidelines in order to exploit the utilization of productive soils in the region under studied.

Digging a Little Deeper: Microbial Communities, Molecular Composition and Soil Organic Matter Turnover along Tropical Forest Soil Depth Profiles

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; McFarlane, K. J.; Heckman, K. A.; Reed, S.; Green, E. A.; Nico, P. S.; Tfaily, M. M.; Wood, T. E.; Plante, A. F.

2016-12-01

Tropical forest soils store more carbon (C) than any other terrestrial ecosystem and exchange vast amounts of CO2, water, and energy with the atmosphere. Much of this C is leached and stored in deep soil layers where we know little about its fate or the microbial communities that drive deep soil biogeochemistry. Organic matter (OM) in tropical soils appears to be associated with mineral particles, suggesting deep soils may provide greater C stabilization. However, few studies have evaluated sub-surface soils in tropical ecosystems, including estimates of the turnover times of deep soil C, the sensitivity of this C to global environmental change, and the microorganisms involved. We quantified bulk C pools, microbial communities, molecular composition of soil organic matter, and soil radiocarbon turnover times from surface soils to 1.5m depths in multiple soil pits across the Luquillo Experimental Forest, Puerto Rico. Soil C, nitrogen, and root and microbial biomass all declined exponentially with depth; total C concentrations dropped from 5.5% at the surface to <0.5% at 140cm depth. High-throughput sequencing highlighted distinct microbial communities in surface soils (Acidobacteria and Proteobacteria) versus those below the active rooting zone (Verrucomicrobia and Thaumarchaea). High resolution mass spectrometry (FTICR-MS) analyses suggest a shift in the composition of OM with depth (especially in the water soluble fraction), an increase in oxidation, and decreasing H/C with depth (indicating higher aromaticity). Additionally, surface samples were rich in lignin-like compounds of plant origin that were absent with depth. Soil OM 14C and mean turnover times were variable across replicate horizons, ranging from 3-1500 years at the surface, to 5000-40,000 years at depth. In comparison to temperate deciduous forests, these 14C values reflect far older soil C. Particulate organic matter (free light fraction), with a relatively modern 14C was found in low but measureable concentration in even the deepest soil horizons. Our results indicate these tropical subsoils contain small but metabolically active microbial communities that are highly OM limited and may persist via degradation of recent inputs.

Soil biochemical properties of grassland ecosystems under anthropogenic emission of nitrogen compounds

NASA Astrophysics Data System (ADS)

Kudrevatykh, Irina; Ivashchenko, Kristina; Ananyeva, Nadezhda

2016-04-01

Inflow of pollutants in terrestrial ecosystems nowadays increases dramatically, that might be led to disturbance of natural biogeochemical cycles and landscapes structure. Production of nitrogen fertilizers is one of the air pollution sources, namely by nitrogen compounds (NH4+, NO3-, NO2-). Air pollution by nitrogen compounds of terrestrial ecosystems might be affected on soil biochemical properties, which results increasing mineral nitrogen content in soil, changing soil P/N and Al/Ca ratios, and, finally, the deterioration of soil microbial community functioning. The research is focused on the assessment of anthropogenic emission of nitrogen compounds on soil properties of grassland ecosystems in European Russia. Soil samples (Voronic Chernozem Pachic, upper 10 cm mineral layer, totally 10) were taken from grassland ecosystem: near (5-10 m) nitrogen fertilizer factory (NFF), and far from it (20-30 km, served as a control) in Tula region. In soil samples the NH4+ and NO3- (Kudeyarov's photocolorimetric method), P, Ca, Al (X-ray fluorescence method) contents were measured. Soil microbial biomass carbon (Cmic) was analyzed by substrate-induced respiration method. Soil microbial respiration (MR) was assessed by CO2 rate production. Soil microbial metabolic quotient (qCO2) was calculated as MR/Cmic ratio. Near NFF the soil ammonium and nitrate nitrogen contents were a strongly varied, variation coefficient (CV) was 42 and 86This study was supported by Russian Foundation of Basic Research Grant No. 14-04-00098, 15-44-03220, 15-04-00915.

Plant tolerance to diesel minimizes its impact on soil microbial characteristics during rhizoremediation of diesel-contaminated soils.

PubMed

Barrutia, O; Garbisu, C; Epelde, L; Sampedro, M C; Goicolea, M A; Becerril, J M

2011-09-01

Soil contamination due to petroleum-derived products is an important environmental problem. We assessed the impacts of diesel oil on plants (Trifolium repens and Lolium perenne) and soil microbial community characteristics within the context of the rhizoremediation of contaminated soils. For this purpose, a diesel fuel spill on a grassland soil was simulated under pot conditions at a dose of 12,000 mg diesel kg(-1) DW soil. Thirty days after diesel addition, T. repens (white clover) and L. perenne (perennial ryegrass) were sown in the pots and grown under greenhouse conditions (temperature 25/18 °C day/night, relative humidity 60/80% day/night and a photosynthetic photon flux density of 400 μmol photon m(-2) s(-1)) for 5 months. A parallel set of unplanted pots was also included. Concentrations of n-alkanes in soil were determined as an indicator of diesel degradation. Seedling germination, plant growth, maximal photochemical efficiency of photosystem II (F(v)/F(m)), pigment composition and lipophylic antioxidant content were determined to assess the impacts of diesel on the studied plants. Soil microbial community characteristics, such as enzyme and community-level physiological profiles, were also determined and used to calculate the soil quality index (SQI). The presence of plants had a stimulatory effect on soil microbial activity. L. perenne was far more tolerant to diesel contamination than T. repens. Diesel contamination affected soil microbial characteristics, although its impact was less pronounced in the rhizosphere of L. perenne. Rhizoremediation with T. repens and L. perenne resulted in a similar reduction of total n-alkanes concentration. However, values of the soil microbial parameters and the SQI showed that the more tolerant species (L. perenne) was able to better maintain its rhizosphere characteristics when growing in diesel-contaminated soil, suggesting a better soil health. We concluded that plant tolerance is of crucial importance for the recovery of soil health during rhizoremediation of contaminated soils. Copyright © 2011 Elsevier B.V. All rights reserved.

[Effects of exogenous glucose and starch on soil carbon metabolism of root zone and root function in potted sweet cherry].

PubMed

Zhou, Wen-jie; Zhang, Peng; Qin, Si-jun; Lyu, De-guo

2015-11-01

One-year-old potted sweet cheery trees were treated with 4 g · kg(-1) exogenous glucose or starch and with non-addition of exogenous carbon as the control for up to 60 days. Soil of root zone was sampled to analyze soil microbial biomass carbon, activities of invertase and amylase and microbial community functional diversity during the 60-day treatment, and roots were sampled for analysis of root respiratory rate, respiratory pathways and root viability after treatment for 30 days. Results showed that the invertase activity and the microbial biomass carbon initially increased and decreased subsequently, with the maxima which were 14.0% and 13.1% higher in the glucose treatment than in the control treatment appeared after 15 and 7 days of treatments, respectively. Soil organic matter content increased first then decreased and finally moderately increased again. Amylase activity was 7.5-fold higher in the starch treatment than in the control treatment after 15-day treatment. Soil microbial biomass carbon was higher in the starch treatment than in the control treatment except after 7-day treatment. Soil organic matter content initially increased and then decreased, but it was still 19.8% higher than in the control after 60-day treatment. BIOLOG results showed that the maximum average well color development (AWCD) value and microbial activity appeared after 15-day treatment in the following order: starch>glucose>control. After 30-day treatment, glucose treatment resulted in a significant increase in the soil microbial utilization of carbohydrates, carboxylic acid, amino acids, phenolic acids and amines, and starch treatment significantly increased the soil microbial utilization of carbohydrates, carboxylic acid, polymers and phenolic acids. After 30-day treatment, the total root respiratory rate and root viability were 21.4%, 19.4% and 65.5%, 37.0% higher in glucose treatment than in the control and starch treatments, respectively. These results indicated exogenous glucose and starch affected soil carbon metabolism and enhanced soil microbial activity, the root respiratory rate and root viability.

Maintenance of soil functioning following erosion of microbial diversity.

PubMed

Wertz, Sophie; Degrange, Valérie; Prosser, James I; Poly, Franck; Commeaux, Claire; Freitag, Thomas; Guillaumaud, Nadine; Roux, Xavier Le

2006-12-01

The paradigm that soil microbial communities, being very diverse, have high functional redundancy levels, so that erosion of microbial diversity is less important for ecosystem functioning than erosion of plant or animal diversity, is often taken for granted. However, this has only been demonstrated for decomposition/respiration functions, performed by a large proportion of the total microbial community, but not for specialized microbial groups. Here, we determined the impact of a decrease in soil microbial diversity on soil ecosystem processes using a removal approach, in which less abundant species were removed preferentially. This was achieved by inoculation of sterile soil microcosms with serial dilutions of a suspension obtained from the same non-sterile soil and subsequent incubation, to enable recovery of community size. The sensitivity to diversity erosion was evaluated for three microbial functional groups with known contrasting taxonomic diversities (ammonia oxidizers < denitrifiers < heterotrophs). Diversity erosion within each functional group was characterized using molecular fingerprinting techniques: ribosomal intergenic spacer analysis (RISA) for the eubacterial community, denaturing gradient gel electrophoresis (DGGE) analysis of nirK genes for denitrifiers, and DGGE analysis of 16S rRNA genes for betaproteobacterial ammonia oxidizers. In addition, we simulated the impact of the removal approach by dilution on the number of soil bacterial species remaining in the inoculum using values of abundance distribution of bacterial species reported in the literature. The reduction of the diversity of the functional groups observed from genetic fingerprints did not impair the associated functioning of these groups, i.e. carbon mineralization, denitrification and nitrification. This was remarkable, because the amplitude of diversity erosion generated by the dilution approach was huge (level of bacterial species loss was estimated to be around 99.99% for the highest dilution). Our results demonstrate that the vast diversity of the soil microbiota makes soil ecosystem functioning largely insensitive to biodiversity erosion even for functions performed by specialized groups.

Contributions of available substrates and activities of trophic microbial community to methanogenesis in vegetative and reproductive rice rhizospheric soil.

PubMed

Chawanakul, Sansanee; Chaiprasert, Pawinee; Towprayoon, Sirintornthep; Tanticharoen, Morakot

2009-01-01

Potential of methane production and trophic microbial activities at rhizospheric soil during rice cv. Supanbunri 1 cultivation were determined by laboratory anaerobic diluents vials. The methane production was higher from rhizospheric than non-rhizospheric soil, with the noticeable peaks during reproductive phase (RP) than vegetative phase (VP). Glucose, ethanol and acetate were the dominant available substrates found in rhizospheric soil during methane production at both phases. The predominance activities of trophic microbial consortium in methanogenesis, namely fermentative bacteria (FB), acetogenic bacteria (AGB), acetate utilizing bacteria (AB) and acetoclastic methanogens (AM) were also determined. At RP, these microbial groups were enhanced in the higher of methane production than VP. This correlates with our finding that methane production was greater at the rhizospheric soil with the noticeable peaks during RP (1,150 +/- 60 nmol g dw(-1) d(-1)) compared with VP (510 +/- 30 nmol g dw(-1) d(-1)). The high number of AM showed the abundant (1.1x10(4) cell g dw(-1)) with its high activity at RP, compared to the less activity with AM number at VP (9.8x10(2) cell g dw(-1)). Levels of AM are low in the total microbial population, being less than 1% of AB. These evidences revealed that the microbial consortium of these two phases were different.

Role of cosubstrate and bioaccessibility played in the enhanced anaerobic biodegradation of organochlorine pesticides (OCPs) in a paddy soil by nitrate and methyl-β-cyclodextrin amendments.

PubMed

Ye, Mao; Sun, Mingming; Ni, Ni; Chen, Yinwen; Liu, Zongtang; Gu, Chengang; Bian, Yongrong; Hu, Feng; Li, Huixin; Kengara, Fredrick Orori; Jiang, Xin

2014-01-01

The present study was conducted to investigate the anaerobic biodegradation potential of biostimulation by nitrate (KNO3) and methyl-β-cyclodextrin (MCD) addition on an aged organochlorine pesticide (OCP)-contaminated paddy soil. After 180 days of incubation, total OCP biodegradation was highest in soil receiving the addition of nitrate and MCD simultaneously and then followed by nitrate addition, MCD addition, and control. The highest biodegradation of chlordanes, hexachlorocyclohexanes, endosulfans, and total OCPs was 74.3, 63.5, 51.2, and 65.1%, respectively. Meanwhile, MCD addition significantly increased OCP bioaccessibility (p < 0.05) evaluated by Tenax TA extraction and a three-compartment model method. Moreover, the addition of nitrate and MCD also obtained the highest values of soil microbial activities, including soil microbial biomass carbon and nitrogen, ATP production, denitrifying bacteria count, and nitrate reductase activity. Such similar trend between OCP biodegradation and soil-denitrifying activities suggests a close relationship between OCP biodegradation and N cycling and the indirect/direct involvement of soil microorganisms, especially denitrifying microorganisms in the anaerobic biodegradation of OCPs.

The microbial communities and potential greenhouse gas production in boreal acid sulphate, non-acid sulphate, and reedy sulphidic soils.

PubMed

Šimek, Miloslav; Virtanen, Seija; Simojoki, Asko; Chroňáková, Alica; Elhottová, Dana; Krištůfek, Václav; Yli-Halla, Markku

2014-01-01

Acid sulphate (AS) soils along the Baltic coasts contain significant amounts of organic carbon and nitrogen in their subsoils. The abundance, composition, and activity of microbial communities throughout the AS soil profile were analysed. The data from a drained AS soil were compared with those from a drained non-AS soil and a pristine wetland soil from the same region. Moreover, the potential production of methane, carbon dioxide, and nitrous oxide from the soils was determined under laboratory conditions. Direct microscopic counting, glucose-induced respiration (GIR), whole cell hybridisation, and extended phospholipid fatty acid (PLFA) analysis confirmed the presence of abundant microbial communities in the topsoil and also in the deepest Cg2 horizon of the AS soil. The patterns of microbial counts, biomass and activity in the profile of the AS soil and partly also in the non-AS soil therefore differed from the general tendency of gradual decreases in soil profiles. High respiration in the deepest Cg2 horizon of the AS soil (5.66 μg Cg(-1)h(-1), as compared to 2.71 μg Cg(-1)h(-1) in a top Ap horizon) is unusual but reasonable given the large amount of organic carbon in this horizon. Nitrous oxide production peaked in the BCgc horizon of the AS and in the BC horizon of the non-AS soil, but the peak value was ten-fold higher in the AS soil than in the non-AS soil (82.3 vs. 8.6 ng Ng(-1)d(-1)). The data suggest that boreal AS soils on the Baltic coast contain high microbial abundance and activity. This, together with the abundant carbon and total and mineral nitrogen in the deep layers of AS soils, may result in substantial gas production. Consequently, high GHG emissions could occur, for example, when the generally high water table is lowered because of arable farming. © 2013.

Lignin decomposition and microbial community in paddy soils: effects of alternating redox conditions

NASA Astrophysics Data System (ADS)

Cerli, Chiara; Liu, Qin; Hanke, Alexander; Kaiser, Klaus; Kalbitz, Karsten

2013-04-01

Paddy soils are characterised by interchanging cycles of anaerobic and aerobic conditions. Such fluctuations cause continuous changes in soil solution chemistry as well as in the composition and physiological responses of the microbial community. Temporary deficiency in oxygen creates conditions favourable to facultative or obligates anaerobic bacteria, while aerobic communities can thrive in the period of water absence. These alterations can strongly affect soil processes, in particular organic matter (OM) accumulation and mineralization. In submerged soils, lignin generally constitutes a major portion of the total OM because of hampered degradation under anoxic conditions. The alternating redox cycles resulting from paddy soil management might promote both degradation and preservation of lignin, affecting the overall composition and reactivity of total and dissolved OM. We sampled soils subjected to cycles of anoxic (rice growing period) and oxic (harvest and growth of other crops) conditions since 700 and 2000 years. We incubated suspended Ap material, sampled from the two paddy plus two corresponding non-paddy control soils under oxic and anoxic condition, for 3 months, interrupted by a short period of three weeks (from day 21 to day 43) with reversed redox conditions. At each sampling time (day 2, 21, 42, 63, 84), we determined lignin-derived phenols (by CuO oxidation) as well as phospholipids fatty acids contents and composition. We aimed to highlight changes in lignin decomposition as related to the potential rapid changes in microbial community composition. Since the studied paddy soils had a long history of wet rice cultivation, the microbial community should be well adapted to interchanging oxic and anoxic cycles, therefore fully expressing its activity at both conditions. In non-paddy soil changes in redox conditions caused modification of quantity and composition of the microbial community. On the contrary, in well-established paddy soils the microbial community appeared to be affected by alternating redox conditions more in quantity that in quality. Bacteria represented the largest portion of the living microorganisms, responding promptly to changes in soil redox status. However we did not detect any sign of lignin biodegradation. Relative short (3 weeks) changes in redox conditions had no effect on lignin decomposition or oxidation state. Also, lignin was not altered during oxic incubation. Since fungi represented only small portion of the microbial biomass in the studied soils, they were obviously not capable to cause much degradation, even under favourable conditions. On the contrary, changes in redox conditions strongly affected lignin extractability, regardless of the initial content and direction of change in both paddy and non-paddy soils. This was likely a result of (partial) dissolution and/or pH-induced changes of the surface properties of Fe and Mn hydrous oxides causing the release of mineral-associated lignin-derived phenols. Thus, we speculate that oxidised lignin fragments produced during the (oxic) dry period do not remain in the soils but percolate with water drainage during the flooding period.

Effects of Plant Functional Group Loss on Soil Microbial Community and Litter Decomposition in a Steppe Vegetation.

PubMed

Xiao, Chunwang; Zhou, Yong; Su, Jiaqi; Yang, Fan

2017-01-01

Globally, many terrestrial ecosystems are experiencing a rapid loss of biodiversity. Continued improvements in our understanding of interrelationships between plant diversity and soil microbes are critical to address the concern over the consequences of the decline in biodiversity on ecosystem functioning and services. By removing forbs, or grasses, or, to an extreme scenario, both forbs and grasses in a steppe vegetation in Inner Mongolia, we studied how plant functional group (PFG) loss affects soil microbial community composition using phospholipid fatty acid analysis (PLFA) and litter decomposition using a litter-bag method. PFG loss significantly decreased above- and below-ground plant biomass, soil microbial biomass carbon (SMBC) and nitrogen (SMBN), but had no effect on the ratio of SMBC to SMBN. Although the ratio of fungal to bacterial PLFAs remained unaffected, PFG loss significantly reduced the amount of bacterial, fungal, and total PLFAs. PFG loss decreased litter monthly mass loss and decay constant, and such decrease was significant when both forbs and grasses were removed. Our results provide robust evidence that PFG loss in grassland ecosystem can lead to a rapid response of soil microbial activity which may affect litter decomposition and soil nutrient cycling, suggesting that the assessment of plant-microbe interactions in soils is an integral component of ecosystem response to biodiversity loss.

Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient.

PubMed

Scola, Vincent; Ramond, Jean-Baptiste; Frossard, Aline; Zablocki, Olivier; Adriaenssens, Evelien M; Johnson, Riegardt M; Seely, Mary; Cowan, Don A

2018-01-01

The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.

Chemical manipulation of soil biota in a fescue meadow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malone, C. R.; Reichle, D. E.

Formalin, phorate, and sodium chlorate were used in field enclosures to create artificial habitats in a fescue meadow containing (1) reduced number of earthworms, (2) reduced numbers of earthworms and soil arthropods, and (3) reduction of total soil fauna and rate of microbial decomposition. Under these conditions, confined fescue litter initially decomposed more rapidly where arthropods or earthworms were suppressed than in controls with full complements of soil animals. After one year, reduction in numbers of soil animals had no net effect on litter decomposition, with faunal activity apparently having been compensated for by increased microbial activity. Where animals andmore » microbial activity were reduced, rate of litter loss was depressed initially but recovered after 10 months as the effects of chemical suppression of microbial populations subsided. Contrary to the effects on annual loss of litter, elimination of all or portions of the soil fauna depressed rates of loss of confined and buried roots, reflecting the role of animals in fragmenting roots before their decomposition by microorganisms. Habitat manipulations had pronounced effects on the mobility of 134Cs, and loss of the radionuclide from labelled litter was retarded despite an accelerated rate of decomposition. This effect apparently was associated with proliferation of microorganisms on litter and microbial immobilization of the radionuclide. Immobilization of 134Cs occurred following chemical perturbations, but only after an initial period of rapid loss resulting from increased microbial activity. Distribution of 134Cs in soil beneath tagged litter bags reflected the role of animals in element redistribution within soil. Finally, restricted vertical mobility of the nuclide occurred except where chemical application killed vegetation within the experimental enclosures.« less

Atmospheric Nitrogen Deposition and the Properties of Soils in Forests of Vologda Region

NASA Astrophysics Data System (ADS)

Kudrevatykh, I. Yu.; Ivashchenko, K. V.; Ananyeva, N. D.; Ivanishcheva, E. A.

2018-02-01

Twenty plots (20 m2 each) were selected in coniferous and mixed forests of the industrial Vologda district and the Vytegra district without developed industries in Vologda region. In March, snow cores corresponding to the snow cover depth were taken on these plots. In August, soil samples from the 0- to 20-cm layer of litter-free soddy-podzolic soil (Albic Retisol (Ochric)) were taken on the same plots in August. The content of mineral nitrogen (Nmin), including its ammonium (NH+ 4) and nitrate (NO- 3) forms, was determined in the snow (meltwater) and soil. The contents of total organic carbon, total nitrogen, and elements (Al, Ca); pH; particle size distribution; and microbiological parameters―carbon of microbial biomass (Cmic) and microbial respiration (MR)―were determined in the soil. The ratio MR/Cmic = qCO2 (specific respiration of microbial biomass, or soil microbial metabolic quotient) was calculated. The content of Nmic in meltwater of two districts was 1.7 mg/L on the average (1.5 and 0.3 mg/L for the NH+ 4 and NO- 3 forms, respectively). The annual atmospheric deposition was 0.6-8.9 kg Nmin/ha, the value of which in the Vologda district was higher than in the Vytegra district by 40%. Reliable correlations were found between atmospheric NH+ 4 depositions and Cmic (-0.45), between NH+ 4 and qCO2 (0.56), between atmospheric NO- 3 depositions and the soil NO- 3 (-0.45), and between NO- 3 and qCO2 (-0.58). The content of atmospheric Nmin depositions correlated with the ratios C/N (-0.46) and Al/Ca (-0.52) in the soil. In forests with the high input of atmospheric nitrogen (>2.0 kg NH+ 4/(ha yr) and >6.4 kg Nmin/(ha yr)), a tendency of decreasing Cmic, C/N, and Al/Ca, as well as increasing qCO2, was revealed, which could be indicative of deterioration in the functioning of microbial community and the chemical properties of the soil.

Bioremediation of diesel oil in a co-contaminated soil by bioaugmentation with a microbial formula tailored with native strains selected for heavy metals resistance.

PubMed

Alisi, Chiara; Musella, Rosario; Tasso, Flavia; Ubaldi, Carla; Manzo, Sonia; Cremisini, Carlo; Sprocati, Anna Rosa

2009-04-01

The aim of the work is to assess the feasibility of bioremediation of a soil, containing heavy metals and spiked with diesel oil (DO), through a bioaugmentation strategy based on the use of a microbial formula tailored with selected native strains. The soil originated from the metallurgic area of Bagnoli (Naples, Italy). The formula, named ENEA-LAM, combines ten bacterial strains selected for multiple resistance to heavy metals among the native microbial community. The biodegradation process of diesel oil was assessed in biometer flasks by monitoring the following parameters: DO composition by GC-MS, CO2 evolution rate, microbial load and composition of the community by T-RFLP, physiological profile in Biolog ECOplates and ecotoxicity of the system. The application of this microbial formula allowed to obtain, in the presence of heavy metals, the complete degradation of n-C(12-20), the total disappearance of phenantrene, a 60% reduction of isoprenoids and an overall reduction of about 75% of the total diesel hydrocarbons in 42 days. Concurrently with the increase of metabolic activity at community level and the microbial load, the gradual abatement of the ecotoxicity was observed. The T-RFLP analysis highlighted that most of the ENEA-LAM strains survived and some minor native strains, undetectable in the soil at the beginning of the experiment, developed. Such a bioaugmentation approach allows the newly established microbial community to strike a balance between the introduced and the naturally present microorganisms. The results indicate that the use of a tailored microbial formula may efficiently facilitate and speed up the bioremediation of matrices co-contaminated with hydrocarbons and heavy metals. The study represents the first step for the scale up of the system and should be verified at a larger scale. In this view, this bioaugmentation strategy may contribute to overcome a critical bottleneck of the bioremediation technology.

Evaluation of the effect of an additional fertilizer on the dynamics of microbial community and the decomposition of organic matter in soil

NASA Astrophysics Data System (ADS)

Fabiola, B.; Olivier, M.; Houdusse, F.; Fuentes, M.; Garcia, M. J. M.; Lévêque, J.; Yvin, J. C.; Maron, P. A.; Lemenager, D.

2012-04-01

Organic matter (OM) influences many of the soil functions and occupies a central position in the global carbon cycle. At the scale of the agro-ecosystem, primary productivity is dependent on the recycling of soil organic matter (SOM) by the action of decomposers (mainly bacteria and fungi), which mineralize organic compounds, releasing the nutrients needed for plant growth. At a global scale, the recycling of the SOM determines the carbon flux between soil and atmosphere, with major consequences in terms of environmental quality. In this context, the management of SOM stocks in agro-ecosystems is a major issue from which depend the maintenance of the productivity and sustainability of agricultural practices. The use of additional fertilizer appears to be a promising way to achieve such management. These products have been proven effectives in many field trials. However, their mode of action, particularly in terms of impact on soil microbial component, is still nearly unknown. In this context, this study aims to test the influence of an additional fertilizer on (i) soil microbial communities (total biomass, density of bacteria and fungi), and (ii) soil functioning in terms of dynamics of organic matter. It is based on experiments in soil microcosms which follow in parallel the kinetics of mineralization of different organic carbon compartments (endogenous compartment: soil organic matter; exogenous compartment: wheat residue provided) and the dynamics of microbial communities after the addition of wheat residues in soil. Two different soils were used to evaluate the influence of soil physicochemical characteristics on the effect induced by the addition in terms of fertilization. The first results show a significant effect of the input of additional fertilizer on the dynamics of soil organic matter. They also show that soil pH as well as the dose at which the additional fertilizer is applied are important for modulating the observed effect. Characterization of microbial communities by molecular tools (quantification of molecular biomass, quantitative PCR of 16S and 18S ribosomal genes to quantify bacteria and fungi, respectively) will allow linking the changes of the mineralization of carbon compartments with the response of the soil microbial communities.

A comparative assessment of the biological properties of soils in the cultural and native cenoses of the Central Caucasus (using the example of the Terskii variant of altitudinal zonality in Kabardino-Balkaria)

NASA Astrophysics Data System (ADS)

Gorobtsova, O. N.; Gedgafova, F. V.; Uligova, T. S.; Tembotov, R. Kh.

2016-01-01

The biological properties of the most widespread automorphic and hydromorphic soils of cultural and native cenoses in the Terskii variant of the altitudinal zonality (Kabardino-Balkaria) are compared. The data on the humus reserves in the 0- to 20-cm soil layer and those on the carbon content in the microbial biomass calculated on the basis of the results of substrate-induced respiration measurements are presented. The share of carbon in the microbial biomass of the total organic carbon in the soils was determined. Long-term (more than 70 years) farming on the studied soils significantly changed their biological properties. The humus content and its reserves became lower by 25-40%. The physiological activity of the microbial biomass in the cultural soils decreased by more than 60%. Presently, the soils of the cultural cenoses function as an entire natural system, but at a lower level of fertility; the loss of more than 30% of the bioorganic potential (the critical threshold of soil system stability) indicates the disturbance of soil ecological functions, their stability, and the capability of self-restoration.

[Effects of litter and root exclusion on soil microbial community composition and function of four plantations in subtropical sandy coastal plain area, China].

PubMed

Sang, Chang Peng; Wan, Xiao Hua; Yu, Zai Peng; Wang, Min Huang; Lin, Yu; Huang, Zhi Qun

2017-04-18

We conducted detritus input and removal treatment (DIRT) to examine the effects of shifting above- and belowground carbon (C) inputs on soil microbial biomass, community composition and function in subtropical Pinus elliottii, Eucalyptus urophylla × Eucalyptus grandis, Acacia aulacocarpa and Casuarina equisetifolia coastal sandy plain forests, and the treatments included: root trenching, litter removal and control. Up to September 2015, one year after the experiment began, we collected the 0-10 cm soil samples from each plot. Phospholipid fatty acid (PLFA) analysis was used to characterize the microbial community composition, and micro-hole enzymatic detection technology was utilized to determine the activity of six kinds of soil enzymes. Results showed that changes in microbial biomass induced by the C input manipulations differed among tree species, and mainly affected by litter and root qualily. In E. urophylla × E. grandis stands, root trenching significantly decreased the contents of total PLFAs, Gram-positive bacteria, Gram-negative bacteria, fungi and actinomycetes by 31%, 30%, 32%, 36% and 26%, respectively. Litter removal reduced the contents of Gram-positive bacteria, fungi and actinomycetes by 24%, 27% and 24%, respectively. However, C input manipulations had no significant effect on soil microbial biomassunder other three plantations. According to the effect of C input manipulations on soil microbial community structure, litter and root exclusion decreased fungi abundance and increased actinomycetes abundance. Different treatments under different plantations resulted in various soil enzyme activities. Litter removal significantly decreased the activities of cellobiohydrolase, β-glucosidase, acid phosphatase and N-acetyl-β-d-glucosaminidase of P. elliottii, A. aulacocarpa and C. equisetifolia, root exclusion only decreased and increased the activities of β-glucosidase in P. elliottii and A. aulacocarpa forest soils, respectively. Litter removal also decreased the activities of polyphenol oxidase (PPO) and peroxidase (PER) in P. elliottii and C. equisetifolia forest soils, while root trenching had no significant effect on the activities of PPO and PER under all plantations. The properties of litter and root were the important factors in determining the soil microbial community and enzyme activity, and the change of soil microenvironment, such as temperature and moisture, caused by C input manipulations was also the important driver for the change of soil microbial property.

Improved Flotation Technique for Microscopy of In Situ Soil and Sediment Microorganisms

PubMed Central

Bone, T. L.; Balkwill, D. L.

1986-01-01

An improved flotation method for microscopy of in situ soil and sediment microorganisms was developed. Microbial cells were released into gellike flotation films that were stripped from soil and sediment aggregates as these aggregates were submerged in 0.5% solutions of polyvinylpyrrolidone. The use of polyvinylpyrrolidone solutions instead of water facilitated the release of films from saturated samples such as aquifer sediments as well as from typical surface soils. In situ microbial morphological characteristics could then be surveyed rapidly by light microscopy of films stained with acridine orange. This method effectively determined the ranges of morphological diversity in a variety of sample types. It also detected microcolonies and other spatial relationships among microbial cells. Only a small fraction (3.4 to 10.1%) of the microflora was released into the flotation films, but plating and direct evaluations by microscopy showed that this fraction was representative of the total population. Images PMID:16347005

[Effects of controlled release blend bulk urea on soil nitrogen and soil enzyme activity in wheat and rice fields].

PubMed

Zhang, Jing Sheng; Wang, Chang Quan; Li, Bing; Liang, Jing Yue; He, Jie; Xiang, Hao; Yin, Bin; Luo, Jing

2017-06-18

A field experiment was conducted to investigate the effect of controlled-release fertilizer (CRF) combined with urea (UR) on the soil fertility and environment in wheat-rice rotation system. Changes in four forms of nitrogen (total nitrogen, ammonium nitrogen, nitrate nitrogen, and microbial biomass nitrogen) and in activities of three soil enzymes participating in nitrogen transformation (urease, protease, and nitrate reductase) were measured in seven fertilization treatments (no fertilization, routine fertilization, 10%CRF+90%UR, 20%CRF+80%UR, 40%CRF+60%UR, 80%CRF+20%UR, and 100%CRF). The results showed that soil total nitrogen was stable in the whole growth period of wheat and rice. There was no significant difference among the treatments of over 20% CRF in soil total nitrogen content of wheat and rice. The soil inorganic nitrogen content was increased dramatically in treatments of 40% or above CRF during the mid-late growing stages of wheat and rice. With the advance of the growth period, conventional fertilization significantly decreased soil microbial biomass nitrogen, but the treatments of 40% and above CRF increased the soil microbial biomass nitrogen significantly. The soil enzyme activities were increased with over 40% of CRF in the mid-late growing stage of wheat and rice. By increasing the CRF ratio, the soil protease activity and nitrate reductase activity were improved gradually, and peaked in 100% CRF. The treatments of above 20% CRF could decrease the urease activity in tillering stage of rice and delay the peak of ammonium nitrogen, which would benefit nitrogen loss reduction. The treatments of 40% and above CRF were beneficial to improving soil nitrogen supply and enhancing soil urease and protease activities, which could promote the effectiveness of nitrogen during the later growth stages of wheat and rice. The 100% CRF treatment improved the nitrate reductase activity significantly during the later stage of wheat and rice. Compared with the treatments of 40%-80% CRF, 100% CRF reduced the soil nitrate content of 20-40 cm soil layer in wheat significantly suggesting it could reduce the loss of nitrogen.

A Relationship Between Microbial Activity in Soils and Phosphate Levels in Tributaries to Lake Champlain

NASA Astrophysics Data System (ADS)

Larose, R.; Lee, S.; Lane, T.

2015-12-01

Lake Champlain is a large natural freshwater lake. It forms the western boundary of Vermont and drains over half of the state. It is bordered by the state of New York on its western side and drains to the north into Quebec, Canada. Lake Champlain is the source of fresh drinking water for over quarter of a million people and provides for the livelihoods and recreational opportunities of many well beyond its borders. The health of this lake is important. During the summer month's algae blooms plague the lake. These unsightly growths, which affect other aquatic organisms, are the result of excess phosphate flowing into the lake from many sources. Examining whether there is a relationship between microbial activity in the soils bordering tributaries to Lake Champlain and phosphate levels in those tributaries sheds insight into the origins and paths by which phosphate moves into Lake Champlain. Understanding the how phosphate moves into the water system may assist in mitigation efforts.Total Phosphate levels and Total Suspended Solids were measured in second and third order streams in the Lake Champlain Basin over a three-year period. In addition microbial activity was measured within the toe, bank and upland riparian zone areas of these streams during the summer months. In general in areas showing greater microbial activity in the soil(s) there were increased levels of phosphate in the streams.

Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system.

PubMed

Lopes, Ana R; Bello, Diana; Prieto-Fernández, Ángeles; Trasar-Cepeda, Carmen; Manaia, Célia M; Nunes, Olga C

2015-08-01

The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

PubMed

Mendes, Lucas William; Tsai, Siu Mui

2018-01-01

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

[Effects of biochar and sheep manure on rhizospheric soil microbial community in continuous ratooning tea orchards].

PubMed

Li, Yan Chun; Li, Zhao Wei; Lin, Wei Wei; Jiang, Yu Hang; Weng, Bo Qi; Lin, Wen Xiong

2018-04-01

Long-term continuous ratooning of tea could lead to serious soil acidification, nutritional imbalance, and the deterioration of the rhizosphere micro-ecological environment. Understanding the effects of biochar and sheep manure on the growth of tea plants and the rhizosphere microbial community structure and function would provide theoretical basis to improve the soil micro-ecological environment of continuous ratooning tea orchards. Biolog technology combined with phospholipid fatty acid (PLFA) approaches were employed to quantify the effects of biochar (40 t·hm -2 ) and sheep manure on the growth of 20 years continuous ratooning tea plants, soil chemical properties, and the soil microbial community structure and function. The results showed that after one year treatment, biochar and sheep manure both improved soil pH and nutrition, and significantly enhanced tea production. Compared with the routine fertilizer application (CK), the biochar and sheep manure treatments significantly increased the carbon metabolic activity (AWCD) and microorganism diversity in the rhizosphere soils, and increased the relative utilization of the carbon sources such as amines, carbohydrates, and polymers. The total PLFA concentrations in the biochar and sheep manure treatments were significantly increased by 20.9% and 47.5% than that in the routine fertilizers application. In addition, sheep manure treatment significantly decreased the saturated/monosaturated fatty acids In conclusion, biochar and sheep manure could alleviate soil acidification, enhance soil nutrition and the growth of tea plants. Both management strategies could increase the soil microbial activity and biomass, enhance the diversity, and improve the microbial community structure, which could be taken as effective measures to regulate the rhizosphere micro-environment of tea plants.

A protocol for assessing the biotreatability of hydrocarbon contaminated exploration and production site soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tezak, J.; Miller, J.A.; Lawrence, A.W.

1995-12-01

It is estimated that there are over 260,000 natural gas production wells in the continental United States. Production or reserve pits exist which ma require remediation depending on several conditions such as: the manner in which they were initially closed; whether or not they were lined; and the local climate, soil type, and depth to groundwater. As part of the Gas Research Institute (GRI) research program on exploration and production (E&P) site remediation, a treatability Protocol is being developed to facilitate the rapid assessment of the amenability of the contaminated soils to remediation by biological processes. This paper describes themore » treatability protocol and the results of a series of treatability tests on a spectrum of hydrocarbon contaminated E&P soils collected from various operating locations throughout the United States. The soils are subjected to physical and chemical characterization prior to treatability testing. Potential biotoxic characteristics of the soils are determined by a respirometry screening technique. Presuming that the soils are not toxic to aerobic soil microorganisms, 20 percent by weight aqueous slurries of the soils are prepared and subjected to continuous batch aeration for a six week period. Conditions favorable to microbial growth are maintained in the reactors by monitoring and augmentation is needed of pH, microbial nutrients and oxygen for microbial respiration. The extent of microbial degradation of the contaminant hydrocarbons is monitored by periodic measurement of total petroleum hydrocarbons (TPH), oil and grease, and individual hydrocarbon compounds as determined by gas chromatography. Microbial plate counts are prepared to document the biological viability of the treatment process. The factors influencing the amenability of these soils to bioremediation as determined from the test results are discussed.« less

State of microbial communities in paleosols buried under kurgans of the desert-steppe zone in the Middle Bronze Age (27th-26th centuries BC) in relation to the dynamics of climate humidity

NASA Astrophysics Data System (ADS)

Khomutova, T. E.; Demkina, T. S.; Borisov, A. V.; Shishlina, I. I.

2017-02-01

The size and structure of microbial pool in light chestnut paleosols and paleosolonetz buried under kurgans of the Middle Bronze Age 4600-4500 years ago (the burial mound heights are 45-173 cm), as well as in recent analogues in the desert-steppe zone (Western Ergeni, Salo-Manych Ridge), have been studied. In paleosol profiles, the living microbial biomass estimated from the content of phospholipids varies from 35 to 258% of the present-day value; the active biomass (responsive to glucose addition) in paleosols is 1‒3 orders of magnitude lower than in recent analogues. The content of soil phospholipids is recalculated to that of microbial carbon, and its share in the total soil organic carbon is determined: it is 4.5-7.0% in recent soils and up to three times higher in the remained organic carbon of paleosols. The stability of microbial communities in the B1 horizon of paleosols is 1.3-2.2 times higher than in the upper horizon; in recent soils, it has a tendency to a decrease. The share of microorganisms feeding on plant residues in the ecological-trophic structure of paleosol microbial communities is higher by 23-35% and their index of oligotrophy is 3-5 times lower than in recent analogues. The size of microbial pool and its structure indicate a significantly higher input of plant residues into soils 4600-4500 years ago than in the recent time, which is related to the increase in atmospheric humidity in the studied zone. However, the occurrence depths of salt accumulations in profiles of the studied soils contradict this supposition. A short-term trend of increase in climate humidity is supposed, as indicated by microbial parameters (the most sensitive soil characteristics) or changes in the annual variation of precipitation (its increase in the warm season) during the construction of the mounds under study.

Priming effect in topsoil and subsoil induced by earthworm burrows

NASA Astrophysics Data System (ADS)

Thu, Duyen Hoang Thi

2017-04-01

Earthworms (Lumbricus terrestris L.) not only affect soil physics, but they also boost microbial activities and consequently important hotspots of microbial mediated carbon and C turnover through their burrowing activity. However, it is still unknown to which extend earthworms affect priming effect in top- and subsoil horizons. More labile C inputs in earthworm burrows were hypothesized to trigger higher priming of soil organic matter (SOM) decomposition compared to rhizosphere and bulk soil. Moreover, this effect was expected to be more pronounced in subsoil due to its greater C and nutrient limitation. To test these hypotheses, biopores and bulk soil were sampled from topsoil (0-30 cm) and two subsoil depths (45-75 and 75-105 cm). Additionally, rhizosphere samples were taken from the topsoil. Total organic C (Corg), total N (TN), total P (TP) and enzyme activities involved in C-, N-, and P-cycling (cellobiohydrolase, β-glucosidase, xylanase, chitinase, leucine aminopeptidase and phosphatase) were measured. Priming effects were calculated as the difference in SOM-derived CO2 from soil with or without 14C-labelled glucose addition. Enzyme activities in biopores were positively correlated with Corg, TN and TP, but in bulk soil this correlation was negative. The more frequent fresh and labile C inputs to biopores caused 4 to 20 time higher absolute priming of SOM turnover due to enzyme activities that were one order of magnitude higher than in bulk soil. In subsoil biopores, reduced labile C inputs and lower N availability stimulated priming twofold greater than in topsoil. In contrast, a positive priming effect in bulk soil was only detected at 75-105 cm depth. We conclude that earthworm burrows provide not only the linkage between top- and subsoil for C and nutrients, but strongly increase microbial activities and accelerate SOM turnover in subsoil, contributing to nutrient mobilization for roots and CO2 emission increase as a greenhouse gas. Additionally, the mechanisms of native SOM decomposition are distinct between topsoil and subsoil, which relies on the fresh C input and nutrient availability. Keywords: Priming effect; Earthworms; Organic matter decomposition; Biopores; Subsoil; Microbial hotspots.

Potential impacts of CO2 leakage from the CCS sites on seed germination and soil microbial enzyme activities

NASA Astrophysics Data System (ADS)

Wenmei, H.; Yoo, G.; Kim, Y.; Moonis, M.

2015-12-01

To ensure the safety of carbon capture and storage (CCS) technology, it is essential to assess the impacts of potential CO2 leakage on the soil and ecosystem. The changes in soil environment due to the CO2 leakage might have an enormous effect on the plant growth. As a preliminary study, we conducted a research focusing on the germination process because it is known to be especially sensitive to the environmental change. The objective of this study is to investigate the impacts of high soil CO2 concentration on the germination of different species. A laboratory experiment was designed to investigate the effect of high soil CO2 concentration on germination rate and soil physicochemical/microbial parameters. Cabbage, corn, bean, and wheat were selected for this study. The concentrations of the injected CO2 treatments were 10%, 30%, 60% and 100%, and the actual soil CO2 concentration ranged from 3.6% to 53.2%. Two types of controls were employed: the one connected with ambient air tank and the other connected with nothing. The final germination rates of four crops were not different between the controls and 10% treatment, but the delay of germination was observed in cabbage, corn, and bean. At 30% treatment, the germination rates of cabbage, corn and bean were 38%, while that of wheat was 78%. No seed was germinated at 60% and 100% treatments. After the incubation, soil pH decreased from 6.0 in the controls to 5.6 in the 100% treatment. The contents of soil total C and total N were not different among treatments. Activities of microbial fluorescein diacetate hydrolysis were not different among treatments for all plants. Five kinds of soil extracellular enzyme activities were not affected by the CO2 treatments. Our results suggest that: 1) Soil CO2 concentration at 3-4% did not inhibit germination of four crops. 2) Wheat is most resistant to high soil CO2 concentration in this study. 3) Soil microbial parameters were more tolerant during the short term injection.

The combined effects of urea application and simulated acid rain on soil acidification and microbial community structure.

PubMed

Liu, Xingmei; Zhou, Jian; Li, Wanlu; Xu, Jianming; Brookes, Philip C

2014-05-01

Our aim was to test the effects of simulated acid rain (SAR) at different pHs, when applied to fertilized and unfertilized soils, on the leaching of soil cations (K, Ca, Mg, Na) and Al. Their effects on soil pH, exchangeable H(+) and Al(3+) and microbial community structure were also determined. A Paleudalfs soil was incubated for 30 days, with and without an initial application of urea (200 mg N kg(-1)soil) as nitrogen (N) fertilizer. The soil was held in columns and leached with SAR at three pH levels. Six treatments were tested: SAR of pH 2.5, 4.0 and 5.6 leaching on unfertilized soil (T1, T2 and T3), and on soils fertilized with urea (T4, T5 and T6). Increasing acid inputs proportionally increased cation leaching in both unfertilized and fertilized soils. Urea application increased the initial Ca and Mg leaching, but had no effect on the total concentrations of Ca, Mg and K leached. There was no significant difference for the amount of Na leached between the different treatments. The SAR pH and urea application had significant effects on soil pH, exchangeable H(+) and Al(3+). Urea application, SAR treated with various pH, and the interactions between them all had significant impacts on total phospholipid fatty acids (PLFAs). The highest concentration of total PLFAs occurred in fertilized soils with SAR pH5.6 and the lowest in soils leached with the lowest SAR pH. Soils pretreated with urea then leached with SARs of pH 4.0 and 5.6 had larger total PLFA concentrations than soil without urea. Bacterial, fungal, actinomycete, Gram-negative and Gram-positive bacterial PLFAs had generally similar trends to total PLFAs.

Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities.

PubMed

Rojas, Xavier; Guo, Jingqi; Leff, Jonathan W; McNear, David H; Fierer, Noah; McCulley, Rebecca L

2016-07-01

Tall fescue (Schedonorus arundinaceus) is a widespread grass that can form a symbiotic relationship with a shoot-specific fungal endophyte (Epichloë coenophiala). While the effects of fungal endophyte infection on fescue physiology and ecology have been relatively well studied, less attention has been given to how this relationship may impact the soil microbial community. We used high-throughput DNA sequencing and phospholipid fatty acid analysis to determine the structure and biomass of microbial communities in both bulk and rhizosphere soils from tall fescue stands that were either uninfected with E. coenophiala or were infected with the common toxic strain or one of several novel strains of the endophyte. We found that rhizosphere and bulk soils harbored distinct microbial communities. Endophyte presence, regardless of strain, significantly influenced soil fungal communities, but endophyte effects were less pronounced in prokaryotic communities. E. coenophiala presence did not change total fungal biomass but caused a shift in soil and rhizosphere fungal community composition, increasing the relative abundance of taxa within the Glomeromycota phylum and decreasing the relative abundance of genera in the Ascomycota phylum, including Lecanicillium, Volutella, Lipomyces, Pochonia, and Rhizoctonia. Our data suggests that tripartite interactions exist between the shoot endophyte E. coenophiala, tall fescue, and soil fungi that may have important implications for the functioning of soils, such as carbon storage, in fescue-dominated grasslands.

Role of microbial inoculation and industrial by-product phosphogypsum in growth and nutrient uptake of maize (Zea mays L.) grown in calcareous soil.

PubMed

Al-Enazy, Abdul-Aziz R; Al-Oud, Saud S; Al-Barakah, Fahad N; Usman, Adel Ra

2017-08-01

Alkaline soils with high calcium carbonate and low organic matter are deficient in plant nutrient availability. Use of organic and bio-fertilizers has been suggested to improve their properties. Therefore, a greenhouse experiment was conducted to evaluate the integrative role of phosphogypsum (PG; added at 0.0, 10, 30, and 50 g PG kg -1 ), cow manure (CM; added at 50 g kg -1 ) and mixed microbial inoculation (Incl.; Azotobacter chroococcum, and phosphate-solubilizing bacteria Bacillus megaterium var. phosphaticum and Pseudomonas fluorescens) on growth and nutrients (N, P, K, Fe, Mn, Zn and Cu) uptake of maize (Zea mays L.) in calcareous soil. Treatment effects on soil chemical and biological properties and the Cd and Pb availability to maize plants were also investigated. Applying PG decreased soil pH. The soil available P increased when soil was inoculated and/or treated with CM, especially with PG. The total microbial count and dehydrogenase activity were enhanced with PG+CM+Incl. Inoculated soils treated with PG showed significant increases in NPK uptake and maize plant growth. However, the most investigated treatments showed significant decreases in shoot micronutrients. Cd and Pb were not detected in maize shoots. Applying PG with microbial inoculation improved macronutrient uptake and plant growth. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Impact of Wildfire on Microbial Biomass in Critical Zone Observatory

NASA Astrophysics Data System (ADS)

Murphy, M. A.; Fairbanks, D.; Chorover, J.; Gallery, R. E.; Rich, V. I.

2014-12-01

The recovery of the critical zone following disturbances such as wildfire is not fully understood. Wildfires have increased in size and intensity in western US forests in recent years and these fires influence soil microbial communities, both in composition and overall biomass. Studies have typically shown a 50% post-fire decline in overall microbial biomass (µg per g soil) that can persist for years. There is however, some variability in the severity of biomass decline, and its relationship with burn severity and landscape position have not yet been studied. Since microbial biomass has a cascade of impacts in soil systems, from helping control the rate and diversity the biogeochemical processes occurring, to promoting soil fertility, to impacting the nature and structure of soil carbon (C), fire's lasting impact on it is one mechanistic determinant of the overall post-fire recovery of impacted ecosystems. Additionally, microbial biomass measurements hold potential for testing and incorporation into land surface models (NoahMP, CLM, etc.) in order to improve estimates of long-term effects of climate change and disturbances such as fire on the C cycle. In order to refine our understanding of the impact of fire on microbial biomass and then relate that to biogeochemical processes and ecosystem recovery, we used chloroform fumigation extraction to quantify total microbial biomass C (Cmic ). One year after the June 2013 Thompson Ridge fire in the Jemez River Basin Critical Zone Observatory, we are measuring the Cmic of 22 sites across a gradient of burn severities and 4 control unburned sites, from six depth intervals at each site (0-2, 2-5, 5-10, 10-20, 20-30, and 30-40 cm). We hypothesize that the decrease in microbial biomass in burned sites relative to control sites will correlate with changes in soil biogeochemistry related to burn severity; and that the extent of the impact on biomass will be inversely related to depth in the soil column. Additionally, as the project progresses, we will relate microbial biomass to microbial functional assays as proxy for biogeochemical activity, and test variation by landscape position and aspect.

Effects of heavy metal contamination of soils on micronucleus induction in Tradescantia and on microbial enzyme activities: a comparative investigation.

PubMed

Majer, Bernhard J; Tscherko, Dagmar; Paschke, Albrecht; Wennrich, Rainer; Kundi, Michael; Kandeler, Ellen; Knasmüller, Siegfried

2002-03-25

The aim of this study was to investigate correlation between genotoxic effects and changes of microbial parameters caused by metal contamination in soils. In total, 20 soils from nine locations were examined; metal contents and physicochemical soil parameters were measured with standard methods. In general, a pronounced induction of the frequency of micronuclei (MN) in the Tradescantia micronucleus (Trad-MN) assay was seen with increasing metal concentration in soils from identical locations. However, no correlations were found between metal contents and genotoxicity of soils from different locations. These discrepancies are probably due to differences of the physicochemical characteristics of the samples. Also, the microbial parameters depended on the metal content in soils from identical sampling locations. Inconsistent responses of the individual enzymes were seen in soils from different locations, indicating that it is not possible to define a specific marker enzyme for metal contamination. The most sensitive microbial parameters were dehydrogenase and arylsulfatase activity, biomass C, and biomass N. Statistical analyses showed an overall correlation between genotoxicity in Tradescantia on the one hand and dehydrogenase activity, biomass C, and the metabolic quotient on the other hand. In conclusion, the results of the present study show that the Trad-MN assay is suitable for the detection of genotoxic effects of metal contamination in soils and furthermore, that the DNA-damaging potential of soils from different origin cannot be predicted on the basis of chemical analyses of their metal concentrations.

Biological properties of disturbed and undisturbed Cerrado sensu stricto from Northeast Brazil.

PubMed

Araújo, A S F; Magalhaes, L B; Santos, V M; Nunes, L A P L; Dias, C T S

2017-03-01

The aim of this study was to measure soil microbial biomass and soil surface fauna in undisturbed and disturbed Cerrado sensu stricto (Css) from Sete Cidades National Park, Northeast Brazil. The following sites were sampled under Cerrado sensu stricto (Css) at the park: undisturbed and disturbed Css (slash-and-burn agricultural practices). Total organic and microbial biomass C were higher in undisturbed than in disturbed sites in both seasons. However, microbial biomass C was higher in the wet than in the dry season. Soil respiration did not vary among sites but was higher in the wet than in the dry season. The densities of Araneae, Coleoptera, and Orthoptera were higher in the undisturbed site, whereas the densities of Formicidae were higher in the disturbed site. Non-metric multidimensional scaling analysis separated undisturbed from disturbed sites according to soil biological properties. Disturbance by agricultural practices, such as slash-and-burn, probably resulted in the deterioration of the biological properties of soil under native Cerrado sensu stricto in the Sete Cidades National Park.

Post-fire soil functionality and microbial community structure in a Mediterranean shrubland subjected to experimental drought.

PubMed

Hinojosa, M Belén; Parra, Antonio; Laudicina, Vito Armando; Moreno, José M

2016-12-15

Fire may cause significant alterations in soil properties. Post-fire soil dynamics can vary depending, among other factors, on rainfall patterns. However, little is known regarding variations in response to post-fire drought. This is relevant in arid and semiarid areas with poor soils, like much of the western Mediterranean. Furthermore, climate change projections in such areas anticipate reduced precipitation and longer annual drought periods, together with an increase in fire severity and frequency. This research evaluates the effects of experimental drought after fire on soil dynamics of a Cistus-Erica shrubland (Central Spain). A replicated (n=4) field experiment was conducted in which the total rainfall and its patterns were manipulated by means of a rain-out shelters and irrigation system. The treatments were: environmental control (natural rainfall), historical control (average rainfall, 2months drought), moderate drought (25% reduction of historical control, 5months drought) and severe drought (45% reduction, 7months drought). After one growing season under these rainfall treatments, the plots were burned. One set of unburned plots under natural rainfall served as an additional control. Soils were collected seasonally. Fire increased soil P and N availability. Post-fire drought treatments reduced available soil P but increased N concentration (mainly nitrate). Fire reduced available K irrespective of drought treatments. Fire reduced enzyme activities and carbon mineralization rate, a reduction that was higher in post-fire drought-treated soils. Fire decreased soil microbial biomass and the proportion of fungi, while that of actinomycetes increased. Post-fire drought decreased soil total microbial biomass and fungi, with bacteria becoming more abundant. Our results support that increasing drought after fire could compromise the resilience of Mediterranean ecosystems to fire. Copyright © 2016 Elsevier B.V. All rights reserved.

Single application of Sewage Sludge to an Alluvial Agricultural Soil - impacts on Soil Quality

NASA Astrophysics Data System (ADS)

Suhadolc, M.; Graham, D. B.; Hagn, A.; Doerfler, U.; Schloter, M.; Schroll, R.; Munch, J. C.; Lobnik, F.

2009-04-01

Limited information exists on the effects of sewage sludge on soil quality with regard to their ability to maintain soil functions. We studied effects of sewage sludge amendment on soil chemical properties, microbial community structure and microbial degradation of the herbicide glyphosate. Three months soil column leaching experiment has been conducted using alluvial soils (Eutric Fluvisol) with no prior history of sludge application. The soil was loamy with pH 7,4 and organic matter content of 3,5%. Soil material in the upper 2 cm of columns was mixed with dehydrated sewage sludge which was applied in amounts corresponding to the standards governing the use of sewage sludge for agricultural land. Sludge did increase some nutrients (total N, NH4+, available P and K, organic carbon) and some heavy metals contents (Zn, Cu, Pb) in soil. However, upper limits for heavy metals in agricultural soils were not exceeded. Results of heavy metal availability in soil determined by sequential extraction will be also presented. Restriction fragment length polymorphism (RFLP) analyses of 16s/18s rDNA, using universal fungal and bacterial primers, revealed clear shifts in bacterial and fungal community structure in the upper 2 cm of soils after amendment. Fungal fingerprints showed greater short term effects of sewage sludge, whereas sewage sludge seems to have prolonged effects on soil bacteria. Furthermore, sewage sludge amendment significantly increased glyphosate degradation from 21.6±1% to 33.6±1% over a 2 months period. The most probable reasons for shifts in microbial community structure and increased degradation of glyphosate are beneficial alterations to the physical-chemical characteristics of the soil. Negative effects of potentially toxic substances present in the sewage sludge on soil microbial community functioning were not observed with the methods used in our study.

Effects of biochar and maize straw on the short-term carbon and nitrogen dynamics in a cultivated silty loam in China.

PubMed

Zhu, Li-Xia; Xiao, Qian; Shen, Yu-Fang; Li, Shi-Qing

2017-01-01

Application of maize straw and biochar can potentially improve soil fertility and sequester carbon (C) in the soil, but little information is available about the effects of maize straw and biochar on the mineralization of soil C and nitrogen (N). We conducted a laboratory incubation experiment with five treatments of a cultivated silty loam, biochar produced from maize straw and/or maize straw: soil only (control), soil + 1 % maize straw (S), soil + 4 % biochar (B1), soil + 4 % biochar + 1 % maize straw (B1S), and soil + 8 % biochar + 1 % maize straw (B2S). CO 2 emissions, soil organic C, dissolved organic C, easily oxidized C, total N, mineral N, net N mineralization, and microbial biomass C and N of three replicates were measured periodically during the 60-day incubation using destructive sampling method. C mineralization was highest in treatment S, followed by B2S, B1S, the control, and B1. Total net CO 2 emissions suggested that negative or positive priming effect may occur between the biochar and straw according to the biochar addition rate, and biochar mineralization was minimal. By day 35, maize straw, irrespective of the rate of biochar addition, significantly increased microbial biomass C and N but decreased dissolved organic N. Biochar alone, however, had no significant effect on either microbial biomass C or N but decreased dissolved organic N. Mixing the soil with biochar and/or straw significantly increased soil organic C, easily oxidized C and total N contents, and decreased dissolved organic N content. Dissolved organic C contents showed mixed results. Notably, N was immobilized in soil mixed with straw and/or biochar, but the effect was stronger for soil mixed with straw, which may cause N deficiency for plant growth. The application of biochar and maize straw can thus affect soil C and N cycles, and the appropriate proportion of biochar and maize straw need further studies to increase C sequestration.

Spectral Characteristics of Salinized Soils during Microbial Remediation Processes.

PubMed

Ma, Chuang; Shen, Guang-rong; Zhi, Yue-e; Wang, Zi-jun; Zhu, Yun; Li, Xian-hua

2015-09-01

In this study, the spectral reflectance of saline soils, the associated soil salt content (SSC) and the concentrations of salt ions were measured and analysed by tracing the container microbial remediation experiments for saline soil (main salt is sodium chloride) of Dongying City, Shandong Province. The sensitive spectral reflectance bands of saline soils to SSC, Cl- and Na+ in the process of microbial remediation were analysed. The average-dimension reduction of these bands was conducted by using a combination of correlation coefficient and decision coefficient, and by gradually narrowing the sampling interval method. Results showed that the tendency and magnitude of the average spectral reflectance in all bands of saline soils during the total remediation processes were nearly consistent with SSC and with Cl- coocentration, respectively. The degree of salinity of the soil, including SSC and salt ion concentrations, had a significant positive correlation with the spectral reflectance of all bands, particularly in the near-infrared band. The optimal spectral bands of SSC were 1370 to 1445 nm and 1447 to 1608 nm, whereas the optimal spectral bands of Cl- and Na+ were 1336 to 1461 nm and 1471 to 1561 nm, respectively. The relationship model among SSC, soil salt ion concentrations (Cl- and Na+) and soil spectral reflectance of the corresponding optimal spectral band was established. The largest R2 of relationship model between SSC and the average reflectance of associated optimal band reached to 0.95, and RMSEC and RMSEP were 1.076 and 0.591, respectively. Significant statistical analysis of salt factors and soil reflectance for different microbial remediation processes indicated that the spectral response characteristics and sensitivity of SSC to soil reflectance, which implied the feasibility of high spectrum test on soil microbial remediation monitoring, also provided the basis for quick nondestructive monitoring soil bioremediation process by soil spectral reflectance.

Methane production potential and microbial community structure for different forest soils

NASA Astrophysics Data System (ADS)

Matsumoto, Y.; Ueyama, M.; Kominami, Y.; Endo, R.; Tokumoto, H.; Hirano, T.; Takagi, K.; Takahashi, Y.; Iwata, H.; Harazono, Y.

2017-12-01

Forest soils are often considered as a methane (CH4) sink, but anaerobic microsites potentially decrease the sink at the ecosystem scale. In this study, we measured biological CH4 production potential of soils at various ecosystems, including upland forests, a lowland forest, and a bog, and analyzed microbial community structure using 16S ribosomal RNA (rRNA) genes. Three different types of soil samples (upland, bank of the stream, and center of the stream) were collected from Yamashiro forest meteorology research site (YMS) at Kyoto, Japan, on 11 May 2017. The soils were incubated at dark and anaerobic conditions under three different temperatures (37°C, 25°C, and 10°C) from 9 June 2017. The upland soils emitted CH4 with largest yields among the three soils at 37°C and 25°C, although no CH4 emission was observed at 10°C. For all temperature ranges, the emission started to increase with a 14- to 20-days lag after the start of the incubation. The lag indicates a slow transition to anaerobic conditions; as dissolved oxygen in water decreased, the number and/or activity of anaerobic bacteria like methanogens increased. The soils at the bank and center of the stream emitted CH4 with smaller yields than the upland soils in the three temperature ranges. The microbial community analyses indicate that methanogenic archaea presented at the three soils including the aerobic upland soil, but compositions of methanogenic archaea were different among the soils. In upland soils, hydrogenotrophic methanogens, such as Methanobacterium and Methanothermobacter, consisted almost all of the total methanogen detected. In the bank and center of the stream, soils contained approximately 10-25% of acetoclastic methanogens, such as Methanosarcina and Methanosaeta, among the total methanogen detected. Methanotrophs, a genus of Methanobacteriaceae, was appeared in the all types of soils. We will present results from same incubation and 16S rRNA analyses for other ecosystems, including a larch forest on volcanic soils, a young larch forest on Gleyic Cambisol, and a boreal bog and a lowland forest on permafrost. Comparing various soils from temperate and boreal ecosystems, we will discuss differences of biogenic CH4 production potential among the soils with the microbial community analyses.

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China

NASA Astrophysics Data System (ADS)

Zhang, Chuang; Zhang, Xin-Yu; Zou, Hong-Tao; Kou, Liang; Yang, Yang; Wen, Xue-Fa; Li, Sheng-Gong; Wang, Hui-Min; Sun, Xiao-Min

2017-10-01

The nitrate to ammonium ratios in nitrogen (N) compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH4Cl) and nitrate (NaNO3) at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH4Cl) and nitrate (NaNO3) applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs) decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G+) and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF) PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP) than ammonium. The activities of N-acquisition specific enzymes (enzyme activities normalized by total PLFA contents) were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA), we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO) activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate contents. The PLFA biomarker contents were positively correlated with soil pH, soil organic carbon (SOC), and total N contents, but were negatively correlated with the ammonium contents. The soil enzyme activities varied seasonally, and were highest in March and lowest in October. In contrast, the contents of the microbial PLFA biomarkers were higher in October than in March and June. Ammonium may inhibit the contents of PLFA biomarkers more strongly than nitrate because of acidification. This study has provided useful information about the effects of ammonium and nitrate on soil microbial communities and enzyme activities.

Microbial degradation of total petroleum hydrocarbons in crude oil: a field-scale study at the low-land rainforest of Ecuador.

PubMed

Maddela, Naga Raju; Scalvenzi, Laura; Venkateswarlu, Kadiyala

2017-10-01

A field-level feasibility study was conducted to determine total petroleum hydrocarbon (TPH)-degrading potential of two bacterial strains, Bacillus thuringiensis B3 and B. cereus B6, and two fungi, Geomyces pannorum HR and Geomyces sp. strain HV, all soil isolates obtained from an oil field located in north-east region of Ecuador. Crude oil-treated soil samples contained in wooden boxes received a mixture of all the four microorganisms and were incubated for 90 days in an open low-land area of Amazon rainforest. The percent removal of TPHs in soil samples that received the mixed microbial inoculum was 87.45, indicating the great potential of the soil isolates in field-scale removal of crude oil. The TPHs-degrading efficiency was verified by determining the toxicity of residues, remained in soil after biodegradation, toward viability of Artemia salina or seed germination and plant growth of cowpea. Our results clearly suggest that the selected soil isolates of bacteria and fungi could be effectively used for large-scale bioremediation of sites contaminated with crude oil.

Soil microbial response to waste potassium silicate drilling fluid.

PubMed

Yao, Linjun; Naeth, M Anne; Jobson, Allen

2015-03-01

Potassium silicate drilling fluids (PSDF) are a waste product of the oil and gas industry with potential for use in land reclamation. Few studies have examined the influence of PSDF on abundance and composition of soil bacteria and fungi. Soils from three representative locations for PSDF application in Alberta, Canada, with clay loam, loam and sand textures were studied with applications of unused, used once and used twice PSDF. For all three soils, applying ≥40 m3/ha of used PSDF significantly affected the existing soil microbial flora. No microbiota was detected in unused PSDF without soil. Adding used PSDF to soil significantly increased total fungal and aerobic bacterial colony forming units in dilution plate counts, and anaerobic denitrifying bacteria numbers in serial growth experiments. Used PSDF altered bacterial and fungal colony forming unit ratios of all three soils. Copyright © 2015. Published by Elsevier B.V.

Endophytic fungus Phomopsis liquidambari and different doses of N-fertilizer alter microbial community structure and function in rhizosphere of rice

PubMed Central

Siddikee, Md. Ashaduzzaman; Zereen, Mst Israt; Li, Cai-Feng; Dai, Chuan-Chao

2016-01-01

Microbial community structure and functions of rhizosphere soil of rice were investigated after applying low and high doses of nitrogenous fertilizer and Phomopsis liquidambari. Average well color development, substrate richness, catabolic diversity and soil enzymes activities varied after applying N-fertilizer and P. liquidambari and were greater in P. liquidambari treated soil than only N-fertilization. Multivariate analysis distinctly separated the catabolic and enzymes activity profile which statistically proved alteration of microbial functional diversity. Nitrogen fertilizer altered microbial community structure revealed by the increased content of total PLFAs, specific subgroup marker PLFAs except fungal PLFAs and by the decreased ratio of G+/G−, sat/monunsat, iso/anteiso, F/B except trans/cis while P. liquidambari inoculation enhanced N-fertilization effect except increased fungal PLFA and decreased trans/cis. PCA using identified marker PLFAs revealed definite discrimination among the treatments which further statistically confirmed structural changed of microbial community. Nitrogenase activity representative of N-fixing community decreased in N-fertilizer treatment while P. liquidambari inoculation increased. In short, application of P. liquidambari with low doses of N-fertilizer improved rice growth and reduced N-fertilizer requirement by increasing enzymes activities involved in C, N and P cycling, structural and functional diversity of microbes, nitrogenase activity involved in N2 fixation and accumulation of total-N. PMID:27596935

Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

PubMed

Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

2012-07-01

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.

Response of the soil microbial community to imazethapyr application in a soybean field.

PubMed

Xu, Jun; Guo, Liqun; Dong, Fengshou; Liu, Xingang; Wu, Xiaohu; Sheng, Yu; Zhang, Ying; Zheng, Yongquan

2013-01-01

The objective of this study was to determine the effects of imazethapyr on soil microbial communities combined with its effect on soybean growth. A short-term field experiment was conducted, and imazethapyr was applied to the soil at three different doses [1-fold, 10-fold, and 50-fold of the recommended field rate (H1, H10, H50)] during the soybean seedling period (with two leaves). Soil sampling was performed after 1, 7, 30, 60, 90, and 120 days of application to determine the imazethapyr concentration and microbial community structure by investigating phospholipid fatty acids (PLFA) and microbial biomass carbon (MBC). The half-lives of the imazethapyr in the field soil varied from 30.1 to 43.3 days. Imazethapyr at H1 was innocuous to soybean plants, but imazethapyr at H10 and H50 led to a significant inhibition in soybean plant height and leaf number. The soil MBC, total PLFA, and bacterial PLFA were decreased by the application of imazethapyr during the initial period and could recover by the end of the experiment. The ratio of Gram-negative/Gram-positive (GN/GP) bacteria during the three treatments went through increases and decreases, and then recovered at the end of the experiment. The fungal PLFA of all three treatments increased during the initial period and then declined, and only the fungal PLFA at H50 recovered by the end of the treatment. A principal component analysis (PCA) of the PLFA clearly separated the treatments and sampling times, and the results demonstrate that imazethapyr alters the microbial community structure. This is the first systemic study reporting the effects of imazethapyr on the soil microbial community structure under soybean field conditions.

Microbial composition and diversity are associated with plant performance: a case study on long-term fertilization effect on wheat growth in an Ultisol.

PubMed

Li, Lihua; Fan, Fenliang; Song, Alin; Yin, Chang; Cui, Peiyuan; Li, Zhaojun; Liang, Yongchao

2017-06-01

The association between microbial communities and plant growth in long-term fertilization system has not been fully studied. In the present study, impacts of long-term fertilization have been determined on the size and activity of soil microbial communities and wheat performance in a red soil (Ultisol) collected from Qiyang Experimental Station, China. For this, different microbial communities originating from long-term fertilized pig manure (M), mineral fertilizer (NPK), pig manure plus mineral fertilizer (MNPK), and no fertilizer (CK) were used as inocula for the Ultisol tested. Changes in total bacterial and fungal community composition and structures using Ion Torrent sequencing were determined. The results show that the biomass of wheat was significantly higher in both sterilized soil inoculated with NPK (SNPK) and sterilized soil inoculated with MNPK (SMNPK) treatments than in other treatments (P < 0.05). The activities of β-1,4-N-acetylglucosaminidase (NAG) and cellobiohydrolase (CBH) were significantly correlated with wheat biomass. Among the microbial communities, the largest Ascomycota phylum in soils was negatively correlated with β-1,4-glucosidase (βG) (P < 0.05). The phylum Basidiomycota was negatively correlated with plant biomass (PB) and tillers per plant (TI) (P < 0.05). Nonmetric multidimensional scaling analysis shows that fungal community was strongly correlated with long-term fertilization strategy, while the bacterial community was strongly correlated with β-1,4-N-acetylglucosaminidase activity. According to the Mantel test, the growth of wheat was affected by fungal community. Taken together, microbial composition and diversity in soils could be a good player in predicting soil fertility and consequently plant growth.

Bioremediation assessment of diesel-biodiesel-contaminated soil using an alternative bioaugmentation strategy.

PubMed

Colla, Tatiana Simonetto; Andreazza, Robson; Bücker, Francielle; de Souza, Marcela Moreira; Tramontini, Letícia; Prado, Gerônimo Rodrigues; Frazzon, Ana Paula Guedes; Camargo, Flávio Anastácio de Oliveira; Bento, Fátima Menezes

2014-02-01

This study investigated the effectiveness of successive bioaugmentation, conventional bioaugmentation, and biostimulation of biodegradation of B10 in soil. In addition, the structure of the soil microbial community was assessed by polymerase chain reaction-denaturing gradient gel electrophoresis. The consortium was inoculated on the initial and the 11th day of incubation for successive bioaugmentation and only on the initial day for bioaugmentation and conventional bioaugmentation. The experiment was conducted for 32 days. The microbial consortium was identified based on sequencing of 16S rRNA gene and consisted as Pseudomonas aeruginosa, Achromobacter xylosoxidans, and Ochrobactrum intermedium. Nutrient introduction (biostimulation) promoted a positive effect on microbial populations. The results indicate that the edaphic community structure and dynamics were different according to the treatments employed. CO2 evolution demonstrated no significant difference in soil microbial activity between biostimulation and bioaugmentation treatments. The total petroleum hydrocarbon (TPH) analysis indicated a biodegradation level of 35.7 and 32.2 % for the biostimulation and successive bioaugmentation treatments, respectively. Successive bioaugmentation displayed positive effects on biodegradation, with a substantial reduction in TPH levels.

[Ozone effects on soil microbial community of rice investigated by 13C isotope labeling].

PubMed

Chen, Zhan; Wang, Xiao-Ke; Shang, He

2014-10-01

This study was initiated to explore the effects of dynamic ozone (O3) exposure on soil microbial biomass and phospholipid fatty acids (PLFAs) under potted rice. A pulse-chase labeling experiment was designed to expose potted rice with 13CO2 for 6 h after one and two months, the rice were fumigated by elevated O3 concentration with an 8 h mean of 110 nL · L(-1) (O3). The allocation of the assimilated 13C to soil microorganisms was estimated by analyzing the 13C profile of microbial phospholipid fatty acids (PLFAs). After one month O3 exposure, the soil microbial biomass carbon was not affected, while the 13C-microbial biomass was significantly decreased with elevated O3. Both the total and 13C microbial biomass carbon was remarkably lower than that of control treatment after two months O3 exposure. Principal components analysis of 13C-PLFA data showed that elevated O3 significantly changed soil microbial structure after two month exposures, while there was no difference of 13C-PLFA structure between control and elevated O3 treatments after one month exposure. Δδ13C per hundred thousand of individual PLFA was significantly affected by O3 after both one and two month exposures. Only did ozone change the relative abundance of individual 13C-PLFA (13C%) of bacterial fatty acids after one month exposure, while after two month exposures, the 13C% of fungal and actinomycetic fatty acids were markedly changed by elevated O3.

Effects of Grazing and Fire Frequency on Floristic Quality and its Relationship to Indicators of Soil Quality in Tallgrass Prairie

NASA Astrophysics Data System (ADS)

Manning, George C.; Baer, Sara G.; Blair, John M.

2017-12-01

Fire and grazing are widely used to manage grasslands for conservation purposes, but few studies have evaluated the effects of these drivers on the conservation value of plant communities measured by the floristic quality index (FQI). Further, the influence of fire and grazing on soil properties and functions are difficult for land managers and restoration practitioners to assess. The objectives of this study were to: (1) quantify the independent and interactive effects of grazing and fire frequency on floristic quality in native tallgrass prairie to provide potential benchmarks for community assessment, and (2) to explore whether floristic quality can serve as an indicator of soil structure and function for more holistic ecosystem assessments. A factorial combination of fire frequencies (1-2, 4, and 20 years return intervals) and grazing (by bison or ungrazed) treatments were sampled for plant species composition, and for several indicators of soil quality in lowland tallgrass prairie. Floristic quality, diversity, and richness were higher in grazed than ungrazed prairie over all fire frequencies ( P < 0.05). Available inorganic N, microbial biomass N, total N, and soil bulk density were also higher in grazed prairie soil over all fire frequencies ( P < 0.05). Microbial biomass C, total organic C, and total soil N were positively correlated with FQI ( P < 0.05). This study shows that floristic quality and soil N pools are more strongly influenced by grazing than fire and that floristic quality can be an indicator of total soil C and N stocks in never cultivated lowland prairie.

Effects of Grazing and Fire Frequency on Floristic Quality and its Relationship to Indicators of Soil Quality in Tallgrass Prairie.

PubMed

Manning, George C; Baer, Sara G; Blair, John M

2017-12-01

Fire and grazing are widely used to manage grasslands for conservation purposes, but few studies have evaluated the effects of these drivers on the conservation value of plant communities measured by the floristic quality index (FQI). Further, the influence of fire and grazing on soil properties and functions are difficult for land managers and restoration practitioners to assess. The objectives of this study were to: (1) quantify the independent and interactive effects of grazing and fire frequency on floristic quality in native tallgrass prairie to provide potential benchmarks for community assessment, and (2) to explore whether floristic quality can serve as an indicator of soil structure and function for more holistic ecosystem assessments. A factorial combination of fire frequencies (1-2, 4, and 20 years return intervals) and grazing (by bison or ungrazed) treatments were sampled for plant species composition, and for several indicators of soil quality in lowland tallgrass prairie. Floristic quality, diversity, and richness were higher in grazed than ungrazed prairie over all fire frequencies (P < 0.05). Available inorganic N, microbial biomass N, total N, and soil bulk density were also higher in grazed prairie soil over all fire frequencies (P < 0.05). Microbial biomass C, total organic C, and total soil N were positively correlated with FQI (P < 0.05). This study shows that floristic quality and soil N pools are more strongly influenced by grazing than fire and that floristic quality can be an indicator of total soil C and N stocks in never cultivated lowland prairie.

Passive warming effect on soil microbial community and humic substance degradation in maritime Antarctic region.

PubMed

Kim, Dockyu; Park, Ha Ju; Kim, Jung Ho; Youn, Ui Joung; Yang, Yung Hun; Casanova-Katny, Angélica; Vargas, Cristina Muñoz; Venegas, Erick Zagal; Park, Hyun; Hong, Soon Gyu

2018-06-01

Although the maritime Antarctic has undergone rapid warming, the effects on indigenous soil-inhabiting microorganisms are not well known. Passive warming experiments using open-top chamber (OTC) have been performed on the Fildes Peninsula in the maritime Antarctic since 2008. When the soil temperature was measured at a depth of 2-5 cm during the 2013-2015 summer seasons, the mean temperature inside OTC (OTC-In) increased by approximately 0.8 °C compared with outside OTC (OTC-Out), while soil chemical and physical characteristics did not change. Soils (2015 summer) from OTC-In and OTC-Out were subjected to analysis for change in microbial community and degradation rate of humic substances (HS, the largest pool of recalcitrant organic carbon in soil). Archaeal and bacterial communities in OTC-In were minimally affected by warming compared with those in OTC-Out, with archaeal methanogenic Thermoplasmata slightly increased in abundance. The abundance of heterotrophic fungi Ascomycota was significantly altered in OTC-In. Total bacterial and fungal biomass in OTC-In increased by 20% compared to OTC-Out, indicating that this may be due to increased microbial degradation activity for soil organic matter (SOM) including HS, which would result in the release of more low-molecular-weight growth substrates from SOM. Despite the effects of warming on the microbial community over the 8-years-experiments warming did not induce any detectable change in content or structure of polymeric HS. These results suggest that increased temperature may have significant and direct effects on soil microbial communities inhabiting maritime Antarctic and that soil microbes would subsequently provide more available carbon sources for other indigenous microbes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Soil Microbial Response to a Massive Natural Gas Leak

NASA Astrophysics Data System (ADS)

Tavormina, P. L.; Newman, S.; Shen, L.; Connon, S. A.; Okumura, M.; Orphan, V. J.

2016-12-01

The 2015/2016 gas leak in the Porter Ranch community (Southern California) was the largest natural gas leak in US history. While considerable attention has focused on the amount of methane released to the atmosphere and the effects of other gas components on human well-being, less attention has been given to the response of soil microbes to this event. These microbes represent natural pathways for utilization of C1 compounds in soils and, possibly, untapped potential to remediate natural and anthropogenic gas emissions. We monitored onsite and background soil methane concentrations and microbial communities during and following the Porter Ranch gas leak. Soil core samples (25cm depth, collected twice monthly beginning in January 2016) were preserved for DNA, RNA, microscopic, stable isotope probing, and chromatographic methods. Simultaneously to coring, gas from soil pore spaces was collected for cavity ringdown spectroscopy to measure carbon dioxide, methane and ethane concentrations, and estimate corresponding isotopic values in carbon dioxide and methane. By pairing these measurements with high throughput sequencing, transcript analysis, and cultivation, we demonstrate discrete shifts in the total microbial community in surface (0 - 5 cm) and deep (20 - 25 cm) soils. Importantly, we find that methane consumption likely occurred in surface soils during and following the leak. The lineages most significantly correlated with elevated methane from the leak event were five orders of magnitude more abundant near the leak event in space and time, indicating a microbial bloom. These lineages are previously unrecognized members of Sphingomonadaceae, and they encode at least two biochemical pathways for methane oxidation. Cultivation of the first representative of this group now allows more detailed investigation into its capacity for microbially-mediated soil methane oxidation and mitigation.

[Effects of long-term fertilization on microbial biomass carbon and nitrogen and on carbon source utilization of microbes in a red soil].

PubMed

Sun, Feng-xia; Zhang, Wei-hua; Xu, Ming-gang; Zhang, Wen-ju; Li, Zhao-qiang; Zhang, Jing-ye

2010-11-01

In order to explore the effects of long-term fertilization on the microbiological characters of red soil, soil samples were collected from a 19-year long-term experimental field in Qiyang of Hunan, with their microbial biomass carbon (MBC) and nitrogen (MBN) and microbial utilization ratio of carbon sources analyzed. The results showed that after 19-year fertilization, the soil MBC and MBN under the application of organic manure and of organic manure plus inorganic fertilizers were 231 and 81 mg x kg(-1) soil, and 148 and 73 mg x kg(-1) soil, respectively, being significantly higher than those under non-fertilization, inorganic fertilization, and inorganic fertilization plus straw incorporation. The ratio of soil MBN to total N under the application of organic manure and of organic manure plus inorganic fertilizers was averagely 6.0%, significantly higher than that under non-fertilization and inorganic fertilization. Biolog-ECO analysis showed that the average well color development (AWCD) value was in the order of applying organic manure plus inorganic fertilizers = applying organic manure > non-fertilization > inorganic fertilization = inorganic fertilization plus straw incorporation. Under the application of organic manure or of organic manure plus inorganic fertilizers, the microbial utilization rate of carbon sources, including carbohydrates, carboxylic acids, amino acids, polymers, phenols, and amines increased; while under inorganic fertilization plus straw incorporation, the utilization rate of polymers was the highest, and that of carbohydrates was the lowest. Our results suggested that long-term application of organic manure could increase the red soil MBC, MBN, and microbial utilization rate of carbon sources, improve soil fertility, and maintain a better crop productivity.

Comparative Toxicities of Salts on Microbial Processes in Soil

PubMed Central

Maheshwari, Arpita; Bengtson, Per; Rousk, Johannes

2016-01-01

Soil salinization is a growing threat to global agriculture and carbon sequestration, but to date it remains unclear how microbial processes will respond. We studied the acute response to salt exposure of a range of anabolic and catabolic microbial processes, including bacterial (leucine incorporation) and fungal (acetate incorporation into ergosterol) growth rates, respiration, and gross N mineralization and nitrification rates. To distinguish effects of specific ions from those of overall ionic strength, we compared the addition of four salts frequently associated with soil salinization (NaCl, KCl, Na2SO4, and K2SO4) to a nonsaline soil. To compare the tolerance of different microbial processes to salt and to interrelate the toxicity of different salts, concentration-response relationships were established. Growth-based measurements revealed that fungi were more resistant to salt exposure than bacteria. Effects by salt on C and N mineralization were indistinguishable, and in contrast to previous studies, nitrification was not found to be more sensitive to salt exposure than other microbial processes. The ion-specific toxicity of certain salts could be observed only for respiration, which was less inhibited by salts containing SO42− than Cl− salts, in contrast to the microbial growth assessments. This suggested that the inhibition of microbial growth was explained solely by total ionic strength, while ion-specific toxicity also should be considered for effects on microbial decomposition. This difference resulted in an apparent reduction of microbial growth efficiency in response to exposure to SO42− salts but not to Cl− salts; no evidence was found to distinguish K+ and Na+ salts. PMID:26801570

Role of soil sorption and microbial degradation on dissipation of mesotrione in plant-available soil water.

PubMed

Shaner, Dale; Brunk, Galen; Nissen, Scott; Westra, Phil; Chen, Wenlin

2012-01-01

Mesotrione is a carotenoid biosynthesis-inhibiting herbicide labeled for pre-emergence and postemergence weed control in corn production. Understanding the factors that influence the dissipation of mesotrione in soil and in the plant-available water (PAW) is important for the environmental fate assessment and optimal weed management practices. The present research investigated the role of soil properties and microbial activities on the interrelated sorption and degradation processes of mesotrione in four soils by direct measurements of PAW. We found that mesotrione bound to the soils time dependently, with approximately 14 d to reach equilibrium. The 24-h batch-slurry equilibrium experiments provided the sorption partition coefficient ranging from 0.26 to 3.53 L kg(-1), depending on soil organic carbon and pH. The dissipation of mesotrione in the soil-bound phase was primarily attributed to desorption to the PAW. Degradation in the PAW was rapid and primarily dependent on microbial actions, with half-degradation time (DT(50)) <3 d in all four soils tested. The rapid degradation in the PAW became rate limited by sorption as more available molecules were depleted in the soil pore water, resulting in a more slowed overall process for the total soil-water system (DT(50) <26 d). The dissipation of mesotrione in the PAW was due to microbial metabolism and time-dependent sorption to the soils. A coupled kinetics model calibrated with the data from the laboratory centrifugation technique provided an effective approach to investigate the interrelated processes of sorption and degradation in realistic soil moisture conditions. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO).

PubMed

Touceda-González, M; Prieto-Fernández, Á; Renella, G; Giagnoni, L; Sessitsch, A; Brader, G; Kumpiene, J; Dimitriou, I; Eriksson, J; Friesl-Hanl, W; Galazka, R; Janssen, J; Mench, M; Müller, I; Neu, S; Puschenreiter, M; Siebielec, G; Vangronsveld, J; Kidd, P S

2017-12-01

Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg -1 soil, respiration increased from 7.4 to 40.1 mg C-CO 2 kg -1 soil d -1 , and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term. Copyright © 2017 Elsevier Ltd. All rights reserved.

Impact of Long-Term Forest Enrichment Planting on the Biological Status of Soil in a Deforested Dipterocarp Forest in Perak, Malaysia

PubMed Central

Karam, D. S.; Arifin, A.; Radziah, O.; Shamshuddin, J.; Majid, N. M.; Hazandy, A. H.; Zahari, I.; Nor Halizah, A. H.; Rui, T. X.

2012-01-01

Deforestation leads to the deterioration of soil fertility which occurs rapidly under tropical climates. Forest rehabilitation is one of the approaches to restore soil fertility and increase the productivity of degraded areas. The objective of this study was to evaluate and compare soil biological properties under enrichment planting and secondary forests at Tapah Hill Forest Reserve, Perak after 42 years of planting. Both areas were excessively logged in the 1950s and left idle without any appropriate forest management until 1968 when rehabilitation program was initiated. Six subplots (20 m × 20 m) were established within each enrichment planting (F1) and secondary forest (F2) plots, after which soil was sampled at depths of 0–15 cm (topsoil) and 15–30 cm (subsoil). Results showed that total mean microbial enzymatic activity, as well as biomass C and N content, was significantly higher in F1 compared to F2. The results, despite sample variability, suggest that the rehabilitation program improves the soil biological activities where high rate of soil organic matter, organic C, N, suitable soil acidity range, and abundance of forest litter is believed to be the predisposing factor promoting higher population of microbial in F1 as compared to F2. In conclusion total microbial enzymatic activity, biomass C and biomass N evaluation were higher in enrichment planting plot compared to secondary forest. After 42 years of planting, rehabilitation or enrichment planting helps to restore the productivity of planted forest in terms of biological parameters. PMID:22606055

Microbial Repopulation Following In Situ STAR Remediation

NASA Astrophysics Data System (ADS)

Gerhard, J.; Overbeeke, G.; Edwards, E.; Lomheim, L.; Grant, G.

2016-12-01

STAR (Self-sustaining Treatment for Active Remediation) is an emerging remediation technology that employs a self-sustaining smouldering reaction to destroy nonaqueous phase liquids (NAPLs) in the subsurface. The reaction front travels outwards from an ignition well at approximately 0.5 per day and subjects the soil to temperatures of 400°C-1000°C. The objectives of this work were to monitor re-saturation of the soil over time and quantify the microbial repopulation of the treated zone. STAR is currently being applied as a full scale, in situ remedy for coal tar beneath a former creosol manufacturing facility in New Jersey, USA. This study analyzed soil cores taken at regular intervals following STAR treatment, allowing time for groundwater to re-infiltrate and for microbial populations to potentially reestablish. Soil and groundwater were analyzed for total number of microorganisms via quantitative Polymerase Chain Reaction (qPCR), as well as microbial diversity via amplicon sequencing. Results demonstrate that microbes rapidly repopulated over a 2 month period to 106 gene copies/g of soil. However, concentrations in the treated zone did not rise above this concentration over 6 months post-STAR, indicating a low carrying capacity of the treated soil. To examine the system in more detail and consider the effects of bio-stimulation, a bench top column study using site soil and artificial groundwater explored the rate at which STAR-treated soil is repopulated with naturally occurring microorganisms in the presence and absence of lactate and a terminal electron acceptor. Results demonstrated that biostimulation did not increase the carrying capacity of the STAR treated sol, but rather shifted the microbial community to reflect the TEA provided, in this case, promoting sulfate reducers. Overall, the work illustrates that microbial populations in STAR treated soil do recover via groundwater infiltration but robust communities will take time to naturally establish.

Effects of Different Organic Manures on the Biochemical and Microbial Characteristics of Albic Paddy Soil in a Short-Term Experiment

PubMed Central

Zhang, Qian; Zhou, Wei; Liang, Guoqing; Wang, Xiubin; Sun, Jingwen; He, Ping; Li, Lujiu

2015-01-01

This study aimed to evaluate the effects of chemical fertilizer (NPK), NPK with livestock manure (NPK+M), NPK with straw (NPK+S), and NPK with green manure (NPK+G) on soil enzyme activities and microbial characteristics of albic paddy soil, which is a typical soil with low productivity in China. The responses of extracellular enzyme activities and the microbial community diversity (determined by phospholipid fatty acid analysis [PLFA] and denaturing gradient gel electrophoresis [DGGE]) were measured. The results showed that NPK+M and NPK+S significantly increased rice yield, with NPK+M being approximately 24% greater than NPK. The NPK+M significantly increased soil organic carbon (SOC) and available phosphate (P) and enhanced phosphatase, β-cellobiosidase, L-leucine aminopeptidase and urease activities. The NPK+S significantly increased SOC and available potassium (K) and significantly enhanced N-acetyl-glucosamidase, β-xylosidase, urease, and phenol oxidase activities. The NPK+G significantly improved total nitrogen (N), ammonium N, available P, and N-acetyl-glucosamidase activity. The PLFA biomass was highest under NPK+S, followed by NPK+M and NPK+G treatments. Principal component analysis (PCA) of the PLFA indicated that soils with NPK+M and NPK+S contained higher proportions of unsaturated and cyclopropane fatty acids (biomarkers of fungi and gram-negative bacteria) and soil under NPK+G contained more straight chain saturated fatty acids (representing gram-positive bacteria). PCA of the DGGE patterns showed that organic amendments had a greater influence on fungal community. Cluster analysis of fungal DGGE patterns revealed that NPK+G was clearly separated. Meanwhile, the bacterial community of NPK+M treatment was the most distinct. RDA analysis revealed changes of microbial community composition mostly depended on β-xylosidase, β-cellobiosidase activities, total N and available K contents. The abundances of gram-negative bacterial and fungal PLFAs probably effective in improving fertility of low-yield albic paddy soil because of their significant influence on DGGE profile. PMID:25879759

Effects of different organic manures on the biochemical and microbial characteristics of albic paddy soil in a short-term experiment.

PubMed

Zhang, Qian; Zhou, Wei; Liang, Guoqing; Wang, Xiubin; Sun, Jingwen; He, Ping; Li, Lujiu

2015-01-01

This study aimed to evaluate the effects of chemical fertilizer (NPK), NPK with livestock manure (NPK+M), NPK with straw (NPK+S), and NPK with green manure (NPK+G) on soil enzyme activities and microbial characteristics of albic paddy soil, which is a typical soil with low productivity in China. The responses of extracellular enzyme activities and the microbial community diversity (determined by phospholipid fatty acid analysis [PLFA] and denaturing gradient gel electrophoresis [DGGE]) were measured. The results showed that NPK+M and NPK+S significantly increased rice yield, with NPK+M being approximately 24% greater than NPK. The NPK+M significantly increased soil organic carbon (SOC) and available phosphate (P) and enhanced phosphatase, β-cellobiosidase, L-leucine aminopeptidase and urease activities. The NPK+S significantly increased SOC and available potassium (K) and significantly enhanced N-acetyl-glucosamidase, β-xylosidase, urease, and phenol oxidase activities. The NPK+G significantly improved total nitrogen (N), ammonium N, available P, and N-acetyl-glucosamidase activity. The PLFA biomass was highest under NPK+S, followed by NPK+M and NPK+G treatments. Principal component analysis (PCA) of the PLFA indicated that soils with NPK+M and NPK+S contained higher proportions of unsaturated and cyclopropane fatty acids (biomarkers of fungi and gram-negative bacteria) and soil under NPK+G contained more straight chain saturated fatty acids (representing gram-positive bacteria). PCA of the DGGE patterns showed that organic amendments had a greater influence on fungal community. Cluster analysis of fungal DGGE patterns revealed that NPK+G was clearly separated. Meanwhile, the bacterial community of NPK+M treatment was the most distinct. RDA analysis revealed changes of microbial community composition mostly depended on β-xylosidase, β-cellobiosidase activities, total N and available K contents. The abundances of gram-negative bacterial and fungal PLFAs probably effective in improving fertility of low-yield albic paddy soil because of their significant influence on DGGE profile.

Microbial activity in Alaskan taiga soils contaminated by crude oil in 1976

DOE Office of Scientific and Technical Information (OSTI.GOV)

Monroe, E.M.; Lindstrom, J.E.; Brown, E.J.

1995-12-31

Biodegradation, often measured via microbial activity, includes destruction of environmental pollutants by living microorganisms and is dependent upon many physical and chemical factors. Effects of mineral nutrients and organic matter on biodegradation of Prudhoe Bay crude oil were investigated at a nineteen-year-old oil spill site in Alaskan taiga. Microcosms of two different soil types from the spill site; one undeveloped soil with forest litter and detritus (O horizon) and one more developed with lower organic content (A horizon), were treated with various nitrogen and phosphorus amendments, and incubated for up to six weeks. Each microcosm was sampled periodically and assayedmore » for hydrocarbon mineralization potential using radiorespirometry, for total carbon dioxide respired using gas chromatography, and for numbers of hydrocarbon-degrading bacteria and heterotrophic bacteria using most probable number counting techniques. Organic matter in the O horizon soil along with combinations of mineral nutrients were found to stimulate microbial activity. No combination of mineral nutrient additions to the A horizon soil stimulated any of the parameters above those measured in control microcosms. The results of this study indicate that adding mineral nutrients and tilling the O horizon into the A horizon of subarctic soils contaminated with crude oil, would stimulate microbial activity, and therefore the biodegradation potential, ultimately increasing the rate of destruction of crude oil in these soils.« less

Effect of a residue after evaporation from industrial vitamin C fermentation on chemical and microbial properties of alkali-saline soil.

PubMed

Kong, Tao; Xu, Hui; Wang, Zhenyu; Sun, Hao; Wang, Lihua

2014-07-01

Residue after evaporation (RAE) from industrial vitamin C fermentation is emitted as a waste product at an amount of 60,000 tons per year in China. The disposal of RAE is difficult because of its high chemical oxygen demand (1.17×10(6) mg/l) and low pH (0.27). We hypothesized that RAE could be used as an ameliorant for alkali-saline soils, and tried to verify it by carrying out a pot experiment of pakchoi cultivation and to explore its effect on soil chemical and microbial properties. The results showed that pakchoi yield was increased by 28.13% and pakchoi quality was also enhanced under RAE treatment. The improved chemical and microbial properties of treated soil were also observed: soil pH was decreased from 9.19 to 9.03; total organic carbon, available phosphorus and available potassium were increased by 49.15%, 34.91% and 42.02%, respectively; number of culturable bacteria, actinomycetes and fungi, microbial biomass carbon and enzyme activity number were improved by 52.97%, 104.05%, 79.09%, 57.82% and 31.16%, respectively. These results suggested the residue application led to an improved soil quality and subsequently a higher yield and quality of pakchoi. This study provided a strong evidence for the feasibility of RAE as an ameliorant for alkali-saline soil.

Genetic Linkage of Soil Carbon Pools and Microbial Functions in Subtropical Freshwater Wetlands in Response to Experimental Warming

PubMed Central

Wang, Hang; He, Zhili; Lu, Zhenmei; Zhou, Jizhong; Van Nostrand, Joy D.; Xu, Xinhua

2012-01-01

Rising climate temperatures in the future are predicted to accelerate the microbial decomposition of soil organic matter. A field microcosm experiment was carried out to examine the impact of soil warming in freshwater wetlands on different organic carbon (C) pools and associated microbial functional responses. GeoChip 4.0, a functional gene microarray, was used to determine microbial gene diversity and functional potential for C degradation. Experimental warming significantly increased soil pore water dissolved organic C and phosphorus (P) concentrations, leading to a higher potential for C emission and P export. Such losses of total organic C stored in soil could be traced back to the decomposition of recalcitrant organic C. Warming preferentially stimulated genes for degrading recalcitrant C over labile C. This was especially true for genes encoding cellobiase and mnp for cellulose and lignin degradation, respectively. We confirmed this with warming-enhanced polyphenol oxidase and peroxidase activities for recalcitrant C acquisition and greater increases in recalcitrant C use efficiency than in labile C use efficiency (average percentage increases of 48% versus 28%, respectively). The relative abundance of lignin-degrading genes increased by 15% under warming; meanwhile, soil fungi, as the primary decomposers of lignin, were greater in abundance by 27%. This work suggests that future warming may enhance the potential for accelerated fungal decomposition of lignin-like compounds, leading to greater microbially mediated C losses than previously estimated in freshwater wetlands. PMID:22923398

Enhancement and inhibition of microbial activity in hydrocarbon- contaminated arctic soils: Implications for nutrient-amended bioremediation

USGS Publications Warehouse

Braddock, J.F.; Ruth, M.L.; Catterall, P.H.; Walworth, J.L.; McCarthy, K.A.

1997-01-01

Bioremediation is being used or proposed as a treatment option at many hydrocarbon-contaminated sites. One such site is a former bulk-fuel storage facility near Barrow, AK, where contamination persists after approximately 380 m3 of JP-5 was spilled in 1970. The soil at the site is primarily coarse sand with low organic carbon (<1%) end low moisture (1-3%) contents. We examined the effects of nutrient additions on microorganisms in contaminated soil from this site in laboratory microcosms and in mesocosms incubated for 6 weeks in the field. Nitrogen was the major limiting nutrient in this system, but microbial populations and activity were maximally enhanced by additions of both nitrogen and phosphorus. When nutrients were added to soil in the field at three levels of N:P (100:45, 200:90, and 300:135 mg/kg soil), the greatest stimulation in microbial activity occurred at the lowest, rather than the highest, level of nutrient addition. The total soil-water potentials ranged from -2 to -15 bar with increasing levels of fertilizer. Semivolatile hydrocarbon concentrations declined significantly only in the soils treated at the low fertilizer level. These results indicate that an understanding of nutrient effects at a specific site is essential for successful bioremediation.Bioremediation is being used or proposed as a treatment option at many hydrocarbon-contaminated sites. One such site is a former bulk-fuel storage facility near Barrow, AK, where contamination persists after approximately 380 m3 of JP-5 was spilled in 1970. The soil at the site is primarily coarse sand with low organic carbon (<1%) and low moisture (1-3%) contents. We examined the effects of nutrient additions on microorganisms in contaminated soil from this site in laboratory microcosms and in mesocosms incubated for 6 weeks in the field. Nitrogen was the major limiting nutrient in this system, but microbial populations and activity were maximally enhanced by additions of both nitrogen and phosphorus. When nutrients were added to soil in the field at three levels of N:P (100:45, 200:90, and 300:135 mg/kg soil), the greatest stimulation in microbial activity occurred at the lowest, rather than the highest, level of nutrient addition. The total soil-water potentials ranged from -2 to -15 bar with increasing levels of fertilizer. Semi-volatile hydrocarbon concentrations declined significantly only in the soils treated at the low fertilizer level. These results indicate that an understanding of nutrient effects at a specific site is essential for successful bioremediation.

Carbon and Nitrogen Mineralization in Relation to Soil Particle-Size Fractions after 32 Years of Chemical and Manure Application in a Continuous Maize Cropping System.

PubMed

Cai, Andong; Xu, Hu; Shao, Xingfang; Zhu, Ping; Zhang, Wenju; Xu, Minggang; Murphy, Daniel V

2016-01-01

Long-term manure application is recognized as an efficient management practice to enhance soil organic carbon (SOC) accumulation and nitrogen (N) mineralization capacity. A field study was established in 1979 to understand the impact of long-term manure and/or chemical fertilizer application on soil fertility in a continuous maize cropping system. Soil samples were collected from field plots in 2012 from 9 fertilization treatments (M0CK, M0N, M0NPK, M30CK, M30N, M30NPK, M60CK, M60N, and M60NPK) where M0, M30, and M60 refer to manure applied at rates of 0, 30, and 60 t ha(-1) yr(-1), respectively; CK indicates no fertilizer; N and NPK refer to chemical fertilizer in the forms of either N or N plus phosphorus (P) and potassium (K). Soils were separated into three particle-size fractions (2000-250, 250-53, and <53 μm) by dry- and wet-sieving. A laboratory incubation study of these separated particle-size fractions was used to evaluate the effect of long-term manure, in combination with/without chemical fertilization application, on the accumulation and mineralization of SOC and total N in each fraction. Results showed that long-term manure application significantly increased SOC and total N content and enhanced C and N mineralization in the three particle-size fractions. The content of SOC and total N followed the order 2000-250 μm > 250-53 μm > 53 μm fraction, whereas the amount of C and N mineralization followed the reverse order. In the <53 μm fraction, the M60NPK treatment significantly increased the amount of C and N mineralized (7.0 and 10.1 times, respectively) compared to the M0CK treatment. Long-term manure application, especially when combined with chemical fertilizers, resulted in increased soil microbial biomass C and N, and a decreased microbial metabolic quotient. Consequently, long-term manure fertilization was beneficial to both soil C and N turnover and microbial activity, and had significant effect on the microbial metabolic quotient.

Bacterial diversity of soil aggregates of different sizes in various land use conditions

NASA Astrophysics Data System (ADS)

Ivanova, Ekaterina; Azida, Thakahova; Olga, Kutovaya

2014-05-01

The patterns of soil microbiome structure may be a universal and very sensitive indicator of soil quality (soil "health") used for optimization and biologization of agricultural systems. The understanding of how microbial diversity influenses, and is influenced by, the environment can only be attained by analyses at scales relevant to those at which processes influencing microbial diversity actually operate. The basic structural and functional unit of the soil is a soil aggregate, which is actually a microcosm of the associative co-existing groups of microorganisms that form characteristic ecological food chains. It is known that many important microbial processes occur in spatially segregated microenvironments in soil leading to a microscale biogeography. The Metagenomic library of typical chernozem in conditions of different land use systems was created. Total genomic DNA was extracted from 0.5 g of the frozen soil after mechanical destruction. Sample preparation and sequencing was performed on a GS Junior ("Roche»", Switzerland) according to manufacturer's recommendations, using the universal primers to the variable regions V4 gene 16S - rRNA - F515 (GTGCCAGCMGCCGCGGTAA) and R806 (GGACT-ACVSGGGTATCTAAT). It is shown that the system of land use is a stronger determinant of the taxonomic composition of the soil microbial community, rather than the size of the structural units. In soil samples from different land use systems the presence of accessory components was revealed. They may be used as indicators of processes of soil recovery, soil degradation or soil exhaustion processes occuring in the agroecosystems. The comparative analysis of microbial communities of chernozem aggregates investigated demonstrates the statistically valuable differences in the amount of bacterial phyla and Archean domain content as well as the species richness in aggregates of various size fractions. The occurrence of specific components in the taxonomic structure of micro-and macro-aggregates may indicate the presence of a certain size fraction in the structure of the investigated soil. The study of soils' metagenome is promising for the development of both soil microbiology, and for the soil processes trends in soils of anthropogenic origin.

Changes in microbial activity of soils during the natural restoration of abandoned lands in central Russia

NASA Astrophysics Data System (ADS)

Ovsepyan, Lilit; Mostovaya, Anna; Lopes de Gerenyu, Valentin; Kurganova, Irina

2015-04-01

Most changes in land use affect significantly the amount of soil organic carbon (SOC) and alter the nutrition status of soil microbial community. The arable lands withdrawal induced usually the carbon sequestration in soil, the significant shifts in quality of soil organic matter and structure of microbial community. This study was aimed to determine the microbial activity of the abandoned lands in Central Russia due to the process of natural self-restoration. For the study, two representative chronosequences were selected in Central Russia: (1) deciduous forest area, DFA (Moscow region, 54o49N'; 37o34'E; Haplic Luvisols) and (2) forest steppe area, FSA (Belgorod region 50o36'N, 36o01'E Luvic Phaeozems). Each chronosequence included current arable, abandoned lands of different age, and forest plots. The total soil organic carbon (Corg, automatic CHNS analyzer), carbon immobilized in microbial biomass (Cmic, SIR method), and respiratory activity (RA) were determined in the topsoil (0-5, 5-10, 10-20 and 20-30 cm layers) for each plots. Relationships between Corg, Cmic, and RA were determined by liner regression method. Our results showed that the conversion of croplands to the permanent forest induced the progressive accumulation Corg, Cmic and acceleration of RA in the top 10-cm layer for both chronosequences. Carbon stock increased from 24.1 Mg C ha-1 in arable to 45.3 Mg C ha-1 in forest soil (Luvic Phaeozems, Belgorod region). In Haplic Luvisols (Moscow region), SOC build up was 2 time less: from 13.5 Mg C ha-1 in arable to 27.9 Mg C ha-1 in secondary forest. During post-agrogenic evolution, Cmic also increased significantly: from 0.34 to 1.43 g C kg-1 soil in Belgorod region and from 0.34 to 0.64 g C kg-1 soil in Moscow region. RA values varied widely in soils studied: from 0.54-0.63 mg C kg-1h-1 in arable plots to 2.02-3.4 mg C kg-1h-1 in forest ones. The close correlations between Cmic, RA and Corg in the top 0-5cm layer (R2 = 0.81-0.90; P<0.01-0.05) were observed for both soils. Concluding, the conversion of former arable soils to native vegetation led to significant increase in respiratory and enzymatic activity, total and microbial carbon in the former plough layer. This study was supported by RFBR (projects NN 12-04-00201a, 12-05-00198a), grant of Russian Government (SSc -6123.2014.4) and program KONTAKT II of the Czech Ministry of Education, Youth and Sports.

Resistance and resilience responses of a range of soil eukaryote and bacterial taxa to fungicide application

PubMed Central

Howell, Christopher C.; Hilton, Sally; Semple, Kirk T.; Bending, Gary D.

2014-01-01

The application of plant protection products has the potential to significantly affect soil microbial community structure and function. However, the extent to which soil microbial communities from different trophic levels exhibit resistance and resilience to such compounds remains poorly understood. The resistance and resilience responses of a range of microbial communities (bacteria, fungi, archaea, pseudomonads, and nematodes) to different concentrations of the strobilurin fungicide, azoxystrobin were studied. A significant concentration-dependent decrease, and subsequent recovery in soil dehydrogenase activity was recorded, but no significant impact on total microbial biomass was observed. Impacts on specific microbial communities were studied using small subunit (SSU) rRNA terminal restriction fragment length polymorphism (T-RFLP) profiling using soil DNA and RNA. The application of azoxystrobin significantly affected fungal and nematode community structure and diversity but had no impact on other communities. Community impacts were more pronounced in the RNA-derived T-RFLP profiles than in the DNA-derived profiles. qPCR confirmed that azoxystrobin application significantly reduced fungal, but not bacterial, SSU rRNA gene copy number. Azoxystrobin application reduced the prevalence of ascomycete fungi, but increased the relative abundance of zygomycetes. Azoxystrobin amendment also reduced the relative abundance of nematodes in the order Enoplia, but stimulated a large increase in the relative abundance of nematodes from the order Araeolaimida. PMID:25048906

Resistance and resilience responses of a range of soil eukaryote and bacterial taxa to fungicide application.

PubMed

Howell, Christopher C; Hilton, Sally; Semple, Kirk T; Bending, Gary D

2014-10-01

The application of plant protection products has the potential to significantly affect soil microbial community structure and function. However, the extent to which soil microbial communities from different trophic levels exhibit resistance and resilience to such compounds remains poorly understood. The resistance and resilience responses of a range of microbial communities (bacteria, fungi, archaea, pseudomonads, and nematodes) to different concentrations of the strobilurin fungicide, azoxystrobin were studied. A significant concentration-dependent decrease, and subsequent recovery in soil dehydrogenase activity was recorded, but no significant impact on total microbial biomass was observed. Impacts on specific microbial communities were studied using small subunit (SSU) rRNA terminal restriction fragment length polymorphism (T-RFLP) profiling using soil DNA and RNA. The application of azoxystrobin significantly affected fungal and nematode community structure and diversity but had no impact on other communities. Community impacts were more pronounced in the RNA-derived T-RFLP profiles than in the DNA-derived profiles. qPCR confirmed that azoxystrobin application significantly reduced fungal, but not bacterial, SSU rRNA gene copy number. Azoxystrobin application reduced the prevalence of ascomycete fungi, but increased the relative abundance of zygomycetes. Azoxystrobin amendment also reduced the relative abundance of nematodes in the order Enoplia, but stimulated a large increase in the relative abundance of nematodes from the order Araeolaimida. Copyright © 2014. Published by Elsevier Ltd.

Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations.

PubMed

Liu, Q; Tang, J; Liu, X; Song, B; Zhen, M; Ashbolt, N J

2017-10-01

Study the response of microbial communities and selected petroleum hydrocarbon (PH)-degrading genes on simulated PH spills in soils/sediments from different geographic locations. A microcosm experiment was conducted by spiking mixtures of petroleum hydrocarbons (PHs) to soils/sediments collected from four different regions of China, including the Dagang Oilfield (DG), Sand of Bohai Sea (SS), Northeast China (NE) and Xiamen (XM). Changes in bacterial community and the abundance of PH-degrading genes (alkB, nah and phe) were analysed by denaturing gradient electrophoresis (DGGE) and qPCR, respectively. Degradation of alkanes and PAHs in SS and NE materials were greater (P < 0·05) than those in DG and XM. Clay content was negatively correlated with the degradation of total alkanes by 112 days and PAHs by 56 days, while total organic carbon content was negatively correlated with initial degradation of total alkanes as well as PAHs. Abundances of alkB, nah and phe genes increased 10- to 100-fold and varied by soil type over the incubation period. DGGE fingerprints identified the dominance of α-, β- and γ-Proteobacteria (Gram -ve) and Actinobacteria (Gram +ve) bacteria associated with degradation of PHs in the materials studied. The geographic divergence resulting from the heterogeneity of physicochemical properties of soils/sediments appeared to influence the abundance of metabolic genes and community structure of microbes capable of degrading PHs. When developing practical in-situ bioremediation approaches for PHs contamination of soils/sediment, appropriate microbial community structures and the abundance of PH-degrading genes appear to be influenced by geographic location. © 2017 The Society for Applied Microbiology.

[Soil soluble organic matter, microbial biomass, and enzyme activities in forest plantations in degraded red soil region of Jiangxi Province, China].

PubMed

Jiang, Yu-mei; Chen, Cheng-long; Xu, Zhi-hong; Liu, Yuan-qiu; Ouyang, Jing; Wang, Fang

2010-09-01

Taking the adjacent 18-year-old pure Pinus massoniana pure forest (I), P. massoniana, Liquidamber fomosana, and Schima superba mixed forest (II), S. superba pure forest (III), L. fomosana (IV) pure forest, and natural restoration fallow land (CK) in Taihe County of Jiangxi Province as test sites, a comparative study was made on their soil soluble organic carbon (SOC) and nitrogen (SON), soil microbial biomass C (MBC) and N (MBN), and soil urease and asparaginase activities. In 0-10 cm soil layer, the pool sizes of SOC, SON, MBC, and MBN at test sites ranged in 354-1007 mg x kg(-1), 24-73 mg x kg(-1), 203-488 mg x kg(-1), and 24-65 mg x kg(-1), and the soil urease and asparaginase activities were 95-133 mg x kg(-1) x d(-1) and 58-113 mg x kg(-1) x d(-1), respectively. There were significant differences in the pool sizes of SOC, SON, MBC, and MBN and the asparaginase activity among the test sites, but no significant difference was observed in the urease activity. The pool sizes of SOC and SON were in the order of IV > CK > III > I > II, those of MBC and MBN were in the order of CK > IV > III > I > II, and asparaginase activity followed the order of IV > CK > III > II > I. With the increase of soil depth, the pool sizes of SOC, SON, MBC, and MBN and the activities of soil asparaginase and urease decreased. In 0-20 cm soil layer, the SOC, SON, MBC, MBN, total C, and total N were highly correlated with each other, soil asparaginase activity was highly correlated with SOC, SON, TSN, total C, total N, MBC, and MBN, and soil urease activity was highly correlated with SON, TSN, total C, MBC and MBN.

Soil microbial communities and enzyme activities under various poultry litter application rates.

PubMed

Acosta-Martínez, V; Harmel, R Daren

2006-01-01

The potential excessive nutrient and/or microbial loading from mismanaged land application of organic fertilizers is forcing changes in animal waste management. Currently, it is not clear to what extent different rates of poultry litter impact soil microbial communities, which control nutrient availability, organic matter quality and quantity, and soil degradation potential. From 2002 to 2004, we investigated the microbial community and several enzyme activities in a Vertisol soil (fine, smectitic, thermic, Udic Haplustert) at 0 to 15 cm as affected by different rates of poultry litter application to pasture (0, 6.7, and 13.4 Mg ha(-1)) and cultivated sites (0, 4.5, 6.7, 9.0, 11.2, and 13.4 Mg ha(-1)) in Texas, USA. No differences in soil pH (average: 7.9), total N (pasture: 2.01-3.53, cultivated: 1.09-1.98 g kg(-1) soil) or organic C (pasture average: 25-26.7, cultivated average: 13.9-16.1 g kg(-1) soil) were observed following the first four years of litter application. Microbial biomass carbon (MBC) and nitrogen (MBN) increased at litter rates greater than 6.7 Mg ha(-1) (pasture: MBC = >863, MBN = >88 mg kg(-1) soil) compared to sites with no applied litter (MBC = 722, MBN = 69 mg kg(-1) soil). Enzyme activities of C (beta-glucosidase, alpha-galactosidase, beta-glucosaminidase) or N cycling (beta-glucosaminidase) were increased at litter rates greater than 6.7 Mg ha(-1). Enzyme activities of P (alkaline phosphatase) and S (arylsulfatase) mineralization showed the same response in pasture, but they were only increased at the highest (9.0, 11.2, and 13.4 Mg ha(-1)) litter application rates in cultivated sites. According to fatty acid methyl ester (FAME) analysis, the pasture soils experienced shifts to higher bacterial populations at litter rates of 6.7 Mg ha(-1), and shifts to higher fungal populations at the highest litter application rates in cultivated sites. While rates greater than 6.7 Mg ha(-1) provided rapid enhancement of the soil microbial populations and enzymatic activities, they result in P application in excess of crop needs. Thus, studies will continue to investigate whether litter application at rates below 6.7 Mg ha(-1), previously recommended to maintain water quality, will result in similar improved soil microbial and biochemical functioning with continued annual litter application.

[Effects of intercropping Sedum plumbizincicola and Apium graceolens on the soil chemical and microbiological properties under the contamination of zinc and cadmium from sewage sludge application].

PubMed

Nai, Feng-Jiao; Wu, Long-Hua; Liu, Hong-Yan; Ren, Jing; Liu, Wu-Xing; Luo, Yong-Ming

2013-05-01

Taking the vegetable soil with zinc- and cadmium contamination from a long-term sewage sludge application as the object, a pot experiment was conducted to study the remediation effect of Sedum plumbizincicola and Apium graceolens under continuous monoculture and intercropping. With the remediation time increased, both S. plumbizincicola and A. graceolens under monoculture grew poorly, but S. plumbizincicola under intercropping grew well. Under intercropping, the soil organic matter, total N, extractable N, and total P contents decreased significantly while the soil extractable K content had a significant increase, the counts of soil bacteria and fungi increased by 7.9 and 18.4 times and 3.7 and 4.3 times, respectively, but the soil urease and catalase activities remained unchanged, as compared with those under A. graceolens and S. plumbizincicola monoculture. The BIOLOG ECO micro-plates also showed that the carbon sources utilization level and the functional diversity index of soil microbial communities were higher under intercropping than under monoculture, and the concentrations of soil zinc and cadmium under intercropping decreased by 5.8% and 50.0%, respectively, with the decrements being significantly higher than those under monoculture. It was suggested that soil microbial effect could be one of the important factors affecting plant growth.

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming

DOE PAGES

Feng, Wenting; Liang, Junyi; Hale, Lauren E.; ...

2017-06-09

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon–climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming.more » Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change.« less

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Wenting; Liang, Junyi; Hale, Lauren E.

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon–climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming.more » Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change.« less

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming.

PubMed

Feng, Wenting; Liang, Junyi; Hale, Lauren E; Jung, Chang Gyo; Chen, Ji; Zhou, Jizhong; Xu, Minggang; Yuan, Mengting; Wu, Liyou; Bracho, Rosvel; Pegoraro, Elaine; Schuur, Edward A G; Luo, Yiqi

2017-11-01

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon-climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming. Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change. © 2017 John Wiley & Sons Ltd.

Addition of Rubber to soil damages the functional diversity of soil.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-07-01

Rubber is a polymer of isoprene, consisting mainly of cis-1,4-polyisoprene units. The unmanageable production and its irresponsible disposal pose severe threats to environmental ecology. Therefore, the current study focuses extensively on the ill-effects of Rubber disposal on soil microbial functional diversity as it reflects the health of ecosystem by acting as a key component in ecosystem productivity. To investigate the effect of Rubber on soil microbial functional diversity, soil samples were collected from landfill sites and three different soil microcosms (Rubber treated, untreated, and sterile soil) were prepared. The soil enzymatic activity was determined by fluorescein diacetate hydrolysis followed by the determination of the microbial metabolic potential and functional diversity by average well color development and Shannon-Weaver index (H), respectively. BiOLOG ECO plates were used for determining the microbial functional diversity of the soil microcosms. Higher heterotrophic microbial count as well as higher soil microbial activity was observed in Rubber untreated soil than Rubber treated soil microcosm. The result indicated that the addition of Rubber to soil reduced soil heterotrophic microbial count and soil microbial activity considerably. Similarly, soil microbial metabolic potential as well as microbial functional diversity of soil had been decreased by the addition of Rubber gloves in it. Variation in soil microbial metabolic spectrum between Rubber treated and untreated microcosm was confirmed by multivariate analysis. Collectively, all the results demonstrated that the addition of Rubber to soil reduced the soil microbial functional diversity considerably. Therefore, it is necessary for the commission of serious steps regarding Rubber disposal and protection of the environment from serious environmental issues.

Engineering soil organic matter quality: Biodiesel Co-Product (BCP) stimulates exudation of nitrogenous microbial biopolymers

PubMed Central

Redmile-Gordon, Marc A.; Evershed, Richard P.; Kuhl, Alison; Armenise, Elena; White, Rodger P.; Hirsch, Penny R.; Goulding, Keith W.T.; Brookes, Philip C.

2015-01-01

Biodiesel Co-Product (BCP) is a complex organic material formed during the transesterification of lipids. We investigated the effect of BCP on the extracellular microbial matrix or ‘extracellular polymeric substance’ (EPS) in soil which is suspected to be a highly influential fraction of soil organic matter (SOM). It was hypothesised that more N would be transferred to EPS in soil given BCP compared to soil given glycerol. An arable soil was amended with BCP produced from either 1) waste vegetable oils or 2) pure oilseed rape oil, and compared with soil amended with 99% pure glycerol; all were provided with 15N labelled KNO3. We compared transfer of microbially assimilated 15N into the extracellular amino acid pool, and measured concomitant production of exopolysaccharide. Following incubation, the 15N enrichment of total hydrolysable amino acids (THAAs) indicated that intracellular anabolic products had incorporated the labelled N primarily as glutamine and glutamate. A greater proportion of the amino acids in EPS were found to contain 15N than those in the THAA pool, indicating that the increase in EPS was comprised of bioproducts synthesised de novo. Moreover, BCP had increased the EPS production efficiency of the soil microbial community (μg EPS per unit ATP) up to approximately double that of glycerol, and caused transfer of 21% more 15N from soil solution into EPS-amino acids. Given the suspected value of EPS in agricultural soils, the use of BCP to stimulate exudation is an interesting tool to consider in the theme of delivering sustainable intensification. PMID:26635420

Vertical variation of a black soil's properties in response to freeze-thaw cycles and its links to shift of microbial community structure.

PubMed

Han, Ziming; Deng, Mingwen; Yuan, Anqi; Wang, Jiahui; Li, Hao; Ma, Jincai

2018-06-01

Soil freeze-thaw cycles (FTCs) change soil physical, chemical, and biological properties, however information regarding their vertical variations in response to FTCs is limited. In this work, black soil (silty loam) packed soil columns were exposed to 8 FTCs, and soil properties were determined for each of vertical layer of soil columns. The results revealed that after FTCs treatment, moisture and electrical conductivity (EC) salinity tended to increase in upper soil layers. Increments of ammonium nitrogen (NH 4 + -N) and nitrate nitrogen (NO 3 - -N) in top layers (0-10cm) were greater than those in other layers, and increments of water soluble organic carbon (WSOC) and decrease of microbial biomass carbon (MBC) in middle layers (10-20cm) were greater than those in both ends. Overall, microbial community structure was mainly influenced by soil physical properties (moisture and EC) and chemical properties (pH and WSOC). For bacterial (archaeal) and fungal communities, soil physical properties, chemical properties and their interaction explained 79.73% and 82.66% of total variation, respectively. Our results provided insights into the vertical variation of soil properties caused by FTCs, and such variation had a major impact on the change of structure and composition of soil bacterial and fungal communities. Copyright © 2017 Elsevier B.V. All rights reserved.

Arbuscular Mycorrhizal Fungal Hyphae Alter Soil Bacterial Community and Enhance Polychlorinated Biphenyls Dissipation

PubMed Central

Qin, Hua; Brookes, Philip C.; Xu, Jianming

2016-01-01

We investigated the role of arbuscular mycorrhizal fungal (AMF) hyphae in alternation of soil microbial community and Aroclor 1242 dissipation. A two-compartment rhizobox system with double nylon meshes in the central was employed to exclude the influence of Cucurbita pepo L. root exudates on hyphal compartment soil. To assess the quantitative effect of AMF hyphae on soil microbial community, we separated the hyphal compartment soil into four horizontal layers from the central mesh to outer wall (e.g., L1–L4). Soil total PCBs dissipation rates ranged from 35.67% of L4 layer to 57.39% of L1 layer in AMF inoculated treatment, which were significant higher than the 17.31% of the control (P < 0.05). The dissipation rates of tri-, tetrachlorinated biphenyls as well as the total PCBs were significantly correlated with soil hyphal length (P < 0.01). Real-time quantitative PCR results indicated that the Rhodococcus-like bphC gene was 2–3 orders of magnitude more than that of Pseudomonas-like bphC gene, and was found responded positively to AMF. Phylogenetic analyses of the 16S rDNA sequenced by the Illumina Miseq sequencing platform indicated that AMF hyphae altered bacterial community compositions. The phylum Betaproteobacteria and Actinobacteria were dominated in the soil, while Burkholderiales and Actinomycetales were dominated at the order level. Taxa from the Comamonadaceae responded positively to AMF and trichlorinated biphenyl dissipation, while taxa from the Oxalobacteraceae and Streptomycetaceae responded negatively to AMF and PCB congener dissipation. Our results suggested that the AMF hyphal exudates as well as the hyphae per se did have quantitative effects on shaping soil microbial community, and could modify the PCBs dissipation processes consequently. PMID:27379068

Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth System Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Xiaofeng; Schimel, Joshua; Thornton, Peter E

2014-01-01

Microbial assimilation of soil organic carbon is one of the fundamental processes of global carbon cycling and it determines the magnitude of microbial biomass in soils. Mechanistic understanding of microbial assimilation of soil organic carbon and its controls is important for to improve Earth system models ability to simulate carbon-climate feedbacks. Although microbial assimilation of soil organic carbon is broadly considered to be an important parameter, it really comprises two separate physiological processes: one-time assimilation efficiency and time-dependent microbial maintenance energy. Representing of these two mechanisms is crucial to more accurately simulate carbon cycling in soils. In this study, amore » simple modeling framework was developed to evaluate the substrate and environmental controls on microbial assimilation of soil organic carbon using a new term: microbial annual active period (the length of microbes remaining active in one year). Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality (lower C:N ratio) leads to higher ratio of microbial carbon to soil organic carbon and vice versa. Increases in microbial annual active period from zero stimulate microbial assimilation of soil organic carbon; however, when microbial annual active period is longer than an optimal threshold, increasing this period decreases microbial biomass. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global dataset at the biome-level. The modeling framework of microbial assimilation of soil organic carbon and its controls developed in this study offers an applicable ways to incorporate microbial contributions to the carbon cycling into Earth system models for simulating carbon-climate feedbacks and to explain global patterns of microbial biomass.« less

Profile Changes in the Soil Microbial Community When Desert Becomes Oasis

PubMed Central

Li, Chen-hua; Tang, Li-song; Jia, Zhong-jun; Li, Yan

2015-01-01

The conversion of virgin desert into oasis farmland creates two contrasting types of land-cover. During oasis formation with irrigation and fertilizer application, however, the changes in the soil microbial population, which play critical roles in the ecosystem, remain poorly understood. We applied high-throughput pyrosequencing to investigate bacterial and archaeal communities throughout the profile (0–3 m) in an experimental field, where irrigation and fertilization began in 1990 and cropped with winter wheat since then. To assess the effects of cultivation, the following treatments were compared with the virgin desert: CK (no fertilizer), PK, NK, NP, NPK, NPKR, and NPKM (R: straw residue; M: manure fertilizer). Irrigation had a greater impact on the overall microbial community than fertilizer application. The greatest impact occurred in topsoil (0–0.2 m), e.g., Cyanobacteria (25% total abundance) were most abundant in desert soil, while Actinobacteria (26%) were most abundant in oasis soil. The proportions of extremophilic and photosynthetic groups (e.g., Deinococcus-Thermus and Cyanobacteria) decreased, while the proportions of R-strategy (e.g., Gammaproteobacteria including Xanthomonadales), nitrifying (e.g., Nitrospirae), and anaerobic bacteria (e.g., Anaerolineae) increased throughout the oasis profile. Archaea occurred only in oasis soil. The impact of fertilizer application was mainly reflected in the non-dominant communities or finer taxonomic divisions. Oasis formation led to a dramatic shift in microbial community and enhanced soil enzyme activities. The rapidly increased soil moisture and decreased salt caused by irrigation were responsible for this shift. Furthermore, difference in fertilization and crop growth altered the organic carbon contents in the soil, which resulted in differences of microbial communities within oasis. PMID:26426279

[Effects of different crop rotations on growth of continuous cropping sorghum and its rhizosphere soil micro-environment.

PubMed

Wang, Jin Song; Fan, Fang Fang; Guo, Jun; Wu, Ai Lian; Dong, Er Wei; Bai, Wen Bin; Jiao, Xiao Yan

2016-07-01

The effects of crop rotation on sorghum [Sorghum biocolor (L) Moench] growth, rhizosphere microbial community and the activity of soil enzymes for successive crops of sorghum were evaluated. Five years of continuous monoculture sorghum as the control (CK) was compared to alfalfa and scallion planted in the fourth year. The results showed that incorporation of alfalfa and scallion into the rotation significantly improved sorghum shoot growth. Specifically, sorghum grain yield increased by 16.5% in the alfalfa rotation plots compared to the CK. The rotations also increased sorghum root system growth, with alfalfa or scallion rotation increasing sorghum total root length by 0.3 and 0.4 times, total root surface area by 0.6 and 0.5 times, root volume by 1.2 and 0.6 times, and root biomass by 1.0 and 0.3 times, respectively. Alfalfa rotation also expanded sorghum root distribution below the 10 cm soil depth. A Biolog analysis on biome functions in the sorghum flowering period indicated significantly higher microbial activity in the rotation plots. The alfalfa and scallion rotation increased the Shannon index by 0.2 and 0.1 times compared to the CK, and improved the sucrose activity in the rhizosphere soil. It was concluded that including alfalfa in rotation with sorghum improved sorghum rhizosphere soil environment, enhanced soil microbial enzyme activity, alleviated the obstacle of continuous cropping and thus increased the sorghum yield.

Biocrusts role on nitrogen cycle and microbial communities from underlying soils in drylands

NASA Astrophysics Data System (ADS)

Anguita-Maeso, Manuel; Miralles*, Isabel; van Wesemael, Bas; Lázaro, Roberto; Ortega, Raúl; Garcia-Salcedo, José Antonio; Soriano**, Miguel

2017-04-01

Biocrusts are distributed in arid areas widely covering most of the soil surface and playing an essential role in the functioning of nitrogen cycle. The absence of biocrust coverage might affect the soil nitrogen content and the quantity and diversity of microbial communities in underlying biocrust soils. To analyse this mater, we have collected three underlying soils biocrusts samples dominated by the lichen Diploschistes diacapsis and Squamarina lentigera from Tabernas desert (southeast of Spain) at two extremes of its spatial distribution range: one with a high percentage of biocrust coverage and other with a huge degradation and low percentage of biocrust coverage in order to determine differences on the total nitrogen content and microbial communities from these underlying soils. DNA from these samples was isolated though a commercial kit and it was used as template for metagenomic analysis. We accomplished a sequencing of the amplicons V4-V5 of the 16S rRNA gene with Next-Generation Sequencing (NGS) Illumina MiSeq platform and a relative quantity of bacteria (rRNA 16S) and fungi (ITS1-5.8S) were conducted by quantitative qPCR. Total nitrogen was measured by the Kjeldahl method. Statistical analyses were based on ANOVAs, heatmap and Generalized Linear Models (GLM). The results showed 1.89E+09 bacteria per gram of soil in the high biocrust coverage position while 6.98E+08 microorganisms per gram of soil were found in the less favourable position according to the lower percentage of biocrust coverage. Similarly, 1.19E+12 was the amount of fungi per gram of soil located in the favourable position with higher biocrust coverage and 7.62E+11 was found in the unfavourable position. Furthermore, the soil under high percentage of biocrust coverage showed the greatest total nitrogen content (1.1 g kg-1) whereas the soil sampled under depressed percentage of biocrust coverage displayed the fewest quantity of total nitrogen content (0.9 g kg-1). Metagenomic and statistical analysis exhibited different bacteria communities according to underlying soils with unlike percentage of biocrust coverage. Opitutus and Adhaeribacter predominated in soil under high biocrust coverage percentage whereas Chelatococcus was found as prevalent bacteria community in soils under low biocrust coverage percentage. Our data illustrate that the percentage of biocrust coverage influence the total nitrogen content in underlying biocrust soils and also affects the amount and the variety of bacteria communities in these underlying soils. (*) Financial support by Marie Curie Intra-European Fellowship (FP7-577 PEOPLE-2013-IEF, Proposal n° 623393) and (**) by the Ministerio de Economía y Competitividad (MINECO) cofinanced with FEDER funds (project CGL2015-71709-R) is acknowledged.

Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function. ?? 2006 Springer Science+Business Media, Inc.

Soil biochemical properties and microbial resilience in agroforestry systems: effects on wheat growth under controlled drought and flooding conditions.

PubMed

Rivest, David; Lorente, Miren; Olivier, Alain; Messier, Christian

2013-10-01

Agroforestry is increasingly viewed as an effective means of maintaining or even increasing crop and tree productivity under climate change while promoting other ecosystem functions and services. This study focused on soil biochemical properties and resilience following disturbance within agroforestry and conventional agricultural systems and aimed to determine whether soil differences in terms of these biochemical properties and resilience would subsequently affect crop productivity under extreme soil water conditions. Two research sites that had been established on agricultural land were selected for this study. The first site included an 18-year-old windbreak, while the second site consisted in an 8-year-old tree-based intercropping system. In each site, soil samples were used for the determination of soil nutrient availability, microbial dynamics and microbial resilience to different wetting-drying perturbations and for a greenhouse pot experiment with wheat. Drying and flooding were selected as water stress treatments and compared to a control. These treatments were initiated at the beginning of the wheat anthesis period and maintained over 10 days. Trees contributed to increase soil nutrient pools, as evidenced by the higher extractable-P (both sites), and the higher total N and mineralizable N (tree-based intercropping site) found in the agroforestry compared to the conventional agricultural system. Metabolic quotient (qCO2) was lower in the agroforestry than in the conventional agricultural system, suggesting higher microbial substrate use efficiency in agroforestry systems. Microbial resilience was higher in the agroforestry soils compared to soils from the conventional agricultural system (windbreak site only). At the windbreak site, wheat growing in soils from agroforestry system exhibited higher aboveground biomass and number of grains per spike than in conventional agricultural system soils in the three water stress treatments. At the tree-based intercropping site, higher wheat biomass, grain yield and number of grains per spike were observed in agroforestry than in conventional agricultural system soils, but in the drought treatment only. Drought (windbreak site) and flooding (both sites) treatments significantly reduced wheat yield and 1000-grain weight in both types of system. Relationships between soil biochemical properties and soil microbial resilience or wheat productivity were strongly dependent on site. This study suggests that agroforestry systems may have a positive effect on soil biochemical properties and microbial resilience, which could operate positively on crop productivity and tolerance to severe water stress. Copyright © 2013 Elsevier B.V. All rights reserved.

Rice to vegetables: short- versus long-term impact of land-use change on the indigenous soil microbial community.

PubMed

Sun, Bo; Dong, Zhi-Xing; Zhang, Xue-Xian; Li, Yun; Cao, Hui; Cui, Zong-Li

2011-08-01

Land-use change is known to have a significant effect on the indigenous soil microbial community, but it is unknown if there are any general trends regarding how this effect varies over time. Here, we describe a comparative analysis of microbial communities from three adjacent agricultural fields: one-century-old paddy field (OP) and two vegetable fields (new vegetable field (NV) and old vegetable field (OV)) that were established on traditional paddy fields 10 and 100 years ago, respectively. Soil chemical and physical analysis showed that both vegetable fields were more nutrient rich than the paddy field in terms of organic C, total N, total P, and available K. The vegetable fields possessed relatively higher abundance of culturable bacteria, fungi, and specific groups of bacteria (Actinomyces, nitrifying bacteria, and cellulose-decomposing bacteria) but lower levels of microbial biomass C and N. Notably, the decrease of biomass was further confirmed by analysis of seven additional soils in chronosequence sampled from the same area. Next we examined the metabolic diversity of the microbial community using the EcoPlate(TM) system from Biolog Inc. (Hayward, CA, USA). The utilization patterns of 31 unique C substrates (i.e., community-level physiological profile) showed that microorganisms in vegetable soil and paddy soil prefer to use different C substrates (polymeric compounds for NV and OV soils, phenolic acids for OP soil). Principal component analysis and the average well color development data showed that the NV is metabolically more distinct from the OV and OP. The effect was likely attributable to the elevated soil pH in NV soil. Furthermore, we assessed the diversity of soil bacterial populations using the cultivation-independent technology of amplified ribosomal DNA restriction analysis (ARDRA). Results showed that levels of bacterial diversity in OP and NV soils were similar (Shannon's diversity index H = 4.83 and 4.79, respectively), whereas bacteria in OV soil have the lowest score of diversity (H = 3.48). The low level of bacterial diversity in OV soil was supported by sequencing of ten randomly selected 16S rDNA clones from each of the three rDNA libraries. Phylogenetic analysis showed that all the ten OV clones belonged to Proteobacteria with eight in the gamma-subdivision and two in the alpha-subdivision. In contrast, the ten clones from NV and OP soils were classified into four and eight bacterial classes or unclassified groups, respectively. Taken together, our data suggest that land-use change from rice to vegetables resulted in a decrease of bacterial diversity and soil biomass despite an increase in the abundance of culturable microorganisms and, moreover, the decrease of bacterial diversity occurred during long-term rather than short-term vegetable cultivation.

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

PubMed Central

Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

2015-01-01

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation. PMID:26067226

Soil aggregate mediates the impacts of land uses on organic carbon, total nitrogen, and microbial activity in a Karst ecosystem

NASA Astrophysics Data System (ADS)

Xiao, Shuangshuang; Zhang, Wei; Ye, Yingying; Zhao, Jie; Wang, Kelin

2017-02-01

Understanding the effect of land use on soil carbon, nitrogen, and microbial activity associated with aggregates is critical for thorough comprehension of the C and N dynamics of karst landscapes/ecosystems. We monitored soil organic carbon (SOC), total nitrogen (TN), microbial biomass carbon (MBC), and Cmic: Corg ratio in large macro- (>2 mm), small macro- (0.25-2 mm), and micro- (0.053-0.25 mm) aggregates to determine the changes in soil properties under different land uses in the karst area of Southwest China. Five common land-use types—enclosure land (natural system, control), prescribed-burning land, fuel-wood shrubland, pasture and maize fields—were selected. Results showed that pasture and maize fields remarkably decreased the SOC and TN concentrations in aggregates. Conversion of natural system to other land uses decreased MBC (except for prescribed-burning) and increased Cmic: Corg ratios in aggregates. The extent of the response to land uses of SOC and TN concentrations was similar whereas that of MBC and Cmic: Corg ratios differed across the three aggregate sizes. Further, the SOC concentrations were significantly higher in macro-aggregates than micro-aggregates; the MBC and Cmic: Corg ratios were highest in small macro-aggregates. Therefore, small macro-aggregates might have more active C dynamics.

Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

PubMed

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem.

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing

PubMed Central

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G.

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world’s highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1–10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem. PMID:25078273

Mechanisms for increased soil C storage with increasing temporal and spatial plant diversity in Agroecosystems

NASA Astrophysics Data System (ADS)

Tiemann, L. K.; Grandy, S.; Marin-Spiotta, E.; Atkinson, E. E.

2012-12-01

Generally, there are positive relationships between plant species diversity and net primary production and other key ecosystem functions. However, the effects of aboveground diversity on soil microbial communities and ecosystem processes they mediate, such as soil C sequestration, remain unclear. In this study, we used an 11-y cropping diversity study where increases in diversity have increased crop yields. At the experimental site, temporal diversity is altered using combinations of annual crop rotations, while spatial diversity is altered using cover crop species. We used five treatments ranging in diversity from one to five species consisting of continuous corn with no cover crop or one cover crop and corn-soy-wheat rotations with no cover, one cover or two cover crop species. We collected soils from four replicate plots of each treatment and measured the distribution of mega- (>2 mm), macro- (0.25-2 mm), and micro- (0.053-0.25 mm) aggregates. Within each aggregate size class, we also measured total soil C and N, permanganate oxidizable C (POXC), extracellular enzyme activities (EEA), and microbial community structure with phospholipid fatty acid (PLFA) analysis. We use these data to address the impacts of both rotational and cover crop diversity on soil physical structure, associated microbial community structure and activity and soil C storage. As spatial diversity increased, we found concurrent increases in mega-aggregate abundance as well as increasing soil C in the mega- and micro-aggregates but not macro-aggregates. The proportion of total soil C in each aggregate size class that is relatively labile (POXC) was highest in the micro-aggregates, as was enzyme activity associated with labile C acquisition across all levels of diversity. Enzyme activity associated with more recalcitrant forms of soil C was highest in the mega-aggregate class, also across all diversity levels; however, the ratio of labile to recalcitrant EEA increased with increasing diversity in the mega- and micro-aggregates. In addition, soil N increased with diversity such that microbial C:N EEA simultaneously decreased in mega-aggregates. We also found that cropping diversity has created distinctive soil microbial communities, highlighted by variation in the abundance of gram positive bacteria and Actinomycetes. Further research will help us determine how these changes in community structure with increasing diversity are related to concomitant changes in aggregation and enzyme activities. We suggest that the additional organic matter inputs from cover crops in the high diversity treatments have increased aggregation processes and C pools. While microbial activity has also increased in association with this increased C availability, the activity of recalcitrant and N-acquiring enzymes has declined, suggesting an overall decrease in SOM mineralization with possible increased SOM stabilization. The addition of crop species in rotation (temporal diversity) had minimal influence on any of the measured parameters. We thus conclude that spatial diversity is a more important driver of soil structure and microbial activity, likely due to the high quality organic matter inputs derived from the leguminous cover crops; however, spatial diversity alone did not lead to the same level of C storage potential as mixtures of temporal and spatial diversity.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

PubMed

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-03-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

PubMed Central

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-01-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites. PMID:20861922

Effects of moso bamboo encroachment into native, broad-leaved forests on soil carbon and nitrogen pools.

PubMed

Bai, Shangbin; Conant, Richard T; Zhou, Guomo; Wang, Yixiang; Wang, Nan; Li, Yanhua; Zhang, Kaiqiang

2016-08-16

Across southern China, Moso bamboo has been encroaching on most neighboring secondary broad-leaved forests and/or coniferous plantations, leading to the land cover changes that alter abiotic and biotic conditions. Little is known about how this conversion alters soil carbon (C) and nitrogen (N). We selected three sites, each with three plots arrayed along the bamboo encroachment pathway: moso bamboo forest (BF); transition zone, mixed forest plots (MF); and broad-leaved forest (BLF), and examined how bamboo encroachment affects soil organic C (SOC), soil total N, microbial biomass C (MBC), microbial biomass N (MBN), water-soluble organic C (WSOC), and water-soluble organic N (WSON) in three forests. Over nine years, moso bamboo encroachment leads to a decrease in SOC and total soil N, an increase in MBC and WSOC, and a decrease in MBN and WSON. Changes in soil C and N occurred mainly in the topsoil. We conclude that moso bamboo encroachment on broadleaved forest not only substantially altered soil C and N pools, but also changed the distribution pattern of C and N in the studied forest soils. Continued bamboo encroachment into evergreen broadleaved forests seems likely to lead to net CO2 emissions to the atmosphere as ecosystem C stocks decline.

Fungal role in post-fire ecosystem recovery in Sierra Nevada National Park (Spain)

NASA Astrophysics Data System (ADS)

Bárcenas-Moreno, Gema; Jiménez-Morillo, Nicasio T.; Mataix-Beneyto, Jorge; Martín Sánchez, Ines

2016-04-01

Fire effect on soil microorganisms has been studies for decades in several ecosystems and different microbial response can be found in the bibliography depending on numerous intrinsic and extrinsic soil factors. These factors will determine preliminary soil microbial community composition, subsequent pos-fire initial colonizers and even post-fire growth media characteristics that microbial community will find to start recolonisation. Fire-induced soil bacterial proliferation is a common pattern found after fire, usually related to pH and C availability increased. But when original soil pH is not altered by fire in acid soils, microbial response can be different and fungal response can be crucial to ecosystem recovery. In this study we have compile data related to high mountain soil from Sierra Nevada National park which was affected by a wildfire in 2006 and data obtained by laboratory heating experiment, trying to elucidate the ecological role of fungi in this fragile ecosystem. On the one hand we can observe fire-induced fungal abundance proliferation estimated by plate count method 8 and 32 months after wildfire and even in a short-term (21 d) after laboratory heating at 300 °C. Six years after fire, fungal abundance was similar between samples collected in burnt and unburnt-control area but we found higher proportion of species capable to degrade PAHs (lacase activity) in burnt soil than I the unburnt one. This finding evidences the crucial role of fungal enzymatic capacities to detoxify burnt soils when fire-induced recalcitrant and even toxic carbon compounds could be partially limiting total ecosystem recovery.

Short-time effect of heavy metals upon microbial community activity.

PubMed

Wang, Fei; Yao, Jun; Si, Yang; Chen, Huilun; Russel, Mohammad; Chen, Ke; Qian, Yiguang; Zaray, Gyula; Bramanti, Emilia

2010-01-15

Microcalorimetry was applied to assess and compare the toxic effect of heavy metals, such as As, Cu, Cd, Cr, Co, Pb and Zn, on the soil microbial activities and community. About 1.0 g soil spiked 5.0mg glucose and 5.0mg ammonium sulfate, the microbial activities were recorded as power-time curves, and their indices, microbial growth rate constant k, total heat evolution Q(T), metabolic enthalpy Delta H(met) and mass specific heat rate J(Q/S), were calculated. Comparing these thermodynamic parameters associated with growth yield, a general order of toxicity to the soil was found to be Cr>Pb>As>Co>Zn>Cd>Cu. When soil was exposed to heavy metals, the amount of bacteria and fungi decreased with the incubation time, and the bacterial number diminished sharply. It illustrates that fungi are more tolerant, and bacteria-fungi ratio would be altered under metal stress. To determine the status of the glucose consumed, a glucose biosensor with eggshell membrane was used to measure the remaining glucose in soil sample. Results showed that the time at which glucose was consumed completely was agreed with the microcalorimetric time to a large extent, and depended on the toxicity of heavy metals as well.

[Bioremediation of oil-polluted soils: using the [13C]/[12C] ratio to characterize microbial products of oil hydrocarbon biodegradation].

PubMed

Ziakun, A M; Brodskiĭ, E S; Baskunov, B P; Zakharchenko, V N; Peshenko, V P; Filonov, A E; Vetrova, A A; Ivanova, A A; Boronin, A M

2014-01-01

We compared data on the extent of bioremediation in soils polluted with oil. The data were obtained using conventional methods of hydrocarbon determination: extraction gas chromatography-mass spectrometry, extraction IR spectroscopy, and extraction gravimetry. Due to differences in the relative abundances of the stable carbon isotopes (13C/12C) in oil and in soil organic matter, these ratios could be used as natural isotopic labels of either substance. Extraction gravimetry in combination with characteristics of the carbon isotope composition of organic products in the soil before and after bioremediation was shown to be the most informative approach to an evaluation of soil bioremediation. At present, it is the only method enabling quantification of the total petroleum hydrocarbons in oil-polluted soil, as well as of the amounts of hydrocarbons remaining after bioremediation and those microbially transformed into organic products and biomass.

Microbial activity and community composition during bioremediation of diesel-oil-contaminated soil: effects of hydrocarbon concentration, fertilizers, and incubation time.

PubMed

Margesin, Rosa; Hämmerle, Marion; Tscherko, Dagmar

2007-02-01

We investigated the influence of three factors-diesel oil concentration [2500, 5000, 10,000, 20,000 mg total petroleum hydrocarbons (TPH) kg(-1) soil], biostimulation (unfertilized, inorganic fertilization with NPK nutrients, or oleophilic fertilization with Inipol EAP22), and incubation time-on hydrocarbon removal, enzyme activity (lipase), and microbial community structure [phospholipid fatty acids (PLFA)] in a laboratory soil bioremediation treatment. Fertilization enhanced TPH removal and lipase activity significantly (P < or = 0.001). The higher the initial contamination, the more marked was the effect of fertilization. Differences between the two fertilizers were not significant (P > 0.05). Microbial communities, as assessed by PLFA patterns, were primarily influenced by the TPH content, followed by fertilization, and the interaction of these two factors, whereas incubation time was of minor importance. This was demonstrated by three-factorial analysis of variance and multidimensional scaling analysis. Low TPH content had no significant effect on soil microbial community, independent of the treatment. High TPH content generally resulted in increased PLFA concentrations, whereby a significant increase in microbial biomass with time was only observed with inorganic fertilization, whereas oleophilic fertilization (Inipol EAP22) tended to inhibit microbial activity and to reduce PLFA contents with time. Among bacteria, PLFA indicative of the Gram-negative population were significantly (P < or = 0.05) increased in soil samples containing high amounts of diesel oil and fertilized with NPK after 21-38 days of incubation at 20 degrees C. The Gram-positive population was not significantly influenced by TPH content or biostimulation treatment.

The fate of fertilizer nitrogen in a high nitrate accumulated agricultural soil

PubMed Central

Quan, Zhi; Huang, Bin; Lu, Caiyan; Shi, Yi; Chen, Xin; Zhang, Haiyang; Fang, Yunting

2016-01-01

Well-acclimatized nitrifiers in high-nitrate agricultural soils can quickly nitrify NH4+ into NO3− subject to leaching and denitrifying loss. A 120-day incubation experiment was conducted using a greenhouse soil to explore the fates of applied fertilizer N entering into seven soil N pools and to examine if green manure (as ryegrass) co-application can increase immobilization of the applied N into relatively stable N pools and thereby reduce NO3− accumulation and loss. We found that 87–92% of the applied 15N-labelled NH4+ was rapidly recovered as NO3− since day 3 and only 2–4% as microbial biomass and soil organic matter (SOM), while ryegrass co-application significantly decreased its recovery as NO3− but enhanced its recovery as SOM (17%) at the end of incubation. The trade-off relationship between 15N recoveries in microbial biomass and SOM indicated that ryegrass co-application stabilized newly immobilized N via initial microbial uptake and later breakdown. Nevertheless, ryegrass application didn’t decrease soil total NO3− accumulation due to its own decay. Our results suggest that green manure co-application can increase immobilization of applied N into stable organic N via microbial turnover, but the quantity and quality of green manure should be well considered to reduce N release from itself. PMID:26868028

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat.

PubMed

Perazzolli, Michele; Herrero, Noemí; Sterck, Lieven; Lenzi, Luisa; Pellegrini, Alberto; Puopolo, Gerardo; Van de Peer, Yves; Pertot, Ilaria

2016-10-27

Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms. A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of A. mellea. This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic or neutral intruders.

Biological Chlorine Cycling in Arctic Peat Soils

NASA Astrophysics Data System (ADS)

Zlamal, J. E.; Raab, T. K.; Lipson, D.

2014-12-01

Soils of the Arctic tundra near Barrow, Alaska are waterlogged and anoxic throughout most of the profile due to underlying permafrost. Microbial communities in these soils are adapted for the dominant anaerobic conditions and are capable of a surprising diversity of metabolic pathways. Anaerobic respiration in this environment warrants further study, particularly in the realm of electron cycling involving chlorine, which preliminary data suggest may play an important role in arctic anaerobic soil respiration. For decades, Cl was rarely studied outside of the context of solvent-contaminated sites due to the widely held belief that it is an inert element. However, Cl has increasingly become recognized as a metabolic player in microbial communities and soil cycling processes. Organic chlorinated compounds (Clorg) can be made by various organisms and used metabolically by others, such as serving as electron acceptors for microbes performing organohalide respiration. Sequencing our arctic soil samples has uncovered multiple genera of microorganisms capable of participating in many Cl-cycling processes including organohalide respiration, chlorinated hydrocarbon degradation, and perchlorate reduction. Metagenomic analysis of these soils has revealed genes for key enzymes of Cl-related metabolic processes such as dehalogenases and haloperoxidases, and close matches to genomes of known organohalide respiring microorganisms from the Dehalococcoides, Dechloromonas, Carboxydothermus, and Anaeromyxobacter genera. A TOX-100 Chlorine Analyzer was used to quantify total Cl in arctic soils, and these data were examined further to separate levels of inorganic Cl compounds and Clorg. Levels of Clorg increased with soil organic matter content, although total Cl levels lack this trend. X-ray Absorption Near Edge Structure (XANES) was used to provide information on the structure of Clorg in arctic soils, showing great diversity with Cl bound to both aromatic and alkyl groups. Incubations were conducted in the laboratory providing arctic soils with Clorg, and measurements taken to assess rates of organohalide respiration show an increase in chloride production due to microbial activity. Investigating these soils with diverse techniques affirms the importance of Cl-cycling in a pristine arctic tundra ecosystem.

[Effects of different straw recycling and tillage methods on soil respiration and microbial activity].

PubMed

Li, Xiao-sha; Wu, Ning; Liu, Ling; Feng, Yu-peng; Xu, Xu; Han, Hui-fang; Ning, Tang-yuan; Li, Zeng-jia

2015-06-01

To explore the effects of different tillage methods and straw recycling on soil respiration and microbial activity in summer maize field during the winter wheat and summer maize double cropping system, substrate induced respiration method and CO2 release method were used to determine soil microbial biomass carbon, microbial activity, soil respiration, and microbial respiratory quotient. The experiment included 3 tillage methods during the winter wheat growing season, i.e., no-tillage, subsoiling and conventional tillage. Each tillage method was companied with 2 straw management patterns, i.e., straw recycling and no straw. The results indicated that the conservation tillage methods and straw recycling mainly affected 0-10 cm soil layer. Straw recycling could significantly improve the microbial biomass carbon and microbial activity, while decrease microbial respiratory quotient. Straw recycling could improve the soil respiration at both seedling stage and anthesis, however, it could reduce the soil respiration at filling stage, wax ripeness, and harvest stage. Under the same straw application, compared with conventional tillage, the soil respiration and microbial respiratory quotient in both subsoiling and no-tillage were reduced, while the microbial biomass carbon and microbial activity were increased. During the summer maize growing season, soil microbial biomass carbon and microbial activity were increased in straw returning with conservation tillage, while the respiratory quotient was reduced. In 0-10 cm soil layer, compared with conventional tillage, straw recycling with subsoiling and no-tillage significantly increased soil microbial biomass carbon by 95.8% and 74.3%, and increased soil microbial activity by 97.1% and 74.2%, respectively.

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

Accelerated decay rates drive soil organic matter persistence and storage in temperate forests via greater mineral stabilization of microbial residues.

NASA Astrophysics Data System (ADS)

Phillips, R.; Craig, M.; Turner, B. L.; Liang, C.

2017-12-01

Climate predicts soil organic matter (SOM) stocks at the global scale, yet controls on SOM stocks at finer spatial scales are still debated. A current hypothesis predicts that carbon (C) and nitrogen (N) storage in soils should be greater when decomposition is slow owing to microbial competition for nutrients or the recalcitrance of organic substrates (hereafter the `slow decay' hypothesis). An alternative hypothesis predicts that soil C and N storage should be greater in soils with rapid decomposition, owing to the accelerated production of microbial residues and their stabilization on soil minerals (hereafter the `stabilization hypothesis'). To test these alternative hypotheses, we quantified soil C and N to 1-m depth in temperate forests across the Eastern and Midwestern US that varied in their biotic, climatic, and edaphic properties. At each site, we sampled (1) soils dominated by arbuscular mycorrhizal (AM) tree species, which typically have fast decay rates and accelerated N cycling, (2) soils dominated by ectomycorrhizal (ECM) tree species, which generally have slow decay rates and slow N cycling, and (3) soils supporting both AM and ECM trees. To the extent that trees and theor associated microbes reflect and reinforce soil conditions, support for the slow decay hypothesis would be greater SOM storage in ECM soils, whereas support for the stabilization hypothesis would be greater SOM storage in AM soils. We found support for both hypotheses, as slow decomposition in ECM soils increased C and N storage in topsoil, whereas fast decomposition in AM soils increased C and N storage in subsoil. However, at all sites we found 57% greater total C and N storage in the entire profile in AM- soils (P < 0.0001), supporting the stabilization hypothesis. Amino sugar biomarkers (an indicator of microbial necromass) and particle size fractionation revealed that the greater SOM storage in AM soils was driven by an accumulation of microbial residues on clay minerals and metal oxides. Taken together, our results indicate that tree species influence soil C and N storage owing to how differences in decay rates affect mineral stabilization of organic matter. Further, our findings indicate that slow decay promotes soil C and N stocks at the soil surface, whereas fast decay promotes greater soil C and N stocks at depth.

Elevated atmospheric CO2 increases microbial growth rates and enzymes activity in soil

NASA Astrophysics Data System (ADS)

Blagodatskaya, Evgenia; Blagodatsky, Sergey; Dorodnikov, Maxim; Kuzyakov, Yakov

2010-05-01

Increasing the belowground translocation of assimilated carbon by plants grown under elevated CO2 can cause a shift in the structure and activity of the microbial community responsible for the turnover of organic matter in soil. We investigated the long-term effect of elevated CO2 in the atmosphere on microbial biomass and specific growth rates in root-free and rhizosphere soil. The experiments were conducted under two free air carbon dioxide enrichment (FACE) systems: in Hohenheim and Braunschweig, as well as in the intensively managed forest mesocosm of the Biosphere 2 Laboratory (B2L) in Oracle, AZ. Specific microbial growth rates (μ) were determined using the substrate-induced respiration response after glucose and/or yeast extract addition to the soil. We evaluated the effect of elevated CO2 on b-glucosidase, chitinase, phosphatase, and sulfatase to estimate the potential enzyme activity after soil amendment with glucose and nutrients. For B2L and both FACE systems, up to 58% higher μ were observed under elevated vs. ambient CO2, depending on site, plant species and N fertilization. The μ-values increased linearly with atmospheric CO2 concentration at all three sites. The effect of elevated CO2 on rhizosphere microorganisms was plant dependent and increased for: Brassica napus=Triticum aestivum

Rhizosphere priming effects in two contrasting soils

NASA Astrophysics Data System (ADS)

Lloyd, Davidson; Kirk, Guy; Ritz, Karl

2015-04-01

Inputs of fresh plant-derived carbon may stimulate the turnover of existing soil organic matter by so-called priming effects. Priming may occur directly, as a result of nutrient 'mining' by existing microbial communities, or indirectly via population adjustments. However the mechanisms are poorly understood. We planted C4 Kikuyu grass (Pennisetum clandestinum) in pots with two contrasting C3 soils (clayey, fertile TB and sandy, acid SH), and followed the soil CO2 efflux and its δ13C. The extent of C deposition in the rhizosphere was altered by intermittently clipping the grass in half the pots; there were also unplanted controls. At intervals, pots were destructively sampled for root and shoot biomass. Total soil CO2 efflux was measured using a gas-tight PVC chamber fitted over bare soil, and connected to an infra-red gas analyser; the δ13C of efflux was measured in air sub-samples withdrawn by syringe. The extent of priming was inferred from the δ13C of efflux and the δ13C of the plant and soil end-members. In unclipped treatments, in both soils, increased total soil respiration and rhizosphere priming effects (RPE) were apparent compared to the unplanted controls. The TB soil had greater RPE overall. The total respiration in clipped TB soil was significantly greater than in the unplanted controls, but in the clipped SH soil it was not significantly different from the controls. Clipping affected plant C partitioning with greater allocation to shoot regrowth from about 4 weeks after planting. Total plant biomass decreased in the order TB unclipped > SH unclipped >TB clipped > SH clipped. The results are consistent with priming driven by microbial activation stimulated by rhizodeposits and by nitrogen demand from the growing plants under N limited conditions. Our data suggest that photosynthesis drives RPE and soil differences may alter the rate and intensity of RPE but not the direction.

Comparative bioremediation of soils contaminated with diesel oil by natural attenuation, biostimulation and bioaugmentation.

PubMed

Bento, Fatima M; Camargo, Flávio A O; Okeke, Benedict C; Frankenberger, William T

2005-06-01

Bioremediation of diesel oil in soil can occur by natural attenuation, or treated by biostimulation or bioaugmentation. In this study we evaluated all three technologies on the degradation of total petroleum hydrocarbons (TPH) in soil. In addition, the number of diesel-degrading microorganisms present and microbial activity as indexed by the dehydrogenase assay were monitored. Soils contaminated with diesel oil in the field were collected from Long Beach, California, USA and Hong Kong, China. After 12 weeks of incubation, all three treatments showed differing effects on the degradation of light (C12-C23) and heavy (C23-C40) fractions of TPH in the soil samples. Bioaugmentation of the Long Beach soil showed the greatest degradation in the light (72.7%) and heavy (75.2%) fractions of TPH. Natural attenuation was more effective than biostimulation (addition of nutrients), most notably in the Hong Kong soil. The greatest microbial activity (dehydrogenase activity) was observed with bioaugmentation of the Long Beach soil (3.3-fold) and upon natural attenuation of the Hong Kong sample (4.0-fold). The number of diesel-degrading microorganisms and heterotrophic population was not influenced by the bioremediation treatments. Soil properties and the indigenous soil microbial population affect the degree of biodegradation; hence detailed site specific characterization studies are needed prior to deciding on the proper bioremediation method.

The soil microbial community composition and soil microbial carbon uptake are more affected by soil type than by different vegetation types (C3 and C4 plants) and seasonal changes

NASA Astrophysics Data System (ADS)

Griselle Mellado Vazquez, Perla; Lange, Markus; Gleixner, Gerd

2016-04-01

This study investigates the influence of different vegetation types (C3 and C4 plants), soil type and seasonal changes on the soil microbial biomass, soil microbial community composition and soil microbial carbon (C) uptake. We collected soil samples in winter (non-growing season) and summer (growing season) in 2012 from an experimental site cropping C3 and C4 plants for 6 years on two different soil types (sandy and clayey). The amount of phospholipid fatty acids (PLFAs) and their compound-specific δ13C values were used to determined microbial biomass and the flow of C from plants to soil microorganisms, respectively. Higher microbial biomass was found in the growing season. The microbial community composition was mainly explained by soil type. Higher amounts of SOC were driving the predominance of G+ bacteria, actinobacteria and cyclic G- bacteria in sandy soils, whereas root biomass was significantly related to the increased proportions of G- bacteria in clayey soils. Plant-derived C in G- bacteria increased significantly in clayey soils in the growing season. This increase was positively and significantly driven by root biomass. Moreover, changes in plant-derived C among microbial groups pointed to specific capabilities of different microbial groups to decompose distinct sources of C. We concluded that soil texture and favorable growth conditions driven by rhizosphere interactions are the most important factors controlling the soil microbial community. Our results demonstrate that a change of C3 plants vs. C4 plants has only a minor effect on the soil microbial community. Thus, such experiments are well suited to investigate soil organic matter dynamics as they allow to trace the C flow from plants into the soil microbial community without changing the community abundance and composition.

Profile analysis of microbiomes in soils of solonetz complex in the Caspian Lowland

NASA Astrophysics Data System (ADS)

Chernov, T. I.; Lebedeva, M. P.; Tkhakakhova, A. K.; Kutovaya, O. V.

2017-01-01

The taxonomic structure of the microbiota in two associated soils—solonetz on a microhigh and meadow-chestnut soil in a microlow—was studied in the semidesert of the Caspian Lowland. A highthroughput sequencing of the 16S rRNA gene was used for the soil samples from genetic horizons. A considerable reduction in the bacterial diversity was found in the lower horizons of the solonetz and compact solonetzic horizon with a high content of exchangeable sodium. In the meadow-chestnut soil, the microbial diversity little decreased with the depth. In both soils, a portion of archaea from the Thaumarchaeota group also decreased in the deeper horizons. In the soil horizons with the lower total bacterial diversity, a share of proteobacteria of the Enterobacteriaceae, Pseudomonadaceae, and Sphingomonadaceae families became higher. The difference between the structure of the microbial population in the solonetz and meadow- chestnut soil can be first explained by the different water regimes and soil consistence.

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition.

PubMed

Baldrian, Petr; Kolařík, Miroslav; Stursová, Martina; Kopecký, Jan; Valášková, Vendula; Větrovský, Tomáš; Zifčáková, Lucia; Snajdr, Jaroslav; Rídl, Jakub; Vlček, Cestmír; Voříšková, Jana

2012-02-01

Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.

Microbial community dynamics and methane, carbon dioxide, oxygen, and nitrous oxide concentrations in upland forest and riparian soils across a seasonal gradient of fully saturated soils to completely dried soils

NASA Astrophysics Data System (ADS)

Jones, R. T.; McGlynn, B. L.; McDermott, T.; Dore, J. E.

2015-12-01

Gas concentrations (CH4, CO2, N2O, and O2), soil properties (soil water content and pH), and microbial community composition were measured from soils at 32 sites across the Stringer Creek Watershed in the Tenderfoot Creek Experimental Forest 7 times between June 3, 2013 and September 20, 2013. Soils were fully saturated during the initial sampling period and dried down over the course of the summer. Soils and gas were sampled from 5cm and 20cm at each site and also at 50cm at eight riparian sites. In total, 496 individual soil samples were collected. Soil moisture ranged from 3.7% to fully saturated; soil pH ranged from 3.60 to 6.68. Methane concentrations in soils ranged from 0.426 ppm to 218 ppm; Carbon dioxide concentrations ranged from 550 ppm to 42,990 ppm; Nitrous oxide concentrations ranged from 0.220 ppm to 2.111 ppm; Oxygen concentrations ranged from 10.2% to 21.5%. Soil microbial communities were characterized by DNA sequences covering the V4 region of the 16S rRNA gene. DNA sequences were generated (~30,000,000 sequences) from the 496 soil samples using the Illumina MiSeq platform. Operational Taxonomic Units were generated using USEARCH, and representative sequences were taxonomically classified according the Ribosomal Database Project's taxonomy scheme. Analysis of similarity revealed that microbial communities found within a landscape type (high upland forest, low upland forest, riparian) were more similar than among landscape types (R = 0.600; p<0.001). Similarly, communities from unique site x depths were similar across the 7 collection periods (R = 0.646; p<0.001) despite changes in soil moisture. Euclidean distances of soil properties and gas concentrations were compared to Bray-Curtis community dissimilarity matrices using Mantel tests to determine how community structure co-varies with the soil environment and gas concentrations. All variables measured significantly co-varied with microbial community membership (pH: R = 0.712, p < 0.001; CO2: R = 0.578, p < 0.001; O2: R = 0.517, p < 0.001; Soil moisture: R = 0.408, p < 0.001; N2O: R = 0.218, p = 0.003; CH4: R = 0.195, p = 0.008). Despite the rather low co-variation between methane concentrations and microbial community composition, relative abundances of methanotrophic and methanogenic lineages did co-vary strongly with methane concentrations.

Effects of forest conversion on soil microbial communities depend on soil layer on the eastern Tibetan Plateau of China.

PubMed

He, Ruoyang; Yang, Kaijun; Li, Zhijie; Schädler, Martin; Yang, Wanqin; Wu, Fuzhong; Tan, Bo; Zhang, Li; Xu, Zhenfeng

2017-01-01

Forest land-use changes have long been suggested to profoundly affect soil microbial communities. However, how forest type conversion influences soil microbial properties remains unclear in Tibetan boreal forests. The aim of this study was to explore variations of soil microbial profiles in the surface organic layer and subsurface mineral soil among three contrasting forests (natural coniferous forest, NF; secondary birch forest, SF and spruce plantation, PT). Soil microbial biomass, activity and community structure of the two layers were investigated by chloroform fumigation, substrate respiration and phospholipid fatty acid analysis (PLFA), respectively. In the organic layer, both NF and SF exhibited higher soil nutrient levels (carbon, nitrogen and phosphorus), microbial biomass carbon and nitrogen, microbial respiration, PLFA contents as compared to PT. However, the measured parameters in the mineral soils often did not differ following forest type conversion. Irrespective of forest types, the microbial indexes generally were greater in the organic layer than in the mineral soil. PLFAs biomarkers were significantly correlated with soil substrate pools. Taken together, forest land-use change remarkably altered microbial community in the organic layer but often did not affect them in the mineral soil. The microbial responses to forest land-use change depend on soil layer, with organic horizons being more sensitive to forest conversion.

Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

PubMed

Dey, Samrat; Tribedi, Prosun

2018-03-01

Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both microbial functional diversity and PHB degradation suggesting a strong positive correlation ( r  = 0.95) between microbial functional diversity and PHB degradation. Thus, the results demonstrate that microbial functional diversity plays an important role in PHB degradation in soil by exhibiting versatile microbial metabolic potentials that lead to the enhanced degradation of PHB.

Biochemical and microbial soil functioning after application of the insecticide imidacloprid.

PubMed

Cycoń, Mariusz; Piotrowska-Seget, Zofia

2015-01-01

Imidacloprid is one of the most commonly used insecticides in agricultural practice, and its application poses a potential risk for soil microorganisms. The objective of this study was to assess whether changes in the structure of the soil microbial community after imidacloprid application at the field rate (FR, 1mg/kg soil) and 10 times the FR (10× FR, 10mg/kg soil) may also have an impact on biochemical and microbial soil functioning. The obtained data showed a negative effect by imidacloprid applied at the FR dosage for substrate-induced respiration (SIR), the number of total bacteria, dehydrogenase (DHA), both phosphatases (PHOS-H and PHOS-OH), and urease (URE) at the beginning of the experiment. In 10× FR treated soil, decreased activity of SIR, DHA, PHOS-OH and PHOS-H was observed over the experimental period. Nitrifying and N2-fixing bacteria were the most sensitive to imidacloprid. The concentration of NO3(-) decreased in both imidacloprid-treated soils, whereas the concentration of NH4(+) in soil with 10× FR was higher than in the control. Analysis of the bacterial growth strategy revealed that imidacloprid affected the r- or K-type bacterial classes as indicated also by the decreased eco-physiological (EP) index. Imidacloprid affected the physiological state of culturable bacteria and caused a reduction in the rate of colony formation as well as a prolonged time for growth. Principal component analysis showed that imidacloprid application significantly shifted the measured parameters, and the application of imidacloprid may pose a potential risk to the biochemical and microbial activity of soils. Copyright © 2014. Published by Elsevier B.V.

A meta-analysis of soil microbial biomass responses to forest disturbances

PubMed Central

Holden, Sandra R.; Treseder, Kathleen K.

2013-01-01

Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm) and biotic (insect, pathogen) disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7, 19.1, and 41.7% reductions in microbial biomass, respectively). In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics. PMID:23801985

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

PubMed Central

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-01-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha. PMID:25367357

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

NASA Astrophysics Data System (ADS)

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-11-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

Native-plant amendments and topsoil addition enhance soil function in post-mining arid grasslands.

PubMed

Kneller, Tayla; Harris, Richard J; Bateman, Amber; Muñoz-Rojas, Miriam

2018-04-15

One of the most critical challenges faced in restoration of disturbed arid lands is the limited availability of topsoil. In post-mining restoration, alternative soil substrates such as mine waste could be an adequate growth media to alleviate the topsoil deficit, but these materials often lack appropriate soil characteristics to support the development and survival of seedlings. Thus, addition of exogenous organic matter may be essential to enhance plant survival and soil function. Here, we present a case study in the arid Pilbara region (north-west Western Australia), a resource-rich area subject to intensive mining activities. The main objective of our study was to assess the effects of different restoration techniques such as soil reconstruction by blending available soil materials, sowing different compositions of plant species, and addition of a locally abundant native soil organic amendment (Triodia pungens biomass) on: (i) seedling recruitment and growth of Triodia wiseana, a dominant grass in Australian arid ecosystems, and (ii) soil chemical, physical, and biological characteristics of reconstructed soils, including microbial activity, total organic C, total N, and C and N mineralisation. The study was conducted in a 12-month multifactorial microcosms setting in a controlled environment. Our results showed that the amendment increased C and N contents of re-made soils, but these values were still lower than those obtained in the topsoil. High microbial activity and C mineralisation rates were found in the amended waste that contrasted the low N mineralisation but this did not translate into improved emergence or survival of T. wiseana. These results suggest a short- or medium-term soil N immobilisation caused by negative priming effect of fresh un-composted amendment on microbial communities. We found similar growth and survival rates of T. wiseana in topsoil and a blend of topsoil and waste (50:50) which highlights the importance of topsoil, even in a reduced amount, for plant establishment in arid land restoration. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of different agricultural managements in soil microbial community structure in a semi-arid Mediterranean region.

NASA Astrophysics Data System (ADS)

García-Orenes, Fuensanta; Morugan, Alicia; Mataix-Solera, Jorge; Scow, Kate

2013-04-01

Agriculture has been practiced in semi-arid Mediterranean regions for 10.000 years and in many cases these practices have been unsuitable causing land degradation for millennium and an important loss of soil quality. The land management can provide solutions to find the best agricultural practices in order to maintain the soil quality and get a sustainable agriculture model. Microbiological properties are the most sensitive and rapid indicators of soil perturbations and land use managements. The study of microbial community and diversity has an important interest as indicators of changes in soil quality. The main objective of this work was to asses the effect of different agricultural management practices in soil microbial community (evaluated as abundance of phospholipid fatty acids, PLFA). Four different treatments were selected, based on the most commonly practices applied by farmers in the study area, "El Teularet Experimental Station", located at the Enguera Range in the southern part of the Valencia province (eastern Spain). These treatments were: a) ploughing, b) herbicides c) mulch, using the types applied by organic farmers to develop a sustainable agriculture, such as oat straw and d) control that was established as plot where the treatment was abandonment after farming. An adjacent area with the same type of soil, but with natural vegetation was used as a standard or reference high quality soil. Soil samples were taken to evaluate the changes in microbial soil structure, analysing the abundance of PLFA. The results showed a major content of total PLFA in soils treated with oats straw, being these results similar to the content of PLFA in the soil with natural vegetation, also these soils were similar in the distribution of abundance of different PLFA studied. However, the herbicide and tillage treatments showed great differences regarding the soil used as reference (soil under natural vegetation).

Soil carbon stabilization and turnover at alley-cropping systems, Eastern Germany

NASA Astrophysics Data System (ADS)

Medinski, T.; Freese, D.

2012-04-01

Alley-cropping system is seen as a viable land-use practice for mitigation of greenhouse gas CO2, energy-wood production and soil carbon sequestration. The extent to which carbon is stored in soil varies between ecosystems, and depends on tree species, soil types and on the extent of physical protection of carbon within soil aggregates. This study investigates soil carbon sequestration at alley-cropping systems presented by alleys of fast growing tree species (black locust and poplar) and maize, in Brandenburg, Eastern Germany. Carbon accumulation and turnover are assessed by measuring carbon fractions differing in decomposition rates. For this purpose soil samples were fractionated into labile and recalcitrant soil-size fractions by wet-sieving: macro (>250 µm), micro (53-250 µm) and clay + silt (<53 µm), followed by determination of organic carbon and nitrogen by gas-chromatography. Soil samples were also analysed for the total C&N content, cold-water extractable OC, and microbial C. Litter decomposition was evaluated by litter bags experiment. Soil CO2 flux was measured by LiCor automated device LI-8100A. No differences for the total and stable (clay+silt, <53 µm) carbon fraction were observed between treatment. While cold water-extractable carbon was significantly higher at maize alley compared to black locust alley. This may indicate faster turnover of organic matter at maize alley due to tillage, which influenced greater incorporation of plant residues into the soil, greater soil respiration and microbial activity.

Effects of agricultural intensification in the tropics on soil carbon losses and soil fertility

NASA Astrophysics Data System (ADS)

Guillaume, Thomas; Buttler, Alexandre; Kuzyakov, Yakov

2016-04-01

Tropical forest conversion to agricultural land leads to strong decrease of soil organic carbon (SOC). Nonetheless, the impacts of SOC losses on soil fertility remain unclear. We quantified SOC losses in forest, oil palm plantations, extensive rubber plantations and rubber monocultures on Sumatra Island (Indonesia). Furthermore, we assessed the response of biological (basal respiration, microbial biomass, acid phosphatase) and chemical fertility indicators (light fraction of OM, DOC, total N, available P) to SOC losses. We used a new approach based on (non-)linear regressions between SOC losses and the indicators, normalized to natural ecosystem values, to assess the sensitivity or resistance of fertility indicators to SOC losses. Carbon contents in the Ah horizon under oil palm and intensive rubber plantations were strongly reduced: up to 70% and 62%, respectively. The decrease was lower under extensive rubber (41%). The negative impact of land-use changes on all measured indicators increased in the following sequence: extensive rubber < rubber < oil palm. Basal respiration, microbial biomass and nutrients were comparatively resistant to SOC losses, whereas the light fraction of OM was lost faster than the SOC. The resistance of the microbial activity to SOC losses is an indication that microbial-mediated soil functions sustain SOC losses. However, responses of basal respiration and microbial biomass to SOC losses were non-linear. Below 2.7% C content, the relationship was reversed. The basal respiration decreased faster than the SOC, resulting in a stronger drop of microbial activity under oil palm compared to rubber, despite small difference in C content. We conclude that the new approach allows a quantitative assessment of the sensitivity and threshold of various soil functions to land-use changes and consequently, can be used to assess their resistance to agricultural intensification. Therefore, this method is appropriate to evaluate the environmental impacts associated with various scenarios of agricultural intensification in tropical regions, but needs also to be tested in different tropical climate and soil (mineral vs organic) conditions.

Significance of microbial asynchronous anabolism to soil carbon dynamics driven by litter inputs

PubMed Central

Fan, Zhaosheng; Liang, Chao

2015-01-01

Soil organic carbon (SOC) plays an important role in the global carbon cycle. However, it remains largely unknown how plant litter inputs impact magnitude, composition and source configuration of the SOC stocks over long term through microbial catabolism and anabolism, mostly due to uncoupled research on litter decomposition and SOC formation. This limits our ability to predict soil system responses to changes in land-use and climate. Here, we examine how microbes act as a valve controlling carbon sequestrated from plant litters versus released to the atmosphere in natural ecosystems amended with plant litters varying in quantity and quality. We find that litter quality – not quantity – regulates long-term SOC dynamics under different plausible scenarios. Long-term changes in bulk SOC stock occur only when the quality of carbon inputs causes asynchronous change in a microbial physiological trait, defined as “microbial biosynthesis acceleration” (MBA). This is the first theoretical demonstration that the response of the SOC stocks to litter inputs is critically determined by the microbial physiology. Our work suggests that total SOC at an equilibrium state may be an intrinsic property of a given ecosystem, which ultimately is controlled by the asynchronous MBA between microbial functional groups. PMID:25849864

Significance of microbial asynchronous anabolism to soil carbon dynamics driven by litter inputs

DOE PAGES

Fan, Zhaosheng; Liang, Chao

2015-04-02

Soil organic carbon (SOC) plays an important role in the global carbon cycle. However, it remains largely unknown how plant litter inputs impact magnitude, composition and source configuration of the SOC stocks over long term through microbial catabolism and anabolism, mostly due to uncoupled research on litter decomposition and SOC formation. This limits our ability to predict soil system responses to changes in land-use and climate. Here, we examine how microbes act as a valve controlling carbon sequestrated from plant litters versus released to the atmosphere in natural ecosystems amended with plant litters varying in quantity and quality. We findmore » that litter quality – not quantity – regulates long-term SOC dynamics under different plausible scenarios. Long-term changes in bulk SOC stock occur only when the quality of carbon inputs causes asynchronous change in a microbial physiological trait, defined as ‘‘microbial biosynthesis acceleration’’ (MBA). This is the first theoretical demonstration that the response of the SOC stocks to litter inputs is critically determined by the microbial physiology. Our work suggests that total SOC at an equilibrium state may be an intrinsic property of a given ecosystem, which ultimately is controlled by the asynchronous MBA between microbial functional groups.« less

Organic matter characteristics in boreal forest soils under stands of silver birch, Norway spruce, and Norway spruce with a mixture of silver birch

NASA Astrophysics Data System (ADS)

Smolander, A.; Kitunen, V.

2012-04-01

The aim was to study how tree species and a tree species mixture affect microbial C and N transformations and two major plant secondary compound groups, terpenes and phenolic compounds in soil. The study site was a tree-species experiment in middle-eastern part of Finland containing plots of 43-year-old silver birch, Norway spruce and Norway spruce with a mixture of silver birch (22 and 37 % birch of the total stem number). Soil was podzol and humus type mor. Samples were taken from the organic layer. C and N in the microbial biomass, rates of C mineralization (CO2 evolution), net N mineralization and nitrification, and concentrations of total water-soluble phenolic compounds, condensed tannins and different kind of terpenes were measured. Amounts of C and N in the microbial biomass and the rates of C mineralization and net N mineralization were all lower under spruce than birch, and particularly net N mineralization was stimulated by birch mixture. Concentrations of total water-soluble phenolic compounds were on a similar level, irrespective of tree species. However, there were less low-molecular-weight phenolics and more high-molecular-weight phenolics under spruce than birch. Concentrations of condensed tannins and both sesqui- and diterpenes were all higher under spruce than birch but the concentrations of triterpenes were similar in all soils. The difference between tree species was greatest with monoterpenes which were measured from both organic layer and soil atmosphere: high concentrations under spruce and negligible under birch. Birch mixture tended to decrease the concentrations of condensed tannins and mono-, sesqui- and diterpenes.

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lipson, David A.; Raab, Theodore K.; Parker, Melanie

2015-08-01

Summary This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth andmore » were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes,« less

Use of urban composts for the regeneration of a burnt Mediterranean soil: a laboratory approach.

PubMed

Cellier, Antoine; Francou, Cédric; Houot, Sabine; Ballini, Christine; Gauquelin, Thierry; Baldy, Virginie

2012-03-01

In Mediterranean region, forest fires are a major problem leading to the desertification of the environment. Use of composts is considered as a solution for soil and vegetation rehabilitation. In this study, we determined under laboratory conditions the effects of three urban composts and their mode of application (laid on the soil surface or mixed into the soil) on soil restoration after fire: a municipal waste compost (MWC), a compost of sewage sludge mixed with green waste (SSC) and a green waste compost (GWC). Carbon (C) and nitrogen (N) mineralisation, total microbial biomass, fungal biomass and soil characteristics were measured during 77-day incubations in microcosms. The impact of composts input on hydrological behaviour related to erodibility was estimated by measuring runoff, retention and percolation (i.e. infiltration) of water using a rainfall simulator under laboratory conditions. Input of composts increased organic matter and soil nutrient content, and enhanced C and N mineralisation and total microbial biomass throughout the incubations, whereas it increased sporadically fungal biomass. For all these parameters, the MWC induced the highest improvement while GWC input had no significant effect compared to the control. Composts mixed with soil weakly limited runoff and infiltration whereas composts laid at the soil surface significantly reduced runoff and increased percolation and retention, particularly with the MWC. Copyright © 2010 Elsevier Ltd. All rights reserved.

Nitrogen losses, uptake and abundance of ammonia oxidizers in soil under mineral and organo-mineral fertilization regimes.

PubMed

Florio, Alessandro; Felici, Barbara; Migliore, Melania; Dell'Abate, Maria Teresa; Benedetti, Anna

2016-05-01

A laboratory incubation experiment and greenhouse studies investigated the impact of organo-mineral (OM) fertilization as an alternative practice to conventional mineral (M) fertilization on nitrogen (N) uptake and losses in perennial ryegrass (Lolium perenne) as well as on soil microbial biomass and ammonia oxidizers. While no significant difference in plant productivity and ammonia emissions between treatments could be detected, an increase in soil total N content and an average 17.9% decrease in nitrates leached were observed in OM fertilization compared with M fertilization. The microbial community responded differentially to treatments, suggesting that the organic matter fraction of the OM fertilizer might have influenced N immobilization in the microbial biomass in the short-medium term. Furthermore, nitrate contents in fertilized soils were significantly related to bacterial but not archaeal amoA gene copies, whereas in non-fertilized soils a significant relationship between soil nitrates and archaeal but not bacterial amoA copies was found. The application of OM fertilizer to soil maintained sufficient productivity and in turn increased N use efficiency and noticeably reduced N losses. Furthermore, in this experiment, ammonia-oxidizing bacteria drove nitrification when an N source was added to the soil, whereas ammonia-oxidizing archaea were responsible for ammonia oxidation in non-fertilized soil. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Effect of soil structure on the growth of bacteria in soil quantified using CARD-FISH

NASA Astrophysics Data System (ADS)

Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Otten, Wilfred

2014-05-01

It has been reported that compaction of soil due to use of heavy machinery has resulted in the reduction of crop yield. Compaction affects the physical properties of soil such as bulk density, soil strength and porosity. This causes an alteration in the soil structure which limits the mobility of nutrients, water and air infiltration and root penetration in soil. Several studies have been conducted to explore the effect of soil compaction on plant growth and development. However, there is scant information on the effect of soil compaction on the microbial community and its activities in soil. Understanding the effect of soil compaction on microbial community is essential as microbial activities are very sensitive to abrupt environmental changes in soil. Therefore, the aim of this work was to investigate the effect of soil structure on growth of bacteria in soil. The bulk density of soil was used as a soil physical parameter to quantify the effect of soil compaction. To detect and quantify bacteria in soil the method of catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used. This technique results in high intensity fluorescent signals which make it easy to quantify bacteria against high levels of autofluorescence emitted by soil particles and organic matter. In this study, bacterial strains Pseudomonas fluorescens SBW25 and Bacillus subtilis DSM10 were used. Soils of aggregate size 2-1mm were packed at five different bulk densities in polyethylene rings (4.25 cm3).The soil rings were sampled at four different days. Results showed that the total number of bacteria counts was reduced significantly (P

Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales.

PubMed

Zeglin, L H; Bottomley, P J; Jumpponen, A; Rice, C W; Arango, M; Lindsley, A; McGowan, A; Mfombep, P; Myrold, D D

2013-10-01

Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting "Ambient" and "Altered" (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential = -0.01 and -0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracellular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 +/- 0.03 > 0.46 +/- 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (beta-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal:bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet-up and between seasons and treatments. Overall, microbial activity may directly (C respiration) and indirectly (enzyme potential) reduce soil organic matter pools less in drier soils, and soil C sequestration potential (CUE) may be higher in soils with a history of extended dry periods between rainfall events. The implications include that soil C loss may be reduced or compensated for via different mechanisms at varying time scales, and that microbial taxa with better stress tolerance or growth efficiency may be associated with these functional shifts.

Consistency between health risks and microbial response mechanism of various petroleum components in a typical wastewater-irrigated farmland.

PubMed

Zhang, Juan; Fan, Shu-kai

2016-06-01

Various petroleum components possess distinctive migration and toxicity characteristics. Evaluation of contamination levels on the basis of total concentrations of petroleum hydrocarbons in soil and groundwater is limited. Hunpu, a typical wastewater-irrigated area, is located at the southwest of Shenyang City, Liaoning Province, China. In this study, various fractions, exposure pathways, and soil microbial communities were taken into account to make petroleum contamination evaluation more effective and precise in the region. The concentrations and hazard quotients of aliphatic fractions, as the bulk of an oil, verified that the groundwater must not be drunk directly. The total concentrations of aliphatic hydrocarbons (TAHs) for C10-34 were 68.90-199.87 μg g(-1) in soil in Hunpu, which required cleanup according to Oklahoma criteria. However, both health and ecological risks indicated that petroleum contamination in surface soil was not serious. Microbes may use aliphatic fractions as carbon and energy source for their growth, which was indicated by positive correlation between them. TAHsC12-16 posed highest human health risks and had the most significant effect on the soil microbial composition, although its concentration was low in both the groundwater and the soil. Straight-, branched-chain saturated, and cyclopropyl phospholipid fatty acids had more closely positive correlation with TAHsC12-16, which indicated that regulation of bacterial membrane fluidity to toxic petroleum pollutants. This study can also provide the guidelines for assessment and management of petroleum contamination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Plant and soil effects on bacterial communities associated with Miscanthus  ×  giganteus rhizosphere and rhizomes

DOE PAGES

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

2015-02-11

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Plant and soil effects on bacterial communities associated with Miscanthus  ×  giganteus rhizosphere and rhizomes

DOE PAGES

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

2015-04-30

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Succession of Bacterial Community Structure and Diversity in Soil along a Chronosequence of Reclamation and Re-Vegetation on Coal Mine Spoils in China

PubMed Central

Li, Yuanyuan; Wen, Hongyu; Chen, Longqian; Yin, Tingting

2014-01-01

The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important phase of microbial community recovery occurs between 15 and 20 years after reclamation. PMID:25502754

Tree Plantation Systems Influence Nitrogen Retention and the Abundance of Nitrogen Functional Genes in the Solomon Islands

PubMed Central

Reverchon, Frédérique; Bai, Shahla H.; Liu, Xian; Blumfield, Timothy J.

2015-01-01

Tree mono-plantations are susceptible to soil nutrient impoverishment and mixed species plantations have been proposed as a way of maintaining soil fertility while enhancing biodiversity. In the Solomon Islands, mixed species plantations where teak (Tectona grandis) is inter-planted with a local tree species (Flueggea flexuosa) have been used as an alternative to teak mono-plantations and are expected to increase soil microbial diversity and modify microbial biogeochemical processes. In this study, we quantified the abundance of microbial functional genes involved in the nitrogen (N) cycle from soil samples collected in teak, flueggea, and mixed species plantations. Furthermore, we measured soil properties such as pH, total carbon (C) and total N, stable N isotope composition (δ15N), and inorganic N pools. Soil pH and δ15N were higher under teak than under flueggea, which indicates that intercropping teak with flueggea may decrease bacterial activities and potential N losses. Higher C:N ratios were found under mixed species plantations than those under teak, suggesting an enhancement of N immobilization that would help preventing fast N losses. However, inorganic N pools remained unaffected by plant cover. Inter-planting teak with flueggea in mixed species plantations generally increased the relative abundance of denitrification genes and promoted the enrichment of nosZ-harboring denitrifiers. However, it reduced the abundance of bacterial amoA (ammonia monooxygenase) genes compared to teak mono-plantations. The abundance of most denitrification genes correlated with soil total N and C:N ratio, while bacterial and archeal nitrification genes correlated positively with soil NH4+ concentrations. Altogether, these results show that the abundance of bacterial N-cycling functional guilds vary under teak and under mixed species plantations, and that inter-planting teak with flueggea may potentially alleviate N losses associated with nitrification and denitrification and favor N retention. Mixed plantations could also allow an increase in soil C and N stocks without losing the source of income that teak trees represent for local communities. PMID:26733978

Effects of forest conversion on soil microbial communities depend on soil layer on the eastern Tibetan Plateau of China

PubMed Central

He, Ruoyang; Yang, Kaijun; Li, Zhijie; Schädler, Martin; Yang, Wanqin; Wu, Fuzhong; Tan, Bo; Zhang, Li

2017-01-01

Forest land-use changes have long been suggested to profoundly affect soil microbial communities. However, how forest type conversion influences soil microbial properties remains unclear in Tibetan boreal forests. The aim of this study was to explore variations of soil microbial profiles in the surface organic layer and subsurface mineral soil among three contrasting forests (natural coniferous forest, NF; secondary birch forest, SF and spruce plantation, PT). Soil microbial biomass, activity and community structure of the two layers were investigated by chloroform fumigation, substrate respiration and phospholipid fatty acid analysis (PLFA), respectively. In the organic layer, both NF and SF exhibited higher soil nutrient levels (carbon, nitrogen and phosphorus), microbial biomass carbon and nitrogen, microbial respiration, PLFA contents as compared to PT. However, the measured parameters in the mineral soils often did not differ following forest type conversion. Irrespective of forest types, the microbial indexes generally were greater in the organic layer than in the mineral soil. PLFAs biomarkers were significantly correlated with soil substrate pools. Taken together, forest land-use change remarkably altered microbial community in the organic layer but often did not affect them in the mineral soil. The microbial responses to forest land-use change depend on soil layer, with organic horizons being more sensitive to forest conversion. PMID:28982191

Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment

NASA Astrophysics Data System (ADS)

Muñoz-Rojas, Miriam; Martini, Dylan; Erickson, Todd; Merritt, David; Dixon, Kingsley

2015-04-01

Introduction In semi-arid areas such as northern Western Australia, wildfires are a natural part of the environment and many ecosystems in these landscapes have evolved and developed a strong relationship with fire. Soil microbial communities play a crucial role in ecosystem processes by regulating the cycling of nutrients via decomposition, mineralization, and immobilization processes. Thus, the structure (e.g. soil microbial biomass) and functioning (e.g. soil microbial activity) of microbial communities, as well as their changes after ecosystem disturbance, can be useful indicators of soil quality and health recovery. In this research, we assess the impacts of fire on soil microbial communities and their recovery in a biodiverse semi-arid environment of Western Australia (Pilbara region). New methods for determining soil microbial respiration as an indicator of microbial activity and soil health are also tested. Methodology Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25°C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years 'undisturbed' levels (53.18±3.68 ppm CO2-CO and 14.07±0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5-7 years post fire (70.70±8.94 ppm CO2-CO and 21.67±2.62 mg kg-1, respectively). Microbial activity measured with the Solvita test was significantly correlated (R Pearson > 0.7; P < 0.001) with microbial parameters analysed with PLFA such as microbial biomass, bacteria biomass or mycorrhizhal fungi. This method has proven to be reliable, fast and easy to interpret for assessment of soil microbial activity in the recovery of soil quality during the recovery after fire. Keywords Pilbara region, biodiverse ecosystems, microbial biomass, microbial respiration, Solvita test, CO2 burst.

Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Shengmu; Xue, Kai; He, Zhili

2010-05-17

Increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity are three main environmental changes occurring on a global scale. The BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve started in 1997, to better understand how these changes would affect soil systems. To understand how increasing nitrogen deposition affects the microbial community diversity, heterogeneity, and functional structure impact soil microbial communities, 12 samples were collected from the BioCON plots in which nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition and 12 samples from without added fertilizer. DNAmore » from the 24 samples was extracted using a freeze-grind protocol, amplified, labeled with a fluorescent dye, and then hybridized to GeoChip, a functional gene array containing probes for genes involved in N, S and C cycling, metal resistance and organic contaminant degradation. Detrended correspondence analysis (DCA) of all genes detected was performed to analyze microbial community patterns. The first two axes accounted for 23.5percent of the total variation. The samples fell into two major groups: fertilized and non-fertilized, suggesting that nitrogenous fertilizer had a significant impact on soil microbial community structure and diversity. The functional gene numbers detected in fertilized samples was less that detected in non-fertilizer samples. Functional genes involving in the N cycling were mainly discussed.« less

Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review.

PubMed

Zhu, Xiaomin; Chen, Baoliang; Zhu, Lizhong; Xing, Baoshan

2017-08-01

Biochars have attracted tremendous attention due to their effects on soil improvement; they enhance carbon storage, soil fertility and quality, and contaminant (organic and heavy metal) immobilization and transformation. These effects could be achieved by modifying soil microbial habitats and (or) directly influencing microbial metabolisms, which together induce changes in microbial activity and microbial community structures. This review links microbial responses, including microbial activity, community structures and soil enzyme activities, with changes in soil properties caused by biochars. In particular, we summarized possible mechanisms that are involved in the effects that biochar-microbe interactions have on soil carbon sequestration and pollution remediation. Special attention has been paid to biochar effects on the formation and protection of soil aggregates, biochar adsorption of contaminants, biochar-mediated transformation of soil contaminants by microorganisms, and biochar-facilitated electron transfer between microbial cells and contaminants and soil organic matter. Certain reactive organic compounds and heavy metals in biochar may induce toxicity to soil microorganisms. Adsorption and hydrolysis of signaling molecules by biochar interrupts microbial interspecific communications, potentially altering soil microbial community structures. Further research is urged to verify the proposed mechanisms involved in biochar-microbiota interactions for soil remediation and improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China.

PubMed

Sun, Xiaoyan; Zhou, Yanling; Tan, Yinjing; Wu, Zhaoxiang; Lu, Ping; Zhang, Guohua; Yu, Faxin

2018-05-25

To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.

Comparison of model microbial allocation parameters in soils of varying texture

NASA Astrophysics Data System (ADS)

Hagerty, S. B.; Slessarev, E.; Schimel, J.

2017-12-01

The soil microbial community decomposes the majority of carbon (C) inputs to the soil. However, not all of this C is respired—rather, a substantial portion of the carbon processed by microbes may remain stored in the soil. The balance between C storage and respiration is controlled by microbial turnover rates and C allocation strategies. These microbial community properties may depend on soil texture, which has the potential to influence both the nature and the fate of microbial necromass and extracellular products. To evaluate the role of texture on microbial turnover and C allocation, we sampled four soils from the University of California's Hastings Reserve that varied in texture (one silt loam, two sandy loam, and on clay soil), but support similar grassland plant communities. We added 14C- glucose to the soil and measured the concentration of the label in the carbon dioxide (CO2), microbial biomass, and extractable C pools over 7 weeks. The labeled biomass turned over the slowest in the clay soil; the concentration of labeled biomass was more than 1.5 times the concentration of the other soils after 8 weeks. The clay soil also had the lowest mineralization rate of the label, and mineralization slowed after two weeks. In contrast, in the sandier soils mineralization rates were higher and did not plateau until 5 weeks into the incubation period. We fit the 14C data to a microbial allocation model and estimated microbial parameters; assimilation efficiency, exudation, and biomass specific respiration and turnover for each soil. We compare these parameters across the soil texture gradient to assess the extent to which models may need to account for variability in microbial C allocation across soils of different texture. Our results suggest that microbial C turns over more slowly in high-clay soils than in sandy soils, and that C lost from microbial biomass is retained at higher rates in high-clay soils. Accounting for these differences in microbial allocation and carbon stabilization could improve model representations of C cycling across a range of soil types.

Near infrared spectroscopy for determination of various physical, chemical and biochemical properties in Mediterranean soils.

PubMed

Zornoza, R; Guerrero, C; Mataix-Solera, J; Scow, K M; Arcenegui, V; Mataix-Beneyto, J

2008-07-01

The potential of near infrared (NIR) reflectance spectroscopy to predict various physical, chemical and biochemical properties in Mediterranean soils from SE Spain was evaluated. Soil samples (n=393) were obtained by sampling thirteen locations during three years (2003-2005 period). These samples had a wide range of soil characteristics due to variations in land use, vegetation cover and specific climatic conditions. Biochemical properties also included microbial biomarkers based on phospholipid fatty acids (PLFA). Partial least squares (PLS) regression with cross validation was used to establish relationships between the NIR spectra and the reference data from physical, chemical and biochemical analyses. Based on the values of coefficient of determination (r(2)) and the ratio of standard deviation of validation set to root mean square error of cross validation (RPD), predicted results were evaluated as excellent (r(2)>0.90 and RPD>3) for soil organic carbon, Kjeldahl nitrogen, soil moisture, cation exchange capacity, microbial biomass carbon, basal soil respiration, acid phosphatase activity, β-glucosidase activity and PLFA biomarkers for total bacteria, Gram positive bacteria, actinomycetes, vesicular-arbuscular mycorrhizal fungi and total PLFA biomass. Good predictions (0.81

Biochar alters microbial community and carbon sequestration potential across different soil pH.

PubMed

Sheng, Yaqi; Zhu, Lizhong

2018-05-01

Biochar application to soil has been proposed for soil carbon sequestration and global warming mitigation. While recent studies have demonstrated that soil pH was a main factor affecting soil microbial community and stability of biochar, little information is available for the microbiome across different soil pH and the subsequently CO 2 emission. To investigate soil microbial response and CO 2 emission of biochar across different pH levels, comparative incubation studies on CO 2 emission, degradation of biochar, and microbial communities in a ferralsol (pH5.19) and a phaeozems (pH7.81) with 4 biochar addition rates (0.5%, 1.0%, 2.0%, 5.0%) were conducted. Biochar induced higher CO 2 emission in acidic ferralsol, largely due to the higher biochar degradation, while the more drastic negative priming effect (PE) of SOC resulted in decreased total CO 2 emission in alkaline phaeozems. The higher bacteria diversity, especially the enrichment of copiotrophic bacteria such as Bacteroidetes, Gemmatimonadetes, and decrease of oligotrophic bacteria such as Acidobacteria, were responsible for the increased CO 2 emission and initial positive PE of SOC in ferralsol, whereas biochar did not change the relative abundances of most bacteria at phylum level in phaeozems. The relative abundances of other bacterial taxa (i.e. Actinobacteria, Anaerolineae) known to degrade aromatic compounds were also elevated in both soils. Soil pH was considered to be the dominant factor to affect CO 2 emission by increasing the bioavailability of organic carbon and abundance of copiotrophic bacteria after biochar addition in ferralsol. However, the decreased bioavailability of SOC via adsorption of biochar resulted in higher abundance of oligotrophic bacteria in phaeozems, leading to the decrease in CO 2 emission. Copyright © 2017. Published by Elsevier B.V.

Carbon turnover in topsoil and subsoil: The microbial response to root litter additions and different environmental conditions in a reciprocal soil translocation experiment

NASA Astrophysics Data System (ADS)

Preusser, Sebastian; Poll, Christian; Marhan, Sven; Kandeler, Ellen

2017-04-01

At the global scale, soil organic carbon (SOC) represents the largest active terrestrial organic carbon (OC) pool. Carbon dynamics in subsoil, however, vary from those in topsoil with much lower C concentrations in subsoil than in topsoil horizons, although more than 50 % of SOC is stored in subsoils below 30 cm soil depth. In addition, microorganisms in subsoil are less abundant, more heterogeneously distributed and the microbial communities have a lower diversity than those in topsoil. Especially in deeper soil, the impact of changes in habitat conditions on microorganisms involved in carbon cycling are largely unexplored and consequently the understanding of microbial functioning is limited. A reciprocal translocation experiment allowed us to investigate the complex interaction effects of altered environmental and substrate conditions on microbial decomposer communities in both topsoil and subsoil habitats under in situ conditions. We conducted this experiment with topsoil (5 cm soil depth) and subsoil (110 cm) samples of an acid and sandy Dystric Cambisol from a European beech (Fagus sylvatica L.) forest in Lower Saxony, Germany. In total 144 samples were buried into three depths (5 cm, 45 cm and 110 cm) and 13C-labelled root litter was added to expose the samples to different environmental conditions and to increase the substrate availability, respectively. Samples were taken in three month intervals up to a maximum exposure time of one year to follow the temporal development over the experimental period. Analyses included 13Cmic and 13C PLFA measurements to investigate the response of microbial abundance, community structure and 13C-root decomposition activity under the different treatments. Environmental conditions in the respective soil depths such as soil temperature and water content were recorded throughout the experimental period. All microbial groups (gram+ and gram- bacteria, fungi) showed highest relative 13C incorporation in 110 cm depth and samples with root addition had generally higher microbial abundances than those with no root addition. Here, especially fungi benefited from the additional carbon source with highly increased abundances in all incorporation depths. Also the altered environmental conditions in the different incorporation depths significantly influenced the different microbial groups. The steepest decrease with depth was detected in fungal abundance, while bacteria were less affected and increased in relative abundance in soil samples incorporated into subsoil layers. The highest seasonal variability in microbial abundance, however, was determined in 5 cm incorporation depth demonstrating the higher amplitude in micro-climatic and micro-environmental conditions in this near-surface soil habitat. In summary, this experiment demonstrated that carbon quality and quantity are the main factors restricting fungal abundance in deeper soil layers, while bacterial decomposer communities are adapted to a wider range of habitat conditions.

[Soil fertility characteristics under different land use patterns in depressions between karst hills].

PubMed

Liu, Yan; Song, Tong-Qing; Cai, De-Suo; Zeng, Fu-Ping; Peng, Wan-Xia; Du, Hu

2014-06-01

Soil samples were collected from the depressions between karst hills by grid sampling method (5 m x 5 m), soil pH, soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) in surface layer (0-20 cm) under different land use patterns (burning, cutting, cutting plus root removal, enclosure, maize plantation, and pasture plantation) were measured, the main factors of influencing the soil fertility was identified by principal component analysis (PCA), and the relationships between soil nutrients and microorganisms were demonstrated by canonical correlation analysis (CCA). The results showed that the soil was slightly alkaline (pH 7.83-7.98), and the soil fertility differed under the different land use patterns, with 76.78-116.05 g x kg(-1) of SOC, 4.29-6.23 g x kg(-1) of TN, 1.15-1.47 g x kg(-1) of TP, 3.59-6.05 g x kg(-1) of TK, 331.49-505.49 mg x kg(-1) of AN), 3.92-10.91 mg x kg(-1) of AP, and 136.28-198.10 mg x kg(-1) of AK. These soil indexes except pH showed moderate or strong variation. Different land use patterns had various impacts on soil fertility: Soil nutrients such as SOC, TN, TP, and AN were most significantly influenced by land use patterns in the depressions between karst hills; Followed by soil microorganisms, especially soil actinomycetes, and the effect decreased with the increasing gradient of human disturbance from enclosure, burning, cutting, cutting plus root removal, pasture plantation, and maize plantation. CCA elucidated that considerable interactions existed in soil TP with MBP (microbial biomass phosphorus), TK with MBC (microbial biomass carbon), TN with actinomycetes in the burned area, while TN and MBC in the cutting treatment, AP and MBN (microbial biomass nitrogen) in the treatment of cutting plus root removal, pH with MBC and fungus in the enclosure treatment, TN and TK with MBP in the maize plantation, pH with fungi and actinomycetes in the pasture plantation. Land use patterns changed the soil fertility in the depressions between karst hills; therefore, in the ecological restoration and reconstruction of karst region with fragmented landforms and shallow soil, rational land use patterns should be adopted to improve the soil quality of degraded ecosystems.

Functional Diversity of Microbial Communities in Sludge-Amended Soils

NASA Astrophysics Data System (ADS)

Sun, Y. H.; Yang, Z. H.; Zhao, J. J.; Li, Q.

The BIOLOG method was applied to exploration of functional diversity of soil microbial communities in sludge-amended soils sampled from the Yangtze River Delta. Results indicated that metabolic profile, functional diversity indexes and Kinetic parameters of the soil microbial communities changed following soil amendment with sewage sludge, suggesting that the changes occurred in population of the microbes capable of exploiting carbon substrates and in this capability as well. The kinetic study of the functional diversity revealed that the metabolic profile of the soil microbial communities exhibited non-linear correlation with the incubation time, showing a curse of sigmoid that fits the dynamic model of growth of the soil microbial communities. In all the treatments, except for treatments of coastal fluvo-aquic soil amended with fresh sludge and dried sludge from Hangzhou, kinetic parameters K and r of the functional diversity of the soil microbial communities decreased significantly and parameter S increased. Changes in characteristics of the functional diversity well reflected differences in C utilizing capacity and model of the soil microbial communities in the sludge-amended soils, and changes in functional diversity of the soil microbial communities in a particular eco-environment, like soil amended with sewage sludge.

Carbon and Nitrogen Mineralization in Relation to Soil Particle-Size Fractions after 32 Years of Chemical and Manure Application in a Continuous Maize Cropping System

PubMed Central

Shao, Xingfang; Zhu, Ping; Zhang, Wenju; Xu, Minggang; Murphy, Daniel V.

2016-01-01

Long-term manure application is recognized as an efficient management practice to enhance soil organic carbon (SOC) accumulation and nitrogen (N) mineralization capacity. A field study was established in 1979 to understand the impact of long-term manure and/or chemical fertilizer application on soil fertility in a continuous maize cropping system. Soil samples were collected from field plots in 2012 from 9 fertilization treatments (M0CK, M0N, M0NPK, M30CK, M30N, M30NPK, M60CK, M60N, and M60NPK) where M0, M30, and M60 refer to manure applied at rates of 0, 30, and 60 t ha−1 yr−1, respectively; CK indicates no fertilizer; N and NPK refer to chemical fertilizer in the forms of either N or N plus phosphorus (P) and potassium (K). Soils were separated into three particle-size fractions (2000–250, 250–53, and <53 μm) by dry- and wet-sieving. A laboratory incubation study of these separated particle-size fractions was used to evaluate the effect of long-term manure, in combination with/without chemical fertilization application, on the accumulation and mineralization of SOC and total N in each fraction. Results showed that long-term manure application significantly increased SOC and total N content and enhanced C and N mineralization in the three particle-size fractions. The content of SOC and total N followed the order 2000–250 μm > 250–53μm > 53 μm fraction, whereas the amount of C and N mineralization followed the reverse order. In the <53 μm fraction, the M60NPK treatment significantly increased the amount of C and N mineralized (7.0 and 10.1 times, respectively) compared to the M0CK treatment. Long-term manure application, especially when combined with chemical fertilizers, resulted in increased soil microbial biomass C and N, and a decreased microbial metabolic quotient. Consequently, long-term manure fertilization was beneficial to both soil C and N turnover and microbial activity, and had significant effect on the microbial metabolic quotient. PMID:27031697

[Variations of soil labile organic carbon along an altitude gradient in Wuyi Mountain].

PubMed

Xu, Xia; Chen, Yue-Qin; Wang, Jia-She; Fang, Yan-Hong; Quan, Wei; Ruan, Hong-Hua; Xu, Zi-Kun

2008-03-01

By using sequential fumigation-incubation method, this paper determined the soil labile organic carbon (LOC) content under evergreen broadleaf forest, coniferous forest, sub-alpine dwarf forest, and alpine meadow along an altitude gradient in Wuyi Mountain National Nature Reserve in Fujian Province of China, with its relations to soil microbial biomass carbon (MBC), total organic carbon (TOC), total nitrogen (TN), and fine root biomass (FRB) analyzed. The results showed that soil LOC occupied 3.40%-7.46% of soil TOC, and soil MBC occupied 26.87%-80.38% of the LOC. The LOC under different forest stands increased significantly with altitude, and decreased with soil depth. Soil LOC had very significant correlations with soil MBC, TOC, TN and FRB, and its content was obviously higher at higher altitudes than at lower altitudes.

[Characteristics of soil microorganisms and soil nutrients in different sand-fixation shrub plantations in Kubuqi Desert, China].

PubMed

Zhang, Li-Xin; Duan, Yu Xi; Wang, Bo; Wang, Wei Feng; Li, Xiao Jing; Liu, Jin Jie

2017-12-01

Three types of sand-fixation shrub plantations, including Artemisia ordosica + Hedysarum fruticosum, Caragana korshinskii and Salix psammophila, were selected in the eastern area of Kubuqi Desert to study the changes in soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), quantities of soil microorganisms, contents of soil nutrients and the relations among these variables under the different plantation types and shifting sandy land. The restoration effects of each plantation type on soil quality were assessed by synthetic index method. The results showed that the contents of soil organic matter, total nitrogen and phosphorus, and available nitrogen and phosphorus under different plantations were all significantly greater than those under shifting sandy land, and the order of increase was A. ordosica + H. fruticosum ＞ C. korshinskii ＞ S. psammophila. The soil nutrient contents decreased with the increase of soil depth under all plantation types. The quantities of soil microorganisms and the contents of soil MBC and MBN under the plantations were higher at different degrees than those under shifting sandy land. MBC, MBN and the relative numbers of bacteria under A. ordosica+H. fruticosum plantation were higher than those under C. korshinskii plantation and S. psammophila plantation. The relative numbers of fungi and actinobacteria decreased in the order of C. korshinskii ＞ S. psammophila ＞ A. ordosica + H. fruticosum. The relative number of bacteria, MBC and MBN under the plantations were mainly affected by the contents of soil organic matter, total nitrogen, total phosphorus, available nitrogen, available phosphorus, as well as C/N, and the relative numbers of actinobacteria and fungi were primarily affected by the contents of soil total phosphorus, available nitrogen and available phosphorus. Soil quality was ranked in the order of A. ordosica + H. fruticosum ＞ C. korshinskii ＞ S. psammophila ＞ shifting sandy land. These results demonstrated that different sand-fixation shrub plantations could improve the quality of the desert soil and the A. ordosica + H. fruticosum plantation was the best for soil restoration and quality improvement in the desert.

Soil aggregate mediates the impacts of land uses on organic carbon, total nitrogen, and microbial activity in a Karst ecosystem

PubMed Central

Xiao, Shuangshuang; Zhang, Wei; Ye, Yingying; Zhao, Jie; Wang, Kelin

2017-01-01

Understanding the effect of land use on soil carbon, nitrogen, and microbial activity associated with aggregates is critical for thorough comprehension of the C and N dynamics of karst landscapes/ecosystems. We monitored soil organic carbon (SOC), total nitrogen (TN), microbial biomass carbon (MBC), and Cmic: Corg ratio in large macro- (>2 mm), small macro- (0.25–2 mm), and micro- (0.053–0.25 mm) aggregates to determine the changes in soil properties under different land uses in the karst area of Southwest China. Five common land-use types—enclosure land (natural system, control), prescribed-burning land, fuel-wood shrubland, pasture and maize fields—were selected. Results showed that pasture and maize fields remarkably decreased the SOC and TN concentrations in aggregates. Conversion of natural system to other land uses decreased MBC (except for prescribed-burning) and increased Cmic: Corg ratios in aggregates. The extent of the response to land uses of SOC and TN concentrations was similar whereas that of MBC and Cmic: Corg ratios differed across the three aggregate sizes. Further, the SOC concentrations were significantly higher in macro-aggregates than micro-aggregates; the MBC and Cmic: Corg ratios were highest in small macro-aggregates. Therefore, small macro-aggregates might have more active C dynamics. PMID:28211507

The importance of plant-soil interactions for N mineralisation in different soil types

NASA Astrophysics Data System (ADS)

Murphy, Conor; Paterson, Eric; Baggs, Elizabeth; Morley, Nicholas; Wall, David; Schulte, Rogier

2013-04-01

The last hundred years has seen major advancements in our knowledge of nitrogen mineralisation in soil, but key drivers and controls remain poorly understood. Due to an increase in the global population there is a higher demand on food production. To accommodate this demand agriculture has increased its use of N based fertilizers, but these pose risks for water quality and GHG emissions as N can be lost through nitrate leaching, ammonia volatilization, and denitrification processes (Velthof, et al., 2009). Therefore, understanding the underlying processes that determine the soils ability to supply N to the plant is vital for effective optimisation of N-fertilisation with crop demand. Carbon rich compounds exuded from plant roots to the rhizosphere, which are utilized by the microbial biomass and support activities including nutrient transformations, may be a key unaccounted for driver of N mineralisation. The main aim of this study was to study the impact of root exudates on turnover of C and N in soil, as mediated by the microbial community. Two soil types, known to contrast in N-mineralisation capacity, were used to determine relationships between C inputs, organic matter mineralisation (priming effects) and N fluxes. 15N and 13C stable isotope approaches were used to quantify the importance of rhizosphere processes on C and N mineralisation. Gross nitrogen mineralisation was measured using 15N pool dilution. Total soil CO2 efflux was measured and 13C isotope partitioning was applied to quantify SOM turnover and microbial biomass respiration. Also, 13C was traced through the microbial biomass (chloroform fumigation) to separate pool-substitution effects (apparent priming) from altered microbial utilisation of soil organic matter (real priming effects). Addition of labile carbon resulted in an increase in N-mineralisation from soil organic matter in both soils. Concurrent with this there was an increase in microbial biomass size, indicating that labile C elicited real priming effects that mobilised N from organic matter. The results from this experiment indicate that rhizosphere processes play an important role in mediating rates of C and N mineralisation and should be accounted for in estimating soil N-supply capacities. Velthof, G.L., Oudendag, D., Witzke, H.P., Asman, W.A.H., Klimont, Z., Oenema, O., 2009. Integrated assessment of nitrogen losses from agriculture in EU-27 using MITERRA-EUROPE. Journal of Environmental Quality 38, 402-417.

High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils.

PubMed

Min, Xiaobo; Wang, Yangyang; Chai, Liyuan; Yang, Zhihui; Liao, Qi

2017-09-01

To explore how heavy metal contamination in Chromite Ore Processing Residue (COPR) disposal sites determine the dissimilarities of indigenous microbial communities, 16S rRNA gene MiSeq sequencing and advanced statistical methods were applied. 13 soil samples were collected from three COPR disposal sites in Mouding of southwestern, Shangnan of northwestern and Yima of central China. The results of analyses of variance (ANOVA), similarities (ANOSIM), and non-metric multidimensional scaling (NMDS) showed that the structural diversity of the microbial communities in the samples with high total chromium (Cr) content (more than 300 mg kg -1 ; High group) were significantly lesser than in the Low group (less than 90 mg kg -1 ) regardless of their geographical distribution. But their diversity had virtually rehabilitated under the pressures of long-term metal contamination. Furthermore, the similarity percentage (SIMPER) analysis indicated that the major dissimilarity contributors Micrococcaceae, Delftia, and Streptophyta, possibly having Cr(VI)-resistant and/or Cr(VI)-reducing capability, were dominant in the High group, while Ramlibacter and Gemmatimonas with potential resistances to other heavy metals were prevalent in the Low group. In addition, the multivariate regression tree (MRT), aggregated boosted tree (ABT), and Mantel test revealed that total Cr content affiliated with Cr(VI) was the principal factor shaping the dissimilarities between the soil microbial communities in the COPR sites. Our findings provide a deep insight of the influence of these heavy metals on the microbial communities in the COPR disposal sites and will facilitate bioremediation on such site. Copyright © 2017 Elsevier Ltd. All rights reserved.

454 pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas.

PubMed

Li, Yuanyuan; Chen, Longqian; Wen, Hongyu; Zhou, Tianjian; Zhang, Ting; Gao, Xiali

2014-03-28

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coalmining reclamation areas was suggested.

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

PubMed Central

Xue, Kai; Wu, Liyou; Deng, Ye; He, Zhili; Van Nostrand, Joy; Robertson, Philip G.; Schmidt, Thomas M.

2013-01-01

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO3−, NH4+, available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO3− concentration and denitrification genes, NH4+ concentration and ammonification genes, and N2O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes. PMID:23241975

Effects of heavy metals on soil microbial community

NASA Astrophysics Data System (ADS)

Chu, Dian

2018-02-01

Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.

Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest

USGS Publications Warehouse

Waldrop, M.P.; Harden, J.W.

2008-01-01

Boreal forests contain significant quantities of soil carbon that may be oxidized to CO2 given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short-term effects of wildfire to the long-term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both 13C lignin decomposition and microbial respiration in incubation studies. Taken together, these results indicate that reductions in fungal biomass in postfire soils and lower soil moisture in nonpermafrost soils reduced the potential of soil heterotrophs to decompose soil carbon. Although in the field increased rates of microbial respiration can be observed in postfire soils due to warmer soil conditions, reductions in fungal biomass and activity may limit rates of decomposition. ?? 2008 The Authors Journal compilation ?? 2008 Blackwell Publishing.

Organic and inorganic fertilizer effect on soil CO2 flux, microbial biomass, and growth of Nigella sativa L.

NASA Astrophysics Data System (ADS)

Salehi, Aliyeh; Fallah, Seyfollah; Sourki, Ali Abasi

2017-01-01

Cattle manure has a high carbon/nitrogen ratio and may not decompose; therefore, full-dose application of urea fertilizer might improve biological properties by increasing manure decomposition. This study aimed to investigate the effect of combining cattle manure and urea fertilizer on soil CO2 flux, microbial biomass carbon, and dry matter accumulation during Nigella sativa L. (black cumin) growth under field conditions. The treatments were control, cattle manure, urea, different levels of split and full-dose integrated fertilizer. The results showed that integrated application of cattle manure and chemical fertilizer significantly increased microbial biomass carbon by 10%, soil organic carbon by 2.45%, total N by 3.27%, mineral N at the flowering stage by 7.57%, and CO2 flux by 9% over solitary urea application. Integrated application increased microbial biomass carbon by 10% over the solitary application and the full-dose application by 5% over the split application. The soil properties and growth parameters of N. sativa L. benefited more from the full-dose application than the split application of urea. Cattle manure combined with chemical fertilizer and the full-dose application of urea increased fertilizer efficiency and improved biological soil parameters and plant growth. This method decreased the cost of top dressing urea fertilizer and proved beneficial for the environment and medicinal plant health.

Changes of microbial activities and soil aggregation in rhizosphere soil of lettuce plants by drought and the possible influence of inoculation with AM fungi and/or PGPR

NASA Astrophysics Data System (ADS)

Kohler, J.; Caravaca, F.; Roldán, A.

2009-04-01

The effect of different arbuscular mycorrhizal (AM) fungi, Glomus intraradices (Schenk & Smith) or Glomus mosseae (Nicol & Gerd.) Gerd. & Trappe, and plant growth-promoting rhizobacteria (PGPR) (Pseudomonas mendocina Palleroni), alone or in combination, on structural stability and microbial activity in the rhizosphere soil of Lactuca sativa L. was assessed under well-watered conditions and two levels of drought. Desiccation caused an increase in aggregate stability and water-soluble and total carbohydrates but there were no significant differences among treated soils and the control soil. The glomalin-related soil protein (GRSP) levels in both the <2 mm and 0.2-4 mm soil fractions increased with medium water stress, whereas under severe water stress they did not differ with respect to those of well-watered soils. The values of GRSP in soils inoculated with PGPR and AM fungi were higher than in the control or fertilised soil under well-watered and severe-drought conditions, while under medium-drought conditions all soils showed similar GRSP values. Soils inoculated with AM fungi and PGPR generally presented higher dehydrogenase and phosphatase activities than the control soil, independent of the water regime.

Influence of altered precipitation pattern on greenhouse gas emissions and soil enzyme activities in Pannonian soils

NASA Astrophysics Data System (ADS)

Forstner, Stefan Johannes; Michel, Kerstin; Berthold, Helene; Baumgarten, Andreas; Wanek, Wolfgang; Zechmeister-Boltenstern, Sophie; Kitzler, Barbara

2013-04-01

Precipitation patterns are likely to be altered due to climate change. Recent models predict a reduction of mean precipitation during summer accompanied by a change in short-term precipitation variability for central Europe. Correspondingly, the risk for summer drought is likely to increase. This may especially be valid for regions which already have the potential for rare, but strong precipitation events like eastern Austria. Given that these projections hold true, soils in this area will receive water irregularly in few, heavy rainfall events and be subjected to long-lasting dry periods in between. This pattern of drying/rewetting can alter soil greenhouse gas fluxes, creating a potential feedback mechanism for climate change. Microorganisms are the key players in most soil carbon (C) and nitrogen (N) transformation processes including greenhouse gas exchange. A conceptual model proposed by Schimel and colleagues (2007) links microbial stress-response physiology to ecosystem-scale biogeochemical processes: In order to cope with decreasing soil water potential, microbes modify resource allocation patterns from growth to survival. However, it remains unclear how microbial resource acquisition via extracellular enzymes and microbial-controlled greenhouse gas fluxes respond to water stress induced by soil drying/rewetting. We designed a laboratory experiment to test for effects of multiple drying/rewetting cycles on soil greenhouse gas fluxes (CO2, CH4, N2O, NO), microbial biomass and extracellular enzyme activity. Three soils representing the main soil types of eastern Austria were collected in June 2012 at the Lysimeter Research Station of the Austrian Agency for Health and Food Safety (AGES) in Vienna. Soils were sieved to 2mm, filled in steel cylinders and equilibrated for one week at 50% water holding capacity (WHC) for each soil. Then soils were separated into two groups: One group received water several times per week (C=control), the other group received water only once in two weeks (D=dry). Both groups received same water totals for each soil. At the end of each two week drying period, greenhouse gas fluxes were measured via an open-chamber-system (CO2, NO) and a closed-chamber-approach (CH4, N2O, CO2). Additional cylinders were harvested destructively to quantify inorganic N forms, microbial biomass C, N and extracellular enzyme activity (Cellulase, Xylanase, Protease, Phenoloxidase, Peroxidase). We hypothesize that after rewetting (1) rates of greenhouse gas fluxes will generally increase, as well as (2) extracellular enzyme activity indicating enhanced microbial activity. However, response may be different for gases and enzymes involved in the C and N cycle, respectively, as drying/rewetting stress may uncouple microbial mediated biogeochemical cycles. Results will be presented at the EGU General Assembly. Reference: Schimel, J., Balser, T.C., and Wallenstein, M. (2007). Microbial stress-response physiology and its implications for ecosystem function. Ecology 88, 1386-1394.

Soil Microbial Properties and Plant Growth Responses to Carbon and Water Addition in a Temperate Steppe: The Importance of Nutrient Availability

PubMed Central

Guo, Chengyuan; Wang, Renzhong; Xiao, Chunwang

2012-01-01

Background Global climatic change is generally expected to stimulate net primary production, and consequently increase soil carbon (C) input. The enhanced C input together with potentially increased precipitation may affect soil microbial processes and plant growth. Methodology/Principal Findings To examine the effects of C and water additions on soil microbial properties and plant growth, we conducted an experiment lasting two years in a temperate steppe of northeastern China. We found that soil C and water additions significantly affected microbial properties and stimulated plant growth. Carbon addition significantly increased soil microbial biomass and activity but had a limited effect on microbial community structure. Water addition significantly increased soil microbial activity in the first year but the response to water decreased in the second year. The water-induced changes of microbial activity could be ascribed to decreased soil nitrogen (N) availability and to the shift in soil microbial community structure. However, no water effect on soil microbial activity was visible under C addition during the two years, likely because C addition alleviated nutrient limitation of soil microbes. In addition, C and water additions interacted to affect plant functional group composition. Water addition significantly increased the ratio of grass to forb biomass in C addition plots but showed only minor effects under ambient C levels. Our results suggest that soil microbial activity and plant growth are limited by nutrient (C and N) and water availability, and highlight the importance of nutrient availability in modulating the responses of soil microbes and plants to potentially increased precipitation in the temperate steppe. Conclusions/Significance Increased soil C input and precipitation would show significant effects on soil microbial properties and plant growth in the temperate steppe. These findings will improve our understanding of the responses of soil microbes and plants to the indirect and direct climate change effects. PMID:22496905

Bioremediation of petroleum-contaminated soil using aged refuse from landfills.

PubMed

Liu, Qingmei; Li, Qibin; Wang, Ning; Liu, Dan; Zan, Li; Chang, Le; Gou, Xuemei; Wang, Peijin

2018-05-10

This study explored the effects and mechanisms of petroleum-contaminated soil bioremediation using aged refuse (AR) from landfills. Three treatments of petroleum-contaminated soil (47.28 mg·g -1 ) amended with AR, sterilized aged refuse (SAR) and petroleum-contaminated soil only (as a control) were tested. During 98 days of incubation, changes in soil physicochemical properties, residual total petroleum hydrocarbon (TPH), biodegradation kinetics, enzyme activities and the microbial community were investigated. The results demonstrated that AR was an effective soil conditioner and biostimulation agent that could comprehensively improve the quality of petroleum-contaminated soil and promote microbial growth, with an 74.64% TPH removal rate, 22.36 day half-life for SAR treatment, compared with the control (half-life: 138.63 days; TPH removal rate: 22.40%). In addition, the petroleum-degrading bacteria isolation results demonstrated that AR was also a petroleum-degrading microbial agent containing abundant microorganisms. AR addition significantly improved both the biotic and abiotic conditions of petroleum-contaminated soil without other additives. The cooperation of conditioner addition, biostimulation and bioaugmentation in AR treatment led to better bioremediation effects (half-life: 13.86 days; TPH removal rate: 89.83%). In conclusion, AR amendment is a cost-effective, easy-to-use method facilitating in situ large-scale application while simultaneously recycling huge amounts of AR from landfills. Copyright © 2018 Elsevier Ltd. All rights reserved.

Native soil organic matter conditions the response of microbial communities to organic inputs with different stability

NASA Astrophysics Data System (ADS)

Yanardaǧ, Ibrahim H.; Zornoza, Raúl; Bastida, Felipe; Büyükkiliç-Yanardaǧ, Asuman; Acosta, Jose A.; García, Carlos; Faz, Ángel; Mermut, Ahmet R.

2017-04-01

The response of soil microbial communities from soils with different soil organic matter (SOM) content to organic inputs with different stability is still poorly understood. Thus, an incubation experiment was designed to study how the addition of pig slurry (PS), its manure (M) and its biochar (BC) affect soil microbial community and activity in three soils differing in SOM content (Regosol, Luvisol and Kastanozem). The evolution of different C and N fractions, microbial biomass C and N, enzyme activities and microbial community structure by the use of phospholipid fatty acid (PLFA) analysis was assessed for 60 days. Results showed that the different amendments had different effect on microbial properties depending on the soil type. The addition of M caused the highest increase in all microbial properties in the three soils, followed by PS. These changes were more intense in the soil with the lowest SOM (Regosol). The addition of M and PS caused changes in the microbial community structure in all soils, which were more related to the presence of available sources of N than to the labile fractions of C. The addition of BC was followed by increases in the proportions of fungi and Gram positive bacteria in the Regosol, while enhanced the proportion of actinobacteria in all soil types, related to increments in pH and soil C recalcitrance. Thus, native SOM determined the response of microbial communities to external inputs with different stability, soils with low SOM being more prone to increase microbial biomass and activity and change microbial community structure.

Will anticipated future climatic conditions affect belowground C utilization? - Insights into the role of microbial functional groups in a temperate heath/grassland.

NASA Astrophysics Data System (ADS)

Reinsch, Sabine; Michelsen, Anders; Sárossy, Zsuzsa; Egsgaard, Helge; Kappel Schmidt, Inger; Jakobsen, Iver; Ambus, Per

2013-04-01

The global terrestrial soil organic matter stock is the biggest terrestrial carbon pool (1500 Pg C) of which about 4 % is turned over annually. Thus, terrestrial ecosystems have the potential to accelerate or diminish atmospheric climate change effects via belowground carbon processes. We investigated the effect of elevated CO2 (510 ppm), prolonged spring/summer droughts and increased temperature (1 ˚C) on belowground carbon allocation and on the recovery of carbon by the soil microbial community. An in-situ 13C-carbon pulse-labeling experiment was carried out in a temperate heath/grassland (Denmark) in May 2011. Recently assimilated 13C-carbon was traced into roots, soil and microbial biomass 1, 2 and 8 days after pulse-labeling. The importance of the microbial community in C utilization was investigated using 13C enrichment patterns in microbial functional groups on the basis of phospholipid fatty acids (PLFAs) in roots. Gram-negative and gram-positive bacteria were distinguished from the decomposer groups of actinomycetes (belonging to the group of gram-positive bacteria) and saprophytic fungi. Mycorrhizal fungi specific PLFAs were not detected probably due to limited sample size in combination with restricted sensitivity of the used GC-c-IRMS setup. Climate treatments did not affect 13C allocation into roots, soil and microbial biomass carbon and also the total microbial biomass size stayed unchanged as frequently observed. However, climate treatments changed the composition of the microbial community: elevated CO2 significantly reduced the abundance of gram-negative bacteria (17:0cy) but did not affect the abundance of decomposers. Drought favored the bacterial community whereas increased temperatures showed reduced abundance of gram-negative bacteria (19:0cy) and changed the actinomycetes community (10Me16:0, 10Me18:0). However, not only the microbial community composition was affected by the applied climatic conditions, but also the activity of microbial functional groups in their utilization of recently assimilated carbon. Particularly the negative effect of the future treatment combination (CO2×T×D) on actinomycetes activity was surprising. By means of activity patterns of gram-negative bacteria, we observed the fastest carbon turnover rate under elevated CO2, and the slowest under extended drought conditions. A changed soil microbial community in combination with altered activities of different microbial functional groups leads to the conclusion that carbon allocation belowground was different under ambient and future climatic conditions and indicated reduced utilization of soil organic matter in the future due to a change of actinomycetes abundance and activity.

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

DOE PAGES

Penton, Christopher R.; St. Louis, Derek; Pham, Amanda; ...

2015-07-21

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

Rhizobial Inoculation Increases Soil Microbial Functioning and Gum Arabic Production of 13-Year-Old Senegalia senegal (L.) Britton, Trees in the North Part of Senegal.

PubMed

Fall, Dioumacor; Bakhoum, Niokhor; Nourou Sall, Saïdou; Zoubeirou, Alzouma Mayaki; Sylla, Samba N; Diouf, Diegane

2016-01-01

Rhizobial inoculation has been widely used in controlled conditions as a substitute for chemical fertilizers to increase plants growth and productivity. However, very little is known about such effects on mature trees in natural habitats. In this study, we investigated the effect of rhizobial inoculation on soil total microbial biomass, mineral nitrogen content, potential CO2 respiration, fluorescein diacetate (FDA), acid phosphatase activities, and gum arabic production by 13-year-old Senegalia senegal (synonym: Acacia senegal) under natural conditions in the north part of Senegal during two consecutive years. Rhizobial inoculation was performed at the beginning of the rainy season (July) for both years with a cocktail of four strains (CIRADF 300, CIRADF 301, CIRADF 302, and CIRADF 303). Rhizospheric soils were collected in both dry and rainy seasons to a depth of 0-25 cm under uninoculated and inoculated trees. Trees were tapped in November (beginning of dry season) using traditional tools. Gum arabic was harvested every 15 days from December to March. The results obtained from both years demonstrated that rhizobial inoculation increased significantly the percentage of trees producing gum arabic, gum arabic production per tree, soil microbial biomass, FDA, and acid phosphatase activities. However, there was no significant effect on C mineralization and mineral nitrogen (N) content. Gum arabic production was positively correlated to rainfall, soil microbial biomass, and mineral nitrogen content. Our results showed a positive effect of rhizobial inoculation on soil microbial functioning and gum arabic production by mature S. senegal trees. These important findings deserve to be conducted in several contrasting sites in order to improve gum arabic production and contribute to increase rural population incomes.

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Penton, Christopher R.; St. Louis, Derek; Pham, Amanda

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

Rhizobial Inoculation Increases Soil Microbial Functioning and Gum Arabic Production of 13-Year-Old Senegalia senegal (L.) Britton, Trees in the North Part of Senegal

PubMed Central

Fall, Dioumacor; Bakhoum, Niokhor; Nourou Sall, Saïdou; Zoubeirou, Alzouma Mayaki; Sylla, Samba N.; Diouf, Diegane

2016-01-01

Rhizobial inoculation has been widely used in controlled conditions as a substitute for chemical fertilizers to increase plants growth and productivity. However, very little is known about such effects on mature trees in natural habitats. In this study, we investigated the effect of rhizobial inoculation on soil total microbial biomass, mineral nitrogen content, potential CO2 respiration, fluorescein diacetate (FDA), acid phosphatase activities, and gum arabic production by 13-year-old Senegalia senegal (synonym: Acacia senegal) under natural conditions in the north part of Senegal during two consecutive years. Rhizobial inoculation was performed at the beginning of the rainy season (July) for both years with a cocktail of four strains (CIRADF 300, CIRADF 301, CIRADF 302, and CIRADF 303). Rhizospheric soils were collected in both dry and rainy seasons to a depth of 0–25 cm under uninoculated and inoculated trees. Trees were tapped in November (beginning of dry season) using traditional tools. Gum arabic was harvested every 15 days from December to March. The results obtained from both years demonstrated that rhizobial inoculation increased significantly the percentage of trees producing gum arabic, gum arabic production per tree, soil microbial biomass, FDA, and acid phosphatase activities. However, there was no significant effect on C mineralization and mineral nitrogen (N) content. Gum arabic production was positively correlated to rainfall, soil microbial biomass, and mineral nitrogen content. Our results showed a positive effect of rhizobial inoculation on soil microbial functioning and gum arabic production by mature S. senegal trees. These important findings deserve to be conducted in several contrasting sites in order to improve gum arabic production and contribute to increase rural population incomes. PMID:27656192

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau.

PubMed

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Zhou, Huakun; Ganjurjav, Hasbagan; Wang, Xuexia

2016-08-15

Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, <10% variations of microbial diversity was explained by soil properties; and the soil microbial communities among different treatments were similar. The soil microbial community in the cultivated grassland was varied from it in native grasslands. Over 50% variations of soil microbial communities among different treatments were explained by soil nutrients and moisture in each grassland type. Our results suggest that climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter.

PubMed

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; Koechli, Chantal; Campbell, Ashley; Buckley, Daniel H; Lehmann, Johannes

2016-12-01

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.

Organic matter composition and substrate diversity under elevated CO2 in the Mojave Desert

NASA Astrophysics Data System (ADS)

Tfaily, M. M.; Hess, N. J.; Koyama, A.; Evans, R. D.

2016-12-01

Little is known about how rising atmospheric CO2 concentration will impact long-term plant biomass or the dynamics of soil organic matter (SOM) in arid ecosystems. In this study, we investigated the change in the molecular composition of SOM by high resolution mass spectrometry after 10 years exposure to elevated atmospheric CO2 concentrations at the Nevada Desert FACE Facility. Samples were collected from soil profiles from 0 to 1m in 0.2m increments under the dominant evergreen shrub (Larrea tridentata). The differences in the composition of SOM were more evident in soils close to the surface and consistent with higher bulk soil organic carbon (C) and total nitrogen (N) concentrations under elevated than ambient CO2, reflecting increased net productivity of shrubs under elevated CO2, which could be attributed to increased litter input from above-ground biomass and/or shallow roots, root exudation and/or microbial residues. This was further supported by the significant increase in the abundance of amino sugars-, protein- and carbohydrate-like compounds. These compounds are involved in diverse pathways ranging from sugars and amino-acid metabolism to lipid biosynthesis. This indicates increased activity and metabolism under elevated CO2 and suggests that elevated CO2 have altered microbial C use patterns, reflecting changes in the quality and quantity of soil C inputs. A significant increase in the mineral-bound soil organic C was also observed in the surface soils under elevated CO2. This was accompanied by increased microbial residues as identified by mass spectrometry that supports microbial lipid analysis, and reflecting accelerated microbial turnover under elevated CO2. Fungal neutral lipid fatty acids (NLFA) abundance doubled under elevated CO2. When provided with excess labile compounds, such as root exudates, and with limited supply of nutrients, fungi assimilate the excess labile C and store it as NLFA likely contributing to increased total N concentrations. This was further supported by the presence of acetyl glucosamine, a typical amino sugar, present in the chitin of fungi, under elevated than ambient CO2. Our results suggest that arid ecosystems, limited by water, may have a different C storage potential under changing climates than other ecosystems that are limited by N or P.

Stereoselective accumulations of hexachlorocyclohexanes (HCHs) are correlated with Sphingomonas spp. in agricultural soils across China.

PubMed

Xu, Yang; Niu, Lili; Qiu, Jiguo; Zhou, Yuting; Lu, Huijie; Liu, Weiping

2018-05-02

The wide usage of hexachlorocyclohexanes (HCHs) as pesticides has caused soil pollution and adverse health effects through direct contact or bioaccumulation in the food chain. This study quantified major HCH isomers in farmland topsoils across China, and evaluated their correlations with microbial community structure, function, and abiotic variables (e.g., moisture, pH, and temperature). Recalcitrant β-HCH was more abundant than α-, γ-, and δ-HCHs, and α-HCH enantiomeric fractions (EF) were larger than 0.5, indicating preferential degradation of (-)-α-HCH. Sphingomonas was not only a predominant population (especially in samples collected in the south), but also a promising biomarker indicating total- and β-HCH residuals, and EF values of α-HCH. Soil moisture and temperature were among the most influential factors that structured the diversity and function of soil microbial communities. The results suggested that increasing soil moisture (in the range of 5-45%) would benefit the growth of HCH-degrading populations and the enrichment of HCH-degradation related pathways. Revealing the site-specific relationships between topsoil physical, chemical, and microbial properties will benefit the in situ bioremediation of farmlands with relatively low HCH residuals across the world. Copyright © 2018 Elsevier Ltd. All rights reserved.

Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils.

PubMed

Wu, Meng; Liu, Jia; Li, Weitao; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2017-10-01

Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There has been few studies evaluating the toxicological effects of CAP on soil-associated microbes. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP in three types of paddy soils in subtropical China. The effects of CAP on microbial activities (microbial biomass carbon-MBC, basal soil respiration-BSR, microbial metabolic quotient-qCO 2 , acid phosphatase and sucrose invertase activities) in the soils were periodically evaluated. Microbial phospholipid fatty acid (PLFA) analysis was used to evaluate the change of soil microbial community composition on day 14 and 50 of the experiment. CAP residues were extracted using the quick, easy, cheap, effective, rugged, and safe (QuChERS) method and quantification was measured by high performance liquid chromatography (HPLC). The half-lives (DT 50 ) of CAP were in the range of 41.0-53.0 days in the three soils. The results showed that CAP did not impart negative effects on MBC during the incubation. CAP inhibited BSR, qCO 2 , acid phosphatase and sucrose invertase activities in the first 14 days of incubation in all the soils. After day 14, the soil microbial parameters of CAP-treated soils became statistically at par with their controls. Principal component analysis (PCA) determining abundance of biomarker PLFAs indicated that the application of CAP significantly changed the compositions of microbial communities in all three paddy soils on day 14 but the compositions of soil microbial communities recovered by day 50. This study indicates that CAP does not ultimately impair microbial activities and microbial compositions of these three paddy soil types. Copyright © 2017 Elsevier Inc. All rights reserved.

[Effect of long-term fertilization on microbial community functional diversity in black soil].

PubMed

Liu, Jing-xin; Chi, Feng-qin; Xu, Xiu-hong; Kuang, En-jun; Zhang, Jiu-ming; Su, Qing-rui; Zhou, Bao-ku

2015-10-01

In order to study the effects of long-term different fertilization on microbial community functional diversity in arable black. soil, we examined microbial metabolic activities in two soil la- yers (0-20 cm, 20-40 cm) under four treatments (CK, NPK, M, MNPK) from a 35-year continuous fertilization field at the Ministry of Agriculture Key Field Observation Station of Harbin Black Soil Ecology Environment using Biolog-ECO method. The results showed that: in the 0-20 cm soil layer, combined application of organic and inorganic fertilizer(MNPK) increased the rate of soil microbial carbon source utilization and community metabolism richness, diversity and dominance; In the 20-40 cm layer, these indices of the MNPK treatment was lower than that of the NPK treat- ment; while NPK treatment decreased soil microbial community metabolism evenness in both layers. Six groups of carbon sources used by soil microbes of all the treatments were different between the two soil layers, and the difference was significant among all treatments in each soil layer (P < 0.05) , while the variations among treatments were different in the two soil layers. Canonical correspondence analysis (CCA) showed that soil microbial community metabolic function of all the treatments was different between the two soil layers, and there was difference among all treatments in each soil layer, while the influences of soil nutrients on soil microbial community metabolic function of all treatments were similar in each soil layer. It was concluded that long-term different fertilization affected soil microbial community functional diversity in both tillage soil layer and down soil layers, and chemical fertilization alone had a larger influence on the microbial community functional diversity in the 20-40 cm layer.

Carbon use efficiency (CUE) and biomass turnover of soil microbial communities as affected by bedrock, land management and soil temperature and moisture

NASA Astrophysics Data System (ADS)

Zheng, Qing; Hu, Yuntao; Richter, Andreas; Wanek, Wolfgang

2017-04-01

Soil microbial carbon use efficiency (CUE), defined as the proportion of organic C taken up that is allocated to microbial growth, represents an important synthetic representation of microbial community C metabolism that describes the flux partitioning between microbial respiration and growth. Therefore, studying microbial CUE is critical for the understanding of soil C cycling. Microbial CUE is thought to vary with environmental conditions (e.g. temperature and soil moisture). Microbial CUE is thought to decrease with increasing temperature and declining soil moisture, as the latter may trigger stress responses (e.g. the synthesis of stress metabolites), which may consequently lower microbial community CUE. However, these effects on microbial CUE have not been adequately measured so far due to methodological restrictions. The most widely used methods for microbial CUE estimation are based on tracing 13C-labeled substrates into microbial biomass and respiratory CO2, approaches that are known to overestimate microbial CUE of native organic matter in soil. Recently, a novel substrate-independent approach based on the measurement of (i) respiration rates and (ii) the incorporation rates of 18O from labelled water into newly formed microbial DNA has been developed in our laboratory for measuring microbial CUE. This approach overcomes the shortcomings of previously used methods and has already been shown to yield realistic estimations of soil microbial CUE. This approach can also be applied to concurrently measure microbial biomass turnover rates, which also influence the sequestration of soil organic C. Microbial turnover rates are also thought to be impacted by environmental factors, but rarely have been directly measured so far. Here, we aimed at determining the short-term effects of environmental factors (soil temperature and soil moisture) on microbial CUE and microbial biomass turnover rates based on the novel 18O approach. Soils from three land-use types (arable fields, pasture and forest) sampled from two geologies (silicate versus limestone) in the same region in Austria were incubated at three temperatures (5, 15 and 25 ˚ C) for 1 day and at three moisture levels (30, 60, 90% water-holding capacity) for 7 days in the laboratory, respectively. We will present the results and discuss major effects of environmental factors as well as of land management and geology on microbial growth, respiration, microbial CUE and microbial biomass turnover, and set those in relation to microbial community composition.

Assessment of Cu applications in two contrasting soils-effects on soil microbial activity and the fungal community structure.

PubMed

Keiblinger, Katharina M; Schneider, Martin; Gorfer, Markus; Paumann, Melanie; Deltedesco, Evi; Berger, Harald; Jöchlinger, Lisa; Mentler, Axel; Zechmeister-Boltenstern, Sophie; Soja, Gerhard; Zehetner, Franz

2018-03-01

Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community. Two contrasting agricultural soils, an acidic sandy loam and an alkaline silt loam, were used for an eco-toxicological greenhouse pot experiment. The soils were spiked with a Cu-based fungicide in seven concentrations (0-5000 mg Cu kg -1 soil) and alfalfa was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test Cu toxicity effects on total microbial biomass, basal respiration and enzyme activities. Fungal abundance was analysed by ergosterol at both samplings, and for the second sampling, fungal community structure was evaluated via ITS amplicon sequences. Soil microbial biomass C as well as microbial respiration rate decreased with increasing Cu concentrations, with EC 50 ranging from 76 to 187 mg EDTA-extractable Cu kg -1 soil. Oxidative enzymes showed a trend of increasing activity at the first sampling, but a decline in peroxidase activity was observed for the second sampling. We found remarkable Cu-induced changes in fungal community abundance (EC 50 ranging from 9.2 to 94 mg EDTA-extractable Cu kg -1 soil) and composition, but not in diversity. A large number of diverse fungi were able to thrive under elevated Cu concentrations, though within the order of Hypocreales several species declined. A remarkable Cu-induced change in the community composition was found, which depended on the soil properties and, hence, on Cu availability.

Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community.

PubMed

Wang, Yi; Li, Chunyue; Tu, Cong; Hoyt, Greg D; DeForest, Jared L; Hu, Shuijin

2017-12-31

Intensive tillage and high inputs of chemicals are frequently used in conventional agriculture management, which critically depresses soil properties and causes soil erosion and nonpoint source pollution. Conservation practices, such as no-tillage and organic farming, have potential to enhance soil health. However, the long-term impact of no-tillage and organic practices on soil microbial diversity and community structure has not been fully understood, particularly in humid, warm climate regions such as the southeast USA. We hypothesized that organic inputs will lead to greater microbial diversity and a more stable microbial community, and that the combination of no-tillage and organic inputs will maximize soil microbial diversity. We conducted a long-term experiment in the southern Appalachian mountains of North Carolina, USA to test these hypotheses. The results showed that soil microbial diversity and community structure diverged under different management regimes after long term continuous treatments. Organic input dominated the effect of management practices on soil microbial properties, although no-tillage practice also exerted significant impacts. Both no-tillage and organic inputs significantly promoted soil microbial diversity and community stability. The combination of no-tillage and organic management increased soil microbial diversity over the conventional tillage and led to a microbial community structure more similar to the one in an adjacent grassland. These results indicate that effective management through reducing tillage and increasing organic C inputs can enhance soil microbial diversity and community stability. Copyright © 2017 Elsevier B.V. All rights reserved.

Microorganisms in small patterned ground features and adjacent vegetated soils along topographic and climatic gradients in the High Arctic, Canada

Treesearch

G. Gonzalez; F.J. Rivera-Figueroa; W. Gould; S.A. Cantrell; J.R. Pérez-Jiménez

2014-01-01

In this study, we determine differences in total biomass of soil microorganisms and community structure (using the most probable number of bacteria (MPN) and the number of fungal genera) in patterned ground features (PGF) and adjacent vegetated soils (AVS) in mesic sites from three High Arctic islands in order to characterize microbial dynamics as affected by...

[Effects of applying inorganic P and wheat straw on the microbial biomass P and microbial P concentration in a calcareous soil with low concentration available P].

PubMed

Zhao, Xiao-Rong; Zhou, Ran; Li, Gui-Tong; Lin, Qi-Mei

2009-02-01

In an incubation test, a calcareous soil with low concentration of available P was amended with KH2PO4 (0, 25, 50, and 100 mg P x kg(-1)) and ground wheat straw (5 g C x kg(-1)), and incubated at 25 degrees C for 90 days. The aim was to investigate the change patterns of soil microbial biomass P and microbial P concentration as well as their relationships with soil available P. The results showed that both soil microbial biomass P and microbial P concentration increased with increasing inorganic P addition, with the maximum being 71.37 and 105.34 mg x kg(-1), respectively. The combined application of inorganic P (except 100 mg P x kg(-1)) and wheat straw decreased the soil microbial biomass P and microbial P concentration, being most obvious at early incubation period. Soil microbial biomass P and microbial P concentration had significant positive correlations (P < 0.05) with soil available P (R2 = 0.26 and 0.40, n = 49, respectively). The applied P could rapidly transform into microbial biomass P. The maximum apparent contribution rate of applied P to microbial biomass P was 71%. The added wheat straw could further improve the apparent contribution rate.

Effect of different cover crops on C and N cycling in sorghum NT systems.

PubMed

Frasier, Ileana; Quiroga, Alberto; Noellemeyer, Elke

2016-08-15

In many no-till (NT) systems, residue input is low and fallow periods excessive, for which reasons soil degradation occurs. Cover crops could improve organic matter, biological activity, and soil structure. In order to study changes in soil carbon, nitrogen and microbial biomass a field experiment (2010-2012) was set up with sorghum (Sorghum bicolor Moench.) monoculture and with cover crops. Treatments were control (NT with bare fallow), rye (Secale cereale L.) (R), rye with nitrogen fertilization (R+N), vetch (Vicia villosa Roth.) (V), and rye-vetch mixture (VR) cover crops. A completely randomized block design with 4 replicates was used. Soil was sampled once a year at 0.06 and 0.12m depth for total C, microbial biomass carbon (MBC) and-nitrogen (MBN) determinations. Shoot and root biomass of sorghum and cover crops, litter biomass, and their respective carbon and nitrogen contents were determined. Soil temperatures at 0.06 and 0.12m depth, volumetric water contents and nitrate concentrations were determined at sowing, and harvest of each crop, and during sorghum's vegetative phase. NT led to a small increase in MBC and MBN, despite low litter and root biomass residue. Cover crops increased litter, root biomass, total C, MBC, and MBN. Relationships between MBC, MBN, and root-C and -N adjusted to logistic models (R(2)=0.61 and 0.43 for C and N respectively). Litter cover improved soil moisture to 45-50% water filled pore space and soil temperatures not exceeding 25°C during the warmest month. Microbial biomass stabilized at 20.1gCm(-2) and 1.9gNm(-2) in the upper 0.06m. Soil litter disappearance was a good indicator of mineral N availability. These findings support the view that cover crops, specifically legumes in NT systems can increase soil ecosystem services related to water and carbon storage, habitat for biodiversity, and nutrient availability. Copyright © 2016 Elsevier B.V. All rights reserved.

Anthropogenic nitrogen deposition enhances carbon sequestration in boreal soils.

PubMed

Maaroufi, Nadia I; Nordin, Annika; Hasselquist, Niles J; Bach, Lisbet H; Palmqvist, Kristin; Gundale, Michael J

2015-08-01

It is proposed that carbon (C) sequestration in response to reactive nitrogen (Nr ) deposition in boreal forests accounts for a large portion of the terrestrial sink for anthropogenic CO2 emissions. While studies have helped clarify the magnitude by which Nr deposition enhances C sequestration by forest vegetation, there remains a paucity of long-term experimental studies evaluating how soil C pools respond. We conducted a long-term experiment, maintained since 1996, consisting of three N addition levels (0, 12.5, and 50 kg N ha(-1) yr(-1) ) in the boreal zone of northern Sweden to understand how atmospheric Nr deposition affects soil C accumulation, soil microbial communities, and soil respiration. We hypothesized that soil C sequestration will increase, and soil microbial biomass and soil respiration will decrease, with disproportionately large changes expected compared to low levels of N addition. Our data showed that the low N addition treatment caused a non-significant increase in the organic horizon C pool of ~15% and a significant increase of ~30% in response to the high N treatment relative to the control. The relationship between C sequestration and N addition in the organic horizon was linear, with a slope of 10 kg C kg(-1) N. We also found a concomitant decrease in total microbial and fungal biomasses and a ~11% reduction in soil respiration in response to the high N treatment. Our data complement previous data from the same study system describing aboveground C sequestration, indicating a total ecosystem sequestration rate of 26 kg C kg(-1) N. These estimates are far lower than suggested by some previous modeling studies, and thus will help improve and validate current modeling efforts aimed at separating the effect of multiple global change factors on the C balance of the boreal region. © 2015 John Wiley & Sons Ltd.

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

DOE PAGES

Xue, Kai; Xie, Jianping; Zhou, Aifen; ...

2016-05-06

Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on microbial functional gene expressions. Here, we applied functional gene array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA to assess expressed functional genes in active soil microbial communities after nine years of experimental warming in a tallgrass prairie. Our results showed that warming significantly altered the community wide gene expressions. Specifically, expressed genes for degrading more recalcitrant carbon were stimulated by warming, likely linked to the plant community shift toward moremore » C 4 species under warming and to decrease the long-term soil carbon stability. In addition, warming changed expressed genes in labile C degradation and N cycling in different directions (increase and decrease), possibly reflecting the dynamics of labile C and available N pools during sampling. However, the average abundances of expressed genes in phosphorus and sulfur cycling were all increased by warming, implying a stable trend of accelerated P and S processes which might be a mechanism to sustain higher plant growth. Furthermore, the expressed gene composition was closely related to both dynamic (e.g., soil moisture) and stable environmental attributes (e.g., C 4 leaf C or N content), indicating that RNA analyses could also capture certain stable trends in the long-term treatment. Overall, this study revealed the importance of elucidating functional gene expressions of soil microbial community in enhancing our understanding of ecosystem responses to warming.« less

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

PubMed Central

Xue, Kai; Xie, Jianping; Zhou, Aifen; Liu, Feifei; Li, Dejun; Wu, Liyou; Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Luo, Yiqi; Zhou, Jizhong

2016-01-01

Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on microbial functional gene expressions. Here, we applied functional gene array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA to assess expressed functional genes in active soil microbial communities after nine years of experimental warming in a tallgrass prairie. Our results showed that warming significantly altered the community wide gene expressions. Specifically, expressed genes for degrading more recalcitrant carbon were stimulated by warming, likely linked to the plant community shift toward more C4 species under warming and to decrease the long-term soil carbon stability. In addition, warming changed expressed genes in labile C degradation and N cycling in different directions (increase and decrease), possibly reflecting the dynamics of labile C and available N pools during sampling. However, the average abundances of expressed genes in phosphorus and sulfur cycling were all increased by warming, implying a stable trend of accelerated P and S processes which might be a mechanism to sustain higher plant growth. Furthermore, the expressed gene composition was closely related to both dynamic (e.g., soil moisture) and stable environmental attributes (e.g., C4 leaf C or N content), indicating that RNA analyses could also capture certain stable trends in the long-term treatment. Overall, this study revealed the importance of elucidating functional gene expressions of soil microbial community in enhancing our understanding of ecosystem responses to warming. PMID:27199978

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xue, Kai; Xie, Jianping; Zhou, Aifen

Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on microbial functional gene expressions. Here, we applied functional gene array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA to assess expressed functional genes in active soil microbial communities after nine years of experimental warming in a tallgrass prairie. Our results showed that warming significantly altered the community wide gene expressions. Specifically, expressed genes for degrading more recalcitrant carbon were stimulated by warming, likely linked to the plant community shift toward moremore » C 4 species under warming and to decrease the long-term soil carbon stability. In addition, warming changed expressed genes in labile C degradation and N cycling in different directions (increase and decrease), possibly reflecting the dynamics of labile C and available N pools during sampling. However, the average abundances of expressed genes in phosphorus and sulfur cycling were all increased by warming, implying a stable trend of accelerated P and S processes which might be a mechanism to sustain higher plant growth. Furthermore, the expressed gene composition was closely related to both dynamic (e.g., soil moisture) and stable environmental attributes (e.g., C 4 leaf C or N content), indicating that RNA analyses could also capture certain stable trends in the long-term treatment. Overall, this study revealed the importance of elucidating functional gene expressions of soil microbial community in enhancing our understanding of ecosystem responses to warming.« less

Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

NASA Astrophysics Data System (ADS)

Wieczorek, A. S.; Hetz, S. A.; Kolb, S.

2014-06-01

Microbial degradation of chitin in soil substantially contributes to carbon cycling in terrestrial ecosystems. Chitin is globally the second most abundant biopolymer after cellulose and can be deacetylated to chitosan or can be hydrolyzed to N,N'-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities is unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, and carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation, along with ammonification, were likely responsible for anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of less than 50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions on community level.

Carbon availability structures microbial community composition and function in soil aggregate fractions

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

2014-12-01

Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of microbial communities on terrestrial C and N cycling.

[Effects of biochar on microbial ecology in agriculture soil: a review].

PubMed

Ding, Yan-Li; Liu, Jie; Wang, Ying-Ying

2013-11-01

Biochar, as a new type of soil amendment, has been obtained considerable attention in the research field of environmental sciences worldwide. The studies on the effects of biochar in improving soil physical and chemical properties started quite earlier, and already covered the field of soil microbial ecology. However, most of the studies considered the soil physical and chemical properties and the microbial ecology separately, with less consideration of their interactions. This paper summarized and analyzed the interrelationships between the changes of soil physical and chemical properties and of soil microbial community after the addition of biochar. Biochar can not only improve soil pH value, strengthen soil water-holding capacity, increase soil organic matter content, but also affect soil microbial community structure, and alter the abundance of soil bacteria and fungi. After the addition of biochar, the soil environment and soil microorganisms are interacted each other, and promote the improvement of soil microbial ecological system together. This review was to provide a novel perspective for the in-depth studies of the effects of biochar on soil microbial ecology, and to promote the researches on the beneficial effects of biochar to the environment from ecological aspect. The methods to improve the effectiveness of biochar application were discussed, and the potential applications of biochar in soil bioremediation were further analyzed.

Greatest soil microbial diversity found in micro-habitats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

Toxic industrial deposit remediation by ant activity

NASA Astrophysics Data System (ADS)

Jilkova, Veronika; Frouz, Jan

2016-04-01

Toxic industrial deposits are often contaminated by heavy metals and the substrates have low pH values. In such systems, soil development is thus slowed down by high toxicity and acidic conditions which are unfavourable to soil fauna. Ants (Hymenoptera, Formicidae) are considered tolerant to heavy metal pollution and are known to increase organic matter content and microbial activity in their nests. Here, we focused on soil remediation caused by three ant species (Formica sanguinea, Lasius niger, and Tetramorium sp.) in an ore-washery sedimentation basin near Chvaletice (Czech Republic). Soil samples were taken from the centre of ant nests and from the nest surroundings (>3 m from nests). Samples were then analyzed for microbial activity and biomass and contents of organic matter and nutrients. As a result, ant species that most influenced soil properties was F. sanguinea as there were higher microbial activity and total nitrogen and ammonia contents in ant nests than in the surrounding soil. We expected such a result because F. sanguinea builds conspicuous large nests and is a carnivorous species that brings substantial amounts of nitrogen in insect prey to their nests. Effects of the other two ant species might be lower because of smaller nests and different feeding habits as they rely mainly on honeydew from aphids or on plant seeds that do not contain much nutrients.

Phytoremediation of a nitrogen-contaminated desert soil by native shrubs and microbial processes

DOE PAGES

Glenn, Edward P.; Jordan, Fiona; Waugh, W. Joseph

2016-02-24

Here, we combined phytoremediation and soil microbial nitrification and denitrification cycles to reduce nitrate and ammonium levels at a former uranium mill site near Monument Valley, Arizona. Ammonia used in uranium extraction was present throughout the soil profile. Sulfate,applied as sulfuric acid to solubilize uranium, was also present in the soil. These contaminants were leaching from a denuded area where a tailings pile had been removed and were migrating away from the site in groundwater. We planted the source area with two deep-rooted native shrubs, Atriplex cansescens and Sarcobatus vermiculatus, and irrigated transplants for 11 years at 20% the ratemore » of potential evapotranspiration to stimulate growth, then discontinued irrigation for 4 years. Over 15 years, total nitrogen levels dropped 82%, from 347 to 64 mg kg –1. Analysis of δ 15N supported our hypothesis that coupled microbial nitrification and denitrification processes were responsible for the loss of N. Soil sulfate levels changed little; however, evapotranspiration reduced sulfate leaching into the aquifer. For arid sites where traditional pump-and-treat methods are problematic, the Monument Valley data suggest that alternatives that incorporate native plants and rely on vadose zone biogeochemistry and hydrology could be a sustainable remediation for nitrogen contaminated soil.« less

Occurrence and quantitative microbial risk assessment of Cryptosporidium and Giardia in soil and air samples.

PubMed

Balderrama-Carmona, Ana Paola; Gortáres-Moroyoqui, Pablo; Álvarez-Valencia, Luis Humberto; Castro-Espinoza, Luciano; Mondaca-Fernández, Iram; Balderas-Cortés, José de Jesús; Chaidez-Quiroz, Cristóbal; Meza-Montenegro, María Mercedes

2014-09-01

Cryptosporidium oocysts and Giardia cysts can be transmitted by the fecal-oral route and may cause gastrointestinal parasitic zoonoses. These zoonoses are common in rural zones due to the parasites being harbored in fecally contaminated soil. This study assessed the risk of illness (giardiasis and cryptosporidiosis) from inhaling and/or ingesting soil and/or airborne dust in Potam, Mexico. To assess the risk of infection, Quantitative Microbial Risk Assessment (QMRA) was employed, with the following steps: (1) hazard identification, (2) hazard exposure, (3) dose-response, and (4) risk characterization. Cryptosporidium oocysts and Giardia cysts were observed in 52% and 57%, respectively, of total soil samples (n=21), and in 60% and 80%, respectively, of air samples (n=12). The calculated annual risks were higher than 9.9 × 10(-1) for both parasites in both types of sample. Soil and air inhalation and/or ingestion are important vehicles for these parasites. To our knowledge, the results obtained in the present study represent the first QMRAs for cryptosporidiosis and giardiasis due to soil and air inhalation/ingestion in Mexico. In addition, this is the first evidence of the microbial air quality around these parasites in rural zones. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Phytoremediation of a nitrogen-contaminated desert soil by native shrubs and microbial processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glenn, Edward P.; Jordan, Fiona; Waugh, W. Joseph

Here, we combined phytoremediation and soil microbial nitrification and denitrification cycles to reduce nitrate and ammonium levels at a former uranium mill site near Monument Valley, Arizona. Ammonia used in uranium extraction was present throughout the soil profile. Sulfate,applied as sulfuric acid to solubilize uranium, was also present in the soil. These contaminants were leaching from a denuded area where a tailings pile had been removed and were migrating away from the site in groundwater. We planted the source area with two deep-rooted native shrubs, Atriplex cansescens and Sarcobatus vermiculatus, and irrigated transplants for 11 years at 20% the ratemore » of potential evapotranspiration to stimulate growth, then discontinued irrigation for 4 years. Over 15 years, total nitrogen levels dropped 82%, from 347 to 64 mg kg –1. Analysis of δ 15N supported our hypothesis that coupled microbial nitrification and denitrification processes were responsible for the loss of N. Soil sulfate levels changed little; however, evapotranspiration reduced sulfate leaching into the aquifer. For arid sites where traditional pump-and-treat methods are problematic, the Monument Valley data suggest that alternatives that incorporate native plants and rely on vadose zone biogeochemistry and hydrology could be a sustainable remediation for nitrogen contaminated soil.« less

Biophysical processes supporting the diversity of microbial life in soil

PubMed Central

Tecon, Robin

2017-01-01

Abstract Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure—the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning. PMID:28961933

Selective progressive response of soil microbial community to wild oat roots.

PubMed

DeAngelis, Kristen M; Brodie, Eoin L; DeSantis, Todd Z; Andersen, Gary L; Lindow, Steven E; Firestone, Mary K

2009-02-01

Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of beta-Proteobacteria and Actinobacteria at about 10(8) copies of 16S rRNA genes per g soil, with Nitrospira having about 10(5) copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

PubMed Central

Luo, Chengwei; Rodriguez-R, Luis M.; Johnston, Eric R.; Wu, Liyou; Cheng, Lei; Xue, Kai; Tu, Qichao; Deng, Ye; He, Zhili; Shi, Jason Zhou; Yuan, Mengting Maggie; Sherry, Rebecca A.; Li, Dejun; Luo, Yiqi; Schuur, Edward A. G.; Chain, Patrick; Tiedje, James M.

2014-01-01

Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO2 production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations. PMID:24375144

The influence of microbial-based inoculants on N2O emissions from soil planted with corn (Zea mays L.) under greenhouse conditions with different nitrogen fertilizer regimens.

PubMed

Calvo, Pamela; Watts, Dexter B; Kloepper, Joseph W; Torbert, H Allen

2016-12-01

Nitrous oxide (N 2 O) emissions are increasing at an unprecedented rate owing to the increased use of nitrogen (N) fertilizers. Thus, new innovative management tools are needed to reduce emissions. One potential approach is the use of microbial inoculants in agricultural production. In a previous incubation study, we observed reductions in N 2 O emissions when microbial-based inoculants were added to soil (no plants present) with N fertilizers under laboratory incubations. This present study evaluated the effects of microbial-based inoculants on N 2 O and carbon dioxide (CO 2 ) emissions when applied to soil planted with corn (Zea mays L.) under controlled greenhouse conditions. Inoculant treatments consisted of (i) SoilBuilder (SB), (ii) a metabolite extract of SoilBuilder (SBF), and (iii) a mixture of 4 strains of plant-growth-promoting Bacillus spp. (BM). Experiments included an unfertilized control and 3 N fertilizers: urea, urea - ammonium nitrate with 32% N (UAN-32), and calcium - ammonium nitrate with 17% N (CAN-17). Cumulative N 2 O fluxes from pots 41 days after planting showed significant reductions in N 2 O of 15% (SB), 41% (BM), and 28% (SBF) with CAN-17 fertilizer. When UAN-32 was used, reductions of 34% (SB), 35% (SBF), and 49% (BM) were obtained. However, no reductions in N 2 O emissions occurred with urea. Microbial-based inoculants did not affect total CO 2 emissions from any of the fertilized treatments or the unfertilized control. N uptake was increased by an average of 56% with microbial inoculants compared with the control (nonmicrobial-based treatments). Significant increases in plant height, SPAD chlorophyll readings, and fresh and dry shoot mass were also observed when the microbial-based treatments were applied (with and without N). Overall, results demonstrate that microbial inoculants can reduce N 2 O emissions following fertilizer application depending on the N fertilizer type used and can enhance N uptake and plant growth. Future studies are planned to evaluate the effectiveness of these microbial inoculants in field-based trials and determine the mechanisms involved in N 2 O reduction.

Land-use and soil depth affect resource and microbial stoichiometry in a tropical mountain rainforest region of southern Ecuador.

PubMed

Tischer, Alexander; Potthast, Karin; Hamer, Ute

2014-05-01

Global change phenomena, such as forest disturbance and land-use change, significantly affect elemental balances as well as the structure and function of terrestrial ecosystems. However, the importance of shifts in soil nutrient stoichiometry for the regulation of belowground biota and soil food webs have not been intensively studied for tropical ecosystems. In the present account, we examine the effects of land-use change and soil depth on soil and microbial stoichiometry along a land-use sequence (natural forest, pastures of different ages, secondary succession) in the tropical mountain rainforest region of southern Ecuador. Furthermore, we analyzed (PLFA-method) whether shifts in the microbial community structure were related to alterations in soil and microbial stoichiometry. Soil and microbial stoichiometry were affected by both land-use change and soil depth. After forest disturbance, significant decreases of soil C:N:P ratios at the pastures were followed by increases during secondary succession. Microbial C:N ratios varied slightly in response to land-use change, whereas no fixed microbial C:P and N:P ratios were observed. Shifts in microbial community composition were associated with soil and microbial stoichiometry. Strong positive relationships between PLFA-markers 18:2n6,9c (saprotrophic fungi) and 20:4 (animals) and negative associations between 20:4 and microbial N:P point to land-use change affecting the structure of soil food webs. Significant deviations from global soil and microbial C:N:P ratios indicated a major force of land-use change to alter stoichiometric relationships and to structure biological systems. Our results support the idea that soil biotic communities are stoichiometrically flexible in order to adapt to alterations in resource stoichiometry.

A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

PubMed

Shang, Shuanghua; Yi, Yanli

2015-12-01

The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

Microbial Community Dynamics during the Bioremediation Process of Chlorimuron-Ethyl-Contaminated Soil by Hansschlegelia sp. Strain CHL1

PubMed Central

Yang, Liqiang; Li, Xinyu; Li, Xu; Su, Zhencheng; Zhang, Chenggang; Zhang, Huiwen

2015-01-01

Long-term and excessive application of chlorimuron-ethyl has led to a series of environmental problems. Strain Hansschlegelia sp. CHL1, a highly efficient chlorimuron-ethyl degrading bacterium isolated in our previous study, was employed in the current soil bioremediation study. The residues of chlorimuron-ethyl in soils were detected, and the changes of soil microbial communities were investigated by phospholipid fatty acid (PLFA) analysis. The results showed that strain CHL1 exhibited significant chlorimuron-ethyl degradation ability at wide range of concentrations between 10μg kg-1 and 1000μg kg-1. High concentrations of chlorimuron-ethyl significantly decreased the total concentration of PLFAs and the Shannon-Wiener indices and increased the stress level of microbes in soils. The inoculation with strain CHL1, however, reduced the inhibition on soil microbes caused by chlorimuron-ethyl. The results demonstrated that strain CHL1 is effective in the remediation of chlorimuron-ethyl-contaminated soil, and has the potential to remediate chlorimuron-ethyl contaminated soils in situ. PMID:25689050

Deriving site-specific soil clean-up values for metals and metalloids: Rationale for including protection of soil microbial processes

PubMed Central

Kuperman, Roman G; Siciliano, Steven D; Römbke, Jörg; Oorts, Koen

2014-01-01

Although it is widely recognized that microorganisms are essential for sustaining soil fertility, structure, nutrient cycling, groundwater purification, and other soil functions, soil microbial toxicity data were excluded from the derivation of Ecological Soil Screening Levels (Eco-SSL) in the United States. Among the reasons for such exclusion were claims that microbial toxicity tests were too difficult to interpret because of the high variability of microbial responses, uncertainty regarding the relevance of the various endpoints, and functional redundancy. Since the release of the first draft of the Eco-SSL Guidance document by the US Environmental Protection Agency in 2003, soil microbial toxicity testing and its use in ecological risk assessments have substantially improved. A wide range of standardized and nonstandardized methods became available for testing chemical toxicity to microbial functions in soil. Regulatory frameworks in the European Union and Australia have successfully incorporated microbial toxicity data into the derivation of soil threshold concentrations for ecological risk assessments. This article provides the 3-part rationale for including soil microbial processes in the development of soil clean-up values (SCVs): 1) presenting a brief overview of relevant test methods for assessing microbial functions in soil, 2) examining data sets for Cu, Ni, Zn, and Mo that incorporated soil microbial toxicity data into regulatory frameworks, and 3) offering recommendations on how to integrate the best available science into the method development for deriving site-specific SCVs that account for bioavailability of metals and metalloids in soil. Although the primary focus of this article is on the development of the approach for deriving SCVs for metals and metalloids in the United States, the recommendations provided in this article may also be applicable in other jurisdictions that aim at developing ecological soil threshold values for protection of microbial processes in contaminated soils. PMID:24376192

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests.

PubMed

Flores-Rentería, Dulce; Curiel Yuste, Jorge; Rincón, Ana; Brearley, Francis Q; García-Gil, Juan Carlos; Valladares, Fernando

2015-05-01

Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

USGS Publications Warehouse

Waldrop, Mark P.; Holloway, JoAnn M.; Smith, David; Goldhaber, Martin B.; Drenovsky, R.E.; Scow, K.M.; Dick, R.; Howard, Daniel M.; Wylie, Bruce K.; Grace, James B.

2017-01-01

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils.

[Responses of microbial biomass P to the changes of organic C and P in paddy soils under different fertilization systems].

PubMed

Chen, An-Lei; Wang, Kai-Rong; Xie, Xiao-Li; Liu, Ying-Xin

2007-12-01

Based on a fifteen years field experiment in double rice-cropping region of subtropical China, the responses of microbial biomass P (MB-P) to organic C and P in red paddy soils under different fertilization systems were investigated. The results indicated that a long-term input of organic carbon sources and the increasing soil organic carbon made soil microbial biomass remain at a high level (MB-C > 800 mg x kg(-1)), being a main reason of the increase of MB-P. Under long-term zero chemical P fertilization, there was a significant decrease in soil total P (P < 0.05), but soil organic P increased by 29.3% on average. The inorganic P forms in deficit were mainly Al-P, Fe-P, Ca-P and O-P, with the lowest content of Al-P (only 0.5 mg x kg(-1) on average). The content of soil MB-P under zero chemical P fertilization was much higher than that of Olsen-P. Correlation analysis showed that there was a significant relationship (P < 0.05) between MB-P and Al-P, from which, it was deduced that the utilization of Al-P, Fe-P, Ca-P and O-P by soil microbes could be the key approach of promoting these P forms transformed into available P. Chemical P fertilization combined with organic nutrient recycling could not only enlarge the soil P pool, but also improve the P availability.

Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey.

PubMed

Yao, Huaiying; Campbell, Colin D; Chapman, Stephen J; Freitag, Thomas E; Nicol, Graeme W; Singh, Brajesh K

2013-09-01

The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is explained by geographical location or soil pH. Soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) are excellent models for such study due to their functional, agronomic and environmental importance and their relative ease of characterization. To identify the dominant drivers of different ammonia oxidizers, we used samples (n = 713) from the National Soil Inventory of Scotland (NSIS). Our results indicate that 40-45% of the variance in community compositions can be explained by 71 environmental variables. Soil pH and substrate, which have been regarded as the two main drivers, only explained 13-16% of the total variance. We provide strong evidence of multi-factorial drivers (land use, soil type, climate and N deposition) of ammonia-oxidizing communities, all of which play a significant role in the creation of specific niches that are occupied by unique phylotypes. For example, one AOA phylotype was strongly linked to woodland/semi-natural grassland, rainfall and N deposition. Some soil typologies, namely regosols, have a novel AOA community composition indicating typology as one of the factors which defines this ecological niche. AOA abundance was high and strongly linked the rate of potential nitrification in the highly acidic soils supporting the argument that AOA are main ammonia oxidizers in acidic soils. However, for AOB, soil pH and substrate (ammonia) were the main drivers for abundance and community composition. These results highlight the importance of multiple drivers of microbial niche formation and their impact on microbial biogeography that have significant consequences for ecosystem functioning. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Microbial Community Diversities and Taxa Abundances in Soils along a Seven-Year Gradient of Potato Monoculture Using High Throughput Pyrosequencing Approach

PubMed Central

Liu, Xing; Zhang, Junlian; Gu, Tianyu; Zhang, Wenming; Shen, Qirong; Yin, Shixue; Qiu, Huizhen

2014-01-01

Background Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. Methodology/Principal Findings Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H Shannon) and richness (S Chao1) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. Conclusions Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait. Correlations between abundance of Fusarium with several other bacterial taxa suggested their similar behaviors in responses to potato monoculture and/or soil variables, providing insights into the ecological behaviors of these taxa in the environment. PMID:24497959

The impact of cotton growing practices on soil microbiology and its relation to plant and soil health

NASA Astrophysics Data System (ADS)

Pereg, Lily

2013-04-01

Crop production and agricultural practices heavily impact the soil microbial communities, which differ among varying types of soils and environmental conditions. Soil-borne microbial communities in cotton production systems, as in every other cropping system, consist of microbial populations that may either be pathogenic, beneficial or neutral with respect to the cotton crop. Crop production practices have major roles in determining the composition of microbial communities and function of microbial populations in soils. The structure and function of any given microbial community is determined by various factors, including those that are influenced by farming and those not controlled by farming activities. Examples of the latter are environmental conditions such as soil type, temperature, daylight length and UV radiation, air humidity, atmospheric pressure and some abiotic features of the soil. On the other hand, crop production practices may determine other abiotic soil properties, such as water content, density, oxygen levels, mineral and elemental nutrient levels and the load of other crop-related soil amendments. Moreover, crop production highly influences the biotic properties of the soil and has a major role in determining the fate of soil-borne microbial communities associated with the crop plant. Various microbial strains react differently to the presence of certain plants and plant exudates. Therefore, the type of plant and crop rotations are important factors determining microbial communities. In addition, practice management, e.g. soil cultivation versus crop stubble retention, have a major effect on the soil conditions and, thus, on microbial community structure and function. All of the above-mentioned factors can lead to preferential selection of certain microbial population over others. It may affect not only the composition of microbial communities (diversity and abundance of microbial members) but also the function of the community (the ability of different microbes to perform certain activities). Therefore, agricultural practices may determine the ability of beneficial microbes to realise their plant growth promoting potential or the pathogenic expression of others. This presentation will review the current knowledge about the impact of cotton growing practices on microbial communities and soil health in different environments as well as endeavour to identify gaps worthwhile exploring in future research for promoting plant growth in healthy soils.

Temperature dependence and coupling of iron and arsenic reduction and release during flooding of a contaminated soil.

PubMed

Weber, Frank-Andreas; Hofacker, Anke F; Voegelin, Andreas; Kretzschmar, Ruben

2010-01-01

Arsenic (As) in soils and sediments is commonly mobilized when anoxic conditions promote microbial iron (Fe) and As reduction. Recent laboratory studies and field observations have suggested a decoupling between Fe and As reduction and release, but the links between these processes are still not well understood. In microcosm experiments, we monitored the formation of Fe(II) and As(III) in the porewater and in the soil solid-phase during flooding of a contaminated floodplain soil at temperatures of 23, 14, and 5 degrees C. At all temperatures, flooding induced the development of anoxic conditions and caused increasing concentrations of dissolved Fe(II) and As(III). Decreasing the temperature from 23 to 14 and 5 degrees C strongly slowed down soil reduction and Fe and As release. Speciation of As in the soil solid-phase by X-ray absorption spectroscopy (XAS) and extraction of the Fe(II) that has formed by reductive Fe(III) (hydr)oxide dissolution revealed that less than 3.9% of all As(III) and less than 3.2% of all Fe(II) formed during 52 days of flooding at 23 degrees C were released into the porewater, although 91% of the initially ascorbate-extractable Fe and 66% of the total As were reduced. The amount of total As(III) formed during soil reduction was linearly correlated to the amount of total Fe(II) formed, indicating that the rate of As(V) reduction was controlled by the rate of microbial Fe(III) (hydr)oxide reduction.

Soil Bacterial Community Structure Responses to Precipitation Reduction and Forest Management in Forest Ecosystems across Germany

PubMed Central

Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E.; Ellerbrock, Ruth; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

2015-01-01

Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season. PMID:25875835

Soil bacterial community structure responses to precipitation reduction and forest management in forest ecosystems across Germany.

PubMed

Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E; Ellerbrock, Ruth; Bruelheide, Helge; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

2015-01-01

Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season.

Phosphorus, carbon- and nitrogen interactions in productive and degraded tropical pastures

NASA Astrophysics Data System (ADS)

Oberson, A.; Hegglin, D. D.; Nesper, M.; Rao, I.; Fonte, S.; Ramirez, B.; Velasquez, J.; Tamburini, F.; Bünemann, E. K.; Frossard, E.

2011-12-01

Pastures are the main land use in deforested areas of tropical South America. The highly weathered soils of these regions usually have low total and available phosphorus (P) contents. Low P availability can strongly limit plant and animal productivity and other soil ecosystem functions. Most introduced pastures of Brachiaria spp. are grass-alone (GA) while some are grass-legume (GL) pastures. The majority of the introduced pastures, particularly the grass-alone are at some state of degradation (GD). Pasture degradation induces severe loss of plant biomass production, with drastic ecological and economic implications. Although the importance of P deficiency in pasture degradation has been recognized, the knowledge generated on stoichiometry of carbon (C), nitrogen (N) and P along pathways of the nutrient cycles of pastures, with different botanical composition and productivity, has been very limited. We will present results of a case study realized during 2010 to 2011 in the forest margins agro-ecosystem of the department of Caquetá, Colombia. Our objectives were to determine: i) whether P availability is lower in degraded compared to productive pastures, and ii) whether the introduction of legumes in the pasture increases P availability through enhanced biological P cycling through plant growth, plant litter decomposition and the soil microbial biomass; and iii) whether pasture types (GA vs GL) and the state of pasture degradation affect the C:N:P ratios in nutrient pools of the soil-plant system. An on-farm study was conducted on nine farms in the department of Caquetá, Colombia. On every farm three different pasture types were studied: degraded grass alone pastures (GD), productive grass-alone pastures (GA) and productive grass-legume pastures (GL). Basic soil characteristics and indicators on soil P status, microbial P cycling, plant biomass production, plant litter deposition and nutrient concentrations in plant tissue were determined. Analysis of P, C and N in the microbial biomass, particulate organic matter and soil aggregates is in progress. Results showed that plant biomass production, litter deposition, soil organic P and basal soil respiration rate were significantly lower in GD than GA pastures. Moreover, clear trends towards lower total C, N, total P and microbial P per unit soil mass and higher Al saturation were observed in soils of GD compared to GA pastures while available soil P content and P concentration in plant biomass did not differ. No significant differences were found in any of the measured soil parameters between the two productive pasture types, GA and GL, but legume biomass has significantly higher N concentration and tends to have higher P concentration than grasses. 15-N natural abundance data indicated that legume N was largely derived from symbiotic N2 fixation. Biological P cycling was clearly reduced in GD compared to productive GA and GL pastures. This work highlights the importance of biological P cycling for developing sustainable pastoral systems and provides new knowledge on interactions of P with C and N.

Leaf and root C-to-N ratios are poor predictors of soil microbial biomass C and respiration across 32 tree species.

PubMed

Ferlian, Olga; Wirth, Christian; Eisenhauer, Nico

2017-11-01

Soil microorganisms are the main primary decomposers of plant material and drive biogeochemical processes like carbon and nitrogen cycles. Hence, knowledge of their nutritional demands and limitations for activity and growth is of particular importance. However, potential effects of the stoichiometry of soil and plant species on soil microbial activity and carbon use efficiency are poorly understood. Soil properties and plant traits are assumed to drive microbial carbon and community structure. We investigated the associations between C and N concentrations of leaf, root, and soil as well as their ratios and soil microbial biomass C and activity (microbial basal respiration and specific respiratory quotient) across 32 young native angiosperm tree species at two locations in Central Germany. Correlations between C:N ratios of leaves, roots, and soil were positive but overall weak. Only regressions between root and leaf C:N ratios as well as between root and soil C:N ratios were significant at one site. Soil microbial properties differed significantly between the two sites and were significantly correlated with soil C:N ratio across sites. Soil C concentrations rather than N concentrations drove significant effects of soil C:N ratio on soil microbial properties. No significant correlations between soil microbial properties and leaf as well as root C:N ratios were found. We found weak correlations of C:N ratios between plant aboveground and belowground tissues. Furthermore, microorganisms were not affected by the stoichiometry of plant tissues in the investigated young trees. The results suggest that soil stoichiometry represents a consistent determinant of soil microbial biomass and respiration. Our study indicates that stoichiometric relationships among tree organs can be weak and poor predictors of soil microbial properties in young tree stands. Further research in controlled experimental settings with a wide range of tree species is needed to study the role of plant chemical traits like the composition and stoichiometry of root exudates in determining interactions between above- and belowground compartments.

Microbial diversity in firework chemical exposed soil and water samples collected in Virudhunagar district, Tamil Nadu, India.

PubMed

Dhasarathan, P; Theriappan, P; Ashokraja, C

2010-03-01

Microbial diversity of soil and water samples collected from pyrochemicals exposed areas of Virdhunagar district (Tamil Nadu, India) was studied. Soil and water samples from cultivable area, waste land and city area of the same region were also studied for a comparative acount. There is a remarkable reduction in total heterotrophic bacterial population (THB) in pyrochemicals exposed soil and water samples (42 × 10(4) CFU/g and 5.6 × 10(4) CFU/ml respectively), compared to the THB of cultivable area soil and water samples (98 × 10(7) CFU/g and 38.6 × 10(7) CFU/ml). The generic composition the THB of the pyrochemicals exposed samples too exhibited considerable change compared to other samples. Pseudomonas sp. was the predominant one (41.6%) followed by Achromobacter sp. (25%) in pyrochemical exposed soil and Pseudomonas sp. was the predominant one (25%) in pyrochemical exposed water samples followed by Bacillus sp. (25%) and Micrococcus sp. (16.6%). It was observed that Cornybacterium sp. and Micrococcus sp. were absent completely in pyrochemical exposed soil and Achromobacter sp. was missing in the pyrochemical exposed water samples, which were present in the other samples. The outcome of this study clearly demonstrates that pollutants such as chemicals used in pyrotechniques affect the microbial biodiversity and suitable measures have to be taken to control the pollution level and to save biodiversity.

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lipson, David A.; Raab, Theodore K.; Parker, Melanie

2015-07-21

This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska, and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and weremore » most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography, but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes, dominated by fermenters ( Bacteroidetes and Firmicutes).« less

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils.

PubMed

Lipson, David A; Raab, Theodore K; Parker, Melanie; Kelley, Scott T; Brislawn, Colin J; Jansson, Janet

2015-08-01

This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes, dominated by fermenters (Bacteroidetes and Firmicutes). © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska

DOE PAGES

Kao-Kniffin, J.; Woodcroft, B. J.; Carver, S. M.; ...

2015-12-18

We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the activemore » layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Effects of interactions between Collembola and soil microbial community on the degradation of glyphosate-based herbicide

NASA Astrophysics Data System (ADS)

Wee, J.; Lee, Y. S.; Son, J.; Kim, Y.; Nam, T. H.; Cho, K.

2017-12-01

Glyphosate is the most widely used herbicide because of its broad spectrum activity and effectiveness, however, little is known about adverse effects on non-target species and their interactions. Therefore, in this study, we investigated the effects of glyphosate on interactions between Collembola and soil microbial community and the effect of Collembola on degradation of glyphosate. The experiment carried out in PS container filled with 30g of soil according to OECD 232 guidelines. Investigating the effects of soil microbial community and Collembola on degradation of glyphosate, we prepared defaunated field soil (only maintaining soil microbial community, sampling in May and September, 2016.) and autoclaved soil with 0, 10, 30 adults of Paronychiurus kimi (Collembola) respectively. Survived adults and hatched juveniles of P. kimi were counted after 28-day exposures in both soils spiked with 100 mg/kg of glyphosate. Glyphosate in soil of 7, 14, 21, 28 days after spiking of glyphosate based herbicide was analyzed by spectrophotometer (Jan et al., 2009). Also soil microbial community structure was investigated using phospholipid fatty acids (PLFAs) composition analysis of soils following the procedures given by the Sherlock Microbial Identification System (MIDI Inc., Newark, DE). Glyphosate (100mg/kg soil) has no effects on reproduction and survival of P. kimi in any soils. Also, glyphosate in soils with Collembola was more rapidly degraded. Rapid increase of soil microbial biomass(PLFAs) was shown in soil with Collembola addition. This result showed that glyphosate affected interactions between Collembola and soil microorganisms, and also soil microbial community affected by Collembola changed degradation of glyphosate.

Tillage system affects microbiological properties of soil

NASA Astrophysics Data System (ADS)

Delgado, A.; de Santiago, A.; Avilés, M.; Perea, F.

2012-04-01

Soil tillage significantly affects organic carbon accumulation, microbial biomass, and subsequently enzymatic activity in surface soil. Microbial activity in soil is a crucial parameter contributing to soil functioning, and thus a basic quality factor for soil. Since enzymes remain soil after excretion by living or disintegrating cells, shifts in their activities reflect long-term fluctuations in microbial biomass. In order to study the effects of no-till on biochemical and microbiological properties in comparison to conventional tillage in a representative soil from South Spain, an experiment was conducted since 1982 on the experimental farm of the Institute of Agriculture and Fisheries Research of Andalusia (IFAPA) in Carmona, SW Spain (37o24'07''N, 5o35'10''W). The soil at the experimental site was a very fine, montomorillonitic, thermic Chromic Haploxerert (Soil Survey Staff, 2010). A randomized complete block design involving three replications and the following two tillage treatments was performed: (i) Conventional tillage, which involved mouldboard plowing to a depth of 50 cm in the summer (once every three years), followed by field cultivation to a depth of 15 cm before sowing; crop residues being burnt, (ii) No tillage, which involved controlling weeds before sowing by spraying glyphosate and sowing directly into the crop residue from the previous year by using a planter with double-disk openers. For all tillage treatments, the crop rotation (annual crops) consisted of winter wheat, sunflower, and legumes (pea, chickpea, or faba bean, depending on the year), which were grown under rainfed conditions. Enzymatic activities (ß-glucosidase, dehydrogenase, aryl-sulphatase, acid phosphatase, and urease), soil microbial biomass by total viable cells number by acridine orange direct count, the density of cultivable groups of bacteria and fungi by dilution plating on semi-selective media, the physiological profiles of the microbial communities by BiologR, and the Shannon (H') and Gini (1-G) diversity index of microbial communities were determined in soil samples (0-10 cm depth) taken in autumn 2009. All the enzymatic activities and the biomass estimated by viable cell counting were significantly higher under no-till than under conventional tillage. However, only fluorescents pseudomonas population was increased under no-till, meanwhile oligotrophic bacteria and actinomycetes populations were higher with conventional tillage than with no-till. Overall, there was a higher use all the group of carbon sources used in the BiologR test with conventional tillage than with no-till, by except amines and phenols which showed non-significant differences. This reveals different physiological profiles in the microbial communities under both tillage systems. The Gini diversity was significantly lower with no-till than with conventional tillage. It can be concluded that no-till increases microbial biomass in soil and subsequently enzymatic activities likely ascribed to an increased organic matter content. Under low availability of hydrocarbon sources in soil due to conventional tillage, which promotes a decrease in the organic matter content of the soil, populations of oligotrophods and the diversity of microbial communities are increased. Under these conditions, there must not be dominant carbon sources promoting the selection of microorganisms with a given physiological profile. The reduced hydrocarbon availability and the higher diversity contribute to explain the increased use of carbon sources used in Biolog with conventional tillage than with no-till.

Plant species influence on soil C after afforestation of Mediterranean degraded soils

NASA Astrophysics Data System (ADS)

Dominguez, Maria T.; García-Vargas, Carlos; Madejón, Engracia; Marañón, Teodoro

2015-04-01

Increasing C sequestration in terrestrial ecosystems is one of the main current environmental challenges to mitigate climate change. Afforestation of degraded and contaminated lands is one of the key strategies to achieve an increase in C sequestration in ecosystems. Plant species differ in their mechanisms of C-fixation, C allocation into different plant organs, and interaction with soil microorganisms, all these factors influencing the dynamics of soil C following the afforestation of degraded soils. In this work we examine the influence of different woody plant species on soil C dynamics in degraded and afforested Mediterranean soils. The soils were former agricultural lands that were polluted by a mining accident and later afforested with different native plant species. We analysed the effect of four of these species (Olea europaea var. sylvestris Brot., Populus alba L., Pistacia lentiscus L. and Retama sphaerocarpa (L.) Boiss.) on different soil C fractions, soil nutrient availability, microbial activity (soil enzyme activities) and soil CO2 fluxes 15 years after the establishment of the plantations. Results suggest that the influence of the planted trees and shrubs is still limited, being more pronounced in the more acidic and nutrient-poor soils. Litter accumulation varied among species, with the highest C accumulated in the litter under the deciduous species (Populus alba L.). No differences were observed in the amount of total soil organic C among the studied species, or in the concentrations of phenols and sugars in the dissolved organic C (DOC), which might have indicated differences in the biodegradability of the DOC. Microbial biomass and activity was highly influenced by soil pH, and plant species had a significant influence on soil pH in the more acidic site. Soil CO2 fluxes were more influenced by the plant species than total soil C content. Our results suggest that changes in total soil C stocks after the afforestation of degraded Mediterranean soils are hardly detectable at decadal time-scales, and that more dynamic pools and fluxes must be monitored to determine which plant species should be promote to enhance C sequestration capacity.

Shifts in microbial use of carbon sources after 8 years of elevated CO2 and warming simulation in a semiarid grassland: linkages to soil C stocks

NASA Astrophysics Data System (ADS)

Carrillo, Y.; Dijkstra, F. A.; Pendall, E.

2016-12-01

Atmospheric CO2 and temperature will continue to increase in the future, potentially generating feedbacks to climate change. There is a high degree of uncertainty on the combined effects of CO2 and climate warming and on soil organic matter (SOM), which stores most terrestrial C. Although C input is an important driver of soil C dynamics, the use of this C by decomposer communities ultimately determines if inputs are retained in the ecosystem or lost to the atmosphere. We investigated impacts of eCO2 and warming on microbial assimilation and respiration of C at the Prairie Heating and CO2 Enrichment (PHACE) experiment in Wyoming, USA. We exposed this grassland to 8 years of free-air CO2 enrichment (FACE) and 7 years of warming. In this system, plant aboveground and belowground biomass were stimulated by eCO2 and this effect was enhanced by warming -with interannual variation. However, no changes in soil C have been detected. We evaluated microbial communities, heterotrophic respiration, susceptibility to priming when exposed to labile C, microbial N cycling and use of FACE-labelled C and pre-experimental soil C by individual microbial groups using 13C-PLFA.After 8 years of experimental manipulation we found main effects of both warming and eCO2, but mainly eCO2 the composition of the microbial community, specifically, an increase in the fungi to bacteria ratio. eCO2 led to greater soil respiration which was explained by a greater amount of substrate for decomposition as well as microbial biomass, both consistent with greater plant inputs. However, eCO2 led to lower susceptibility of C to priming, thus potentially counteracting enhanced respiration. Warming did not appear to have impacts on short-term total respiration or priming. However, it modified microbial use of C sources. Under eCO2 warming increased microbial use of FACE C (plant-derived C from the start of the CO2 treatment). We determined that this was explained by ca. 30% increase in the use of FACE-C by the bacterial groups (gram negative, gram positive and the actinobacteria), while the fungal use of C was not altered. Hence, increased plant inputs in future warmer, eCO2 conditions are likely being assimilated and rapidly respired by bacteria, leading to no significant changes in soil C.

Microbial responses to southward and northward Cambisol soil transplant

DOE PAGES

Wang, Mengmeng; Liu, Shanshan; Wang, Feng; ...

2015-10-26

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

Rapid determination of soil quality and earthworm impacts on soil microbial communities using fluorescence-based respirometry

NASA Astrophysics Data System (ADS)

Prendergast-Miller, Miranda T.; Thurston, Josh; Taylor, Joe; Helgason, Thorunn; Ashauer, Roman; Hodson, Mark E.

2017-04-01

We applied a fluorescence-based respirometry method currently devised for aquatic ecotoxicology studies to rapidly measure soil microbial oxygen consumption as a function of soil quality. In this study, soil was collected from an arable wheat field and the field margin. These two soil habitats are known to differ in their soil quality due to differences in their use and management as well as plant, microbial and earthworm community. The earthworm Lumbricus terrestris was incubated in arable or margin soil for three weeks. After this initial phase, a transfer experiment was then conducted to test the hypothesis that earthworm 'migration' alters soil microbial community function and diversity. In this transfer experiment, earthworms incubated in margin soil were transferred to arable soil. The converse transfer (i.e. earthworms incubated in arable soil) was also conducted. Soils of each type with no earthworms were also incubated as controls. After a further four week incubation, the impact of earthworm migration on the soil microbial community was tested by measuring oxygen consumption. Replicated soil slurry subsamples were aliquoted into individual respirometer wells (600 μl volume) on a glass 24-well microplate (Loligo Systems, Denmark) fitted with non-invasive, reusable oxygen sensor spots. The sealed microplate was then attached to an oxygen fluorescence sensor (SDR SensorDish Reader, PreSens, Germany). Oxygen consumption was measured in real-time over a 2 hr period following standard operating procedures. Soil microbial activity was measured with and without an added carbon source (glucose or cellulose, 50 mg C L-1). Using this system, we were able to differentiate between soil type, earthworm treatment and C source. Earthworm-driven impacts on soil microbial oxygen consumption were also supported by changes in soil microbial community structure and diversity revealed using DNA-based sequencing techniques. This method provides a simple and rapid system for measuring soil quality and has the potential for use in a variety of scenarios investigating impacts on soil microbial function.

Ecotoxicological assessment of pesticides and their combination on rhizospheric microbial community structure and function of Vigna radiata.

PubMed

Walvekar, Varsha Ashok; Bajaj, Swati; Singh, Dileep K; Sharma, Shilpi

2017-07-01

India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin, and a combination of both) with a biopesticide (azadirachtin) at their recommended field application level (L), and three times the recommended dosage (H) on structure and function of microbial community in rhizosphere of Vigna radiata. Effect on culturable fraction was assessed by enumeration on selective media, while PCR-denaturing gradient gel electrophoresis (DGGE) was employed to capture total bacterial community diversity. This was followed by a metabolic sketch using community-level physiological profiling (CLPP), to obtain a broader picture of the non-target effects on rhizospheric microbial community. Although plant parameters were not significantly affected by pesticide application, the microbial community structure experienced an undesirable impact as compared to control devoid of pesticide treatment. Examination of DGGE banding patterns through cluster analysis revealed that microbial community structure of pesticide-treated soils had only 70% resemblance to control rhizospheric soil even at 45 days post application. Drastic changes in the metabolic profiles of pesticide-treated soils were also detected in terms of substrate utilization, rhizospheric diversity, and evenness. It is noteworthy that the effects exacerbated by biopesticide were comparable to that of synthetic pesticides, thus emphasizing the significance of ecotoxicological assessments before tagging biopesticides as "safe alternatives."

Effects of lead contamination on soil microbial activity and rice physiological indices in soil-Pb-rice (Oryza sativa L.) system.

PubMed

Zeng, Lu-Sheng; Liao, Min; Chen, Cheng-Li; Huang, Chang-Yong

2006-10-01

The effect of lead (Pb) treatment on the soil microbial activities (soil microbial biomass and soil basal respiration) and rice physiological indices were studied by greenhouse pot experiment. Pb was applied as lead acetate at six different levels in two different paddy soils, namely 0 (control), 100, 300, 500, 700, 900 mg kg-1 soil. The results showed that the application of Pb at lower level (<300 mg kg-1) as lead acetate resulted in a slight increase in soil microbial activities compared with the control, and had an inhibitory influence at high concentration (>500 mg Pb kg-1 soil), which might be the critical concentration of Pb causing a significant decline in the soil microbial activities. However, the degree of influence on soil microbial activities by Pb was related to the clay and organic matter contents of the soils. On the other hand, when the level of Pb treatments increased to 500 mg kg-1, there was ecological risk for both soil microbial activities and plants. The results also revealed that there was a consistent trend that the chlorophyll contents increased initially, and then decreased gradually with increase in Pb concentration. Pb was effective in inducing proline accumulation and its toxicity causes oxidative stress in rice plants. In a word, soil microbial activities and rice physiological indices, therefore, may be sensitive indicators reflecting environmental stress in soil-Pb-rice system.

Role of vegetation and edaphic factors in controlling diversity and use of different carbon sources in semi-arid ecosystems

NASA Astrophysics Data System (ADS)

Lohse, K. A.; McLain, J. E.; Harman, C. J.; Sivapalan, M.; Troch, P. A.

2010-12-01

Microbially-mediated soil carbon cycling is closely linked to soil moisture and temperature. Climate change is predicted to increase intra-annual precipitation variability (i.e. less frequent yet more intense precipitation events) and alter biogeochemical processes due to shifts in soil moisture dynamics and inputs of carbon. However, the responses of soil biology and chemistry to predicted climate change, and their concomitant feedbacks on ecosystem productivity and biogeochemical processes are poorly understood. We collected soils at three different elevations in the Santa Catalina Mountains, AZ and quantified carbon utilization during pre-monsoon precipitation conditions. Contrasting parent materials (schist and granite) were paired at each elevation. We expected climate to determine the overall activity of soil fungal and bacterial communities and diversity of soil C utilization, and differences in parent material to modify these responses through controls on soil physical properties. We used EcoPlateTM C utilization assays to determine the relative abundance of soil bacterial and fungal populations and rate and diversity of carbon utilization. Additional plates were incubated with inhibitors selective to fungal or bacterial activity to assess relative contribution of these microbial groups to overall C utilization. We analyzed soils for soil organic matter, total C and N, particle size analysis and soil moisture content via both gravimetric and volumetric methods to assess the influences of soil physical and chemical properties on the measured biological responses. Consistent with our expectations, overall microbial activity was highest at the uppermost conifer elevation sites compared to the middle and lower elevation sites. In contrast to our expectations, however, overall activity was lower at the mid elevation oak woodland sites compared to the low elevation desert sites. Also consistent with our expectations was the observation that overall activities were consistently higher in schist parent material compared to granite. Though differences between canopy and intercanopy carbon utilization were subtle, the diversity of carbon utilization differed, suggesting a potential role of root exudates in governing C utilization in these semiarid soils. Findings from this study suggest that soil physical properties due to parent material have primary impacts in constraining microbial growth and carbon utilization under changing climate conditions.

Temporal dynamics of soil microbial communities under different moisture regimes: high-throughput sequencing and bioinformatics analysis

NASA Astrophysics Data System (ADS)

Semenov, Mikhail; Zhuravleva, Anna; Semenov, Vyacheslav; Yevdokimov, Ilya; Larionova, Alla

2017-04-01

Recent climate scenarios predict not only continued global warming but also an increased frequency and intensity of extreme climatic events such as strong changes in temperature and precipitation regimes. Microorganisms are well known to be more sensitive to changes in environmental conditions than to other soil chemical and physical parameters. In this study, we determined the shifts in soil microbial community structure as well as indicative taxa in soils under three moisture regimes using high-throughput Illumina sequencing and range of bioinformatics approaches for the assessment of sequence data. Incubation experiments were performed in soil-filled (Greyic Phaeozems Albic) rhizoboxes with maize and without plants. Three contrasting moisture regimes were being simulated: 1) optimal wetting (OW), a watering 2-3 times per week to maintain soil moisture of 20-25% by weight; 2) periodic wetting (PW), with alternating periods of wetting and drought; and 3) constant insufficient wetting (IW), while soil moisture of 12% by weight was permanently maintained. Sampled fresh soils were homogenized, and the total DNA of three replicates was extracted using the FastDNA® SPIN kit for Soil. DNA replicates were combined in a pooled sample and the DNA was used for PCR with specific primers for the 16S V3 and V4 regions. In order to compare variability between different samples and replicates within a single sample, some DNA replicates treated separately. The products were purified and submitted to Illumina MiSeq sequencing. Sequence data were evaluated by alpha-diversity (Chao1 and Shannon H' diversity indexes), beta-diversity (UniFrac and Bray-Curtis dissimilarity), heatmap, tagcloud, and plot-bar analyses using the MiSeq Reporter Metagenomics Workflow and R packages (phyloseq, vegan, tagcloud). Shannon index varied in a rather narrow range (4.4-4.9) with the lowest values for microbial communities under PW treatment. Chao1 index varied from 385 to 480, being a more flexible indicator than Shannon index. Chao1 had similar values for OW and IW communities, but alpha-diversity of microbial communities has sharply decreased under PW treatment. There was no visible difference in beta-diversity depending on sampling date and wetting regime, however, it could be possible to distinguish microbial communities in soils with maize and without plants. The presence of maize was acting as scattering agent, making microbial communities more distinguished. In all studied samples, the most dominant phyla were Proteobacteria, Firmicutes, Verrucomicrobia, Actinobacteria, and Acidobacteria. Chthoniobacter, Bacillus, Alicyclobacillus, Rhodoplanes, Cohnella, Kaistobacter, and Solibacter were the most abundant genera. Moreover, these genera were found as the most reactive and variable taxa in microbial community. Thus, DNA high-throughput sequencing revealed no dramatic shifts in bacterial community structure in soils under different moisture regimes. However, this technique allowed us to determine the effect of wetting regime and the presence of plants on soil microbial community which were adaptable to insufficient wetting, but lost diversity under periodic wetting. Furthermore, we detected the indicative taxa which dominate in microbial communities and at the same time strongly react to environmental changes.

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

PubMed Central

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. PMID:28611747

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

PubMed

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

The influence of water-soluble As(III) and As(V) on dehydrogenase activity in soils affected by mine tailings.

PubMed

Fernández, Pilar; Sommer, Irene; Cram, Silke; Rosas, Irma; Gutiérrez, Margarita

2005-09-15

Dehydrogenase activity (DHA) in soils contaminated by arsenic-bearing tailings was correlated with total arsenic and total water-soluble arsenic (As(III)+As(V)) to evaluate the impact of tailings dispersion on the oxidative capacity of soil microorganisms. Georeferenced surface soil samples (0-10 cm depth) were collected at different distances from a tailings dam. In the samples farthest from the dam, all water-soluble arsenic (avg. 0.6+/-0.1 mg kg(-1)) was As(V). The highest concentration of water-soluble As(III)+As(V) (>1.9 mg kg(-1)) was found where As(III) was present. DHA averaged 438.9+/-79.3 microg INTF g(-1) h(-1) at the greatest distance from the dam and decreased to 92.3+/-27.1 microg INTF g(-1) h(-1) with decreasing distance from the dam. Pearson correlation coefficient between DHA and samples containing water-soluble As(V) (r=-0.87) was greater than that between DHA and total water-soluble arsenic (r=-0.57). The correlation between DHA and soluble arsenic containing both As(V) and As(III) was not significant (r=0.24). In soils with detectable As(III) concentrations where wet conditions prevail (i.e., reducing conditions), there is an abiotic response in addition to a biotic one. The correlation between DHA and total water-soluble As(III)+ As(V) was higher (r=-0.79) when the abiotic response was excluded. Our study demonstrated the importance of distinguishing between total and available fraction and its species and the need to evaluate biological functions in addition to purely geochemical analyses. DHA bioassay combined with other microbial properties offers a good tool for evaluating soil microbial activity and status and is a suitable indicator of the oxidative capacity of soil microorganisms affected by tailings in an oxidizing environment; however, under reducing conditions, abiotic responses must also be studied.

Soil microbial community responses to contamination with silver, aluminium oxide and silicon dioxide nanoparticles.

PubMed

McGee, C F; Storey, S; Clipson, N; Doyle, E

2017-04-01

Soil microorganisms are key contributors to nutrient cycling and are essential for the maintenance of healthy soils and sustainable agriculture. Although the antimicrobial effects of a broad range of nanoparticulate substances have been characterised in vitro, little is known about the impact of these compounds on microbial communities in environments such as soil. In this study, the effect of three widely used nanoparticulates (silver, silicon dioxide and aluminium oxide) on bacterial and fungal communities in an agricultural pastureland soil was examined in a microcosm-based experiment using a combination of enzyme analysis, molecular fingerprinting and amplicon sequencing. A relatively low concentration of silver nanoparticles (AgNPs) significantly reduced total soil dehydrogenase and urease activity, while Al 2 O 3 and SiO 2 nanoparticles had no effect. Amplicon sequencing revealed substantial shifts in bacterial community composition in soils amended with AgNPs, with significant decreases in the relative abundance of Acidobacteria and Verrucomicrobia and an increase in Proteobacteria. In particular, the relative abundance of the Proteobacterial genus Dyella significantly increased in AgNP amended soil. The effects of Al 2 O 3 and SiO 2 NPs on bacterial community composition were less pronounced. AgNPs significantly reduced bacterial and archaeal amoA gene abundance in soil, with the archaea more susceptible than bacteria. AgNPs also significantly impacted soil fungal community structure, while Al 2 O 3 and SiO 2 NPs had no effect. Several fungal ribotypes increased in soil amended with AgNPs, compared to control soil. This study highlights the need to consider the effects of individual nanoparticles on soil microbial communities when assessing their environmental impact.

Distinct Microbial Limitations in Litter and Underlying Soil Revealed by Carbon and Nutrient Fertilization in a Tropical Rainforest

PubMed Central

Fanin, Nicolas; Barantal, Sandra; Fromin, Nathalie; Schimann, Heidy; Schevin, Patrick; Hättenschwiler, Stephan

2012-01-01

Human-caused alterations of the carbon and nutrient cycles are expected to impact tropical ecosystems in the near future. Here we evaluated how a combined change in carbon (C), nitrogen (N) and phosphorus (P) availability affects soil and litter microbial respiration and litter decomposition in an undisturbed Amazonian rainforest in French Guiana. In a fully factorial C (as cellulose), N (as urea), and P (as phosphate) fertilization experiment we analyzed a total of 540 litterbag-soil pairs after a 158-day exposure in the field. Rates of substrate-induced respiration (SIR) measured in litter and litter mass loss were similarly affected by fertilization showing the strongest stimulation when N and P were added simultaneously. The stimulating NP effect on litter SIR increased considerably with increasing initial dissolved organic carbon (DOC) concentrations in litter, suggesting that the combined availability of N, P, and a labile C source has a particularly strong effect on microbial activity. Cellulose fertilization, however, did not further stimulate the NP effect. In contrast to litter SIR and litter mass loss, soil SIR was reduced with N fertilization and showed only a positive effect in response to P fertilization that was further enhanced with additional C fertilization. Our data suggest that increased nutrient enrichment in the studied Amazonian rainforest can considerably change microbial activity and litter decomposition, and that these effects differ between the litter layer and the underlying soil. Any resulting change in relative C and nutrient fluxes between the litter layer and the soil can have important consequences for biogeochemical cycles in tropical forest ecosystems. PMID:23272052

USE OF FATTY ACID STABLE CARBON ISOTOPE RATIO TO INDICATE MICROBIAL CARBON SOURCE IN TROPICAL SOILS

EPA Science Inventory

We use measurements of the concentration and stable carbon isotope ratio of individual microbial phospholipid fatty acids (PLFAs) in soils as indicators of live microbial biomass levels, broad microbial community structure, and microbial carbon source. For studies of soil o...

Application of manures to mitigate the harmful effects of electrokinetic remediation of heavy metals on soil microbial properties in polluted soils.

PubMed

Tahmasbian, Iman; Safari Sinegani, Ali Akbar; Nguyen, Thi Thu Nhan; Che, Rongxiao; Phan, Thuc D; Hosseini Bai, Shahla

2017-12-01

Ethylenediaminetetraacetic acid (EDTA) used with electrokinetic (EK) to remediate heavy metal-polluted soils is a toxic chelate for soil microorganisms. Therefore, this study aimed to evaluate the effects of alternative organic chelates to EDTA on improving the microbial properties of a heavy metal-polluted soil subjected to EK. Cow manure extract (CME), poultry manure extract (PME) and EDTA were applied to a lead (Pb) and zinc (Zn)-polluted calcareous soil which were subjected to two electric intensities (1.1 and 3.3 v/cm). Soil carbon pools, microbial activity, microbial abundance (e.g., fungal, actinomycetes and bacterial abundances) and diethylenetriaminepentaacetic acid (DTPA)-extractable Pb and Zn (available forms) were assessed in both cathodic and anodic soils. Applying the EK to soil decreased all the microbial variables in the cathodic and anodic soils in the absence or presence of chelates. Both CME and PME applied with two electric intensities decreased the negative effect of EK on soil microbial variables. The lowest values of soil microbial variables were observed when EK was combined with EDTA. The following order was observed in values of soil microbial variables after treating with EK and chelates: EK + CME or EK + PME > EK > EK + EDTA. The CME and PME could increase the concentrations of available Pb and Zn, although the increase was less than that of EDTA. Overall, despite increasing soil available Pb and Zn, the combination of EK with manures (CME or PME) mitigated the negative effects of using EK on soil microbial properties. This study suggested that the synthetic chelates such as EDTA could be replaced with manures to alleviate the environmental risks of EK application.

Soil Microbial Biomass, Basal Respiration and Enzyme Activity of Main Forest Types in the Qinling Mountains

PubMed Central

Cheng, Fei; Peng, Xiaobang; Zhao, Peng; Yuan, Jie; Zhong, Chonggao; Cheng, Yalong; Cui, Cui; Zhang, Shuoxin

2013-01-01

Different forest types exert essential impacts on soil physical-chemical characteristics by dominant tree species producing diverse litters and root exudates, thereby further regulating size and activity of soil microbial communities. However, the study accuracy is usually restricted by differences in climate, soil type and forest age. Our objective is to precisely quantify soil microbial biomass, basal respiration and enzyme activity of five natural secondary forest (NSF) types with the same stand age and soil type in a small climate region and to evaluate relationship between soil microbial and physical-chemical characters. We determined soil physical-chemical indices and used the chloroform fumigation-extraction method, alkali absorption method and titration or colorimetry to obtain the microbial data. Our results showed that soil physical-chemical characters remarkably differed among the NSFs. Microbial biomass carbon (Cmic) was the highest in wilson spruce soils, while microbial biomass nitrogen (Nmic) was the highest in sharptooth oak soils. Moreover, the highest basal respiration was found in the spruce soils, but mixed, Chinese pine and spruce stands exhibited a higher soil qCO2. The spruce soils had the highest Cmic/Nmic ratio, the greatest Nmic/TN and Cmic/Corg ratios were found in the oak soils. Additionally, the spruce soils had the maximum invertase activity and the minimum urease and catalase activities, but the maximum urease and catalase activities were found in the mixed stand. The Pearson correlation and principle component analyses revealed that the soils of spruce and oak stands obviously discriminated from other NSFs, whereas the others were similar. This suggested that the forest types affected soil microbial properties significantly due to differences in soil physical-chemical features. PMID:23840671

Effects of stand age and soil properties on soil bacterial and fungal community composition in Chinese pine plantations on the Loess Plateau

PubMed Central

Dang, Peng; Yu, Xuan; Le, Hien; Liu, Jinliang; Shen, Zhen

2017-01-01

The effects of Chinese pine (Pinus tabuliformis) on soil variables after afforestation have been established, but microbial community changes still need to be explored. Using high-throughput sequencing technology, we analyzed bacterial and fungal community composition and diversity in soils from three stands of different-aged, designated 12-year-old (PF1), 29-year-old (PF2), and 53-year-old (PF3), on a Chinese pine plantation and from a natural secondary forest (NSF) stand that was almost 80 years old. Abandoned farmland (BL) was also analyzed. Shannon index values of both bacterial and fungal community in PF1 were greater than those in PF2, PF3 and NSF. Proteobacteria had the lowest abundance in BL, and the abundance increased with stand age. The abundance of Actinobacteria was greater in BL and PF1 soils than those in other sites. Among fungal communities, the dominant taxa were Ascomycota in BL and PF1 and Basidiomycota in PF2, PF3 and NSF, which reflected the successional patterns of fungal communities during the development of Chinese pine plantations. Therefore, the diversity and dominant taxa of soil microbial community in stands 12 and 29 years of age appear to have undergone significant changes; afterward, the soil microbial community achieved a relatively stable state. Furthermore, the abundances of the most dominant bacterial and fungal communities correlated significantly with organic C, total N, C:N, available N, and available P, indicating the dependence of these microbes on soil nutrients. Overall, our findings suggest that the large changes in the soil microbial community structure of Chinese pine plantation forests may be attributed to the phyla present (e.g., Proteobacteria, Actinobacteria, Ascomycota and Basidiomycota) which were affected by soil carbon and nutrients in the Loess Plateau. PMID:29049349

Effects of stand age and soil properties on soil bacterial and fungal community composition in Chinese pine plantations on the Loess Plateau.

PubMed

Dang, Peng; Yu, Xuan; Le, Hien; Liu, Jinliang; Shen, Zhen; Zhao, Zhong

2017-01-01

The effects of Chinese pine (Pinus tabuliformis) on soil variables after afforestation have been established, but microbial community changes still need to be explored. Using high-throughput sequencing technology, we analyzed bacterial and fungal community composition and diversity in soils from three stands of different-aged, designated 12-year-old (PF1), 29-year-old (PF2), and 53-year-old (PF3), on a Chinese pine plantation and from a natural secondary forest (NSF) stand that was almost 80 years old. Abandoned farmland (BL) was also analyzed. Shannon index values of both bacterial and fungal community in PF1 were greater than those in PF2, PF3 and NSF. Proteobacteria had the lowest abundance in BL, and the abundance increased with stand age. The abundance of Actinobacteria was greater in BL and PF1 soils than those in other sites. Among fungal communities, the dominant taxa were Ascomycota in BL and PF1 and Basidiomycota in PF2, PF3 and NSF, which reflected the successional patterns of fungal communities during the development of Chinese pine plantations. Therefore, the diversity and dominant taxa of soil microbial community in stands 12 and 29 years of age appear to have undergone significant changes; afterward, the soil microbial community achieved a relatively stable state. Furthermore, the abundances of the most dominant bacterial and fungal communities correlated significantly with organic C, total N, C:N, available N, and available P, indicating the dependence of these microbes on soil nutrients. Overall, our findings suggest that the large changes in the soil microbial community structure of Chinese pine plantation forests may be attributed to the phyla present (e.g., Proteobacteria, Actinobacteria, Ascomycota and Basidiomycota) which were affected by soil carbon and nutrients in the Loess Plateau.

Tree specie effects on soil microbial community composition and greenhouse gases emissions in a Mediterranean ecotone forest

NASA Astrophysics Data System (ADS)

Fernandez, Maria Jose; Ortiz, Carlos; Kitzler, Barbara; Curiel, Jorge; Rubio, Agustin

2016-04-01

Over recent decades in the Iberian Peninsula, altitudinal shifts from Pinus sylvestris L. to Quercus pyrenaica Willd species has been observed as a consequence of Global Change, meaning changes in temperature, precipitation, land use and forestry. The forest conversion from pine to oak can alter the litter quality and quantity provided to the soil and thereby the soil microbial community composition and functioning. Since soil microbiota plays an important role in organic matter decomposition, and this in turn is key in biogeochemical cycles and forest ecosystems productivity, the rate in which forests produce and consume greenhouse gases can be also affected by changes in forest composition. In other words, changes in litter decomposition will ultimately affect downstream carbon and nitrogen dynamics although this impact is uncertain. In order to predict changes in carbon and nitrogen stocks in Global Change scenarios, it is necessary to deepen the impact of vegetation changes on soil microbial communities, litter decomposition dynamics (priming effect) and the underlying interactions between these factors. To test this, we conducted a full-factorial transplant microcosms experiment mixing both fresh soils and litter from Pyrenean oak, Scots pine and mixed stands collected inside their transitional area in Central Spain. The microcosms consisted in soil cylinders inside Kilner jars used as chambers inside an incubator. In this experiment, we investigated how and to what extent the addition of litter with different quality (needles, oak leaves and mixed needles-leaves) to soil inoculums with contrasting soil microbiota impact on (i) soil CO2, NO, N2O and CH4 efflux rates, (ii) total organic carbon and nitrogen and (iii) dissolved organic carbon and nitrogen. Furthermore, we assessed if these responses were controlled by changes in the microbial community structure using the PLFA analyses prior and after the incubation period of 54 days.

Long-term Effects of Shrub Encroachment and Grazing on Soil Microbial Composition and Function

NASA Astrophysics Data System (ADS)

Gallery, R. E.; O'Shea, C.; Kwiecien, A.; Predick, K.; Archer, S. R.

2014-12-01

Drylands account for ca. 35% of terrestrial net primary productivity and thus play a significant role in global water and biogeochemical cycles. Replacement of grasses by shrubs has been widespread in these systems and has altered rates of erosion and native plant biodiversity and productivity. The net effect of these changes on biogeochemical cycling is not well understood. Projected warmer and drier conditions may further alter the function and stability of these ecosystems and soil resources through direct effects on soil microbiota and plant-microbe interactions. We quantified microbial community responses to long-term livestock grazing and shrub encroachment in a Sonoran Desert grassland. We sought to characterize tipping points where biotic controls over ecosystem processes shift from being 'grass-driven' to 'shrub-driven.' We asked: How do livestock grazing (the predominant land use in dryland ecosystems) and shrub invasion (a predominant land cover change) interact to influence microbial biomass and the relative abundance of bacteria, archaea, and fungi and their extracellular enzyme activities? Surface soil from bare-ground patches, native and invasive grass rhizospheres, and bole and canopy dripline locations in patches of mature mesquite trees in long-term grazed and long-term (70+ y) protected pastures were collected and analyzed for microbial community composition, biomass, potential exoenzyme activities, and a suite of biogeochemical characteristics. We found no differences in microbial communities or the soils associated with native vs. exotic grasses. Overall, mesquite bole patches differed from other patches in all soil characteristics except potential enzyme activity: soil temperature was significantly lower, and total carbon (C) and soil moisture were significantly higher. Potential activities were lowest for bare ground and highest at shrub dripline patches for all seven exoenzymes tested. Mean potential activities for C and phosphorous (P) hydrolyzing enzymes in long-term protected pastures (C: 21.4 ug activity g-1 h-1 ± 2.3; P: 29.8 ug activity g-1 h-1 ± 3.5) were significantly higher than those in grazed pastures (C: 16.6 ug activity g-1 h-1 ± 2.1; P: 15.8 ug activity g-1 h-1 ± 2.5), suggesting long-term effects of past land use on current soil microbial populations.

Response of Nitrifier and Denitrifier Abundance and Microbial Community Structure to Experimental Warming in an Agricultural Ecosystem

PubMed Central

Waghmode, Tatoba R.; Chen, Shuaimin; Li, Jiazhen; Sun, Ruibo; Liu, Binbin; Hu, Chunsheng

2018-01-01

Soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, the response of the soil nitrifier and denitrifier communities to climate warming is poorly understood. A long-term field warming experiment has been conducted for 8 years at Luancheng Experimental Farm Station on the North China Plain; we used this field to examine how soil microbial community structure, nitrifier, and denitrifier abundance respond to warming under regular irrigation (RI) and high irrigation (HI) at different soil depths (0–5, 5–10, and 10–20 cm). Nitrifier, denitrifier, and the total bacterial abundance were assessed by quantitative polymerase chain reaction of the functional genes and 16S rRNA gene, respectively. Bacterial community structure was studied through high throughput sequencing of the 16S rRNA gene. Under RI, warming significantly (P < 0.05) increased the potential nitrification rate and nitrate concentration and decreased the soil moisture. In most of the samples, warming increased the ammonia-oxidizing bacteria abundance but decreased the ammonia-oxidizing archaea (AOA) and denitrifier (nirK, nirS, and nosZ genes) abundance. Under HI, there was a highly increased AOA and 16S rRNA gene abundance and a slightly higher denitrifier abundance compared with RI. Warming decreased the bacterial diversity and species richness, and the microbial community structure differed greatly between the warmed and control plots. The decrease in bacterial diversity was higher in RI than HI and at the 0–5 cm depths than at the 5–10 and 10–20 cm soil depths. Warming led to an increase in the relative abundance of Actinobacteria, Bacteroidetes, and TM7 but a decrease in Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Nitrospira, and Planctomycetes. The greater shift in microbial community structure was observed only in RI at the 0–5 cm soil depth. This study provides new insight into our understanding of the nitrifier and denitrifier activity and microbial community response to climate warming in agricultural ecosystems. PMID:29593703

Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

PubMed Central

Blagodatskaya, Evgenia; Blagodatsky, Sergey; Anderson, Traute-Heidi; Kuzyakov, Yakov

2014-01-01

Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)–the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed. PMID:24722409

Declining plant nitrogen supply and carbon accumulation in ageing primary boreal forest ecosystems

NASA Astrophysics Data System (ADS)

Högberg, Mona N.; Yarwood, Stephanie A.; Trumbore, Susan; Högberg, Peter

2016-04-01

Boreal forest soils are commonly characterized by a low plant nitrogen (N) supply. A high tree below-ground allocation of carbon (C) to roots and soil microorganisms in response to the shortage of N may lead to high microbial immobilisation of N, thus aggravating the N limitation. We studied the N supply at a Swedish boreal forest ecosystem chronosequence created by new land rising out of the sea due to iso-static rebound. The youngest soils develop with meadows by the coast, followed by a zone of dinitrogen fixing alder trees, and primary boreal conifer forest on ground up to 560 years old. With increasing ecosystem age, the proportion of microbial C out of the total soil C pool from the youngest to the oldest coniferous ecosystem was constant (c. 1-1.5%), whereas immobilised N (microbial N out of total soil N) increased and approached the levels commonly observed in similar boreal coniferous forests (c. 6-7 %), whereas gross N mineralization declined. Simultaneously, plant foliar N % decreased and the natural abundance of N-15 in the soil increased. More specifically, the difference in N-15 between plant foliage and soil increased, which is related to greater retention of N-15 relative to N-14 by ectomycorrhizal fungi as N is taken up from the soil and some N is transferred to the plant host. In the conifer forest, where these changes were greatest, we found increased fungal biomass in the F- and H-horizons of the mor-layer, in which ectomycorrhizal fungi are known to dominate (the uppermost horizon with litter and moss is dominated by saprotrophic fungi). Hence, we propose that the decreasing N supply to the plants and the subsequent decline in plant production in ageing boreal forests is linked to high tree belowground C allocation to C limited ectomycorrhizal fungi (and other soil microorganisms), a strong sink for available soil N. Data on organic matter C-14 suggested that the largest input of recently fixed plant C occurred in the younger coniferous forest ecosystems, whereas the soil C accumulation rate declined as N supply to the plants declined.

Microbial response to modified precipitation patterns in tallgrass prairie soil: molecular mechanisms, activity rates and organic matter dynamics

NASA Astrophysics Data System (ADS)

Zeglin, L. H.; David, M.; Bottomley, P.; Hettich, R. L.; Jansson, J.; Jumpponen, A.; Rice, C. W.; Tringe, S.; VerBerkmoes, N. C.; Myrold, D.

2011-12-01

A significant amount of carbon (C) is processed and stored in prairie soils: grasslands cover 6.1-7.4% of the earth's land surface and hold 7.3-11.4% of global soil C. Global change models predict that the future precipitation regime across the North American Great Plains will entail less frequent but larger rainfall events. The response of prairie soil microbial C processing and allocation to this scenario of higher hydrologic variability is not known, but will be a key determiner of the future capacity for prairie soil C sequestration. We are approaching this problem by assessing soil microbial function (respiration, C utilization efficiency, extracellular enzyme activity) and molecular indicators of dominant C allocation pathways (soil transcriptome, proteome and metabolome) under ambient and experimentally modified precipitation regimes. The rainfall manipulation plots (RaMPs) at the Konza Prairie Long-Term Ecological Research (LTER) site in eastern Kansas, USA is a replicated field manipulation of the magnitude and frequency of natural precipitation that was established in 1998. We collected soil before, during and after a rainfall event in both ambient and modified precipitation treatments and measured the microbial response. Microbial respiration doubled in both treatments during the water addition, and cellobiohydrolase enzyme potential activity (a catalyst of cellulose hydrolysis) increased slightly, but no significant effect of altered precipitation treatment has emerged. The fungal and bacterial ribosomal gene composition was also similar between precipitation treatments. Although pools of genes and extracellular enzymes may be relatively static during short-term dynamic conditions, transcript and intracellular protein abundances may be more indicative of the active microbial metabolic response to rapid shifts in soil moisture. Thus, analysis of transcript and protein composition is underway. In addition, we have implemented a series of lab experiments to optimize and link transcript and protein recovery and analysis procedures using the model soil bacterium Arthrobacter chlorophenicolus strain A6 (ArtchA6). Konza prairie soil was inoculated with ArchA6 and incubated for 72 h with no supplemental C, with acetate or with 4-chlorophenol (a xenobiotic compound that ArtchA6 can utilize as its sole C source), then RNA and protein were extracted from the soil. Quantitatively representative recovery of ArtchA6 genes, rRNA, mRNA and protein was successful. The ratio of ArtchA6 isocitrate lyase (icl, indicative of 2-C metabolism) to succinyl CoA synthetase (suCAB, indicative of total respiratory activity) transcript was highest in soils amended with acetate. Proteomic signatures were distinct in soils with different supplemental C sources. This experiment confirms our capability of recovering transcript and protein from the study soil and of identifying the functional molecules representative of distinct C metabolism pathways.

Soil Microbial Communities and Gas Dynamics Contribute to Arbuscular Mycorrhizal Nitrogen Uptake and Transfer to Plants

NASA Astrophysics Data System (ADS)

Hestrin, R.; Harrison, M. J.; Lehmann, J.

2016-12-01

Arbuscular mycorrhizal fungi (AMF) associate with most terrestrial plants and influence ecosystem ecology and biogeochemistry. There is evidence that AMF play a role in soil nitrogen cycling, in part by taking up nitrogen and transferring it to plants. However, many aspects of this process are poorly understood, including the factors that control fungal access to nitrogen stored in soil organic matter. In this study, we used stable isotopes and root exclusion to track nitrogen movement from organic matter into AMF and host plants. AMF significantly increased total plant biomass and nitrogen content, but both AMF and other soil microbes seemed to compete with plants for nitrogen. Surprisingly, gaseous nitrogen species also contributed significantly to plant nitrogen content under alkaline soil conditions. Our current experiments investigate whether free-living microbial communities that have evolved under a soil nitrogen gradient influence AMF access to soil organic nitrogen and subsequent nitrogen transfer to plants. This research links interactions between plants, mycorrhizal symbionts, and free-living microbes with terrestrial carbon and nitrogen dynamics.

Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards.

PubMed

Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

2014-11-01

It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards* #

PubMed Central

Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

2014-01-01

It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle. PMID:25367788

Earthworms are associated with subpopulations of Gammaproteobacteria irrespective of the total soil microbiota composition and stability.

PubMed

Fjøsne, Trine; Myromslien, Frøydis D; Wilson, Robert C; Rudi, Knut

2018-05-01

Soil represents one of the most complex microbial ecosystems on earth. It is well-known that invertebrates such as earthworms have a major impact on transformations of organic material in soil, while their effect on the soil microbiota remains largely unknown. The aim of our work was therefore to investigate the association of earthworms with temporal stability, composition and diversity in two soil microbiota experimental series. We found that earthworms were consistently associated with an increase in subgroups of Gammaproteobacteria, despite major differences in microbiota composition and temporal stability across the experimental series. Our results therefore suggest that earthworms can affect subpopulation dynamics in the soil microbiota, irrespective of the total microbiota composition. If the soil microbiota is comprised of independent microbiota components, this can contribute to our general understanding of the complexity of the soil microbiota.

Species-specific effects of polyploidisation and plant traits of Centaurea maculosa and Senecio inaequidens on rhizosphere microorganisms.

PubMed

Thébault, Aurélie; Frey, Beat; Mitchell, Edward A D; Buttler, Alexandre

2010-08-01

Invasive plant species represent a threat to terrestrial ecosystems, but their effects on the soil biota and the mechanisms involved are not yet well understood. Many invasive species have undergone polyploidisation, leading to the coexistence of various cytotypes in the native range, whereas, in most cases, only one cytotype is present in the introduced range. Since genetic variation within a species can modify soil rhizosphere communities, we studied the effects of different cytotypes and ranges (native diploid, native tetraploid and introduced tetraploid) of Centaurea maculosa and Senecio inaequidens on microbial biomass carbon, rhizosphere total DNA content and bacterial communities of a standard soil in relation to plant functional traits. There was no overall significant difference in microbial biomass between cytotypes. The variation of rhizosphere total DNA content and bacterial community structure according to cytotype was species specific. The rhizosphere DNA content of S. inaequidens decreased with polyploidisation in the native range but did not vary for C. maculosa. In contrast, the bacterial community structure of C. maculosa was affected by polyploidisation and its diversity increased, whereas there was no significant change for S. inaequidens. Traits of S. inaequidens were correlated to the rhizosphere biota. Bacterial diversity and total DNA content were positively correlated with resource allocation to belowground growth and late flowering, whereas microbial biomass carbon was negatively correlated to investment in reproduction. There were no correlations between traits of the cytotypes of C. maculosa and corresponding rhizosphere soil biota. This study shows that polyploidisation may affect rhizosphere bacterial community composition, but that effects vary among plant species. Such changes may contribute to the success of invasive polyploid genotypes in the introduced range.

Soil micromorphology, geochemistry and microbiology at two sites on James Ross Island, Maritime Antarctica

NASA Astrophysics Data System (ADS)

Meier, Lars A.; Krauze, Patryk; Prater, Isabel; Scholten, Thomas; Wagner, Dirk; Kühn, Peter; Mueller, Carsten W.

2017-04-01

Referring to the fundamental question in ecosystem research, how biotic and abiotic processes interact, only a few studies exist for polar regions that integrate microbiological and soil scientific studies . Soils comprise the complex structure and environment that fosters water storage and nutrient cycling determined by its unique chemical, physical and biological properties with respect to the specific climate and parent material. In the extreme environment of Antarctica, soil biological processes are primarily controlled by microbial communities (Bacteria, Archaea and Fungi), and thus microbiota may also determine soils chemical and physical properties in a landscape lacking higher plants at an average air temperature below 0°C. James Ross Island, Maritime Antarctica, offers a pristine laboratory and an exceptional opportunity to study pedogenesis without the influence of vascular plants and burrowing animals. We analysed micromorphological features, chemical and microbiological measures at two sites on James Ross Island (Brandy Bay and St. Martha Cove) with similar substrates (mostly fine-grained calcareous sandstones and siltstones of the Alpha Member of the Santa Martha Formation with varying amounts of conglomerates and mudstones) at similar topographic positions (small plateaus at similar elevation (80m a.s.l.)). The sites represent luv- and leeward conditions with respect to the main southwesterly winds. The climate on James Ross Island is to be described as semi-arid polar-continental, which is in clear contrast to the Southern Shetlands (e.g. King George Island) north of the Antarctic Peninsula. We will present first results of soil physical (bulk density, soil moisture and grains size distribution), pedochemical (SOC, total N and S, pH, CECeff, and pedogenic oxides) micromorphological and microbial analyses (Microbial DNA content, microbial abundances).

Atrazine contamination in agricultural soils from the Yangtze River Delta of China and associated health risks.

PubMed

Sun, J T; Pan, L L; Zhan, Yu; Tsang, Daniel C W; Zhu, L Z; Li, X D

2017-04-01

Atrazine is one of the most widely applied and persistent herbicides in the world. In view of limited information on the regional contamination of atrazine in soils in China, this study investigated the spatial distribution and environmental impacts of atrazine in agricultural soils collected from the Yangtze River Delta (YRD) as an illustrative analysis of rapidly developing regions in the country. The results showed that the concentrations of atrazine in the YRD agricultural soils ranged from <1.0 to 113 ng/g dry weight, with a mean of 5.7 ng/g, and a detection rate of 57.7 % in soils. Pesticide factory might be a major source for the elevated levels of atrazine in Zhejiang Province. The contamination of atrazine was closely associated with land use types. The concentrations and detection rates of atrazine were higher in corn fields and mulberry fields than in rice paddy fields. There was no significant difference in compositions of soil microbial phospholipids fatty acids among the areas with different atrazine levels. Positive relationship (R = 0.417, p < 0.05, n = 30) was observed between atrazine and total microbial biomass. However, other factors, such as soil type and land management practice, might have stronger influences on soil microbial communities. Human health risks via exposure to atrazine in soils were estimated according to the methods recommended by the US EPA. Atrazine by itself in all the soil samples imposed very low carcinogenic risks (<10 -6 ) and minimal non-cancer risks (hazard index <1) to adults and children.

Seasonal variation of different microorganisms with nickel and cadmium in the industrial wastewater and agricultural soils.

PubMed

Ansari, Mohd Ikram; Malik, Abdul

2010-08-01

Wastewater and soil samples were collected from the industrial area of Ghaziabad City, India from January 2005 to December 2007 and were analyzed for the presence of heavy metals by atomic absorption spectrophotometry. Test samples revealed high levels of Fe, Cr, Cu, Ni, Zn, and Cd as 967.03, 34.63, 27.97, 19.7, 16.70, and 3.20 mg/L of wastewater, respectively. The concentrations of inorganic minerals were higher in the soil samples irrigated with wastewater. Total coliforms were found to be maximum (1,133x10(4) most probable number per 100 mL) during spring and summer followed by winter and postmonsoon in the wastewater samples. The microbial count in soil as well as in wastewater decreases as the metal concentration increases. The concentration 200 microg/mL of nickel and cadmium inhibits majority of the population, while, at some points, it inhibits 100% of the population. The exponential decay model for microbial count at the increasing metal concentrations indicate that asymbiotic N2 fixers were best fitted to the model. In all the seasons, the order of decline in terms of exponential decay of the population of different microbial groups in soil was asymbiotic N2 fixers>actinomycetes>fungi>aerobic heterotrophic bacteria. The different microbial groups that have different values of slope in different seasons indicate that the resistant population of microorganisms was variable with seasons.

Microbial populations and activities of mangrove, restinga and Atlantic forest soils from Cardoso Island, Brazil.

PubMed

Pupin, B; Nahas, E

2014-04-01

Mangroves provide a distinctive ecological environment that differentiates them from other ecosystems. This study deal to evaluate the frequency of microbial groups and the metabolic activities of bacteria and fungi isolated from mangrove, restinga and Atlantic forest soils. Soil samples were collected during the summer and winter at depths of 0-2, 2-5 and 5-10 cm. Except for fungi, the counts of the total, sporulating, Gram-negative, actinomycetes, nitrifying and denitrifying bacteria decreased significantly in the following order: Atlantic forest >mangrove > restinga. The counts of micro-organisms decreased by 11 and 21% from the surface to the 2-5 and 5-10 cm layers, but denitrifying bacteria increased by 44 and 166%, respectively. A larger growth of micro-organisms was verified in the summer compared with the winter, except for actinomycetes and fungi. The average frequency of bacteria isolated from mangrove, restinga and Atlantic forest soils was 95, 77 and 78%, and 93, 90 and 95% for fungi, respectively. Bacteria were amylolytic (33%), producers of acid phosphatase (79%) and solubilizers (18%) of inorganic phosphate. The proportions of fungi were 19, 90 and 27%. The mangrove soil studied had higher chemical characteristics than the Atlantic forest, but the high salinity may have restricted the growth of microbial populations. Estimates of the microbial counts and activities were important to elucidate the differences of mangrove ecosystem from restinga and Atlantic forest. © 2013 The Society for Applied Microbiology.