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Sample records for affect soil microbial

  1. Can transgenic maize affect soil microbial communities?

    PubMed

    Mulder, Christian; Wouterse, Marja; Raubuch, Markus; Roelofs, Willem; Rutgers, Michiel

    2006-09-29

    The aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the microbial community (ability to metabolize sources belonging to different chemical guilds) and/or a change in numerical abundance of their cells. Litter placement is known for its strong influence on the soil decomposer communities. The effects of the addition of crop residues on respiration and catabolic activities of the bacterial community were examined in microcosm experiments. Four cultivars of Zea mays L. of two different isolines (each one including the conventional crop and its Bacillus thuringiensis cultivar) and one control of bulk soil were included in the experimental design. The growth models suggest a dichotomy between soils amended with either conventional or transgenic maize residues. The Cry1Ab protein appeared to influence the composition of the microbial community. The highly enhanced soil respiration observed during the first 72 h after the addition of Bt-maize residues can be interpreted as being related to the presence of the transgenic crop residues. This result was confirmed by agar plate counting, as the averages of the colony-forming units of soils in conventional treatments were about one-third of those treated with transgenic straw. Furthermore, the addition of Bt-maize appeared to induce increased microbial consumption of carbohydrates in BIOLOG EcoPlates. Three weeks after the addition of maize residues to the soils, no differences between the consumption rate of specific chemical guilds by bacteria in soils amended with transgenic maize and bacteria in soils amended with conventional maize were detectable. Reaped crop residues, comparable to post-harvest maize straw (a common practice in current agriculture), rapidly influence the soil bacterial cells at a functional level. Overall, these data support the existence of short

  2. Can Transgenic Maize Affect Soil Microbial Communities?

    PubMed Central

    Mulder, Christian; Wouterse, Marja; Raubuch, Markus; Roelofs, Willem; Rutgers, Michiel

    2006-01-01

    The aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the microbial community (ability to metabolize sources belonging to different chemical guilds) and/or a change in numerical abundance of their cells. Litter placement is known for its strong influence on the soil decomposer communities. The effects of the addition of crop residues on respiration and catabolic activities of the bacterial community were examined in microcosm experiments. Four cultivars of Zea mays L. of two different isolines (each one including the conventional crop and its Bacillus thuringiensis cultivar) and one control of bulk soil were included in the experimental design. The growth models suggest a dichotomy between soils amended with either conventional or transgenic maize residues. The Cry1Ab protein appeared to influence the composition of the microbial community. The highly enhanced soil respiration observed during the first 72 h after the addition of Bt-maize residues can be interpreted as being related to the presence of the transgenic crop residues. This result was confirmed by agar plate counting, as the averages of the colony-forming units of soils in conventional treatments were about one-third of those treated with transgenic straw. Furthermore, the addition of Bt-maize appeared to induce increased microbial consumption of carbohydrates in BIOLOG EcoPlates. Three weeks after the addition of maize residues to the soils, no differences between the consumption rate of specific chemical guilds by bacteria in soils amended with transgenic maize and bacteria in soils amended with conventional maize were detectable. Reaped crop residues, comparable to post-harvest maize straw (a common practice in current agriculture), rapidly influence the soil bacterial cells at a functional level. Overall, these data support the existence of short

  3. Factors Affecting Soil Microbial Community Structure in Tomato Cropping Systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. We identified some of the most important factors controlling microbial biomass and community structure in an agroecosystem utilizing tomato plants with the following nine tre...

  4. Microbial Carbon Cycling in Permafrost-Affected Soils

    SciTech Connect

    Vishnivetskaya, T.; Liebner, Susanne; Wilhelm, Ronald; Wagner, Dirk

    2011-01-01

    The Arctic plays a key role in Earth s climate system as global warming is predicted to be most pronounced at high latitudes and because one third of the global carbon pool is stored in ecosystems of the northern latitudes. In order to improve our understanding of the present and future carbon dynamics in climate sensitive permafrost ecosystems, present studies concentrate on investigations of microbial controls of greenhouse gas fluxes, on the activity and structure of the involved microbial communities, and on their response to changing environmental conditions. Permafrost-affected soils can function as both a source and a sink for carbon dioxide and methane. Under anaerobic conditions, caused by flooding of the active layer and the effect of backwater above the permafrost table, the mineralization of organic matter can only be realized stepwise by specialized microorganisms. Important intermediates of the organic matter decomposition are hydrogen, carbon dioxide and acetate, which can be further reduced to methane by methanogenic archaea. Evolution of methane fluxes across the subsurface/atmosphere boundary will thereby strongly depend on the activity of anaerobic methanogenic archaea and obligately aerobic methane oxidizing proteobacteria, which are known to be abundant and to significantly reduce methane emissions in permafrost-affected soils. Therefore current studies on methane-cycling microorganisms are the object of particular attention in permafrost studies, because of their key role in the Arctic methane cycle and consequently of their significance for the global methane budget.

  5. 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. PMID:26974565

  6. Do long-lived ants affect soil microbial communities?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was designed to test the hypothesis that desert ant species that build nests that remain viable at a particular point in space for more than a decade produce soil conditions that enhance microbial biomass and functional diversity. We studied the effects of a seed-harvester ant, Pogonomyrm...

  7. 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

  8. Land use type significantly affects microbial gene transcription in soil.

    PubMed

    Nacke, Heiko; Fischer, Christiane; Thürmer, Andrea; Meinicke, Peter; Daniel, Rolf

    2014-05-01

    Soil microorganisms play an essential role in sustaining biogeochemical processes and cycling of nutrients across different land use types. To gain insights into microbial gene transcription in forest and grassland soil, we isolated mRNA from 32 sampling sites. After sequencing of generated complementary DNA (cDNA), a total of 5,824,229 sequences could be further analyzed. We were able to assign nonribosomal cDNA sequences to all three domains of life. A dominance of bacterial sequences, which were affiliated to 25 different phyla, was found. Bacterial groups capable of aromatic compound degradation such as Phenylobacterium and Burkholderia were detected in significantly higher relative abundance in forest soil than in grassland soil. Accordingly, KEGG pathway categories related to degradation of aromatic ring-containing molecules (e.g., benzoate degradation) were identified in high abundance within forest soil-derived metatranscriptomic datasets. The impact of land use type forest on community composition and activity is evidently to a high degree caused by the presence of wood breakdown products. Correspondingly, bacterial groups known to be involved in lignin degradation and containing ligninolytic genes such as Burkholderia, Bradyrhizobium, and Azospirillum exhibited increased transcriptional activity in forest soil. Higher solar radiation in grassland presumably induced increased transcription of photosynthesis-related genes within this land use type. This is in accordance with high abundance of photosynthetic organisms and plant-infecting viruses in grassland. PMID:24553913

  9. Microbial community composition as affected by dryland cropping systems and tillage in a semiarid sandy soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study evaluated microbial communities of soil (0-10 cm) as affected by dryland cropping systems under different tillage practices after 5 years. The soil is an Olton sandy loam (Fine, mixed, superactive, thermic Aridic Paleustolls) with an average of 16.4% clay, 67.6% sand and 0.65 g kg-1 of O...

  10. Fly ash addition affects microbial biomass and carbon mineralization in agricultural soils.

    PubMed

    Nayak, A K; Kumar, Anjani; Raja, R; Rao, K S; Mohanty, Sangita; Shahid, Mohammad; Tripathy, Rahul; Panda, B B; Bhattacharyya, P

    2014-02-01

    The microbial biomass carbon (MBC) and carbon mineralization of fly ash (FA) amended soil at (0 %, 1.25 %, 2.5 %, 5 %, 10 % and 20 % FA; v/v) was investigated under laboratory conditions for 120 days at 60 % soil water-holding capacity and 25 ± 1°C temperature. The results demonstrated that soil respiration and microbial activities were not suppressed up to 2.5 % FA amendment and these activities decreased significantly at 10 % and 20 % FA treatment with respect to control. Application of 10 % and 20 % FA treated soils showed a decreasing trend of soil MBC with time; and the decrease was significant throughout the period of incubation. The study concluded that application of FA up to 2.5 % can thus be safely used without affecting the soil biological activity and thereby improve nutrient cycling in agricultural soils. PMID:24362819

  11. Microbial Functional Potential and Community Composition in Permafrost-Affected Soils of the NW Canadian Arctic

    PubMed Central

    Frank-Fahle, Béatrice A.; Yergeau, Étienne; Greer, Charles W.; Lantuit, Hugues; Wagner, Dirk

    2014-01-01

    Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic. PMID:24416279

  12. Arid soil microbial enzymatic activity profile as affected by geographical location and soil degradation status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Evaluating soil health is critical for any successful remediation effort. Arid lands, with their minimal carbon and water contents, low nutritional status and restricted, seasonal microbial activity pose specific challenges to soil health restoration and by extension, restoration of ecosystem repr...

  13. 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. PMID:24532178

  14. Microbial response following straw application in a soil affected by a wildfire

    NASA Astrophysics Data System (ADS)

    Barreiro, Ana; Lombao, Alba; Díaz-Raviña, Montserrat; Martin, Angela; Fontúrbel, Maria Teresa; Vega, Jose Antonio; Fernández, Cristina; Carballas, Tarsy

    2015-04-01

    Mulching treatment is often recommended to reduce post-fire erosion and sediments yields but information concerning their effects on soil microorganisms is scarce. In the present investigation the evolution of several parameters related with the mass and activity of soil microorganisms was examined in a hillslope shrubland located in Saviñao (Lugo, NW Spain) and susceptible to suffer post-fire erosion (38% slope). In this area, affected by a medium-high severity wildfire in September 2012, different treatments with wheat straw applied to the burnt soil in mulch strips (800 and 1000 kg ha-1) were established by quadruplicate (10 m x 40 m plots) and compared with the corresponding burnt untreated control. Soil samples were collected from the A horizon (0-2.5 cm depth) at different sampling times over one year after the wildfire and different soil biochemical properties (microbial biomass C, soil respiration, bacterial activity, -glucosidase, urease and phosphatase activities) were analyzed. The results showed large variation among the four field replicates of the same treatment (spatial variability), which makes difficult to evaluate the effect of mulch treatment. The evolution of the different biochemical properties in the post-fire stabilization treatments with the wheat straw applied in mulch strips were mainly related to the time passed after the fire (short- and medium- term changes in soil physical and chemical properties induced by both fire and climatic conditions) rather than to the straw mulching effects; in addition, a different temporal pattern was observed depending on the variable considered. The results pointed out the usefulness of examining intra-annual natural variability (spatial variation, seasonal fluctuations) when different indices of mass and activity of microorganisms were used as monitoring tools in soil ecosystems affected by fire. Acknowledgements. A. Barreiro and A. Lombao are recipients of FPU grants from Spanish Ministry of

  15. Drought induced changes of plant belowground carbon allocation affect soil microbial community function in a subalpine meadow

    NASA Astrophysics Data System (ADS)

    Fuchslueger, L.; Bahn, M.; Fritz, K.; Hasibeder, R.; Richter, A.

    2012-12-01

    There is growing evidence that climate extremes may affect ecosystem carbon dynamics more strongly than gradual changes in temperatures or precipitation. Climate projections suggest more frequent heat waves accompanied by extreme drought periods in many parts of Europe, including the Alps. Drought is considered to decrease plant C uptake and turnover, which may in turn decrease belowground C allocation and potentially has significant consequences for microbial community composition and functioning. However, information on effects of drought on C dynamics at the plant-soil interface in real ecosystems is still scarce. Our study aimed at understanding how summer drought affects soil microbial community composition and the uptake of recently assimilated plant C by different microbial groups in grassland. We hypothesized that under drought 1) the microbial community shifts, fungi being less affected than bacteria, 2) plants decrease belowground C allocation, which further reduces C transfer to soil microbes and 3) the combined effects of belowground C allocation, reduced soil C transport due to reduced soil moisture and shift in microbial communities cause an accumulation of extractable organic C in the soil. Our study was conducted as part of a rain-exclusion experiment in a subalpine meadow in the Austrian Central Alps. After eight weeks of rain exclusion we pulse labelled drought and control plots with 13CO2 and traced C in plant biomass, extractable organic C (EOC) and soil microbial communities using phospholipid fatty acids (PLFA). Drought induced a shift of the microbial community composition: gram-positive bacteria became more dominant, whereas gram-negative bacteria were not affected by drought. Also the relative abundance of fungal biomass was not affected by drought. While total microbial biomass (as estimated by total microbial PLFA content) increased during drought, less 13C was taken up. This reduction was pronounced for bacterial biomarkers. It reflects

  16. Factors affecting microbial 2,4,6-trinitrotoluene mineralization in contaminated soil

    USGS Publications Warehouse

    Bradley, P.M.; Chapelle, F.H.

    1995-01-01

    The influence of selected environmental factors on microbial TNT mineralization in soils collected from a TNT-contaminated site at Weldon Spring, MO, was examined using uniformly ring-labeled [14C]TNT. Microbial TNT mineralization was significantly inhibited by the addition of cellobiose and syringate. This response suggests that the indigenous microorganisms are capable of metabolizing TNT but preferentially utilize less recalcitrant substrates when available. The observed inhibition of TNT mineralization by TNT concentrations higher than 100 ??mol/kg of soil and by dry soil conditions suggests that toxic inhibition of microbial activity at high TNT concentrations and the periodic drying of these soils have contributed to the long-term persistence of TNT at Weldon Spring. In comparison to aerobic microcosms, mineralization was inhibited in anaerobic microcosms and in microcosms with a headspace of air amended with oxygen, suggesting that a mosaic of aerobic and anaerobic conditions may optimize TNT degradation at this site.

  17. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland

    PubMed Central

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

    Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the

  18. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland.

    PubMed

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

    Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the

  19. Reduced Soil Tillage Affects the Concentration, Production and Stabilization of Microbial Biomass

    NASA Astrophysics Data System (ADS)

    van Groenigen, K.; Jones, M.

    2008-12-01

    Soil microbial communities dominated by fungi have been associated with reduced N losses and increased soil aggregation. Moreover, fungal residues have been found to degrade slower than bacterial residues. For these reasons, fungi-dominated communities may be more conducive to ecosystem C storage. In agricultural systems, a shift towards a fungal decomposition pathway might help to regain some of the soil C that was lost due to cultivation. However, measurements on standing microbial biomass alone do not fully reveal fungal and bacterial contributions to SOM dynamics. Therefore, we compared the effect of reduced and conventional tillage on both the growth and concentration of fungal and bacterial biomass, by using leucine and acetate incorporation techniques and epifluorescence microscopy. We also measured the concentration of fungal and bacterial residues, by quantifying amino sugars glucosamine, galactosamine and muramic acid. Soil samples were collected at two different depths from spring barley field plots that were under conventional vs. reduced tillage management for 7.5 growing seasons. Reduced tillage strongly increased both fungal and bacterial biomass in the top soil layer. However, microbial growth rates only showed small responses, suggesting a slower turnover of microbial biomass under reduced tillage. Across soil depths and tillage treatments, total amino sugar contents ranged between 440 and 560 mg C per kilo soil. Fungal derived amino sugars increased under reduced tillage, whereas bacterial residues remained unaffected. These results suggest that reduced tillage enhances the fungal contribution to SOM dynamics both by stimulating fungal growth and stabilization of fungal biomass.

  20. Physicochemical and biological quality of soil in hexavalent chromium-contaminated soils as affected by chemical and microbial remediation.

    PubMed

    Liao, Yingping; Min, Xiaobo; Yang, Zhihui; Chai, Liyuan; Zhang, Shujuan; Wang, Yangyang

    2014-01-01

    Chemical and microbial methods are the main remediation technologies for chromium-contaminated soil. These technologies have progressed rapidly in recent years; however, there is still a lack of methods for evaluating the chemical and biological quality of soil after different remediation technologies have been applied. In this paper, microbial remediation with indigenous bacteria and chemical remediation with ferrous sulphate were used for the remediation of soils contaminated with Cr(VI) at two levels (80 and 1,276 mg kg(-1)) through a column leaching experiment. After microbial remediation with indigenous bacteria, the average concentration of water-soluble Cr(VI) in the soils was reduced to less than 5.0 mg kg(-1). Soil quality was evaluated based on 11 soil properties and the fuzzy comprehensive assessment method, including fuzzy mathematics and correlative analysis. The chemical fertility quality index was improved by one grade using microbial remediation with indigenous bacteria, and the biological fertility quality index increased by at least a factor of 6. Chemical remediation with ferrous sulphate, however, resulted in lower levels of available phosphorus, dehydrogenase, catalase and polyphenol oxidase. The result showed that microbial remediation with indigenous bacteria was more effective for remedying Cr(VI)-contaminated soils with high pH value than chemical remediation with ferrous sulphate. In addition, the fuzzy comprehensive evaluation method was proven to be a useful tool for monitoring the quality change in chromium-contaminated soils. PMID:23784058

  1. Soil microbial activity is affected by Roundup WeatherMax and pesticides applied to cotton (Gossypium hirsutum)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Adoption of glyphosate-based weed control systems has led to increased use of the herbicide with continued use of additional pesticides. Combinations of pesticides may affect soil microbial activity differently than pesticides applied alone. Research was conducted to evaluate the influence of glypho...

  2. Soil moisture variations affect short-term plant-microbial competition for ammonium, glycine, and glutamate

    PubMed Central

    Månsson, Katarina F; Olsson, Magnus O; Falkengren-Grerup, Ursula; Bengtsson, Göran

    2014-01-01

    We tested whether the presence of plant roots would impair the uptake of ammonium (), glycine, and glutamate by microorganisms in a deciduous forest soil exposed to constant or variable moisture in a short-term (24-h) experiment. The uptake of 15NH4 and dual labeled amino acids by the grass Festuca gigantea L. and soil microorganisms was determined in planted and unplanted soils maintained at 60% WHC (water holding capacity) or subject to drying and rewetting. The experiment used a design by which competition was tested in soils that were primed by plant roots to the same extent in the planted and unplanted treatments. Festuca gigantea had no effect on microbial N uptake in the constant moist soil, but its presence doubled the microbial uptake in the dried and rewetted soil compared with the constant moist. The drying and rewetting reduced by half or more the uptake by F. gigantea, despite more than 60% increase in the soil concentration of . At the same time, the amino acid and -N became equally valued in the plant uptake, suggesting that plants used amino acids to compensate for the lower acquisition. Our results demonstrate the flexibility in plant-microbial use of different N sources in response to soil moisture fluctuations and emphasize the importance of including transient soil conditions in experiments on resource competition between plants and soil microorganisms. Competition between plants and microorganisms for N is demonstrated by a combination of removal of one of the potential competitors, the plant, and subsequent observations of the uptake of N in the organisms in soils that differ only in the physical presence and absence of the plant during a short assay. Those conditions are necessary to unequivocally test for competition. PMID:24772283

  3. Biochar and soil properties affecting microbial transport through biochar-amended soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incorporation of biochar into soils has been proposed as a means to sequester carbon from the atmosphere. An added environmental benefit is that biochar has also been shown to increase soil retention of nutrients, heavy metals, and pesticides. We have recently conducted a series of experiments t...

  4. [Carbon source metabolic diversity of soil microbial community under different climate types in the area affected by Wenchuan earthquake].

    PubMed

    Zhang, Guang-Shuai; Lin, Yong-Ming; Ma, Rui-Feng; Deng, Hao-Jun; Du, Kun; Wu, Cheng-Zhen; Hong, Wei

    2015-02-01

    The MS8.0 Wenchuan earthquake in 2008 led to huge damage to land covers in northwest Sichuan, one of the critical fragile eco-regions in China which can be divided into Semi-arid dry hot climate zone (SDHC) and Subtropical humid monsoon climate zone (SHMC). Using the method of Bilog-ECO-microplate technique, this paper aimed to determine the functional diversity of soil microbial community in the earthquake-affected areas which can be divided into undamaged area (U), recover area (R) and damaged area without recovery (D) under different climate types, in order to provide scientific basis for ecological recovery. The results indicated that the average-well-color-development (AWCD) in undamaged area and recovery area showed SDHC > SHMC, which was contrary to the AWCD in the damaged area without recovery. The AWCD of damaged area without recovery was the lowest in both climate zones. The number of carbon source utilization types of soil microbial in SHMC zone was significantly higher than that in SDHC zone. The carbon source utilization types in both climate zones presented a trend of recover area > undamaged area > damaged area without recovery. The carbon source metabolic diversity characteristic of soil microbial community was significantly different in different climate zones. The diversity index and evenness index both showed a ranking of undamaged area > recover area > damaged area without recovery. In addition, the recovery area had the highest richness index. The soil microbial carbon sources metabolism characteristic was affected by soil nutrient, aboveground vegetation biomass and vegetation coverage to some extent. In conclusion, earthquake and its secondary disasters influenced the carbon source metabolic diversity characteristic of soil microbial community mainly through the change of aboveground vegetation and soil environmental factors. PMID:26031097

  5. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland

    PubMed Central

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Schnecker, Jörg; Wild, Birgit; Čapek, Petr; Kaiser, Christina; Torsvik, Vigdis L.; Richter, Andreas; Schleper, Christa; Urich, Tim

    2014-01-01

    Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation (“buried topsoils”), resulting from a decrease in fungal abundance compared to recent (“unburied”) topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation. PMID

  6. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland.

    PubMed

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Schnecker, Jörg; Wild, Birgit; Capek, Petr; Kaiser, Christina; Torsvik, Vigdis L; Richter, Andreas; Schleper, Christa; Urich, Tim

    2014-01-01

    Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation. PMID:25360132

  7. Biogas digestates affect crop P uptake and soil microbial community composition.

    PubMed

    Hupfauf, Sebastian; Bachmann, Silvia; Fernández-Delgado Juárez, Marina; Insam, Heribert; Eichler-Löbermann, Bettina

    2016-01-15

    Fermentation residues from biogas production are known as valuable organic fertilisers. This study deals with the effect of cattle slurry, co-digested cattle slurry, co-digested energy crops and mineral fertilisers on the activity and composition of soil microbiota. Furthermore, the effect of solid-liquid separation as a common pre-treatment of digestate was tested. The fertilising effects were analysed in an 8-week pot experiment on loamy sand using two crops, Amaranthus cruentus and Sorghum bicolor. Amaranth, as a crop with significantly higher P uptake, triggered stress for occurring soil microbes and thereby caused a reduction of microbial biomass C in the soil. Irrespective of the crop, microbial basal respiration and metabolic quotient were higher with the digestates than with the untreated slurry or the mineral treatments. Community level physiological profiles with MicroResp showed considerable differences among the treatments, with particularly strong effects of solid-liquid separation. Similar results were also found on a structural level (PCR-DGGE). Alkaline phosphatase gene analyses revealed high sensitivity to different fertilisation regimes. PMID:26410342

  8. Increased nitrogen deposition did not affect the composition and turnover of plant and microbial biomarkers in forest soil density fractions

    NASA Astrophysics Data System (ADS)

    Griepentrog, Marco; Bodé, Samuel; Boeckx, Pascal; Hagedorn, Frank; Wiesenberg, Guido L. B.; Schmidt, Michael W. I.

    2013-04-01

    Increased atmospheric nitrogen (N) deposition and elevated CO2 concentrations affect many forests and their ecosystem functions, including organic matter cycling in soils, the largest carbon pool of terrestrial ecosystems. However, it is still not clear how, and what the underlying mechanisms are. Specific molecules of plant and microbial origin (biomarkers) might respond differently to N deposition, depending on their internal N content. Microbial cell-wall-constituents with high-N content like amino sugars are reliable biomarkers to distinguish between fungal- and bacterial-derived organic residues. Individual lipids are plant-specific biomarkers that lack N in their molecular structure. Here, we tested the effects of elevated CO2 and increased N deposition on the dynamics of plant and microbial biomarkers by studying their composition and turnover in forest soil density fractions. Furthermore, we tested the hypothesis that these biomarkers respond differently to increased N deposition, depending on their internal N content. We used soil samples from a 4-year elevated CO2 and N deposition experiment in model forest ecosystems (open-top chambers), that were fumigated with ambient and 13C-depleted CO2 and treated with two levels of 15N-labeled fertilizer. Bulk soil was separated into free light fraction, occluded light fraction and heavy fraction by density fractionation and ultrasonic dispersion. The heavy fraction was further particle-size fractionated with 20 μm as a cut-off. We determined carbon and N concentrations and their isotopic compositions (δ13C, δ15N) within bulk soil and density fractions. Therein, we extracted and quantified individual amino sugars and lipids and conducted compound-specific stable-isotope-analysis using GC- and LC-IRMS. Results show that amino sugars were mainly stabilized in association with soil minerals. Especially bacterial amino sugars were preferentially associated with soil minerals, exemplified by a consistent decrease

  9. Dissipation and effects of tricyclazole on soil microbial communities and rice growth as affected by amendment with alperujo compost.

    PubMed

    García-Jaramillo, M; Redondo-Gómez, S; Barcia-Piedras, J M; Aguilar, M; Jurado, V; Hermosín, M C; Cox, L

    2016-04-15

    The presence of pesticides in surface and groundwater has grown considerably in the last decades as a consequence of the intensive farming activity. Several studies have shown the benefits of using organic amendments to prevent losses of pesticides from runoff or leaching. A particular soil from the Guadalquivir valley was placed in open air ponds and amended at 1 or 2% (w/w) with alperujo compost (AC), a byproduct from the olive oil industry. Tricyclazole dissipation, rice growth and microbial diversity were monitored along an entire rice growing season. An increase in the net photosynthetic rate of Oryza sativa plants grown in the ponds with AC was observed. These plants produced between 1100 and 1300kgha(-1) more rice than plants from the unamended ponds. No significant differences were observed in tricyclazole dissipation, monitored for a month in soil, surface and drainage water, between the amended and unamended ponds. The structure and diversity of bacteria and fungi communities were also studied by the use of the polymerase chain reaction denaturing gel electrophoresis (PCR-DGGE) from DNA extracted directly from soil samples. The banding pattern was similar for all treatments, although the density of bands varied throughout the time. Apparently, tricyclazole did not affect the structure and diversity of bacteria and fungi communities, and this was attributed to its low bioavailability. Rice cultivation under paddy field conditions may be more efficient under the effects of this compost, due to its positive effects on soil properties, rice yield, and soil microbial diversity. PMID:26849328

  10. Analysis of matrix effects critical to microbial transport in organic waste-affected soils across laboratory and field scales

    NASA Astrophysics Data System (ADS)

    Unc, Adrian; Goss, Michael J.; Cook, Simon; Li, Xunde; Atwill, Edward R.; Harter, Thomas

    2012-06-01

    Organic waste applications to soil (manure, various wastewaters, and biosolids) are among the most significant sources of bacterial contamination in surface and groundwater. Transport of bacteria through the vadose zone depends on flow path geometry and stability and is mitigated by interaction between soil, soil solution, air-water interfaces, and characteristics of microbial surfaces. After initial entry, the transport through soil depends on continued entrainment of bacteria and resuspension of those retained in the porous structure. We evaluated the retention of bacteria-sized artificial microspheres, varying in diameter and surface charge and applied in different suspending solutions, by a range of sieved soils contained in minicolumns, the transport of hydrophobic bacteria-sized microspheres through undisturbed soil columns as affected by waste type under simulated rainfall, and the field-scale transport of Enterococcus spp. to an unconfined sandy aquifer after the application of liquid manure. Microsphere retention reflected microsphere properties. The soil type and suspending solution affected retention of hydrophilic but not hydrophobic particles. Retention was not necessarily facilitated by manure-microsphere-soil interactions but by manure-soil interactions. Undisturbed column studies confirmed the governing role of waste type on vadose-zone microsphere transport. Filtration theory applied as an integrated analysis of transport across length scales showed that effective collision efficiency depended on the distance of travel. It followed a power law behavior with the power coefficient varying from ˜0.4 over short distances to >0.9 over 1 m (i.e., very little filtration for a finite fraction of biocolloids), consistent with reduced influence of soil solution and biocolloid properties at longer travel distances.

  11. 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.

  12. Spatial pattern formation of microbes at the soil microscale affect soil C and N turnover in an individual-based microbial community model

    NASA Astrophysics Data System (ADS)

    Kaiser, Christina; Evans, Sarah; Dieckmann, Ulf; Widder, Stefanie

    2016-04-01

    At the μm-scale, soil is a highly structured and complex environment, both in physical as well as in biological terms, characterized by non-linear interactions between microbes, substrates and minerals. As known from mathematics and theoretical ecology, spatial structure significantly affects the system's behaviour by enabling synergistic dynamics, facilitating diversity, and leading to emergent phenomena such as self-organisation and self-regulation. Such phenomena, however, are rarely considered when investigating mechanisms of microbial soil organic matter turnover. Soil organic matter is the largest terrestrial reservoir for organic carbon (C) and nitrogen (N) and plays a pivotal role in global biogeochemical cycles. Still, the underlying mechanisms of microbial soil organic matter buildup and turnover remain elusive. We explored mechanisms of microbial soil organic matter turnover using an individual-based, stoichiometrically and spatially explicit computer model, which simulates the microbial de-composer system at the soil microscale (i.e. on a grid of 100 x 100 soil microsites). Soil organic matter dynamics in our model emerge as the result of interactions among individual microbes with certain functional traits (f.e. enzyme production rates, growth rates, cell stoichiometry) at the microscale. By degrading complex substrates, and releasing labile substances microbes in our model continusly shape their environment, which in turn feeds back to spatiotemporal dynamics of the microbial community. In order to test the effect of microbial functional traits and organic matter input rate on soil organic matter turnover and C and N storage, we ran the model into steady state using continuous inputs of fresh organic material. Surprisingly, certain parameter settings that induce resource limitation of microbes lead to regular spatial pattern formation (f.e. moving spiral waves) of microbes and substrate at the μm-scale at steady-state. The occurrence of these

  13. Habitat management affects soil chemistry and allochthonous organic inputs mediating microbial structure and exo-enzyme activity in Wadden Sea salt-marsh soils

    NASA Astrophysics Data System (ADS)

    Mueller, Peter; Granse, Dirk; Thi Do, Hai; Weingartner, Magdalena; Nolte, Stefanie; Hoth, Stefan; Jensen, Kai

    2016-04-01

    The Wadden Sea (WS) region is Europe's largest wetland and home to approximately 20% of its salt marsh area. Mainland salt marshes of the WS are anthropogenically influenced systems and have traditionally been used for livestock grazing in wide parts. After foundation of WS National Parks in the late 1980s and early 1990s, artificial drainage has been abandoned; however, livestock grazing is still common in many areas of the National Parks and is under ongoing discussion as a habitat-management practice. While studies so far focused on effects of livestock grazing on biodiversity, little is known about how biogeochemical processes, element cycling, and particularly carbon sequestration are affected. Here, we present data from a recent field study focusing on grazing effects on soil properties, microbial exo-enzyme activity, microbial abundance and structure. Exo-enzyme activity was studied conducting digestive enzyme assays for various enzymes involved in C- and N cycling. Microbial abundance and structure was assessed measuring specific gene abundance of fungi and bacteria using quantitative PCR. Soil compaction induced by grazing led to higher bulk density and decreases in soil redox (∆ >100 mV). Soil pH was significantly lower in grazed parts. Further, the proportion of allochthonous organic matter (marine input) was significantly smaller in grazed vs. ungrazed sites, likely caused by a higher sediment trapping capacity of the taller vegetation in the ungrazed sites. Grazing induced changes in bulk density, pH and redox resulted in reduced activity of enzymes involved in microbial C acquisition; however, there was no grazing effect on enzymes involved in N acquisition. While changes in pH, bulk density or redox did not affect microbial abundance and structure, the relative amount of marine organic matter significantly reduced the relative abundance of fungi (F:B ratio). We conclude that livestock grazing directly affects microbial exo-enzyme activity, thus

  14. DMPP-added nitrogen fertilizer affects soil N2O emission and microbial activity in Southern Italy

    NASA Astrophysics Data System (ADS)

    Vitale, Luca; De Marco, Anna; Maglione, Giuseppe; Polimeno, Franca; Di Tommasi, Paul; Magliulo, Vincenzo

    2014-05-01

    plots, whereas an opposite trend for basal respiration was observed, thus evidencing a stressful condition for nitrifying microbial population. After 57 and 71 DAS, when fertilizer was applied as 30 kg N ha-1, the microbial biomass was similar between C and DMPP plots, whereas basal respiration resulted statistically lower in DMPP plots than C plots. During these periods, average DMPP N2O fluxes were also comparable or lower. In conclusion, our data evidence a stressful condition for soil microbes and in particular for nitrifiers when a higher DMPP quantity is supplied. On the contrary, when lower quantities of DMPP-added fertilizers are supplied (e.s. 30 kg N ha-1) effectiveness of DMPP in reducing soil N2O emission is guaranteed by reducing the nitrifiers activity without negatively affecting their growth.

  15. Microbial indicators of soil quality

    SciTech Connect

    Turco, R.F.; Kennedy, A.C.; Jawson, M.

    1992-01-01

    Soil quality is an elusive term; however, the quality of a soil can greatly impact land use, sustainability, and productivity. Soil microbial processes are an integral part of soil quality and a better understanding of these processes and microbial community structure is needed. Microbial biomass, respiration, and labile nutrient pool size have generally been used as intrinsic parameters of a soil's microbial status. These analyses may not fully identify inherent differences in soil quality, especially if environmental conditions or manmade pertubations alter microbial community structure. Assessment of microbial community structure is necessary to determine the long-term effects of stress on soil quality. Measurement of microbial diversity should include nucleic acid and fatty acid phospholipid profiles as well as substrate utilization patterns. Microbial indicators will allow us to characterize the ecological status of the soil microbial community. For soil quality indicators to be successful, integration with other soil parameters is essential.

  16. Biochar addition impacts soil microbial community in tropical soils

    NASA Astrophysics Data System (ADS)

    Paz-Ferreiro, Jorge; Fu, Shenglei; Méndez, Ana; Gascó, Gabriel

    2014-05-01

    Studies on the effect of biochar on soil microbial activity and community structure in tropical areas are scarce. In this study we report the effect of several types of biochar (sewage sludge biochar, paper mill waste biochar, miscanthus biochar and pinewood biochar) in the soil microbial community of two tropical soils, an Acrisol and an Oxisol. In addition we study the effect of the presence or absence of earthworms in soil microbial community. Soil microbial community was more strongly affected by biochar than by the presence or absence of macrofauna.

  17. Temperature Effects on Microbial CH4 and CO2 Production in Permafrost-Affected Soils From the Barrow Environmental Observatory

    NASA Astrophysics Data System (ADS)

    Graham, D. E.; Roy Chowdhury, T.; Zheng, J.; Moon, J. W.; Yang, Z.; Gu, B.; Wullschleger, S. D.

    2015-12-01

    Warmer Arctic temperatures are increasing the annual soil thaw depth and prolonging the thaw season in Alaskan permafrost zones. This change exposes organic matter buried in the soils and permafrost to microbial degradation and mineralization to form CO2 and CH4. The proportion and fluxes of these greenhouse gases released into the atmosphere control the global feedback on warming. To improve representations of these biogeochemical processes in terrestrial ecosystem models we compared soil properties and microbial activities in core samples of polygonal tundra from the Barrow Environmental Observatory. Measurements of soil water potential through the soil column characterized water binding to the organic and mineral components. This suction combines with temperature to control freezing, gas diffusion and microbial activity. The temperature-dependence of CO2 and CH4 production from anoxic soil incubations at -2, +4 or +8 °C identified a significant lag in methanogenesis relative to CO2 production by anaerobic respiration and fermentation. Changes in the abundance of methanogen signature genes during incubations indicate that microbial population shifts caused by thawing and warmer temperatures drive changes in the mixtures of soil carbon degradation products. Comparisons of samples collected across the microtopographic features of ice-wedge polygons address the impacts of water saturation, iron reduction and organic matter content on CH4 production and oxidation. These combined measurements build process understanding that can be applied across scales to constrain key response factors in models that address Arctic soil warming.

  18. Biological soil crusts: a microenvironment characterized by complex microbial interrelations affected by the presence of the exopolysaccharidic matrix.

    NASA Astrophysics Data System (ADS)

    De Philippis, Roberto

    2015-04-01

    Biological Soil Crusts (BSCs) are complex microbial communities, commonly found in arid and semiarid areas of the world. The capability of the microorganisms residing in BSCs to withstand the harsh environmental conditions typical of these habitats, namely drought and high solar irradiation, is related with the presence of a matrix constituted by microbial-produced extracellular polysaccharides (EPSs), which also accomplish for a wide array of key ecological roles. EPSs represent a huge carbon source directly available to heterotrophic organisms, affect soil characteristics, water regimes, and establish complex interactions with plants. The induction of BSCs on degraded soils is considered a feasible approach to amend and maintain land fertility, as it was reported in a number of recent studies. It was recently shown that BSC induction is beneficial in enhancing SOC (Soil Organic Carbon) and in increasing the abundance of phototrophic organisms and vegetation cover. This lecture will describe the results of a study showing that cyanobacterial-EPS resulted advantageous to the growth and metabolism of seedlings of Caragana korshinskii, a desert sub-shrub widely diffused in the area under study, also contributing a defensive effect against the damaging effects of reactive oxygen species (ROS), generated under UV-irradiation, salt stress and desiccation. A study aimed at investigating the possible correlation between the chemical composition and the macromolecular features of the EPS matrix of induced BSCs of different age, collected in the hyper-arid plateau of Hobq desert, Inner Mongolia, China, will be also presented. The results of this study showed that the characteristics of the EPS of the matrix of the investigated IBSCs cannot be put only in relation with the age of the crusts and the activity of phototrophic microorganisms but, more properly, it has to be taken into account the biotic interactions ongoing between EPS producers (cyanobacteria, green microalgae

  19. Persistence of bifenthrin in sandy loam soil as affected by microbial community.

    PubMed

    Sharma, Divya; Singh, Shashi Bala

    2012-06-01

    Soil was fortified with bifenthrin at the level of 10 μg g(-1) soil. Soil samples were drawn at regular intervals of 0, 10, 20, 30 and 40 days. For extraction of bifenthrin, soil was extracted with acetone. Clean up was done by liquid-liquid partitioning with dichloromethane after diluting with brine solution. Quantification of bifenthrin residues was done by GC using mega bore column and ECD detector. Recovery of bifenthrin in soil ranged between 92.6 % and 93.8 % at 0.5 and 1.0 μg g(-1). The instrumental limit of detection of bifenthrin was 0.005 μg mL(-1) and LOQ for soil by this method was found to be 0.05 μg g(-1). The calibration curve was found to be linear within range the range of 0.01 and 0.10 μg mL(-1) concentration. The DT(50) (disappearance time for 50 % loss) of bifenthrin at the level of 10 μg g(-1) in sterile and non sterile soil were found to be 330 and 147 days, respectively. A vast difference in the half life of sterile and non sterile soil indicated the presence of potential microbes for bifenthrin degradation. PMID:22476257

  20. MICROBIAL INDICATORS OF SOIL QUALITY

    EPA Science Inventory

    Soil quality is an elusive term; however, the quality of a soil can greatly impact land use, sustainability, and productivity. Soil microbial processes are an integral part of soil quality and a better understanding of these processes and microbial community structure is needed. ...

  1. Microbial Transformation of Triadimefon to Triadimenol in Soils: Selective Production Rates of Triadimenol Stereoisomers Affect Exposure and Risk

    EPA Science Inventory

    The microbial transformation of triadimefon, an agricultural fungicide of the 1,2,4-triazole class, was followed at a nominal concentration of 50 μg/mL over 4 months under aerobic conditions in three different soil types. Rates and products of transformation were measured, as wel...

  2. Climate change interactions affect soil carbon dioxide efflux and microbial functioning in a post-harvest forest.

    PubMed

    McDaniel, M D; Kaye, J P; Kaye, M W; Bruns, M A

    2014-04-01

    Forest disturbances, including whole-tree harvest, will increase with a growing human population and its rising affluence. Following harvest, forests become sources of C to the atmosphere, partly because wetter and warmer soils (relative to pre-harvest) increase soil CO2 efflux. This relationship between soil microclimate and CO2 suggests that climate changes predicted for the northeastern US may exacerbate post-harvest CO2 losses. We tested this hypothesis using a climate-manipulation experiment within a recently harvested northeastern US forest with warmed (H; +2.5 °C), wetted (W; +23% precipitation), warmed + wetted (H+W), and ambient (A) treatments. The cumulative soil CO2 effluxes from H and W were 35% (P = 0.01) and 22% (P = 0.07) greater than A. However, cumulative efflux in H+W was similar to A and W, and 24% lower than in H (P = 0.02). These findings suggest that with higher precipitation soil CO2 efflux attenuates rapidly to warming, perhaps due to changes in substrate availability or microbial communities. Microbial function measured as CO2 response to 15 C substrates in warmed soils was distinct from non-warmed soils (P < 0.001). Furthermore, wetting lowered catabolic evenness (P = 0.04) and fungi-to-bacteria ratios (P = 0.03) relative to non-wetted treatments. A reciprocal transplant incubation showed that H+W microorganisms had lower laboratory respiration on their home soils (i.e., home substrates) than on soils from other treatments (P < 0.01). We inferred that H+W microorganisms may use a constrained suite of C substrates that become depleted in their "home" soils, and that in some disturbed ecosystems, a precipitation-induced attenuation (or suppression) of soil CO2 efflux to warming may result from fine-tuned microbe-substrate linkages. PMID:24362535

  3. Soil microbial abundance, activity and diversity response in two different altitude-adapted plant communities affected by wildfire in Sierra Nevada National Park (Granada, Spain)

    NASA Astrophysics Data System (ADS)

    Bárcenas-Moreno, Gema; Zavala, Lorena; Jordan, Antonio; Bååth, Erland; Mataix-Beneyto, Jorge

    2013-04-01

    Plant communities can play an important role in fire severity and post-fire ecosystem recovery due to their role as combustible and different plant-soil microorganisms interactions. Possible differences induced by plant and microorganisms response after fire could affect the general ecosystem short and long-term response and its sustainability. The main objective of this work was the evaluation of the effect of wildfire on soil microbial abundance, activity and diversity in two different plant communities associated to different altitudes in Sierra Nevada National Park (Granada, Spain). Samples were collected in two areas located on the Sierra Nevada Mountain between 1700 and 2000 m above sea level which were affected by a large wildfire in 2005. Two samplings were carried out 8 and 20 months after fire and samples were collected in both burned and unburned (control) zones in each plant community area. Area A is located at 1700m and it is formed by Quercus rotundifolia forest while area B is located at 2000 m altitude and is composed of alpine vegetation formed by creeping bearing shrubs. Microbial biomass measured by Fumigation-Extraction method followed the same trend in both areas showing slight and no significant differences between burned and unburned area during the study period while viable and cultivable bacteria abundance were markedly higher in fire affected samples than in the control ones in both samplings. Viable and cultivable filamentous fungi had different behavior depending of plant vegetation community studied showing no differences between burned and unburned area in area A while was significantly higher in burned samples than in the control ones in area B. Microbial activity monitoring with soil microbial respiration appears to had been affected immediately after fire since microbial respiration was lower in burned samples from area A than in unburned one only 8 months after fire and no significant differences were observed between burned and

  4. Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season

    PubMed Central

    Zhou, Dinggang; Xu, Liping; Gao, Shiwu; Guo, Jinlong; Luo, Jun; You, Qian; Que, Youxiong

    2016-01-01

    Cry1Ac transgenic sugarcane provides a promising way to control stem-borer pests. Biosafety assessment of soil ecosystem for cry1Ac transgenic sugarcane is urgently needed because of the important role of soil microorganisms in nutrient transformations and element cycling, however little is known. This study aimed to explore the potential impact of cry1Ac transgenic sugarcane on rhizosphere soil enzyme activities and microbial community diversity, and also to investigate whether the gene flow occurs through horizontal gene transfer. We found no horizontal gene flow from cry1Ac sugarcane to soil. No significant difference in the population of culturable microorganisms between the non-GM and cry1Ac transgenic sugarcane was observed, and there were no significant interactions between the sugarcane lines and the growth stages. A relatively consistent trend at community-level, represented by the functional diversity index, was found between the cry1Ac sugarcane and the non-transgenic lines. Most soil samples showed no significant difference in the activities of four soil enzymes: urease, protease, sucrose, and acid phosphate monoester between the non-transgenic and cry1Ac sugarcane lines. We conclude, based on one crop season, that the cry1Ac sugarcane lines may not affect the microbial community structure and functional diversity of the rhizosphere soil and have few negative effects on soil enzymes. PMID:27014291

  5. Biodegradability of nonaqueous-phase liquids affects the mineralization of phenanthrene in soil because of microbial competition

    SciTech Connect

    Morrison, D.E.; Alexander, M.

    1997-08-01

    A study was conducted to determine the effects of biodegradability of nonaqueous-phase liquids (NAPLs) and microbial competition on the biodegradation in soil of a constituent of the NAPLs. The rates of mineralization of phenanthrene dissolved in 8 mg of 2,2,4,4,6,8,8-heptamethylnonane (HMN), di(2-ethylhexyl) phthalate (DEHP), or pristane per g of soil were faster than the rates when the compound was dissolved in hexadecane or dodecane. Addition of inorganic N and P to the soil increased the mineralization rate in the first two but not the last two NAPLs. N and P addition did not enhance mineralization of phenanthrene when added in 500 {micro}g of hexadecane, pristane, or HMN per g of soil. Hexadecane was rapidly degraded, pristane was slowly metabolized, DEHP was still slower, and HMN was not mineralized in the test period. Mixing the soil stimulated mineralization of phenanthrene dissolved in HMN but not in hexadecane. Mineralization of phenanthrene dissolved in HMN was the same if the gas phase contained 21%, 2.1%, or traces of O{sub 2}. In contrast, the biodegradation of phenanthrene dissolved in hexadecane, although the same at 21 and 2.1% O{sub 2}, was not observed if traces of O{sub 2} were present. The mineralization was slower in unshaken soil-water mixtures if phenanthrene was added in hexadecane than in HMN or pristane, but the rates with the 3 NAPLs were increased by shaking the suspensions. The authors suggest that the biodegradability of major components of NAPLs and microbial competition for N, P, or O{sub 2} will have a major impact on the rate of transformation of minor constituents of NAPLs.

  6. Soil Microbial Mineralization of Cellulose in Frozen Soils

    NASA Astrophysics Data System (ADS)

    Segura, J.; Haei, M.; Sparrman, T.; Nilsson, M. B.; Schleucher, J.; Oquist, M. G.

    2014-12-01

    Soils of high-latitude ecosystems store a large fraction of the global soil carbon pool. In boreal forests, the mineralization of soil organic matter (SOM) during winter by soil heterotrophic activity can affect the ecosystems net carbon balance. Recent research has shown that microorganisms in the organic surface layer of boreal forest soil can mineralize and grow on simple, monomeric substrates under frozen conditions. However, any substantial impacts of microbial activity in frozen soils on long-term soil carbon balances depend on whether soil microorganisms can utilize the more complex, polymeric substrates in SOM. In order to evaluate the potential for soil microorganisms to metabolize carbon polymers at low temperatures, we incubated boreal forest soil samples amended with [13C]-cellulose and studied the microbial catabolic and anabolic utilization of the substrate under frozen and unfrozen conditions (-4 and +4°C). The [13C]-CO2 production rate in the samples at +4°C were 0.524 mg CO2 SOM -1 day-1 while rates in the frozen samples (-4°C) were 0.008 mg CO2 SOM -1 day-1. Thus, freezing of the soil markedly reduced microbial utilization of the cellulose. However, newly synthetized [13C]-enriched cell membrane lipids, PLFAs, were detected in soil samples incubated both above and below freezing, confirming microbial growth also in the frozen soil matrix. The reduced metabolic rates induced by freezing indicate constraints on exoenzymatic activity, as well as substrate diffusion rates that we can attribute to reduced liquid water content of the frozen soil. We conclude that the microbial population in boreal forest soil has the capacity to metabolize, and grow, on polymeric substrates at temperatures below zero. This also involves maintaining exoenzymatic activity in frozen soils. This capacity manifests the importance of SOM mineralization during the winter season and its importance for the net carbon balance of soils of high-latitude ecosystems.

  7. Microbial control over carbon cycling in soil

    PubMed Central

    Schimel, Joshua P.; Schaeffer, Sean M.

    2012-01-01

    A major thrust of terrestrial microbial ecology is focused on understanding when and how the composition of the microbial community affects the functioning of biogeochemical processes at the ecosystem scale (meters-to-kilometers and days-to-years). While research has demonstrated these linkages for physiologically and phylogenetically “narrow” processes such as trace gas emissions and nitrification, there is less conclusive evidence that microbial community composition influences the “broad” processes of decomposition and organic matter (OM) turnover in soil. In this paper, we consider how soil microbial community structure influences C cycling. We consider the phylogenetic level at which microbes form meaningful guilds, based on overall life history strategies, and suggest that these are associated with deep evolutionary divergences, while much of the species-level diversity probably reflects functional redundancy. We then consider under what conditions it is possible for differences among microbes to affect process dynamics, and argue that while microbial community structure may be important in the rate of OM breakdown in the rhizosphere and in detritus, it is likely not important in the mineral soil. In mineral soil, physical access to occluded or sorbed substrates is the rate-limiting process. Microbial community influences on OM turnover in mineral soils are based on how organisms allocate the C they take up – not only do the fates of the molecules differ, but they can affect the soil system differently as well. For example, extracellular enzymes and extracellular polysaccharides can be key controls on soil structure and function. How microbes allocate C may also be particularly important for understanding the long-term fate of C in soil – is it sequestered or not? PMID:23055998

  8. Short-time effect of salvage harvesting on microbial soil properties in a Mediterranean area affected by a wildfire: preliminary results

    NASA Astrophysics Data System (ADS)

    Moltó, Jorge; Mataix-Solera, Jorge; Arcenegui, Victoria; Morugan, Alicia; Girona, Antonio; Garcia-orenes, Fuensanta

    2014-05-01

    In the Mediterranean region, wildfires are considered one of the main ecological factors, which, in addition to and in relation to changes in soil use, may cause soil loss and degradation, one of the most important environmental problems that humanity must face up to. As is well known, the soil-plant system is one of the key factors determining ecological recovery after the occurrence of a wildfire. Traditionally, a variety of forestry practices have been implemented on spanish sites after the incidence of a wildfire. Among them stands out the complete extraction of the burned wood, which consist in getting rid of the branches and other wooden debris using small controlled bonfires, splintering or mechanical extraction. This set of post-fire management practices is known as salvage logging or salvage harvesting. Despite the remarkable relevance and influence that this conjunction of techniques has on land management after a wildfire, very little experimental research focused on assessing the impact of salvage logging on the vegetal community has been done. Furthermore, even less research inquiring into the mode and grade of incidence that the salvage logging produces on soil properties has taken place. The aim of this research is to assess the effects that the salvage harvesting has on different soil microbial properties and other related properties. The study area is located in the Natural Park of the "Sierra de Mariola" in the province of Alicante, southeastern Spain. This location was affected by a wildfire whose extension reached more than 500 Ha in July 2012. Different post-fire treatments were proposed by the authorities, including salvage harvesting in some areas. Two different treatments were distinguished for the study, "control" (without any kind of burned wood removal) and "harvest" (where salvage logging was carried out), in each area three 4 m2 sampling plots were set up. These two treatments were established on the same slope with the same orography

  9. Microbial effect on soil hydraulic properties

    NASA Astrophysics Data System (ADS)

    Furman, Alex; Rosenzweig, Ravid; Volk, Elazar; Rosenkranz, Hella; Iden, Sascha; Durner, Wolfgang

    2014-05-01

    Although largely ignored, the soil contains large amount of biofilms (attached microbes) that can affect many processes. While biochemical processes are studied, biophysical processes receive only little attention. Biofilms may occupy some of the pore space, and by that affect the soil hydraulic properties. This effect on unsaturated soils, however, was not intensively studied. In this research we directly measure the hydraulic properties, namely the soil's unsaturated hydraulic conductivity function and retention curve, for soils containing real biofilm. To do that we inoculate soil with biofilm-forming bacteria and incubate it with sufficient amounts of nutrient until biofilm is formed. The hydraulic properties of the incubated soil are then measured using several techniques, including multi-step outflow and evaporation method. The longer measurements (evaporation method) are conducted under refrigeration conditions to minimize microbial activity during the experiment. The results show a clear effect of the biofilm, where the biofilm-affected soil (sandy loam in our case) behaves like a much finer soil. This qualitatively makes sense as the biofilm generates an effective pore size distribution that is characterized by smaller pores. However, the effect is much more complex and needs to be studied carefully considering (for example) dual porosity models. We compare our preliminary results with other experiments, including flow-through column experiments and experiments with biofilm analogues. Clearly a better understanding of the way microbial activity alters the hydraulic properties may help designing more efficient bioremediation, irrigation, and other soil-related processes.

  10. Factors affecting soil cohesion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil erodibility is a measure of a soil’s resistance against erosive forces and is affected by both intrinsic (or inherent) soil property and the extrinsic condition at the time erodibility measurement is made. Since soil erodibility is usually calculated from results obtained from erosion experimen...

  11. Soil microbial biomass and community structure affected by repeated additions of sewage sludge in four Swedish long-term field experiments

    NASA Astrophysics Data System (ADS)

    Börjesson, G.; Kätterer, T.; Kirchmann, H.

    2012-04-01

    and soil organic matter levels. Correlations between soil organic matter and total PLFA contents showed highly positive correlations at all sites (with R-values between 0.72 and 0.88). To find out whether sewage sludge through its metal impurities could impose stress on the microbial biomass, we compared the correlations between all different fertilisers used and PLFAs. The slopes of these comparisons revealed that sludge did not differ from other fertiliser treatments, which means that our results contrast earlier reports on negative effects of metals in sludge on soil microbes. The microbial community structure, studied with principal component analysis of individual PLFAs, was strongly affected by changes in soil pH, and at those sites where sewage sludge had caused a low pH, Gram-positive bacteria were more dominant than in the other treatments. However, differences in community structure were larger between sites than between the treatments investigated in this study, thus indicating that the original soil properties were more important for the microbial community structure than the fertiliser treatments.

  12. Post fumigation recovery of soil microbial community structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil fumigants have been extensively used to control target soil-borne pathogens and weeds for the past few decades. It is known that the fumigants with broad biocidal activity can affect both target and non-target soil organisms, but the recovery of soil microbial communities are unknown until rece...

  13. Microbial hotspots and hot moments in soil

    NASA Astrophysics Data System (ADS)

    Kuzyakov, Yakov; Blagodatskaya, Evgenia

    2015-04-01

    Soils are the most heterogeneous parts of the biosphere, with an extremely high differentiation of properties and processes within nano- to macroscales. The spatial and temporal heterogeneity of input of labile organics by plants creates microbial hotspots over short periods of time - the hot moments. We define microbial hotspots as small soil volumes with much faster process rates and much more intensive interactions compared to the average soil conditions. Such hotspots are found in the rhizosphere, detritusphere, biopores (including drilosphere) and on aggregate surfaces, but hotspots are frequently of mixed origin. Hot moments are short-term events or sequences of events inducing accelerated process rates as compared to the averaged rates. Thus, hotspots and hot moments are defined by dynamic characteristics, i.e. by process rates. For this hotspot concept we extensively reviewed and examined the localization and size of hotspots, spatial distribution and visualization approaches, transport of labile C to and from hotspots, lifetime and process intensities, with a special focus on process rates and microbial activities. The fraction of active microorganisms in hotspots is 2-20 times higher than in the bulk soil, and their specific activities (i.e. respiration, microbial growth, mineralization potential, enzyme activities, RNA/DNA ratio) may also be much higher. The duration of hot moments in the rhizosphere is limited and is controlled by the length of the input of labile organics. It can last a few hours up to a few days. In the detritusphere, however, the duration of hot moments is regulated by the output - by decomposition rates of litter - and lasts for weeks and months. Hot moments induce succession in microbial communities and intense intra- and interspecific competition affecting C use efficiency, microbial growth and turnover. The faster turnover and lower C use efficiency in hotspots counterbalances the high C inputs, leading to the absence of strong

  14. Effects of biochar amendments on soil microbial biomass and activity.

    PubMed

    Zhang, H; Voroney, R P; Price, G W

    2014-11-01

    Environmental benefits reported in the literature of using biochar as a soil amendment are generally increased microbial activity and reduced greenhouse gas (GHG) emissions. This study determined the effects of amendment with biomass feedstocks (spent coffee grounds, wood pellets, and horse bedding compost) and that of biochars (700°C) produced from these feedstocks on soil microbial biomass (C and N) and activity. Soils were amended with these substrates at 0.75% by weight and incubated for up to 175 d under laboratory conditions. Biochar residual effects on soil microbial activity were also studied by amending these soils with either ammonium nitrate (NHNO, 35 mg N kg) or with glucose (864 mg C kg) plus NHNO. Soil microbial biomass C and N, net N mineralization, and CO, NO, and CH emissions were measured. Amendment with biomass feedstocks significantly increased soil microbial biomass and activity, whereas amendment with the biochars had no significant effect. Also, biochar amendment had no significant effect on either net N mineralization or NO and CH emissions from soil. These results indicate that production of biochars at this high temperature eliminated potential substrates. Microbial biomass C in biochar-amended and unamended soils was not significantly different following additions of NHNO or glucose plus NHNO, suggesting that microbial access to otherwise labile C and N was not affected. This study shows that biochars produced at 700°C, regardless of feedstock source, do not enhance soil microbial biomass or activity. PMID:25602227

  15. Microbial Contribution to Organic Carbon Sequestration in Mineral Soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil productivity and sustainability are dependent on soil organic matter (SOM). Our understanding on how organic inputs to soil from microbial processes become converted to SOM is still limited. This study aims to understand how microbes affect carbon (C) sequestration and the formation of recalcit...

  16. Interactions between allelochemicals and the microbial community affect weed suppresion following cover crop residue incorporation into soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study is to understand how soil microorganisms interact with cover crop-derived allelochemicals to suppress weed germination and growth following cover crop residue incorporation. We conducted a time series experiment by crossing sterilized and non-sterilized soil with four dif...

  17. Experimental warming effects on the microbial community of a temperate mountain forest soil

    PubMed Central

    Schindlbacher, A.; Rodler, A.; Kuffner, M.; Kitzler, B.; Sessitsch, A.; Zechmeister-Boltenstern, S.

    2011-01-01

    Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO2 (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency. PMID:21760644

  18. Soil microbial communities respond differently to three chemically defined polyphenols

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High molecular weight polyphenols (tannins) that leach into the soil may affect microbial populations, for example by serving as substrates for microbial respiration or by selecting for certain microbes . In this study we examined how three phenolic compounds that represent environmentally widespre...

  19. Out of sight - Profiling soil characteristics, nutrients and microbial communities affected by organic amendments down to one meter in a long-term maize cultivation experiment

    NASA Astrophysics Data System (ADS)

    Lehtinen, Taru; Mikkonen, Anu; Zavattaro, Laura; Grignani, Carlo; Baumgarten, Andreas; Spiegel, Heide

    2016-04-01

    Soil characteristics, nutrients and microbial activity in the deeper soil layers are topics not of-ten covered in agricultural studies since the main interest lies within the most active topsoils and deep soils are more time-consuming to sample. Studies have shown that deep soil does matter, although biogeochemical cycles are not fully understood yet. The main aim of this study is to investigate the soil organic matter dynamics, nutrients and microbial community composition in the first meter of the soil profiles in the long-term maize cropping system ex-periment Tetto Frati, in the vicinity of the Po River in Northern Italy. The trial site lies on a deep, calcareous, free-draining soil with a loamy texture. The following treatments have been applied since 1992: 1) maize for silage with 250 kg mineral N ha-1 (crop residue removal, CRR), 2) maize for grain with 250 kg mineral N ha-1 (crop residue incorporation, CRI), 3) maize for silage with 250 kg bovine slurry N ha-1 (SLU), 4) maize for silage with 250 kg farm yard manure N ha-1 (FYM). Soil characteristics (pH, carbonate content, soil organic carbon (SOC), aggregate stability (WSA)), and nutrients (total nitrogen (Nt), CAL-extractable phos-phorous (P) and potassium (K), potential N mineralisation) were investigated. Bacteri-al community composition was investigated with Ion PGM high-throughput sequencing at the depth of 8000 sequences per sample. Soil pH was moderately alkaline in all soil samples, in-creasing with increasing soil depth, as the carbonate content increased. SOC was significantly higher in the treatments with organic amendments (CRI, SLU and FYM) compared to CRR in 0-25 cm (11.1, 11.6, 14.7 vs. 9.8 g kg-1, respectively), but not in the deeper soil. At 50-75 cm soil depth FYM treatment revealed higher WSA compared to CRR, as well as higher CAL-extractable K (25 and 15 mg kg-1, respectively) and potential N mineralisation (11.30 and 8.78 mg N kg-1 7d-1, respectively). At 75-100 cm soil depth, SLU and

  20. Hydrological connectivity drives microbial responses to soil moisture (Invited)

    NASA Astrophysics Data System (ADS)

    Schimel, J.

    2013-12-01

    Biogeochemical models generally fit microbial responses to moisture with smooth functions--as soils dry, processes slow. Microbial physiology, in contrast, has focused on how cells synthesize organic solutes to remain hydrated. Increasingly, however, we recognize that drying affects soil processes through resource constraints that develop when hydrological connection breaks down and organisms and resources become isolated in disconnected water pockets. Thus, microbial activity is regulated by abrupt breaks in connectivity and resources become unavailable to synthesize organic osmolytes; i.e. both biogeochemical models and pure-culture physiology perspectives are flawed. Hydrological connectivity fails before microbes become substantially stressed and before extracellular enzymes become inactive. Thus, resources can accumulate in dry soils, even as microbial activity shuts down because of resource limitation. The differential moisture responses of enzymes, organisms, and transport explains why microbial biomass and extractable C pools increase through the dry summer in California annual grasslands, why the size of the respiration pulse on rewetting increases with the length of drought, and even why soils from a wide range of biomes show the same relative response to soil moisture. I will discuss the evidence that supports the hydrological connectivity hypothesis for soil microbial moisture responses, how it affects a range of ecosystem processes, and how we can use it to develop simple, yet mechanistically rich, models of soil dynamics.

  1. Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

    PubMed

    Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

    2015-07-01

    In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen. PMID:25391237

  2. SOIL MICROBIAL COMMUNITIES UNDER CONVENTIONAL-TILL AND NO-TILL CONTINUOUS COTTON SYSTEMS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil management practices affect soil microbial communities, which in turn influence soil ecosystem processes. In this study, the effects of conventional- and no-tillage practices on soil microbial communities were examined under long-term continuous cotton (Gossypium hirsutum L.) systems on a Deca...

  3. ACID RAIN AND SOIL MICROBIAL ACTIVITY: EFFECTS AND THEIR MECHANISMS

    EPA Science Inventory

    In the investigation, our aim was to determine if acid rain affects soil microbial activity and to identify possible mechanisms of observed effects. A Sierran forest soil (pH 6.4) planted with Ponderosa pine seedlings was exposed to simulated rain (pH 2.0, 3.0, 4.0 and 5.6) with ...

  4. Soil microbial community dynamics as influenced by composted dairy manure, soil properties and landscape position

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding factors that affect plant growth, whether it is manure addition, season, or soil-type and landscape variability may also impact soil microbial activity, biomass and community structure. Thus an in situ study was conducted to evaluate microbiological properties of three different soil t...

  5. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    transformation of added substrates into complex SOM and stability is measured biologically using 13C isotopes. The first 4 mo of the incubation demonstrate a significant influence of both soil mineralogy and substrate quality on microbial physiology with subsequent effects on total newly formed soil C concentrations. However, treatment differences in total C changed when only the biologically stable fraction was considered. There was an interaction between mineralogy and substrate with soil respiration, enzyme activity and microbial biomass. Py-GC/MS results show a transformation of simple substrates into chemically complex SOM, rich in proteins, lipids, and phenolics. The abundances of proteins and lipids varied however, across soil and substrate treatments, suggesting divergent SOM chemistries due to substrate quality and organo-mineral interactions. Preliminary results from this long-term study demonstrate the microbial production of complex SOM where difference in accumulation and stability are influenced by the conditions and microbial community in which it is formed. From this work, we can develop a better understanding of the ecological context in which SOM is formed and how altering microbial community function and resource inputs may affect the development of stable SOM.

  6. BIOLOGICAL AMENDMENTS AND CROP ROTATIONS FOR MANAGING SOIL MICROBIAL COMMUNITIES AND SOILBORNE DISEASES OF POTATO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Various biological amendments, including commercial biocontrol agents, microbial inoculants, mycorrhizae, and an aerobic compost tea (CT), were evaluated, alone and in conjunction with different crop rotations, for their efficacy in introducing beneficial microorganisms, affecting soil microbial com...

  7. Linking microbial carbon utilization with microbially-derived soil organic matter

    NASA Astrophysics Data System (ADS)

    Kallenbach, Cynthia M.; Grandy, A. Stuart

    2014-05-01

    , microbial activity and biomass, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial transformation of added substrates into complex SOM and stability is measured biologically using 13C isotopes. The first 6 mo of the incubation demonstrate a significant influence of both soil mineralogy and substrate quality on microbial physiology with subsequent effects on total newly formed soil C concentrations. However, treatment differences in total C changed when only the biologically stable fraction was considered. There was an interaction between mineralogy and substrate with soil respiration, enzyme activity and microbial biomass. Py-GC/MS results show a transformation of simple substrates into chemically complex SOM, rich in proteins, lipids, and phenolics. The abundances of proteins and lipids varied however, across soil and substrate treatments, suggesting divergent SOM chemistries due to substrate quality and organo-mineral interactions. Preliminary results from this long-term study demonstrate the microbial production of complex SOM where difference in accumulation and stability are influenced by the interactions between resources and the microbial community. From this work, we can develop a better understanding of the ecological context in which SOM is formed and how altering microbial community function and resource inputs may affect the development of stable SOM.

  8. 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

  9. Soil microbial communities respond differently to three chemically defined polyphenols.

    PubMed

    Schmidt, Michael A; Kreinberg, Allison J; Gonzalez, Javier M; Halvorson, Jonathan J; French, Elizabeth; Bollmann, Annette; Hagerman, Ann E

    2013-11-01

    High molecular weight polyphenols (e.g. tannins) that enter the soil may affect microbial populations, by serving as substrates for microbial respiration or by selecting for certain microbes. In this study we examined how three phenolic compounds that represent some environmentally widespread tannins or their constituent functional groups were respired by soil microorganisms and how the compounds affected the abundance and diversity of soil bacteria and archaea, including ammonia oxidizers. An acidic, silt loam soil from a pine forest was incubated for two weeks with the monomeric phenol methyl gallate, the small polyphenol epigallocatechin gallate, or the large polyphenol oenothein B. Respiration of the polyphenols during the incubation was measured using the Microresp™ system. After incubation, metabolic diversity was determined by community level physiological profiling (CLPP), and genetic diversity was determined using denaturing gradient gel electrophoresis (DGGE) analysis on DNA extracted from the soil samples. Total microbial populations and ammonia-oxidizing populations were measured using real time quantitative polymerase chain reaction (qPCR). Methyl gallate was respired more efficiently than the higher molecular weight tannins but not as efficiently as glucose. Methyl gallate and epigallocatechin gallate selected for genetically or physiologically unique populations compared to glucose. None of the polyphenols supported microbial growth, and none of the polyphenols affected ammonia-oxidizing bacterial populations or ammonia-oxidizing archaea. Additional studies using both a wider range of polyphenols and a wider range of soils and environments are needed to elucidate the role of polyphenols in determining soil microbiological diversity. PMID:23545181

  10. Soil disturbance increases soil microbial enzymatic activity in arid ecoregion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functional diversity of the soil microbial community is commonly used in the assessment of soil health as it relates to the activity of soil microflora involved in carbon cycling. Soil microbes in different microenvironments will have varying responses to different substrates, thus catabolic fingerp...

  11. Arctic soil microbial diversity in a changing world.

    PubMed

    Blaud, Aimeric; Lerch, Thomas Z; Phoenix, Gareth K; Osborn, A Mark

    2015-12-01

    The Arctic region is a unique environment, subject to extreme environmental conditions, shaping life therein and contributing to its sensitivity to environmental change. The Arctic is under increasing environmental pressure from anthropogenic activity and global warming. The unique microbial diversity of Arctic regions, that has a critical role in biogeochemical cycling and in the production of greenhouse gases, will be directly affected by and affect, global changes. This article reviews current knowledge and understanding of microbial taxonomic and functional diversity in Arctic soils, the contributions of microbial diversity to ecosystem processes and their responses to environmental change. PMID:26275598

  12. 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

  13. The subzero microbiome: microbial activity in frozen and thawing soils.

    PubMed

    Nikrad, Mrinalini P; Kerkhof, Lee J; Häggblom, Max M

    2016-06-01

    Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change. PMID:27106051

  14. Role of soil microbial processes in integrated pest management

    SciTech Connect

    Francis, A.J.

    1987-01-01

    Soil microorganisms play a significant role in the carbon, nitrogen, phosphorus, and sulfur cycles in nature and are critical to the functioning of ecosystems. Microorganisms affect plant growth directly by regulating the availability of plant nutrients in soil, or indirectly by affecting the population dynamics of plant pathogens in soil. Any adverse effect on soil microorganisms or on the microbial processes will affect the soil fertility, availability of plant nutrients and the overall biogeochemical cycling of elements in nature. Soil microorganisms are responsible for the degradation and detoxification of pesticides; they control many insect pests, nematodes, and other plant pathogenic microorganisms by parasitism, competition, production of antibiotics and other toxic substances. Also, they regulate the availability of major and minor nutrients as well as essential elements. The long-term effects of continuous and, in some instances, excessive application of pesticides on soil fertility is not fully understood. Although much information is available on the integrated pest management (IPM) system, we have very little understanding of the extent of soil microbial processes which modulate the overall effectiveness of various strategies employed in IPM. The purpose of this paper is to review briefly the key microbial processes and their relationship to the IPM system.

  15. Controls on soil microbial community stability under climate change

    PubMed Central

    de Vries, Franciska T.; Shade, Ashley

    2013-01-01

    Soil microbial communities are intricately linked to ecosystem functioning because they play important roles in carbon and nitrogen cycling. Still, we know little about how soil microbial communities will be affected by disturbances expected with climate change. This is a significant gap in understanding, as the stability of microbial communities, defined as a community's ability to resist and recover from disturbances, likely has consequences for ecosystem function. Here, we propose a framework for predicting a community's response to climate change, based on specific functional traits present in the community, the relative dominance of r- and K-strategists, and the soil environment. We hypothesize that the relative abundance of r- and K-strategists will inform about a community's resistance and resilience to climate change associated disturbances. We also propose that other factors specific to soils, such as moisture content and the presence of plants, may enhance a community's resilience. For example, recent evidence suggests microbial grazers, resource availability, and plant roots each impact on microbial community stability. We explore these hypotheses by offering three vignettes of published data that we re-analyzed. Our results show that community measures of the relative abundance of r- and K-strategists, as well as environmental properties like resource availability and the abundance and diversity of higher trophic levels, can contribute to explaining the response of microbial community composition to climate change-related disturbances. However, further investigation and experimental validation is necessary to directly test these hypotheses across a wide range of soil ecosystems. PMID:24032030

  16. Microbial respiration per unit microbial biomass increases with carbon-to-nutrient ratios in soils

    NASA Astrophysics Data System (ADS)

    Spohn, Marie; Chodak, Marcin

    2015-04-01

    The ratio of carbon-to-nutrient in forest floors is usually much higher than the ratio of carbon-to-nutrient that soil microorganisms require for their nutrition. In order to understand how this mismatch affects carbon cycling, the respiration rate per unit soil microbial biomass carbon - the metabolic quotient (qCO2) - was studied. This was done in a field study (Spohn and Chodak, 2015) and in a meta-analysis of published data (Spohn, 2014). Cores of beech, spruce, and mixed spruce-beech forest soils were cut into slices of 1 cm from the top of the litter layer down to 5 cm in the mineral soil, and the relationship between the qCO2 and the soil carbon-to-nitrogen (C:N) and the soil carbon-to-phosphorus (C:P) ratio was analyzed. We found that the qCO2 was positively correlated with soil C:N ratio in spruce soils (R = 0.72), and with the soil C:P ratio in beech (R = 0.93), spruce (R = 0.80) and mixed forest soils (R = 0.96). We also observed a close correlation between the qCO2 and the soil C concentration in all three forest types. Yet, the qCO2 decreased less with depth than the C concentration in all three forest types, suggesting that the change in qCO2 is not only controlled by the soil C concentration. We conclude that microorganisms increase their respiration rate per unit biomass with increasing soil C:P ratio and C concentration, which adjusts the substrate to their nutritional demands in terms of stoichiometry. In an analysis of literature data, I tested the effect of the C:N ratio of soil litter layers on microbial respiration in absolute terms and per unit microbial biomass C. For this purpose, a global dataset on the microbial respiration rate per unit microbial biomass C - termed the metabolic quotient (qCO2) - was compiled form literature data. It was found that the qCO2 in the soil litter layers was positively correlated with the litter C:N ratio and negatively related with the litter nitrogen (N) concentration. The positive relation between the qCO2

  17. Substrate and nutrient limitation regulating microbial growth in soil

    NASA Astrophysics Data System (ADS)

    Bååth, Erland

    2015-04-01

    Microbial activity and growth in soil is regulated by several abiotic factors, including temperature, moisture and pH as the most important ones. At the same time nutrient conditions and substrate availability will also determine microbial growth. Amount of substrate will not only affect overall microbial growth, but also affect the balance of fungal and bacterial growth. The type of substrate will also affect the latter. Furthermore, according to Liebig law of limiting factors, we would expect one nutrient to be the main limiting one for microbial growth in soil. When this nutrient is added, the initial second liming factor will become the main one, adding complexity to the microbial response after adding different substrates. I will initially describe different ways of determining limiting factors for bacterial growth in soil, especially a rapid method estimating bacterial growth, using the leucine incorporation technique, after adding C (as glucose), N (as ammonium nitrate) and P (as phosphate). Scenarios of different limitations will be covered, with the bacterial growth response compared with fungal growth and total activity (respiration). The "degree of limitation", as well as the main limiting nutrient, can be altered by adding substrate of different stoichiometric composition. However, the organism group responding after alleviating the nutrient limitation can differ depending on the type of substrate added. There will also be situations, where fungi and bacteria appear to be limited by different nutrients. Finally, I will describe interactions between abiotic factors and the response of the soil microbiota to alleviation of limiting factors.

  18. 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. PMID:26590854

  19. Microbial Life in Soil - Linking Biophysical Models with Observations

    NASA Astrophysics Data System (ADS)

    Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

    2014-12-01

    Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that

  20. Microbial Life in Soil - Linking Biophysical Models with Observations

    NASA Astrophysics Data System (ADS)

    Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

    2015-04-01

    Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools

  1. Soil Microbial Community Dynamics as Influenced by Soil Properties and Landscape Position

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Factors that affect plant growth, whether it is manure addition, season, or soil-type and landscape variability may provide insight on how to better manage agricultural fields through the evaluation of soil microbial activity, biomass and community structure. Thus, an in situ study was conducted to ...

  2. Desert gerbils affect bacterial composition of soil.

    PubMed

    Kuznetsova, Tatyana A; Kam, Michael; Khokhlova, Irina S; Kostina, Natalia V; Dobrovolskaya, Tatiana G; Umarov, Marat M; Degen, A Allan; Shenbrot, Georgy I; Krasnov, Boris R

    2013-11-01

    Rodents affect soil microbial communities by burrow architecture, diet composition, and foraging behavior. We examined the effect of desert rodents on nitrogen-fixing bacteria (NFB) communities by identifying bacteria colony-forming units (CFU) and measuring nitrogen fixation rates (ARA), denitrification (DA), and CO2 emission in soil from burrows of three gerbil species differing in diets. Psammomys obesus is folivorous, Meriones crassus is omnivorous, consuming green vegetation and seeds, and Dipodillus dasyurus is predominantly granivorous. We also identified NFB in the digestive tract of each rodent species and in Atriplex halimus and Anabasis articulata, dominant plants at the study site. ARA rates of soil from burrows of the rodent species were similar, and substantially lower than control soil, but rates of DA and CO2 emission differed significantly among burrows. Highest rates of DA and CO2 emission were measured in D. dasyurus burrows and lowest in P. obesus. CFU differed among bacteria isolates, which reflected dietary selection. Strains of cellulolytic representatives of the family Myxococcaceae and the genus Cytophaga dominated burrows of P. obesus, while enteric Bacteroides dominated burrows of D. dasyurus. Burrows of M. crassus contained both cellulolytic and enteric bacteria. Using discriminant function analysis, differences were revealed among burrow soils of all rodent species and control soil, and the two axes accounted for 91 % of the variance in bacterial occurrences. Differences in digestive tract bacterial occurrences were found among these rodent species. Bacterial colonies in P. obesus and M. crassus burrows were related to bacteria of A. articulata, the main plant consumed by both species. In contrast, bacteria colonies in the burrow soil of D. dasyurus were related to bacteria in its digestive tract. We concluded that gerbils play an important role as ecosystem engineers within their burrow environment and affect the microbial complex of

  3. Plant diversity increases soil microbial activity and soil carbon storage.

    PubMed

    Lange, Markus; Eisenhauer, Nico; Sierra, Carlos A; Bessler, Holger; Engels, Christoph; Griffiths, Robert I; Mellado-Vázquez, Perla G; Malik, Ashish A; Roy, Jacques; Scheu, Stefan; Steinbeiss, Sibylle; Thomson, Bruce C; Trumbore, Susan E; Gleixner, Gerd

    2015-01-01

    Plant diversity strongly influences ecosystem functions and services, such as soil carbon storage. However, the mechanisms underlying the positive plant diversity effects on soil carbon storage are poorly understood. We explored this relationship using long-term data from a grassland biodiversity experiment (The Jena Experiment) and radiocarbon ((14)C) modelling. Here we show that higher plant diversity increases rhizosphere carbon inputs into the microbial community resulting in both increased microbial activity and carbon storage. Increases in soil carbon were related to the enhanced accumulation of recently fixed carbon in high-diversity plots, while plant diversity had less pronounced effects on the decomposition rate of existing carbon. The present study shows that elevated carbon storage at high plant diversity is a direct function of the soil microbial community, indicating that the increase in carbon storage is mainly limited by the integration of new carbon into soil and less by the decomposition of existing soil carbon. PMID:25848862

  4. A biophysical index for predicting hydration-mediated microbial diversity in soils

    NASA Astrophysics Data System (ADS)

    Wang, G.; Or, D.

    2012-04-01

    Exploring the origins of soil microbial diversity represents an immense and uncharted scientific frontier. Progress in resolving mechanisms that promote and sustain the unparalleled soil microbial diversity found in soil requires development of process-based predictive tools that consider dynamic biophysical interactions at highly resolved spatial and temporal scales. We report a novel biophysical metric for hydration-mediated microbial coexistence in soils by integrating key biophysical variables, such as aquatic habitat size and connectivity, nutrient diffusion affecting microbial growth, and aqueous films controlling motility and dispersal, into a predictive index. Results show a surprisingly narrow range of hydration conditions (a few kPa) that mark a sharp transition from suppression (wet) to promotion (dry) of microbial diversity in unsaturated soils in agreement with limited observations and with simulation results based on individual-based models of competing populations. The framework enables systematic hypothesis testing for key factors that regulate microbial populations and affect soil bio-geochemical functions, and represents a step towards deciphering key mechanisms that support soil microbial diversity. New insights into the different roles of biophysical mechanisms in promoting soil microbial diversity enable predictions concerning microbial consortia function and bioremediation activities in soils, and may shape how we quantify microbial diversity within the context of land resources and biogeochemical cycling.

  5. 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. PMID:24652702

  6. Water management history affects GHG kinetics and microbial communities composition of an Italian rice paddy

    NASA Astrophysics Data System (ADS)

    Lagomarsino, Alessandra; Agnelli, Allessandroelio; Pastorelli, Roberta; Pallara, Grazia; Rasse, Daniel; Silvennoinen, Hanna

    2015-04-01

    The water management system of cultivated soils is one of the most important factors affecting the respective magnitudes of CH4 and N2O emissions. We hypothesized an effect of past management on soil microbial communities and greenhouse gas (GHG) production potential The objective of this study were to i) assess the influence of water management history on GHG production potential and microbial community structure, ii) relate GHGs fluxes to the microbial communities involved in CH4 and N2O production inhabiting the different soils. Moreover, the influence of different soil conditioning procedures on GHG potential fluxes was determined. To reach this aim, four soils with different history of water management were compared, using dried and sieved, pre-incubated and fresh soils. Soil conditioning procedures strongly affected GHG emissions potential: drying and sieving determined the highest emission rates and the largest differences among soil types, probably through the release of labile substrates. Conversely, soil pre-incubation tended to homogenize and level out the differences among soils. Microbial communities composition drove GHG emissions potential and was affected by past management. The water management history strongly affected microbial communities structure and the specific microbial pattern of each soil was strictly linked to the gas (CH4 or N2O) emitted. Aerobic soil stimulated N2O peaks, given a possible major contribution of coupled nitrification/denitrification process. As expected, CH4 was lower in aerobic soil, which showed a less abundant archeal community. This work added evidences to support the hypothesis of an adaptation of microbial communities to past land management that reflected in the potential GHG fluxes.

  7. Soil microbial community and its interaction with soil carbon and nitrogen dynamics following afforestation in central China.

    PubMed

    Deng, Qi; Cheng, Xiaoli; Hui, Dafeng; Zhang, Qian; Li, Ming; Zhang, Quanfa

    2016-01-15

    Afforestation may alter soil microbial community structure and function, and further affect soil carbon (C) and nitrogen (N) dynamics. Here we investigated soil microbial carbon and nitrogen (MBC and MBN) and microbial community [e.g. bacteria (B), fungi (F)] derived from phospholipid fatty acids (PLFAs) analysis in afforested (implementing woodland and shrubland plantations) and adjacent croplands in central China. Relationships of microbial properties with biotic factors [litter, fine root, soil organic carbon (SOC), total nitrogen (TN) and inorganic N], abiotic factors (soil temperature, moisture and pH), and major biological processes [basal microbial respiration, microbial metabolic quotient (qCO2), net N mineralization and nitrification] were developed. Afforested soils had higher mean MBC, MBN and MBN:TN ratios than the croplands due to an increase in litter input, but had lower MBC:SOC ratio resulting from low-quality (higher C:N ratio) litter. Afforested soils also had higher F:B ratio, which was probably attributed to higher C:N ratios in litter and soil, and shifts of soil inorganic N forms, water, pH and disturbance. Alterations in soil microbial biomass and community structure following afforestation were associated with declines in basal microbial respiration, qCO2, net N mineralization and nitrification, which likely maintained higher soil carbon and nitrogen storage and stability. PMID:26410698

  8. 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. PMID:25766028

  9. Spatial Variations of Soil Microbial Activities in Saline Groundwater-Irrigated Soil Ecosystem

    NASA Astrophysics Data System (ADS)

    Chen, Li-Juan; Feng, Qi; Li, Chang-Sheng; Song, You-Xi; Liu, Wei; Si, Jian-Hua; Zhang, Bao-Gui

    2016-05-01

    Spatial variations of soil microbial activities and its relationship with environmental factors are very important for estimating regional soil ecosystem function. Based on field samplings in a typical saline groundwater-irrigated region, spatial variations of soil microbial metabolic activities were investigated. Combined with groundwater quality analysis, the relationship between microbial activities and water salinity was also studied. The results demonstrated that moderate spatial heterogeneity of soil microbial activities presented under the total dissolved solids (TDS) of groundwater ranging from 0.23 to 12.24 g L-1. Groundwater salinity and microbial activities had almost opposite distribution characteristics: slight saline water was mainly distributed in west Baqu and south Quanshan, while severe saline and briny water were dominant in east Baqu and west Huqu; however, total AWCD was higher in the east-center and southwest of Baqu and east Huqu, while it was lower in east Baqu and northwest Huqu. The results of correlation analyses demonstrated that high-salinity groundwater irrigation had significantly adverse effects on soil microbial activities. Major ions Ca2+, Mg2+, Cl_, and SO4 2- in groundwater decisively influenced the results. Three carbon sources, carbohydrates, amines, and phenols, which had minor utilization rates in all irrigation districts, were extremely significantly affected by high-salinity groundwater irrigation. The results presented here offer an approach for diagnosing regional soil ecosystem function changes under saline water irrigation.

  10. Spatial Variations of Soil Microbial Activities in Saline Groundwater-Irrigated Soil Ecosystem.

    PubMed

    Chen, Li-Juan; Feng, Qi; Li, Chang-Sheng; Song, You-Xi; Liu, Wei; Si, Jian-Hua; Zhang, Bao-Gui

    2016-05-01

    Spatial variations of soil microbial activities and its relationship with environmental factors are very important for estimating regional soil ecosystem function. Based on field samplings in a typical saline groundwater-irrigated region, spatial variations of soil microbial metabolic activities were investigated. Combined with groundwater quality analysis, the relationship between microbial activities and water salinity was also studied. The results demonstrated that moderate spatial heterogeneity of soil microbial activities presented under the total dissolved solids (TDS) of groundwater ranging from 0.23 to 12.24 g L(-1). Groundwater salinity and microbial activities had almost opposite distribution characteristics: slight saline water was mainly distributed in west Baqu and south Quanshan, while severe saline and briny water were dominant in east Baqu and west Huqu; however, total AWCD was higher in the east-center and southwest of Baqu and east Huqu, while it was lower in east Baqu and northwest Huqu. The results of correlation analyses demonstrated that high-salinity groundwater irrigation had significantly adverse effects on soil microbial activities. Major ions Ca(2+), Mg(2+), Cl(_), and SO4 (2-) in groundwater decisively influenced the results. Three carbon sources, carbohydrates, amines, and phenols, which had minor utilization rates in all irrigation districts, were extremely significantly affected by high-salinity groundwater irrigation. The results presented here offer an approach for diagnosing regional soil ecosystem function changes under saline water irrigation. PMID:26872886

  11. Soil warming affects soil organic matter chemistry of all density fractions of a mountain forest soil

    NASA Astrophysics Data System (ADS)

    Schnecker, Jörg; Wanek, Wolfgang; Borken, Werner; Schindlbacher, Andreas

    2016-04-01

    Rising temperatures enhance microbial decomposition of soil organic matter (SOM) and increase thereby the soil CO2 efflux. Elevated microbial activity might differently affect distinct SOM pools, depending on their stability and accessibility. Soil fractions derived from density fractionation have been suggested to represent SOM pools with different turnover times and stability against microbial decomposition. We here investigated the chemical and isotopic composition of bulk soil and three different density fractions of forest soils from a long term warming experiment in the Austrian Alps. At the time of sampling the soils in this experiment had been warmed during the snow-free period for 8 consecutive years. During that time no thermal adaptation of the microbial community could be identified and CO2 release from the soil continued to be elevated by the warming treatment. Our results which included organic C content, total N content, δ13C, δ 14C, δ 15N and the chemical composition, identified by pyrolysis-GC/MS, showed no significant differences in bulk soil between warming treatment and control. The differences in the three individual fractions (free particulate organic matter, occluded particulate organic matter and mineral associated organic matter) were mostly small and the direction of warming induced change was variable with fraction and sampling depth. We did however find statistically significant effects of warming in all density fractions from 0-10 cm depth, 10-20 cm depth or both. Our results also including significant changes in the supposedly more stable mineral associated organic matter fraction where δ 13C values decreased at both sampling depths and the relative proportion of N-bearing compounds decreased at a sampling depth of 10-20 cm. All the observed changes can be attributed to an interplay of enhanced microbial decomposition of SOM and increased root litter input. This study suggests that soil warming destabilizes all density fractions of

  12. [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. PMID:24564164

  13. Non-microbial methane emissions from soils

    NASA Astrophysics Data System (ADS)

    Wang, Bin; Hou, Longyu; Liu, Wei; Wang, Zhiping

    2013-12-01

    Traditionally, methane (CH4) is anaerobically formed by methanogenic archaea. However, non-microbial CH4 can also be produced from geologic processes, biomass burning, animals, plants, and recently identified soils. Recognition of non-microbial CH4 emissions from soils remains inadequate. To better understand this phenomenon, a series of laboratory incubations were conducted to examine effects of temperature, water, and hydrogen peroxide (H2O2) on CH4 emissions under both aerobic and anaerobic conditions using autoclaved (30 min, 121 °C) soils and aggregates (>2000 μm, A1; 2000-250 μm, A2; 250-53 μm, M1; and <53 μm, M2). Results show that applying autoclaving to pre-treat soils is effective to inhibit methanogenic activity, ensuring the CH4 emitted being non-microbial. Responses of non-microbial CH4 emissions to temperature, water, and H2O2 were almost identical between aerobic and anaerobic conditions. Increasing temperature, water of proper amount, and H2O2 could significantly enhance CH4 emissions. However, the emission rates were inhibited and enhanced by anaerobic conditions without and with the existence of H2O2, respectively. As regards the aggregates, aggregate-based emission presented an order of M1 > A2 > A1 > M2 and C-based emission an order of M2 > M1 > A1 > A2, demonstrating that both organic carbon quantity and property are responsible for CH4 emissions from soils at the scale of aggregate. Whole soil-based order of A2 > A1 > M1 > M2 suggests that non-microbial CH4 release from forest soils is majorly contributed by macro-aggregates (i.e., >250 μm). The underlying mechanism is that organic matter through thermal treatment, photolysis, or reactions with free radicals produce CH4, which, in essence, is identical with mechanisms of other non-microbial sources, indicating that non-microbial CH4 production may be a widespread phenomenon in nature. This work further elucidates the importance of non-microbial CH4 formation which should be distinguished

  14. Bioremediation of petroleum contaminated soil using vegetation. A microbial study

    SciTech Connect

    Lee, E.; Banks, M.K. )

    1993-12-01

    The degradation of selected petroleum hydrocarbons in the rhizosphere of alfalfa was investigated in a greenhouse experiment. Petroleum contaminated and uncontaminated soils were spiked with 100 ppm of polynuclear aromatic and aliphatic hydrocarbons. Unspiked, uncontaminated soil was used as a control. Microbial counts for soils with and without plants for each soil treatment were performed 4, 8, 16, and 24 weeks after planting. Microbial numbers were substantially greater in soil with plants when compared to soil containing no plants, indicating that plant roots enhanced microbial populations in contaminated soil. Soil treatments had no effect on microbial numbers in the presence of plants. 12 refs., 3 figs., 1 tab.

  15. Relative Effects of Biological Amendments and Crop Rotations on Soil Microbial Communities and Soilborne Diseases of Potato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Various biological amendments, including commercial biocontrol agents, microbial inoculants, mycorrhizae, and an aerobic compost tea (ACT), were evaluated, alone and in conjunction with different crop rotations, for their efficacy in introducing beneficial microorganisms, affecting soil microbial co...

  16. Specific microbial attachment to root knot nematodes in suppressive soil.

    PubMed

    Adam, Mohamed; Westphal, Andreas; Hallmann, Johannes; Heuer, Holger

    2014-05-01

    Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity. PMID:24532076

  17. Specific Microbial Attachment to Root Knot Nematodes in Suppressive Soil

    PubMed Central

    Adam, Mohamed; Westphal, Andreas; Hallmann, Johannes

    2014-01-01

    Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity. PMID:24532076

  18. Biofuel intercropping effects on soil carbon and microbial activity.

    PubMed

    Strickland, Michael S; Leggett, Zakiya H; Sucre, Eric B; Bradford, Mark A

    2015-01-01

    Biofuels will help meet rising demands for energy and, ideally, limit climate change associated with carbon losses from the biosphere to atmosphere. Biofuel management must therefore maximize energy production and maintain ecosystem carbon stocks. Increasingly, there is interest in intercropping biofuels with other crops, partly because biofuel production on arable land might reduce availability and increase the price of food. One intercropping approach involves growing biofuel grasses in forest plantations. Grasses differ from trees in both their organic inputs to soils and microbial associations. These differences are associated with losses of soil carbon when grasses become abundant in forests. We investigated how intercropping switchgrass (Panicum virgalum), a major candidate for cellulosic biomass production, in loblolly pine (Pinus taeda) plantations affects soil carbon, nitrogen, and microbial dynamics. Our design involved four treatments: two pine management regimes where harvest residues (i.e., biomass) were left in place or removed, and two switchgrass regimes where the grass was grown with pine under the same two biomass scenarios (left or removed). Soil variables were measured in four 1-ha replicate plots in the first and second year following switchgrass planting. Under switchgrass intercropping, pools of mineralizable and particulate organic matter carbon were 42% and 33% lower, respectively. These declines translated into a 21% decrease in total soil carbon in the upper 15 cm of the soil profile, during early stand development. The switchgrass effect, however, was isolated to the interbed region where switchgrass is planted. In these regions, switchgrass-induced reductions in soil carbon pools with 29%, 43%, and 24% declines in mineralizable, particulate, and total soil carbon, respectively. Our results support the idea that grass inputs to forests can prime the activity of soil organic carbon degrading microbes, leading to net reductions in stocks

  19. Characterization of redox-related soil microbial communities along a river floodplain continuum by fatty acid methyl ester (FAME) and 16S rRNA genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Redox states affect substrate availability and energy transformation, and, thus, play a crucial role in regulating soil microbial abundance, diversity, and community structure. We evaluated microbial communities in soils under oxic, intermittent, and anoxic conditions along a river floodplain conti...

  20. 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

  1. Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

    SciTech Connect

    Xiao, Shengmu; Xue, Kai; He, Zhili; VanNostrand, Joy D.; Liu, Jianshe; Hobbie, Sarah E.; Reich, Peter B.; Zhou, Jizhong

    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. DNA 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.

  2. Conservation tillage, rotations, and cover crop affect soil quality in the Tennessee Valley: Particulate organic matter, organic matter, and microbial biomass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Monocropping cotton (Gossypium hirsutum L.) with conventional tillage provides little carbon input to soil, increases erosion and promotes rapid oxidation of existing soil organic carbon (SOC). Management practices like conservation tillage, crop rotation, and cover cropping can impact soil carbon, ...

  3. Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China.

    PubMed

    Zeng, Jun; Wang, Xiao-Xia; Lou, Kai; Eusufzai, Moniruzzaman Khan; Zhang, Tao; Lin, Qing; Shi, Ying-Wu; Yang, Hong-Mei; Li, Zhong-Qing

    2015-02-01

    We investigated the primary successions of soil enzyme activity and heterotrophic microbial communities at the forefields of the Tianshan Mountains No. 1 Glacier by investigating soil microbial processes (microbial biomass and nitrogen mineralization), enzyme activity and community-level physiological profiling. Soils deglaciated between 1959 and 2008 (0, 5, 17, 31 and 44 years) were collected. Soils >1,500 years in age were used as a reference (alpine meadow soils). Soil enzyme activity and carbon-source utilization ability significantly increased with successional time. Amino-acid utilization rates were relatively higher in early, unvegetated soils (0 and 5 years), but carbohydrate utilization was higher in later stages (from 31 years to the reference soil). Discriminant analysis, including data on microbial processes and soil enzyme activities, revealed that newly exposed soils (0-5 years) and older soils (17-44 years) were well-separated from each other and obviously different from the reference soil. Correlation analysis revealed that soil organic carbon, was the primary factor influencing soil enzyme activity and heterotrophic microbial community succession. Redundancy analysis suggested that soil pH and available P were also affect microbial activity to a considerable degree. Our results indicated that glacier foreland soils have continued to develop over 44 years and soils were significantly affected by the geographic location of the glacier and the local topography. Soil enzyme activities and heterotrophic microbial communities were also significantly influenced by these variables. PMID:25472706

  4. Soil microbial activities beneath Stipa tenacissima L. and in surrounding bare soil

    NASA Astrophysics Data System (ADS)

    Novosadová, I.; Ruiz Sinoga, J. D.; Záhora, J.; Fišerová, H.

    2010-05-01

    Open steppes dominated by Stipa tenacissima L. constitute one of the most representative ecosystems of the semi-arid zones of Eastern Mediterranean Basin (Iberian Peninsula, North of Africa). These steppes show a higher degree of variability in composition and structure. Ecosystem functioning is strongly related to the spatial pattern of grass tussocks. Soils beneath S. tenacissima grass show higher fertility and improved microclimatic conditions, favouring the formation of "resource islands" (Maestre et al., 2007). On the other hand in "resource islands" and in surrounding bare soil exists the belowground zone of influence. The competition for water and resources between plants and microorganisms is strong and mediated trough an enormous variety of exudates and resource depletion intended to regulate soil microbial communities in the rhizosphere, control herbivory, encourage beneficial symbioses, and change chemical and physical properties in soil (Pugnaire et Armas, 2008). Secondary compounds and allelopathy restrict other species growth and contribute to patchy plant distribution. Active root segregation affects not only neighbourś growth but also soil microbial activities. The objective of this study was to assess the effect of Stipa tenacissima on the key soil microbial activities under controlled incubation conditions (basal and potential respiration; net nitrogen mineralization). The experimental plots were located in the province Almería in Sierra de los Filabres Mountains near the village Gérgal (southeast Spain) in the small catchment which is situated between 1090 - 1165 m a.s.l. The area with extent of 82 000 m2 is affected by soil degradation. The climate is semiarid Mediterranean. The mean annual rainfall is of about 240 mm mostly concentrated in autumn and spring. The mean annual temperature is 13.9° C. The studied soil has a loam to sandy clay texture and is classified as Lithosol (FAO-ISRIC and ISSS, 1998). The vegetation of these areas is an

  5. Soil health, plant-microbial interactions and relationships with herbicides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil biological properties critical for successful crop production include microbial diversity and soil carbon content and quality. Soil microbial diversity, or soil biodiversity, may be the most valuable property of any ecosystem because greater diversity provides a greater range of pathways for pr...

  6. 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

  7. Biotic and abiotic properties mediating plant diversity effects on soil microbial communities in an experimental grassland.

    PubMed

    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

  8. Limited recovery of soil microbial activity after transient exposure to gasoline vapors.

    PubMed

    Modrzyński, Jakub J; Christensen, Jan H; Mayer, Philipp; Brandt, Kristian K

    2016-09-01

    During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial growth ([(3)H]leucine incorporation). Microbial activity was strongly stimulated and inhibited at low and high exposure levels, respectively. Microbial growth efficiency decreased with increasing exposure, but rebounded during the recovery phase for low-dose treatments. Although benzene, toluene, ethylbenzene and xylene (BTEX) concentrations decreased by 83-97% during the recovery phase, microbial activity in high-dose treatments did not recover and numbers of viable bacteria were 3-4 orders of magnitude lower than in control soil. Re-inoculation with active soil microorganisms failed to restore microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient exposure to high, but environmentally relevant, levels of gasoline VOCs which therefore may compromise ecosystem services provided by microorganisms even after extensive soil VOC dissipation. PMID:27376993

  9. Mechanisms Controlling the Plant Diversity Effect on Soil Microbial Community Composition and Soil Microbial Diversity

    NASA Astrophysics Data System (ADS)

    Mellado Vázquez, P. G.; Lange, M.; Griffiths, R.; Malik, A.; Ravenek, J.; Strecker, T.; Eisenhauer, N.; Gleixner, G.

    2015-12-01

    Soil microorganisms are the main drivers of soil organic matter cycling. Organic matter input by living plants is the major energy and matter source for soil microorganisms, higher organic matter inputs are found in highly diverse plant communities. It is therefore relevant to understand how plant diversity alters the soil microbial community and soil organic matter. In a general sense, microbial biomass and microbial diversity increase with increasing plant diversity, however the mechanisms driving these interactions are not fully explored. Working with soils from a long-term biodiversity experiment (The Jena Experiment), we investigated how changes in the soil microbial dynamics related to plant diversity were explained by biotic and abiotic factors. Microbial biomass quantification and differentiation of bacterial and fungal groups was done by phospholipid fatty acid (PLFA) analysis; terminal-restriction fragment length polymorphism was used to determine the bacterial diversity. Gram negative (G-) bacteria predominated in high plant diversity; Gram positive (G+) bacteria were more abundant in low plant diversity and saprotrophic fungi were independent from plant diversity. The separation between G- and G+ bacteria in relation to plant diversity was governed by a difference in carbon-input related factors (e.g. root biomass and soil moisture) between plant diversity levels. Moreover, the bacterial diversity increased with plant diversity and the evenness of the PLFA markers decreased. Our results showed that higher plant diversity favors carbon-input related factors and this in turn favors the development of microbial communities specialized in utilizing new carbon inputs (i.e. G- bacteria), which are contributing to the export of new C from plants to soils.

  10. Antibiotic effects on microbial community characteristics in soils under conservation management practices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Veterinary antibiotics (VAs) administered to livestock are introduced to agroecosystems via land application of manure, posing a potential human and environmental health risk. These Antibiotics may adversely affect soil microbial communities. The objectives of this research were to investigate poten...

  11. Environmental Controls of Microbial Resource Partitioning in Soils

    NASA Astrophysics Data System (ADS)

    Kandeler, Ellen; Poll, Christian; Kramer, Susanne; Mueller, Karolin; Marhan, Sven

    2015-04-01

    The mineralization and flow of plant-derived carbon in soils is relevant to global carbon cycling. Current models of organismic carbon fluxes in soil assume that separate bacterial and fungal energy channels exist in soil. Recent studies disentangle the herbivore and detritivore pathways of microbial resource use, identify the key players contributing to these two different pathways, and determine to what extent microbial substrate use is affected by environmental controls. To follow the kinetics of litter and root decomposition and to quantify the contribution of key players, it is necessary to use isotopic approaches like PLFA-SIP and ergosterol-SIP. It was shown that bacteria and sugar consuming fungi initiated litter decomposition in an incubation experiment during the first two weeks, whereas higher fungi started to grow after the depletion of low molecular weight substrates. Analyses of PLFA-SIP revealed, for example, that fungi assimilated C directly from the litter, whereas bacteria took up substrates in the soil and therefore depended more on external transport processes than fungi. In addition, we will present data from a field experiment showing the incorporation of root and shoot litter C into organic and microbial C pools under field conditions over a period of two years. Similar amounts of C derived from the two resources differing in substrate quality and amount were incorporated into microbial C and ergosterol pools over time, indicating the importance of root-derived C for the soil food web. High incorporation of maize C (up to 76%) into ergosterol suggests fast and high assimilation of maize C into fungal biomass. Nevertheless, there is still a debate whether bacteria, archaea and fungi start feeding on new substrates at the same time or if their activity occurs at different successional stages. This presentation gives a summery of current knowledge on microbial resource partitioning under lab and field conditions.

  12. Effects of Plant Diversity, Functional Group Composition, and Fertilization on Soil Microbial Properties in Experimental Grassland

    PubMed Central

    Strecker, Tanja; Barnard, Romain L.; Niklaus, Pascal A.; Scherer-Lorenzen, Michael; Weigelt, Alexandra; Scheu, Stefan; Eisenhauer, Nico

    2015-01-01

    Background Loss of biodiversity and increased nutrient inputs are two of the most crucial anthropogenic factors driving ecosystem change. Although both received considerable attention in previous studies, information on their interactive effects on ecosystem functioning is scarce. In particular, little is known on how soil biota and their functions are affected by combined changes in plant diversity and fertilization. Methodology/Principal Findings We investigated the effects of plant diversity, functional community composition, and fertilization on the biomass and respiration of soil microbial communities in a long-term biodiversity experiment in semi-natural grassland (Jena Experiment). Plant species richness enhanced microbial basal respiration and microbial biomass, but did not significantly affect microbial specific respiration. In contrast, the presence of legumes and fertilization significantly decreased microbial specific respiration, without altering microbial biomass. The effect of legumes was superimposed by fertilization as indicated by a significant interaction between the presence of legumes and fertilization. Further, changes in microbial stoichiometry (C-to-N ratio) and specific respiration suggest the presence of legumes to reduce N limitation of soil microorganisms and to modify microbial C use efficiency. Conclusions/Significance Our study highlights the role of plant species and functional group diversity as well as interactions between plant community composition and fertilizer application for soil microbial functions. Our results suggest soil microbial stoichiometry to be a powerful indicator of microbial functioning under N limited conditions. Although our results support the notion that plant diversity and fertilizer application independently affect microbial functioning, legume effects on microbial N limitation were superimposed by fertilization, indicating significant interactions between the functional composition of plant communities and

  13. 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

  14. Soil microbial biomass, basal respiration and enzyme activity of main forest types in the Qinling Mountains.

    PubMed

    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

  15. 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

  16. Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils.

    PubMed

    Nemir, Audra; David, Maude M; Perrussel, Ronan; Sapkota, Amy; Simonet, Pascal; Monier, Jean-Michel; Vogel, Timothy M

    2010-07-01

    The arrival of chemicals in a soil or groundwater ecosystem could upset the natural balance of the microbial community. Since soil microorganisms are the first to be exposed to the chemicals released into the soil environment, we evaluated the use of a phylogenetic microarray as a bio-indicator of community perturbations due to the exposure to trichloroethylene (TCE). The phylogenetic microarray, which measures the presence of different members of the soil community, was used to evaluate unpolluted soils exposed to TCE as well as to samples from historically TCE polluted sites. We were able to determine an apparent threshold at which the microbial community structure was significantly affected (about 1ppm). In addition, the members of the microbial community most affected were identified. This approach could be useful for assessing environmental impact of chemicals on the biosphere as well as important members of the microbial community involved in TCE degradation. PMID:20444493

  17. Comparative resistance and resilience of soil microbial communities and enzyme activities in adjacent native forest and agricultural soils.

    PubMed

    Chaer, Guilherme; Fernandes, Marcelo; Myrold, David; Bottomley, Peter

    2009-08-01

    Degradation of soil properties following deforestation and long-term soil cultivation may lead to decreases in soil microbial diversity and functional stability. In this study, we investigated the differences in the stability (resistance and resilience) of microbial community composition and enzyme activities in adjacent soils under either native tropical forest (FST) or in agricultural cropping use for 14 years (AGR). Mineral soil samples (0 to 5 cm) from both areas were incubated at 40 degrees C, 50 degrees C, 60 degrees C, or 70 degrees C for 15 min in order to successively reduce the microbial biomass. Three and 30 days after the heat shocks, fluorescein diacetate (FDA) hydrolysis, cellulase and laccase activities, and phospholipid-derived fatty acids-based microbial community composition were measured. Microbial biomass was reduced up to 25% in both soils 3 days after the heat shocks. The higher initial values of microbial biomass, enzyme activity, total and particulate soil organic carbon, and aggregate stability in the FST soil coincided with higher enzymatic stability after heat shocks. FDA hydrolysis activity was less affected (more resistance) and cellulase and laccase activities recovered more rapidly (more resilience) in the FST soil relative to the AGR counterpart. In the AGR soil, laccase activity did not show resilience to any heat shock level up to 30 days after the disturbance. Within each soil type, the microbial community composition did not differ between heat shock and control samples at day 3. However, at day 30, FST soil samples treated at 60 degrees C and 70 degrees C contained a microbial community significantly different from the control and with lower biomass regardless of high enzyme resilience. Results of this study show that deforestation followed by long-term cultivation changed microbial community composition and had differential effects on microbial functional stability. Both soils displayed similar resilience to FDA hydrolysis, a

  18. Microbial Mechanisms Enhancing Soil C Storage

    SciTech Connect

    Zak, Donald

    2015-09-24

    Human activity has globally increased the amount of nitrogen (N) entering ecosystems, which could foster higher rates of C sequestration in the N-limited forests of the Northern Hemisphere. Presently, these ecosystems are a large global sink for atmospheric CO2, the magnitude of which could be influenced by the input of human-derived N from the atmosphere. Nevertheless, empirical studies and simulation models suggest that anthropogenic N deposition could have either an important or inconsequential effect on C storage in forests of the Northern Hemisphere, a set of observations that continues to fuel scientific discourse. Although a relatively simple set of physiological processes control the C balance of terrestrial ecosystems, we still fail to understand how these processes directly and indirectly respond to greater N availability in the environment. The uptake of anthropogenic N by N-limited forest trees and a subsequent enhancement of net primary productivity have been the primary mechanisms thought to increase ecosystem C storage in Northern Hemisphere forests. However, there are reasons to expect that anthropogenic N deposition could slow microbial activity in soil, decrease litter decay, and increase soil C storage. Fungi dominate the decay of plant detritus in forests and, under laboratory conditions, high inorganic N concentrations can repress the transcription of genes coding for enzymes which depolymerize lignin in plant detritus; this observation presents the possibility that anthropogenic N deposition could elicit a similar effect under field conditions. In our 18-yr-long field experiment, we have been able to document that simulated N deposition, at a rate expected in the near future, resulted in a significant decline in cellulolytic and lignolytic microbial activity, slowed plant litter decay, and increased soil C storage (+10%); this response is not portrayed in any biogeochemical model simulating the effect of atmospheric N deposition on ecosystem C

  19. Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

    PubMed Central

    Kim, Minsu; Or, Dani

    2016-01-01

    Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

  20. Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces.

    PubMed

    Kim, Minsu; Or, Dani

    2016-01-01

    Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

  1. Soil microbial communities associated with Bt and non-Bt corn in three soils.

    PubMed

    Blackwood, Christopher B; Buyer, Jeffrey S

    2004-01-01

    The effects of expression of Cry endotoxin by Bt corn (transgenic corn engineered to express Bacillus thuringiensis toxin) on soil microbial community structure were assessed in a growth chamber experiment. Two lines of transgenic corn expressing different Cry endotoxins were compared with their respective non-transgenic isolines in three soil types with differing textures. Phospholipid fatty acid (PLFA) profiles from bulk soil and community-level physiological profiles (CLPP) from the rhizosphere community were used to assess community structure. Differences in PLFA profiles due to soil type were significant, accounting for 73% of the total variability in the dataset. Differences in bacterial and fungal CLPP profiles due to soil type were statistically significant, but probably not biologically important, accounting for 6.3 and 3.8% of the total variability, respectively. Neither expression of Cry endotoxin nor corn line had a significant effect on microbial profiles, except in the high-clay soil where both factors significantly affected bacterial CLPP profiles (accounting for 6.6 and 6.1% of the variability in that soil, respectively). Expression of Cry endotoxin also significantly reduced the presence of eukaryotic PLFA biomarker in bulk soils, although it is unclear which groups of eukaryotes were affected. We conclude that the effects of transgenic Bt corn in this short-term experiment are small, and longer-term investigations are necessary. PMID:15224917

  2. Soil amendments yield persisting changes in the microbial communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil microbial communities are sensitive to carbon amendments and largely control the decomposition and accumulation of soil organic matter. In this study, we evaluated whether the type of carbon amendment applied to wheat-cropped or fallow soil imparted lasting effects on the microbial community w...

  3. Manipulating soil microbial communities in extensive green roof substrates.

    PubMed

    Molineux, Chloe J; Connop, Stuart P; Gange, Alan C

    2014-09-15

    There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition. PMID:24992459

  4. Soil microbial communities as suitable bioindicators of trace metal pollution in agricultural volcanic soils

    NASA Astrophysics Data System (ADS)

    Parelho, Carolina; dos Santos Rodrigues, Armindo; do Carmo Barreto, Maria; Gonçalo Ferreira, Nuno; Garcia, Patrícia

    2015-04-01

    Summary: The biological, chemical and physical properties of soil confer unique characteristics that enhance or influence its overall biodiversity. The adaptive character of soil microbial communities (SMCs) to metal pollution allows discriminating soil health, since changes in microbial populations and activities may function as excellent indicators of soil pollutants. Volcanic soils are unique naturally fertile resources, extensively used for agricultural purposes and with particular physicochemical properties that may result in accumulation of toxic substances, such as trace metals (TM). In our previous works, we identified priority TM affecting agricultural Andosols under different agricultural land uses. Within this particular context, the objectives of this study were to (i) assess the effect of soil TM pollution in different agricultural systems (conventional, traditional and organic) on the following soil properties: microbial biomass carbon, basal soil respiration, metabolic quotient, enzymatic activities (β-glucosidase, acid phosphatase and dehydrogenase) and RNA to DNA ratio; and (ii) evaluate the impact of TM in the soil ecosystem using the integrated biomarker response (IBR) based on a set of biochemical responses of SMCs. This multi-biomarker approach will support the development of the "Trace Metal Footprint" for different agricultural land uses in volcanic soils. Methods: The study was conducted in S. Miguel Island (Azores, Portugal). Microbial biomass carbon was measured by chloroform-fumigation-incubation-assay (Vance et al., 1987). Basal respiration was determined by the Jenkinson & Powlson (1976) technique. Metabolic quotient was calculated as the ratio of basal respiration to microbial biomass C (Sparkling & West, 1988). The enzymatic activities of β-glucosidase and acid phosphatase were determined by the Dick et al. (1996) method and dehydrogenase activity by the Rossel et al. (1997) method. The RNA and DNA were co-extracted from the same

  5. Response of Microbial Soil Carbon Mineralization Rates to Oxygen Limitations

    NASA Astrophysics Data System (ADS)

    Keiluweit, M.; Denney, A.; Nico, P. S.; Fendorf, S. E.

    2014-12-01

    The rate of soil organic matter (SOM) mineralization is known to be controlled by climatic factors as well as molecular structure, mineral-organic associations, and physical protection. What remains elusive is to what extent oxygen (O2) limitations impact overall rates of microbial SOM mineralization (oxidation) in soils. Even within upland soils that are aerobic in bulk, factors limiting O2 diffusion such as texture and soil moisture can result in an abundance of anaerobic microsites in the interior of soil aggregates. Variation in ensuing anaerobic respiration pathways can further impact SOM mineralization rates. Using a combination of (first) aggregate model systems and (second) manipulations of intact field samples, we show how limitations on diffusion and carbon bioavailability interact to impose anaerobic conditions and associated respiration constraints on SOM mineralization rates. In model aggregates, we examined how particle size (soil texture) and amount of dissolved organic carbon (bioavailable carbon) affect O2 availability and distribution. Monitoring electron acceptor profiles (O2, NO3-, Mn and Fe) and SOM transformations (dissolved, particulate, mineral-associated pools) across the resulting redox gradients, we then determined the distribution of operative microbial metabolisms and their cumulative impact on SOM mineralization rates. Our results show that anaerobic conditions decrease SOM mineralization rates overall, but those are partially offset by the concurrent increases in SOM bioavailability due to transformations of protective mineral phases. In intact soil aggregates collected from soils varying in texture and SOM content, we mapped the spatial distribution of anaerobic microsites. Optode imaging, microsensor profiling and 3D tomography revealed that soil texture regulates overall O2 availability in aggregate interiors, while particulate SOM in biopores appears to control the fine-scale distribution of anaerobic microsites. Collectively, our

  6. [Soil microbial community structure of monoculture and mixed plantation stands of native tree species in south subtropical China].

    PubMed

    Luo, Da; Shi, Zuo-Min; Tang, Jing-Chao; Liu, Shi-Rong; Lu, Li-Hua

    2014-09-01

    The effects of three plantation stands, Erythrophleumf ordii (EF), Pinus massoniana (PM), and their mixed plantation (MP), on soil microbial biomass and microbial community structure in south subtropical China were studied by the method of phospholipid fatty acids (PLFAs) analysis. The results showed that the amounts of microbial total PLFAs and PLFAs of each microbial group in these three plantation stand soils were significantly higher in dry season than in rainy season. In dry season, the amounts of microbial total PLFAs, bacteria PLFAs, fungi PLFAs, and actinomycetes PLFAs were the highest in the PM soil, moderate in the MP soil, and the lowest in the EF soil. But in rainy season, the amounts of microbial total PLFAs, bacteria PLFAs, fungi PLFAs, and arbuscular mycorrhizal fungi (AMF) PLFAs in the EF soil were higher than in the MP soil, and were significantly higher than in the PM soil. Principal component analysis (PCA) indicated that the variations in soil microbial community structure composition were affected by both plantation types and seasons. Redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil temperature and moisture, pH, total nitrogen content, and ammonium nitrogen content had significant correlations with PLFA signatures. In addition, the ratio of fungi PLFAs to bacteria PLFAs in the MP soil was the highest among the three stand soils within the whole year, indicating that mixed plantation stands could facilitate the stability of the soil ecosystem. PMID:25757303

  7. Soil water repellency affects production and transport of CO2 and CH4 in soil

    NASA Astrophysics Data System (ADS)

    Urbanek, Emilia; Qassem, Khalid

    2016-04-01

    Soil moisture is known to be vital in controlling both the production and transport of C gases in soil. Water availability regulates the decomposition rates of soil organic matter by the microorganisms, while the proportion of water/air filled pores controls the transport of gases within the soil and at the soil-atmosphere interface. Many experimental studies and process models looking at soil C gas fluxes assume that soil water is uniformly distributed and soil is easily wettable. Most soils, however, exhibit some degree of soil water repellency (i.e. hydrophobicity) and do not wet spontaneously when dry or moderately moist. They have restricted infiltration and conductivity of water, which also results in extremely heterogeneous soil water distribution. This is a world-wide occurring phenomenon which is particularly common under permanent vegetation e.g. forest, grass and shrub vegetation. This study investigates the effect of soil water repellency on microbial respiration, CO2 transport within the soil and C gas fluxes between the soil and the atmosphere. The results from the field monitoring and laboratory experiments show that soil water repellency results in non-uniform water distribution in the soil which affects the CO2 and CH4 gas fluxes. The main conclusion from the study is that water repellency not only affects the water relations in the soil, but has also a great impact on greenhouse gas production and transport and therefore should be included as an important parameter during the sites monitoring and modelling of gas fluxes.

  8. 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. PMID:25724140

  9. RELATIONSHIPS BETWEEN CULTURABLE SOIL MICROBIAL POPULATIONS AND GROSS NITROGEN TRANSFORMATION PROCESSES IN A CLAY LOAM SOIL ACROSS ECOSYSTEMS

    EPA Science Inventory

    The size and quality of soil organic matter (SOM) pool can vary between ecosystems and can affect many soil properties. The objective of this study was to examine the relationship between gross N transformation rates and microbial populations and to investigate the role that SOM...

  10. Soil microbial characteristics and seed bank dynamics of stock-piled top soils in ther western Rio Grande Plains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increased energy extraction has impacted rangelands throughout the western U.S. Ecological restoration can be enhanced with proper management of affected top soils. Little information exists on effects of stockpiling on soil microbial community composition and functionality and seed bank dynamics. T...

  11. Microbial mobilization of plutonium and other actinides from contaminated soil.

    PubMed

    Francis, A J; Dodge, C J

    2015-12-01

    We examined the dissolution of Pu, U, and Am in contaminated soil from the Nevada Test Site (NTS) due to indigenous microbial activity. Scanning transmission x-ray microscopy (STXM) analysis of the soil showed that Pu was present in its polymeric form and associated with Fe- and Mn- oxides and aluminosilicates. Uranium analysis by x-ray diffraction (μ-XRD) revealed discrete U-containing mineral phases, viz., schoepite, sharpite, and liebigite; synchrotron x-ray fluorescence (μ-XRF) mapping showed its association with Fe- and Ca-phases; and μ-x-ray absorption near edge structure (μ-XANES) confirmed U(IV) and U(VI) oxidation states. Addition of citric acid or glucose to the soil and incubated under aerobic or anaerobic conditions enhanced indigenous microbial activity and the dissolution of Pu. Detectable amount of Am and no U was observed in solution. In the citric acid-amended sample, Pu concentration increased with time and decreased to below detection levels when the citric acid was completely consumed. In contrast, with glucose amendment, Pu remained in solution. Pu speciation studies suggest that it exists in mixed oxidation states (III/IV) in a polymeric form as colloids. Although Pu(IV) is the most prevalent and generally considered to be more stable chemical form in the environment, our findings suggest that under the appropriate conditions, microbial activity could affect its solubility and long-term stability in contaminated environments. PMID:26406590

  12. Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits.

    PubMed

    Lau, Jennifer A; Lennon, Jay T

    2011-10-01

    • Below-ground microbial communities influence plant diversity, plant productivity, and plant community composition. Given these strong ecological effects, are interactions with below-ground microbes also important for understanding natural selection on plant traits? • Here, we manipulated below-ground microbial communities and the soil moisture environment on replicated populations of Brassica rapa to examine how microbial community structure influences selection on plant traits and mediates plant responses to abiotic environmental stress. • In soils with experimentally simplified microbial communities, plants were smaller, had reduced chlorophyll content, produced fewer flowers, and were less fecund when compared with plant populations grown in association with more complex soil microbial communities. Selection on plant growth and phenological traits also was stronger when plants were grown in simplified, less diverse soil microbial communities, and these effects typically were consistent across soil moisture treatments. • Our results suggest that microbial community structure affects patterns of natural selection on plant traits. Thus, the below-ground microbial community can influence evolutionary processes, just as recent studies have demonstrated that microbial diversity can influence plant community and ecosystem processes. PMID:21658184

  13. Microbial carbon recycling: an underestimated process controlling soil carbon dynamics

    NASA Astrophysics Data System (ADS)

    Basler, A.; Dippold, M.; Helfrich, M.; Dyckmans, J.

    2015-07-01

    The mean residence times (MRT) of different compound classes of soil organic matter (SOM) do not match their inherent recalcitrance to decomposition. One reason for this is the stabilisation within the soil matrix, but recycling, i.e. the reuse of "old" organic material to form new biomass may also play a role as it uncouples the residence times of organic matter from the lifetime of discrete molecules in soil. We analysed soil sugar dynamics in a natural 30 years old labelling experiment after a~wheat-maize vegetation change to determine the extent of recycling and stabilisation in plant and microbial derived sugars: while plant derived sugars are only affected by stabilisation processes, microbial sugars may be subject to both, stabilisation and recycling. To disentangle the dynamics of soil sugars, we separated different density fractions (free particulate organic matter (fPOM), light occluded particulate organic matter (≤1.6 g cm-3; oPOM1.6), dense occluded particulate organic matter (≤2 g cm-3; oPOM2) and mineral-associated organic matter (>2 g cm-3; Mineral)) of a~silty loam under long term wheat and maize cultivation. The isotopic signature of sugars was measured by high pressure liquid chromatography coupled to isotope ratio mass spectrometry (HPLC/IRMS), after hydrolysis with 4 M Trifluoroacetic acid (TFA). While apparent mean residence times (MRT) of sugars were comparable to total organic carbon in the bulk soil and mineral fraction, the apparent MRT of sugars in the oPOM fractions were considerably lower than those of the total carbon of these fractions. This indicates that oPOM formation was fuelled by microbial activity feeding on new plant input. In the bulk soil, mean residence times of the mainly plant derived xylose (xyl) were significantly lower than those of mainly microbial derived sugars like galactose (gal), rhamnose (rha), fucose (fuc), indicating that recycling of organic matter is an important factor regulating organic matter dynamics

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

    PubMed Central

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

    2015-01-01

    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. PMID:26195343

  15. 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

    2015-01-01

    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. PMID:26195343

  16. 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.

  17. Soil microbial community and endemic earthworm Allolobophora hrabei in soils of steppe fragments of central Europe

    NASA Astrophysics Data System (ADS)

    Elhottová, Dana; Jirout, Jiří; Pižl, Václav

    2016-04-01

    The earthworm activity is generally recognized as an important factor changing the intrinsic heterogeneity of soil environment including the microbial constituents. In central Europe, about 40% of earthworm species are endemic to this region, some of them dominating forest and grassland ecosystems and playing a keystone role in the soil food-web. However, current knowledge about the effects of earthworms on soil microorganisms derives from studies on a few peregrine species only. Our study brought a view on the microbial component of the steppe soil affected by the activity of Allolobophora hrabei, an endemic earthworm fragmentary distributed in the border regions of the Czech Republic, Austria, Slovakia and Hungary. The study was carried out in three steppe fragments, where A. hrabei represented a key earthworm species. Comprehensive approach based on bio-indicating quantitative and qualitative options of extended phospholipid fatty acids analysis (PLFA) of bulk soil, drilosphere sensu lato and casts was used on data from two-years monitoring. In situ observation was completed by detailed observation of the casts-microbiota succession under controlled laboratory conditions. Our results showed that A. hrabei significantly affected soil microorganisms mainly via its extremely high casting activity. The doubled biomass, new qualitative composition, better growth and nutritional status of microbial community together with significantly higher availability of phosphorus and organic carbon in casts in contrast to bulk soil confirmed beneficial impact of A. hrabei on the soil environment. A. hrabei has burrowed up to more than one metre depths and produced more than 3 kg . m-2 of casts per year.

  18. Microbial life in variably saturated soil aggregates - upscaling gaseous fluxes across distributed aggregate sizes in a soil profile

    NASA Astrophysics Data System (ADS)

    Or, D.; Ebrahimi, A.

    2015-12-01

    Recent studies revealed highly dynamic and rich behavior of microbial communities inhabiting soil aggregates. Modeling of these processes in three dimensional (unsaturated) pore networks provided insights into the unique conditions essential for coexistence of oxic and anoxic microsites that shape (and respond to) aerobic and anaerobic microbial communities. Soil hydration dynamics continuously alter the spatial extent of anoxic niches (hotspots) that flicker in time (hot moments) and support anaerobic microbial activity even in unsaturated and oxic soil profiles. We extend a model for individual-based microbial community growth in 3-D angular pore networks mimicking soil aggregates of different sizes placed in different ambient boundary conditions reflecting profiles of water, carbon, and oxygen in soil. An upscaling scheme was developed to account for aerobic and anaerobic activity within each aggregate class size and soil depth integrated over the aggregate size distribution in the soil for a range of hydration conditions. Results show that dynamic adjustments in microbial community composition affect CO2 and N2O production rates in good agreement with experimental data. The modeling approach addresses a long-standing challenge of linking hydration conditions to dynamic adjustments of microbial communities within "hotspots" with the emergence of "hot moments" reflecting high rates of denitrification and organic matter decomposition.

  19. Microbial Communities and Enzymatic Activities as Affected by Various Poultry Litter Application Rates to Pasture and Cultivated Soils of the Texas Blackland Prairies Ecosystem

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Land application is the most common and usually most desirable method of utilizing manure because of nutrient and organic matter addition to soils. In recent years, as a result of the shift to fewer and larger confined animal operations, environmental and economic issues associated with utilization...

  20. Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

    SciTech Connect

    Cusack, Daniela F.; Silver, Whendee; Torn, Margaret S.; Burton, Sarah D.; Firestone, Mary

    2011-03-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

  1. Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests.

    PubMed

    Cusack, Daniela F; Silver, Whendee L; Torn, Margaret S; Burton, Sarah D; Firestone, Mary K

    2011-03-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types. PMID:21608471

  2. Soil microbial biomass nitrogen and Beta-Glucosaminidase activity response to compaction, poultry litter application and cropping in a claypan soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Compaction-induced changes in soil physical properties may significantly affect soil microbial activity, especially nitrogen-cycling processes, in many agroecosystems. The objective of this study was to determine the effect of soil compaction on soil microbiological properties related to N in a clay...

  3. The Potential of Hyperspectral Patterns of Winter Wheat to Detect Changes in Soil Microbial Community Composition

    PubMed Central

    Carvalho, Sabrina; van der Putten, Wim H.; Hol, W. H. G.

    2016-01-01

    Reliable information on soil status and crop health is crucial for detecting and mitigating disasters like pollution or minimizing impact from soil-borne diseases. While infestation with an aggressive soil pathogen can be detected via reflected light spectra, it is unknown to what extent hyperspectral reflectance could be used to detect overall changes in soil biodiversity. We tested the hypotheses that spectra can be used to (1) separate plants growing with microbial communities from different farms; (2) to separate plants growing in different microbial communities due to different land use; and (3) separate plants according to microbial species loss. We measured hyperspectral reflectance patterns of winter wheat plants growing in sterilized soils inoculated with microbial suspensions under controlled conditions. Microbial communities varied due to geographical distance, land use and microbial species loss caused by serial dilution. After 3 months of growth in the presence of microbes from the two different farms plant hyperspectral reflectance patterns differed significantly from each other, while within farms the effects of land use via microbes on plant reflectance spectra were weak. Species loss via dilution on the other hand affected a number of spectral indices for some of the soils. Spectral reflectance can be indicative of differences in microbial communities, with the Renormalized Difference Vegetation Index the most common responding index. Also, a positive correlation was found between the Normalized Difference Vegetation Index and the bacterial species richness, which suggests that plants perform better with higher microbial diversity. There is considerable variation between the soil origins and currently it is not possible yet to make sufficient reliable predictions about the soil microbial community based on the spectral reflectance. We conclude that measuring plant hyperspectral reflectance has potential for detecting changes in microbial

  4. The Potential of Hyperspectral Patterns of Winter Wheat to Detect Changes in Soil Microbial Community Composition.

    PubMed

    Carvalho, Sabrina; van der Putten, Wim H; Hol, W H G

    2016-01-01

    Reliable information on soil status and crop health is crucial for detecting and mitigating disasters like pollution or minimizing impact from soil-borne diseases. While infestation with an aggressive soil pathogen can be detected via reflected light spectra, it is unknown to what extent hyperspectral reflectance could be used to detect overall changes in soil biodiversity. We tested the hypotheses that spectra can be used to (1) separate plants growing with microbial communities from different farms; (2) to separate plants growing in different microbial communities due to different land use; and (3) separate plants according to microbial species loss. We measured hyperspectral reflectance patterns of winter wheat plants growing in sterilized soils inoculated with microbial suspensions under controlled conditions. Microbial communities varied due to geographical distance, land use and microbial species loss caused by serial dilution. After 3 months of growth in the presence of microbes from the two different farms plant hyperspectral reflectance patterns differed significantly from each other, while within farms the effects of land use via microbes on plant reflectance spectra were weak. Species loss via dilution on the other hand affected a number of spectral indices for some of the soils. Spectral reflectance can be indicative of differences in microbial communities, with the Renormalized Difference Vegetation Index the most common responding index. Also, a positive correlation was found between the Normalized Difference Vegetation Index and the bacterial species richness, which suggests that plants perform better with higher microbial diversity. There is considerable variation between the soil origins and currently it is not possible yet to make sufficient reliable predictions about the soil microbial community based on the spectral reflectance. We conclude that measuring plant hyperspectral reflectance has potential for detecting changes in microbial

  5. Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.).

    PubMed

    Coats, V C; Pelletreau, K N; Rumpho, M E

    2014-03-01

    The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure. PMID:24118303

  6. Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert.

    PubMed

    Stomeo, Francesca; Valverde, Angel; Pointing, Stephen B; McKay, Christopher P; Warren-Rhodes, Kimberley A; Tuffin, Marla I; Seely, Mary; Cowan, Don A

    2013-03-01

    The Namib Desert is considered the oldest desert in the world and hyperarid for the last 5 million years. However, the environmental buffering provided by quartz and other translucent rocks supports extensive hypolithic microbial communities. In this study, open soil and hypolithic microbial communities have been investigated along an East-West transect characterized by an inverse fog-rainfall gradient. Multivariate analysis showed that structurally different microbial communities occur in soil and in hypolithic zones. Using variation partitioning, we found that hypolithic communities exhibited a fog-related distribution as indicated by the significant East-West clustering. Sodium content was also an important environmental factor affecting the composition of both soil and hypolithic microbial communities. Finally, although null models for patterns in microbial communities were not supported by experimental data, the amount of unexplained variation (68-97 %) suggests that stochastic processes also play a role in the assembly of such communities in the Namib Desert. PMID:23397517

  7. Microbial community structure and functionality under peanut based cropping systems in a sandy soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is little information on soil microbial and biochemical properties, important for nutrient cycling and organic matter dynamics, as affected by different peanut (Arachis hypogaea L.) cropping systems and how they relate to soil quality and functioning and system sustainability. We studied a sa...

  8. Microbial community structure and functionality under peanut based cropping systems in a sandy soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Little information is available on soil microbial and biochemical properties, important for understanding nutrient cycling and organic matter (OM) dynamics, as affected by different peanut (Arachis hypogaea L.) cropping systems and how they relate to soil functioning. Peanut is typically produced i...

  9. Microbial community structure and functionality under peanut based cropping systems in a sandy soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Little information is available on soil microbial and biochemical properties, important for understanding nutrient cycling and organic matter (OM) dynamics, as affected by different peanut cropping systems and how they relate to soil functioning. Thus, we studied a Tifton loamy sand (fine-loamy, ka...

  10. Temperature and Microbial Activity Effects on Soil Carbon Stabilization

    NASA Astrophysics Data System (ADS)

    Fissore, C.; van Diepen, L.; Wixon, D.; Marin-Spiotta, E.; Giardina, C. P.

    2014-12-01

    Uncertainties on the importance of environmental controls on soil C stabilization and turnover limit accurate predictions of the rate and magnitude of the response of soils to climate change. Here we report results from a study of interactions among vegetation and soil microbial communities in North American forests across a highly constrained, 22OC gradient mean annual temperature (MAT) as a proxy for understanding changes with climate. Previous work indicated that turnover and amount of labile SOC responded negatively to MAT, whereas stable SOC was insensitive to temperature variation. Hardwood forests stored a larger amount of stable SOC, but with shorter mean residence times than paired pine forests. Our findings suggest that the interaction between vegetation composition and microbial communities may affect SOC accumulation and stabilization responses to rising temperature. To investigate these relationships, we characterized the microbial communities with Phospholipid Fatty Acid (PLFA) analysis. PLFA analyses indicate complex microbial responses to increased MAT and vegetation composition. Microbial biomass declined with MAT in conifer forests and increased in hardwood forests. Relative abundance of actinomycetes increased with MAT for both forest types, and was correlated with amount and turnover of active SOC. The relative abundance of fungi decreased with increasing MAT, while gram+ bacteria increased, such that fungi:bacteria ratio decreased with MAT, with this trend being more pronounced for hardwood cover type. These results are consistent with a long-term warming experiment in a hardwood forest at the Harvard Forest LTER site, where after 12 years of warming the relative abundance of gram positive bacteria and actinomycetes increased, while fungal biomass decreased. In contrast, relationships between microbial groups and the stable fraction of SOC along the gradient were only observed in conifers. Increases in mean residence time of stable SOC were

  11. Response of soil microbial communities during changes in land management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The response of soil microbial communities to restoration following disturbances is poorly understood. We studied the soil microbial communities in a forest disturbance-restoration series comprising a native deciduous forest (DF), conventionally tilled cropland (CT) and mid-succession forest (SF) re...

  12. Soil degradation and amendment effects on soil properties, microbial communities, and plant growth

    NASA Astrophysics Data System (ADS)

    Gebhardt, M.; Fehmi, J. S.; Rasmussen, C.; Gallery, R. E.

    2015-12-01

    Human activities that disrupt soil properties are fundamentally changing ecosystems. Soil degradation, caused by anthropogenic disturbance can decrease microbial abundance and activity, leading to changes in nutrient availability, soil organic matter, and plant establishment. The addition of amendments to disturbed soils have the potential ameliorate these negative consequences. We studied the effects of soil degradation, via an autoclave heat shock method, and the addition of amendments (biochar and woodchips) on microbial activity, soil carbon and nitrogen availability, microbial biomass carbon and nitrogen content, and plant growth of ten plant species native to the semi-arid southwestern US. Relative to non-degraded soils, microbial activity, measured via extracellular enzyme assays, was significantly lower for all seven substrates assayed. These soils also had significantly lower amounts of carbon assimilated into microbial biomass but no change in microbial biomass nitrogen. Soil degradation had no effect on plant biomass. Amendments caused changes in microbial activity: biochar-amended soils had significant increases in potential activity with five of the seven substrates measured; woodchip amended soils had significant increases with two. Soil carbon increased with both amendments but this was not reflected in a significant change in microbial biomass carbon. Biochar-amended soils had increases in soil nitrogen availability but neither amendment caused changes in microbial biomass nitrogen. Biochar amendments had no significant effect on above- or belowground plant biomass while woodchips significantly decreased aboveground plant biomass. Results show that soil degradation decreases microbial activity and changes nutrient dynamics, but these are not reflected in changes in plant growth. Amendments provide nutrient sources and change soil pore space, which cause microbial activities to fluctuate and may, in the case of woodchips, increase plant drought

  13. 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

  14. Medusahead: available soil N and microbial communities in native and invasive soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To better understand why medusahead (Taeniatherum caput-medusae) is invasive, we quantified soil N availability and characterized soil microbial communities between native and invasive populations. No consistent differences in soil N mineralization potentials were noted between native medusahead sit...

  15. Microbial responses to southward and northward Cambisol soil transplant

    SciTech Connect

    Wang, Mengmeng; Liu, Shanshan; Wang, Feng; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

    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 at 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 (NO3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.

  16. Microbial responses to southward and northward Cambisol soil transplant

    DOE PAGESBeta

    Wang, Mengmeng; Liu, Shanshan; Wang, Feng; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

    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 (NO3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

  17. Soil Microbial Community Responses to Long-Term Global Change Factors in a California Grassland

    NASA Astrophysics Data System (ADS)

    Qin, K.; Peay, K.

    2015-12-01

    Soil fungal and bacterial communities act as mediators of terrestrial carbon and nutrient cycling, and interact with the aboveground plant community as both pathogens and mutualists. However, these soil microbial communities are sensitive to changes in their environment. A better understanding of the response of soil microbial communities to global change may help to predict future soil microbial diversity, and assist in creating more comprehensive models of terrestrial carbon and nutrient cycles. This study examines the effects of four global change factors (increased temperature, increased variability in precipitation, nitrogen deposition, and CO2 enrichment) on soil microbial communities at the Jasper Ridge Global Change Experiment (JRGCE), a full-factorial global change manipulative experiment on three hectares of California grassland. While similar studies have examined the effects of global change on soil microbial communities, few have manipulated more factors or been longer in duration than the JRGCE, which began field treatments in 1998. We find that nitrogen deposition, CO2 enrichment, and increased variability in precipitation significantly affect the structure of both fungal and bacterial communities, and explain more of the variation in the community structures than do local soil chemistry or aboveground plant community. Fungal richness is correlated positively with soil nitrogen content and negatively with soil water content. Arbuscular mycorrhizal fungi (AMF), which associate closely with herbaceous plants' roots and assist in nutrient uptake, decrease in both richness and relative abundance in elevated CO2 treatments.

  18. Flooding Effects on Soil Microbial Communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flooding of a riparian forest affects the ecosystem both above- and below-ground. While the below-ground changes may be hidden from sight, they are no less important than the above-ground changes that are readily visible. Similar to their above-ground counterparts, soil microorganisms are sensitive...

  19. Connecting soil microbial communities to soil functioning and soil health

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One of the most important functions soils perform, is the capacity to buffer anthropogenic disturbances to sustain productivity while improving water and air quality. At the core of a healthy soil is a biological active and diverse community that provides internal nutrient cycling and is resilient t...

  20. Influence of geogenic factors on microbial communities in metallogenic Australian soils.

    PubMed

    Reith, Frank; Brugger, Joel; Zammit, Carla M; Gregg, Adrienne L; Goldfarb, Katherine C; Andersen, Gary L; DeSantis, Todd Z; Piceno, Yvette M; Brodie, Eoin L; Lu, Zhenmei; He, Zhili; Zhou, Jizhong; Wakelin, Steven A

    2012-11-01

    Links between microbial community assemblages and geogenic factors were assessed in 187 soil samples collected from four metal-rich provinces across Australia. Field-fresh soils and soils incubated with soluble Au(III) complexes were analysed using three-domain multiplex-terminal restriction fragment length polymorphism, and phylogenetic (PhyloChip) and functional (GeoChip) microarrays. Geogenic factors of soils were determined using lithological-, geomorphological- and soil-mapping combined with analyses of 51 geochemical parameters. Microbial communities differed significantly between landforms, soil horizons, lithologies and also with the occurrence of underlying Au deposits. The strongest responses to these factors, and to amendment with soluble Au(III) complexes, was observed in bacterial communities. PhyloChip analyses revealed a greater abundance and diversity of Alphaproteobacteria (especially Sphingomonas spp.), and Firmicutes (Bacillus spp.) in Au-containing and Au(III)-amended soils. Analyses of potential function (GeoChip) revealed higher abundances of metal-resistance genes in metal-rich soils. For example, genes that hybridised with metal-resistance genes copA, chrA and czcA of a prevalent aurophillic bacterium, Cupriavidus metallidurans CH34, occurred only in auriferous soils. These data help establish key links between geogenic factors and the phylogeny and function within soil microbial communities. In particular, the landform, which is a crucial factor in determining soil geochemistry, strongly affected microbial community structures. PMID:22673626

  1. Hydrazine degradation and its effect on microbial activity in soil

    SciTech Connect

    Ou, L.T.; Street, J.J.

    1987-01-01

    Considerable information has been accumulated on the toxicity of hydrazine to soil bacterial cultures and on the degradation of hydrazne by soil bacterial cultures. The activities of the autotrophic nitrifiers Nitrosomonas and Nitrobacter and of denitrifying bacteria, and the growth of Enterobacter cloacae, were all inhibited by hydrazine. An enzyme system has been found in heterotrophic N/sub 2/-fixing bacteria capable of degrading hydrazine. Information concerning the effect of hydrazine on microbial activity in soils is not available, however. Accidental spills to soil can occur during transportation and storage. Therefore, this study was initiated to determine degradation rates of hydrazine in soils and its effect on soil microbial activity.

  2. Effects of soil water repellency on microbial community structure and functions in Mediterranean pine forests

    NASA Astrophysics Data System (ADS)

    Lozano, Elena; Grayston, Sue J.; Mataix-Solera, Jorge; Arcenegui, Victoria; Jimenez-Pinilla, Patricia; Mataix-Beneyto, Jorge

    2015-04-01

    Soil water repellency (SWR) is a property commonly observed in forest areas showing wettable and water repellent patches with high spatial variability. SWR can greatly influence the hydrology and the ecology of forest soils. The capacity of soil microorganisms to degrade different organic compounds depends upon species composition, so this may affect changes in SWR on the microsite scale (such as the presence of soil water repellent patches; Mülleret al., 2010). In the Mediterranean forest context, SWR has been found to be related to microbial community composition. The accumulation of different hydrophobic compounds might be causing the shifts in microbial community structure (Lozano et al., 2014). In this study we investigated the effects of SWR persistence on soil microbial community structure and enzyme activity under Pinus halepensis forest in three different sites: Petrer, Gorga and Jávea (Alicante, E Spain). Soil samples were classified into three different water repellency classes (wettable, slight or strongly water repellent samples) depending on the SWR persistence. The soil microbial community was determined through phospholipid fatty acids (PLFAs). Enzyme activities chosen for this study were cellulase, β-glucosidase and N-acetyl-β-glucosaminide (NAG). The relationships between microbiological community structure and some soil properties such as pH, Glomalin Related Soil Protein, soil organic matter content and soil respiration were also studied. Redundancy analyses and decomposition of the variances were performed to clarify how microbial community composition and enzyme activities are affected by SWR and soil properties. The effect of SWR on microbial community composition differed between locations. This effect was clearer in the Petrer site. Enzyme activity varied considerably depending on SWR persistence. The highest activities were found in slightly SWR samples and the lowest mostly in the strongly water repellent ones. These preliminary

  3. Stoichiometry of Microbial Decomposition Priming in Plant Litter and Soil

    NASA Astrophysics Data System (ADS)

    Schaefer, D.; Qiao, N.

    2011-12-01

    Microbial priming is accelerated conversion of plant residues and soil organic carbon to CO2. It is caused by small additions of labile carbon and nitrogen compounds, but microbial stoichiometry suggests that this description is incomplete. The temperature dependence of soil organic carbon cycling models may be related to diffusion of labile resources to microbial cells. Incomplete treatment of stoichiometrically significant elements in these models may also limit their ability to predict carbon fluxes if plant species, diseases or defoliators are affected by climate changes. We explore this by incubating decomposable substrates (leaves, wood, humus and mineral soil) with resources added as dissolved inorganic nitrogen (ammonium and nitrate separately), phosphorus and sugar, added in different amounts and proportions. We measure CO2 production by infrared absorption. Contribution of sugar to CO2 production is assessed by mass spectrometry. High concentrations for each resource are 16X the low, and middle concentrations are 4X the low. The ratios are centered on 200:10:1. We explore C:N:P resource ratios and additions over wide ranges; subsequently to examine narrower ranges of interest. For C:N:P incubations, C and N effects are always significant on CO2 production, with P in only half of the treatments. Literature suggests that leaf-litter decomposition is stimulated by N (occasionally P) additions, but results for soils have been mixed. We find N to be inhibitory only when added in "stoichiometic excess" to added C. Stimulation of microbial respiration is generally strongest with C:N:P additions in "Redfield-like" ratios, but the response is far below linear. Humus has a stronger response to C than do leaves and wood. This is consistent with a chronic energy limitation for soil microbes, even where their environments contain large amounts of total C. For all substrates, the addition of N as nitrate leads to significantly more CO2 than the same amount of ammonium

  4. Organic matter mineralization in frozen boreal soils-environmental constraints on catabolic and anabolic microbial activity

    NASA Astrophysics Data System (ADS)

    Oquist, Mats G.; Sparrman, Tobias; Schleucher, Jürgen; Nilsson, Mats B.

    2014-05-01

    Heterotrophic microbial mineralization of soil organic matter (SOM) and associated production and emission of atmospheric trace gases proceed during the winter months in the frozen soils of high latitude ecosystems. However, in what ways this microbial activity is constrained by the environmental conditions prevailing in a frozen soil matrix is uncertain. This presentation will address how temperature, water availability and substrate availability combine to regulate rates of microbial activity at below freezing temperatures and the implications of this activity for SOM mineralization in the surface layers of boreal forest soils experiencing seasonal freezing. We show that the amount and availability of liquid water is an integral factor regulating rates of microbial activity in the frozen soil matrix and can also explain frequently observed deviations in the temperature responses of biogenic CO2 production in frozen soils, as compared to unfrozen soils. Using stable isotope labeling (13C) we also show that the partitioning of substrate carbon, in the form of monomeric sugar (glucose), for catabolic and anabolic metabolism remain constant in the temperature range of -4C to 9C. This confirms that microbial growth may proceed even when soils are frozen. In addition we present corresponding data for organisms metabolizing polymeric substrates (cellulose) requiring exoenzymatic activity prior to substrate uptake. We conclude that the metabolic response of soil microorganism to controlling factors may change substantially across the freezing point of soil water, and also the patterns of interaction among controlling factors are affected. Thus, it is evident that metabolic response functions derived from investigations of unfrozen soils cannot be superimposed on frozen soils. Nonetheless, the soil microbial population appear very adapted to seasonal freezing with respect to their metabolic performance.

  5. Microbial communities play important roles in modulating paddy soil fertility

    NASA Astrophysics Data System (ADS)

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-02-01

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production.

  6. Microbial communities play important roles in modulating paddy soil fertility

    PubMed Central

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-01-01

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production. PMID:26841839

  7. Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

    PubMed

    You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

    2014-03-01

    Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations. PMID

  8. Microbial degradation of sulfentrazone in a Brazilian rhodic hapludox soil

    PubMed Central

    Martinez, Camila O.; Silva, Celia Maria M. S.; Fay, Elisabeth F.; Abakerli, Rosangela B.; Maia, Aline H. N.; Durrant, Lucia R.

    2010-01-01

    Sulfentrazone is amongst the most widely used herbicides for treating the main crops in the State of São Paulo, Brazil, but few studies are available on the biotransformation of this compound in Brazilian soils. Soil samples of Rhodic Hapludox soil were supplemented with sulfentrazone (0.7 µg active ingredient (a.i.) g-1 soil) and maintained at 27°C. The soil moisture content was corrected to 30, 70 or 100 % water holding capacity (WHC) and maintained constant until the end of the experimental period. Herbicide-free soil samples were used as controls. Another experiment was carried out using soil samples maintained at a constant moisture content of 70% WHC, supplemented or otherwise with the herbicide, and submitted to different temperatures of 15, 30 and 40° C. In both experiments, aliquots were removed after various incubation periods for the quantitative analysis of sulfentrazone residues by gas chromatography. Herbicide-degrading microorganisms were isolated and identified. After 120 days a significant effect on herbicide degradation was observed for the factor of temperature, degradation being higher at 30 and 40° C. A half-life of 91.6 days was estimated at 27° C and 70 % WHC. The soil moisture content did not significantly affect sulfentrazone degradation and the microorganisms identified as potential sulfentrazone degraders were Nocardia brasiliensis and Penicillium sp. The present study enhanced the prospects for future studies on the bio-prospecting for microbial populations related to the degradation of sulfentrazone, and may also contribute to the development of strategies for the bioremediation of sulfentrazone-polluted soils. PMID:24031483

  9. Microbial degradation of sulfentrazone in a Brazilian rhodic hapludox soil.

    PubMed

    Martinez, Camila O; Silva, Celia Maria M S; Fay, Elisabeth F; Abakerli, Rosangela B; Maia, Aline H N; Durrant, Lucia R

    2010-01-01

    Sulfentrazone is amongst the most widely used herbicides for treating the main crops in the State of São Paulo, Brazil, but few studies are available on the biotransformation of this compound in Brazilian soils. Soil samples of Rhodic Hapludox soil were supplemented with sulfentrazone (0.7 µg active ingredient (a.i.) g(-1) soil) and maintained at 27°C. The soil moisture content was corrected to 30, 70 or 100 % water holding capacity (WHC) and maintained constant until the end of the experimental period. Herbicide-free soil samples were used as controls. Another experiment was carried out using soil samples maintained at a constant moisture content of 70% WHC, supplemented or otherwise with the herbicide, and submitted to different temperatures of 15, 30 and 40° C. In both experiments, aliquots were removed after various incubation periods for the quantitative analysis of sulfentrazone residues by gas chromatography. Herbicide-degrading microorganisms were isolated and identified. After 120 days a significant effect on herbicide degradation was observed for the factor of temperature, degradation being higher at 30 and 40° C. A half-life of 91.6 days was estimated at 27° C and 70 % WHC. The soil moisture content did not significantly affect sulfentrazone degradation and the microorganisms identified as potential sulfentrazone degraders were Nocardia brasiliensis and Penicillium sp. The present study enhanced the prospects for future studies on the bio-prospecting for microbial populations related to the degradation of sulfentrazone, and may also contribute to the development of strategies for the bioremediation of sulfentrazone-polluted soils. PMID:24031483

  10. Microbial response to salinity stress in a tropical sandy soil amended with native shrub residues or inorganic fertilizer.

    PubMed

    Sall, Saïdou Nourou; Ndour, Ndèye Yacine Badiane; Diédhiou-Sall, Siré; Dick, Richard; Chotte, Jean-Luc

    2015-09-15

    Soil degradation and salinization caused by inappropriate cultivation practices and high levels of saltwater intrusion are having an adverse effect on agriculture in Central Senegal. The residues of Piliostigma reticulatum, a local shrub that coexists with crops, were recently shown to increase particulate organic matter and improve soil quality and may be a promising means of alleviating the effects of salinization. This study compared the effects of inorganic fertilizer and P. reticulatum residues on microbial properties and the ability of soil to withstand salinity stress. We hypothesized that soils amended with P. reticulatum would be less affected by salinity stress than soils amended with inorganic fertilizer and control soil. Salinity stress was applied to soil from a field site that had been cultivated for 5 years under a millet/peanut crop rotation when microbial biomass, phospholipid fatty acid (PLFA) community profile, catabolic diversity, microbial activities were determined. Microbial biomass, nitrification potential and dehydrogenase activity were higher by 20%, 56% and 69% respectively in soil with the organic amendment. With salinity stress, the structure and activities of the microbial community were significantly affected. Although the biomass of actinobacteria community increased with salinity stress, there was a substantial reduction in microbial activity in all soils. The soil organically amended was, however, less affected by salinity stress than the control or inorganic fertilizer treatment. This suggests that amendment using P. reticulatum residues may improve the ability of soils to respond to saline conditions. PMID:26143083

  11. 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

  12. Effects of biochar blends on microbial community composition in two coastal plain soils

    EPA Science Inventory

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

  13. Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities

    PubMed Central

    Deng, Ye; He, Zhili; Xu, Meiying; Qin, Yujia; Van Nostrand, Joy D.; Wu, Liyou; Roe, Bruce A.; Wiley, Graham; Hobbie, Sarah E.; Reich, Peter B.

    2012-01-01

    Pyrosequencing analysis of 16S rRNA genes was used to examine impacts of elevated CO2 (eCO2) on soil microbial communities from 12 replicates each from ambient CO2 (aCO2) and eCO2 settings. The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO2, which was closely associated with soil and plant properties. PMID:22307288

  14. Responses of soil microbial community to experimental warming and precipitation manipulation

    NASA Astrophysics Data System (ADS)

    Li, G.; Kim, S.; Park, M. J.; Han, S. H.; Lee, J.; Son, Y.

    2015-12-01

    An experimental nursery was established with two-year-old Pinus densiflora seedlings at Korea University to study soil microbial community responses to air warming (+3°C) and precipitation manipulation (-30% and +30%). Soil samplings were collected monthly from July to November, 2014. Substrate utilization profile of microbial community was examined using BIOLOG EcoPlate. Microbial community composition was assessed by high-throughput sequencing technology. The results showed that warming significantly affected the substrate utilization profile of microbial community (P<0.05), which labile substrates were degraded more quickly in warming plots than unwarmed plots. Only significant effects of warming on fungal community richness and abundance were observed (all P<0.05). Compared with unwarmed and precipitation control treatment, fungal community richness in the others were significantly decreased by 1.22%-15.27% (P<0.05), but community diversity in those treatments were slightly increased (P>0.05). In contrast, compared with unwarmed and precipitation control treatment, the bacterial community richness in the others were increased, but community abundance and diversity in those treatments were decreased (all P>0.05). These changes in microbial community structure resulted in the changes in community functional composition, which microbial metabolic functions were higher in warming plots than unwarmed plots. Since microorganisms differ in their susceptibility to stressors, changes in the soil environment affect the microbial community. Therefore, the results indicated that effects of warming and precipitation manipulation on soil microbial community might be related to warming and precipitation manipulation-induced changes in soil moisture. We suggested that shifts in the microbial community may be important implications for soil carbon and nitrogen dynamics in a warmer world. This study was supported by National Research Foundation of Korea (NRF-2013R1A1A2012242).

  15. Decreases in Soil Moisture and Organic Matter Quality Suppress Microbial Decomposition Following a Boreal Forest Fire

    SciTech Connect

    Holden, Sandra R.; Berhe, Asmeret A.; Treseder, Kathleen K.

    2015-08-01

    Climate warming is projected to increase the frequency and severity of wildfires in boreal forests, and increased wildfire activity may alter the large soil carbon (C) stocks in boreal forests. Changes in boreal soil C stocks that result from increased wildfire activity will be regulated in part by the response of microbial decomposition to fire, but post-fire changes in microbial decomposition are poorly understood. Here, we investigate the response of microbial decomposition to a boreal forest fire in interior Alaska and test the mechanisms that control post-fire changes in microbial decomposition. We used a reciprocal transplant between a recently burned boreal forest stand and a late successional boreal forest stand to test how post-fire changes in abiotic conditions, soil organic matter (SOM) composition, and soil microbial communities influence microbial decomposition. We found that SOM decomposing at the burned site lost 30.9% less mass over two years than SOM decomposing at the unburned site, indicating that post-fire changes in abiotic conditions suppress microbial decomposition. Our results suggest that moisture availability is one abiotic factor that constrains microbial decomposition in recently burned forests. In addition, we observed that burned SOM decomposed more slowly than unburned SOM, but the exact nature of SOM changes in the recently burned stand are unclear. Finally, we found no evidence that post-fire changes in soil microbial community composition significantly affect decomposition. Taken together, our study has demonstrated that boreal forest fires can suppress microbial decomposition due to post-fire changes in abiotic factors and the composition of SOM. Models that predict the consequences of increased wildfires for C storage in boreal forests may increase their predictive power by incorporating the observed negative response of microbial decomposition to boreal wildfires.

  16. Microbial community structures and metabolic profiles response differently to physiochemical properties between three landfill cover soils.

    PubMed

    Long, Xi-En; Wang, Juan; Huang, Ying; Yao, Huaiying

    2016-08-01

    Landfills are always the most important part of solid waste management and bear diverse metabolic activities involved in element biogeochemical cycling. There is an increasing interest in understanding the microbial community and activities in landfill cover soils. To improve our knowledge of landfill ecosystems, we determined the microbial physiological profiles and communities in three landfill cover soils (Ninghai: NH, Xiangshan: XS, and Fenghua: FH) of different ages using the MicroResp(TM), phospholipid fatty acid (PLFA), and high-throughput sequencing techniques. Both total PLFAs and glucose-induced respiration suggested more active microorganisms occurred in intermediate cover soils. Microorganisms in all landfill cover soils favored L-malic acid, ketoglutarate, and citric acid. Gram-negative bacterial PLFAs predominated in all samples with the representation of 16:1ω7, 18:1ω7, and cy19:0 in XS and NH sites. Proteobacteria dominated soil microbial phyla across different sites, soil layers, and season samples. Canonical correspondence analysis showed soil pH, dissolved organic C (DOC), As, and total nitrogen (TN) contents significantly influenced the microbial community but TN affected the microbial physiological activities in both summer and winter landfill cover soils. PMID:27117156

  17. Effect of elevated CO2 on degradation of azoxystrobin and soil microbial activity in rice soil.

    PubMed

    Manna, Suman; Singh, Neera; Singh, V P

    2013-04-01

    An experiment was conducted in open-top chambers (OTC) to study the effect of elevated CO2 (580 ± 20 μmol mol(-1)) on azoxystrobin degradation and soil microbial activities. Results indicated that elevated CO2 did not have any significant effect on the persistence of azoxystrobin in rice-planted soil. The half-life values for the azoxystrobin in rice soils were 20.3 days in control (rice grown at ambient CO2 outdoors), 19.3 days in rice grown under ambient CO2 atmosphere in OTC, and 17.5 days in rice grown under elevated CO2 atmosphere in OTC. Azoxystrobin acid was recovered as the only metabolite of azoxystrobin, but it did not accumulate in the soil/water and was further metabolized. Elevated CO2 enhanced soil microbial biomass (MBC) and alkaline phosphatase activity of soil. Compared with rice grown at ambient CO2 (both outdoors and in OTC), the soil MBC at elevated CO2 increased by twofold. Elevated CO2 did not affect dehydrogenase, fluorescein diacetate, and acid phosphatase activity. Azoxystrobin application to soils, both ambient and elevated CO2, inhibited alkaline phosphates activity, while no effect was observed on other enzymes. Slight increase (1.8-2 °C) in temperature inside OTC did not affect microbial parameters, as similar activities were recorded in rice grown outdoors and in OTC at ambient CO2. Higher MBC in soil at elevated CO2 could be attributed to increased carbon availability in the rhizosphere via plant metabolism and root secretion; however, it did not significantly increase azoxystrobin degradation, suggesting that pesticide degradation was not the result of soil MBC alone. Study suggested that increased CO2 levels following global warming might not adversely affect azoxystrobin degradation. However, global warming is a continuous and cumulative process, therefore, long-term studies are necessary to get more realistic assessment of global warming on fate of pesticide. PMID:22773147

  18. Testing nickel tolerance of Sorghastrum nutans and its associated soil microbial community from serpentine and prairie soils.

    PubMed

    Doherty, Jennifer H; Ji, Baoming; Casper, Brenda B

    2008-02-01

    Ecotypes of Sorghastrum nutans from a naturally metalliferous serpentine grassland and the tallgrass prairie were assessed for Ni tolerance and their utility in remediation of Ni-polluted soils. Plants were inoculated with serpentine arbuscular mycorrhizal (AM) root inoculum or whole soil microbial communities, originating from either prairie or serpentine, to test their effects on plant performance in the presence of Ni. Serpentine plants had marginally higher Ni tolerance as indicated by higher survival. Ni reduced plant biomass and AM root colonization for both ecotypes. The serpentine AM fungi and whole microbial community treatments decreased plant biomass relative to uninoculated plants, while the prairie microbial community had no effect. Differences in how the soil communities affect plant performance were not reflected in patterns of root colonization by AM fungi. Thus, serpentine plants may be suited for reclamation of Ni-polluted soils, but AM fungi that occur on serpentine do not improve Ni tolerance. PMID:17555852

  19. Priming and turnover of soil microbial biomass C and N

    NASA Astrophysics Data System (ADS)

    Voroney, Paul; Paul, Eldor

    2015-04-01

    Priming is the altered rate of mineralization of native soil organic matter (SOM) induced by an organic substrate and, depending on the nature of the amendment, can be either positive or negative. Coupled with the use of tracer (14C, 13C, 15N) techniques, measurements of the rates of CO2 evolution and organic N mineralization are typically used to assess priming effects. In this study priming was also assessed from measurements of soil microbial biomass. Soil was amended with 14C-glucose and 15N-nitrate and incubated for 42 d during which unlabelled and labelled microbial biomass C and N were measured using the chloroform-incubation method. All of the 14C-glucose was metabolized within 24-30 h at a C-use efficiency of ~60%, and resulted in a labelled biomass C:N of 9. After this period of rapid microbial growth, labelled microbial biomass C decayed at a rate of 19.3 x 10-3 d-1. Unlabelled microbial biomass C in the amended treatment decayed at 8.6 x 10-3 d-1 whereas in the unamended soil microbial biomass C decayed at half this rate (4.9 x 10-3 d-1). These data suggest that ~25% of the native microbial biomass C responded to the addition of glucose-C and when it was depleted the newly formed microbial biomass, comprised of both labelled and unlabelled- C, collapsed and subsequently was mineralized. The period of rapid microbial biomass decay coincided with an increased evolution of soil (unlabelled) CO2 and accumulation of (unlabelled) mineral N compared to that in the unamended soil. Thus, the apparent priming of soil C and N following addition of glucose can be attributed to biological recycling and increased turnover of native microbial biomass C and N. There was no evidence of priming of native soil organic matter during the first 21 days of the incubation.

  20. Precipitation regime drives soil microbial responses to warming in temperate steppes

    NASA Astrophysics Data System (ADS)

    Liu, W.; Xia, J.; Liu, L.; Wan, S.

    2014-12-01

    Although numerous warming experiments have been done to examine the impacts of elevated temperature on soil microbial actives, most of them were based on responses from a single site. To investigate how precipitation regime regulate warming's effects on carbon cycle, field manipulative warming experiments were conducted at 3 types of steppes (desert, typical and meadow steppe) along a precipitation gradient in northern China. Soil temperature, moisture, dissolved organic C (DOC), inorganic nitrogen (N) concentration, microbial biomass C (MBC), N (MBN) and respiration (MR) were measured once a year from 2006 to 2009. The results showed that soil moisture was significantly decreased in the typical steppe whereas not affected in the desert and meadow steppe, respectively. Across the 4 years, warming decreased MBC and MR in the desert and typical steppe while did not affect them in the meadow steppe. The magnitude of reductions in warming-induced MBC and MR declined with increasing precipitation gradient at a regional scale. Across the precipitation gradient, all changes in soil MBC, MBN and MR were positively correlated with both annual precipitation and changes in belowground net primary productivity (BNPP), suggesting that soil microbial responses to warming may be regulated by annual precipitation and substrate availability. However, the lab-incubation revealed that soil moisture is more important in regulating soil microbial activities than substrate across the 3 steppes. In addition, soil microbial responses to warming showed year-to-year variations during the first 4 years coincided with the fluctuations in annual precipitation across the 3 steppes. Our results suggested that precipitation regime controls the spatial and interannual responses of soil microbes to warming, mainly by regulating soil moisture and substrate availability. With the increase in precipitation, the positive responses of soil microbes to warming started to outweigh the negative impacts

  1. Soil microbial communities of postpyrogenic pine forests (case study in Russia)

    NASA Astrophysics Data System (ADS)

    Maksimova, Ekaterina

    2015-04-01

    Soil microbial communities of postpyrogenic pine forests (case study in Russia) Ekaterina Maksimova Saint-Petersburg State University, Department of Applied Ecology, Saint-Petersburg, Russian Federation Institute of Ecology of Volga basin, Togljatty city, Russian Federation Soils, affected by catastrophic wildfires in 2010, were investigated in pine woods of Togljatty city, Samara region with the special reference to soil biological parameters. The analysis of microbial community of pine wood soils was carried out. It was revealed that wildfires have a negative impact on structure and functional activity of the microbial community postpyrogenic soils. In particular, they influence on values of eukaryotes-prokaryotes ratios, on CO2 emission intensity and on microorganisms functional state (as it was determined by microbial metabolic quotient) after wildfires. It has been revealed that microbial biomass values and basal respiration rate shows the trend to decrease in case of postfire sites compared with control (in 6.5 and 3.4 times respectively). The microbial biomass and basal respiration values have annual natural variability that testifies to a correlation of this process with soil hydrothermal conditions. However, it was also noted that wildfires don't affect on measured microbiological parameters in layers situated deeper than top 10 cm of soil. An increasing of the values, mentioned above, was observed 2-3 years after wildfires. Zone of microorganisms' activity has been moved to the lowermost soil layers. A disturbance of soil microbial communities' ecophysiological status after the fire is diagnosed by an increase of microbial metabolic quotient value. The metabolic activity of the microbial community decreases in a row: control→crown fire→ground fire. That testifies to certain intensive changes in the microbial community. High-temperature influence on microbial community has a significant effect on a total amount of bacteria, on a length of actinomycetes

  2. Fractal scaling of microbial colonies affects growth

    NASA Astrophysics Data System (ADS)

    Károlyi, György

    2005-03-01

    The growth dynamics of filamentary microbial colonies is investigated. Fractality of the fungal or actinomycetes colonies is shown both theoretically and in numerical experiments to play an important role. The growth observed in real colonies is described by the assumption of time-dependent fractality related to the different ages of various parts of the colony. The theoretical results are compared to a simulation based on branching random walks.

  3. Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

    PubMed Central

    Leite, D.C.A.; Balieiro, F.C.; Pires, C.A.; Madari, B.E.; Rosado, A.S.; Coutinho, H.L.C.; Peixoto, R.S.

    2014-01-01

    Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples. PMID:24948928

  4. Comparison of DNA extraction protocols for microbial communities from soil treated with biochar.

    PubMed

    Leite, D C A; Balieiro, F C; Pires, C A; Madari, B E; Rosado, A S; Coutinho, H L C; Peixoto, R S

    2014-01-01

    Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples. PMID:24948928

  5. Enhancing Potato System Sustainability: Soilborne Diseases and Soil Microbial Communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Four different potato cropping systems, designed to address specific management goals of soil conservation (SC), soil improvement (SI), disease suppression (DS), and a status quo (standard rotation) control (SQ), were evaluated for their effects on soilborne diseases of potato and soil microbial com...

  6. Effects of soil type and farm management on soil ecological functional genes and microbial activities.

    PubMed

    Reeve, Jennifer R; Schadt, Christopher W; Carpenter-Boggs, Lynne; Kang, Sanghoon; Zhou, Jizhong; Reganold, John P

    2010-09-01

    Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes. PMID:20376100

  7. Effects of soil type and farm management on soil ecological functional genes and microbial activities

    SciTech Connect

    Reeve, Jennifer; Schadt, Christopher Warren; Carpenter-Boggs, Lynne; Kang, S.; Zhou, Jizhong; Reganold, John P.

    2010-01-01

    Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.

  8. Soil organic matter transformation in cryoturbated horizons of permafrost affected soils

    NASA Astrophysics Data System (ADS)

    Capek, Petr; Diakova, Katerina; Dickopp, Jan-Erik; Barta, Jiri; Santruckova, Hana; Wild, Birgit; Schnecker, Joerg; Guggenberg, Georg; Gentsch, Norman; Hugelius, Gustaf; Kuhry, Peter; Lashchinsky, Nikolaj; Gittel, Antje; Schleper, Christa; Mikutta, Robert; Palmtag, Juri; Shibistova, Olga; Urich, Tim; Zimov, Sergey; Richter, Andreas

    2014-05-01

    Cryoturbated soil horizons are special feature of permafrost affected soils. These soils are known to store great amount of organic carbon and cryoturbation undoubtedly contribute to it to large extent. Despite this fact there is almost no information about soil organic matter (SOM) transformation in cryoturbated horizons. Therefore we carried out long term incubation experiment in which we inspect SOM transformation in cryoturbated as well as in organic and mineral soil horizons under different temperature and redox regimes as potential drivers. We found out that lower SOM transformation in cryoturbated horizons compared to organic horizons was mainly limited by the amount of microbial biomass, which is extremely low in absolute numbers or expressed to SOM concentration. The biochemical transformation ensured by extracellular enzymes is relatively high leading to high concentrations of dissolved organic carbon in cryoturbated horizons. Nevertheless the final step of SOM transformation leading to C mineralization to CO2 or CH4 seems to be restricted by low microbial biomass. Critical step of biochemical transformation of complex SOM is dominated by phenoloxidases, which break down complex organic compounds to simple ones. Their oxygen consumption greatly overwhelms oxygen consumption of the whole microbial community. However the phenoloxidase activity shows strong temperature response with optimum at 13.7° C. Therefore we suggest that apparent SOM stability in cryoturbated horizons, which is expressed in old C14 dated age, is caused by low amount of microbial biomass and restricted diffusion of oxygen to extracellular enzymes in field.

  9. Exploring Microbial Iron Oxidation in Wetland Soils

    NASA Astrophysics Data System (ADS)

    Wang, J.; Muyzer, G.; Bodelier, P. L. E.; den Oudsten, F.; Laanbroek, H. J.

    2009-04-01

    Iron is one of the most abundant elements on earth and is essential for life. Because of its importance, iron cycling and its interaction with other chemical and microbial processes has been the focus of many studies. Iron-oxidizing bacteria (FeOB) have been detected in a wide variety of environments. Among those is the rhizosphere of wetland plants roots which release oxygen into the soil creating suboxic conditions required by these organisms. It has been reported that in these rhizosphere microbial iron oxidation proceeds up to four orders of magnitude faster than strictly abiotic oxidation. On the roots of these wetland plants iron plaques are formed by microbial iron oxidation which are involved in the sequestering of heavy metals as well organic pollutants, which of great environmental significance.Despite their important role being catalysts of iron-cycling in wetland environments, little is known about the diversity and distribution of iron-oxidizing bacteria in various environments. This study aimed at developing a PCR-DGGE assay enabling the detection of iron oxidizers in wetland habitats. Gradient tubes were used to enrich iron-oxidizing bacteria. From these enrichments, a clone library was established based on the almost complete 16s rRNA gene using the universal bacterial primers 27f and 1492r. This clone library consisted of mainly α- and β-Proteobacteria, among which two major clusters were closely related to Gallionella spp. Specific probes and primers were developed on the basis of this 16S rRNA gene clone library. The newly designed Gallionella-specific 16S rRNA gene primer set 122f/998r was applied to community DNA obtained from three contrasting wetland environments, and the PCR products were used in denaturing gradient gel electrophoresis (DGGE) analysis. A second 16S rRNA gene clone library was constructed using the PCR products from one of our sampling sites amplified with the newly developed primer set 122f/998r. The cloned 16S rRNA gene

  10. 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

  11. Short-term precipitation exclusion alters microbial responses to soil moisture in a wet tropical forest.

    PubMed

    Waring, Bonnie G; Hawkes, Christine V

    2015-05-01

    Many wet tropical forests, which contain a quarter of global terrestrial biomass carbon stocks, will experience changes in precipitation regime over the next century. Soil microbial responses to altered rainfall are likely to be an important feedback on ecosystem carbon cycling, but the ecological mechanisms underpinning these responses are poorly understood. We examined how reduced rainfall affected soil microbial abundance, activity, and community composition using a 6-month precipitation exclusion experiment at La Selva Biological Station, Costa Rica. Thereafter, we addressed the persistent effects of field moisture treatments by exposing soils to a controlled soil moisture gradient in the lab for 4 weeks. In the field, compositional and functional responses to reduced rainfall were dependent on initial conditions, consistent with a large degree of spatial heterogeneity in tropical forests. However, the precipitation manipulation significantly altered microbial functional responses to soil moisture. Communities with prior drought exposure exhibited higher respiration rates per unit microbial biomass under all conditions and respired significantly more CO2 than control soils at low soil moisture. These functional patterns suggest that changes in microbial physiology may drive positive feedbacks to rising atmospheric CO2 concentrations if wet tropical forests experience longer or more intense dry seasons in the future. PMID:24889286

  12. Soil microbial community successional patterns during forest ecosystem restoration.

    PubMed

    Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

    2011-09-01

    Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

  13. Soil microbial biomass and mineralizable carbon as a function of crop rotation and soil acidity amendment in a no-tillage system in Brazil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tropical climate and weathered soil conditions create significant challenges for increasing soil organic matter content. However, crop management strategies could affect short-term dynamics of active fractions of soil organic matter. Thus, our aim was to evaluate the microbial biomass and mineraliza...

  14. Long- and short-term temperature responses of microbially-mediated boreal soil organic matter transformations

    NASA Astrophysics Data System (ADS)

    Min, K.; Buckeridge, K. M.; Edwards, K. A.; Ziegler, S. E.; Billings, S. A.

    2015-12-01

    Microorganisms use exoenzymes to decay soil organic matter into assimilable substrates, some of which are transformed into CO2. Microbial CO2 efflux contributes up to 60% of soil respiration, a feature that can change with temperature due to altered exoenzyme activities (short-term) and microbial communities producing different exoenzymes (longer-term). Often, however, microbial temperature responses are masked by factors that also change with temperature in soil, making accurate projections of microbial CO2 efflux with warming challenging. Using soils along a natural climate gradient similar in most respects except for temperature regime (Newfoundland Labrador Boreal Ecosystem Latitudinal Transect), we investigated short-vs. long-term temperature responses of microbially-mediated organic matter transformations. While incubating soils at 5, 15, and 25°C for 84 days, we measured exoenzyme activities, CO2 efflux rates and biomass, and extracted DNA at multiple times. We hypothesized that short-term, temperature-induced increases in exoenzyme activities and CO2 losses would be smaller in soils from warmer regions, because microbes presumably adapted to warmer regions should use assimilable substrates more efficiently and thus produce exoenzymes at a lower rate. While incubation temperature generally induced greater exoenzyme activities (p<0.001), exoenzymes' temperature responses depended on enzymes and regions (p<0.001). Rate of CO2 efflux was affected by incubation temperature (P<0.001), but not by region. Microbial biomass and DNA sequencing will reveal how microbial community abundance and composition change with short-vs. longer-term temperature change. Though short-term microbial responses to temperature suggest higher CO2 efflux and thus lower efficiency of resource use with warming, longer-term adaptations of microbial communities to warmer climates remain unknown; this work helps fill that knowledge gap.

  15. Enhanced microbial degradation of deethylatrazine in atrazine-history soils

    SciTech Connect

    Kruger, E.L.; Chaplin, J.A.; Anderson, T.A.

    1995-12-01

    Persistence and degradation of deethylatrazine, the primary metabolite of atrazine, was measured in soil with atrazine history (15 consecutive years of atrazine application) and no atrazine history (no atrazine application for 15 consecutive years). Uniformly ring-labeled {sup 14}C-deethylatrazine was applied to surface and subsurface soils for metabolism studies. After 60 d of incubation, mineralization of deethylatrazine to {sup 14}CO{sub 2} in the atrazine-history surface soil was twice that in the no-history surface soils (34% and 17% of the applied {sup 14}C, respectively). In surface soils, 25% of the applied {sup 14}C remained as deethylatrazine in the atrazine-history soil, compared with 35% in the no-history soil. Microbial plate counts indicated an increase in numbers of bacteria and fungi in soils incubated with deethylatrazine compared to control soils. Total microbial biomass of soils incubated with deethylatrazine, as determined by CO{sub 2} efflux using an infrared (IR) gas analyzer, showed no significant difference between atrazine-history, and no-history soil, but did show an increase above untreated control soils. Prior to treating soils with deethylatrazine, specific deethylatrazine degraders were quantified using a {sup 14}C-most-probable-number procedure. Deethylatrazine degraders were more numerous in atrazine-history surface soil compared to no-history surface soil. After incubation of soils with deethylatrazine, deethylatrazine degraders were more numerous in both history soils as compared to control soils. From these studies, it appears that deethylatrazine is degraded microbially to a greater extent in soils that have had long-term exposure to atrazine at field application rates compared to soils with no long-term exposure. Decreased persistence of this major metabolite of atrazine in atrazine-history soils is important in that there will be less available for movement in surface runoff and to groundwater.

  16. Explicitly representing soil microbial processes in Earth system models

    NASA Astrophysics Data System (ADS)

    Wieder, William R.; Allison, Steven D.; Davidson, Eric A.; Georgiou, Katerina; Hararuk, Oleksandra; He, Yujie; Hopkins, Francesca; Luo, Yiqi; Smith, Matthew J.; Sulman, Benjamin; Todd-Brown, Katherine; Wang, Ying-Ping; Xia, Jianyang; Xu, Xiaofeng

    2015-10-01

    Microbes influence soil organic matter decomposition and the long-term stabilization of carbon (C) in soils. We contend that by revising the representation of microbial processes and their interactions with the physicochemical soil environment, Earth system models (ESMs) will make more realistic global C cycle projections. Explicit representation of microbial processes presents considerable challenges due to the scale at which these processes occur. Thus, applying microbial theory in ESMs requires a framework to link micro-scale process-level understanding and measurements to macro-scale models used to make decadal- to century-long projections. Here we review the diversity, advantages, and pitfalls of simulating soil biogeochemical cycles using microbial-explicit modeling approaches. We present a roadmap for how to begin building, applying, and evaluating reliable microbial-explicit model formulations that can be applied in ESMs. Drawing from experience with traditional decomposition models, we suggest the following: (1) guidelines for common model parameters and output that can facilitate future model intercomparisons; (2) development of benchmarking and model-data integration frameworks that can be used to effectively guide, inform, and evaluate model parameterizations with data from well-curated repositories; and (3) the application of scaling methods to integrate microbial-explicit soil biogeochemistry modules within ESMs. With contributions across scientific disciplines, we feel this roadmap can advance our fundamental understanding of soil biogeochemical dynamics and more realistically project likely soil C response to environmental change at global scales.

  17. Explicitly Representing Soil Microbial Processes In Earth System Models

    SciTech Connect

    Wieder, William R.; Allison, Steven D.; Davidson, Eric A.; Georgiou, Katrina; Hararuk, Oleksandra; He, Yujie; Hopkins, Francesca; Luo, Yiqi; Smith, Mathew J.; Sulman, Benjamin; Todd-Brown, Katherine EO; Wang, Ying-Ping; Xia, Jianyang; Xu, Xiaofeng

    2015-10-26

    Microbes influence soil organic matter (SOM) decomposition and the long-term stabilization of carbon (C) in soils. We contend that by revising the representation of microbial processes and their interactions with the physicochemical soil environment, Earth system models (ESMs) may make more realistic global C cycle projections. Explicit representation of microbial processes presents considerable challenges due to the scale at which these processes occur. Thus, applying microbial theory in ESMs requires a framework to link micro-scale process-level understanding and measurements to macro-scale models used to make decadal- to century-long projections. Here, we review the diversity, advantages, and pitfalls of simulating soil biogeochemical cycles using microbial-explicit modeling approaches. We present a roadmap for how to begin building, applying, and evaluating reliable microbial-explicit model formulations that can be applied in ESMs. Drawing from experience with traditional decomposition models we suggest: (1) guidelines for common model parameters and output that can facilitate future model intercomparisons; (2) development of benchmarking and model-data integration frameworks that can be used to effectively guide, inform, and evaluate model parameterizations with data from well-curated repositories; and (3) the application of scaling methods to integrate microbial-explicit soil biogeochemistry modules within ESMs. With contributions across scientific disciplines, we feel this roadmap can advance our fundamental understanding of soil biogeochemical dynamics and more realistically project likely soil C response to environmental change at global scales.

  18. Insights into the resistance and resilience of the soil microbial community.

    PubMed

    Griffiths, Bryan S; Philippot, Laurent

    2013-03-01

    Soil is increasingly under environmental pressures that alter its capacity to fulfil essential ecosystem services. To maintain these crucial soil functions, it is important to know how soil microorganisms respond to disturbance or environmental change. Here, we summarize the recent progress in understanding the resistance and resilience (stability) of soil microbial communities and discuss the underlying mechanisms of soil biological stability together with the factors affecting it. Biological stability is not solely owing to the structure or diversity of the microbial community but is linked to a range of other vegetation and soil properties including aggregation and substrate quality. We suggest that resistance and resilience are governed by soil physico-chemical structure through its effect on microbial community composition and physiology, but that there is no general response to disturbance because stability is particular to the disturbance and soil history. Soil stability results from a combination of biotic and abiotic soil characteristics and so could provide a quantitative measure of soil health that can be translated into practice. PMID:22568555

  19. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Ali; Or, Dani

    2016-04-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Mechanistic models of microbial processes in unsaturated aggregate pore networks revealed dynamic interplay between oxic and anoxic microsites that are jointly shaped by hydration and by aerobic and anaerobic microbial communities. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support significant anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3-D angular pore networks with profiles of water, carbon, and oxygen that vary with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain biogeochemical fluxes over the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of interest for hydrological and climate models.

  20. Hydration and diffusion dynamics shape microbial community composition and function in soil aggregates.

    NASA Astrophysics Data System (ADS)

    Or, D.; Ebrahimi, A.

    2014-12-01

    Natural variations in soil hydration conditions (rainfall, evaporation, root water uptake) affect gas and nutrient diffusion and soil microbial community composition and function. The conditions in soil aggregates are of particular interest due to limitations to oxygen diffusion into the core often containing organic carbon (as aggregation agent). The constantly varying soil hydration conditions affect the spatial extent of anoxic conditions in aggregates and thus the sized and self-organization of aerobic and anaerobic microbial communities. We developed an artificial soil aggregate composed of 3-D angular pore network combined with individual based models of motile microbial cells that grow, move, intercept nutrients and are inhibited by presence or absence of oxygen. The hydration conditions in the model aggregate affect community size, spatial segregation, and growth rates. The opposing diffusion directions of oxygen and carbon were essential to maintenance of aerobic and anaerobic communities within an aggregate (anaerobes become extinct when carbon sources are external). Cohabited soil aggregates promoted onset of anaerobic conditions by oxygen consumption by peripheral aerobes. Model predictions of CO2 and N2O production rates were in good agreement with experimental data. Results illustrate how aerobic and anaerobic microbial communities are activated by certain hydration conditions that enhance either nitrogen losses or decomposition of organic matter both contributing to GHG emissions.

  1. Microbial carbon mineralization in tropical lowland and montane forest soils of Peru.

    PubMed

    Whitaker, Jeanette; Ostle, Nicholas; McNamara, Niall P; Nottingham, Andrew T; Stott, Andrew W; Bardgett, Richard D; Salinas, Norma; Ccahuana, Adan J Q; Meir, Patrick

    2014-01-01

    Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., "positive priming effects" that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding (13)C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils. PMID:25566230

  2. Microbial carbon mineralization in tropical lowland and montane forest soils of Peru

    PubMed Central

    Whitaker, Jeanette; Ostle, Nicholas; McNamara, Niall P.; Nottingham, Andrew T.; Stott, Andrew W.; Bardgett, Richard D.; Salinas, Norma; Ccahuana, Adan J. Q.; Meir, Patrick

    2014-01-01

    Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., “positive priming effects” that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding 13C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils. PMID:25566230

  3. Matrix Effects and Measuring Microbial Responses to Xenobiotics in Soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Compartmentalization due to tortuous pore space promotes great diversity and functional redundancy in unsaturated soils. It is difficult to simultaneously expose discontiguous pore space (and organisms therein) to the same substance, which creates some challenges in measuring microbial responses to ...

  4. Microbial activity promotes carbon storage in temperate soils

    NASA Astrophysics Data System (ADS)

    Lange, Markus; Eisenhauer, Nico; Sierra, Carlos; Gleixner, Gerd

    2014-05-01

    Soils are one of the most important carbon sink and sources. Soils contain up to 3/4 of all terrestrial carbon. Beside physical aspects of soil properties (e.g. soil moisture and texture) plants play an important role in carbon sequestration. The positive effect of plant diversity on carbon storage is already known, though the underlying mechanisms remain still unclear. In the frame of the Jena Experiment, a long term biodiversity experiment, we are able to identify these processes. Nine years after an land use change from an arable field to managed grassland the mean soil carbon concentrations increased towards the concentrations of permanent meadows. The increase was positively linked to a plant diversity gradient. High diverse plant communities produce more biomass, which in turn results in higher amounts of litter inputs. The plant litter is transferred to the soil organic matter by the soil microbial community. However, higher plant diversity also causes changes in micro-climatic condition. For instance, more diverse plant communities have a more dense vegetation structure, which reduced the evaporation of soils surface and thus, increases soil moisture in the top layer. Higher inputs and higher soil moisture lead to an enlarged respiration of the soil microbial community. Most interestingly, the carbon storage in the Jena Experiment was much more related to microbial respiration than to plant root inputs. Moreover, using radiocarbon, we found a significant younger carbon age in soils of more diverse plant communities than in soils of lower diversity, indicating that more fresh carbon is integrated into the carbon pool. Putting these findings together, we could show, that the positive link between plant diversity and carbon storage is due to a higher microbial decomposition of plant litter, pointing out that carbon storage in soils is a function of the microbial community.

  5. Soil microbial community structure and nitrogen cycling responses to agroecosystem management and carbon substrate addition

    NASA Astrophysics Data System (ADS)

    Berthrong, S. T.; Buckley, D. H.; Drinkwater, L. E.

    2011-12-01

    Fertilizer application in conventional agriculture leads to N saturation and decoupled soil C and N cycling, whereas organic practices, e.g. complex rotations and legume incorporation, often results in increased SOM and tightly coupled cycles of C and N. These legacy effects of management on soils likely affect microbial community composition and microbial process rates. This project tested if agricultural management practices led to distinct microbial communities and if those communities differed in ability to utilize labile plant carbon substrates and to produce more plant available N. We addressed several specific questions in this project. 1) Do organic and conventional management legacies on similar soils produce distinct soil bacterial and fungal community structures and abundances? 2) How do these microbial community structures change in response to carbon substrate addition? 3) How do the responses of the microbial communities influence N cycling? To address these questions we conducted a laboratory incubation of organically and conventionally managed soils. We added C-13 labelled glucose either in one large dose or several smaller pulses. We extracted genomic DNA from soils before and after incubation for TRFLP community fingerprinting. We measured C in soil pools and respiration and N in soil extracts and leachates. Management led to different compositions of bacteria and fungi driven by distinct components in organic soils. Biomass did not differ across treatments indicating that differences in cycling were due to composition rather than abundance. C substrate addition led to convergence in bacterial communities; however management still strongly influenced the difference in communities. Fungal communities were very distinct between managements and plots with substrate addition not altering this pattern. Organic soils respired 3 times more of the glucose in the first week than conventional soils (1.1% vs 0.4%). Organic soils produced twice as much

  6. Soil microbial activity as influenced by compaction and straw mulching

    NASA Astrophysics Data System (ADS)

    Siczek, A.; Frąc, M.

    2012-02-01

    Field study was performed on Haplic Luvisol soil to determine the effects of soil compaction and straw mulching on microbial parameters of soil under soybean. Treatments with different compaction were established on unmulched and mulched with straw soil. The effect of soil compaction and straw mulching on the total bacteria number and activities of dehydrogenases, protease, alkaline and acid phosphatases was studied. The results of study indicated the decrease of enzymes activities in strongly compacted soil and their increase in medium compacted soil as compared to no-compacted treatment. Mulch application caused stimulation of the bacteria total number and enzymatic activity in the soil under all compaction levels. Compaction and mulch effects were significant for all analyzed microbial parameters (P<0.001).

  7. 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

  8. Principal methods for isolation and identification of soil microbial communities.

    PubMed

    Stefanis, Christos; Alexopoulos, Athanasios; Voidarou, Chrissa; Vavias, Stavros; Bezirtzoglou, Eugenia

    2013-01-01

    Soil microbial populations play crucial role in soil properties and influence below-ground ecosystem processes. Microbial composition and functioning changes the soil quality through decomposition of organic matter, recycling of nutrients, and biological control of parasites of plants. Moreover, the discovery that soil microbes may translate into benefits for biotechnology, management of agricultural, forest, and natural ecosystems, biodegradation of pollutants, and waste treatment systems maximized the need of scientists for the isolation and their characterization. Operations such as the production of antibiotics and enzymic activities from microorganisms of soil constitute objectives of industry in her effort to cope with the increase of population of earth and disturbance of environment and may ameliorate the effects of global climate change. In the past decades, new biochemical and molecular techniques have been developed in our effort to identify and classify soil bacteria. The goal of measuring the soil microbial diversity is difficult because of the limited knowledge about bacteria species and classification through families and orders. Molecular techniques extend our knowledge about microbial diversity and help the taxonomy of species. Measuring and monitoring soil microbial communities can lead us to better understanding of their composition and function in many ecosystem processes. PMID:22791233

  9. 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. PMID:26122574

  10. 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. PMID:26631020

  11. Distinct microbial communities associated with buried soils in the Siberian tundra

    NASA Astrophysics Data System (ADS)

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Mikutta, Robert; Owens, Sarah; Gilbert, Jack; Schnecker, Jörg; Wild, Birgit; Hannisdal, Bjarte; Maerz, Joeran; Lashchinskiy, Nikolay; Čapek, Petr; Šantrůčková, Hana; Gentsch, Norman; Shibistova, Olga; Guggenberger, Georg; Richter, Andreas; Torsvik, Vigdis; Schleper, Christa; Urich, Tim

    2014-05-01

    Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze-thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.

  12. Long-term forest soil warming alters microbial communities in temperate forest soils

    PubMed Central

    DeAngelis, Kristen M.; Pold, Grace; Topçuoğlu, Begüm D.; van Diepen, Linda T. A.; Varney, Rebecca M.; Blanchard, Jeffrey L.; Melillo, Jerry; Frey, Serita D.

    2015-01-01

    Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming. PMID:25762989

  13. Different Degrees of Plant Invasion Significantly Affect the Richness of the Soil Fungal Community

    PubMed Central

    Si, Chuncan; Liu, Xueyan; Wang, Congyan; Wang, Lei; Dai, Zhicong; Qi, Shanshan; Du, Daolin

    2013-01-01

    Several studies have shown that soil microorganisms play a key role in the success of plant invasion. Thus, ecologists have become increasingly interested in understanding the ecological effects of biological invasion on soil microbial communities given continuing increase in the effects of invasive plants on native ecosystems. This paper aims to provide a relatively complete depiction of the characteristics of soil microbial communities under different degrees of plant invasion. Rhizospheric soils of the notorious invasive plant Wedelia trilobata with different degrees of invasion (uninvaded, low-degree, and high-degree using its coverage in the invaded ecosystems) were collected from five discrete areas in Hainan Province, P. R. China. Soil physicochemical properties and community structure of soil microorganisms were assessed. Low degrees of W. trilobata invasion significantly increased soil pH values whereas high degrees of invasion did not significantly affected soil pH values. Moreover, the degree of W. trilobata invasion exerted significant effects on soil Ca concentration but did not significantly change other indices of soil physicochemical properties. Low and high degrees of W. trilobata invasion increased the richness of the soil fungal community but did not pose obvious effects on the soil bacterial community. W. trilobata invasion also exerted obvious effects on the community structure of soil microorganisms that take part in soil nitrogen cycling. These changes in soil physicochemical properties and community structure of soil microbial communities mediated by different degrees of W. trilobata invasion may present significant functions in further facilitating the invasion process. PMID:24392015

  14. Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material

    USGS Publications Warehouse

    Steven, Blaire; Gallegos-Graves, La Verne; Belnap, Jayne; Kuske, Cheryl R.

    2013-01-01

    Biological soil crusts (biocrusts) are common to drylands worldwide. We employed replicated, spatially nested sampling and 16S rRNA gene sequencing to describe the soil microbial communities in three soils derived from different parent material (sandstone, shale, and gypsum). For each soil type, two depths (biocrusts, 0–1 cm; below-crust soils, 2–5 cm) and two horizontal spatial scales (15 cm and 5 m) were sampled. In all three soils, Cyanobacteria and Proteobacteria demonstrated significantly higher relative abundance in the biocrusts, while Chloroflexi and Archaea were significantly enriched in the below-crust soils. Biomass and diversity of the communities in biocrusts or below-crust soils did not differ with soil type. However, biocrusts on gypsum soil harbored significantly larger populations of Actinobacteria and Proteobacteria and lower populations of Cyanobacteria. Numerically dominant operational taxonomic units (OTU; 97% sequence identity) in the biocrusts were conserved across the soil types, whereas two dominant OTUs in the below-crust sand and shale soils were not identified in the gypsum soil. The uniformity with which small-scale vertical community differences are maintained across larger horizontal spatial scales and soil types is a feature of dryland ecosystems that should be considered when designing management plans and determining the response of biocrusts to environmental disturbances.

  15. Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material.

    PubMed

    Steven, Blaire; Gallegos-Graves, La Verne; Belnap, Jayne; Kuske, Cheryl R

    2013-10-01

    Biological soil crusts (biocrusts) are common to drylands worldwide. We employed replicated, spatially nested sampling and 16S rRNA gene sequencing to describe the soil microbial communities in three soils derived from different parent material (sandstone, shale, and gypsum). For each soil type, two depths (biocrusts, 0-1 cm; below-crust soils, 2-5 cm) and two horizontal spatial scales (15 cm and 5 m) were sampled. In all three soils, Cyanobacteria and Proteobacteria demonstrated significantly higher relative abundance in the biocrusts, while Chloroflexi and Archaea were significantly enriched in the below-crust soils. Biomass and diversity of the communities in biocrusts or below-crust soils did not differ with soil type. However, biocrusts on gypsum soil harbored significantly larger populations of Actinobacteria and Proteobacteria and lower populations of Cyanobacteria. Numerically dominant operational taxonomic units (OTU; 97% sequence identity) in the biocrusts were conserved across the soil types, whereas two dominant OTUs in the below-crust sand and shale soils were not identified in the gypsum soil. The uniformity with which small-scale vertical community differences are maintained across larger horizontal spatial scales and soil types is a feature of dryland ecosystems that should be considered when designing management plans and determining the response of biocrusts to environmental disturbances. PMID:23621290

  16. Microbial dynamics and arsenic speciation in rice paddy soil under two water management practices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Arsenic (As) undergoes several microbial transformations, including oxidation/reduction, methylation/demethylation, and volatilization in soil, which impact As bioavailability. Different water management systems for rice cultivation alter soil-redox conditions and As biogeochemistry. Soil microbial ...

  17. The Effect of Biochar and Its Interaction with the Earthworm Pontoscolex corethrurus on Soil Microbial Community Structure in Tropical Soils

    PubMed Central

    Paz-Ferreiro, Jorge; Liang, Chenfei; Fu, Shenglei; Mendez, Ana; Gasco, Gabriel

    2015-01-01

    Biochar effects on soil microbial abundance and community structure are keys for understanding the biogeochemical cycling of nutrients and organic matter turnover, but are poorly understood, in particular in tropical areas. We conducted a greenhouse experiment in which we added biochars produced from four different feedstocks [sewage sludge (B1), deinking sewage sludge (B2), Miscanthus (B3) and pine wood (B4)] at a rate of 3% (w/w) to two tropical soils (an Acrisol and a Ferralsol) planted with proso millet (Panicum milliaceum L.). The interactive effect of the addition of earthworms was also addressed. For this purpose we utilized soil samples from pots with or without the earthworm Pontoscolex corethrurus, which is a ubiquitous earthworm in tropical soils. Phospholipid fatty acid (PLFA) measurements showed that biochar type, soil type and the presence of earthworms significantly affected soil microbial community size and structure. In general, biochar addition affected fungal but not bacterial populations. Overall, biochars rich in ash (B1 and B2) resulted in a marked increase in the fungi to bacteria ratio, while this ratio was unaltered after addition of biochars with a high fixed carbon content (B3 and B4). Our study remarked the contrasting effect that both, biochar prepared from different materials and macrofauna, can have on soil microbial community. Such changes might end up with ecosystem-level effects. PMID:25898344

  18. The effect of biochar and its interaction with the earthworm Pontoscolex corethrurus on soil microbial community structure in tropical soils.

    PubMed

    Paz-Ferreiro, Jorge; Liang, Chenfei; Fu, Shenglei; Mendez, Ana; Gasco, Gabriel

    2015-01-01

    Biochar effects on soil microbial abundance and community structure are keys for understanding the biogeochemical cycling of nutrients and organic matter turnover, but are poorly understood, in particular in tropical areas. We conducted a greenhouse experiment in which we added biochars produced from four different feedstocks [sewage sludge (B1), deinking sewage sludge (B2), Miscanthus (B3) and pine wood (B4)] at a rate of 3% (w/w) to two tropical soils (an Acrisol and a Ferralsol) planted with proso millet (Panicum milliaceum L.). The interactive effect of the addition of earthworms was also addressed. For this purpose we utilized soil samples from pots with or without the earthworm Pontoscolex corethrurus, which is a ubiquitous earthworm in tropical soils. Phospholipid fatty acid (PLFA) measurements showed that biochar type, soil type and the presence of earthworms significantly affected soil microbial community size and structure. In general, biochar addition affected fungal but not bacterial populations. Overall, biochars rich in ash (B1 and B2) resulted in a marked increase in the fungi to bacteria ratio, while this ratio was unaltered after addition of biochars with a high fixed carbon content (B3 and B4). Our study remarked the contrasting effect that both, biochar prepared from different materials and macrofauna, can have on soil microbial community. Such changes might end up with ecosystem-level effects. PMID:25898344

  19. Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

    PubMed

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. PMID:27100017

  20. Microbial ecology and transformations associated with munitions contaminated soils

    SciTech Connect

    Martin, J.L.; Li, Z.; Kokjohn, T.A.; Shea, P.J.; Comfort, S.D.

    1994-12-31

    Many acres of soil at the former Nebraska Ordnance Plant (NOP) are contaminated with TNT and other munitions residues. In some areas, solid phase TNT is present and controls the concentration of the soil solution. Native microbial populations in uncontaminated soils similar to those at the NOP site were severely reduced when solid phase TNT was allowed to control the soil solution TNT concentration. However, examination of NOP soil revealed an active population of Pseudomonas sp. A single species that could utilize TNT as a sole C source was isolated from the contaminated soil and tentatively identified as Pseudomonas corrugata through the BIOLOG system. Subsequent growth and characterization experiments indicate that the Pseudomonad metabolizes TNT while in the exponential phase of growth in medium containing glucose as a sole N source. Low TNT mineralization rates (measured by CO{sub 2} evolution) in soil and media using the various isolates suggest reduced availability due to sorption and incorporation of transformation intermediates into the organic matrix and microbial biomass. Pretreatment of TNT by acid-metal catalyzed reduction resulted in an initially higher rate of mineralization following addition to TNT-contaminated soil. Observations indicate more rapid microbial utilization of the 2,4,6-triaminotoluene (TAT) reduction product and its spontaneous decay product, methylphloroglucinol (2,4,6-trihydroxytoluene), than TNT. Abiotic pretreatment may be useful in enhancing microbial transformation and detoxification of TNT in highly contaminated soils.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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 ((14)C-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

  3. 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

  4. 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

  5. Impact of Fungicide Mancozeb at Different Application Rates on Soil Microbial Populations, Soil Biological Processes, and Enzyme Activities in Soil

    PubMed Central

    Mehta, Preeti; Guleria, Shiwani; Chauhan, Anjali; Shirkot, C. K.

    2014-01-01

    The use of fungicides is the continuous exercise particularly in orchard crops where fungal diseases, such as white root rot, have the potential to destroy horticultural crops rendering them unsaleable. In view of above problem, the present study examines the effect of different concentrations of mancozeb (0–2000 ppm) at different incubation periods for their harmful side effects on various microbiological processes, soil microflora, and soil enzymes in alluvial soil (pH 6.8) collected from apple orchards of Shimla in Himachal Pradesh (India). Low concentrations of mancozeb were found to be deleterious towards fungal and actinomycetes population while higher concentrations (1000 and 2000 ppm) were found to be detrimental to soil bacteria. Mancozeb impaired the process of ammonification and nitrification. Similar results were observed for nitrifying and ammonifying bacteria. Phosphorus solubilization was increased by higher concentration of mancozeb, that is, 250 ppm and above. In unamended soil, microbial biomass carbon and carbon mineralization were adversely affected by mancozeb. Soil enzymes, that is, amylase, invertase, and phosphatase showed adverse and disruptive effect when mancozeb used was above 10 ppm in unamended soil. These results conclude that, to lessen the harmful effects in soil biological processes caused by this fungicide, addition of higher amount of nitrogen based fertilizers is required. PMID:25478598

  6. Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Ali; Or, Dani

    2015-12-01

    The constantly changing soil hydration status affects gas and nutrient diffusion through soil pores and thus the functioning of soil microbial communities. The conditions within soil aggregates are of particular interest due to limitations to oxygen diffusion into their core, and the presence of organic carbon often acting as binding agent. We developed a model for microbial life in simulated soil aggregates comprising of 3-D angular pore network model (APNM) that mimics soil hydraulic and transport properties. Within these APNM, we introduced individual motile (flagellated) microbial cells with different physiological traits that grow, disperse, and respond to local nutrients and oxygen concentrations. The model quantifies the dynamics and spatial extent of anoxic regions that vary with hydration conditions, and their role in shaping microbial community size and activity and the spatial (self) segregation of anaerobes and aerobes. Internal carbon source and opposing diffusion directions of oxygen and carbon within an aggregate were essential to emergence of stable coexistence of aerobic and anaerobic communities (anaerobes become extinct when carbon sources are external). The model illustrates a range of hydration conditions that promote or suppress denitrification or decomposition of organic matter and thus affect soil GHG emissions. Model predictions of CO2 and N2O production rates were in good agreement with limited experimental data. These limited tests support the dynamic modeling approach whereby microbial community size, composition, and spatial arrangement emerge from internal interactions within soil aggregates. The upscaling of the results to a population of aggregates of different sizes embedded in a soil profile is underway.

  7. Microbial biomass as a significant source of soil organic matter

    NASA Astrophysics Data System (ADS)

    Miltner, Anja; Kindler, Reimo; Schweigert, Michael; Achtenhagen, Jan; Bombach, Petra; Fester, Thomas; Kästner, Matthias

    2014-05-01

    Soil organic matter (SOM) plays an important role for soil fertility and in the global carbon cycle. SOM management should be based on knowledge about the chemical composition as well as the spatial distribution of SOM and its individual components in soils. Both parameters strongly depend on the direct precursors of SOM. In the past, microbial biomass has been neglected as a potential source of SOM, mainly because of its small pool size. Recent studies, however, show that a substantial portion of SOM is derived from microbial biomass residues. We therefore investigated the fate of microbial biomass residues in soils by means of incubation experiments with 13C-labelled microbial biomass. For our studies, we selected model organisms representing the three types of soil microorganisms and their characteristic cell wall structures: Escherichia coli (a Gram-negative bacterium), Bacillus subtilis (a Gram-positive bacterium) and Laccaria bicolor (an ectomycorrhizal fungus). We labelled the organisms by growing them on 13C glucose and incubated them in soil. During incubation, we followed the mineralisation of the labelled C, its incorporation into microbial biomass, and its transformation to non-living SOM. We found that 50-65% of the microbial biomass C remained in the soil during incubation. However, only a small part remained in the microbial biomass, the majority was transformed to SOM. In particular, proteins seemed to be rather stable in our experiments. In addition, we used scanning electron microscopy to identify microbial residues in soils and, for comparison, in artificial groundwater microcosms. Scanning electron micrographs showed a low number of intact cells, but mainly fragments of about 200-500 nm size. Similar fragments were found in artificial groundwater microcosms where the only possible origin was microbial biomass residues. Based on the results obtained, we provide a mechanistic model which explains how microbial biomass residues are formed and

  8. Response of soil microbial community composition to afforestation with pure and mixed tree species

    NASA Astrophysics Data System (ADS)

    Gunina, Anna; Smith, Andrew; Godbold, Douglas; Kuzyakov, Yakov; Jones, Davey

    2016-04-01

    Afforestation of agricultural land affects soil ecosystem functions by inducing carbon (C) and nitrogen (N) sequestration and promoting shifts in microbial community structure. Soil C and N stocks undergo progressive changes over several decades after forest establishment, particularly in successional forests. In contrast, microbial community structure can be shifted already in the first decade and thus, direct effect of tree species can be revealed. Thus, the aim of this study was to determine how soil microbial community composition is altered by afforestation with either one, two or three species mixtures of trees, which possess strongly contrasting functional traits. The study was conducted at the BangorDIVERSE temperate forest experiment established in 2004 on a former arable soil. Soil samples were collected under single, two and three species mixtures of alder, birch, beech and oak, while contiguous field was chosen as a control. Soil samples were analysed for key quality indicators (total C and N, pH, nitrate and ammonium), and microbial community structure was determined by phospholipid fatty acids (PLFAs) analysis. Ten years after afforestation, total soil C, N and C/N ratios were not strongly affected, with the highest positive changes (up to 20%) for the birch, alder+oak and birch+beech plots. Decrease of C and N contents were observed for the pure beech plot. pH decreased by 1-1.2 units for all forest plots compare to the control soil. Total PLFAs content (370-630 nmol g‑1 soil) increased in comparison to the control (315 nmol g‑1 soil), resulting in the changes in total PLFAs content from 20 to 100%. Thus, changes of chemical properties (C, N) occur slower than changes of microbial biomarkers at the early stage of afforestation. Bacterial PLFA content was shifted by 20-120%, whereas fungal PLFAs were changed by 50-300%, reflecting stronger impact of afforestation on the recovery of fungal communities than on bacterial. Principal component analysis

  9. Spatial Variation in Anaerobic Microbial Communities in Wetland Margin Soils

    NASA Astrophysics Data System (ADS)

    Rich, H.; Kannenberg, S.; Ludwig, S.; Nelson, L. C.; Spawn, S.; Porterfield, J.; Schade, J. D.

    2012-12-01

    Climate change is predicted to increase the severity and frequency of precipitation and drought events, which may result in substantial temporal variation in the size of wetlands. Wetlands are the world's largest natural emitter of methane, a greenhouse gas that is 20 times more effective at trapping heat than carbon dioxide. Changes in the dynamics of wetland size may lead to changes in the extent and timing of inundation of soils in ephemeral margins, which is likely to influence microbes that rely on anoxic conditions. The impact on process rates may depend on the structure of the community of microbes present in the soil, however, the link between microbial structure and patterns in process rates in soils is not well understood. Our goal was to use molecular techniques to compare microorganism communities in two wetlands that differ in the extent and duration of inundation of marginal soils to assess how these communities may change with changes in climate, and the potential consequences for methane production. This will allow us to examine how community composition changes with soil conditions such as moisture content, frequency of drought and abundance of available carbon. The main focus of this project was to determine the presence or absence of acetoclastic (AC) and hydrogenotrophic (HT) methanogens. AC methanogens use acetate as their main substrate, while HT methanogens use Hydrogen and Carbon dioxide. The relative proportion of these pathways depends on soil conditions, such as competition with other anaerobic microbes and the amount of labile carbon, and spatial patterns in the presence of each can give insight into the soil conditions of a wetland site. We sampled soil from three different wetland ponds of varying permanence in the St Olaf Natural Lands in Northfield, Minnesota, and extracted DNA from these soil samples with a MoBio PowerSoil DNA Isolation Kit. With PCR and seven different primer sets, we tested the extracted DNA for the presence of

  10. Microbial community composition of transiently wetted Antarctic Dry Valley soils

    PubMed Central

    Niederberger, Thomas D.; Sohm, Jill A.; Gunderson, Troy E.; Parker, Alexander E.; Tirindelli, Joëlle; Capone, Douglas G.; Carpenter, Edward J.; Cary, Stephen C.

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm3 for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas. PMID:25674080

  11. Soil microbes and plant invasions—how soil-borne pathogens regulate plant populations and affect plant invasions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Exotic plant invaders are a major global threat to biodiversity and ecosystem function. Here I present multiple lines of evidence suggesting that soil microbial communities affect the population growth rates of Prunus serotina in its native range and affect its invasiveness abroad. Research often ...

  12. EFFECTS OF COVER CROPPING AND PLASTICULTURE ON SOIL AND RHIZOSPHERE MICROBIAL COMMUNITY STRUCTURE IN TOMATO PRODUCTION SYSTEMS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In a previous study (Carrera et al., submitted for publication) we found that soil microbial community structure was distinctly different under black polyethylene film than under hairy vetch cover crops in tomato production systems. In order to determine the major factors affecting microbial communi...

  13. EFFECTS OF COVER CROPPING AND PLASTICULTURE ON SOIL AND RHIZOSPHERE MICROBIAL COMMUNITY STRUCTURE IN TOMATO PRODUCTION SYSTEMS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In a previous study (Carrera et al., submitted for publication) we found that soil microbial community structure was distinctly different under plasticulture than under hairy vetch cover crops in tomato production systems. In order to determine the major factors affecting microbial communities we se...

  14. Long-Term Effects of Multiwalled Carbon Nanotubes and Graphene on Microbial Communities in Dry Soil.

    PubMed

    Ge, Yuan; Priester, John H; Mortimer, Monika; Chang, Chong Hyun; Ji, Zhaoxia; Schimel, Joshua P; Holden, Patricia A

    2016-04-01

    Little is known about the long-term effects of engineered carbonaceous nanomaterials (ECNMs) on soil microbial communities, especially when compared to possible effects of natural or industrial carbonaceous materials. To address these issues, we exposed dry grassland soil for 1 year to 1 mg g(-1) of either natural nanostructured material (biochar), industrial carbon black, three types of multiwalled carbon nanotubes (MWCNTs), or graphene. Soil microbial biomass was assessed by substrate induced respiration and by extractable DNA. Bacterial and fungal communities were examined by terminal restriction fragment length polymorphism (T-RFLP). Microbial activity was assessed by soil basal respiration. At day 0, there was no treatment effect on soil DNA or T-RFLP profiles, indicating negligible interference between the amended materials and the methods for DNA extraction, quantification, and community analysis. After a 1-year exposure, compared to the no amendment control, some treatments reduced soil DNA (e.g., biochar, all three MWCNT types, and graphene; P < 0.05) and altered bacterial communities (e.g., biochar, carbon black, narrow MWCNTs, and graphene); however, there were no significant differences across the amended treatments. These findings suggest that ECNMs may moderately affect dry soil microbial communities but that the effects are similar to those from natural and industrial carbonaceous materials, even after 1-year exposure. PMID:26962674

  15. Integrating microbial diversity in soil carbon dynamic models parameters

    NASA Astrophysics Data System (ADS)

    Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

    2015-04-01

    Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten

  16. MICROBIAL COMMUNITY STRUCTURE AND ENZYME ACTIVITIES IN SEMIARID AGRICULTURAL SOILS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effect of management on the microbial community structure and enzyme activities of three semiarid soils from Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in cotton -peanut (Arachis h...

  17. Development of soil microbial communities during tallgrass prairie restoration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil microbial communities were examined in a chronosequence of four different land-use treatments at the Konza Prairie Biological Station, Kansas. The time series comprised a conventionally tilled cropland (CTC) developed on former prairie soils, two restored grasslands that were initiated on forme...

  18. Measurements of microbial community activities in individual soil macroaggregates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for ß-glucosidase, N-acetyl-ß-D-glucosaminidase, lipase, and leucine...

  19. Soil microbial communities following bush removal in a Namibian savanna

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Savanna ecosystems are subject to desertification and bush encroachment, which reduce the grazing value of the land and hence the carrying capacity for wildlife and livestock. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil at a chronose...

  20. Microbial functional diversity in a mediterranean forest soil: impact of soil nitrogen availability

    NASA Astrophysics Data System (ADS)

    Dalmonech, D.; Lagomarsino, A.; Moscatelli, M. C.

    2009-04-01

    Beneficial or negative effects of N deposition on forest soil are strongly linked to the activity of microbial biomass and enzyme activities because they regulate soil quality and functioning due to their involvement in organic matter dynamics, nutrient cycling and decomposition processes. Moreover, because the ability of an ecosystem to withstand serious disturbances may depend in part on the microbial component of the system, by characterizing microbial functional diversity we may be able to better understand and manipulate ecosystem processes. Changes in the biodiversity of the soil microbial community are likely to be important in relation to maintenance of soil ecosystem function because the microbial communities influence the potential of soils for enzyme-mediated substrate catalysis. Objective of this study was to evaluate how soil N availability affected microbial functional diversity in a 4 months laboratory experiment. The incubation experiment was carried out with an organo-mineral soil collected in a Quercus cerris forest at the Roccarespampani site (Central Italy, Viterbo). All samples were incubated at 28°C and were kept to a water content between 55 and 65% of the water holding capacity. Different amount of N (NH4NO3) were added as solution once a week in order to mimic the N wet deposition and to let microbial community deal with a slow increase in time of inorganic N content. The amount of nutrient solutions was chosen depending on the average soil-water loss due to evaporation in one week. The total amount of N-NH4NO3 was chosen to be comparable with the range of N depositions currently reported in European forests, i.e. between 1 and 75 kg N ha-1 y-1. The total amount added at the end of incubation varied from 0, 10, 25, 50 and 75 kg N ha-1. Distilled water was added in the control soil in order to provide the same amount of solution as the treated soils. In order to discriminate the effect of N, the NH4NO3 solutions were adjusted to soil pH and

  1. Soil microbial community function, structure, and glomalin in response to tall fescue endophyte infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tall fescue [Lolium arundinaceum (Schreb.) S.J. Darbyshire] is naturally infected with a fungal endophyte, Neotyphodium coenophialum, which produces toxic ergot alkaloids that negatively affect herbivores and may alter soil microbial communities. A 60-week mesocosm study with a factorial arrangemen...

  2. Soil microbial responses to a subambient to elevated gradient of atmospheric CO2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increasing atmospheric CO2 has been shown to significantly affect terrestrial ecosystems through increased primary production. This response is thought to be mitigated by changes to the soil microbial community, which can alter nutrient availability in these systems. In this study we examine the e...

  3. Combined effects of cadmium and butachlor on soil enzyme activities and microbial community structure

    NASA Astrophysics Data System (ADS)

    Wang, Jinhua; Lu, Yitong; Shen, Guoqing

    2007-02-01

    The combined effects of cadmium (Cd, 10 mg/kg of soil) and butachlor (5, 10 and 50 mg/kg of soil) on enzyme activities and microbial community structure were assessed in phaeozem soil. The result showed that phosphatase activities were decreased in soils with Cd (10 mg/kg of soil) alone whereas urease acitivities were unaffected by Cd. Urease and phosphatase activities were significantly reduced by high butachlor concentration (50 mg/kg of soil). When Cd and butachlor concentrations in soils were added at milligram ratio of 2:1 or 1:2, urease and phosphatase activities were decreased, while enzyme activities were greatly improved at the ratio of 1:5. This study indicates that the combined effects of Cd and butachlor on soil urease and phosphatase activities depend largely on the addition concentration ratios to soils. The random amplified polymorphic DNA (RAPD) analysis showed that the changes occurring in RAPD profiles of different treated samples included variation in loss of normal bands and appearance of new bands compared with the control soil. The RAPD fingerprints showed substantial differences between the control and treated soil samples, with apparent changes in the number and size of amplified DNA fragments. The results showed that the addition of high concentration butachlor and the combined applied Cd and butachlor significantly affected the diversity of microbial community. The present results suggest that RAPD analysis in conjunction with other biomarkers such as soil enzyme parameter etc. would prove a powerful ecotoxicological tool.

  4. Relationships between soil microbial communities and soil carbon turnover along a vegetation and moisture gradient in interior Alaska

    NASA Astrophysics Data System (ADS)

    Waldrop, M. P.; Harden, J. W.; Turetsky, M. R.; Petersen, D. G.; McGuire, A. D.; Briones, M. J.; Churchill, A. C.; Doctor, D. H.; Pruett, L. E.

    2010-12-01

    Boreal landscapes are characterized by a mosaic of uplands and lowlands, which differ in plant species composition, litter biochemistry, and biogeochemical cycling rates. Boreal ecosystems, from upland black spruce stands to lowland fens, are structured largely by water table position and contain quantitatively and qualitatively different forms of soil organic matter. Differences in carbon (C) availability among ecosystems likely translate to differences in the structure of soil microbial communities, which in turn could affect rates of organic matter decomposition and turnover. We examined relationships between microbial communities and soil C turnover in near-surface soils along a topographic soil moisture and vegetation gradient in interior Alaska. We tested the hypothesis that upland black spruce sites would be dominated by soil fungi and have slow rates of C turnover, whereas lowland ecosystems would be dominated by bacteria and mesofauna (enchytraeids) and have more rapid rates of C turnover. We utilized several isotopic measures of soil C turnover including bomb radiocarbon techniques, the δ15N of SOM, and the difference between δ13C of SOM, DOC, and respired CO2. All three measures indicated greater C turnover rates in the surface soils of the lowland fen sites compared to the more upland locations. Quantitative PCR analyses of soil bacteria and archaea, combined with enchytraed counts, confirmed that surface soils from the lowland fen ecosystems had the highest abundances of these functional groups. Fungal biomass was highly variable and tended to be more abundant in the upland forest sites. Soil enzymatic results were mixed: potential cellulase activities were higher in the more upland soils even though rates of microbial activity were generally lower. Oxidative enzyme activities were higher in fens, even though these ecosystems are saturated and partly anaerobic. Overall our data support soil food web theory which argues that rapidly cycling systems

  5. Microbial ecology and biogeochemistry of continental Antarctic soils

    PubMed Central

    Cowan, Don A.; Makhalanyane, Thulani P.; Dennis, Paul G.; Hopkins, David W.

    2014-01-01

    The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities. PMID:24782842

  6. Evaluation of pasture soil productivity in the semi-arid zone of Brazil by microbial analyses

    PubMed Central

    de Luna, Rômulo Gil; Coutinho, Henrique Douglas Melo; Grisi, Breno Machado

    2008-01-01

    The productivity of a pasture soil (caatinga) located in the region of São João do Cariri, PB, Brazil was evaluated based an the following microbiological parameters: biomass (measured by fumigation-incubation method), activity (estimated from basal respiration and cellulose decomposition rate), qCO2, and Cmic : Corg ratio. This analysis demonstrated that livestock management in the ‘caatinga’ is probably causing environment damage by affecting the soil properties, reducing the microbial biomass and soil respiration and increasing the qCO2, affecting the recovery of this ecosystem. PMID:24031238

  7. Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities.

    PubMed

    Deng, Ye; He, Zhili; Xiong, Jinbo; Yu, Hao; Xu, Meiying; Hobbie, Sarah E; Reich, Peter B; Schadt, Christopher W; Kent, Angela; Pendall, Elise; Wallenstein, Matthew; Zhou, Jizhong

    2016-02-01

    Although elevated CO2 (eCO2 ) significantly affects the α-diversity, composition, function, interaction and dynamics of soil microbial communities at the local scale, little is known about eCO2 impacts on the geographic distribution of micro-organisms regionally or globally. Here, we examined the β-diversity of 110 soil microbial communities across six free air CO2 enrichment (FACE) experimental sites using a high-throughput functional gene array. The β-diversity of soil microbial communities was significantly (P < 0.05) correlated with geographic distance under both CO2 conditions, but declined significantly (P < 0.05) faster at eCO2 with a slope of -0.0250 than at ambient CO2 (aCO2 ) with a slope of -0.0231 although it varied within each individual site, indicating that the spatial turnover rate of soil microbial communities was accelerated under eCO2 at a larger geographic scale (e.g. regionally). Both distance and soil properties significantly (P < 0.05) contributed to the observed microbial β-diversity. This study provides new hypotheses for further understanding their assembly mechanisms that may be especially important as global CO2 continues to increase. PMID:26414247

  8. Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators.

    PubMed

    Trivedi, Pankaj; Delgado-Baquerizo, Manuel; Anderson, Ian C; Singh, Brajesh K

    2016-01-01

    Agricultural intensification is placing tremendous pressure on the soil's capacity to maintain its functions leading to large-scale ecosystem degradation and loss of productivity in the long term. Therefore, there is an urgent need to find early indicators of soil health degradation in response to agricultural management. In recent years, major advances in soil meta-genomic and spatial studies on microbial communities and community-level molecular characteristics can now be exploited as 'biomarker' indicators of ecosystem processes for monitoring and managing sustainable soil health under global change. However, a continental scale, cross biome approach assessing soil microbial communities and their functional potential to identify the unifying principles governing the susceptibility of soil biodiversity to land conversion is lacking. We conducted a meta-analysis from a dataset generated from 102 peer-reviewed publications as well as unpublished data to explore how properties directly linked to soil nutritional health (total C and N; C:N ratio), primary productivity (NPP) and microbial diversity and composition (relative abundance of major bacterial phyla determined by next generation sequencing techniques) are affected in response to agricultural management across the main biomes of Earth (arid, continental, temperate and tropical). In our analysis, we found strong statistical trends in the relative abundance of several bacterial phyla in agricultural (e.g., Actinobacteria and Chloroflexi) and natural (Acidobacteria, Proteobacteria, and Cyanobacteria) systems across all regions and these trends correlated well with many soil properties. However, main effects of agriculture on soil properties and productivity were biome-dependent. Our meta-analysis provides evidence on the predictable nature of the microbial community responses to vegetation type. This knowledge can be exploited in future for developing a new set of indicators for primary productivity and soil

  9. 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. PMID:27100015

  10. Recovery of Soil Microbial Community Structure in a Wildfire Impacted Forest Soil

    NASA Astrophysics Data System (ADS)

    Tate, Robert, III; Mikita, Robyn

    2010-05-01

    between the biological and physical variables. The bacterial community in the mineral layer soil samples from 2 and 5 months after the fire were positively correlated with soil copper and iron concentrations. Molecular analysis of the soil archaeal community revealed that while the unburned and burned samples share common bands, the samples from the unburned site clustered separately from those of the burned site collected 2, 13, and 25 months after the fire. The identities of the dominant phylotypes are being further evaluated. The results will bring insight into how disturbances associated with the changing climate affect belowground microbial ecology.

  11. Microbial decomposer communities in Alaskan permafrost soils and their response to thaw

    NASA Astrophysics Data System (ADS)

    Waldrop, M. P.; Wickland, K.; Harden, J.; Striegl, R.; Aiken, G.

    2007-12-01

    Permafrost protected soil carbon in boreal forest ecosystems represents a significant portion of the approximately 500 Gt C in the soil organic matter of boreal regions. The magnitude of this thermally-protected carbon pool makes it a particularly important to the global C cycle within the context of global climatic change. Permafrost has acted as a C sink for thousands of years yet currently has been warming at a rate of 1°C per decade, making the C contained within it potentially available for decomposition. Thawing permafrost opens a latch into a globally important C reservoir that could be released to the atmosphere (as CO2) and rivers (as dissolved organic carbon, DOC), affecting greenhouse warming and aquatic chemistry. A gap in our current knowledge is the extent to which permafrost-protected C is available for microbial metabolism once soils thaw. Current indications are that organic matter contained within permafrost is relatively labile since it is not protected from decomposition by physical protection or humification mechanisms. However, we have little understanding of the microbiology of permafrost soils, which could significantly affect the rate of decomposition of permafrost C after thaw. Our aim was to use quantitative molecular techniques to examine the abundance of microbial decomposer functional groups in permafrost soils, the enzymes they encode, and their rates of respiration under both aerobic and anaerobic conditions in a simulated summer thaw at 5°C. We compared microbial and chemical characteristics of active layer and permafrost soils from black spruce stands in three distinct geographic regions: Coldfoot, Hess Creek, and Smith Lake, AK. We chose these regions because they span a range of permafrost conditions from shallow active layers and mineral-associated permafrost layers to thick active layers and deep organic permafrost soils. Soil carbon and nitrogen concentrations did not differ between active layer and permafrost soils within

  12. Soil moisture and land use are major determinants of soil microbial community composition and biomass at a regional scale in northeastern China

    NASA Astrophysics Data System (ADS)

    Ma, L.; Guo, C.; Lü, X.; Yuan, S.; Wang, R.

    2015-04-01

    Global environmental factors impact soil microbial communities and further affect organic matter decomposition, nutrient cycling and vegetation dynamic. However, little is known about the relative contributions of climate factors, soil properties, vegetation types, land management practices and spatial structure (which serves as a proxy for underlying effects of temperature and precipitation for spatial variation) on soil microbial community composition and biomass at large spatial scales. Here, we compared soil microbial communities using phospholipid fatty acid method across 7 land use types from 23 locations at a regional scale in northeastern China (850 × 50 km). The results showed that soil moisture and land use changes were most closely related to microbial community composition and biomass at the regional scale, while soil total C content and climate effects were weaker but still significant. Factors such as spatial structure, soil texture, nutrient availability and vegetation types were not important. Higher contributions of gram-positive bacteria were found in wetter soils, whereas higher contributions of gram-negative bacteria and fungi were observed in drier soils. The contributions of gram-negative bacteria and fungi were lower in heavily disturbed soils than historically disturbed and undisturbed soils. The lowest microbial biomass appeared in the wettest and driest soils. In conclusion, dominant climate and soil properties were not the most important drivers governing microbial community composition and biomass because of inclusion of irrigated and managed practices, and thus soil moisture and land use appear to be primary determinants of microbial community composition and biomass at the regional scale in northeastern China.

  13. Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration

    NASA Astrophysics Data System (ADS)

    Alster, Charlotte J.; Koyama, Akihiro; Johnson, Nels G.; Wallenstein, Matthew D.; Fischer, Joseph C.

    2016-06-01

    There is compelling evidence that microbial communities vary widely in their temperature sensitivity and may adapt to warming through time. To date, this sensitivity has been largely characterized using a range of models relying on versions of the Arrhenius equation, which predicts an exponential increase in reaction rate with temperature. However, there is growing evidence from laboratory and field studies that observe nonmonotonic responses of reaction rates to variation in temperature, indicating that Arrhenius is not an appropriate model for quantitatively characterizing temperature sensitivity. Recently, Hobbs et al. (2013) developed macromolecular rate theory (MMRT), which incorporates thermodynamic temperature optima as arising from heat capacity differences between isoenzymes. We applied MMRT to measurements of respiration from soils incubated at different temperatures. These soils were collected from three grassland sites across the U.S. Great Plains and reciprocally transplanted, allowing us to isolate the effects of microbial community type from edaphic factors. We found that microbial community type explained roughly 30% of the variation in the CO2 production rate from the labile C pool but that temperature and soil type were most important in explaining variation in labile and recalcitrant C pool size. For six out of the nine soil × inoculum combinations, MMRT was superior to Arrhenius. The MMRT analysis revealed that microbial communities have distinct heat capacity values and temperature sensitivities sometimes independent of soil type. These results challenge the current paradigm for modeling temperature sensitivity of soil C pools and understanding of microbial enzyme dynamics.

  14. Soil microbial communities following bush removal in a Namibian savanna

    NASA Astrophysics Data System (ADS)

    Buyer, Jeffrey S.; Schmidt-Küntzel, Anne; Nghikembua, Matti; Maul, Jude E.; Marker, Laurie

    2016-03-01

    Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

  15. Soil microbial communities following bush removal in a Namibian savanna

    NASA Astrophysics Data System (ADS)

    Buyer, J. S.; Schmidt-Küntzel, A.; Nghikembua, M.; Maul, J. E.; Marker, L.

    2015-12-01

    Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

  16. [Soil microbial functional diversity of different altitude Pinus koraiensis forests].

    PubMed

    Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan

    2015-12-01

    In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity. PMID:27112001

  17. Effects of assimilate supply on root and microbial components of soil respiration in a mountain grassland.

    NASA Astrophysics Data System (ADS)

    Schmitt, M.; Siegwolf, R.; Ekblad, A.; Pfahringer, N.; Bahn, M.

    2012-04-01

    Soil respiration is the main source of carbon emitted from terrestrial ecosystems. Soil CO2 originates from multiple processes, comprising respiration by plant roots, mycorrhizae and microbes in the rhizosphere, as well as respiration due to soil organic matter (SOM) decomposition. Thus, components of soil respiration have different controls and show varying responses to changing environmental conditions and to the supply of fresh assimilates from photosynthesis. For grasslands there is still little information available as to what extent root and microbial respiration respond to reduced or enhanced assimilate supply. The aim of this study was to assess effects of assimilate supply on root and microbial components of soil respiration in a temperate mountain grassland. Root and microbial components were separated and quantified by applying the Substrate Induced Respiration method (SIR) in situ using a δ13C labelled sucrose solution, and analysing δ13C of the subsequently respired CO2. Assimilate supply was modified by clipping and shading treatments, which strongly reduced photosynthetic C supply, and by applying a sucrose solution 8 days after clipping and shading. We tested the hypotheses that (1) due to a reduction of assimilate supply, soil respiration would be lower in the clipped and shaded than in the control treatment, that (2) the microbial contribution to soil respiration would be lower in the assimilate-limited than in the control treatments, and that (3) priming effects following the addition of sucrose would be stronger in shaded and mowed treatments than in control plots. Our results showed that clipping and shading reduced soil respiration significantly. Whilst the microbial contribution to soil respiration was 61% in control plots, it amounted to only 50-48% in clipped and shaded plots, respectively. Sucrose application did not affect root respiration in any of the plots, but generally stimulated microbial respiration. The measured priming effect

  18. Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils using ''Omics''

    SciTech Connect

    Myrold, David D.; Bottomely, Peter J.; Jumpponen, Ari; Rice, Charles W.; Zeglin, Lydia H.; David, Maude M.; Jansson, Janet K.; Prestat, Emmanuel; Hettich, Robert L.

    2014-09-17

    Soils process and store large amounts of C; however, considerable uncertainty still exists about the details of that influence microbial partitioning of C into soil C pools, and what are the main influential forces that control the fraction of the C input that is stabilized. The soil microbial community is genotypically and phenotypically diverse. Despite our ability to predict the kinds of regional environmental changes that will accompany global climate change, it is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C deposited into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts genotypically and physiologically to changes in soil moisture brought about by shifts in precipitation. Our overarching goal is to harness the power of multiple meta-omics tools to gain greater understanding of the functioning of whole-soil microbial communities and their role in C cycling. We will do this by meeting the following three objectives: 1. Further develop and optimize a combination of meta-omics approaches to study how environmental factors affect microbially-mediated C cycling processes. 2. Determine the impacts of long-term changes in precipitation timing on microbial C cycling using an existing long-term field manipulation of a tallgrass prairie soil. 3. Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes. We took advantage of our state-of-the-art expertise in community “omics” to better understand the functioning soil C cycling within the Great Prairie ecosystem, including our ongoing Konza Prairie soil metagenome flagship project at JGI and the unique rainfall manipulation plots (RaMPs) established at this site more than a decade ago. We employed a systems

  19. Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes-to-Amazon elevation gradient

    PubMed Central

    Whitaker, Jeanette; Ostle, Nicholas; Nottingham, Andrew T; Ccahuana, Adan; Salinas, Norma; Bardgett, Richard D; Meir, Patrick; McNamara, Niall P; Austin, Amy

    2014-01-01

    1. The Andes are predicted to warm by 3–5 °C this century with the potential to alter the processes regulating carbon (C) cycling in these tropical forest soils. This rapid warming is expected to stimulate soil microbial respiration and change plant species distributions, thereby affecting the quantity and quality of C inputs to the soil and influencing the quantity of soil-derived CO2 released to the atmosphere. 2. We studied tropical lowland, premontane and montane forest soils taken from along a 3200-m elevation gradient located in south-east Andean Peru. We determined how soil microbial communities and abiotic soil properties differed with elevation. We then examined how these differences in microbial composition and soil abiotic properties affected soil C-cycling processes, by amending soils with C substrates varying in complexity and measuring soil heterotrophic respiration (RH). 3. Our results show that there were consistent patterns of change in soil biotic and abiotic properties with elevation. Microbial biomass and the abundance of fungi relative to bacteria increased significantly with elevation, and these differences in microbial community composition were strongly correlated with greater soil C content and C:N (nitrogen) ratios. We also found that RH increased with added C substrate quality and quantity and was positively related to microbial biomass and fungal abundance. 4. Statistical modelling revealed that RH responses to changing C inputs were best predicted by soil pH and microbial community composition, with the abundance of fungi relative to bacteria, and abundance of gram-positive relative to gram-negative bacteria explaining much of the model variance. 5. Synthesis. Our results show that the relative abundance of microbial functional groups is an important determinant of RH responses to changing C inputs along an extensive tropical elevation gradient in Andean Peru. Although we do not make an experimental test of the effects of climate

  20. Microbial Decomposition of Extracellular DNA in Clay Soils

    NASA Astrophysics Data System (ADS)

    Morrissey, E. M.; McHugh, T. A.; Schwartz, E.; Preteska, L.; Hayer, M.; Hungate, B. A.

    2014-12-01

    Genomic analysis of soil communities can only be useful in predicting ecosystem processes if the genetic data gathered is representative of the microbial community. Consequently, extracellular DNA (eDNA) represents a pool of unexpressed genetic information that may skew genomic analyses. To date, our understanding of the representation of eDNA in metagenomic data and its decomposition in soil is very limited. To address this deficit, we performed a laboratory experiment wherein soils were amended with eDNA and/or clay minerals in a full factorial design. Specifically, the decomposition of 13C labeled E. coli DNA was monitored over a 30-day period in control, Kaolinite-amended, and Montmorillonite-amended soils. The amount of added eDNA carbon (C) remaining in the soil declined exponentially over time, with the majority of decomposition occurring in the first two weeks. Kaolinite significantly decreased eDNA decomposition rates and retained a higher fraction of eDNA-C (~70% remaining) than unamended and Montmorillonite-soils (~40% remaining) after 30 days. Phylogenetic (16S rRNA) sequencing of DNA extracted over the course of the incubation period enabled detection of the added eDNA. The relative abundance of added E. coli DNA decreased ~10-100 fold over 30 days. These results indicate that while a significant fraction of eDNA-C remained in the soil, this carbon was likely no longer in the form of intact strands of DNA amenable to sequencing. In addition, the eDNA affected the composition of the bacterial community. Specifically, the relative abundance of Planctomycetes and TM7 were elevated in soils that received eDNA regardless of clay addition, suggesting these phyla may be particularly effective at degrading eDNA and using it for growth. In conclusion these results indicate that the representation of eDNA in metagenomic sequence data declines rapidly, likely due to fragmentation. However, a fraction of eDNA material was resistant to decomposition, suggesting a

  1. Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community

    PubMed Central

    Xu, Zhuofei; Hansen, Martin Asser; Hansen, Lars H.; Jacquiod, Samuel; Sørensen, Søren J.

    2014-01-01

    As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function. PMID:24691166

  2. Global biogeography of microbial nitrogen-cycling traits in soil.

    PubMed

    Nelson, Michaeline B; Martiny, Adam C; Martiny, Jennifer B H

    2016-07-19

    Microorganisms drive much of the Earth's nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little-studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N-cycling specialists or generalists. For instance, taxa within the Deltaproteobacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait-based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils. PMID:27432978

  3. Global biogeography of microbial nitrogen-cycling traits in soil

    PubMed Central

    Nelson, Michaeline B.; Martiny, Jennifer B. H.

    2016-01-01

    Microorganisms drive much of the Earth’s nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little-studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N-cycling specialists or generalists. For instance, taxa within the Deltaproteobacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait-based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils. PMID:27432978

  4. Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

    PubMed

    Xu, Zhuofei; Hansen, Martin Asser; Hansen, Lars H; Jacquiod, Samuel; Sørensen, Søren J

    2014-01-01

    As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function. PMID:24691166

  5. Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

    NASA Astrophysics Data System (ADS)

    Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

    2002-12-01

    The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

  6. Dynamics of organic matter and microbial populations in amended soil: a multidisciplinary approach

    NASA Astrophysics Data System (ADS)

    Gigliotti, Giovanni; Pezzolla, Daniela; Zadra, Claudia; Albertini, Emidio; Marconi, Gianpiero; Turchetti, Benedetta; Buzzini, Pietro

    2013-04-01

    The application of organic amendments to soils, such as pig slurry, sewage sludge and compost is considered a tool for improving soil fertility and enhancing C stock. The addition of these different organic materials allows a good supply of nutrients for plants but also contributes to C sequestration, affects the microbial activity and the transformation of soil organic matter (SOM). Moreover, the addition of organic amendment has gained importance as a source of greenhouse gas (GHG) emissions and then as a cause of the "Global Warming". Therefore, it is important to investigate the factors controlling the SOM mineralization in order to improve soil C sequestration and decreasing at the same time the GHG emissions. The quality of organic matter added to the soil will play an important role in these dynamics, affecting the microbial activity and the changes in microbial community structure. A laboratory, multidisciplinary experiment was carried out to test the effect of the amendment by anaerobic digested livestock-derived organic materials on labile organic matter evolution and on dynamics of microbial population, this latter both in terms of consistence of microbial biomass, as well as in terms of microbial biodiversity. Different approaches were used to study the microbial community structure: chemical (CO2 fluxes, WEOC, C-biomass, PLFA), microbiological (microbial enumeration) and molecular (DNA extraction and Roche 454, Next Generation Sequencing, NGS). The application of fresh digestate, derived from the anaerobic treatment of animal wastes, affected the short-term dynamics of microbial community, as reflected by the increase of CO2 emissions immediately after the amendment compared to the control soil. This is probably due to the addition of easily available C added with the digestate, demonstrating that this organic material was only partially stabilized by the anaerobic process. In fact, the digestate contained a high amounts of available C, which led to

  7. Effects of biochar and elevated soil temperature on soil microbial activity and abundance in an agricultural system

    NASA Astrophysics Data System (ADS)

    Bamminger, Chris; Poll, Christian; Marhan, Sven

    2014-05-01

    As a consequence of Global Warming, rising surface temperatures will likely cause increased soil temperatures. Soil warming has already been shown to, at least temporarily, increase microbial activity and, therefore, the emissions of greenhouse gases like CO2 and N2O. This underlines the need for methods to stabilize soil organic matter and to prevent further boost of the greenhouse gas effect. Plant-derived biochar as a soil amendment could be a valuable tool to capture CO2 from the atmosphere and sequestrate it in soil on the long-term. During the process of pyrolysis, plant biomass is heated in an oxygen-low atmosphere producing the highly stable solid matter biochar. Biochar is generally stable against microbial degradation due to its chemical structure and it, therefore, persists in soil for long periods. Previous experiments indicated that biochar improves or changes several physical or chemical soil traits such as water holding capacity, cation exchange capacity or soil structure, but also biotic properties like microbial activity/abundance, greenhouse gas emissions and plant growth. Changes in the soil microbial abundance and community composition alter their metabolism, but likely also affect plant productivity. The interaction of biochar addition and soil temperature increase on soil microbial properties and plant growth was yet not investigated on the field scale. To investigate whether warming could change biochar effects in soil, we conducted a field experiment attached to a soil warming experiment on an agricultural experimental site near the University of Hohenheim, already running since July 2008. The biochar field experiment was set up as two-factorial randomized block design (n=4) with the factors biochar amendment (0, 30 t ha-1) and soil temperature (ambient, elevated=ambient +2.5° C) starting from August 2013. Each plot has a dimension of 1x1m and is equipped with combined soil temperature and moisture sensors. Slow pyrolysis biochar from the C

  8. Microbial activity and soil organic matter decay in roadside soils polluted with petroleum hydrocarbons

    NASA Astrophysics Data System (ADS)

    Mykhailova, Larysa; Fischer, Thomas; Iurchenko, Valentina

    2015-04-01

    It has been demonstrated previously that hydrocarbon addition to soil provokes soil organic matter priming (Zyakun et al., 2011). It has further been shown that petroleum hydrocarbons deposit to roadside soils bound to fine mineral particles and together with vehicle spray (Mykhailova et al., 2014), and that hydrocarbon concentrations decrease to safe levels within the first 15 m from the road, reaching background concentrations at 60-100 m distance (Mykhailova et al., 2013). It was the aim of this study to (I) identify the bioavailability of different petroleum hydrocarbon fractions to degradation and to (II) identify the native (i.e. pedogenic) C fraction affected by hydrocarbon-mediated soil organic matter priming during decay. To address this aim, we collected soil samples at distances from 1 to 100 m (sampling depth 15 cm) near the Traktorostroiteley avenue and the Pushkinskaya street in Kharkov, as well as near the country road M18 near Kharkov, Ukraine. The roads have been under exploitation for several decades, so microbial adaptation to enhanced hydrocarbon levels and full expression of effects could be assumed. The following C fractions were quantified using 13C-CP/MAS-NMR: Carbohydrates, Proteins, Lignin, Aliphates, Carbonyl/Carboxyl as well as black carbon according to Nelson and Baldock (2005). Petroleum hydrocarbons were determind after hexane extraction using GC-MS and divided into a light fraction (chain-length C27, Mykhailova et al., 2013). Potential soil respiration was determined every 48 h by trapping of CO2 evolving from 20 g soil in NaOH at 20 ° C and at 60% of the maximum water holding capacity and titration after a total incubation period of 4 weeks in the lab. It was found that soil respiration positively correlated with the ratio of the light fraction to the sum of medium and heavy fractions of petroleum hydrocarbons, which indicates higher biodegradation primarily of the light petroleum hydrocarbon fraction. Further, soil respiration was

  9. Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators

    PubMed Central

    Trivedi, Pankaj; Delgado-Baquerizo, Manuel; Anderson, Ian C.; Singh, Brajesh K.

    2016-01-01

    Agricultural intensification is placing tremendous pressure on the soil’s capacity to maintain its functions leading to large-scale ecosystem degradation and loss of productivity in the long term. Therefore, there is an urgent need to find early indicators of soil health degradation in response to agricultural management. In recent years, major advances in soil meta-genomic and spatial studies on microbial communities and community-level molecular characteristics can now be exploited as ‘biomarker’ indicators of ecosystem processes for monitoring and managing sustainable soil health under global change. However, a continental scale, cross biome approach assessing soil microbial communities and their functional potential to identify the unifying principles governing the susceptibility of soil biodiversity to land conversion is lacking. We conducted a meta-analysis from a dataset generated from 102 peer-reviewed publications as well as unpublished data to explore how properties directly linked to soil nutritional health (total C and N; C:N ratio), primary productivity (NPP) and microbial diversity and composition (relative abundance of major bacterial phyla determined by next generation sequencing techniques) are affected in response to agricultural management across the main biomes of Earth (arid, continental, temperate and tropical). In our analysis, we found strong statistical trends in the relative abundance of several bacterial phyla in agricultural (e.g., Actinobacteria and Chloroflexi) and natural (Acidobacteria, Proteobacteria, and Cyanobacteria) systems across all regions and these trends correlated well with many soil properties. However, main effects of agriculture on soil properties and productivity were biome-dependent. Our meta-analysis provides evidence on the predictable nature of the microbial community responses to vegetation type. This knowledge can be exploited in future for developing a new set of indicators for primary productivity and

  10. Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale

    PubMed Central

    Cao, Haichuan; Chen, Ruirui; Wang, Libing; Jiang, Lanlan; Yang, Fen; Zheng, Shixue; Wang, Gejiao; Lin, Xiangui

    2016-01-01

    Considering the extensive functional redundancy in microbial communities and great difficulty in elucidating it based on taxonomic structure, studies on the biogeography of soil microbial activity at large spatial scale are as important as microbial community structure. Eighty-four soil samples were collected across a region from south to north China (about 1,000 km) to address the questions if microbial activity displays biogeographic patterns and what are driving forces. These samples represented different soil types, land use and climate. Redundancy analysis and nonmetric multidimensional scaling clearly revealed that soil microbial activities showed distinct differentiation at different sites over a regional spatial scale, which were strongly affected by soil pH, total P, rainfall, temperature, soil type and location. In addition, microbial community structure was greatly influenced by rainfall, location, temperature, soil pH and soil type and was correlated with microbial activity to some extent. Our results suggest that microbial activities display a clear geographic pattern that is greatly altered by geographic distance and reflected by climate, soil pH and total P over large spatial scales. There are common (distance, climate, pH and soil type) but differentiated aspects (TP, SOC and N) in the biogeography of soil microbial community structure and activity. PMID:27170469

  11. Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale.

    PubMed

    Cao, Haichuan; Chen, Ruirui; Wang, Libing; Jiang, Lanlan; Yang, Fen; Zheng, Shixue; Wang, Gejiao; Lin, Xiangui

    2016-01-01

    Considering the extensive functional redundancy in microbial communities and great difficulty in elucidating it based on taxonomic structure, studies on the biogeography of soil microbial activity at large spatial scale are as important as microbial community structure. Eighty-four soil samples were collected across a region from south to north China (about 1,000 km) to address the questions if microbial activity displays biogeographic patterns and what are driving forces. These samples represented different soil types, land use and climate. Redundancy analysis and nonmetric multidimensional scaling clearly revealed that soil microbial activities showed distinct differentiation at different sites over a regional spatial scale, which were strongly affected by soil pH, total P, rainfall, temperature, soil type and location. In addition, microbial community structure was greatly influenced by rainfall, location, temperature, soil pH and soil type and was correlated with microbial activity to some extent. Our results suggest that microbial activities display a clear geographic pattern that is greatly altered by geographic distance and reflected by climate, soil pH and total P over large spatial scales. There are common (distance, climate, pH and soil type) but differentiated aspects (TP, SOC and N) in the biogeography of soil microbial community structure and activity. PMID:27170469

  12. Assessing the soil microbial carbon budget: Probing with salt stress

    NASA Astrophysics Data System (ADS)

    Rath, Kristin; Rousk, Johannes

    2014-05-01

    The amount of carbon stored as soil organic matter (SOM) constitutes a pool more than double the size of the atmospheric carbon pool. Soil respiration represents one of the largest fluxes of carbon between terrestrial ecosystems and the atmosphere. A large fraction of the CO2 released by soils is produced by the microbial decomposition of SOM. The microbial carbon budget is characterized by their carbon use efficiency, i.e. the partitioning of substrate into growth and respiration. This will shape the role of the soil as a net source or sink for carbon. One of the canonical factors known to influence microbial processes in soil is pH. In aquatic systems salinity has been found to have a comparably strong influence as pH. However salinity remains understudied in soil, despite its growing relevance due to land use change and agricultural practices. The aim of this project is to understand how microbial carbon dynamics respond to disturbance by changing environmental conditions, using salinity as a reversible stressor. First, we compiled a comparative analysis of the sensitivity of different microbial processes to increasing salt concentrations. Second, we compared different salts to determine whether salt toxicity depended on the identity of the salt. Third, we used samples from a natural salinity gradient to assess if a legacy of salt exposure can influence the microbial response to changing salt concentrations. If salt had an ecologically significant effect in shaping these communities, we would assume that microbial processes would be less sensitive to an increase in salt concentrations. The sensitivity of microbial processes to salt was investigated by establishing inhibition curves in order to estimate EC50 values (the concentration resulting in 50% inhibition). These EC50 values were used to compare bacterial and fungal growth responses, as well as catabolic processes such as respiration and nitrogen mineralisation. Initial results suggest that growth related

  13. 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

  14. Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China.

    PubMed

    Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

    2016-01-01

    The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community. PMID:27241173

  15. Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China

    NASA Astrophysics Data System (ADS)

    Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

    2016-05-01

    The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community.

  16. Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China

    PubMed Central

    Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

    2016-01-01

    The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community. PMID:27241173

  17. Microbial destruction of chitin in soils under different moisture conditions

    NASA Astrophysics Data System (ADS)

    Yaroslavtsev, A. M.; Manucharova, N. A.; Stepanov, A. L.; Zvyagintsev, D. G.; Sudnitsyn, I. I.

    2009-07-01

    The most favorable moisture conditions for the microbial destruction of chitin in soils are close to the total water capacity. The water content has the most pronounced effect on chitin destruction in soils in comparison with other studied substrates. It was found using gas-chromatographic and luminescent-microscopic methods that the maximum specific activity of the respiration of the chitinolytic community was at a rather low redox potential with the soil moisture close to the total water capacity. The range of moisture values under which the most intense microbial transformation of chitin occurred was wider in clayey and clay loamy soils as compared with sandy ones. The increase was observed due to the contribution of mycelial bacteria and actinomycetes in the chitinolytic complex as the soil moisture increased.

  18. Impact of some selected insecticides application on soil microbial respiration.

    PubMed

    Latif, M A; Razzaque, M A; Rahman, M M

    2008-08-15

    The aim of present study was to investigate the impact of selected insecticides used for controlling brinjal shoot and fruit borer on soil microorganisms and to find out the insecticides or nontoxic to soil microorganism the impact of nine selected insecticides on soil microbial respiration was studied in the laboratory. After injection of different insecticides solutions, the soil was incubated in the laboratory at room temperature for 32 days. The amount of CO2 evolved due to soil microbial respiration was determined at 2, 4, 8, 16, 24 and 32 days of incubation. Flubendiamide, nimbicidine, lambda-cyhalothrin, abamectin and thiodicarb had stimulatory effect on microbial respiration during the initial period of incubation. Chlorpyriphos, cartap and carbosulfan had inhibitory effect on microbial respiration and cypermethrin had no remarkable effect during the early stage of incubation. The negative effect of chlorpyriphos, cartap and carbosulfan was temporary, which was disappeared after 4 days of insecticides application. No effect of the selected insecticides on soil microorganisms was observed after 24 or 32 days of incubation. PMID:19266909

  19. Biotic interactions mediate soil microbial feedbacks to climate change.

    PubMed

    Crowther, Thomas W; Thomas, Stephen M; Maynard, Daniel S; Baldrian, Petr; Covey, Kristofer; Frey, Serita D; van Diepen, Linda T A; Bradford, Mark A

    2015-06-01

    Decomposition of organic material by soil microbes generates an annual global release of 50-75 Pg carbon to the atmosphere, ∼7.5-9 times that of anthropogenic emissions worldwide. This process is sensitive to global change factors, which can drive carbon cycle-climate feedbacks with the potential to enhance atmospheric warming. Although the effects of interacting global change factors on soil microbial activity have been a widespread ecological focus, the regulatory effects of interspecific interactions are rarely considered in climate feedback studies. We explore the potential of soil animals to mediate microbial responses to warming and nitrogen enrichment within a long-term, field-based global change study. The combination of global change factors alleviated the bottom-up limitations on fungal growth, stimulating enzyme production and decomposition rates in the absence of soil animals. However, increased fungal biomass also stimulated consumption rates by soil invertebrates, restoring microbial process rates to levels observed under ambient conditions. Our results support the contemporary theory that top-down control in soil food webs is apparent only in the absence of bottom-up limitation. As such, when global change factors alleviate the bottom-up limitations on microbial activity, top-down control becomes an increasingly important regulatory force with the capacity to dampen the strength of positive carbon cycle-climate feedbacks. PMID:26038557

  20. Biotic interactions mediate soil microbial feedbacks to climate change

    PubMed Central

    Crowther, Thomas W.; Thomas, Stephen M.; Maynard, Daniel S.; Baldrian, Petr; Covey, Kristofer; Frey, Serita D.; van Diepen, Linda T. A.; Bradford, Mark A.

    2015-01-01

    Decomposition of organic material by soil microbes generates an annual global release of 50–75 Pg carbon to the atmosphere, ∼7.5–9 times that of anthropogenic emissions worldwide. This process is sensitive to global change factors, which can drive carbon cycle–climate feedbacks with the potential to enhance atmospheric warming. Although the effects of interacting global change factors on soil microbial activity have been a widespread ecological focus, the regulatory effects of interspecific interactions are rarely considered in climate feedback studies. We explore the potential of soil animals to mediate microbial responses to warming and nitrogen enrichment within a long-term, field-based global change study. The combination of global change factors alleviated the bottom-up limitations on fungal growth, stimulating enzyme production and decomposition rates in the absence of soil animals. However, increased fungal biomass also stimulated consumption rates by soil invertebrates, restoring microbial process rates to levels observed under ambient conditions. Our results support the contemporary theory that top-down control in soil food webs is apparent only in the absence of bottom-up limitation. As such, when global change factors alleviate the bottom-up limitations on microbial activity, top-down control becomes an increasingly important regulatory force with the capacity to dampen the strength of positive carbon cycle–climate feedbacks. PMID:26038557

  1. Sterol-inhibiting fungicide impacts on soil microbial ecology in Atlantic Coastal Plain soils

    NASA Astrophysics Data System (ADS)

    White, P. M.; Potter, T. L.; Strickland, T. C.

    2008-12-01

    Seventy-five percent of the peanuts (Arachus hypogaia) produced in the United States are grown in the Atlantic Coastal Plain region. Portions of this area, including Alabama and Georgia, exhibit a subtropical climate that promotes soil-borne plant fungal diseases. Most fields receive repeated fungicide applications during the growing season to suppress the disease causing organisms, such as Sclerotium rolfsii, Rhizoctonia solani, and Cylindrocladium parasiticum. Information regarding fungicide effects on the soil microbial community, with components principally responsible for transformation and fate of fungicides and other soil-applied pesticides, is limited. The objectives of the study were to assess soil microbial community response to (1) varying rates of the sterol-inhibiting fungicide tebuconazole (0, single application, season max, 2x season max), and (2) field rates of the sterol-inhibitors cyproconazole, prothioconazole, tebuconazole, and flutriafol, and thiol-competitor chlorothalonil. The sterol-inhibitors exhibited different half lives, as listed in the FOOTPRINT database, ranging from <1 day to >1300 d. Chlorothalonil was chosen because it is the most frequently applied fungicide to peanut. Shifts in the fungi, gram positive and gram negative bacteria, were monitored during the experiments using phospholipid fatty acid (PLFA) profiles. Ergosterol levels and pesticide decay rates were also monitored to evaluate the effectiveness of the fungicide and soil residence time, respectively. In the rate study, the highest rate of tebuconazole reduced the fungal biomarker 18:2ω6,9c to 2.6 nmol g-1 dry soil at 17 d, as compared to the control (4.1 nmol g-1 dry soil). However, levels of the fungal PLFA biomarker were similar regardless of rate at 0 and 32 d. The gram negative bacterial PLFA mole percent was greater at 17 d for the two highest rates of tebuconazole, but was similar at 0 and 32 d. Gram positive and fungal mole percents were not affected at any time

  2. Modeling microbial dynamics in heterogeneous environments: Growth on soil carbon sources

    SciTech Connect

    Resat, Haluk; Bailey, Vanessa L.; McCue, Lee Ann; Konopka, Allan

    2012-01-01

    We have developed a new hybrid model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment. The modeling framework can represent porous media such as soil. The individual based biological model can explicitly simulate microbial diversity, and cell metabolism is regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by local environmental conditions and by the functional attributes of individual microbes. Different strategies for acquisition of carbon from polymeric cellulose were investigated. Bacteria that express membrane-associated hydrolase had different growth and survival dynamics in soil pores than bacteria that release extracellular hydrolases. The kinetic differences may suggest different functional roles for these two classes of microbes in cellulose utilization. Our model predicted an emergent behavior in which co-existence led to higher cellulose utilization efficiency and reduced stochasticity. Microbial community dynamics were simulated at two spatial scales: micro-pores that resemble 6-20 {micro}m size portions of the soil physical structure and in 111 {micro}m size soil aggregates with a random pore structure. Trends in dynamic properties were very similar at these two scales, implying that micro-scale studies can be useful approximations to aggregate scale studies when local effects on microbial dynamics are studied.

  3. Recovery of soil microbial communities after fumigation with time

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the past few decades, soil fumigants have been extensively used to control target soil borne pathogens and weeds for high value cash crops. However, the fumigants with broad biocidal activity can affect both target and non-target or beneficial microorganisms in soil, but the recovery of soil micr...

  4. Measurements of Microbial Community Activities in Individual Soil Macroaggregates

    SciTech Connect

    Bailey, Vanessa L.; Bilskis, Christina L.; Fansler, Sarah J.; McCue, Lee Ann; Smith, Jeff L.; Konopka, Allan

    2012-05-01

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for {beta}-glucosidase, N-acetyl-{beta}-D-glucosaminidase, lipase, and leucine aminopeptidase to measure of the enzyme potential of individual aggregates (250-1000 {mu}m diameter). Across all enzymes, the smallest aggregates had the greatest activity and the range of enzyme activities observed in all aggregates supports the hypothesis that functional potential in soil may be distributed in a patchy fashion. Paired analyses of ATP as a surrogate for active microbial biomass and {beta}-glucosidase on the same aggregates suggest the presence of both extracellular {beta}-glucosidase functioning in aggregates with no detectable ATP and also of relatively active microbial communities (high ATP) that have low {beta}-glucosidase potentials. Studying function at a scale more consistent with microbial habitat presents greater opportunity to link microbial community structure to microbial community function.

  5. Effect of activated carbon on microbial bioavailability of phenanthrene in soils

    SciTech Connect

    Yang, Y.; Hunter, W.; Tao, S.; Crowley, D.; Gan, J.

    2009-11-15

    Bioavailability is a governing factor that controls the rate of biological degradation of hydrophobic organic contaminants in soil. Among the solid phases that can adsorb hydrophobic organic contaminants in soil, black carbon (BC) exerts a particularly significant effect on phase distribution. However, knowledge on the effect of BC on the microbial availability of polycyclic aromatic hydrocarbons in soil is still limited. In the present study, the effect of a coal-derived activated carbon on the bioavailability of phenanthrene (PHE) during its degradation by Mycobacterium vanbaalenii PYR-1 was measured in three soils. The freely dissolved concentration of PHE was concurrently determined in soil solutions using disposable polydimethylsiloxane fibers. The results showed that PHE mineralization was significantly inhibited after addition of activated carbon in all test soils. After 216 h, only 5.20, 5.83, and 6.85% of PHE was degraded in the 0.5% BC-amended soils initially containing organic carbon at 0.23, 2.1, and 7.1%, respectively. Significant correlation was found between PHE degradability and freely dissolved concentration, suggesting that BC affected PHE bioavailability by decreasing chemical activity. The effect of activated carbon in the amended soils was attributed to its enhancement of soil surface areas and pore volumes. Results from the present study clearly highlighted the importance of BC for influencing the microbial availability of polycyclic aromatic hydrocarbons in soils.

  6. Microbial composition affects the functioning of estuarine sediments

    PubMed Central

    Reed, Heather E; Martiny, Jennifer BH

    2013-01-01

    Although microorganisms largely drive many ecosystem processes, the relationship between microbial composition and their functioning remains unclear. To tease apart the effects of composition and the environment directly, microbial composition must be manipulated and maintained, ideally in a natural ecosystem. In this study, we aimed to test whether variability in microbial composition affects functional processes in a field setting, by reciprocally transplanting riverbed sediments between low- and high-salinity locations along the Nonesuch River (Maine, USA). We placed the sediments into microbial ‘cages' to prevent the migration of microorganisms, while allowing the sediments to experience the abiotic conditions of the surroundings. We performed two experiments, short- (1 week) and long-term (7 weeks) reciprocal transplants, after which we assayed a variety of functional processes in the cages. In both experiments, we examined the composition of bacteria generally (targeting the 16S rDNA gene) and sulfate-reducing bacteria (SRB) specifically (targeting the dsrAB gene) using terminal restriction fragment length polymorphism (T-RFLP). In the short-term experiment, sediment processes (CO2 production, CH4 flux, nitrification and enzyme activities) depended on both the sediment's origin (reflecting differences in microbial composition between salt and freshwater sediments) and the surrounding environment. In the long-term experiment, general bacterial composition (but not SRB composition) shifted in response to their new environment, and this composition was significantly correlated with sediment functioning. Further, sediment origin had a diminished effect, relative to the short-term experiment, on sediment processes. Overall, this study provides direct evidence that microbial composition directly affects functional processes in these sediments. PMID:23235294

  7. Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

    NASA Astrophysics Data System (ADS)

    Wang, Qiufeng; Tian, Jing; Yu, Guirui

    2014-05-01

    Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

  8. Carbon and Nitrogen Use Efficiency in Microbial Communities in Antarctic Soils

    NASA Astrophysics Data System (ADS)

    Prommer, Judith; Spohn, Marie; Klaus, Karoline; Kusch, Stephanie; Wanek, Wolfgang; Dercon, Gerd; Richter, Andreas

    2016-04-01

    Terrestrial ecosystems in the Antarctic experience harsh environmental conditions including very low temperatures and a low carbon input leading to poorly developed ecosystems with low diversity and a low soil organic matter content, which may be vulnerable to perturbations in a future climate. Microbial transformation and decomposition of soil organic matter under the extreme climatic conditions in the Antarctic has received little attention so far. Specifically, little is known about microbial process rates and how they might be affected by climate warming. We here report on C and N transformation rates and their corresponding microbial use efficiencies in two soil horizons of two sites on King George Island, the maritime Antarctica. We used novel isotope techniques to estimate microbial carbon use efficiency (CUE; based on incorporation of 18O from water into DNA) and nitrogen use efficiency (NUE; based on a 15N isotope pool dilution assays). The investigated two contrasting sites at marine terraces on basaltic rocks that were characterized by a stable surface. While both sites were similar in exposition, distance from sea and elevation, they differed in their vegetation cover and several biogeochemical parameters, such as soil pH and soil organic carbon and nitrogen content. Surprisingly, we found low soil C:N ratios at both sites and for both horizons, i.e. below 12 in the organic crust and below 8 in the first mineral horizon. This indicates a low carbon availability relative to nitrogen and would thus imply a high microbial CUE. However, our results showed also a low CUE at both sites and in both horizons (CUE of 24% and 9% in the organic crust and mineral layer, respectively). In contrast, NUE was very high in organic layers (98%), pointing towards a strong nitrogen limitation, while in the mineral horizons, NUE was lower (between 84% and 72%), as expected for soil horizons with a C:N ratio below 8. Thus, the NUE pattern followed stoichiometric theory (i

  9. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    SciTech Connect

    Terence L. Marsh

    2004-05-26

    The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

  10. Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng.

    PubMed

    Wu, Zhaoxiang; Hao, Zhipeng; Zeng, Yan; Guo, Lanping; Huang, Luqi; Chen, Baodong

    2015-11-01

    Rhizosphere and root-associated microbial communities are known to be related to soil-borne disease and plant health. In the present study, the microbial communities in rhizosphere soils and roots of both healthy and diseased Panax notoginseng were analyzed by high-throughput sequencing of 16S rRNA for bacteria and 18S rRNA internal transcribed spacer for fungi, to reveal the relationship of microbial community structure with plant health status. In total, 5593 bacterial operational taxonomic units (OTUs) and 963 fungal OTUs were identified in rhizosphere soils, while 1794 bacterial and 314 fungal OTUs were identified from root samples respectively. Principal coordinate analysis separated the microbial communities both in the rhizosphere soils and roots of diseased P. notoginseng from healthy plants. Compared to those of healthy P. notoginseng, microbial communities in rhizosphere soils and roots of diseased plants showed a decrease in alpha diversity. By contrast, bacterial community dissimilarity increased and fungal community dissimilarity decreased in rhizosphere soils of diseased plants, while both bacterial and fungal community dissimilarity in roots showed no significant difference between healthy and diseased plants. Redundancy analysis at the phylum level showed that mycorrhizal colonization and soil texture significantly affected microbial community composition in rhizosphere soils, whereas shoot nutrition status had a significant effect on microbial community composition in root samples. Our study provided strong evidence for the hypothesis that microbial diversity could potentially serve as an indicator for disease outbreak of medicinal plants, and supported the ecological significance of microbial communities in maintaining plant healthy and soil fertility. PMID:26296378

  11. 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. PMID:26122566

  12. 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

  13. 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. PMID:22885757

  14. Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

    PubMed Central

    2013-01-01

    The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research. PMID:23957006

  15. Contribution of microbial carbon to soil fractions: significance of diverse microbial group biochemistry

    NASA Astrophysics Data System (ADS)

    Throckmorton, H.; Bird, J. A.; Dane, L.; Firestone, M. K.; Horwath, W. R.

    2011-12-01

    The importance of diverse microbial groups to soil C maintenance is still a matter of debate. This study follows the turnover of 13C labeled nonliving residues from diverse microbial groups into soil physical fractions in situ in a temperate forest in California (CA) and a tropical forest in Puerto Rico (PR), during 5 sampling points per site- over a 3 and 2 year period, respectively. Microbial groups include fungi, actinomycetes, Gm(+) bacteria, and Gm(-) bacteria, isolated from CA and PR soils to obtain temperate and tropical isolates composited of 3-4 species per group. The selected density fractionation approach isolated: a "light fraction" (LF), non-mineral aggregate "occluded fraction" (OF), and a "mineral bound fraction" (MF). Pyrolysis gas chromatography mass spectrometry (Py-GC-MS) was employed to characterize microbial group isolates, whole soils, and fractions. Microbial isolates contained unique biochemical fingerprints: temperate and tropical fungi and tropical Gm(-) were characterized by a low abundance of phenol, benzene, and N-compounds compared with other microbial group isolates. Py-GC-MS revealed compositional differences among soil fractions at both sites, likely attributed to differences in the decomposition stage and C source material (ie. plant vs. microbial). For both sites, benzene and N-compounds were greatest in the MF; lignin and phenol compounds were greatest in the LF; and lipids were greatest in the OF. The trend for polysaccharides differed between sites, with the greatest concentration in the CA OF; and for PR with the lowest concentration in the OF, and similar concentrations in the LF and MF. SOM chemistry was most similar between sites in the LF, compared with the OF and MF, suggesting that differences in SOM chemistry between sites may be more attributed to differential decomposition processes than unique litter quality inputs. A substantial portion of microbial C moved from the LF into the OF, and the MF by the first sampling

  16. Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

    NASA Astrophysics Data System (ADS)

    Wilton, E.; Flanagan, L. B.

    2014-12-01

    Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex

  17. Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation

    PubMed Central

    Xie, Yan; Fan, Jibiao; Zhu, Weixi; Amombo, Erick; Lou, Yanhong; Chen, Liang; Fu, Jinmin

    2016-01-01

    Heavy metal pollution is a serious global environmental problem as it adversely affects plant growth and genetic variation. It also alters the composition and activity of soil microbial communities. The objectives of this study were to determine the soil microbial diversity, bermudagrass genetic variation in Cd contaminated or uncontaminated soils from Hunan province of China, and to evaluate Cd-tolerance of bermudagrass at different soils. The Biolog method, hydroponic experiments and simple sequence repeat markers were used to assess the functional diversity of microorganisms, Cd-tolerance and the genetic diversity of bermudagrass, respectively. Four of the sampling sites were heavily contaminated with heavy metals. The total bioactivity, richness, and microbial diversity decreased with increasing concentration of heavy metal. The hydroponic experiment revealed that bermudagrass populations collected from polluted sites have evolved, encompassing the feature of a higher resistance to Cd toxicity. Higher genetic diversity was observed to be more in contaminated populations than in uncontaminated populations. Heavy metal pollution can result in adverse effects on plant growth, soil microbial diversity and activity, and apparently has a stronger impact on the genetic structure. The results of this study provide new insights and a background to produce a genetic description of populations in a species that is suitable for use in phytoremediation practices. PMID:27303431

  18. Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation.

    PubMed

    Xie, Yan; Fan, Jibiao; Zhu, Weixi; Amombo, Erick; Lou, Yanhong; Chen, Liang; Fu, Jinmin

    2016-01-01

    Heavy metal pollution is a serious global environmental problem as it adversely affects plant growth and genetic variation. It also alters the composition and activity of soil microbial communities. The objectives of this study were to determine the soil microbial diversity, bermudagrass genetic variation in Cd contaminated or uncontaminated soils from Hunan province of China, and to evaluate Cd-tolerance of bermudagrass at different soils. The Biolog method, hydroponic experiments and simple sequence repeat markers were used to assess the functional diversity of microorganisms, Cd-tolerance and the genetic diversity of bermudagrass, respectively. Four of the sampling sites were heavily contaminated with heavy metals. The total bioactivity, richness, and microbial diversity decreased with increasing concentration of heavy metal. The hydroponic experiment revealed that bermudagrass populations collected from polluted sites have evolved, encompassing the feature of a higher resistance to Cd toxicity. Higher genetic diversity was observed to be more in contaminated populations than in uncontaminated populations. Heavy metal pollution can result in adverse effects on plant growth, soil microbial diversity and activity, and apparently has a stronger impact on the genetic structure. The results of this study provide new insights and a background to produce a genetic description of populations in a species that is suitable for use in phytoremediation practices. PMID:27303431

  19. Carbon Accumulation and Microbial Community Structure in Reclaimed Mine Soils

    NASA Astrophysics Data System (ADS)

    Pfiffner, S. M.; Palumbo, A. V.; Tarver, J. D.; Fisher, S.; Cantu, J.; Brandt, C. C.

    2002-12-01

    The objective of this study was to investigate the potential for soil amendments to increase accumulation of carbon in reclaimed soils and the relationship between carbon and microbial community structure. Changes in community structure were determined by signature lipid biomarkers (SLBs) or phospholipid fatty acid methyl esters. PLFA provide estimates of the viable biomass, diversity of prokaryotic and eukaryotic diversity, and indications of physiological stress to the microbial community. Artificial neural network (ANN) analysis has been used to examine the relationship between microbial community structure and soil geochemistry. It was hypothesized that (1) soil amendments would cause changes in the structure of the microbial community and carbon content (2) changes in the structure of the microbial community would be vary between the types of amendments, and (3) analysis of the SLB with an artificial neural network (ANN) would distinguish treatment and provide a insight in to the relationship between changes in soil geochemistry and microbial community. Twenty soils samples from different field plots and at different soil horizon depths were analyzed. Biomass as estimated by PLFA analysis, ranged from 1.9 to 265 nmol/g, which corresponded to cell densities of 4.8 x107 to 6.6 x109 cells/g. In the Wall's Farm and Jenkin's Farm samples the microbial biomass decreased with depth. A horizon soils had biomass values of greater or equal to 120 nmol/g, followed by the A2 horizon,(70 to 100 nmol/g) and the weak B horizon at and (40 to 80 nmo/g). The A2 and B horizon samples showed higher relative abundance of mid-chain branched saturates that are indicative of gram positive prokaryotes and actinomycetes. At Well's Farm, the polyunsaturates indicative of eukaryotes were observed at higher abundances. These changes were related to both the prokaryotic and eukaryotic influences in the microbial community in response to the soil amendments. The correlation between

  20. 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...

  1. Comparative Toxicities of Salts on Microbial Processes in Soil.

    PubMed

    Rath, Kristin M; 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 SO4 (2-) 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 SO4 (2-) salts but not to Cl(-) salts; no evidence was found to distinguish K(+) and Na(+) salts. PMID:26801570

  2. Switchgrass ecotypes alter microbial contribution to deep-soil C

    NASA Astrophysics Data System (ADS)

    Roosendaal, Damaris; Stewart, Catherine E.; Denef, Karolien; Follett, Ronald F.; Pruessner, Elizabeth; Comas, Louise H.; Varvel, Gary E.; Saathoff, Aaron; Palmer, Nathan; Sarath, Gautam; Jin, Virginia L.; Schmer, Marty; Soundararajan, Madhavan

    2016-05-01

    Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland), little is known about the impact of plant belowground productivity on microbial communities down deep in the soil profiles. Microbial dynamics in deeper soils are likely to exert considerable control on ecosystem services, including C and nutrient cycles, due to their involvement in such processes as soil formation and ecosystem biogeochemistry. Differences in root biomass and rooting characteristics of switchgrass ecotypes could lead to distinct differences in belowground microbial biomass and microbial community composition. We quantified root abundance and root architecture and the associated microbial abundance, composition, and rhizodeposit C uptake for two switchgrass ecotypes using stable-isotope probing of microbial phospholipid fatty acids (PLFAs) after 13CO2 pulse-chase labeling. Kanlow, a lowland ecotype with thicker roots, had greater plant biomass above- and belowground (g m-2), greater root mass density (mg cm-3), and lower specific root length (m g-1) compared to Summer, an upland ecotype with finer root architecture. The relative abundance of bacterial biomarkers dominated microbial PLFA profiles for soils under both Kanlow and Summer (55.4 and 53.5 %, respectively; P = 0.0367), with differences attributable to a greater relative abundance of Gram-negative bacteria in soils under Kanlow (18.1 %) compared to soils under Summer (16.3 %; P = 0.0455). The two ecotypes also had distinctly different microbial communities process rhizodeposit C: greater relative atom % 13C excess in Gram-negative bacteria (44.1 ± 2.3 %) under the thicker roots of Kanlow and greater relative atom % 13C excess in saprotrophic fungi under the thinner roots of Summer (48.5 ± 2.2 %). For bioenergy production systems, variation between switchgrass

  3. Variations in Soil Microbial Communities and Residues Along an Altitude Gradient on the Northern Slope of Changbai Mountain, China

    PubMed Central

    Zhang, Bin; Liang, Chao; He, Hongbo; Zhang, Xudong

    2013-01-01

    Altitudinally-defined climate conditions provide specific vegetation types and soil environments that could influence soil microbial communities, which in turn may affect microbial residues. However, the knowledge is limited in terms of the degree to which microbial communities and residues present and differ along altitude. In this study, we examined the soil microbial communities and residues along the northern slope of Changbai Mountain, China using phospholipid fatty acid (PLFA) and amino sugar analysis, respectively. Soil samples were taken from five different vegetation belts defined by climates. Principal component analysis (PCA) revealed substantial differences in soil microbial community composition among study sites, appeared to be driven primarily by soil pH and C/N ratio on the first principal component (PC1) which accounted for 50.7% of the total sample variance. The alpine tundra was separated from forest sites on the second principal component (PC2) by a signifiscantly higher amount of fungal PLFA (18:2ω6,9). Soil pH and C/N ratio were also correlated with the ratios of Gram-positive to Gram-negative bacteria (Gm+/Gm−), glucosamine to galactosamine (GluN/GalN), and glucosamine to muramic acid (GluN/MurA). Both total PLFAs and amino sugars were positively correlated with soil organic carbon, inorganic nitrogen, available phosphorus and potassium. We concluded that soil pH and C/N ratio were the most important drivers for microbial community structure and amino sugar pattern, while substrate availability was of great importance in determining the concentrations of microbial communities and residues. These findings could be used to facilitate interpretation of soil microbial community and amino sugar data derived from measurements in latitude or managed forests. PMID:23776630

  4. Integrating microbial physiology and physiochemical principles in soils with the MIcrobial-MIneral Carbon Stabilization (MIMICS) model

    NASA Astrophysics Data System (ADS)

    Wieder, W. R.; Grandy, A. S.; Kallenbach, C. M.; Bonan, G. B.

    2014-01-01

    Previous modeling efforts document divergent responses of microbial explicit soil biogeochemistry models when compared to traditional models that implicitly simulate microbial activity, particularly following environmental perturbations. However, microbial models are needed that capture current soil biogeochemical theories emphasizing the relationships between litter quality, functional differences in microbial physiology, and the physical protection of microbial byproducts in forming stable soil organic matter (SOM). To address these limitations we introduce the MIcrobial-MIneral Carbon Stabilization (MIMICS) model. In MIMICS, the turnover of litter and SOM pools are governed by temperature sensitive Michaelis-Menten kinetics and the activity of two physiologically distinct microbial functional types. The production of microbial residues through microbial turnover provides inputs to SOM pools that are considered physically or chemically protected. Soil clay content determines the physical protection of SOM in different soil environments. MIMICS adequately simulates the mean rate of leaf litter decomposition observed at a temperate and boreal forest sites, and captures observed effects of litter quality on decomposition rates. Initial results from MIMICS suggest that soil C storage can be maximized in sandy soils with low-quality litter inputs, whereas high-quality litter inputs may maximize SOM accumulation in finely textured soils that physically stabilize microbial products. Assumptions in MIMICS about the degree to which microbial functional types differ in the production, turnover, and stabilization of microbial residues provides a~mechanism by which microbial communities may influence SOM dynamics in mineral soils. Although further analyses are needed to validate model results, MIMICS allows us to begin exploring theoretical interactions between substrate quality, microbial community abundance, and the formation of stable SOM.

  5. [Effects of antimicrobial drugs on soil microbial respiration].

    PubMed

    Liu, Feng; Ying, Guang-Guo; Zhou, Qi-Xing; Tao, Ran; Su, Hao-Chang; Li, Xu

    2009-05-15

    The effects on soil microbial respiration of sulfonamides, tetracyclines, macrolides and so on were studied using the direct absorption method. The results show sulfamethazine, sulfamethoxazole, chlortetracycline, tetracycline, tylosin and trimethoprim inhibit soil respiration 34.33%, 34.43%, 2.71%, 3.08%, 7.13%, 38.08% respectively. Sulfamethoxazole and trimethoprim have the highest inhibition rates among all the antibiotics. In early incubation period (0-2 d), the concentrations above 10 mg x kg(-1) of sulfamethazine, sulfamethoxazole and trimethoprim remarkably decrease soil CO2 emission. The effects of these antibiotics vary with their concentrations too. Sulfamethoxazole and trimethoprim show good dose-response relationships. According to the standard of pesticide safety evaluation protocol, the six antibiotics pose a little risk to soil microbial environment. PMID:19558090

  6. Understory vegetation leads to changes in soil acidity and in microbial communities 27 years after reforestation.

    PubMed

    Fu, Xiaoli; Yang, Fengting; Wang, Jianlei; Di, Yuebao; Dai, Xiaoqin; Zhang, Xinyu; Wang, Huimin

    2015-01-01

    Experiments with potted plants and removed understories have indicated that understory vegetation often affects the chemical and microbial properties of soil. In this study, we examined the mechanism and extent of the influence of understory vegetation on the chemical and microbial properties of soil in plantation forests. The relationships between the vegetational structure (diversity for different functional layers, aboveground biomass of understory vegetation, and species number) and soil properties (pH, microbial community structure, and levels of soil organic carbon, total nitrogen, and inorganic nitrogen) were analyzed across six reforestation types (three pure needleleaf forests, a needle-broadleaf mixed forest, a broadleaf forest, and a shrubland). Twenty-seven years after reforestation, soil pH significantly decreased by an average of 0.95 across reforestation types. Soil pH was positively correlated with the aboveground biomass of the understory. The levels of total, bacterial, and fungal phospholipid fatty acids, and the fungal:bacterial ratios were similar in the shrubland and the broadleaf forest. Both the aboveground biomass of the understory and the diversity of the tree layer positively influenced the fungal:bacterial ratio. Improving the aboveground biomass of the understory could alleviate soil acidification. An increase in the aboveground biomass of the understory, rather than in understory diversity, enhanced the functional traits of the soil microbial communities. The replacement of pure plantations with mixed-species stands, as well as the enhancement of understory recruitment, can improve the ecological functions of a plantation, as measured by the alleviation of soil acidification and increased fungal dominance. PMID:25261818

  7. The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils.

    PubMed

    Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

    2016-01-01

    Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations

  8. The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils

    PubMed Central

    Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

    2016-01-01

    Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations

  9. Effect of biosolid waste compost on soil respiration in salt-affected soils

    NASA Astrophysics Data System (ADS)

    Raya, Silvia; Gómez, Ignacio; García, Fuensanta; Navarro, José; Jordán, Manuel Miguel; Belén Almendro, María; Martín Soriano, José

    2013-04-01

    A great part of mediterranean soils are affected by salinization. This is an important problem in semiarid areas increased by the use of low quality waters, the induced salinization due to high phreatic levels and adverse climatology. Salinization affects 25% of irrigated agriculture, producing important losses on the crops. In this situation, the application of organic matter to the soil is one of the possible solutions to improve their quality. The main objective of this research was to asses the relation between the salinity level (electrical conductivity, EC) in the soil and the response of microbial activity (soil respiration rate) after compost addition. The study was conducted for a year. Soil samples were collected near to an agricultural area in Crevillente and Elche, "El Hondo" Natural Park (Comunidad de Regantes from San Felipe Neri). The experiment was developed to determine and quantify the soil respiration rate in 8 different soils differing in salinity. The assay was done in close pots -in greenhouse conditions- containing soil mixed with different doses of sewage sludge compost (2, 4 and 6%) besides the control. They were maintained at 60% of water holding capacity (WHC). Soil samples were analyzed every four months for a year. The equipment used to estimate the soil respiration was a Bac-Trac and CO2 emitted by the soil biota was measured and quantified by electrical impedance changes. It was observed that the respiration rate increases as the proportion of compost added to each sample increases as well. The EC was incremented in each sampling period from the beginning of the experiment, probably due to the fact that soils were in pots and lixiviation was prevented, so the salts couldńt be lost from soil. Over time the compost has been degraded and, it was more susceptible to be mineralized. Salts were accumulated in the soil. Also it was observed a decrease of microbial activity with the increase of salinity in the soil. Keywords: soil

  10. Soil microbial community toxic response to atrazine and its residues under atrazine and lead contamination.

    PubMed

    Chen, Qinglin; Yang, Baoshan; Wang, Hui; He, Fei; Gao, Yongchao; Scheel, Ryan A

    2015-01-01

    Intensive use of atrazine and extensive dispersal of lead (Pb) have occurred in farmland with chemical agriculture development. However, the toxicological effect of their presence on soil microorganism remains unknown. The objective of this study was to investigate the impacts of atrazine or Pb on the soil microbiota, soil net nitrogen mineralization, and atrazine residues over a 28-day microcosm incubation. The Shannon-Wiener diversity index, typical microbe species, and a Neighbor-joining tree of typical species from sequencing denaturing gradient gel electrophoresis (DGGE) bands were determined across periodical sampling times. The results showed that the existence of atrazine or Pb (especially high concentration) in soils reduced microbial diversity (the lowest H value is 2.23) compared to the control (H = 2.59) after a 28-day incubation. The species richness reduced little (from 17~19 species to 16~17 species) over the research time. But soil microbial community was significantly affected by the incubation time after the exposure to atrazine or Pb. The combination of atrazine and Pb had a significant inhibition effect on soil net nitrogen nitrification. Atrazine and Pb significantly stimulated soil cumulative net nitrogen mineralization and nitrification. Pb (300 and 600 mg kg(-1)) accelerated the level of atrazine dissipation. The exposure might stimulate the significant growth of the autochthonous soil degraders which may use atrazine as C source and accelerate the dissipation of atrazine in soils. PMID:25106517

  11. Benchmarking and improving microbial-explicit soil biogeochemistry models

    NASA Astrophysics Data System (ADS)

    Wieder, W. R.; Bonan, G. B.; Hartman, M. D.; Sulman, B. N.; Wang, Y.

    2015-12-01

    Earth system models that are designed to project future carbon (C) cycle - climate feedbacks exhibit notably poor representation of soil biogeochemical processes and generate highly uncertain projections about the fate of the largest terrestrial C pool on Earth. Given these shortcomings there has been intense interest in soil biogeochemical model development, but parallel efforts to create the analytical tools to characterize, improve and benchmark these models have thus far lagged behind. A long-term goal of this work is to develop a framework to compare, evaluate and improve the process-level representation of soil biogeochemical models that could be applied in global land surface models. Here, we present a newly developed global model test bed that is built on the Carnegie Ames Stanford Approach model (CASA-CNP) that can rapidly integrate different soil biogeochemical models that are forced with consistent driver datasets. We focus on evaluation of two microbial explicit soil biogeochemical models that function at global scales: the MIcrobial-MIneral Carbon Stabilization model (MIMICS) and Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model. Using the global model test bed coupled to MIMICS and CORPSE we quantify the uncertainty in potential C cycle - climate feedbacks that may be expected with these microbial explicit models, compared with a conventional first-order, linear model. By removing confounding variation of climate and vegetation drivers, our model test bed allows us to isolate key differences among different soil model structure and parameterizations that can be evaluated with further study. Specifically, the global test bed also identifies key parameters that can be estimated using cross-site observations. In global simulations model results are evaluated with steady state litter, microbial biomass, and soil C pools and benchmarked against independent globally gridded data products.

  12. Soil erosion increases soil microbial activity at the depositional position of eroding slopes

    NASA Astrophysics Data System (ADS)

    Meng, Xu; Cardenas, Laura M.; Donovan, Neil; Zhang, Junling; Murray, Phil; Zhang, Fusuo; Dungait, Jennifer A. J.

    2016-04-01

    Soil erosion is the most widespread form of soil degradation. Estimation of the impact of agricultural soil erosion on global carbon cycle is a topic of scientific debate, with opposing yet similar magnitude estimates of erosion as a net source or sink of atmospheric carbon. The transport and deposition of eroded agricultural soils affects not only the carbon cycle but other nutrient cycles as well. It has been estimated that erosion-induced lateral fluxes of nitrogen (N) and phosphorus (P) could be similar in magnitude to those from fertilizer application and crop removal (Quinton et al., 2010). In particular, the dynamics of soil N in eroding slopes need to be considered because the management of soil N has profound influences on the functioning of soil microorganisms, which are generally considered as the main biotic driver of soil C efflux. Carbon dioxide (CO2) emissions tend to increase in deposition positions of eroded slopes, diminishing the sink potential of eroded soils C (. As the global warming potential of nitrous oxide (N2O) is 310 times relative to that of CO2, the sink potential of agricultural erosion could easily be negated with a small increase in N2O emissions. Therefore, an investigation of the potential emissions of greenhouse gases, and especially N2O from soils affected by agricultural erosion, are required. In the present study, a field experiment was established with contrasting cultivation techniques of a C4 crop (Zea mays; δ13C = -12.2‰) to introduce 13C-enriched SOC to a soil previously cropped with C3 plants (δ13C = -29.3‰). Soils sampled from the top, middle, bottom and foot slope positions along a distinct erosion pathway were analyzed using 13C-phospholipid fatty acid (PLFA) analysis and incubated to investigate the responses of microorganisms and associated potential emissions of greenhouse gases (GHG). The total C and N contents were greatest in soils at the top slope position, whereas soil mineral N (NO3--N and NH4+-N

  13. How agricultural management shapes soil microbial communities: patterns emerging from genetic and genomic studies

    NASA Astrophysics Data System (ADS)

    Daly, Amanda; Grandy, A. Stuart

    2016-04-01

    Agriculture is a predominant land use and thus a large influence on global carbon (C) and nitrogen (N) balances, climate, and human health. If we are to produce food, fiber, and fuel sustainably we must maximize agricultural yield while minimizing negative environmental consequences, goals towards which we have made great strides through agronomic advances. However, most agronomic strategies have been designed with a view of soil as a black box, largely ignoring the way management is mediated by soil biota. Because soil microbes play a central role in many of the processes that deliver nutrients to crops and support their health and productivity, agricultural management strategies targeted to exploit or support microbial activity should deliver additional benefits. To do this we must determine how microbial community structure and function are shaped by agricultural practices, but until recently our characterizations of soil microbial communities in agricultural soils have been largely limited to broad taxonomic classes due to methodological constraints. With advances in high-throughput genetic and genomic sequencing techniques, better taxonomic resolution now enables us to determine how agricultural management affects specific microbes and, in turn, nutrient cycling outcomes. Here we unite findings from published research that includes genetic or genomic data about microbial community structure (e.g. 454, Illumina, clone libraries, qPCR) in soils under agricultural management regimes that differ in type and extent of tillage, cropping selections and rotations, inclusion of cover crops, organic amendments, and/or synthetic fertilizer application. We delineate patterns linking agricultural management to microbial diversity, biomass, C- and N-content, and abundance of microbial taxa; furthermore, where available, we compare patterns in microbial communities to patterns in soil extracellular enzyme activities, catabolic profiles, inorganic nitrogen pools, and nitrogen

  14. Altered soil microbial community at elevated CO2 leads to loss of soil carbon

    PubMed Central

    Carney, Karen M.; Hungate, Bruce A.; Drake, Bert G.; Megonigal, J. Patrick

    2007-01-01

    Increased carbon storage in ecosystems due to elevated CO2 may help stabilize atmospheric CO2 concentrations and slow global warming. Many field studies have found that elevated CO2 leads to higher carbon assimilation by plants, and others suggest that this can lead to higher carbon storage in soils, the largest and most stable terrestrial carbon pool. Here we show that 6 years of experimental CO2 doubling reduced soil carbon in a scrub-oak ecosystem despite higher plant growth, offsetting ≈52% of the additional carbon that had accumulated at elevated CO2 in aboveground and coarse root biomass. The decline in soil carbon was driven by changes in soil microbial composition and activity. Soils exposed to elevated CO2 had higher relative abundances of fungi and higher activities of a soil carbon-degrading enzyme, which led to more rapid rates of soil organic matter degradation than soils exposed to ambient CO2. The isotopic composition of microbial fatty acids confirmed that elevated CO2 increased microbial utilization of soil organic matter. These results show how elevated CO2, by altering soil microbial communities, can cause a potential carbon sink to become a carbon source. PMID:17360374

  15. Microbial Community Responses to Glycine Addition in Kansas Prairie Soils

    NASA Astrophysics Data System (ADS)

    Bottos, E.; Roy Chowdhury, T.; White, R. A., III; Brislawn, C.; Fansler, S.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.

    2015-12-01

    Advances in sequencing technologies are rapidly expanding our abilities to unravel aspects of microbial community structure and function in complex systems like soil; however, characterizing the highly diverse communities is problematic, due primarily to challenges in data analysis. To tackle this problem, we aimed to constrain the microbial diversity in a soil by enriching for particular functional groups within a community through addition of "trigger substrates". Such trigger substrates, characterized by low molecular weight, readily soluble and diffusible in soil solution, representative of soil organic matter derivatives, would also be rapidly degradable. A relatively small energy investment to maintain the cell in a state of metabolic alertness for such substrates would be a better evolutionary strategy and presumably select for a cohort of microorganisms with the energetics and cellular machinery for utilization and growth. We chose glycine, a free amino acid (AA) known to have short turnover times (in the range of hours) in soil. As such, AAs are a good source of nitrogen and easily degradable, and can serve as building blocks for microbial proteins and other biomass components. We hypothesized that the addition of glycine as a trigger substrate will decrease microbial diversity and evenness, as taxa capable of metabolizing it are enriched in relation to those that are not. We tested this hypothesis by incubating three Kansas native prairie soils with glycine for 24 hours at 21 degree Celsius, and measured community level responses by 16S rRNA gene sequencing, metagenomics, and metatranscriptomics. Preliminary evaluation of 16S rRNA gene sequences revealed minor changes in bacterial community composition in response to glycine addition. We will also present data on functional gene abundance and expression. The results of these analyses will be useful in designing sequencing strategies aimed at dissecting and deciphering complex microbial communities.

  16. A GPU Reaction Diffusion Soil-Microbial Model

    NASA Astrophysics Data System (ADS)

    Falconer, Ruth; Houston, Alasdair; Schmidt, Sonja; Otten, Wilfred

    2014-05-01

    Parallelised algorithms are frequent in bioinformatics as a consequence of the close link to informatics - however in the field of soil science and ecology they are less prevalent. A current challenge in soil ecology is to link habitat structure to microbial dynamics. Soil science is therefore entering the 'big data' paradigm as a consequence of integrating data pertinent to the physical soil environment obtained via imaging and theoretical models describing growth and development of microbial dynamics permitting accurate analyses of spatio-temporal properties of different soil microenvironments. The microenvironment is often captured by 3D imaging (CT tomography) which yields large datasets and when used in computational studies the physical sizes of the samples that are amenable to computation are less than 1 cm3. Today's commodity graphics cards are programmable and possess a data parallel architecture that in many cases is capable of out-performing the CPU in terms of computational rates. The programmable aspect is achieved via a low-level parallel programming language (CUDA, OpenCL and DirectX). We ported a Soil-Microbial Model onto the GPU using the DirectX Compute API. We noted a significant computational speed up as well as an increase in the physical size that can be simulated. Some of the drawbacks of such an approach were concerned with numerical precision and the steep learning curve associated with GPGPU technologies.

  17. Soil microbial response to photo-degraded C60 fullerenes.

    PubMed

    Berry, Timothy D; Clavijo, Andrea P; Zhao, Yingcan; Jafvert, Chad T; Turco, Ronald F; Filley, Timothy R

    2016-04-01

    Recent studies indicate that while unfunctionalized carbon nanomaterials (CNMs) exhibit very low decomposition rates in soils, even minor surface functionalization (e.g., as a result of photochemical weathering) may accelerate microbial decay. We present results from a C60 fullerene-soil incubation study designed to investigate the potential links between photochemical and microbial degradation of photo-irradiated C60. Irradiating aqueous (13)C-labeled C60 with solar-wavelength light resulted in a complex mixture of intermediate products with decreased aromaticity. Although addition of irradiated C60 to soil microcosms had little effect on net soil respiration, excess (13)C in the respired CO2 demonstrates that photo-irradiating C60 enhanced its degradation in soil, with ∼ 0.78% of 60 day photo-irradiated C60 mineralized. Community analysis by DGGE found that soil microbial community structure was altered and depended on the photo-treatment duration. These findings demonstrate how abiotic and biotic transformation processes can couple to influence degradation of CNMs in the natural environment. PMID:26774781

  18. Metagenomic analysis of microbial community in uranium-contaminated soil.

    PubMed

    Yan, Xun; Luo, Xuegang; Zhao, Min

    2016-01-01

    Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China. PMID:26433967

  19. Measures of Microbial Biomass for Soil Carbon Decomposition Models

    NASA Astrophysics Data System (ADS)

    Mayes, M. A.; Dabbs, J.; Steinweg, J. M.; Schadt, C. W.; Kluber, L. A.; Wang, G.; Jagadamma, S.

    2014-12-01

    Explicit parameterization of the decomposition of plant inputs and soil organic matter by microbes is becoming more widely accepted in models of various complexity, ranging from detailed process models to global-scale earth system models. While there are multiple ways to measure microbial biomass, chloroform fumigation-extraction (CFE) is commonly used to parameterize models.. However CFE is labor- and time-intensive, requires toxic chemicals, and it provides no specific information about the composition or function of the microbial community. We investigated correlations between measures of: CFE; DNA extraction yield; QPCR base-gene copy numbers for Bacteria, Fungi and Archaea; phospholipid fatty acid analysis; and direct cell counts to determine the potential for use as proxies for microbial biomass. As our ultimate goal is to develop a reliable, more informative, and faster methods to predict microbial biomass for use in models, we also examined basic soil physiochemical characteristics including texture, organic matter content, pH, etc. to identify multi-factor predictive correlations with one or more measures of the microbial community. Our work will have application to both microbial ecology studies and the next generation of process and earth system models.

  20. Arsenic mobility during flooding of contaminated soil: the effect of microbial sulfate reduction.

    PubMed

    Burton, Edward D; Johnston, Scott G; Kocar, Benjamin D

    2014-12-01

    In floodplain soils, As may be released during flooding-induced soil anoxia, with the degree of mobilization being affected by microbial redox processes such as the reduction of As(V), Fe(III), and SO4(2-). Microbial SO4(2-) reduction may affect both Fe and As cycling, but the processes involved and their ultimate consequences on As mobility are not well understood. Here, we examine the effect of microbial SO4(2) reduction on solution dynamics and solid-phase speciation of As during flooding of an As-contaminated soil. In the absence of significant levels of microbial SO4(2-) reduction, flooding caused increased Fe(II) and As(III) concentrations over a 10 week period, which is consistent with microbial Fe(III)- and As(V)-reduction. Microbial SO4(2-) reduction leads to lower concentrations of porewater Fe(II) as a result of FeS formation. Scanning electron microscopy with energy dispersive X-ray fluorescence spectroscopy revealed that the newly formed FeS sequestered substantial amounts of As. Bulk and microfocused As K-edge X-ray absorption near-edge structure spectroscopy confirmed that As(V) was reduced to As(III) and showed that in the presence of FeS, solid-phase As was retained partly via the formation of an As2S3-like species. High resolution transmission electron microscopy suggested that this was due to As retention as an As2S3-like complex associated with mackinawite (tetragonal FeS) rather than as a discrete As2S3 phase. This study shows that mackinawite formation in contaminated floodplain soil can help mitigate the extent of arsenic mobilization during prolonged flooding. PMID:25346449

  1. Database on microbial degradation of soil pollutants

    SciTech Connect

    Gleim, D.; Milch, H.; Kracht, M.

    1995-12-31

    The factual database outlined in this paper has been developed to provide rapid reliable information on the biodegradability of soil pollutants and on possible bioremedial action. It contains information both on degradation in pure and mixed cultures and on degradation in soils. At present the study comprises haloaliphatic compounds, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and polychlorinated dioxins and furans.

  2. Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure

    PubMed Central

    Rizvi, Fariha Z.; Rehman, Yasir; Faisal, Muhammad; Hasnain, Shahida; McInerney, Michael J.; Krumholz, Lee R.

    2012-01-01

    Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways. PMID:22768219

  3. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    PubMed

    Sheik, Cody S; Mitchell, Tyler W; Rizvi, Fariha Z; Rehman, Yasir; Faisal, Muhammad; Hasnain, Shahida; McInerney, Michael J; Krumholz, Lee R

    2012-01-01

    Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways. PMID:22768219

  4. 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. PMID:25597673

  5. Changes in Soil Microbial Community Structure with Flooding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flooding disturbs both above- and below-ground ecosystem processes. Although often ignored, changes in below-ground environments are no less important than those that occur above-ground. Shifts in soil microbial community structure are expected when anaerobic conditions develop from flooding. The ...

  6. Rhizosphere microbial community composition affects cadmium and zinc uptake by the metal-hyperaccumulating plant Arabidopsis halleri.

    PubMed

    Muehe, E Marie; Weigold, Pascal; Adaktylou, Irini J; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas; Behrens, Sebastian

    2015-03-01

    The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a "native" and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, "Candidatus Chloracidobacterium") of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. PMID:25595759

  7. Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri

    PubMed Central

    Muehe, E. Marie; Weigold, Pascal; Adaktylou, Irini J.; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas

    2015-01-01

    The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a “native” and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, “Candidatus Chloracidobacterium”) of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. PMID:25595759

  8. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    NASA Astrophysics Data System (ADS)

    Park, J. E.; Lee, B. T.; Son, A.

    2015-12-01

    Heavy metals leached from exhausted mines have been causing severe environmental problems in nearby soils and groundwater. Environmental mitigation was performed based on the heavy metal stabilization using Calcite and steel slag in Korea. Since the soil stabilization only temporarily immobilizes the contaminants to soil matrix, the potential risk of re-leaching heavy metal still exists. Therefore the follow-up management of stabilized soils and the corresponding evaluation methods are required to avoid the consequent contamination from the stabilized soils. In this study, microbial community analysis using pyrosequencing was performed for assessing the potential leaching of the stabilized soils. As a result of rarefaction curve and Chao1 and Shannon indices, the stabilized soil has shown lower richness and diversity as compared to non-contaminated negative control. At the phyla level, as the degree of contamination increases, most of phyla decreased with only exception of increased proteobacteria. Among proteobacteria, gamma-proteobacteria increased against the heavy metal contamination. At the species level, Methylobacter tundripaludum of gamma-proteobacteria showed the highest relative portion of microbial community, indicating that methanotrophs may play an important role in either solubilization or immobilization of heavy metals in stabilized soils.

  9. Impact of (±)-catechin on soil microbial communities

    PubMed Central

    Kaur, Rajwant; Kaur, Surinder

    2009-01-01

    Catechin is a highly studied but controversial allelochemical reported as a component of the root exudates of Centaurea maculosa. Initial reports of high and consistent exudation rates and soil concentrations have been shown to be highly inaccurate, but the chemical has been found in root exudates at and much less frequently in soil but sporadically at high concentrations. Part of the problem of detection and measuring phytotoxicity in natural soils may be due to the confounding effect of soil microbes, and little is known about interactions between catechin and soil microbes. Here we tested the effect of catechin on soil microbial communities and the feedback of these effects to two plant species. We found that catechin inhibits microbial activity in the soil we tested, and by doing so appears to promote plant growth in the microbe-free environment. This is in striking contrast to other in vitro studies, emphasizing the highly conditional effects of the chemical and suggesting that the phytotoxic effects of catechin may be exerted through the microbes in some soils. PMID:19704908

  10. Climate change-driven treeline advances in the Urals alter soil microbial communities

    NASA Astrophysics Data System (ADS)

    Djukic, Ika; Moiseev, Pavel; Hagedorn, Frank

    2016-04-01

    Climatic warming may affect microbial communities and their functions either directly through increased temperatures or indirectly by changes in vegetation. Treelines are temperature-limited vegetation boundaries from tundra to forests. In unmanaged regions of the Ural mountains, there is evidence that the forest-tundra ecotone has shifted upward in response to climate warming during the 20th century. Little is known about the effects of the treeline advances on the microbial structure and function and hence they feedbacks on the belowground carbon and nitrogen cycling In our study, we aimed to estimate how ongoing upward shifts of the treeline ecotone might affect soil biodiversity and its function and hence soil carbon (C) and nitrogen (N) dynamics in the Southern and Polar Ural mountains. Along altitudinal gradients reaching from the tundra to forests, we determined the soil microbial community composition (using Phospholipid Fatty Acids method) and quantified the activity of several extracellular enzymes involved in the C and nutrient cycling. In addition, we measured C pools in biomass and soils and quantified C and N mineralization. The results for the top soils, both in South Urals and in the Polar Ural, indicate a close link between climate change driven vegetation changes and soil microbial communities. The observed changes in microbial structure are induced through the resulting more favorable conditions than due to a shift in litter quality. The activities of chitinase were significantly higher under trees than under herbaceous plants, while activities of cellulase and protease declined with altitude from the tundra to the closed forest. In contrast to enzymatic activities, soil carbon stocks did not change significantly with altitude very likely as a result of a balancing out of increased C inputs from vegetation by an enhanced C output through mineralization with forest expansion. The accelerated organic matter turnover in the forest than in the tundra

  11. Accessing the Soil Metagenome for Studies of Microbial Diversity▿ †

    PubMed Central

    Delmont, Tom O.; Robe, Patrick; Cecillon, Sébastien; Clark, Ian M.; Constancias, Florentin; Simonet, Pascal; Hirsch, Penny R.; Vogel, Timothy M.

    2011-01-01

    Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome. PMID:21183646

  12. Distinct microbial communities associated with buried soils in the Siberian tundra

    PubMed Central

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Mikutta, Robert; Owens, Sarah; Gilbert, Jack; Schnecker, Jörg; Wild, Birgit; Hannisdal, Bjarte; Maerz, Joeran; Lashchinskiy, Nikolay; Čapek, Petr; Šantrůčková, Hana; Gentsch, Norman; Shibistova, Olga; Guggenberger, Georg; Richter, Andreas; Torsvik, Vigdis L; Schleper, Christa; Urich, Tim

    2014-01-01

    Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze–thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes. PMID:24335828

  13. Soil Mineralogy and Substrate Quality Effects on Microbial Priming

    NASA Astrophysics Data System (ADS)

    Finley, B. K.; Rasmussen, C.; Dijkstra, P.; Schwartz, E.; Mau, R. L.; Liu, X. J. A.; Hungate, B. A.

    2014-12-01

    Soil carbon (C) cycling can slow or accelerate in response to new C inputs from fresh organic matter. This change in native C mineralization, known as the "microbial priming effect," is difficult to predict because the underlying mechanisms of priming are still poorly understood. We hypothesized that soil mineral assemblage, specifically short-range-order (SRO) minerals, influences microbial responses to different quality C substrate inputs. To test this, we added 350 μg C g-1soil weekly of an artificial root exudates mixture primarily comprised of glucose, sucrose, lactate and fructose (a simple C source) or ground ponderosa pine litter (a complex C source) for six weeks to three soil types from similar ecosystems derived from different parent material. The soils, from andesite, basalt, and granite parent materials, had decreasing abundance in SRO minerals, respectively. We found that the simple C substrate induced 63 ±16.3% greater positive priming than the complex C across all soil types. The quantity of soil SRO materials was negatively correlated with soil respiration, but positively correlated with priming. The lowest SRO soil amended with litter primed the least (14 ± 11 μgCO2-C g-1), while the largest priming effect occurring in the highest SRO soil amended with simple substrate (246 ± 18 μgCO2-C g-1). Our results indicate that higher SRO mineral content could accelerate microorganisms' capacity to mineralize native soil organic carbon and respond more strongly to labile C inputs. However, while all treatments exhibited positive priming, the amount of C added over the six-week incubation was greater than total CO2 respired. This suggests that despite a relative stimulation of native C mineralization, these soils act as C sinks rather than sources in response to fresh organic matter inputs.

  14. Can soil drying affect the sorption of pesticides in soil?

    NASA Astrophysics Data System (ADS)

    Chaplain, Véronique; Saint, Philippe; Mamy, Laure; Barriuso, Enrique

    2010-05-01

    The sorption of pesticides in soils mainly controls their further dispersion into the environment. Sorption is usually related to the physico-chemical properties of molecules but it also depends on the hydrophobic features of soils. However, the hydrophobicity of soils changes with wetting and drying cycles and this can be enhanced with climate change. The objective of this study was to measure by using controlled artificial soils the influence of the hydrophobic characteristic of soils on the retention of a model pesticide. Artificial soils consisted in silica particles covered by synthetic cationic polymers. Polymers were characterized by the molar ratio of monomers bearing an alkyl chain of 12C. Two polymers were used, with 20 and 80 % ratios, and the same degree of polymerization. In addition, porous and non-porous particles were used to study the accessibility notion and to measure the influence of diffusion on pesticide sorption kinetics. Lindane was chosen as model molecule because its adsorption is supposed mainly due to hydrophobic interactions. Results on polymers adsorption on silica showed that it was governed by electrostatic interactions, without any dependency of the hydrophobic ratio. Polymers covered the entire surface of porous particles. Kinetic measurements showed that lindane sorption was slowed in porous particles due to the molecular diffusion inside the microporosity. The adsorption of lindane on covered silica particles corresponded to a partition mechanism described by linear isotherms. The slope was determined by the hydrophobic ratio of polymers: the sorption of lindane was highest in the most hydrophobic artificial soil. As a result, modification in soil hydrophobicity, that can happen with climate change, might affect the sorption and the fate of pesticides. However additional experiments are needed to confirm these first results. Such artificial soils should be used as reference materials to compare the reactivity of pesticides, to

  15. Long-term effect on some chemical parameter and microbial diversity in a conifer forest soil

    NASA Astrophysics Data System (ADS)

    Iglesias, T.; Iglesias, M.; Francisco-Álvarez, R.; Ramírez, M.; Fernández-Bermejo, M. C.

    2009-04-01

    Soil microbiota are one of the soil components most affected by wildfires. The data from the present study were obtained from a conifer forest soil at Sierra de Gredos (Ávila, central Spain) twenty years after fire of low-to-moderate intensity. A set of soil characteristics indicated the extent to which the spontaneous recovery of the soil is produced as a result of vegetation regrowth. Ten months after fire a strong increase in soil pH, organic C and N, and exchangeable Ca and K, with respect the control soil. Eighteen years after this fire it was observed a decrease of soil organic C and N, whereas other variables such as pH, exchangeable Ca and K were slightly increased with respect to control soil. Is summe a change in soil microbiota was observed due to wildfire, with a decrease in fungi and bacteria population, Also some changes in microbial community was detected, Key words: Forest Fire, soil microbiology, chemical soil properties

  16. Microbial Succession in Glacial Foreland Soils of the Canadian Subarctic

    NASA Astrophysics Data System (ADS)

    Kazemi, S.; Lanoil, B. D.

    2014-12-01

    The Canadian arctic has experienced increasing temperatures over the past century leading to heightened rate of glacial retreat. Glacial retreat leads to subsequent exposure of foreland soils to atmospheric conditions, thus creating a sequence of change in these ecosystems. Microbes are critical for soil development and nutrient dynamics in glacial systems as they are the primary colonizers of these soils and have been demonstrated to play a role in geochemical weathering and nutrient cycling beneath the glacier. Although viable microbial communities exist beneath glaciers and are known to be important for the glacial ecosystem, the impact of glacial retreat on these communities and development of the resulting foreland ecosystem is not well understood. Here, we investigate how microbial communities respond to changing conditions brought on by glacial retreat and whether a pattern of succession, such as those found in well characterized plant systems, occurs along a soil foreland in these microbial communities. We hypothesis that time since deglaciation is the major determinant of structure and composition of microbial assemblages. To test this, soil samples were collected along two glacier forelands, Trapridge Glacier and Duke River Glacier, located in Kluane National Park, Yukon Territory. Chronosequence dating of satellite images using geographic information system software revealed sampling sites have been ice-free from ~30 years to over 60 years. Soil chemistry analysis of major nutrients revealed no change in chemical parameters along the chronosequence, suggesting that presence of microbes after exposure from subglacial environments does not significantly alter soil characteristics in the timeframe observed. Furthermore, next-generation IonTorrentTM sequencing performed on soil samples revealed over five million sequencing reads, suggesting prominent microbial presence within these soils. Further analysis on sequencing data is needed to establish the

  17. Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil

    PubMed Central

    Wild, Birgit; Schnecker, Jörg; Alves, Ricardo J. Eloy; Barsukov, Pavel; Bárta, Jiří; Čapek, Petr; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Lashchinskiy, Nikolay; Mikutta, Robert; Rusalimova, Olga; Šantrůčková, Hana; Shibistova, Olga; Urich, Tim; Watzka, Margarete; Zrazhevskaya, Galina; Richter, Andreas

    2014-01-01

    Rising temperatures in the Arctic can affect soil organic matter (SOM) decomposition directly and indirectly, by increasing plant primary production and thus the allocation of plant-derived organic compounds into the soil. Such compounds, for example root exudates or decaying fine roots, are easily available for microorganisms, and can alter the decomposition of older SOM (“priming effect”). We here report on a SOM priming experiment in the active layer of a permafrost soil from the central Siberian Arctic, comparing responses of organic topsoil, mineral subsoil, and cryoturbated subsoil material (i.e., poorly decomposed topsoil material subducted into the subsoil by freeze–thaw processes) to additions of 13C-labeled glucose, cellulose, a mixture of amino acids, and protein (added at levels corresponding to approximately 1% of soil organic carbon). SOM decomposition in the topsoil was barely affected by higher availability of organic compounds, whereas SOM decomposition in both subsoil horizons responded strongly. In the mineral subsoil, SOM decomposition increased by a factor of two to three after any substrate addition (glucose, cellulose, amino acids, protein), suggesting that the microbial decomposer community was limited in energy to break down more complex components of SOM. In the cryoturbated horizon, SOM decomposition increased by a factor of two after addition of amino acids or protein, but was not significantly affected by glucose or cellulose, indicating nitrogen rather than energy limitation. Since the stimulation of SOM decomposition in cryoturbated material was not connected to microbial growth or to a change in microbial community composition, the additional nitrogen was likely invested in the production of extracellular enzymes required for SOM decomposition. Our findings provide a first mechanistic understanding of priming in permafrost soils and suggest that an increase in the availability of organic carbon or nitrogen, e.g., by increased

  18. 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

  19. 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

  20. Silver Nanoparticles, Ions, and Shape Governing Soil Microbial Functional Diversity: Nano Shapes Micro

    PubMed Central

    Zhai, Yujia; Hunting, Ellard R.; Wouters, Marja; Peijnenburg, Willie J. G. M.; Vijver, Martina G.

    2016-01-01

    Silver nanoparticles (AgNPs) affect microbial metabolic processes at single cell level or lab-culture strains. However, the impact of different AgNPs properties such as the particle, ion release, and shape on functional responses of natural soil microbial communities remain poorly understood. Therefore, we assessed the relative importance of particles and ions of AgNPs in bacterial toxicity and how the functional diversity of soil microbial communities were impacted by AgNPs shapes (i.e., plates, spheres, and rods) in laboratory incubations. Our results showed that the relative contribution of AgNPs(particle) increased with increasing exposure concentrations (accounted for about 60–68% of the total toxicity at the highest exposure level). In addition, the functional composition of the microbial community differed significantly according to different AgNPs shapes. The various properties of AgNPs thus can significantly and differentially affect the functional composition of microbial communities and associated ecosystem processes depending on the level of environmental exposure. PMID:27504108

  1. Silver Nanoparticles, Ions, and Shape Governing Soil Microbial Functional Diversity: Nano Shapes Micro.

    PubMed

    Zhai, Yujia; Hunting, Ellard R; Wouters, Marja; Peijnenburg, Willie J G M; Vijver, Martina G

    2016-01-01

    Silver nanoparticles (AgNPs) affect microbial metabolic processes at single cell level or lab-culture strains. However, the impact of different AgNPs properties such as the particle, ion release, and shape on functional responses of natural soil microbial communities remain poorly understood. Therefore, we assessed the relative importance of particles and ions of AgNPs in bacterial toxicity and how the functional diversity of soil microbial communities were impacted by AgNPs shapes (i.e., plates, spheres, and rods) in laboratory incubations. Our results showed that the relative contribution of AgNPs(particle) increased with increasing exposure concentrations (accounted for about 60-68% of the total toxicity at the highest exposure level). In addition, the functional composition of the microbial community differed significantly according to different AgNPs shapes. The various properties of AgNPs thus can significantly and differentially affect the functional composition of microbial communities and associated ecosystem processes depending on the level of environmental exposure. PMID:27504108

  2. The influence of ecological and conventional plant production systems on soil microbial quality under hops (Humulus lupulus).

    PubMed

    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

  3. Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities.

    PubMed

    Liu, Jun; He, Xiao-Xin; Lin, Xue-Rui; Chen, Wen-Ce; Zhou, Qi-Xing; Shu, Wen-Sheng; Huang, Li-Nan

    2015-06-01

    The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota. PMID:25919421

  4. 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

  5. Precipitation pulse size effects on Sonoran Desert soil microbial crusts.

    PubMed

    Cable, Jessica M; Huxman, Travis E

    2004-10-01

    Deserts are characterized by low productivity and substantial unvegetated space, which is often covered by soil microbial crust communities. Microbial crusts are important for nitrogen fixation, soil stabilization and water infiltration, but their role in ecosystem production is not well understood. This study addresses the following questions: what are the CO2 exchange responses of crusts to pulses of water, does the contribution of crusts to ecosystem flux differ from the soil respiratory flux, and is this contribution pulse size dependent? Following water application to crusts and soils, CO2 exchange was measured and respiration was partitioned through mixing model analysis of Keeling plots across treatments. Following small precipitation pulse sizes, crusts contributed 80% of soil-level CO2 fluxes to the atmosphere. However, following a large pulse event, roots and soil microbes contributed nearly 100% of the soil-level flux. Rainfall events in southern Arizona are dominated by small pulse sizes, suggesting that crusts may frequently contribute to ecosystem production. Carbon cycle studies of arid land systems should consider crusts as important contributors because of their dynamic responses to different pulse sizes as compared to the remaining ecosystem components. PMID:14669007

  6. Regulation of Soil Microbial Carbon-use Efficiency by Soil Moisture, Substrate Addition, and Incubation Time

    NASA Astrophysics Data System (ADS)

    Stark, J.

    2015-12-01

    Microbial carbon-use efficiency (CUE) is a key variable in biogeochemical cycling that regulates soil C sequestration, greenhouse gas emissions, and retention of inorganic nutrients. Microbial CUE is the fraction of C converted to biomass rather than respired as CO2. Biogeochemical models have been shown to be highly sensitive to variation in CUE; however, we currently have a poor understanding of how CUE responds to environmental variables such as soil moisture and nutrient limitations. We examined the effect of soil moisture and C supply on CUE in soil from a western hemlock / sitka spruce forest in Oregon, USA, using a novel technique which supplies 13C and 15N substrates through the gas phase so that water addition is not necessary. Soil samples (28 g oven-dry equiv. wt) at two water potentials (-0.03 and -3.55 MPa) were exposed to 13C-acetic acid vapor for either 6 or 30 sec to provide two different concentrations of acetate to soil microbial communities. The soils were also injected with small amounts of 15NH3 gas to allow quantification of microbial N assimilation rates and to provide an alternate method of calculating CUE. Rates of 13CO2 respiration were measured continuously during a 48-h incubation using cavity ring-down spectroscopy. Soil samples were extracted at seven time intervals (0, 0.5, 1.5, 4.5, 12, 24, and 48 h) in 0.5 M K2SO4 and analyzed for DO13C, microbial 13C, DO15N, inorganic 15N, and microbial 15N to calculate how gross rates of C and N assimilation and microbial CUE change with incubation time. As expected, microbial C and N assimilation rates and CUE increased with soil moisture and the quantity of acetate added; however, C:N assimilated was higher at lower soil moisture, suggesting that either C-storage compounds were being created, or that fungal communities were responsible for a greater proportion of the assimilation in drier soils. Assimilation rates and CUE also changed with incubation time, demonstrating that estimates of CUE

  7. Fast microbial reduction of ferrihydrite colloids from a soil effluent

    NASA Astrophysics Data System (ADS)

    Fritzsche, Andreas; Bosch, Julian; Rennert, Thilo; Heister, Katja; Braunschweig, Juliane; Meckenstock, Rainer U.; Totsche, Kai U.

    2012-01-01

    Recent studies on the microbial reduction of synthetic iron oxide colloids showed their superior electron accepting property in comparison to bulk iron oxides. However, natural colloidal iron oxides differ in composition from their synthetic counterparts. Besides a potential effect of colloid size, microbial iron reduction may be accelerated by electron-shuttling dissolved organic matter (DOM) as well as slowed down by inhibitors such as arsenic. We examined the microbial reduction of OM- and arsenic-containing ferrihydrite colloids. Four effluent fractions were collected from a soil column experiment run under water-saturated conditions. Ferrihydrite colloids precipitated from the soil effluent and exhibited stable hydrodynamic diameters ranging from 281 (±146) nm in the effluent fraction that was collected first and 100 (±43) nm in a subsequently obtained effluent fraction. Aliquots of these oxic effluent fractions were added to anoxic low salt medium containing diluted suspensions of Geobacter sulfurreducens. Independent of the initial colloid size, the soil effluent ferrihydrite colloids were quickly and completely reduced. The rates of Fe2+ formation ranged between 1.9 and 3.3 fmol h-1 cell-1, and are in the range of or slightly exceeding previously reported rates of synthetic ferrihydrite colloids (1.3 fmol h-1 cell-1), but greatly exceeding previously known rates of macroaggregate-ferrihydrite reduction (0.07 fmol h-1 cell-1). The inhibition of microbial Fe(III) reduction by arsenic is unlikely or overridden by the concurrent enhancement induced by soil effluent DOM. These organic species may have increased the already high intrinsic reducibility of colloidal ferrihydrite owing to quinone-mediated electron shuttling. Additionally, OM, which is structurally associated with the soil effluent ferrihydrite colloids, may also contribute to the higher reactivity due to increasing solubility and specific surface area of ferrihydrite. In conclusion, ferrihydrite

  8. Evaluation of the Effects of Tillage on Selected Soil Enzyme Activities and Soil Microbial Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The number, diversity and distribution of microorganisms in the soil and their ability to function within an ecosystem may refelct on the quality of the soil. Research shows that tillage systems, minimum and no-till (NT) or conventionally tilled (CT) soils may affect the properties of soil. Soil en...

  9. 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

  10. Fungicide Dissipation and Impact on Metolachlor Aerobic Soil Degradation and Soil Microbial Dynamics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pesticides are typically applied as mixtures and or sequentially to soil during crop production. A common scenario is herbicide application at planting followed by sequential fungicide applications post-emergence. Fungicides depending on their spectrum of activity may alter and impact soil microbial...

  11. Relationships among plants, soils and microbial communities along a hydrological gradient in the New Jersey Pinelands, USA

    PubMed Central

    Yu, Shen; Ehrenfeld, Joan G.

    2010-01-01

    Background and Aims Understanding the role of different components of hydrology in structuring wetland communities is not well developed. A sequence of adjacent wetlands located on a catenary sequence of soils and receiving the same sources and qualities of water is used to examine specifically the role of water-table median position and variability in affecting plant and microbial community composition and soil properties. Methods Two replicates of three types of wetland found adjacent to each other along a hydrological gradient in the New Jersey Pinelands (USA) were studied. Plant-community and water-table data were obtained within a 100-m2 plot in each community (pine swamp, maple swamp and Atlantic-white-cedar swamp). Monthly soil samples from each plot were analysed for soil moisture, organic matter, extractable nitrogen fractions, N mineralization rate and microbial community composition. Multivariate ordination methods were used to compare patterns among sites within and between data sets. Key Results The maple and pine wetlands were more similar to each other in plant community composition, soil properties and microbial community composition than either was to the cedar swamps. However, maple and pine wetlands differed from each other in water-table descriptors as much as they differed from the cedar swamps. All microbial communities were dominated by Gram-positive bacteria despite hydrologic differences among the sites. Water-table variability was as important as water-table level in affecting microbial communities. Conclusions Water tables affect wetland communities through both median level and variability. Differentiation of both plant and microbial communities are not simple transforms of differences in water-table position, even when other hydrologic factors are kept constant. Rather, soil genesis, a result of both water-table position and geologic history, appears to be the main factor affecting plant and microbial community similarities. PMID

  12. Carbon input increases microbial nitrogen demand, but not microbial nitrogen mining in boreal forest soils

    NASA Astrophysics Data System (ADS)

    Wild, Birgit; Alaei, Saeed; Bengtson, Per; Bodé, Samuel; Boeckx, Pascal; Schnecker, Jörg; Mayerhofer, Werner; Rütting, Tobias

    2016-04-01

    Plant primary production at mid and high latitudes is often limited by low soil N availability. It has been hypothesized that plants can indirectly increase soil N availability via root exudation, i.e., via the release of easily degradable organic compounds such as sugars into the soil. These compounds can stimulate microbial activity and extracellular enzyme synthesis, and thus promote soil organic matter (SOM) decomposition ("priming effect"). Even more, increased C availability in the rhizosphere might specifically stimulate the synthesis of enzymes targeting N-rich polymers such as proteins that store most of the soil N, but are too large for immediate uptake ("N mining"). This effect might be particularly important in boreal forests, where plants often maintain high primary production in spite of low soil N availability. We here tested the hypothesis that increased C availability promotes protein depolymerization, and thus soil N availability. In a laboratory incubation experiment, we added 13C-labeled glucose to a range of soil samples derived from boreal forests across Sweden, and monitored the release of CO2 by C mineralization, distinguishing between CO2 from the added glucose and from the native, unlabeled soil organic C (SOC). Using a set of 15N pool dilution assays, we further measured gross rates of protein depolymerization (the breakdown of proteins into amino acids) and N mineralization (the microbial release of excess N as ammonium). Comparing unamended control samples, we found a high variability in C and N mineralization rates, even when normalized by SOC content. Both C and N mineralization were significantly correlated to SOM C/N ratios, with high C mineralization at high C/N and high N mineralization at low C/N, suggesting that microorganisms adjusted C and N mineralization rates to the C/N ratio of their substrate and released C or N that was in excess. The addition of glucose significantly stimulated the mineralization of native SOC in soils

  13. Structures of Microbial Communities in Alpine Soils: Seasonal and Elevational Effects

    PubMed Central

    Lazzaro, Anna; Hilfiker, Daniela; Zeyer, Josef

    2015-01-01

    Microbial communities in alpine environments are exposed to several environmental factors related to elevation and local site conditions and to extreme seasonal variations. However, little is known on the combined impact of such factors on microbial community structure. We assessed the effects of seasonal variations on soil fungal and bacterial communities along an elevational gradient (from alpine meadows to a glacier forefield, 1930–2519 m a.s.l.) over 14 months. Samples were taken during all four seasons, even under the winter snowpack and at snowmelt. Microbial community structures and abundances were investigated using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR (qPCR) of the 16S and 18S rRNA genes. Illumina sequencing was performed to identify key bacterial groups in selected samples. We found that the soil properties varied significantly with the seasons and along the elevational gradient. For example, concentrations of soluble nutrients (e.g., NH4+-N, SO42−-S, PO43−-P) significantly increased in October but decreased drastically under the winter snowpack. At all times, the alpine meadows showed higher soluble nutrient concentrations than the glacier forefield. Microbial community structures at the different sites were strongly affected by seasonal variations. Under winter snowpack, bacterial communities were dominated by ubiquitous groups (i.e., beta-Proteobacteria, which made up to 25.7% of the total reads in the glacier forefield). In the snow-free seasons, other groups (i.e., Cyanobacteria) became more abundant (from 1% under winter snow in the glacier forefield samples to 8.1% in summer). In summary, elevation had a significant effect on soil properties, whereas season influenced soil properties as well as microbial community structure. Vegetation had a minor impact on microbial communities. At every elevation analyzed, bacterial, and fungal community structures exhibited a pronounced annual cycle. PMID:26635785

  14. Effects of biochar blends on microbial community composition in two Coastal Plain soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated both positive and negative effects on soil microbial communities. These effect...

  15. STABLE CARBON ISOTOPE RATIO AND COMPOSITION OF MICROBIAL FATTY ACIDS IN TROPICAL SOILS

    EPA Science Inventory

    The soil microbial community plays a critical part in tropical ecosystem functioning through its role in the soil organic matter (SOM) cycle. This study evaluates the relative effects of soil type and land use on: (1) soil microbial community structure and (2) the contribution o...

  16. Synthetic fuel oil effects on microbial activity and nitrogen transformations in soil

    SciTech Connect

    Ward, M.H.; Saylor, G.S.; Luxmoore, R.J.

    1984-12-01

    The effects of a solvent refined coal oil (SRC-II) on microbial processes in a Captina silt loam soil were examined. The soil samples were maintained under environmental conditions favorable for most aerobic microbial activities. Soil was treated with four oil concentrations ranging from 0.2 to 8.6% (wt/wt). Oxygen uptake rates, total viable cell counts, numbers of nitrifying bacteria, and inorganic nitrogen concentrations were monitored before oil addition and at regular intervals for three months thereafter. Organic carbon, total nitrogen, and soil pH were also measured before and after application of the oil. The SRC-II coal oil effected soil processes at all treatment levels. The lowest oil concentration (0.2%) decreased numbers of nitrifying bacteria while increasing total viable cell numbers and net nitrogen mineralization. The higher oil concentrations reduced oxygen uptake rates and total viable cells as well as nitrifier numbers. Soil treated with a 1.7% oil concentration showed significant increases in respiration rates and cell densities after two months, while no significant increases were observed at oil levels of 3.4 and 8.6%. The application of the coal oil to soil samples raised the carbon to nitrogen ratio of the soil. The sum of nitrate and ammonium nitrogen in the oil-treated soils was never significantly lower than the control soil levels, indicating that nitrogen was not limiting to decomposition. However, the toxicity of the oil toward the nitrifying bacteria resulted in an accumulation of ammonium in treated soils. This may affect plant establishment on soils contaminated with a synthetic fuel oil. 104 references, 7 figures, 15 tables.

  17. Nutrient Enrichment Mediates the Relationships of Soil Microbial Respiration with Climatic Factors in an Alpine Meadow

    PubMed Central

    Zong, Ning; Jiang, Jing; Shi, Peili; Song, Minghua; Shen, Zhenxi; Zhang, Xianzhou

    2015-01-01

    Quantifying the effects of nutrient additions on soil microbial respiration (Rm) and its contribution to soil respiration (Rs) are of great importance for accurate assessment ecosystem carbon (C) flux. Nitrogen (N) addition either alone (coded as LN and HN) or in combination with phosphorus (P) (coded as LN + P and HN + P) were manipulated in a semiarid alpine meadow on the Tibetan Plateau since 2008. Either LN or HN did not affect Rm, while LN + P enhanced Rm during peak growing periods, but HN + P did not affect Rm. Nutrient addition also significantly affected Rm/Rs, and the correlations of Rm/Rs with climatic factors varied with years. Soil water content (Sw) was the main factor controlling the variations of Rm/Rs. During the years with large rainfall variations, Rm/Rs was negatively correlated with Sw, while, in years with even rainfall, Rm/Rs was positively correlated with Sw. Meanwhile, in N + P treatments the controlling effects of climatic factors on Rm/Rs were more significant than those in CK. Our results indicate that the sensitivity of soil microbes to climatic factors is regulated by nutrient enrichment. The divergent effects of Sw on Rm/Rs suggest that precipitation distribution patterns are key factors controlling soil microbial activities and ecosystem C fluxes in semiarid alpine meadow ecosystems. PMID:26347902

  18. Microbial control on stability of soil organic matter in drought manipulation experiment

    NASA Astrophysics Data System (ADS)

    Blagodatskaya, E.; Schrumpf, M.; Weber, E.; Wutzler, T.; Gleixner, G.; Reichstein, M.; Trumbore, S.

    2012-04-01

    Extending drought periods as a consequence of global warming affect both the amount and the activity of heterotrophic microorganisms in soil. The studies of drought effect on the decomposition of soil organic matter (SOM) which is microbially mediated still show controversial results mainly due to separated research approaches which do not consider the soil - plant system as a whole. We would like to discuss the results obtained within the QuaSOM experiment (Max Planck Institute for Biogeochemistry Jena, Germany) where continues 13C- CO2-labeling was applied during vegetation of peppermint (Mentha piperita L.) under deficit and optimal moisture regimes. The partitioning of plant-originated and SOM-originated carbon in heterotrophic respiration and in microbial biomass will be related to the changes in the microbial growth parameters and enzymes kinetics. The drought effect on temperature sensitivity of the enzymes responsible for the decomposition of SOM-compounds of different availability will be compared in the rhizosphere of peppermint versus bulk soil. The effect of vegetation on cycling of organic matter in soil will be considered for the contrasting moisture regimes. The changes in carbon sequestration potential due to priming effects caused by repeated drying - rewetting events will be evaluated for the short term time scale.

  19. Nitrogen starvation affects bacterial adhesion to soil

    PubMed Central

    Borges, Maria Tereza; Nascimento, Antônio Galvão; Rocha, Ulisses Nunes; Tótola, Marcos Rogério

    2008-01-01

    One of the main factors limiting the bioremediation of subsoil environments based on bioaugmentation is the transport of selected microorganisms to the contaminated zones. The characterization of the physiological responses of the inoculated microorganisms to starvation, especially the evaluation of characteristics that affect the adhesion of the cells to soil particles, is fundamental to anticipate the success or failure of bioaugmentation. The objective of this study was to investigate the effect of nitrogen starvation on cell surface hydrophobicity and cell adhesion to soil particles by bacterial strains previously characterized as able to use benzene, toluene or xilenes as carbon and energy sources. The strains LBBMA 18-T (non-identified), Arthrobacter aurescens LBBMA 98, Arthrobacter oxydans LBBMA 201, and Klebsiella sp. LBBMA 204–1 were used in the experiments. Cultivation of the cells in nitrogen-deficient medium caused a significant reduction of the adhesion to soil particles by all the four strains. Nitrogen starvation also reduced significantly the strength of cell adhesion to the soil particles, except for Klebsiella sp. LBBMA 204–1. Two of the four strains showed significant reduction in cell surface hydrophobicity. It is inferred that the efficiency of bacterial transport through soils might be potentially increased by nitrogen starvation. PMID:24031246

  20. Soil C and N availability determine the priming effect: microbial N mining and stoichiometric decomposition theories.

    PubMed

    Chen, Ruirui; Senbayram, Mehmet; Blagodatsky, Sergey; Myachina, Olga; Dittert, Klaus; Lin, Xiangui; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2014-07-01

    The increasing input of anthropogenically derived nitrogen (N) to ecosystems raises a crucial question: how does available N modify the decomposer community and thus affects the mineralization of soil organic matter (SOM). Moreover, N input modifies the priming effect (PE), that is, the effect of fresh organics on the microbial decomposition of SOM. We studied the interactive effects of C and N on SOM mineralization (by natural (13) C labelling adding C4 -sucrose or C4 -maize straw to C3 -soil) in relation to microbial growth kinetics and to the activities of five hydrolytic enzymes. This encompasses the groups of parameters governing two mechanisms of priming effects - microbial N mining and stoichiometric decomposition theories. In sole C treatments, positive PE was accompanied by a decrease in specific microbial growth rates, confirming a greater contribution of K-strategists to the decomposition of native SOM. Sucrose addition with N significantly accelerated mineralization of native SOM, whereas mineral N added with plant residues accelerated decomposition of plant residues. This supports the microbial mining theory in terms of N limitation. Sucrose addition with N was accompanied by accelerated microbial growth, increased activities of β-glucosidase and cellobiohydrolase, and decreased activities of xylanase and leucine amino peptidase. This indicated an increased contribution of r-strategists to the PE and to decomposition of cellulose but the decreased hemicellulolytic and proteolytic activities. Thus, the acceleration of the C cycle was primed by exogenous organic C and was controlled by N. This confirms the stoichiometric decomposition theory. Both K- and r-strategists were beneficial for priming effects, with an increasing contribution of K-selected species under N limitation. Thus, the priming phenomenon described in 'microbial N mining' theory can be ascribed to K-strategists. In contrast, 'stoichiometric decomposition' theory, that is, accelerated OM

  1. 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

  2. [Microbial anaerobic dechlorination of polychlorinated biphenyls in paddy soil slurry].

    PubMed

    Yang, Kai; Yao, Xiao-yan; Chen, Chen; Shen, Chao-feng; Qin, Zhi-hui; Huang, Rong-lang

    2015-10-01

    We studied the dechlorination process of Aroclor1260, a high-chlorinated polychlorinated biphenyls (PCBs) mixture in an anaerobic paddy soil slurry, and further analyzed the related microbial community structures. The Aroclor1260 was reduced up to 55.5% in the natural paddy soil slurry in 128 days, and the reduction percentage dropped to 46.9% after incoculating the paddy soil slurry with a PCBs-dechlorination enrichment culture. The dechlorination mainly occurred in congeners of pentachlorobiphenyl, hexachlorobiphenyl, and specially, the heptachlorobiphenyl, with pentachlorobiphenyl accumulated as dechlorination intermediate. Hydrogen gas produced from fermentation of organic matters was maintained at a lower partial pressure due to its consumption during the dechlorination process, so that the methanogens was suppressed as well. The microbial community structure was significantly different between natural and inoculated paddy soils. Introducing the PCBs-dechlorination enrichment culture changed the local microbial community by the competition between the exogenetic dchlorinators and the indigenous bacteria, overall decreasing the dechlorination activity. PMID:26995917

  3. Soil Resources Area Affects Herbivore Health

    PubMed Central

    Garner, James A.; Ahmad, H. Anwar; Dacus, Chad M.

    2011-01-01

    Soil productivity effects nutritive quality of food plants, growth of humans and animals, and reproductive health of domestic animals. Game-range surveys sometimes poorly explained variations in wildlife populations, but classification of survey data by major soil types improved effectiveness. Our study evaluates possible health effects of lower condition and reproductive rates for wild populations of Odocoileus virginianus Zimmerman (white-tailed deer) in some physiographic regions of Mississippi. We analyzed condition and reproductive data for 2400 female deer from the Mississippi Department of Wildlife, Fisheries, and Parks herd health evaluations from 1991–1998. We evaluated age, body mass (Mass), kidney mass, kidney fat mass, number of corpora lutea (CL) and fetuses, as well as fetal ages. Region affected kidney fat index (KFI), which is a body condition index, and numbers of fetuses of adults (P ≤ 0.001). Region affected numbers of CL of adults (P ≤ 0.002). Mass and conception date (CD) were affected (P ≤ 0.001) by region which interacted significantly with age for Mass (P ≤ 0.001) and CD (P < 0.04). Soil region appears to be a major factor influencing physical characteristics of female deer. PMID:21776246

  4. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

    PubMed Central

    Pereira de Castro, Alinne; Sartori da Silva, Maria Regina Silveira; Quirino, Betania Ferraz; da Cunha Bustamante, Mercedes Maria; Krüger, Ricardo Henrique

    2016-01-01

    The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture. PMID:26849674

  5. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils.

    PubMed

    de Castro, Alinne Pereira; Sartori da Silva, Maria Regina Silveira; Quirino, Betania Ferraz; da Cunha Bustamante, Mercedes Maria; Krüger, Ricardo Henrique

    2016-01-01

    The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture. PMID:26849674

  6. Soil depth and temperature effects on microbial degradation of 2,4-D

    SciTech Connect

    Veeh, R.H.; Camper, A.K.; Inskeep, W.P.

    1996-01-01

    Numerous soil factors and climatic conditions affect the degradation rate of pesticides in soils. A major soil factor influencing herbicide degradation is the composition and abundance of the microbiota, which has been shown to vary considerably with soil depth. Another important variable affecting microbial growth and degradation kinetics is temperature. Soil samples from 0- to 30-, 30- to 60-, and 60- to 120-cm depths of two Montana soils were placed in reaction flasks and treated with {sup 14}C-labeled 2,4-D at representative field use rates at temperatures of 10, 17, and 24{degrees}C. A carrier gas was used to continuously evacuate evolved {sup 14}CO{sub 2} into NaOH traps as a measure of 2,4-D degradation. Comparisons of the effects of soil depth and temperature were made by fitting experimental data to both first-order and logistic kinetic models. Degradation rates of 2,4-D decreased significantly with increasing soil depth and were positively correlated with bacterial plate counts. Effects of temperature on degradation rate constants were adequately described using the Arrhenius equation. Degradation rates of 2,4-D and bacterial enumerations were positively correlated with changes in soil organic C as a function of soil depth. These results support the idea that changes in organic C with soil depth could be used as a parameter for estimating changes in degradation rate as a function of soil depth. Efforts to model the transport of 2,4-D in soils should account for variation in degradation rate as a function of soil depth and temperature. 46 refs., 4 figs., 3 tabs.

  7. Impact of Fungicides Chlorothalonil and Propiconazole on Microbial Activities in Groundnut (Arachis hypogaea L.) Soils

    PubMed Central

    Ramudu, A. C.; Mohiddin, G. Jaffer; Srinivasulu, M.; Madakka, M.; Rangaswamy, V.

    2011-01-01

    Introduction of agrochemicals (fungicides) into soil may have lasting effects on soil microbial activities and thus affect soil health. In order to determine the changes in microbial activity in a black clay and red sandy loam soils of groundnut (Arachis hypogaea L.) cultivated fields, a case study was conducted with propiconazole and chlorothalonil to evaluate its effects on soil enzymes (cellulase and invertase) throughout 40 days of incubation under laboratory conditions with different concentrations (1.0, 2.5, 5.0, 7.5, and 10.0 kg ha−1). Individual application of the two fungicides at 1.0, 2.5, and 5.0 kg ha−1 to the soil distinctly enhanced the activities of cellulase and invertase but at higher concentrations of 7.5 and 10 kg ha−1 was toxic or innocuous to both cellulase and invertase activities. In soil samples receiving 2.5–5.0 kg ha−1 of the fungicides, the accumulation of reducing sugar was pronounced more at 20 days, and the activity of the cellulase and invertase was drastically decreased with increasing period of incubation up to 30 and 40 days. PMID:23724306

  8. [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. PMID:27111999

  9. Carbon fiber enhanced bioelectricity generation in soil microbial fuel cells.

    PubMed

    Li, Xiaojing; Wang, Xin; Zhao, Qian; Wan, Lili; Li, Yongtao; Zhou, Qixing

    2016-11-15

    The soil microbial fuel cell (MFC) is a promising biotechnology for the bioelectricity recovery as well as the remediation of organics contaminated soil. However, the electricity production and the remediation efficiency of soil MFC are seriously limited by the tremendous internal resistance of soil. Conductive carbon fiber was mixed with petroleum hydrocarbons contaminated soil and significantly enhanced the performance of soil MFC. The maximum current density, the maximum power density and the accumulated charge output of MFC mixed carbon fiber (MC) were 10, 22 and 16 times as high as those of closed circuit control due to the carbon fiber productively assisted the anode to collect the electron. The internal resistance of MC reduced by 58%, 83% of which owed to the charge transfer resistance, resulting in a high efficiency of electron transfer from soil to anode. The degradation rates of total petroleum hydrocarbons enhanced by 100% and 329% compared to closed and opened circuit controls without the carbon fiber respectively. The effective range of remediation and the bioelectricity recovery was extended from 6 to 20cm with the same area of air-cathode. The mixed carbon fiber apparently enhanced the bioelectricity generation and the remediation efficiency of soil MFC by means of promoting the electron transfer rate from soil to anode. The use of conductively functional materials (e.g. carbon fiber) is very meaningful for the remediation and bioelectricity recovery in the bioelectrochemical remediation. PMID:27162144

  10. Active manipulation of native soil microbial community structure and function to suppress soilborne diseases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The reality of naturally occurring biologically-induced disease suppressive soils suggests opportunity for managing resident soil microbial communities as a disease control method. Disease suppressive soils have yielded a significant body of knowledge concerning operative mechanisms leading to t...

  11. Microbial Ecophysiology is a Missing Link in Emerging Microbial-based Soil Organic Matter Frameworks

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.; Frey, S. D.

    2012-12-01

    Recently, our epistemology of soil C dynamics has been undergoing a major transformation; where in the past soil organic matter (SOM) formation was attributed to the biochemical recalcitrance of plant litter, we now know that microbially transformed plant residues and microbial necromass are key precursors of SOM formation. SOM formation is thus a result of complex ecological interactions between substrate availability, the soil biological community, and the decomposing environment, and is a function of multiple ecosystem processes related to climate, soil type and their interactions with resident decomposer communities. Under this emerging new view, microbial biomass is treated generally, without consideration of the ecophysiological processes that regulate the chemistry and abundance of biomass production. In reality, biomass inputs are far more complex in terms of their input rates and potential to serve as a precursor to SOM formation. We explore microbial growth efficiencies (MGE) and growth rates and how their expression across different soil environments can be incorporated into our emerging conceptual models of microbial-mediated SOM formation. MGE and growth rates are both poorly understood despite their direct impact on SOM formation. Specifically, the physiological trade-offs associated with growth rates and MGE need to be assessed in terms of their relative influence on microbial inputs to SOM. Additionally, we need a better understanding of the variation in chemistry of cellular biomass, metabolites and exocellular excretions across species. At a broad level, we know that fungal and bacterial cell walls differ in their chemical recalcitrance and organo-mineral interactions but the degree to which this variation results in long-term differences in SOM dynamics remains unknown. To explore these uncertainties, we use a model-based approach to examine how potential tradeoffs between MGE and growth rates, and their responses to varying environmental

  12. Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The response of soil microbial communities following soil disturbances is poorly understood. The development of soil microbial communities in two restoration gradients was studied to investigate the impact of land-management regime at the W. K. Kellogg Biological Station, Michigan. The first restora...

  13. 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

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

    PubMed

    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 (t lag ) 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 t lag , indicating that favorable

  15. Microbial diversity and functional capacity in polar soils.

    PubMed

    Makhalanyane, Thulani Peter; Van Goethem, Marc Warwick; Cowan, Don Arthur

    2016-04-01

    Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions. PMID:26921734

  16. Soil microbial properties after long-term swine slurry application to conventional and no-tillage systems in Brazil.

    PubMed

    Balota, Elcio L; Machineski, Oswaldo; Hamid, Karima I A; Yada, Ines F U; Barbosa, Graziela M C; Nakatani, Andre S; Coyne, Mark S

    2014-08-15

    Swine waste can be used as an agricultural fertilizer, but large amounts may accumulate excess nutrients in soil or contaminate the surrounding environment. This study evaluated long-term soil amendment (15 years) with different levels of swine slurry to conventional (plow) tillage (CT) and no tillage (NT) soils. Long-term swine slurry application did not affect soil organic carbon. Some chemical properties, such as calcium, base saturation, and aluminum saturation were significantly different within and between tillages for various application rates. Available P and microbial parameters were significantly affected by slurry addition. Depending on tillage, soil microbial biomass and enzyme activity increased up to 120 m(3) ha(-1) year(-1) in all application rates. The NT system had higher microbial biomass and activity than CT at all application levels. There was an inverse relationship between the metabolic quotient (qCO2) and MBC, and the qCO2 was 53% lower in NT than CT. Swine slurry increased overall acid phosphatase activity, but the phosphatase produced per unit of microbial biomass decreased. A comparison of data obtained in the 3rd and 15th years of swine slurry application indicated that despite slurry application the CT system degraded with time while the NT system had improved values of soil quality indicators. For these Brazilian oxisols, swine slurry amendment was insufficient to maintain soil quality parameters in annual crop production without additional changes in tillage management. PMID:24867704

  17. Microbial contents of soil from fire pits

    NASA Astrophysics Data System (ADS)

    Moon, K.; Esparza, V.; de Sandre, J.; Cheney, S.; Anderson, A.; White, M. A.

    2006-12-01

    Forest fires generate polycylic aromatic hydrocarbons (PAHs) that can lead to carcinogenic compounds, which are potential health risks. PAHs can be degraded to water and carbon dioxide by certain soil microbes. Thus, during participation in a NASA-funded summer research experience at Utah State University, our high school student team sampled soils from a month-old fire pit in which plant materials had been burnt. We detected in soil samples, from surface, 10 and 20 cm depths, microbes that would grow on a defined minimal medium source. Other microbes were cultured from the roots of plants that had established at the fire pit. A diversity of microbes was present in all samples based on visible differences in cell shape and color. It was surprising that the surface ash, although exposed to sunlight over the month interval, had culturable colonies. Many of these culturable bacteria were pigmented perhaps as a protection against UV radiation from the sun. We searched for genes in the microbes that encoded enzymes called dioxygenases that in other bacteria are involved in degradation of PAHs. This test involved using polymerase chain reactions to detect the genes. PCR products were found in two of the fifteen isolates tested although their sizes differed from the control gene product from a PAH-degrading mycobacterium isolate. These results suggest that the soils did contain microbes with the possible potential to alter the PAH compounds generated from vegetation fires. Our findings serve as a starting point for future studies looking at recovery and remediation of fired acreages.

  18. Soil Carbon and Nitrogen Mineralization with Flexible Soil and Microbial C:N Ratios

    NASA Astrophysics Data System (ADS)

    Wang, G.; Mayes, M. A.; Thornton, P. E.; Hoffman, F. M.

    2014-12-01

    Microbial assimilation of C-N and the physicochemical protection of soil organic matter (SOM) play fundamental roles in regulating land-atmosphere interactions. However, these microbial and physicochemical processes are not explicitly represented in current region/global terrestrial ecosystem models, e.g., the Community Land Model (CLM). The lack of explicit representation of microbial pools and functions results in unrealistic fixed-C:N ratios in SOM pools currently in CLM. Thus current soil C-N model configuration is inadequate to model the effects of litter inputs or fertilization on soil carbon and nitrogen mineralization and linkages between plant litter C:N ratios and soil or microbial C:N ratios. We propose a coupled C-N model that allows for flexible C:N ratios in microbe and SOM pools and thus the ability to represent the decomposition response to fertilization and/or litter inputs with various C:N ratios. Our preliminary analysis has shown that the C:N ratios in SOM, dissolved organic matter (DOM), and microbial pools can be well constrained by the new C-N model and microbes regulate the C:N ratios in SOM and DOM pools. We will use this new model framework to evaluate the soil carbon and nitrogen mineralization processes under conditions of excess organic C, excess organic N, or limited mineral N.

  19. Evaluation of Methyl Bromide Alternatives Efficacy against Soil-Borne Pathogens, Nematodes and Soil Microbial Community

    PubMed Central

    Xie, Hongwei; Yan, Dongdong; Mao, Liangang; Wang, Qiuxia; Li, Yuan; Ouyang, Canbin; Guo, Meixia; Cao, Aocheng

    2015-01-01

    Methyl bromide (MB) and other alternatives were evaluated for suppression of Fusarium spp., Phytophthora spp., and Meloidogyne spp. and their influence on soil microbial communities. Both Fusarium spp. and Phytophthora spp. were significantly reduced by the MB (30.74 mg kg-1), methyl iodide (MI: 45.58 mg kg-1), metham sodium (MS: 53.92 mg kg-1) treatments. MS exhibited comparable effectiveness to MB in controlling Meloidogyne spp. and total nematodes, followed by MI at the tested rate. By contrast, sulfuryl fluoride (SF: 33.04 mg kg-1) and chloroform (CF: 23.68 mg kg-1) showed low efficacy in controlling Fusarium spp., Phytophthora spp., and Meloidogyne spp. MB, MI and MS significantly lowered the abundance of different microbial populations and microbial biomass in soil, whereas SF and CF had limited influence on them compared with the control. Diversity indices in Biolog studies decreased in response to fumigation, but no significant difference was found among treatments in PLFA studies. Principal component and cluster analyses of Biolog and PLFA data sets revealed that MB and MI treatments greatly influenced the soil microbial community functional and structural diversity compared with SF treatment. These results suggest that fumigants with high effectiveness in suppressing soil-borne disease could significantly influence soil microbial community. PMID:25723395

  20. Soil Microbial Substrate Properties and Microbial Community Responses under Irrigated Organic and Reduced-Tillage Crop and Forage Production Systems

    PubMed Central

    Ghimire, Rajan; Norton, Jay B.; Stahl, Peter D.; Norton, Urszula

    2014-01-01

    Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC) and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs). Under crop production, dissolved organic C (DOC) content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably influenced soil

  1. Assessing toxic levels of hydrocarbons on microbial degrader communities in vadose zone fill soils

    SciTech Connect

    Schoenberg, T.H.; Long, S.C.

    1995-12-31

    Authentic fill samples were collected from the vadose zone at a highway travel plaza. The contamination at the site is a combination of gasoline, diesel, and waste oil resulting from leaking underground storage tanks. Microbial assessments including plate counts and specific-degrader enumerations were performed to establish the presence of degrader microbial communities, and thus bioremediation potential. Contaminant levels were estimated in samples by quantifying headspace VOCs in collection jars. Physical soil characteristics including soil grain size distribution and moisture content were measured to evaluate the potential ecological variables that would affect implementation of a bioremediation technology. Toxicity screening using the Microtox{trademark} acute toxicity assay was used to compare the level of toxicity present among samples. These analyses were used to assess the potential for using in situ bioventing remediation to clean-up the leaking underground storage tank spill study site. High contaminant levels appear to have exerted a toxic effect and resulted in smaller total microbial community sizes in highly contaminated areas (thousands of ppmv) of the site. Microtox{trademark} EC50 results generally corroborated with the trends of the enumeration experiments. Microbial characterization results indicate that in situ bioremediation would be possible at the study site. Soil heterogeneity appears to pose the greatest challenges to the design and implementation of bioremediation at this site.

  2. The PAMPA datasets: a metagenomic survey of microbial communities in Argentinean pampean soils

    PubMed Central

    2013-01-01

    Background Soil is among the most diverse and complex environments in the world. Soil microorganisms play an essential role in biogeochemical cycles and affect plant growth and crop production. However, our knowledge of the relationship between species-assemblies and soil ecosystem processes is still very limited. The aim of this study was to generate a comprehensive metagenomic survey to evaluate the effect of high-input agricultural practices on soil microbial communities. Results We collected soil samples from three different areas in the Argentinean Pampean region under three different types of land uses and two soil sources (bulk and rhizospheric). We extracted total DNA from all samples and also synthetized cDNA from rhizospheric samples. Using 454-FLX technology, we generated 112 16S ribosomal DNA and 14 16S ribosomal RNA amplicon libraries totaling 1.3 M reads and 36 shotgun metagenome libraries totaling 17.8 million reads (7.7 GB). Our preliminary results suggested that water availability could be the primary driver that defined microbial assemblages over land use and soil source. However, when water was not a limiting resource (annual precipitation >800 mm) land use was a primary driver. Conclusion This was the first metagenomic study of soil conducted in Argentina and our datasets are among the few large soil datasets publicly available. The detailed analysis of these data will provide a step forward in our understanding of how soil microbiomes respond to high-input agricultural systems, and they will serve as a useful comparison with other soil metagenomic studies worldwide. PMID:24450949

  3. Non-target impact of fungicide tetraconazole on microbial communities in soils with different agricultural management.

    PubMed

    Sułowicz, Sławomir; Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2016-08-01

    Effect of the fungicide tetraconazole on microbial community in silt loam soils from orchard with long history of triazole application and from grassland with no known history of fungicide usage was investigated. Triazole tetraconazole that had never been used on these soils before was applied at the field rate and at tenfold the FR. Response of microbial communities to tetraconazole was investigated during 28-day laboratory experiment by determination of changes in their biomass and structure (phospholipid fatty acids method-PLFA), activity (fluorescein diacetate hydrolysis-FDA) as well as changes in genetic (DGGE) and functional (Biolog) diversity. Obtained results indicated that the response of soil microorganisms to tetraconazole depended on the management of the soils. DGGE patterns revealed that both dosages of fungicide affected the structure of bacterial community and the impact on genetic diversity and richness was more prominent in orchard soil. Values of stress indices-the saturated/monounsaturated PLFAs ratio and the cyclo/monounsaturated precursors ratio, were almost twice as high and the Gram-negative/Gram-positive ratio was significantly lower in the orchard soil compared with the grassland soil. Results of principal component analysis of PLFA and Biolog profiles revealed significant impact of tetraconazole in orchard soil on day 28, whereas changes in these profiles obtained for grassland soil were insignificant or transient. Obtained results indicated that orchards soil seems to be more vulnerable to tetraconazole application compared to grassland soil. History of pesticide application and agricultural management should be taken into account in assessing of environmental impact of studied pesticides. PMID:27106012

  4. Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation

    PubMed Central

    Uroz, Stéphane; Ioannidis, Panos; Lengelle, Juliette; Cébron, Aurélie; Morin, Emmanuelle; Buée, Marc; Martin, Francis

    2013-01-01

    In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France). The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource availability impact the

  5. Microbial responses to multi-factor climate change: effects on soil enzymes

    PubMed Central

    Steinweg, J. Megan; Dukes, Jeffrey S.; Paul, Eldor A.; Wallenstein, Matthew D.

    2013-01-01

    The activities of extracellular enzymes, the proximate agents of decomposition in soils, are known to depend strongly on temperature, but less is known about how they respond to changes in precipitation patterns, and the interaction of these two components of climate change. Both enzyme production and turnover can be affected by changes in temperature and soil moisture, thus it is difficult to predict how enzyme pool size may respond to altered climate. Soils from the Boston-Area Climate Experiment (BACE), which is located in an old field (on abandoned farmland), were used to examine how climate variables affect enzyme activities and microbial biomass carbon (MBC) in different seasons and in soils exposed to a combination of three levels of precipitation treatments (ambient, 150% of ambient during growing season, and 50% of ambient year-round) and four levels of warming treatments (unwarmed to ~4°C above ambient) over the course of a year. Warming, precipitation and season had very little effect on potential enzyme activity. Most models assume that enzyme dynamics follow microbial biomass, because enzyme production should be directly controlled by the size and activity of microbial biomass. We observed differences among seasons and treatments in mass-specific potential enzyme activity, suggesting that this assumption is invalid. In June 2009, mass-specific potential enzyme activity, using chloroform fumigation-extraction MBC, increased with temperature, peaking under medium warming and then declining under the highest warming. This finding suggests that either enzyme production increased with temperature or turnover rates decreased. Increased maintenance costs associated with warming may have resulted in increased mass-specific enzyme activities due to increased nutrient demand. Our research suggests that allocation of resources to enzyme production could be affected by climate-induced changes in microbial efficiency and maintenance costs. PMID:23781218

  6. Ecotoxicological assessment of soil microbial community tolerance to glyphosate.

    PubMed

    Allegrini, Marco; Zabaloy, María Celina; Gómez, Elena del V

    2015-11-15

    Glyphosate is the most used herbicide worldwide. While contrasting results have been observed related with its impact on soil microbial communities, more studies are necessary to elucidate the potential effects of the herbicide. Differences in tolerance detected by Pollution Induced Community Tolerance (PICT) approach could reflect these effects. The objective of the present study was to assess the tolerance to glyphosate (the active ingredient and a commercial formulation) of contrasting soils with (H) and without (NH) history of exposure. The hypothesis of a higher tolerance in H soils due to a sustained selection pressure on community structure was tested through the PICT approach. Results indicated that tolerance to glyphosate is not consistent with previous history of exposure to the herbicide either for the active ingredient or for a commercial formulation. Soils of H and NH sites were also characterized in order to determine to what extent they differ in their functional diversity and structure of microbial communities. Denaturant Gradient Gel Electrophoresis (DGGE) and Quantitative Real Time PCR (Q-PCR) indicated high similarity of Eubacteria profiles as well as no significant differences in abundance, respectively, between H and NH sites. Community level physiological profiling (CLPP) indicated some differences in respiration of specific sources but functional diversity was very similar as reflected by catabolic evenness (E). These results support PICT assay, which ideally requires soils with differences in their exposure to the contaminant but minor differences in other characteristics. This is, to our knowledge, the first report of PICT approach with glyphosate examining tolerance at soil microbial community level. PMID:26150308

  7. Assessing microbial activities in metal contaminated agricultural volcanic soils - An integrative approach.

    PubMed

    Parelho, C; Rodrigues, A S; Barreto, M C; Ferreira, N G C; Garcia, P

    2016-07-01

    Volcanic soils are unique naturally fertile resources, extensively used for agricultural purposes and with particular physicochemical properties that may result in accumulation of toxic substances, such as trace metals. Trace metal contaminated soils have significant effects on soil microbial activities and hence on soil quality. The aim of this study is to determine the soil microbial responses to metal contamination in volcanic soils under different agricultural land use practices (conventional, traditional and organic), based on a three-tier approach: Tier 1 - assess soil microbial activities, Tier 2 - link the microbial activity to soil trace metal contamination and, Tier 3 - integrate the microbial activity in an effect-based soil index (Integrative Biological Response) to score soil health status in metal contaminated agricultural soils. Our results showed that microbial biomass C levels and soil enzymes activities were decreased in all agricultural soils. Dehydrogenase and β-glucosidase activities, soil basal respiration and microbial biomass C were the most sensitive responses to trace metal soil contamination. The Integrative Biological Response value indicated that soil health was ranked as: organic>traditional>conventional, highlighting the importance of integrative biomarker-based strategies for the development of the trace metal "footprint" in Andosols. PMID:27057992

  8. Effect of Monospecific and Mixed Sea-Buckthorn (Hippophae rhamnoides) Plantations on the Structure and Activity of Soil Microbial Communities

    PubMed Central

    Yu, Xuan; Liu, Xu; Zhao, Zhong; Liu, Jinliang; Zhang, Shunxiang

    2015-01-01

    This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH4+) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4+ content, nitrate content (NH3−), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations. PMID:25658843

  9. Effect of monospecific and mixed sea-buckthorn (Hippophae rhamnoides) plantations on the structure and activity of soil microbial communities.

    PubMed

    Yu, Xuan; Liu, Xu; Zhao, Zhong; Liu, Jinliang; Zhang, Shunxiang

    2015-01-01

    This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH4(+)) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4(+) content, nitrate content (NH3(-)), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations. PMID:25658843

  10. Evaluation of the Effect of Arsenic Contamination on Selected Soil Enzyme Activities and Microbial Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Environmental impact of different contaminants which enter the soil can alter the diversity of the soil microflora thus disrupting their ability to maintain soil quality and health. Due to the vital role played by the diverse soil microbes in soil, the measurement of the soil microbial diversity has...

  11. Do climate factors govern soil microbial community composition and biomass at a regional scale?

    NASA Astrophysics Data System (ADS)

    Ma, L.; Guo, C.; Lü, X.; Yuan, S.; Wang, R.

    2014-12-01

    Soil microbial communities play important role in organic matter decomposition, nutrient cycling and vegetation dynamic. However, little is known about factors driving soil microbial community composition at large scales. The objective of this study was to determine whether climate dominates among environmental factors governing microbial community composition and biomass at a regional scale. Here, we compared soil microbial communities using phospholipid fatty acid method across 7 land use types from 23 locations in North-East China Transect (850 km x 50 km). The results showed that soil water availability and land use changes exhibited the dominant effects on soil microbial community composition and biomass at the regional scale, while climate factors (expressed as a function of large-scale spatial variation) did not show strong relationships with distribution of microbial community composition. Likewise, factors such as spatial structure, soil texture, nutrient availability and vegetation types were not important. Wetter soils had higher contributions of gram-positive bacteria, whereas drier soils had higher contributions of gram-negative bacteria and fungi. Heavily disturbed soils had lower contributions of gram-negative bacteria and fungi than historically disturbed and undisturbed soils. The lowest microbial biomass appeared in the wettest and driest soils. In conclusion, dominant climate factors, commonly known to structure distribution of macroorganisms, were not the most important drivers governing regional pattern of microbial communities because of inclusion of irrigated and managed practices. In comparison, soil water regime and land use types appear to be primary determinants of microbial community composition and biomass.

  12. Microbial arsenic methylation in soil and rice rhizosphere.

    PubMed

    Jia, Yan; Huang, Hai; Zhong, Min; Wang, Feng-Hua; Zhang, Li-Mei; Zhu, Yong-Guan

    2013-04-01

    Methylated arsenic (As) species are a common constituent of rice grains accounting for 10-90% of the total As. Recent studies have shown that higher plants are unlikely to methylate As in vivo suggesting that As methylation is a microbial mediated process that occurs in soils prior to plant uptake. In this study, we designed primers according to the conserved essential amino acids and structural motifs of arsenite S-adenosylmethionine methyltransferase (ArsM). We report for the first time the successful amplification of the prokaryotic arsM gene in 14 tested soils with wide ranging As concentrations. The abundance and diversity of the arsM gene in the rice rhizosphere soil and roots were analyzed using the designed primers. Results showed that microbes containing arsM genes were phylogenetically diverse, as revealed by the clone library and terminal restriction fragment length polymorphism (T-RFLP) analysis, and were branched into various phyla. Concentration of methylated As species in the soil solution was elevated in the rhizosphere soil and also by the addition of rice straw into the paddy soil, corresponding to the elevated abundance of the arsM gene in the soil. These results, together with evidence of horizontal gene transfer (HGT) of the arsM gene, suggest the genes encoding ArsM in soils are widespread. These findings demonstrate why most rice, when compared with other cereals, contains unusually high concentrations of methylated As species. PMID:23469919

  13. Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

    NASA Astrophysics Data System (ADS)

    Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

    2016-06-01

    Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N•ha‑1•yr‑1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations.

  14. Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

    PubMed Central

    Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

    2016-01-01

    Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N∙ha−1∙yr−1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations. PMID:27302857

  15. Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations.

    PubMed

    Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

    2016-01-01

    Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N∙ha(-1)∙yr(-1). IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations. PMID:27302857

  16. Alaskan Arctic Soils: Relationship between Microbial Carbon Usage and Soil Composition

    NASA Astrophysics Data System (ADS)

    Li, H.; Ziolkowski, L. A.

    2015-12-01

    Carbon stored in Arctic permafrost carbon is sensitive to climate change. Microbes are known to degrade Arctic soil organic carbon (OC) and potentially release vast quantitates of CO2 and CH4. Previously, it has been shown that warming of Arctic soils leads to microbes respiring older carbon. To examine this process, we studied the microbial carbon usage and its relationship to the soil OC composition in active layer soils at five locations along a latitudinal transect on the North Slope of Alaska using the compound specific radiocarbon signatures of the viable microbial community using phospholipid fatty acids (PLFA). Additional geochemical parameters (C/N, 13C, 15N and 14C) of bulk soils were measured. Overall there was a greater change with depth than location. Organic rich surface soils are rich in vegetation and have high PLFA based cell densities, while deeper in the active layer geochemical parameters indicated soil OC was degraded and cell densities decreased. As expected, PLFA indicative of Fungi and Protozoa species dominated in surface soils, methyl-branched PLFAs, indicative of bacterial origin, increased in deeper in the active layer. A group of previously unreported PLFAs, believed to correlate to anaerobic microbes, increased at the transition between the surface and deep microbial communities. Cluster analysis based on individual PLFAs of samples confirmed compositional differences as a function of depth dominated with no site to site differences. Radiocarbon data of soil OC and PLFA show the preferential consumption of younger soil OC by microbes at all sites and older OC being eaten in deep soils. However, in deeper soil, where the C/N ratio suggests lower bioavailability, less soil OC was incorporated into the microbes as indicating by greater differences between bulk and PLFA radiocarbon ages.

  17. Pyrogenic and Fresh Organic Matter Effects on Soil Microbial Communities

    NASA Astrophysics Data System (ADS)

    Whitman, T.; Buckley, D. H.; Lehmann, J.

    2014-12-01

    Soils hold a globally important stock of carbon (C) and can act as both a C source and sink, depending on management and environmental conditions. Pyrogenic organic matter (PyOM) is produced naturally during fires, and contains relatively stable forms of C. Its intentional production has also been proposed as a mechanism for C management (in such cases PyOM is often referred to as "biochar"). However, the impact of natural or anthropogenic PyOM production on soils is complex and depends on many factors. In particular, PyOM additions to soils may have effects on plant growth and on native soil C cycling. The response of the soil microbial community to PyOM additions is likely key to understanding these interactions, but remains poorly characterized. We studied soil C dynamics and soil microbial communities in a field study with 350°C PyOM from 13C-labelled corn stover, a C3-derived soil, and C4 plants (sudangrass). PyOM additions only temporarily increased total soil CO2 fluxes, dramatically less than the increase associated with the addition of corn stover, which likely increased SOC losses. We used high-throughput sequencing of the 16S region on the MiSeq platform to characterize the initial, 12-day and 82-day soil bacterial communiities. We used three-part stable isotopic partitioning after two months to distinguish 334% higher root-derived CO2 fluxes in the plots with PyOM additions than those without, and 45% lower PyOM-C derived CO2 fluxes in the plots with plants present. The 84% increase in estimated cumulative soil CO2 emissions with stover additions was accompanied by a significant shift in the soil bacterial community on days 12 and 82, while the PyOM additions only resulted in significant changes to the overall community on day 82. We investigate which taxa are driving these community shifts, and how they may relate to the soil CO2 fluxes.

  18. [Effects of different cropping patterns on soil enzyme activities and soil microbial community diversity in oasis farmland].

    PubMed

    Li, Rui; Liu, Yu; Chu, Gui-xin

    2015-02-01

    Effects of long-term cropping patterns on the activities of peroxidase, invertase, arylsulfatase, dehydrogenase and protease were investigated in this paper. Four long-term cropping patterns included (1) 10 years continuous cropping of corn, (2) 8 years continuous cropping of wheat followed by 10 years continuous cropping of cotton, (3) 15 years continuous cropping of cotton, and (4) 6 years continuous cropping of cotton followed by 6 years of wheat/sunflower rotation. The responses of soil bacteria, fungi, ammonia oxidizing bacteria (AOB) , and the ammonia oxidizing archaea (AOA) to different copping patterns were analyzed. The results showed that cropping patterns significantly affected the activities of soil peroxidase, arylsulfatase, dehydrogenase and protease, while had no significant effect on soil invertase activity. The cropping patterns significantly influenced the diversity index of AOA, but had no significant influence on that of soil bacteria, fungi and AOB. The community structures of soil fungi and AOB were more sensitive to cropping patterns than soil bacteria and AOA. In conclusion, long-term continuous cropping of cotton decreased the activities of soil enzymes activities and soil microbial diversity in oasis farmland, while crop rotation could alleviate the negative influence. PMID:26094465

  19. Microbial lipids in Paddy Soils of the Yangtze Area

    NASA Astrophysics Data System (ADS)

    Mueller-Niggemann, Cornelia; Bannert, Andrea; Schloter, Michael; Cao, Zhihong; Schwark, Lorenz

    2010-05-01

    Geobiochemical studies of rice paddy soils and their effect on the global carbon cycle are of paramount importance. Paddy soils comprise manmade wetlands because soil flooding is a prerequisite for lowland rice cultivation. Except for sulphate-rich substrates, rice growth is not very sensitive to soil conditions prevailing prior to conversion of marine tidal flat sediments to paddy cultivation. Thus, soil management practices, such as artificial submergence or drainage, ploughing and puddling (i.e. ploughing a submerged soil), manuring, liming, and fertilization, are the major driving factors of paddy soil development. Soil organic matter (SOM) decomposition and humification proceeds in hydromorphic soils at a slower rate than in well-drained, aerated soils. Rice paddy soils thus also represent a suitable model system to study fundamental aspects of redox sensitive soil processes. These processes are of special interest because in flooded rice fields the anaerobic fermentation of SOM leads to the release of methane and to denitrification losses of inorganic nitrogen. Here we present results from a chronosequence study of paddy soils with different and well known starting dates of cultivation, in the Zhejiang province (Yangtze River delta) by land reclamation through the building of protective dikes over the past 2000 years. We here describe the biomarker geochemistry of six paddy soils that developed on marine tidal sediments and where cultivation started 50, 100, 300, 700, 1000 or 2000 years before present. As reference substrates recent marine and lacustrine sediments were selected. The differentiation of the lipid biomass was achieved by investigating glycerol dialkyl glycerol tetraethers (GDGT). These specific organic geochemical biomarkers allow for determining the abundance of fossil microbial consortia (archaea and bacteria input) into paddy soils, justified by the diversity of the archaeal and bacterial cell membrane constituents. The dominant proportion of

  20. Riparian reforestation: are there changes in soil carbon and soil microbial communities?

    PubMed

    Mackay, J E; Cunningham, S C; Cavagnaro, T R

    2016-10-01

    Reforestation of pastures in riparian zones has the potential to decrease nutrient runoff into waterways, provide both terrestrial and aquatic habitat, and help mitigate climate change by sequestering carbon (C). Soil microbes can play an important role in the soil C cycle, but are rarely investigated in studies on C sequestration. We surveyed a chronosequence (0-23years) of mixed-species plantings in riparian zones to investigate belowground (chemical and biological) responses to reforestation. For each planting, an adjacent pasture was surveyed to account for differences in soil type and land-use history among plantings. Two remnant woodlands were included in the survey as indicators of future potential of plantings. Both remnant woodlands had significantly higher soil organic C (SOC) content compared with their adjacent pastures. However, there was no clear trend in SOC content among plantings with time since reforestation. The substantial variability in SOC sequestration among plantings was possibly driven by differences in soil moisture among plantings and the inherent variability of SOC content among reference pastures adjacent to plantings. Soil microbial phospholipid fatty acids (PLFA, an indicator of microbial biomass) and activities of decomposition enzymes (β-glucosidase and polyphenol oxidase) did not show a clear trend with increasing planting age. Despite this, there were positive correlations between total SOC concentration and microbial indicators (total PLFA, fungal PLFA, bacterial PLFA and activities of decomposition enzymes) across all sites. The soil microbial community compositions (explored using PLFA markers) of older plantings were similar to those of remnant woodlands. There was a positive correlation between the soil carbon:nitrogen (C:N) and fungal:bacterial (F:B) ratios. These data indicate that in order to maximise SOC sequestration, we need to take into account not only C inputs, but the microbial processes that regulate SOC cycling

  1. Application of organic amendments to restore degraded soil: effects on soil microbial properties.

    PubMed

    Carlson, Jennifer; Saxena, Jyotisna; Basta, Nicholas; Hundal, Lakhwinder; Busalacchi, Dawn; Dick, Richard P

    2015-03-01

    Topsoil removal, compaction, and other practices in urban and industrial landscapes can degrade soil and soil ecosystem services. There is growing interest to remediate these for recreational and residential purposes, and urban waste materials offers potential to improve degraded soils. Therefore, the objective of this study was to compare the effects of urban waste products on microbial properties of a degraded industrial soil. The soil amendments were vegetative yard waste compost (VC), biosolids (BioS), and a designer mix (DM) containing BioS, biochar (BC), and drinking water treatment residual (WTR). The experiment had a completely randomized design with following treatments initiated in 2009: control soil, VC, BioS-1 (202 Mg ha(-1)), BioS-2 (403 Mg ha(-1)), and DM (202 Mg BioS ha(-1) plus BC and WTR). Soils (0-15-cm depth) were sampled in 2009, 2010, and 2011 and analyzed for enzyme activities (arylsulfatase, β-glucosaminidase, β-glucosidase, acid phosphatase, fluorescein diacetate, and urease) and soil microbial community structure using phospholipid fatty acid analysis (PLFA). In general, all organic amendments increased enzyme activities in 2009 with BioS treatments having the highest activity. However, this was followed by a decline in enzyme activities by 2011 that were still significantly higher than control. The fungal PLFA biomarkers were highest in the BioS treatments, whereas the control soil had the highest levels of the PLFA stress markers (P < 0.10). In conclusion, one-time addition of VC or BioS was most effective on enzyme activities; the BioS treatment significantly increased fungal biomass over the other treatments; addition of BioS to soils decreased microbial stress levels; and microbial measures showed no statistical differences between BioS and VC treatments after 3 years of treatment. PMID:25673270

  2. Invariant soil water potential at zero microbial respiration explained by hydrological discontinuity in dry soils

    NASA Astrophysics Data System (ADS)

    Manzoni, S.; Katul, G.

    2014-10-01

    Soil microbial respiration rates decrease with soil drying, ceasing below water potentials around -15 MPa. A proposed mechanism for this pattern is that under dry conditions, microbes are substrate limited because solute diffusivity is halted due to breaking of water film continuity. However, pore connectivity estimated from hydraulic conductivity and solute diffusivity (at Darcy's scale) is typically interrupted at much less negative water potentials than microbial respiration (-0.1 to -1 MPa). It is hypothesized here that the more negative respiration thresholds than at the Darcy's scale emerge because microbial activity is restricted to microscale soil patches that retain some hydrological connectivity even when it is lost at the macroscale. This hypothesis is explored using results from percolation theory and meta-analyses of respiration-water potential curves and hydrological percolation points. When reducing the spatial scale from macroscale to microscale, hydrological and respiration thresholds become consistent, supporting the proposed hypothesis.

  3. Ecosystem Warming Affects CO2 Flux in an Agricultural Soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Global warming seems likely based on present-day climate predictions. Our objective was to characterize and quantify the interactive effects of ecosystem warming (i.e., canopy temperature, TS), soil moisture content ('S) and microbial biomass (BM: bacteria, fungi) on the intra-row soil CO2 flux (FS)...

  4. The Impact of Climate Change on Microbial Communities and Carbon Cycling in High Arctic Permafrost Soil from Spitsbergen, Northern Norway

    NASA Astrophysics Data System (ADS)

    de Leon, K. C.; Schwery, D.; Yoshikawa, K.; Christiansen, H. H.; Pearce, D.

    2014-12-01

    Permafrost-affected soils are among the most fragile ecosystems in which current microbial controls on organic matter decomposition are changing as a result of climate change. Warmer conditions in the high Arctic will lead to a deepening of the seasonal active layer of permafrost, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. The viable and non-viable fractions of the microbial community in a permafrost soil from Adventdalen, Spitsbergen, Norway were subjected to a comprehensive investigation using culture-dependent and culture-independent methods. Molecular analyses using FISH (with CTC-DAPI) and amplified rDNA restriction analysis (ARDRA) on a 257cm deep core, revealed the presence of all major microbial soil groups, with the active layer having more viable cells, and a higher microbial community diversity. Carbon dioxide (CO2) and methane (CH4) flux measurements were performed to show the amount of C stored in the sample. We demonstrated that the microbial community composition from the soil in the center of the core was most likely influenced by small scale variations in environmental conditions. Community structure showed distinct shift of presence of bacterial groups along the vertical temperature gradient profile and microbial counts and diversity was found to be highest in the surface layers, decreasing with depth. It was observed that soil properties driving microbial diversity and functional potential varied across the permafrost table. Data on the variability of CO2 and CH4 distribution described in peat structure heterogeneity are important for modeling emissions on a larger scale. Furthermore, linking microbial biomass to gas distribution may elucidate the cause of peak CO2 and CH4 and their changes in relation to environmental change and peat composition.

  5. 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.

  6. Colonization patterns of soil microbial communities in the Atacama Desert

    PubMed Central

    2013-01-01

    Background The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life. Results Analyses of high throughput DNA sequence data revealed that bacterial communities from six geographic locations in the hyper-arid core and along a North-South moisture gradient were structurally and phylogenetically distinct (ANOVA test for observed operating taxonomic units at 97% similarity (OTU0.03), P <0.001) and that communities from locations in the hyper-arid zone displayed the lowest levels of diversity. We found bacterial taxa similar to those found in other arid soil communities with an abundance of Rubrobacterales, Actinomycetales, Acidimicrobiales, and a number of families from the Thermoleophilia. The extremely low abundance of Firmicutes indicated that most bacteria in the soil were in the form of vegetative cells. Integrating molecular data with climate and soil geochemistry, we found that air relative humidity (RH) and soil conductivity significantly correlated with microbial communities’ diversity metrics (least squares linear regression for observed OTU0.03 and air RH and soil conductivity, P <0.001; UniFrac PCoA Spearman’s correlation for air RH and soil conductivity, P <0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples, with increased rates in soils from the southern locations. Conclusions Our results suggest that microorganisms in the driest soils of the Atacama Desert are in a state of stasis for most of the time, but can potentially metabolize if presented with liquid water for a sufficient duration. Over geological time, rare rain events and physicochemical factors potentially played a major role in selecting micro-organisms that are most adapted to extreme desiccating

  7. 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

  8. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

    SciTech Connect

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony Wayne; Song, Xia; Thornton, Peter E.; Zhang, Lihua

    2015-11-27

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, P and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg–1 dry soil, 0.1 mmol N Kg–1 dry soil, 0.1 mmol P Kg–1 dry soil, and 0.1 mmol S Kg–1 dry soil, respectively. Lastly, these findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models.

  9. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

    DOE PAGESBeta

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony Wayne; Song, Xia; Thornton, Peter E.; Zhang, Lihua

    2015-11-27

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, Pmore » and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg–1 dry soil, 0.1 mmol N Kg–1 dry soil, 0.1 mmol P Kg–1 dry soil, and 0.1 mmol S Kg–1 dry soil, respectively. Lastly, these findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models.« less

  10. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

    PubMed Central

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony W.; Song, Xia; Thornton, Peter E.; Zhang, Lihua

    2015-01-01

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, P and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg−1 dry soil, 0.1 mmol N Kg−1 dry soil, 0.1 mmol P Kg−1 dry soil, and 0.1 mmol S Kg−1 dry soil, respectively. These findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models. PMID:26612423

  11. Quantification of Microbial Activities in Near-Surface Soils

    NASA Astrophysics Data System (ADS)

    Schroth, M. H.; Nauer, P.; Zeyer, J.

    2007-12-01

    Microbial processes in near-surface soils play an important role in carbon and nutrient cycling, and specifically in the turnover of greenhouse gases such as CO2 and CH4. We modified a recently developed technique, the gas push-pull test (GPPT), to allow for the in-situ quantification of microbial activities in near-surface soils. A GPPT consists of the controlled injection of a gas mixture containing reactive gases (e.g., CH4, O2, CO2) and nonreactive tracer gases (e.g., Ar, Ne) into the soil, followed by the extraction of the gas mixture/soil