Soil structural quality assessment for soil protection regulation

NASA Astrophysics Data System (ADS)

Johannes, Alice; Boivin, Pascal

2017-04-01

Soil quality assessment is rapidly developing worldwide, though mostly focused on the monitoring of arable land and soil fertility. Soil protection regulations assess soil quality differently, focusing on priority pollutants and threshold values. The soil physical properties are weakly considered, due to lack of consensus and experimental difficulties faced with characterization. Non-disputable, easy to perform and inexpensive methods should be available for environmental regulation to be applied, which is unfortunately not the case. As a consequence, quantitative soil physical protection regulation is not applied, and inexpensive soil physical quality indicators for arable soil management are not available. Overcoming these limitations was the objective of a research project funded by the Swiss federal office for environment (FOEN). The main results and the perspectives of application are given in this presentation. A first step of the research was to characterize soils in a good structural state (reference soils) under different land use. The structural quality was assessed with field expertise and Visual Evaluation of the Soil Structure (VESS), and the physical properties were assessed with Shrinkage analysis. The relationships between the physical properties and the soil constituents were linear and highly determined. They represent the reference properties of the corresponding soils. In a second step, the properties of physically degraded soils were analysed and compared to the reference properties. This allowed defining the most discriminant parameters departing the different structure qualities and their threshold limits. Equivalent properties corresponding to these parameters but inexpensive and easy to determine were defined and tested. More than 90% of the samples were correctly classed with this method, which meets, therefore, the requirements for practical application in regulation. Moreover, result-oriented agri-environmental schemes for soil quality are now proposed to farmers based on these indicators.

Afforestation alters community structure of soil fungi.

PubMed

Carson, Jennifer K; Gleeson, Deirdre B; Clipson, Nicholas; Murphy, Daniel V

2010-07-01

Relatively little is known about the effect of afforestation on soil fungal communities. This study demonstrated that afforestation altered fungal community structure and that changes were correlated to pools of soil C. Pasture at three locations on the same soil type was afforested with Eucalyptus globulus or Pinus pinaster. The structure of fungal communities under the three land uses was measured after 13y using automated ribosomal intergenic spacer analysis (ARISA). Afforestation significantly altered the structure of fungal communities. The effect of location on the structure of fungal communities was limited to pasture soils; although these contained the same plant species, the relative composition of each species varied between locations. Differences in the structure of fungal communities between pasture, E. globulus and P. pinaster were significantly correlated with changes in the amount of total organic C and microbial biomass-C in soil. Afforestation of patches of agricultural land may contribute to conserving soil fungi in agricultural landscapes by supporting fungal communities with different composition to agricultural soils. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Soil and Water: Some Teaching Suggestions.

ERIC Educational Resources Information Center

Fischer, Richard B.

1987-01-01

Outlines six soil and water investigations that students can pursue outdoors, in nature centers, or in classrooms: soil characteristics; relationship between soil ph and plant life; what aggregates tell us; differences in soil structure; differences in rate of water absorption by soil; and soil exploration with a Berlesi funnel. (NEC)

The effect of total carbon on microscopic soil properties and implications for crop production

USDA-ARS?s Scientific Manuscript database

Soil structure is a dynamic property affected by physical, chemical, and microbiological processes. Addition of organic matter to soils and the use of different management practices have been reported to impact soil structure and crop production. Moderation in soil temperature and increases in mic...

Influence of Soil Properties on Soldierless Termite Distribution.

PubMed

Bourguignon, Thomas; Drouet, Thomas; Šobotník, Jan; Hanus, Robert; Roisin, Yves

2015-01-01

In tropical rainforests, termites constitute an important part of the soil fauna biomass, and as for other soil arthropods, variations in soil composition create opportunities for niche partitioning. The aim of this study was twofold: first, we tested whether soil-feeding termite species differ in the foraging substrate; second, we investigated whether soil-feeding termites select their foraging sites to enhance nutrients intake. To do so, we collected termites and analysed the composition and structure of their feeding substrates. Although Anoplotermes-group members are all considered soil-feeders, our results show that some species specifically feed on abandoned termite nests and very rotten wood, and that this substrate selection is correlated with previous stable isotope analyses, suggesting that one component of niche differentiation among species is substrate selection. Our results show that the composition and structure of bare soils on which different termite species foraged do not differ, suggesting that there is no species specialization for a particular type of bare soil. Finally, the bare soil on which termites forage does not differ from random soil samples. Overall, our results suggest that few species of the Anoplotermes-group are specialized toward substrates rich in organic matter, but that the vast majority forage on soil independently of its structural and chemical composition, being ecologically equivalent for this factor.

Impact of monovalent cations on soil structure. Part II. Results of two Swiss soils

NASA Astrophysics Data System (ADS)

Farahani, Elham; Emami, Hojat; Keller, Thomas

2018-01-01

In this study, we investigated the impact of adding solutions with different potassium and sodium concentrations on dispersible clay, water retention characteristics, air permeability, and soil shrinkage behaviour using two agricultural soils from Switzerland with different clay content but similar organic carbon to clay ratio. Three different solutions (including only Na, only K, and the combination of both) were added to soil samples at three different cation ratio of soil structural stability levels, and the soil samples were incubated for one month. Our findings showed that the amount of readily dispersible clay increased with increasing Na concentrations and with increasing cation ratio of soil structural stability. The treatment with the maximum Na concentration resulted in the highest water retention and in the lowest shrinkage capacity. This was was associated with high amounts of readily dispersible clay. Air permeability generally increased during incubation due to moderate wetting and drying cycles, but the increase was negatively correlated with readily dispersible clay. Readily dispersible clay decreased with increasing K, while readily dispersible clay increased with increasing K in Iranian soil (Part I of our study). This can be attributed to the different clay mineralogy of the studied soils (muscovite in Part I and illite in Part II).

Assessment the effect of homogenized soil on soil hydraulic properties and soil water transport

NASA Astrophysics Data System (ADS)

Mohawesh, O.; Janssen, M.; Maaitah, O.; Lennartz, B.

2017-09-01

Soil hydraulic properties play a crucial role in simulating water flow and contaminant transport. Soil hydraulic properties are commonly measured using homogenized soil samples. However, soil structure has a significant effect on the soil ability to retain and to conduct water, particularly in aggregated soils. In order to determine the effect of soil homogenization on soil hydraulic properties and soil water transport, undisturbed soil samples were carefully collected. Five different soil structures were identified: Angular-blocky, Crumble, Angular-blocky (different soil texture), Granular, and subangular-blocky. The soil hydraulic properties were determined for undisturbed and homogenized soil samples for each soil structure. The soil hydraulic properties were used to model soil water transport using HYDRUS-1D.The homogenized soil samples showed a significant increase in wide pores (wCP) and a decrease in narrow pores (nCP). The wCP increased by 95.6, 141.2, 391.6, 3.9, 261.3%, and nCP decreased by 69.5, 10.5, 33.8, 72.7, and 39.3% for homogenized soil samples compared to undisturbed soil samples. The soil water retention curves exhibited a significant decrease in water holding capacity for homogenized soil samples compared with the undisturbed soil samples. The homogenized soil samples showed also a decrease in soil hydraulic conductivity. The simulated results showed that water movement and distribution were affected by soil homogenizing. Moreover, soil homogenizing affected soil hydraulic properties and soil water transport. However, field studies are being needed to find the effect of these differences on water, chemical, and pollutant transport under several scenarios.

Effect of Soil Washing for Lead and Zinc Removal on Soil Hydraulic Properties

NASA Astrophysics Data System (ADS)

Kammerer, Gerhard; Zupanc, Vesna; Gluhar, Simon; Lestan, Domen

2017-04-01

Soil washing as a metal pollution remediation process, especially part with intensive mixing of the soil slurry and soil compression after de-watering, significantly deteriorates physical properties of soil compared to those of non-remediated soil. Furthermore, changed physical characteristics of remediated soil influence interaction of plant roots with soil system and affect soil water regime. Remediated soils showed significant differences to their original state in water retention properties and changed structure due to the influence of artificial structure created during remediation process. Disturbed and undisturbed soil samples of remediated and original soils were analyzed. We evaluated soil hydraulic properties as a possible constraint for re-establishing soil structure and soil fertility after the remediation procedure.

Visual assessment of soil structure quality in an agroextractivist system in Southeastern Amazonia

NASA Astrophysics Data System (ADS)

Fernanda Simões da Silva, Laura; Stuchi Boschi, Raquel; Ortega Gomes, Matheus; Cooper, Miguel

2016-04-01

Soil structure is considered a key factor in the functioning of soil, affecting its ability to support plant and animal life, and moderate environmental quality. Numerous methods are available to evaluate soil structure based on physical, chemical and biological indicators. Among the physical indicators, the attributes most commonly used are soil bulk density, porosity, soil resistance to penetration, tensile strength of aggregates, soil water infiltration, and available water. However, these methods are expensive and generally time costly for sampling and laboratorial procedures. Recently, evaluations using qualitative and semi-quantitative indicators of soil structure quality have gained importance. Among these methods, the method known as Visual Evaluation of Soil Structure (VESS) (Ball et al., 2007; Guimarães et al., 2011) can supply this necessity in temperate and tropical regions. The study area is located in the Piranheira Praialta Agroextrativist Settlement Project in the county of Nova Ipixuna, Pará, Brazil. Two toposequences were chosen, one under native forest and the other under pasture. Pits were opened in different landscape positions (upslope, midslope and downslope) for soil morphological, micromorphological and physical characterization. The use of the soil visual evaluation method (SVE) consisted in collecting an undisturbed soil sample of approximately 25 cm in length, 20 cm in width and 10 cm in depth. 12 soil samples were taken for each land use. The samples were manually fragmented, respecting the fracture planes between the aggregates. The SVE was done comparing the fragmented sample with a visual chart and scores were given to the soil structure. The categories that define the soil structure quality (Qe) vary from 1 to 5. Lower scores mean better soil structure. The final score calculation was done using the classification key of Ball et al. (2007) adapted by Guimarães (2011). A change in soil structure was observed between forest and pasture. The presence of layers of different depths, and size and shape of aggregates resulted in a lower Qe in the forest soils (Qe= 2,04 ±0,4), followed by the pasture (Qe= 3,09 ± 1,3). These results indicate certain degradation in the soil structure in the pasture. The variability of the soil structure in the forest samples was lower. The pasture samples presented a worse soil structure when compared to the forest, although their Qe values can be considered good.

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

PubMed Central

Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

2017-01-01

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

[Community structure of soil fauna in Eucalyptus grandis plantations at different slope locations].

PubMed

Zhao, Yu; Zhong, Yu; Zhang, Jian; Yang, Wan-qin

2010-09-01

To understand the effects of slope location on the community structure of soil fauna in Eucalyptus grandis plantation, an investigation was made on the soil fauna in 3 E. grandis plantations at different slope locations in the hilly area of Sichuan Province from January to October 2009. A total of 39,2762 individuals were observed, belonging to 146 groups, 7 phyla, 16 classes, and 31 orders. The community composition, trophic group, diversity, and seasonal dynamics of soil fauna in the plantations all varied with slope. The abundance of macro-fauna, xeric meso- and micro-fauna, saprophagous macro-fauna, and omnivorous xeric meso- and micro-fauna increased with the decrease of slope, indicating that soil fauna had sensitive responses to the soil environmental factors affected by slope. Significant differences in the diversity of soil saprophagous macro-fauna and hygrophilous meso- and micro-fauna were observed at different slope locations, suggesting that these two faunal groups could be used as the indicators of the habitat heterogeneity of E. grandis plantations at different slope. Overall, slope location had definite effects on the community structure and distribution of soil fauna in the E. grandis plantations, but the effects were not statistically significant.

The Vertical Structure of Urban Soils and Their Convergence Across Cities

NASA Astrophysics Data System (ADS)

Herrmann, D.; Schifman, L. A.; Shuster, W.; Schwarz, K.

2017-12-01

The theoretical patterns for vertical soil structure (e.g., A-B-C ordering of horizons) are a basis for research methods and our understanding of ecosystem structure and function in general. A general understanding of how urban soils differ from non-urban soils vertically is needed to inform urban research methods and advance our knowledge of urban ecosystems. We performed a soil taxonomic assessment of 391 deep soil cores (up to 5-m) collected in 11 cities across the U.S. and Puerto Rico. The likely soil series in the absence of urbanization was identified for each soil core and comparison soil taxonomy data for agricultural and wildlands land uses soils of the same soil series was gathered from the NASIS database. We hypothesized that urbanization has modified the vertical arrangement of soil horizons and decreased their vertical complexity (e.g., degree of horizonation). In addition, we hypothesized that soils in each city are becoming more like each other and less like their pre-urbanization soils. Urban soils had fewer soil horizons than their non-urban references; specifically, urban soils had two fewer distinct genetic horizons in the top meter of soil. B horizons were commonly lost or reduced in extent as A horizons deepened and C horizons shallowed in urban relative to reference soils. The order of horizons was also different from reference and theoretical soil structure. Namely A-C transitions with an absence of B horizons was more common in urban than non-urban soils. If these patterns hold across more cities, our results indicate a need to revisit the conventional predictions of vertical soil structure for understanding urban ecosystems. Finally, we found that several attributes for urban soils with evidence of significant disturbance associated with urbanization were converging across cities. Similar findings have been found for surface soils; here we show the structure of urban soil convergence at greater soil depths than previously reported.

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

[Effect of ground mulch managements on soil bacterial community structure and diversity in the non-irrigated apple orchard in Weibei Loess Plateau].

PubMed

Chen, Yuexing; Wen, Xiaoxia; Sun, Yulin; Zhang, Junli; Lin, Xiaoli; Liao, Yuncheng

2015-07-04

We studied the changes in soil bacterial communities induced by ground mulch managements at different apple growth periods. We adopted the denaturing gradient gel electrophoresis (DGGE) with PCR-amplified 16S rRNA fragments to determine soil bacterial community structure and diversity. Soil bacterial community structure with different ground mulch managements were significantly different. Both the mulch management strategies and apple growth periods affected the predominant groups and their abundance in soil bacterial communities. Grass mulch and cornstalk mulch treatments had higher bacterial diversity and richness than the control at young fruit period and fruit expanding period, whereas film mulch treatment had no significant difference compared with the control. During mature period, bacterial diversity in the control reached its maximum, which may be ascribed to the rapid growth and reproduction of the r-selection bacteria. The clustering and detrended correspondence analysis revealed that differences in soil bacterial communities were closely correlated to apple growth periods and ground mulch managements. Soil samples from the grass mulch and cornstalk mulch treatments clustered together while those mulched with plastic film treatment were similar to the control. The most abundant phylum in soil bacterial community was Proteobacteria followed by Bacteroidetes. Some other phyla were also detected, such as Acidobacteria, Firmicutes, Actinobacteria and Chloroflexi. Mulching with plant (Grass/Cornstalk) had great effects on soil bacterial community structure and enhanced the diversity while film mulch management had no significant effects.

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

NASA Astrophysics Data System (ADS)

Jha, Neha; Saggar, Surinder; Giltrap, Donna; Tillman, Russ; Deslippe, Julie

2017-09-01

Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N2O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N2O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N2O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N2O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N2O emissions through denitrification across a wide range of soil types.

Bacterial diversity of soil aggregates of different sizes in various land use conditions

NASA Astrophysics Data System (ADS)

Ivanova, Ekaterina; Azida, Thakahova; Olga, Kutovaya

2014-05-01

The patterns of soil microbiome structure may be a universal and very sensitive indicator of soil quality (soil "health") used for optimization and biologization of agricultural systems. The understanding of how microbial diversity influenses, and is influenced by, the environment can only be attained by analyses at scales relevant to those at which processes influencing microbial diversity actually operate. The basic structural and functional unit of the soil is a soil aggregate, which is actually a microcosm of the associative co-existing groups of microorganisms that form characteristic ecological food chains. It is known that many important microbial processes occur in spatially segregated microenvironments in soil leading to a microscale biogeography. The Metagenomic library of typical chernozem in conditions of different land use systems was created. Total genomic DNA was extracted from 0.5 g of the frozen soil after mechanical destruction. Sample preparation and sequencing was performed on a GS Junior ("Roche»", Switzerland) according to manufacturer's recommendations, using the universal primers to the variable regions V4 gene 16S - rRNA - F515 (GTGCCAGCMGCCGCGGTAA) and R806 (GGACT-ACVSGGGTATCTAAT). It is shown that the system of land use is a stronger determinant of the taxonomic composition of the soil microbial community, rather than the size of the structural units. In soil samples from different land use systems the presence of accessory components was revealed. They may be used as indicators of processes of soil recovery, soil degradation or soil exhaustion processes occuring in the agroecosystems. The comparative analysis of microbial communities of chernozem aggregates investigated demonstrates the statistically valuable differences in the amount of bacterial phyla and Archean domain content as well as the species richness in aggregates of various size fractions. The occurrence of specific components in the taxonomic structure of micro-and macro-aggregates may indicate the presence of a certain size fraction in the structure of the investigated soil. The study of soils' metagenome is promising for the development of both soil microbiology, and for the soil processes trends in soils of anthropogenic origin.

[Effects of different fertilization treatments on soil humic acid structure characteristics].

PubMed

Zhao, Nan; Lü, Yi-Zhong

2012-07-01

The present article used soil humic acid as research object to study effects on the structure characteristics of soil humic acid under the condition of applying cake fertilizer, green manure, straw fertilizer with the same contents of nitrogen and phosphorus. It used element analysis, micro infrared, and solid 13C-NMR for structure analysis, the results indicated that: The chemical composition and structure characteristics of humic acids were similar, but they also had many obvious differences. (1) The atomic ratios of H/C, O/C, and C/N were all different for the humic acids, the soil humic acid of cake fertilizer processing had the highest contents of H and N, green manure processing of soil humic acid contained the highest content of O, while straw fertilizer processing of soil humic acid contained highest content of C. (2) Infrared analysis displayed that the three soil humic acids contained protein Cake fertilizer processing of soil humic acid contained the most amino compounds, green manure processing of soil humic acid contained the maximum contents of hydroxyl and aliphatic hydrocarbon, while straw fertilizer processing of soil humic acid contained the highest contents of alcohol and phenol. (3) Solid 13C-NMR data indicated that cake fertilizer processing of soil humic acid contained the most carboxyl carbon, green manure processing of soil humic acid contained the highest contents of alkyl carbon and carbonyl carbon, while straw fertilizer processing of soil humic acids had the most alkoxy carbon and aromatic carbon

Pore-scale water dynamics during drying and the impacts of structure and surface wettability

NASA Astrophysics Data System (ADS)

Cruz, Brian C.; Furrer, Jessica M.; Guo, Yi-Syuan; Dougherty, Daniel; Hinestroza, Hector F.; Hernandez, Jhoan S.; Gage, Daniel J.; Cho, Yong Ku; Shor, Leslie M.

2017-07-01

Plants and microbes secrete mucilage into soil during dry conditions, which can alter soil structure and increase contact angle. Structured soils exhibit a broad pore size distribution with many small and many large pores, and strong capillary forces in narrow pores can retain moisture in soil aggregates. Meanwhile, contact angle determines the water repellency of soils, which can result in suppressed evaporation rates. Although they are often studied independently, both structure and contact angle influence water movement, distribution, and retention in soils. Here drying experiments were conducted using soil micromodels patterned to emulate different aggregation states of a sandy loam soil. Micromodels were treated to exhibit contact angles representative of those in bulk soil (8.4° ± 1.9°) and the rhizosphere (65° ± 9.2°). Drying was simulated using a lattice Boltzmann single-component, multiphase model. In our experiments, micromodels with higher contact angle surfaces took 4 times longer to completely dry versus micromodels with lower contact angle surfaces. Microstructure influenced drying rate as a function of saturation and controlled the spatial distribution of moisture within micromodels. Lattice Boltzmann simulations accurately predicted pore-scale moisture retention patterns within micromodels with different structures and contact angles.

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

PubMed Central

Zhen, Zhen; Liu, Haitao; Wang, Na; Guo, Liyue; Meng, Jie; Ding, Na; Wu, Guanglei; Jiang, Gaoming

2014-01-01

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils. PMID:25302996

Changes in bacterial diversity associated with bioremediation of used lubricating oil in tropical soils.

PubMed

Meeboon, Naruemon; Leewis, Mary-Cathrine; Kaewsuwan, Sireewan; Maneerat, Suppasil; Leigh, Mary Beth

2017-08-01

Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation.

[Community structure of soil meso- and micro-fauna in different habitats of urbanized region].

PubMed

Qin, Zhong; Zhang, Jia-en; Li, Qing-fang

2009-12-01

Investigations were made in May, June, and November 2007 and January 2008 to study the structural characteristics and their seasonal variations of soil meso- and micro-fauna communities in six habitats of three land use types (forest land, constructed grassland and farmland) in Tianhe District of Guangzhou City. The horizontal spatial distribution of soil fauna differed with habitat. During the investigation periods, the Botanical Garden of South China Agricultural University had the highest individual number (1286) of soil mesa- and micro-fauna, while the farmland, especially in the Fenghuang Street area, had the lowest number of individuals and groups. The seasonal variation of the individual number was in order of autumn (1815) > spring (1623) > winter (1365) > summer (1276). Hierarchical clustering and detrended correspondence analysis also showed that the community composition of soil meso- and micro-fauna in different habitats exhibited distinct seasonal variation. In the same seasons, the community structure and composition of soil meso- and micro-fauna in different habitats were correlated to the degrees of human interferences and the properties of soil environment.

Effects of different regulatory methods on improvement of greenhouse saline soils, tomato quality, and yield.

PubMed

Maomao, Hou; Xiaohou, Shao; Yaming, Zhai

2014-01-01

To identify effective regulatory methods scheduling with the compromise between the soil desalination and the improvement of tomato quality and yield, a 3-year field experiment was conducted to evaluate and compare the effect of straw mulching and soil structure conditioner and water-retaining agent on greenhouse saline soils, tomato quality, and yield. A higher salt removing rate of 80.72% in plough layer with straw mulching was obtained based on the observation of salt mass fraction in 0 ~ 20 cm soil layer before and after the experiment. Salts were also found to move gradually to the deeper soil layer with time. Straw mulching enhanced the content of soil organic matter significantly and was conductive to reserve soil available N, P, and K, while available P and K in soils of plough layer with soil structure conditioner decreased obviously; thus a greater usage of P fertilizer and K fertilizer was needed when applying soil structure conditioner. Considering the evaluation indexes including tomato quality, yield, and desalination effects of different regulatory methods, straw mulching was recommended as the main regulatory method to improve greenhouse saline soils in south China. Soil structure conditioner was the suboptimal method, which could be applied in concert with straw mulching.

The vertical geography of urban soils and its convergence across cities

EPA Science Inventory

The theoretical patterns for vertical soil structure (e.g., A-B-C ordering of horizons) are a basis for research methods and our understanding of ecosystem structure and function in general. A general understanding of how urban soils differ from non-urban soils vertically is need...

Testing the Visual Soil Assessment tool on Estonian farm fields

NASA Astrophysics Data System (ADS)

Reintam, Endla; Are, Mihkel; Selge, Are

2017-04-01

Soil quality estimation plays important role in decision making on farm as well on policy level. Sustaining the production ability and good health of the soil the chemical, physical and biological indicators should be taken into account. The system to use soil chemical parameters is usually quite well established in most European counties, including Estonia. However, measuring soil physical properties, such bulk density, porosity, penetration resistance, structural stability ect is time consuming, needs special tools and is highly weather dependent. In that reason these parameters are excluded from controllable quality parameters in policy in Estonia. Within the project "Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience" (iSQAPER) the visual soil assessment (VSA) tool was developed for easy detection of soil quality as well the different soil friendly agricultural management practices (AMP) were detected. The aim of current study was to test the VSA tool on Estonian farm fields under different management practices and compare the results with laboratory measurements. The main focus was set on soil physical parameters. Next to the VSA, the undisturbed soil samples were collected from the depth of 5-10 cm and 25-30 cm. The study revealed that results of a visually assessed soil physical parameters, such a soil structure, soil structural stability, soil porosity, presence of tillage pan, were confirmed by laboratory measurements in most cases. Soil water stable structure measurement on field (on 1 cm2 net in one 1 l box with 4-6 cm air dry clods for 5-10 min) underestimated very well structured soil on grassland and overestimated the structure aggregates stability of compacted soil. The slightly better soil quality was detected under no-tillage compared to ploughed soils. However, the ploughed soil got higher quality points compared with minimum tillage. The slurry application (organic manuring) had controversial impact - it increased the number of earthworms but decreased soil structural stability. Even the manuring with slurry increases organic matter amount in the soil, the compaction due to the use of heavy machinery during the application, especially on wet soil, reduces the positive effect of slurry.

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

PubMed

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

2013-02-01

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

3D soil structure characterization of Biological Soil Crusts from Alpine Tarfala Valley

NASA Astrophysics Data System (ADS)

Mele, Giacomo; Gargiulo, Laura; Zucconi, Laura; D'Acqui, Luigi; Ventura, Stefano

2017-04-01

Cyanobacteria filaments, microfungal hyphae, lichen rhizinae and anchoring rhizoids of bryophytes all together contribute to induce formation of structure in the thin soil layer beneath the Biological Soil Crusts (BSCs). Quantitative assessment of the soil structure beneath the BSCs is primarily hindered by the fragile nature of the crusts. Therefore, the role of BSCs in affecting such soil physical property has been rarely addressed using direct measurements. In this work we applied non-destructive X-ray microtomography imaging on five different samples of BSCs collected in the Alpine Tarfala Valley (northern Sweden), which have already been characterized in terms of fungal biodiversity in a previous work. We obtained images of the 3D spatial organization of the soil underneath the BSCs and characterized its structure by applying procedures of image analysis allowing to determine pore size distribution, pore connectivity and aggregate size distribution. Results has then been correlated with the different fungal assemblages of the samples.

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.

PubMed

Liu, Peng; Jia, Shuyu; He, Xiwei; Zhang, Xuxiang; Ye, Lin

2017-12-01

Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbiomes structure and diversity in different horizons of full soil profiles

NASA Astrophysics Data System (ADS)

Chernov, Timofey; Tkhakakhova, Azida; Zhelezova, Alena; Semenov, Mikhail; Kutovaya, Olga

2017-04-01

Topsoil is a most common object for soil metagenomic studies; sometimes soil profile is being formally split in layers by depth. However, Russian Soil Science School formulated the idea of soil profile as a complex of soil horizons, which can differ in their properties and genesis. In this research we analyzed 57 genetic soil horizons of 8 different soils from European part of Russia: Albeluvisol, Greyzemic Phaeozem, three Chermozems (different land use - till, fallow, wind-protecting tree line), Rhodic Cambisol, Haplic Kastanozem and Salic Solonetz (WRB classification). Sampling was performed from all genetic horizons in each soil profile starting from topsoil until subsoil. Total DNA was extracted and 16S rRNA sequencing was provided together with chemical analysis of soil (pH measurement, C and N contents, etc.). Structure and diversity of prokaryotic community are significantly different in those soil horizons, which chemical properties and processes of origin are contrasting with nearest horizons: Na-enriched horizon of Solonetz, eluvial horizon of Albeluvisol, plough pan of Agrochernozem. Actinobacteria were abundant in top horizons of soils in warm and dry climate, while Acidobacteria had the highest frequency in soils of moist and cold regions. Concerning Archaea, Thaumarchaeota prevailed in all studied soils. Their rate was higher in microbiomes of upper horizons of steppe soils and it was reducing with depth down the profile. Prokaryotic communities in Chernozems were clustered by soil horizons types: microbiomes of A (organic topsoil) and B (mineral) horizons formed non-overlapping clusters by principal component analysis, cluster formed by prokaryotic communities of transitional soil horizons (AB) take place between clusters of A and B horizons. Moreover, prokaryotic communities of A horizons differ from each other strongly, while microbiomes of B horizons formed a narrow small cluster. It must be explaned by more diverse conditions in upper A horizons. Thus, ecological differences between soil horizons are important factor of differentiation of prokaryotic communities in soil profile; their structure can be specific for horizon type. This study was supported by Russian Science Foundation, project no. 14-26-00079

Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil.

PubMed

Val-Moraes, Silvana Pompeia; de Macedo, Helena Suleiman; Kishi, Luciano Takeshi; Pereira, Rodrigo Matheus; Navarrete, Acacio Aparecido; Mendes, Lucas William; de Figueiredo, Eduardo Barretto; La Scala, Newton; Tsai, Siu Mui; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

2016-12-01

Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.

Effects of imidacloprid on soil microbial communities in different saline soils.

PubMed

Zhang, Qingming; Xue, Changhui; Wang, Caixia

2015-12-01

The effects of imidacloprid in the soil environment are a worldwide concern. However, the impact of imidacloprid on soil microorganisms under salt stress is almost unknown. Therefore, an indoor incubation test was performed, and the denaturing gradient gel electrophoresis (DGGE) approach was used to determine the response of different saline soil bacterial and fungal community structures to the presence of imidacloprid (0.4, 2, 10 mg kg(-1)). The results showed that the soil bacterial diversity slightly declined with increasing imidacloprid concentration in soils with low salinity. In moderately saline soils, a new band in the DGGE profile suggested that imidacloprid could improve the soil bacterial diversity to some degree. An analysis of variance indicated that the measured soil bacterial diversity parameters were significantly affected by dose and incubation time. Compared with the control, the soil fungal community structure showed no obvious changes in low and moderately saline soils treated with imidacloprid. The results of these observations provide a basic understanding of the potential ecological effects of imidacloprid on different microorganisms in saline soils.

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa.

PubMed

van Wyk, Deidré A B; Adeleke, Rasheed; Rhode, Owen H J; Bezuidenhout, Carlos C; Mienie, Charlotte

2017-09-01

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and β-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Land application of tylosin and chlortetracycline swine manure: Impacts to soil nutrients and soil microbial community structure.

PubMed

Stone, James J; Dreis, Erin K; Lupo, Christopher D; Clay, Sharon A

2011-01-01

The land application of aged chortetracycle (CTC) and tylosin-containing swine manure was investigated to determine associated impacts to soil microbial respiration, nutrient (phosphorus, ammonium, nitrate) cycling, and soil microbial community structure under laboratory conditions. Two silty clay loam soils common to southeastern South Dakota were used. Aerobic soil respiration results using batch reactors containing a soil-manure mixture showed that interactions between soil, native soil microbial populations, and antimicrobials influenced CO(2) generation. The aged tylosin treatment resulted in the greatest degree of CO(2) inhibition, while the aged CTC treatment was similar to the no-antimicrobial treatment. For soil columns in which manure was applied at a one-time agronomic loading rate, there was no significant difference in soil-P behavior between either aged CTC or tylosin and the no-antimicrobial treatment. For soil-nitrogen (ammonium and nitrate), the aged CTC treatment resulted in rapid ammonium accumulation at the deeper 40cm soil column depth, while nitrate production was minimal. The aged CTC treatment microbial community structure was different than the no-antimicrobial treatment, where amines/amide and carbohydrate chemical guilds utilization profile were low. The aged tylosin treatment also resulted in ammonium accumulation at 40 cm column depth, however nitrate accumulation also occurred concurrently at 10 cm. The microbial community structure for the aged tylosin was also significantly different than the no-antimicrobial treatment, with a higher degree of amines/amides and carbohydrate chemical guild utilization compared to the no-antimicrobial treatment. Study results suggest that land application of CTC and tylosin-containing manure appears to fundamentally change microbial-mediated nitrogen behavior within soil A horizons.

Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

PubMed

Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

2011-10-01

Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Method for analyzing soil structure according to the size of structural elements

NASA Astrophysics Data System (ADS)

Wieland, Ralf; Rogasik, Helmut

2015-02-01

The soil structure in situ is the result of cropping history and soil development over time. It can be assessed by the size distribution of soil structural elements such as air-filled macro-pores, aggregates and stones, which are responsible for important water and solute transport processes, gas exchange, and the stability of the soil against compacting and shearing forces exerted by agricultural machinery. A method was developed to detect structural elements of the soil in selected horizontal slices of soil core samples with different soil structures in order for them to be implemented accordingly. In the second step, a fitting tool (Eureqa) based on artificial programming was used to find a general function to describe ordered sets of detected structural elements. It was shown that all the samples obey a hyperbolic function: Y(k) = A /(B + k) , k ∈ { 0 , 1 , 2 , … }. This general behavior can be used to develop a classification method based on parameters {A and B}. An open source software program in Python was developed, which can be downloaded together with a selection of soil samples.

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 results suggest a possible influence of SWR on microbial structure and its activity in soils. References: Lozano, E., García-Orenes, F., Bárcenas-Moreno, G., Jiménez-Pinilla, P., Mataix-Solera, J., Arcenegui, V., Morugán-Coronado, A., Mataix-Beneyto, J., 2014. Relationships between soil water repellency and microbial community composition under different plant species in a Mediterranean semiarid forest. J. Hydrol. Hydromech., 62, 101-107 Müller, K., Deurer, M., Newton, P.C.D., 2010. Is there a link between elevated atmospheric carbon dioxide concentration, soil water repellency and soil carbon mineralization? Agric. Ecosyst. Environ., 139, 98-109. Acknowledgements: to the "Ministerio de Economía and Competitividad" of Spanish Government for finance the POSTFIRE project (CGL2013- 47862-C2-1-R), Generalitat Valenciana for PhD grant, and Spanish Soil Science Society and FUEGORED for their support.

Effects of Cd and Pb on soil microbial community structure and activities.

PubMed

Khan, Sardar; Hesham, Abd El-Latif; Qiao, Min; Rehman, Shafiqur; He, Ji-Zheng

2010-02-01

Soil contamination with heavy metals occurs as a result of both anthropogenic and natural activities. Heavy metals could have long-term hazardous impacts on the health of soil ecosystems and adverse influences on soil biological processes. Soil enzymatic activities are recognized as sensors towards any natural and anthropogenic disturbance occurring in the soil ecosystem. Similarly, microbial biomass carbon (MBC) is also considered as one of the important soil biological activities frequently influenced by heavy metal contamination. The polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) has recently been used to investigate changes in soil microbial community composition in response to environmental stresses. Soil microbial community structure and activities are difficult to elucidate using single monitoring approach; therefore, for a better insight and complete depiction of the soil microbial situation, different approaches need to be used. This study was conducted in a greenhouse for a period of 12 weeks to evaluate the changes in indigenous microbial community structure and activities in the soil amended with different application rates of Cd, Pb, and Cd/Pb mix. In a field environment, soil is contaminated with single or mixed heavy metals; so that, in this research, we used the selected metals in both single and mixed forms at different application rates and investigated their toxic effects on microbial community structure and activities, using soil enzyme assays, plate counting, and advanced molecular DGGE technique. Soil microbial activities, including acid phosphatase (ACP), urease (URE), and MBC, and microbial community structure were studied. A soil sample (0-20 cm) with an unknown history of heavy metal contamination was collected and amended with Cd, Pb, and Cd/Pb mix using the CdSO(4) and Pb(NO(3))(2) solutions at different application rates. The amended soils were incubated in the greenhouse at 25 +/- 4 degrees C and 60% water-holding capacity for 12 weeks. During the incubation period, samples were collected from each pot at 0, 2, 9, and 12 weeks for enzyme assays, MBC, numeration of microbes, and DNA extraction. Fumigation-extraction method was used to measure the MBC, while plate counting techniques were used to numerate viable heterotrophic bacteria, fungi, and actinomycetes. Soil DNAs were extracted from the samples and used for DGGE analysis. ACP, URE, and MBC activities of microbial community were significantly lower (p < 0.05) in the metal-amended samples than those in the control. The enzyme inhibition extent was obvious between different incubation periods and varied as the incubation proceeded, and the highest rate was detected in the samples after 2 weeks. However, the lowest values of ACP and URE activities (35.6% and 36.6% of the control, respectively) were found in the Cd(3)/Pb(3)-treated sample after 2 weeks. Similarly, MBC was strongly decreased in both Cd/Pb-amended samples and highest reduction (52.4%) was detected for Cd(3)/Pb(3) treatment. The number of bacteria and actinomycetes were significantly decreased in the heavy metal-amended samples compared to the control, while fungal cells were not significantly different (from 2.3% to 23.87%). In this study, the DGGE profile indicated that the high dose of metal amendment caused a greater change in the number of bands. DGGE banding patterns confirmed that the addition of metals had a significant impact on microbial community structure. In soil ecosystem, heavy metals exhibit toxicological effects on soil microbes which may lead to the decrease of their numbers and activities. This study demonstrated that toxicological effects of heavy metals on soil microbial community structure and activities depend largely on the type and concentration of metal and incubation time. The inhibition extent varied widely among different incubation periods for these enzymes. Furthermore, the rapid inhibition in microbial activities such as ACP, URE, and MBC were observed in the 2 weeks, which should be related to the fact that the microbes were suddenly exposed to heavy metals. The increased inhibition of soil microbial activities is likely to be related to tolerance and adaptation of the microbial community, concentration of pollutants, and mechanisms of heavy metals. The DGGE profile has shown that the structure of the bacterial community changed in amended heavy metal samples. In this research, the microbial community structure was highly affected, consistent with the lower microbial activities in different levels of heavy metals. Furthermore, a great community change in this study, particularly at a high level of contamination, was probably a result of metal toxicity and also unavailability of nutrients because no nutrients were supplied during the whole incubation period. The added concentrations of heavy metals have changed the soil microbial community structure and activities. The highest inhibitory effects on soil microbial activities were observed at 2 weeks of incubation. The bacteria were more sensitive than actinomycetes and fungi. The DGGE profile indicated that bacterial community structure was changed in the Cd/Pb-amended samples, particularly at high concentrations. The investigation of soil microbial community structure and activities together could give more reliable and accurate information about the toxic effects of heavy metals on soil health.

The effect of row structure on soil moisture retrieval accuracy from passive microwave data.

PubMed

Xingming, Zheng; Kai, Zhao; Yangyang, Li; Jianhua, Ren; Yanling, Ding

2014-01-01

Row structure causes the anisotropy of microwave brightness temperature (TB) of soil surface, and it also can affect soil moisture retrieval accuracy when its influence is ignored in the inversion model. To study the effect of typical row structure on the retrieved soil moisture and evaluate if there is a need to introduce this effect into the inversion model, two ground-based experiments were carried out in 2011. Based on the observed C-band TB, field soil and vegetation parameters, row structure rough surface assumption (Q p model and discrete model), including the effect of row structure, and flat rough surface assumption (Q p model), ignoring the effect of row structure, are used to model microwave TB of soil surface. Then, soil moisture can be retrieved, respectively, by minimizing the difference of the measured and modeled TB. The results show that soil moisture retrieval accuracy based on the row structure rough surface assumption is approximately 0.02 cm(3)/cm(3) better than the flat rough surface assumption for vegetated soil, as well as 0.015 cm(3)/cm(3) better for bare and wet soil. This result indicates that the effect of row structure cannot be ignored for accurately retrieving soil moisture of farmland surface when C-band is used.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau.

PubMed

Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong

2014-01-01

In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

PubMed

Fall, S; Nazaret, S; Chotte, J L; Brauman, A

2004-08-01

The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

Transport of four pharmaceuticals in different horizons of three soil types

NASA Astrophysics Data System (ADS)

Kodesova, Radka; Svatkova, Paula; Klement, Ales; Jaksik, Ondrej; Golovko, Oksana; Fer, Miroslav; Kocarek, Martin; Nikodem, Antonin; Grabic, Roman

2015-04-01

Soil structure, which varies in different soil types and the horizons of these soil types, has a significant impact on water flow and contaminant transport in soils. Transport of many contaminants is in addition strongly influenced by their sorption on soil particles. Transport of four pharmaceuticals (sulfamethoxazole, trimethoprim, atenolol and carbamazepine) was studied in soil columns (a diameter of 10.5 cm and a height of 13 cm) taken from all diagnostic horizons of three different soil types (Haplic Luvisol, Greyic Phaeozem and Haplic Cambisol). The irrigation by water contaminated by a mixture of all four compounds followed by ponding infiltration of distilled water was simulated and water outflow and solute concentrations from the bottom of the soil sample was monitored in time. The highest infiltration rates were observed for soil samples from the Bt horizons of the Greyic Phaeozem that exhibited prismatic structure, followed by rates observed in the Ap horizons of the Haplic Luvisol, Greyic Phaeozem and Haplic Cambisol (due to their granular soil structure and presence of root channels). The lowest infiltration rate was measured for the Bw horizon of the Haplic Cambisol, which had a poorly developed soil structure and a low fraction of macropores. Compound discharge was however also highly affected by their sorption on solids. The highest mobility was observed for sulfamethoxazole followed by carbamazepine atenolol and trimethoprim, which corresponds to measured sorption isotherms. Mobility of ionizable compounds in different soil samples was influenced by pH (i.e. degree and form of their ionization) and sites available for absorption. Mobility of sulfamethoxazole decreased with decreasing pH (i.e. the largest sorption measured in horizons of the Haplic Cambisol). While mobility of atenolol and trimethoprim decreased with increasing base cation saturation, and with increasing organic matter content for carbamazepine. As result of both affects (i.e. soil structure and compounds' sorption) the highest discharge of all compounds was observed from the Ap horizon of the Greyic Phaeozem followed by compound discharge from the C horizons of the Greyic Phaeozem and the C and Bt2 horizons of the Haplic Luvisol. Acknowledgement: The authors acknowledge the financial support of the Czech Science Foundation (Project No. 13-12477S, Transport of pharmaceuticals in soils). References: Kodesova, R., Grabic, R., Kocarek, M., Klement, A., Golovko, O., Fer, M., Nikodem, A., Jaksik, O., Pharmaceuticals' sorptions relative to properties of thirteen different soils. Science of the Total Environment 511 (2015) 435-443.

Forest canopy structural controls over throughfall affect soil microbial community structure in an epiphyte-laden maritime oak stand

NASA Astrophysics Data System (ADS)

Van Stan, J. T., II; Rosier, C. L.; Schrom, J. O.; Wu, T.; Reichard, J. S.; Kan, J.

2014-12-01

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to understanding of patterns in nutrient cycling and related ecological services. Since forest canopy structure alters the spatiotemporal patterning of precipitation water and solute supplies to soils (via the "throughfall" mechanism), is it possible changes in SMC structure variability could arise from modifications in canopy elements? Our study investigates this question by monitoring throughfall water and dissolved ion supply to soils beneath a continuum of canopy structure: from a large gap (0% cover) to heavy Tillandsia usneoides L. (Spanish moss) canopy (>90% cover). Throughfall water supply diminished with increasing canopy cover, yet increased washoff/leaching of Na+, Cl-, PO43-, and SO42- from the canopy to the soils (p < 0.01). Presence of T. usneoides diminished throughfall NO3-, but enhanced NH4+, concentrations supplied to subcanopy soils. The mineral soil horizon (0-10 cm) from canopy gaps, bare canopy, and T. usneoides-laden canopy significantly differed (p < 0.05) in soil chemistry parameters (pH, Ca2+, Mg2+, CEC). PCR-DGGE banding patterns beneath similar canopy covers (experiencing similar throughfall dynamics) also produced high similarities per ANalyses Of SIMilarity (ANO-SIM), and clustered together when analyzed by Nonmetric Multidimensional Scaling (NMDS). Correlation analysis of DGGE banding patterns, throughfall dynamics, and soil chemistry yielded significant correlations (p < 0.05) between fungal communities and soil chemical properties significantly differing between canopy cover types (pH: r2 = 0.50; H+ %-base saturation: r2 = 0.48; Ca2+ %-base saturation: r2 = 0.43). Bacterial community structure correlated with throughfall NO3-, NH4+, and Ca2+ concentrations (r2 = 0.37, p = 0.16). These results suggest that modifications of forest canopy structures are capable of affecting mineral-soil horizon SMC structure via the throughfall mechanism when canopies' biomass distribution is highly heterogeneous.

Assessing agricultural management effects on structure related soil hydraulic properties by tension infiltrometry

NASA Astrophysics Data System (ADS)

Bodner, G.; Loiskandl, W.; Kaul, H.-P.

2009-04-01

Soil structure is a dynamic property subject to numerous natural and human influences. It is recognized as fundamental for sustainable functioning of soil. Therefore knowledge of management impacts on the sensitive structural states of soil is decisive in order to avoid soil degradation. The stabilization of the soil's (macro)pore system and eventually the improvement of its infiltrability are essential to avoid runoff and soil erosion, particularly in view of an increasing probability of intense rainfall events. However structure-related soil properties generally have a high natural spatiotemporal variability that interacts with the potential influence of agricultural land use. This complicates a clear determination of management vs. environmental effects and requires adequate measurement methods, allowing a sufficient spatiotemporal resolution to estimate the impact of the targeted management factors within the natural dynamics of soil structure. A common method to assess structure-related soil hydraulic properties is tension infiltrometry. A major advantage of tension infiltrometer measurements is that no or only minimum soil disturbance is necessary and several structure-controlled water transmission properties can readily be derived. The method is more time- and cost-efficient compared to laboratory measurements of soil hydraulic properties, thus enabling more replications. Furthermore in situ measurements of hydraulic properties generally allow a more accurate reproduction of field soil water dynamics. The present study analyses the impact of two common agricultural management options on structure related hydraulic properties based on tension infiltrometer measurements. Its focus is the identification of the role of management within the natural spatiotemporal variability, particularly in respect to seasonal temporal dynamics. Two management approaches are analysed, (i) cover cropping as a "plant-based" agro-environmental measure, and (ii) tillage with different intensities including conventional tillage with a mouldboard plough, reduced tillage with a chisel plough and no-tillage. The results showed that the plant-based management measure of cover cropping had only minor influence on near-saturated hydraulic conductivity (kh) and flow weighted mean pore radius (λm). Substantial over-winter changes were found with a significant increase in kh and a reduction in the pore radius. A spatial trend in soil texture along the cover cropped slope resulted in a higher kh at lower pressure heads at the summit with higher fractions of coarse particles, while kh tended to be highest at the toeslope towards saturation. Cover crop management accounted for a maximum of 9.7% of the total variability in kh, with a decreasing impact towards the unsaturated range. A substantial difference to bare soil in the cover cropped treatments could be identified in relation to a stabilization of macro-pores over winter. The different tillage treatments had a substantial impact on near-saturated kh and pore radius. Although conventional tillage showed the highest values in kh and λm, settling of the soil after the ploughing event tended to reduce differences over time compared to the other tillage methods. The long-term no-tillage (10 years) however had the lowest values of kh at all measurement dates. The high contents of silt and fine sand probably resulted in soil densification that was not counterbalanced sufficiently by biological structure forming agents. The study could show that soil structure related hydraulic properties are subject to a substantial seasonal variability. A comprehensive assessment of agricultural measures such as tillage or cover cropping requires an estimate of these temporal dynamics and their interaction with the management strategies. Particularly for plant-based management measures such as cover cropping, which represent a less intense intervention in the structural states of the soil compared to tillage, this was evident, as the main mechanism revealed for this measure was structure stabilization over time. While spatial variability is mostly controlled in designed experiments, the role of temporal variability is often underestimated. From our study we concluded that (i) a proper understanding of processes involved in management effects on soil structure must take into consideration the dynamic nature of the respective soil properties, (ii) experimental planning for studies regarding management impacts on soil structure should allow an estimation of temporal variability, and (iii) for this purpose tension infiltrometry provides an efficient measurement tool to assess structure related soil hydraulic properties.

Modelling soil-water dynamics in the rootzone of structured and water-repellent soils

NASA Astrophysics Data System (ADS)

Brown, Hamish; Carrick, Sam; Müller, Karin; Thomas, Steve; Sharp, Joanna; Cichota, Rogerio; Holzworth, Dean; Clothier, Brent

2018-04-01

In modelling the hydrology of Earth's critical zone, there are two major challenges. The first is to understand and model the processes of infiltration, runoff, redistribution and root-water uptake in structured soils that exhibit preferential flows through macropore networks. The other challenge is to parametrise and model the impact of ephemeral hydrophobicity of water-repellent soils. Here we have developed a soil-water model, which is based on physical principles, yet possesses simple functionality to enable easier parameterisation, so as to predict soil-water dynamics in structured soils displaying time-varying degrees of hydrophobicity. Our model, WEIRDO (Water Evapotranspiration Infiltration Redistribution Drainage runOff), has been developed in the APSIM Next Generation platform (Agricultural Production Systems sIMulation). The model operates on an hourly time-step. The repository for this open-source code is https://github.com/APSIMInitiative/ApsimX. We have carried out sensitivity tests to show how WEIRDO predicts infiltration, drainage, redistribution, transpiration and soil-water evaporation for three distinctly different soil textures displaying differing hydraulic properties. These three soils were drawn from the UNSODA (Unsaturated SOil hydraulic Database) soils database of the United States Department of Agriculture (USDA). We show how preferential flow process and hydrophobicity determine the spatio-temporal pattern of soil-water dynamics. Finally, we have validated WEIRDO by comparing its predictions against three years of soil-water content measurements made under an irrigated alfalfa (Medicago sativa L.) trial. The results provide validation of the model's ability to simulate soil-water dynamics in structured soils.

The mechanics and energetics of soil bioturbation by earthworms and plant roots - Impacts on soil structure generation and maintenance

NASA Astrophysics Data System (ADS)

Or, Dani; Ruiz, Siul; Schymanski, Stanlislaus

2015-04-01

Soil structure is the delicate arrangement of solids and voids that facilitate numerous hydrological and ecological soil functions ranging from water infiltration and retention to gaseous exchange and mechanical anchoring of plant roots. Many anthropogenic activities affect soil structure, e.g. via tillage and compaction, and by promotion or suppression of biological activity and soil carbon pools. Soil biological activity is critical to the generation and maintenance of favorable soil structure, primarily through bioturbation by earthworms and root proliferation. The study aims to quantify the mechanisms, rates, and energetics associated with soil bioturbation, using a new biomechanical model to estimate stresses required to penetrate and expand a cylindrical cavity in a soil under different hydration and mechanical conditions. The stresses and soil displacement involved are placed in their ecological context (typical sizes, population densities, burrowing rates and behavior) enabling estimation of mechanical energy requirements and impacts on soil organic carbon pool (in the case of earthworms). We consider steady state plastic cavity expansion to determine burrowing pressures of earthworms and plant roots, akin to models of cone penetration representing initial burrowing into soil volumes. Results show that with increasing water content the strain energy decreases and suggest trade-offs between cavity expansion pressures and energy investment for different root and earthworm geometries and soil hydration. The study provides a quantitative framework for estimating energy costs of bioturbation in terms of soil organic carbon or the mechanical costs of soil exploration by plant roots as well as mechanical and hydration limits to such activities.

Soil microbial succession along a chronosequence on a High Arctic glacier foreland, Ny-Ålesund, Svalbard: 10 years' change

NASA Astrophysics Data System (ADS)

Yoshitake, Shinpei; Uchida, Masaki; Iimura, Yasuo; Ohtsuka, Toshiyuki; Nakatsubo, Takayuki

2018-06-01

Rapid glacial retreat in the High Arctic causes the expansion of new habitats, but the successional trajectories of soil microbial communities are not fully understood. We examined microbial succession along a chronosequence twice with a 10-year interval in a High Arctic glacier foreland. Soil samples were collected from five study sites with different ages and phospholipid fatty acids analysis was conducted to investigate the microbial biomass and community structure. Microbial biomass did not differ significantly between the two sampling times but tended to increase with the chronosequence and showed a significant correlation with soil carbon (C) and nitrogen (N) content. Microbial community structure clearly differed along the chronosequence and was correlated with C and N content. The largest shift in community structure over 10 years was observed in the newly exposed sites after deglaciation. The accumulation of soil organic matter was regarded as an important determinant both of microbial biomass and community structure over the successional period. In contrast, the initial microbial community on the newly exposed soil changed rapidly even in the High Arctic, suggesting that some key soil processes such as C and N cycling can also shift within the relatively short period after rapid glacial retreat.

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan

NASA Astrophysics Data System (ADS)

Pershina, E. V.; Ivanova, E. A.; Nagieva, A. G.; Zhiengaliev, A. T.; Chirak, E. L.; Andronov, E. E.; Sergaliev, N. Kh.

2016-06-01

The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.

Soil-borne microbial functional structure across different land uses.

PubMed

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

2014-01-01

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

Impact of soil structure heterogeneity on the degradation of organic pollutants at the centimeter scale : 3D Modeling using graph based method

NASA Astrophysics Data System (ADS)

Sinclair Yemini, Francis; Chenu, Claire; Monga, Olivier; Vieuble Gonond, Laure; Juarez, Sabrina; Pihneiro, Marc; otten, Wilfred; Garnier, Patricia

2014-05-01

Contaminant degradation by microorganisms is very variable in soils because of the very heterogeneous spatial relationship of contaminant/degraders. Repacked Soil columns were carried out to study the degradation of 2,4D pesticide labelled with C14 for different scenarios of microorganisms and pesticide initial location. Measurements of global C14-CO2 emission and C14 distribution in the soil column showed that the initial location play a crucial rule on the dissipation of the pollutant. Experiments were simulated using a 3D model able to model microbial degradation and substrate diffusion between aggregates by considering explicitly the 3D structure of soil from CT images. The initial version of the model (Monga et al., 2008) was improved in order to simulate diffusion in samples of large size. Partial differential equations were implemented using freefem++ solver. The model simulates properly the dynamics of 2,4D in the column for the different initial situations. CT images of the same soil but using undisturbed structure instead of repacked aggregates were also carried out. Significant differences of the simulated results were observed between the repacked and the undisturbed soil. The conclusion of our work is that the heterogeneity of the soil structure and location of pollutants and decomposers has a very strong influence on the dissipation of pollutants.

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.

Urbanization Effects on the Vertical Distribution of Soil Microbial Communities and Soil C Storage across Edge-to-Interior Urban Forest Gradients

NASA Astrophysics Data System (ADS)

Rosier, C. L.; Van Stan, J. T., II; Trammell, T. L.

2017-12-01

Urbanization alters environmental conditions such as temperature, moisture, carbon (C) and nitrogen (N) deposition affecting critical soil processes (e.g., C storage). Urban soils experience elevated N deposition (e.g., transportation, industry) and decreased soil moisture via urban heat island that can subsequently alter soil microbial community structure and activity. However, there is a critical gap in understanding how increased temperatures and pollutant deposition influences soil microbial community structure and soil C/N cycling in urban forests. Furthermore, canopy structural differences between individual tree species is a potentially important mechanism facilitating the deposition of pollutants to the soil. The overarching goal of this study is to investigate the influence of urbanization and tree species structural differences on the bacterial and fungal community and C and N content of soils experiencing a gradient of urbanization pressures (i.e., forest edge to interior; 150-m). Soil cores (1-m depth) were collected near the stem (< 0.5 meter) of two tree species with contrasting canopy and bark structure (Fagus grandifolia, vs. Liriodendron tulipifera), and evaluated for soil microbial structure via metagenomic analysis and soil C/N content. We hypothesize that soil moisture constraints coupled with increases in recalcitrant C will decrease gram negative bacteria (i.e., dependent on labile C) while increasing saprophytic fungal community abundance (i.e., specialist consuming recalcitrant C) within both surface and subsurface soils experiencing the greatest urban pressure (i.e., forest edge). We further expect trees located on the edge of forest fragments will maintain greater surface soil (< 20 cm) C concentrations due to decreased soil moisture constraining microbial activity (e.g., slower decay), and increased capture of recalcitrant C stocks from industrial/vehicle emission sources (e.g., black C). Our initial results support our hypotheses that urbanization alters soil microbial community composition via reduced soil moisture and carbon storage potential via deposition gradients. Further analyses will answer important questions regarding how individual tree species alters urban soil C storage, N retention, and microbial dynamics.

Visual soil evaluation - future research requirements

NASA Astrophysics Data System (ADS)

Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Ball, Bruce; Holden, Nick

2017-04-01

A review of Visual Soil Evaluation (VSE) techniques (Emmet-Booth et al., 2016) highlighted their established utility for soil quality assessment, though some limitations were identified; (1) The examination of aggregate size, visible intra-porosity and shape forms a key assessment criterion in almost all methods, thus limiting evaluation to structural form. The addition of criteria that holistically examine structure may be desirable. For example, structural stability can be indicated using dispersion tests or examining soil surface crusting, while the assessment of soil colour may indirectly indicate soil organic matter content, a contributor to stability. Organic matter assessment may also indicate structural resilience, along with rooting, earthworm numbers or shrinkage cracking. (2) Soil texture may influence results or impeded method deployment. Modification of procedures to account for extreme texture variation is desirable. For example, evidence of compaction in sandy or single grain soils greatly differs to that in clayey soils. Some procedures incorporate separate classification systems or adjust deployment based on texture. (3) Research into impacts of soil moisture content on VSE evaluation criteria is required. Criteria such as rupture resistance and shape may be affected by moisture content. It is generally recommended that methods are deployed on moist soils and quantification of influences of moisture variation on results is necessary. (4) Robust sampling strategies for method deployment are required. Dealing with spatial variation differs between methods, but where methods can be deployed over large areas, clear instruction on sampling is required. Additionally, as emphasis has been placed on the agricultural production of soil, so the ability of VSE for exploring structural quality in terms of carbon storage, water purification and biodiversity support also requires research. References Emmet-Booth, J.P., Forristal. P.D., Fenton, O., Ball, B.C. & Holden, N.M. 2016. A review of visual soil evaluation techniques for soil structure. Soil Use and Management, 32, 623-634.

An examination of the earthquake behaviour of a retaining wall considering soil-structure interaction

NASA Astrophysics Data System (ADS)

Köktan, Utku; Demir, Gökhan; Kerem Ertek, M.

2017-04-01

The earthquake behavior of retaining walls is commonly calculated with pseudo static approaches based on Mononobe-Okabe method. The seismic ground pressure acting on the retaining wall by the Mononobe-Okabe method does not give a definite idea of the distribution of the seismic ground pressure because it is obtained by balancing the forces acting on the active wedge behind the wall. With this method, wave propagation effects and soil-structure interaction are neglected. The purpose of this study is to examine the earthquake behavior of a retaining wall taking into account the soil-structure interaction. For this purpose, time history seismic analysis of the soil-structure interaction system using finite element method has been carried out considering 3 different soil conditions. Seismic analysis of the soil-structure model was performed according to the earthquake record of "1971, San Fernando Pacoima Dam, 196 degree" existing in the library of MIDAS GTS NX software. The results obtained from the analyses show that the soil-structure interaction is very important for the seismic design of a retaining wall. Keywords: Soil-structure interaction, Finite element model, Retaining wall

[Effects of rare earth elements on soil fauna community structure and their ecotoxicity to Holotrichia parallela].

PubMed

Li, Guiting; Jiang, Junqi; Chen, Jie; Zou, Yunding; Zhang, Xincai

2006-01-01

By the method of OECD filter paper contact, this paper studied the effects of applied rare earth elements on soil fauna community structure and their ecological toxicity to Holotrichia parallela in bean field. The results showed that there were no significant differences between the treatments and the control in soil fauna species, quantity of main species, and diversity index. Urgent and chronic toxic test showed that the differences between the treatments and the control were not significant. It was suggested that within the range of test dosages, rare earth elements had little ecological toxicity to Holotrichia parallela, and did not change the soil fauna community structure.

A Comparison of Microbial Community Structures by Depth and Season Under Switchgrass

NASA Astrophysics Data System (ADS)

Fansler, S. J.; Smith, J. L.; Bolton, H.; Bailey, V. L.

2008-12-01

As part of a multidisciplinary study of C sequestration in switchgrass production systems, the soil microbial community structure was monitored at 6 different depths (reaching 90 cm) in both spring and autumn. Microbial community structure was assessed using ribosomal intergenic spacer analysis (RISA), and primers were used specific to either bacteria or fungi, generating microbial community fingerprints for each taxonomic group. Diverse microbial communities for both groups were detected throughout the soil profile. It is notable that while community structure clearly changed with depth, there was the deepest soil samples still retained relatively diverse communities. Seasonally, differences are clearly evident within plots at the surface. As the plots were replicated, significant differences in the community fingerprints with depth and season are reported.

Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides.

PubMed

Shiau, Yo-Jin; Cai, Yuanfeng; Lin, Yu-Te; Jia, Zhongjun; Chiu, Chih-Yu

2018-04-01

Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH 4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of 13 CH 4 DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.

Impacts of soil moisture content on visual soil evaluation

NASA Astrophysics Data System (ADS)

Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Bondi, Giulia; Creamer, Rachel; Holden, Nick

2017-04-01

Visual Soil Examination and Evaluation (VSE) techniques offer tools for soil quality assessment. They involve the visual and tactile assessment of soil properties such as aggregate size and shape, porosity, redox morphology, soil colour and smell. An increasing body of research has demonstrated the reliability and utility of VSE techniques. However a number of limitations have been identified, including the potential impact of soil moisture variation during sampling. As part of a national survey of grassland soil quality in Ireland, an evaluation of the impact of soil moisture on two widely used VSE techniques was conducted. The techniques were Visual Evaluation of Soil Structure (VESS) (Guimarães et al., 2011) and Visual Soil Assessment (VSA) (Shepherd, 2009). Both generate summarising numeric scores that indicate soil structural quality, though employ different scoring mechanisms. The former requires the assessment of properties concurrently and the latter separately. Both methods were deployed on 20 sites across Ireland representing a range of soils. Additional samples were taken for soil volumetric water (θ) determination at 5-10 and 10-20 cm depth. No significant correlation was observed between θ 5-10 cm and either VSE technique. However, VESS scores were significantly related to θ 10-20 cm (rs = 0.40, sig = 0.02) while VSA scores were not (rs = -0.33, sig = 0.06). VESS and VSA scores can be grouped into quality classifications (good, moderate and poor). No significant mean difference was observed between θ 5-10 cm or θ 10-20 cm according to quality classification by either method. It was concluded that VESS scores may be affected by soil moisture variation while VSA appear unaffected. The different scoring mechanisms, where the separate assessment and scoring of individual properties employed by VSA, may limit soil moisture effects. However, moisture content appears not to affect overall structural quality classification by either method. References Guimarães, R.M.C., Ball, B.C. & Tormena, C.A. 2011. Improvements in the visual evaluation of soil structure, Soil Use and Management, 27, 3: 395-403 Shepherd, G.T. 2009. Visual Soil Assessment. Field guide for pastoral grazing and cropping on flat to rolling country. 2nd edn. Horizons regional council, New Zealand.

Differentiate responses of soil structure to natural vegetation and artificial plantation in landslide hazard region of the West Qinling Mountains, China

NASA Astrophysics Data System (ADS)

Wang, X.; Huang, Z.; Zhao, Y.; Hong, M.

2017-12-01

Natural vegetation and artificial plantation are the most important measures for ecological restoration in soil erosion and landslide hazard-prone regions of China. Previous studies have demonstrated that both measures can significantly change the soil structure and decrease soil and water erosion. Few reports have compared the effects of the two contrasting measures on mechanical and hydrological properties and further tested the differentiate responses of soil structure. In the study areas, two vegetation restoration measures-natural vegetation restoration (NVR) and artificial plantation restoration (APR) compared with control site, with similar topographical and geological backgrounds were selected to investigate the different effects on soil structure based on eight-year ecological restoration projects. The results showed that the surface vegetation played an important role in releasing soil erosion and enhance soil structure stability through change the soil aggregates (SA) and total soil porosity (TSP). The SA<0.25mm content in NVR (36.13%) was higher than that in APR (32.14%). The study indicated that SA and TSP were the principal components (PCs) related to soil structure variation. Soil organic carbon, soil water retention, clay and vegetation biomass were more strongly correlated with the PCs in NVR than those in APR. The study indicated that NVR was more beneficial for soil structure stability than APR. These findings will provide a theoretical basis for the decisions around reasonable land use for ecological restoration and conservation in geological hazard-prone regions.

Microbial composition in microcosms amended with natural and mineral fertilizers under different water regimes

NASA Astrophysics Data System (ADS)

Brad, Traian; Chiriac, Cecilia; Szekeres, Edina; Coman, Cristian; Rudi, Knut; Sandor, Mignon

2017-04-01

Twenty microcosm enclosures containing two types of soil (i.e. a rich Chernozemic and a poorer soil) were fertilized with mineral (NPK-complex) and organic (Gülle, manure and a green fertilizer) materials and placed under dry and wet water regimes. After 10, 20 and 30 days of the experiment, soil samples were analyzed for the structure and composition of microbial communities using next generation sequencing techniques (Illumina) and statistical analysis. The differences between bacteria communities in different soil types, and in different fertilization and hydric treatments were analyzed using quantitative phylogenetic distances and the ANOSIM test. The two types of soil especially selected for the structure of microbial communities, while moisture and the type of fertilizer appeared to have a smaller influence on microbial diversity in microcosms. The alpha-diversity indices (species richness, evenness and phylogenetic diversity) had higher values for the poorer soil compared to the rich Chernozemic soil. For both soil types, the highest bacteria diversity values were obtained after fertilization with manure. The microbial communities in the analyzed soils were complex and dominated by sequences belonging to Actinobacteria, Proteobacteria, Acidobacteria and Firmicutes.

[Population structure of soil arthropod in different age Pinus massoniana plantations].

PubMed

Tan, Bo; Wu, Fu-zhong; Yang, Wan-qin; Zhang, Jian; Xu, Zhen-feng; Liu, Yang; Gou, Xiao-lin

2013-04-01

An investigation was conducted on the population structure of soil arthropod community in the 3-, 8-, 14-, 31-, and 40-years old Pinus massoniana plantations in the upper reaches of the Yangtze River in spring (May) and autumn (October), 2011, aimed to search for the scientific management of the plantation. A total of 4045 soil arthropods were collected, belonging to 57 families. Both the individual density and the taxonomic group number of the soil arthropod community decreased obviously with increasing soil depth, and this trend increased with increasing stand age. The dominant groups and ordinary groups of the soil arthropod community varied greatly with the stand age of P. massoniana plantation, and a significant difference (P<0.05) was observed in the individual density and taxonomic group number among different age P. massoniana plantations. In comparison with other stand age P. massoniana plantations, 3years old P. massoniana plantation had a significant difference in the structure and diversity of soil arthropod community, and the similarity index of the soil arthropod community was lower. The individual density, taxonomic group number, and diversity of soil arthropod community were the highest in 8-years old P. massoniana plantation, and then, decreased obviously with increasing stand age. It was suggested that the land fertility of the P. massoniana plantations could be degraded with increasing stand age, and it would be appropriate to make artificial regulation and restoration in 8-years old P. massoniana plantation.

Experimental evidence of the role of pores on movement and distribution of bacteria in soil

NASA Astrophysics Data System (ADS)

Kravchenko, Alexandra N.; Rose, Joan B.; Marsh, Terence L.; Guber, Andrey K.

2014-05-01

It has been generally recognized that micro-scale heterogeneity in soil environments can have a substantial effect on movement, fate, and survival of soil microorganisms. However, only recently the development of tools for micro-scale soil analyses, including X-ray computed micro-tomography (μ-CT), enabled quantitative analyses of these effects. The long-term goal of our work is to explore how differences in micro-scale characteristics of pore structures influence movement, spatial distribution patterns, and activities of soil microorganisms. Using X-ray μ-CT we found that differences in land use and management practices lead to development of contrasting patterns in pore size-distributions within intact soil aggregates. Then our experiments with Escherichia coli added to intact soil aggregates demonstrated that the differences in pore structures can lead to substantial differences in bacteria redistribution and movement within the aggregates. Specifically, we observed more uniform E.coli redistribution in aggregates with homogeneously spread pores, while heterogeneous pore structures resulted in heterogeneous E.coli patterns. Water flow driven by capillary forces through intact aggregate pores appeared to be the main contributor to the movement patterns of the introduced bacteria. Influence of pore structure on E.coli distribution within the aggregates further continued after the aggregates were subjected to saturated water flow. E. coli's resumed movement with saturated water flow and subsequent redistribution within the soil matrix was influenced by porosity, abundance of medium and large pores, pore tortuosity, and flow rates, indicating that greater flow accompanied by less convoluted pores facilitated E. coli transport within the intra-aggregate space. We also found that intra-aggregate heterogeneity of pore structures can have an effect on spatial distribution patterns of indigenous microbial populations. Preliminary analysis showed that in aggregates from an organic agricultural system with cover crops, characterized by greater intra-aggregate pore heterogeneity, bacteria of Actinobacteria and Firmicutes groups were more abundant in presence of large as compared to small pores. In contrast, no differences were observed in the aggregates from conventionally managed soil, overall characterized by homogeneous intra-aggregate pore patterns. Further research efforts are being directed towards quantification of the pore structure effects on activities and community composition of soil microorganisms.

Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure

PubMed Central

Skvortsova, Elena B.; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity. PMID:26010779

Universal spatial correlation functions for describing and reconstructing soil microstructure.

PubMed

Karsanina, Marina V; Gerke, Kirill M; Skvortsova, Elena B; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity.

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

PubMed Central

Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures. PMID:28346463

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses.

PubMed

Li, Tianzhu; Liu, Tongtong; Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures.

Effects of Rainfall-Induced Topsoil Structure Changes on Root-Zone Moisture Regime during the Dry Period

NASA Astrophysics Data System (ADS)

Wang, Feng; Chen, Jiazhou; Lin, Lirong

2018-01-01

Rainfall erosion and subsequent intermittent drought are serious barriers for agricultural production in the subtropical red soil region of China. Although it is widely recognized that rainfall-induced soil structure degradation reduced soil water storage and water-holding capacity, the effects of variation of the rainfall-induced topsoil structure on the subsequent soil water regime during the dry period is still rarely considered. The objective of this study was to ascertain the way of rainfall-induced topsoil structure changes on the subsequent soil water regime during the dry period. In a three-year-long experiment, six practices (CK, only crop; SM, straw mulching; PAM, polyacrylamide surface application; B, contour Bahia-grass strip; SPAM, straw mulching and polyacrylamide surface application; and BPAM, contour Bahia-grass strip and polyacrylamide surface application) were conducted at an 8° farmland with planting summer maize resulting in different topsoil structure and root-zone moisture, to establish and reveal the quantitatively relationship between the factors of topsoil structure and soil drought. Rainfall erosion significantly increased the soil crust coverage, and decreased the WSA 0.25, 0-30 mm soil porosity and mean pore size. There was no significant difference during the raining stage of root-zone water storage between CK and other practices. An index of soil drought intensity ( I) and degree ( D) was established using soil water loss rate and soil drought severity. The larger value of I means a higher rate of water loss. The larger value of D means more severe drought. During the dry period, I and D were significantly higher in CK than in other practices. I and D had significantly positively correlation with the crust size and crust coverage, and negatively with WSA 0.25, 15-30 mm soil porosity and mean pore size. Among of soil structure factors, the soil porosity had the largest effect on I and D. The rainfall-induced topsoil structure changes greatly deteriorated the root-zone regime during the dry period mainly due to significant increasing soil water loss but little improving the raining stage of soil water storage. Straw mulching had greater effects than other practices in alleviating rainfall-induced erosion and intermittent drought, and could be a better strategy applied for this region.

Biogeochemical drivers of microbial community convergence across actively retreating glaciers

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

Castle, Sarah C.; Nemergut, Diana R.; Grandy, A. Stuart

The ecological processes that influence biogeographical patterns of microorganisms are actively debated. To investigate how such patterns emerge during ecosystem succession, we examined the biogeochemical drivers of bacterial community assembly in soils over two environmentally distinct, recently deglaciated chronosequences separated by a distance of more than 1,300 kilometers. Our results show that despite different geographic, climatic, and soil chemical and physical characteristics at the two sites, soil bacterial community structure and decomposer function converged during plant succession. In a comparative analysis, we found that microbial communities in early succession soils were compositionally distinct from a group of diverse, mature forestmore » soils, but that the differences between successional soils and mature soils decreased from early to late stages of succession. Differences in bacterial community composition across glacial sites were largely explained by pH. However, successional patterns and community convergence across sites were more consistently related to soil organic carbon and organic matter chemistry, which appeared to be tightly coupled with bacterial community structure across both young and mature soils.« less

Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function.

PubMed

Ruiz-González, Clara; Archambault, Esther; Laforest-Lapointe, Isabelle; Del Giorgio, Paul A; Kembel, Steven W; Messier, Christian; Nock, Charles A; Beisner, Beatrix E

2018-06-14

Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities. Soil bacterial assemblages showed a strong influence of tree composition, but such community differences were not reflected in the structure of lake communities that developed during the experiment. Bacterial taxa showing the largest abundance increases during incubation were initially present in both lake water and across most soils, and were related to Cytophagales, Burkholderiales and Rhizobiales. No clear metabolic profiles based on inoculum source were found, yet soil-amended communities used 60% more substrate than non-inoculated communities. Overall, we show that terrestrial inputs influence aquatic communities by stimulating the growth and activity of certain ubiquitous taxa distributed across the terrestrial-aquatic continuum, yet different forest soils did not cause predictable changes in lake bacterioplankton assemblages.

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.

PubMed

Patel, Vrutika; Sharma, Anukriti; Lal, Rup; Al-Dhabi, Naif Abdullah; Madamwar, Datta

2016-03-22

Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Minerals in soil select distinct bacterial communities in their microhabitats.

PubMed

Carson, Jennifer K; Campbell, Louise; Rooney, Deirdre; Clipson, Nicholas; Gleeson, Deirdre B

2009-03-01

We tested the hypothesis that different minerals in soil select distinct bacterial communities in their microhabitats. Mica (M), basalt (B) and rock phosphate (RP) were incubated separately in soil planted with Trifolium subterraneum, Lolium rigidum or left unplanted. After 70 days, the mineral and soil fractions were separated by sieving. Automated ribosomal intergenic spacer analysis was used to determine whether the bacterial community structure was affected by the mineral, fraction and plant treatments. Principal coordinate plots showed clustering of bacterial communities from different fraction and mineral treatments, but not from different plant treatments. Permutational multivariate anova (permanova) showed that the microhabitats of M, B and RP selected bacterial communities different from each other in unplanted and L. rigidum, and in T. subterraneum, bacterial communities from M and B differed (P<0.046). permanova also showed that each mineral fraction selected bacterial communities different from the surrounding soil fraction (P<0.05). This study shows that the structure of bacterial communities in soil is influenced by the mineral substrates in their microhabitat and that minerals in soil play a greater role in bacterial ecology than simply providing an inert matrix for bacterial growth. This study suggests that mineral heterogeneity in soil contributes to the spatial variation in bacterial communities.

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

PubMed

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

2013-07-01

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

Sugarcane trash levels in soil affects the fungi but not bacteria in a short-term field experiment.

PubMed

Rachid, C T C C; Pires, C A; Leite, D C A; Coutinho, H L C; Peixoto, R S; Rosado, A S; Salton, J; Zanatta, J A; Mercante, F M; Angelini, G A R; Balieiro, Fabiano de Carvalho

2016-01-01

The sugarcane in Brazil is passing through a management transition that is leading to the abolition of pre-harvest burning. Without burning, large amounts of sugarcane trash is generated, and there is a discussion regarding the utilization of this biomass in the industry versus keeping it in the field to improve soil quality. To study the effects of the trash removal on soil quality, we established an experimental sugarcane plantation with different levels of trash over the soil (0%, 50% and 100% of the original trash deposition) and analyzed the structure of the bacterial and fungal community as the bioindicators of impacts. The soil DNA was extracted, and the microbial community was screened by denaturing gradient gel electrophoresis in two different seasons. Our results suggest that there are no effects from the different levels of trash on the soil chemistry and soil bacterial community. However, the fungal community was significantly impacted, and after twelve months, the community presented different structures among the treatments. Copyright © 2016. Published by Elsevier Editora Ltda.

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

PubMed Central

Lima-Morales, Daiana; Jáuregui, Ruy; Camarinha-Silva, Amelia; Geffers, Robert; Vilchez-Vargas, Ramiro

2016-01-01

Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched. PMID:26850298

Differences between bacterial communities in the gut of a soil-feeding termite (Cubitermes niokoloensis) and its mounds.

PubMed

Fall, Saliou; Hamelin, Jérôme; Ndiaye, Farma; Assigbetse, Komi; Aragno, Michel; Chotte, Jean Luc; Brauman, Alain

2007-08-01

In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.

Differential effects of fine root morphology on water dynamics in the root-soil interface

NASA Astrophysics Data System (ADS)

DeCarlo, K. F.; Bilheux, H.; Warren, J.

2017-12-01

Soil water uptake form plants, particularly in the rhizosphere, is a poorly understood question in the plant and soil sciences. Our study analyzed the role of belowground plant morphology on soil structural and water dynamics of 5 different plant species (juniper, grape, maize, poplar, maple), grown in sandy soils. Of these, the poplar system was extended to capture drying dynamics. Neutron radiography was used to characterize in-situ dynamics of the soil-water-plant system. A joint map of root morphology and soil moisture was created for the plant systems using digital image processing, where soil pixels were connected to associated root structures via minimum distance transforms. Results show interspecies emergent behavior - a sigmoidal relationship was observed between root diameter and bulk/rhizosphere soil water content difference. Extending this as a proxy for extent of rhizosphere development with root age, we observed a logistic growth pattern for the rhizosphere: minimal development in the early stages is superceded by rapid onset of rhizosphere formation, which then stabilizes/decays with the likely root suberization. Dynamics analysis of water content differences between the root/rhizosphere, and rhizosphere/bulk soil interface highlight the persistently higher water content in the root at all water content and root size ranges. At the rhizosphere/bulk soil interface, we observe a shift in soil water dynamics by root size: in super fine roots, we observe that water content is primarily lower in the rhizosphere under wetter conditions, which then gradually increases to a relatively higher water content under drier conditions. This shifts to a persistently higher rhizosphere water content relative to bulk soil in both wet/dry conditions with increased root size, suggesting that, by size, the finest root structures may contribute the most to total soil water uptake in plants.

An ecosystem approach to assess soil quality in organically and conventionally managed farms in Iceland and Austria

NASA Astrophysics Data System (ADS)

van Leeuwen, J. P.; Lehtinen, T.; Lair, G. J.; Bloem, J.; Hemerik, L.; Ragnarsdóttir, K. V.; Gísladóttir, G.; Newton, J. S.; de Ruiter, P. C.

2015-01-01

Intensive agricultural production can be an important driver for the loss of long-term soil quality. For this reason, the European Critical Zone Observatory (CZO) network adopted four pairs of agricultural CZO sites that differ in their management: conventional or organic. The CZO sites include two pairs of grassland farms in Iceland and two pairs of arable farms in Austria. Conventional fields differed from the organic fields in the use of artificial fertilisers and pesticides. Soils of these eight farms were analysed in terms of their physical, chemical, and biological properties, including soil aggregate size distribution, soil organic matter contents, abundance of soil microbes and soil fauna, and taxonomic diversity of soil microarthropods. In Icelandic grasslands, organically farmed soils had larger mean weight diameters of soil aggregates than the conventional farms, while there were no differences on the Austrian farms. Organic farming did not systematically influence organic matter contents or composition, nor soil carbon and nitrogen contents. Also, soil food web structures, in terms of presence of trophic groups of soil organisms, were highly similar among all farms, indicating a low sensitivity of trophic structure to land use or climate. However, soil organism biomass, especially of bacteria and nematodes, was consistently higher on organic farms than on conventional farms. Within the microarthropods, taxonomic diversity was systematically higher in the organic farms compared to the conventional farms. This difference was found across countries and farm, crop, and soil types. The results do not show systematic differences in physical and chemical properties between organic and conventional farms, but confirm that organic farming can enhance soil biomass and that microarthropod diversity is a sensitive and consistent indicator for land management.

Model structures amplify uncertainty in predicted soil carbon responses to climate change.

PubMed

Shi, Zheng; Crowell, Sean; Luo, Yiqi; Moore, Berrien

2018-06-04

Large model uncertainty in projected future soil carbon (C) dynamics has been well documented. However, our understanding of the sources of this uncertainty is limited. Here we quantify the uncertainties arising from model parameters, structures and their interactions, and how those uncertainties propagate through different models to projections of future soil carbon stocks. Both the vertically resolved model and the microbial explicit model project much greater uncertainties to climate change than the conventional soil C model, with both positive and negative C-climate feedbacks, whereas the conventional model consistently predicts positive soil C-climate feedback. Our findings suggest that diverse model structures are necessary to increase confidence in soil C projection. However, the larger uncertainty in the complex models also suggests that we need to strike a balance between model complexity and the need to include diverse model structures in order to forecast soil C dynamics with high confidence and low uncertainty.

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

PubMed

Lee, Seung-Hoon; Kang, Hojeong

2016-02-01

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

Development and assessment of transparent soil and particle image velocimetry in dynamic soil-structure interaction

DOT National Transportation Integrated Search

2007-02-01

This research combines Particle Image Velocimetry (PIV) and transparent soil to investigate the dynamic rigid block and soil interaction. In order to get a low viscosity pore fluid for the transparent soil, 12 different types of chemical solvents wer...

Faunal Drivers of Soil Flux Dynamics via Alterations in Crack Structure

NASA Astrophysics Data System (ADS)

DeCarlo, Keita; Caylor, Kelly

2016-04-01

Organismal activity, in addition to its role in ecological feedbacks, has the potential to serve as instigators or enhancers of atmospheric and hydrologic processes via alterations in soil structural regimes. We investigated the biomechanical effect of faunal activity on soil carbon dynamics via changes in soil crack structure, focusing on three dryland soil systems: bioturbated, biocompacted and undisturbed soils. Carbon fluxes were characterized using a closed-system respiration chamber, with CO2 concentration differences measured using an infrared gas analyzer (IRGA). Results show that faunal influences play a divergent biomechanics role in bulk soil cracking: bioturbation induced by belowground fauna creates "surficial" (shallow, large, well-connected) networks relative to the "systematic" (deep, moderate, poorly connected) networks created by aboveground fauna. The latter also shows a "memory" of past wetting/drying events in the consolidated soil through a crack layering effect. These morphologies further drive differences in soil carbon flux: under dry conditions, bioturbated and control soils show a persistently high and low mean carbon flux, respectively, while biocompacted soils show a large diurnal trend, with daytime lows and nighttime highs comparable to the control and bioturbated soils, respectively. Overall fluxes under wet conditions are considerably higher, but also more variable, though higher mean fluxes are observed in the biocompacted and bioturbated soils. Our results suggest that the increased surface area in the bioturbated soils create enhanced but constant diffusive processes, whereas the increased thermal gradient in the biocompacted soils create novel convective processes that create high fluxes that are diurnal in nature.

[Effects of Phyllostachys edulis cultivation on soil bacterial and fungal community structure and diversity].

PubMed

Zhao, Tian Xin; Mao, Xin Wei; Cheng, Min; Chen, Jun Hui; Qin, Hua; Li, Yong Chun; Liang, Chen Fei; Xu, Qiu Fang

2017-11-01

This study examined how soil bacterial and fungal communities responded to the cultivation history of Moso bamboo in Anji and Changxing counties, Huzhou, Zhejiang, China. Soil samples (0-20 and 20-40 cm) were taken from bamboo plantations subjected to different cultivation histories and analyzed the community structures of soil bacterial and fungal by PCR-DGGE methods. It was found that soil bacterial and fungal communities varied greatly with the development of bamboo plantations which converted from Masson pine forest or formed via invading adjacent broadleaf shrub forest. Soil bacterial community structures exhibited a greater response to bamboo cultivation time than fungal community, but bacteria structure of surface soil displayed an ability of resiliency to disturbance and the tendency to recover to the original state. The cultivation time, sampling site and soil layer significantly affected the biodiversity of soil bacteria and fungi, especially the latter two factors. Redundancy analysis (RDA) of soil properties and bacteria or fungi communities showed that there were no accordant factors to drive the alteration of microbial structure, and the first two axes explained less than 65.0% of variance for most of the sampling sites and soil layers, indicating there existed soil parameters besides the five examined that contributed to microbial community alteration.

A metrics for soil hydrological processes and their intrinsic dimensionality in heterogeneous systems

NASA Astrophysics Data System (ADS)

Lischeid, G.; Hohenbrink, T.; Schindler, U.

2012-04-01

Hydrology is based on the observation that catchments process input signals, e.g., precipitation, in a highly deterministic way. Thus, the Darcy or the Richards equation can be applied to model water fluxes in the saturated or vadose zone, respectively. Soils and aquifers usually exhibit substantial spatial heterogeneities at different scales that can, in principle, be represented by corresponding parameterisations of the models. In practice, however, data are hardly available at the required spatial resolution, and accounting for observed heterogeneities of soil and aquifer structure renders models very time and CPU consuming. We hypothesize that the intrinsic dimensionality of soil hydrological processes, which is induced by spatial heterogeneities, actually is very low and that soil hydrological processes in heterogeneous soils follow approximately the same trajectory. That means, the way how the soil transforms any hydrological input signals is the same for different soil textures and structures. Different soils differ only with respect to the extent of transformation of input signals. In a first step, we analysed the output of a soil hydrological model, based on the Richards equation, for homogeneous soils down to 5 m depth for different soil textures. A matrix of time series of soil matrix potential and soil water content at 10 cm depth intervals was set up. The intrinsic dimensionality of that matrix was assessed using the Correlation Dimension and a non-linear principal component approach. The latter provided a metrics for the extent of transformation ("damping") of the input signal. In a second step, model outputs for heterogeneous soils were analysed. In a last step, the same approaches were applied to 55 time series of observed soil water content from 15 sites and different depths. In all cases, the intrinsic dimensionality in fact was very close to unity, confirming our hypothesis. The metrics provided a very efficient tool to quantify the observed behaviour, depending on depth and soil heterogeneity: Different soils differed primarily with respect to the extent of damping per depth interval rather than to the kind of damping. We will show how that metrics can be used in a very efficient way for representing soil heterogeneities in simulation models.

Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula seedlings in an organic and mineral soil.

PubMed

Priha; Grayston; Pennanen; Smolander

1999-10-01

The aim of this study was to determine whether Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies (L.) Karst.) and silver birch (Betula pendula Roth) seedlings have a selective influence on the soil microbial community structure and activity and whether this varies in different soils. Seedlings of pine, spruce and birch were planted into pots of two soil types: an organic soil and a mineral soil. Pots without seedlings were also included. After one growing season, microbial biomass C (C(mic)) and N (N(mic)), C mineralization, net ammonification, net nitrification, denitrification potential, phospholipid fatty acid (PLFA) patterns and community level physiological profiles (CLPPs) were measured in the rhizosphere soil of the seedlings. In the organic soil, C(mic) and N(mic) were higher in the birch rhizosphere than in pine and spruce rhizosphere. The C mineralization rate was not affected by tree species. Unplanted soil contained the highest amount of mineral N and birch rhizosphere the lowest, but rates of net N mineralization and net nitrification did not differ between treatments. The microbial community structure, measured by PLFAs, had changed in the rhizospheres of all tree species compared to the unplanted soil. Birch rhizosphere was most clearly separated from the others. There was more of the fungal specific fatty acid 18:2omega6,9 and more branched fatty acids, common in Gram-positive bacteria, in this soil. CLPPs, done with Biolog GN plates and 30 additional substrates, separated only birch rhizosphere from the others. In the mineral soil, roots of all tree species stimulated C mineralization in soil and prevented nitrification, but did not affect C(mic) and N(mic), PLFA patterns or CLPPs. The effects of different tree species did not vary in the mineral soil. Thus, in the mineral soil, the strongest effect on soil microbes was the presence of a plant, regardless of the tree species, but in the organic soil, different tree species varied in their influence on soil microbes.

Chemical migration during soil water retention curve evaluation.

PubMed

Pires, Luiz F; Villanueva, Felipe C A; Dias, Nivea M P; Bacchi, Osny O Santos; Reichardt, Klaus

2011-09-01

Wetting and drying (W-D) cycles can induce important elemental migrations in soils. The main purpose of this work was to study the possible existence of soil chemical elemental migrations in samples submitted to repeated W-D cycles during evaluations of soil water retention curve (SWRC). The experimental measurements were carried out by Atomic Absorption Spectrometry (AAS) for Ca(2+), Mg(2+) and K(+) on samples of three different Brazilian tropical soils (Geric Ferralsol, Eutric Nitosol and Rhodic Ferralsol). Results demonstrate an increase in the electrical conductivity of the water extracted from the samples and significant losses of Ca(2+), Mg(2+) and K(+) during the applications of up to nine W-D cycles. It was also observed differences in SWRC for all soils when samples submitted to the application of several W-D cycles were compared with samples not submitted to it. These differences occurred at the region of both structural and textural pores. A possible explanation for these results could be the soil chemical migration during the sequences of W-D cycles, which can affect the soil structure development.

[Effects of grape-replanting on soil bacterial and fungal populations].

PubMed

Li, Kun; Guo, Xiu-wu; Sun, Ying-ni; Zhang, Li-heng; Hu, Xi-xi

2009-12-01

Rhizosphere and non-rhizosphere soil samples were collected from the vineyards having been planted for 3 and 30 years, and PCR-DGGE technique was adopted to study the effects of grape-replanting on the population structure and diversity of soil bacteria and fungi. The bacterial and fungal diversities were higher in 30-year-planted vineyard than in 3-year-planted vineyard, and higher in rhizosphere soil than in non-rhizosphere soil. After 30 years replanting, the population structure of bacteria and fungi approached the same in rhizosphere soil and non-rhizosphere soil but differed from that in fallow soil; while in the 3-year-planted vineyard, the population structure in rhizosphere soil was different from that in non-rhizosphere soil and fallow soil. Comparing with that in 3-year-planted vineyard, the rhizosphere soil microbial population in 30-year-planted vineyard had a greater change. In bacterial population, Flavobacterium sp. (DQ339585) and Bacillus sp. (AY039821) decreased while Pedobacter sp. (AJ871084) increased; in fungal population, Omphalina farinolens (EF413029) appeared, Pestalotiopsis sp. (DQ657877, DQ657875, DQ657871), Phacidium lacerum (DQ470976), and Lecythophora decumbens (AF353597) decreased, while Pilidium acerinum voucher (AY48709) increased. Bacillus sp., Flavobacterium sp. , and Pestalotiopsis sp. had antagonism to pathogen, and their decrease reduced the resistance of grape against pathogen. The increase of Pilidium acerinum voucher might relate to the severe disease after grape-replanting.

The Arctic Soil Bacterial Communities in the Vicinity of a Little Auk Colony

PubMed Central

Zielińska, Sylwia; Kidawa, Dorota; Stempniewicz, Lech; Łoś, Marcin; Łoś, Joanna M.

2016-01-01

Due to deposition of birds' guano, eggshells or feathers, the vicinity of a large seabirds' breeding colony is expected to have a substantial impact on the soil's physicochemical features as well as on diversity of vegetation and the soil invertebrates. Consequently, due to changing physicochemical features the structure of bacterial communities might fluctuate in different soil environments. The aim of this study was to investigate the bacterial assemblages in the Arctic soil within the area of a birds' colony and in a control sample from a topographically similar location but situated away from the colony's impact area. A high number of OTUs found in both areas indicates a highly complex microbial populations structure. The most abundant phyla in both of the tested samples were: Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, with different proportions in the total share. Despite differences in the physicochemical soil characteristics, the soil microbial community structures at the phylum level were similar to some extent in the two samples. The only share that was significantly higher in the control area when compared to the sample obtained within the birds' colony, belonged to the Actinobacteria phylum. Moreover, when analyzing the class level for each phylum, several differences between the samples were observed. Furthermore, lower proportions of Proteobacteria and Acidobacteria were observed in the soil sample under the influence of the bird's colony, which most probably could be linked to higher nitrogen concentrations in that sample. PMID:27667982

An ecosystem approach to assess soil quality in organically and conventionally managed farms in Iceland and Austria

NASA Astrophysics Data System (ADS)

van Leeuwen, J. P.; Lehtinen, T.; Lair, G. J.; Bloem, J.; Hemerik, L.; Ragnarsdóttir, K. V.; Gísladóttir, G.; Newton, J. S.; de Ruiter, P. C.

2014-06-01

Intensive agricultural production can be an important driver for the loss of long-term soil quality. For this reason, the European Critical Zone Observatory (CZO) network adopted four pairs of agricultural CZO sites that differ in their management: conventional or organic. The CZO sites include two pairs of grassland farms in Iceland and two pairs of arable farms in Austria. Conventional fields differed from the organic fields in the use of artificial fertilizers and pesticides. Soils of these eight farms were analysed in terms of their physical, chemical, and biological properties, including soil aggregate size distribution, soil organic matter contents, abundance of soil microbes and soil fauna, and taxonomic diversity of soil microarthropods. In Icelandic grasslands, organically farmed soils had larger mean weight diameters than the conventional farms, while there were no differences in the Austrian farms. Organic farming did neither systematically influence organic matter contents or composition, nor soil carbon and nitrogen contents. Also soil food web structures, in terms of presence of trophic groups of soil organisms, were highly similar among all farms, indicating a low sensitivity of trophic structure to land use or climate. However, soil organism biomass, especially of bacteria and nematodes, was consistently higher in organic farms than in conventional farms. Within the microarthropods, also taxonomic diversity was systematically higher in the organic farms compared to the conventional farms. This difference was found across countries, farm-, crop- and soil-types. The results do not show systematic differences in physical and chemical properties between organic and conventional farms, but confirm that organic farming can enhance soil organism biomass, and that microarthropod diversity is a sensitive and consistent indicator for land management.

[Characteristics of soil ammonia-oxidation microbial communities in different subtropical forests, China].

PubMed

Li, Yong-Chun; Liu, Bu-Rong; Guo, Shuai; Wu, Qi-Feng; Qin, Hua; Wu, Jia-Sen; Xu, Qiu-Fang

2014-01-01

To investigate the effects of different forest stands in subtropical China on the communities of soil ammonia-oxidizing microorganisms, we characterized the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and the community structure of AOA in soils under stands of broad-leaved (BF) , Chinese fir (CF) , Pinus massoniana (PF) and moso bamboo (MB) forests using real-time quantitative PCR and denaturing gradient gel electrophoresis (DGGE). The results showed that the AOA gene copy numbers (1.62 x 10(6)-1.88 x 10(7) per gram of dry soil) were significantly higher than those of AOB genes (2.41 x 10(5)-4.36 x 10(5) per gram of dry soil). Significantly higher soil AOA abundance was detected in the MB than that in the CF (P < 0.05), and the latter was significantly higher than that in the BF and PF soils (P < 0.05). There were no significant differences in the soil AOB abundance among the four forest stands. As indicated by DGGE pattern, soil AOA species varied among the four forest stands. There was a difference in the soil AOA communities between the CF and MB stands. The AOA demonstrated a competitive advantage over the AOB in the soils under these major subtropical forests. Soil pH, concentrations of soil available potassium and organic carbon as well as the forest type were the main factors that influence the variation of AOA community structure and diversity.

Soil Structure - A Neglected Component of Land-Surface Models

NASA Astrophysics Data System (ADS)

Fatichi, S.; Or, D.; Walko, R. L.; Vereecken, H.; Kollet, S. J.; Young, M.; Ghezzehei, T. A.; Hengl, T.; Agam, N.; Avissar, R.

2017-12-01

Soil structure is largely absent in most standard sampling and measurements and in the subsequent parameterization of soil hydraulic properties deduced from soil maps and used in Earth System Models. The apparent omission propagates into the pedotransfer functions that deduce parameters of soil hydraulic properties primarily from soil textural information. Such simple parameterization is an essential ingredient in the practical application of any land surface model. Despite the critical role of soil structure (biopores formed by decaying roots, aggregates, etc.) in defining soil hydraulic functions, only a few studies have attempted to incorporate soil structure into models. They mostly looked at the effects on preferential flow and solute transport pathways at the soil profile scale; yet, the role of soil structure in mediating large-scale fluxes remains understudied. Here, we focus on rectifying this gap and demonstrating potential impacts on surface and subsurface fluxes and system wide eco-hydrologic responses. The study proposes a systematic way for correcting the soil water retention and hydraulic conductivity functions—accounting for soil-structure—with major implications for near saturated hydraulic conductivity. Modification to the basic soil hydraulic parameterization is assumed as a function of biological activity summarized by Gross Primary Production. A land-surface model with dynamic vegetation is used to carry out numerical simulations with and without the role of soil-structure for 20 locations characterized by different climates and biomes across the globe. Including soil structure affects considerably the partition between infiltration and runoff and consequently leakage at the base of the soil profile (recharge). In several locations characterized by wet climates, a few hundreds of mm per year of surface runoff become deep-recharge accounting for soil-structure. Changes in energy fluxes, total evapotranspiration and vegetation productivity are less significant but they can reach up to 10% in specific locations. Significance for land-surface and hydrological modeling and implications for distributed domains are discussed.

Effect of soil structure on the growth of bacteria in soil quantified using CARD-FISH

NASA Astrophysics Data System (ADS)

Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Otten, Wilfred

2014-05-01

It has been reported that compaction of soil due to use of heavy machinery has resulted in the reduction of crop yield. Compaction affects the physical properties of soil such as bulk density, soil strength and porosity. This causes an alteration in the soil structure which limits the mobility of nutrients, water and air infiltration and root penetration in soil. Several studies have been conducted to explore the effect of soil compaction on plant growth and development. However, there is scant information on the effect of soil compaction on the microbial community and its activities in soil. Understanding the effect of soil compaction on microbial community is essential as microbial activities are very sensitive to abrupt environmental changes in soil. Therefore, the aim of this work was to investigate the effect of soil structure on growth of bacteria in soil. The bulk density of soil was used as a soil physical parameter to quantify the effect of soil compaction. To detect and quantify bacteria in soil the method of catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used. This technique results in high intensity fluorescent signals which make it easy to quantify bacteria against high levels of autofluorescence emitted by soil particles and organic matter. In this study, bacterial strains Pseudomonas fluorescens SBW25 and Bacillus subtilis DSM10 were used. Soils of aggregate size 2-1mm were packed at five different bulk densities in polyethylene rings (4.25 cm3).The soil rings were sampled at four different days. Results showed that the total number of bacteria counts was reduced significantly (P

Structure and function of methanotrophic communities in a landfill-cover soil.

PubMed

Henneberger, Ruth; Lüke, Claudia; Mosberger, Lona; Schroth, Martin H

2012-07-01

In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH(4) to CO(2), mitigating emissions of the greenhouse gas CH(4) to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH(4) concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 10(4) to 1.1 × 10(7) (g soil dry weight)(-1)]. Potential CH(4) oxidation rates were high [1.8-58.2 mmol CH(4) (L soil air)(-1) day(-1) ] but showed significant lateral variation and were positively correlated with mean CH(4) concentrations (P < 0.01), MOB abundance (P < 0.05) and MOB diversity (weak correlation, P < 0.17). Our findings indicate that Methylosarcina and closely related MOB are key players and that MOB abundance and community structure are driving factors in CH(4) oxidation at this landfill. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-10-01

Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions. Copyright © 2016. Published by Elsevier B.V.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

Basin-wide variations in Amazon forest structure and function are mediated by both soils and climate

NASA Astrophysics Data System (ADS)

Quesada, C. A.; Phillips, O. L.; Schwarz, M.; Czimczik, C. I.; Baker, T. R.; Patiño, S.; Fyllas, N. M.; Hodnett, M. G.; Herrera, R.; Almeida, S.; Alvarez Dávila, E.; Arneth, A.; Arroyo, L.; Chao, K. J.; Dezzeo, N.; Erwin, T.; di Fiore, A.; Higuchi, N.; Honorio Coronado, E.; Jimenez, E. M.; Killeen, T.; Lezama, A. T.; Lloyd, G.; López-González, G.; Luizão, F. J.; Malhi, Y.; Monteagudo, A.; Neill, D. A.; Núñez Vargas, P.; Paiva, R.; Peacock, J.; Peñuela, M. C.; Peña Cruz, A.; Pitman, N.; Priante Filho, N.; Prieto, A.; Ramírez, H.; Rudas, A.; Salomão, R.; Santos, A. J. B.; Schmerler, J.; Silva, N.; Silveira, M.; Vásquez, R.; Vieira, I.; Terborgh, J.; Lloyd, J.

2012-06-01

Forest structure and dynamics vary across the Amazon Basin in an east-west gradient coincident with variations in soil fertility and geology. This has resulted in the hypothesis that soil fertility may play an important role in explaining Basin-wide variations in forest biomass, growth and stem turnover rates. Soil samples were collected in a total of 59 different forest plots across the Amazon Basin and analysed for exchangeable cations, carbon, nitrogen and pH, with several phosphorus fractions of likely different plant availability also quantified. Physical properties were additionally examined and an index of soil physical quality developed. Bivariate relationships of soil and climatic properties with above-ground wood productivity, stand-level tree turnover rates, above-ground wood biomass and wood density were first examined with multivariate regression models then applied. Both forms of analysis were undertaken with and without considerations regarding the underlying spatial structure of the dataset. Despite the presence of autocorrelated spatial structures complicating many analyses, forest structure and dynamics were found to be strongly and quantitatively related to edaphic as well as climatic conditions. Basin-wide differences in stand-level turnover rates are mostly influenced by soil physical properties with variations in rates of coarse wood production mostly related to soil phosphorus status. Total soil P was a better predictor of wood production rates than any of the fractionated organic- or inorganic-P pools. This suggests that it is not only the immediately available P forms, but probably the entire soil phosphorus pool that is interacting with forest growth on longer timescales. A role for soil potassium in modulating Amazon forest dynamics through its effects on stand-level wood density was also detected. Taking this into account, otherwise enigmatic variations in stand-level biomass across the Basin were then accounted for through the interacting effects of soil physical and chemical properties with climate. A hypothesis of self-maintaining forest dynamic feedback mechanisms initiated by edaphic conditions is proposed. It is further suggested that this is a major factor determining endogenous disturbance levels, species composition, and forest productivity across the Amazon Basin.

Estimating soil erosion risk and evaluating erosion control measures for soil conservation planning at Koga watershed in the highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Molla, Tegegne; Sisheber, Biniam

2017-01-01

Soil erosion is one of the major factors affecting sustainability of agricultural production in Ethiopia. The objective of this paper is to estimate soil erosion using the universal soil loss equation (RUSLE) model and to evaluate soil conservation practices in a data-scarce watershed region. For this purpose, soil data, rainfall, erosion control practices, satellite images and topographic maps were collected to determine the RUSLE factors. In addition, measurements of randomly selected soil and water conservation structures were done at three sub-watersheds (Asanat, Debreyakob and Rim). This study was conducted in Koga watershed at upper part of the Blue Nile basin which is affected by high soil erosion rates. The area is characterized by undulating topography caused by intensive agricultural practices with poor soil conservation practices. The soil loss rates were determined and conservation strategies have been evaluated under different slope classes and land uses. The results showed that the watershed is affected by high soil erosion rates (on average 42 t ha-1 yr-1), greater than the maximum tolerable soil loss (18 t ha-1 yr-1). The highest soil loss (456 t ha-1 yr-1) estimated from the upper watershed occurred on cultivated lands of steep slopes. As a result, soil erosion is mainly aggravated by land-use conflicts and topographic factors and the rugged topographic land forms of the area. The study also demonstrated that the contribution of existing soil conservation structures to erosion control is very small due to incorrect design and poor management. About 35 % out of the existing structures can reduce soil loss significantly since they were constructed correctly. Most of the existing structures were demolished due to the sediment overload, vulnerability to livestock damage and intense rainfall. Therefore, appropriate and standardized soil and water conservation measures for different erosion-prone land uses and land forms need to be implemented in Koga watershed.

Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application

NASA Astrophysics Data System (ADS)

Naliukhin, A. N.; Khamitova, S. M.; Glinushkin, A. P.; Avdeev, Yu. M.; Snetilova, V. S.; Laktionov, Yu. V.; Surov, V. V.; Siluyanova, O. V.; Belozerov, D. A.

2018-03-01

The influence of different systems of fertilization and liming on the changes in the taxonomic structure of prokaryotic community in arable soddy-podzolic soil (Albic Retisol (Loamic, Aric, Cutanic, Differentic, Ochric)) was studied in a stationary field experiment of Vologda State Dairy Farming Academy with the use of high-performance sequencing method of gene 16S rRNA. The 25-year-old fallow plot, in which the intensity of microbiological processes was close to that in the virgin soddy-podzolic soils, was used as a control. At the first stage, dominant phyla were identified: Proteobacteria (45.3-56.2%), Actinobacteria (13.6-20.4%), Bacteroidetes (7.2-19.3%), Acidobacteria (7.1-11.5%), and Verrucomicrobia (4.3-10.3%). Several groups of microorganisms-indicators, whose portion changes in the arable soil under the influence of liming, fertilizer application, and soil treatment in comparison with the control, were determined. The applied approach made it possible to relate the taxonomic structure of the soil microbial cenosis with external factors for assessing changes in the structure of soil microbial complex under the impact of different uses of the arable soil.

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

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

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

PubMed

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

2015-07-21

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

pH dependence and unsuitability of fluorescein dye as a tracer for pesticide mobility studies in acid soil

Treesearch

Chris Peterson

2009-01-01

The mobility of fluorescein and bromide used as tracers in packed soil columns was investigated.Five different soils were used in two application methods: soil surface application and soil incorporation, both of which simulate accepted methods of soil application of termiticides to prevent structural infestation. The...

Land use Effects on Storage, Stability and Structure of Organic Carbon in Soil Density Fractions Revealed by 13C Natural Abundance and CPMAS 13C NMR

NASA Astrophysics Data System (ADS)

Flessa, H.; Helfrich, M.; John, B.; Yamashita, T.; Ludwig, B.

2004-12-01

The type of land use and soil cultivation are important factors controlling organic carbon storage (SOC) in soils and they can also influence the relative importance, the structure, and the stability of different SOC pools. The objectives of our study were: i) to quantify the SOC stocks in different density fractions (mineral-associated soil organic matter > 2 g cm-3 (Mineral-SOM), free particulate organic matter < 1.6 g cm-3 (free POM), light occluded particulate organic matter < 1.6 g cm-3 (occluded POM<1.6) and dense occluded particulate organic matter 1.6 to 2.0 g cm-3 (occluded POM1.6-2.0)) of silty soils under different land use (spruce forest, grassland, maize, wheat), ii) to determine the structure of these SOC fractions by CPMAS 13C NMR spectroscopy, and iii) to analyse the stability of these SOC fractions in the maize soil on the basis of the stable isotope composition of SOC. The SOC concentration in the A horizon increased in the order wheat (12.7 g kg-1) < maize (13.0 g kg-1) < grassland (24.5 g kg-1) < spruce (40.5 g kg-1). The major part (86-91%) of the SOC was associated with the heavy mineral fraction at the grassland, maize and wheat site. In the A horizon of the spruce soil, the particulate organic matter accounted for 52% of the total SOC content. The chemical structure of the soil organic matter (SOM) was influenced by litter quality, the intensity of litter decomposition and the related production and storage of microbially-derived substances. SOM of the acid forest soil was characterized by large amounts of POM with a high content of spruce litter-derived alkyl C. In the biologically more active grassland and maize soil, litter-derived POM was decomposed more rapidly and SOC stocks were dominated by mineral-associated SOM which contained greater proportions of aryl and carbonyl C. The cultivation of the grassland soil induced enhanced mineralization of POM and in particular of mineral-associated SOM. The faster SOC turnover was associated with a relative accumulation of aromatic and carbonyl C structures in the mineral-bound SOM. In all soils, the free particulate organic matter had a smaller proportion of alkyl C and a larger proportion of O-alkyl C than the particulate organic matter occluded in aggregates. The mean age of the SOM in the density fractions of the maize soil increased with increasing aromaticity in the order free POM (22 yr) < occluded POM1.6-2.0 (49 yr) < mineral-associated SOM (63 yr). The results showed that the type of land use influenced the distribution pattern of litter carbon to functionally different SOM pools which represented different stages of SOM decomposition and humification. Additionally, the type of land use influenced the chemical structure of SOM in soil density fractions. Thus, the effect of land use on SOM storage should not only be assessed in terms of total C stocks but also with respect to changes of SOC structure, stability and function.

Environmental impacts of different crop rotations in terms of soil compaction.

PubMed

Götze, Philipp; Rücknagel, Jan; Jacobs, Anna; Märländer, Bernward; Koch, Heinz-Josef; Christen, Olaf

2016-10-01

Avoiding soil compaction caused by agricultural management is a key aim of sustainable land management, and the soil compaction risk should be considered when assessing the environmental impacts of land use systems. Therefore this project compares different crop rotations in terms of soil structure and the soil compaction risk. It is based on a field trial in Germany, in which the crop rotations (i) silage maize (SM) monoculture, (ii) catch crop mustard (Mu)_sugar beet (SB)-winter wheat (WW)-WW, (iii) Mu_SM-WW-WW and (iv) SB-WW-Mu_SM are established since 2010. Based on the cultivation dates, the operation specific soil compaction risks and the soil compaction risk of the entire crop rotations are modelled at two soil depths (20 and 35 cm). To this end, based on assumptions of the equipment currently used in practice by a model farm, two scenarios are modelled (100 and 50% hopper load for SB and WW harvest). In addition, after one complete rotation, in 2013 and in 2014, the physical soil parameters saturated hydraulic conductivity (kS) and air capacity (AC) were determined at soil depths 2-8, 12-18, 22-28 and 32-38 cm in order to quantify the soil structure. At both soil depths, the modelled soil compaction risks for the crop rotations including SB (Mu_SB-WW-WW, SB-WW-Mu_SM) are higher (20 cm: medium to very high risks; 35 cm: no to medium risks) than for those without SB (SM monoculture, Mu_SM-WW-WW; 20 cm: medium risks; 35 cm: no to low risks). This increased soil compaction risk is largely influenced by the SB harvest in years where soil water content is high. Halving the hopper load and adjusting the tyre inflation pressure reduces the soil compaction risk for the crop rotation as a whole. Under these conditions, there are no to low soil compaction risks for all variants in the subsoil (soil depth 35 cm). Soil structure is mainly influenced in the topsoil (2-8 cm) related to the cultivation of Mu as a catch crop and WW as a preceding crop. Concerning kS, Mu_SB-WW-WW (240 cm d(-1)) and Mu_SM-WW-WW (196 cm d(-1)) displayed significantly higher values than the SM monoculture (67 cm d(-1)), indicating better structural stability and infiltration capacity. At other soil depths, and for the parameter AC, there are no systematic differences in soil structure between the variants. Under the circumstances described, all crop rotations investigated are not associated with environmental impacts caused by soil compaction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Changes in soil microbial community structure influenced by agricultural management practices in a mediterranean agro-ecosystem.

PubMed

García-Orenes, Fuensanta; Morugán-Coronado, Alicia; Zornoza, Raul; Cerdà, Artemi; Scow, Kate

2013-01-01

Agricultural practices have proven to be unsuitable in many cases, causing considerable reductions in soil quality. Land management practices can provide solutions to this problem and contribute to get a sustainable agriculture model. The main objective of this work was to assess the effect of different agricultural management practices on soil microbial community structure (evaluated as abundance of phospholipid fatty acids, PLFA). Five different treatments were selected, based on the most common practices used by farmers in the study area (eastern Spain): residual herbicides, tillage, tillage with oats and oats straw mulching; these agricultural practices were evaluated against an abandoned land after farming and an adjacent long term wild forest coverage. The results showed a substantial level of differentiation in the microbial community structure, in terms of management practices, which was highly associated with soil organic matter content. Addition of oats straw led to a microbial community structure closer to wild forest coverage soil, associated with increases in organic carbon, microbial biomass and fungal abundances. The microbial community composition of the abandoned agricultural soil was characterised by increases in both fungal abundances and the metabolic quotient (soil respiration per unit of microbial biomass), suggesting an increase in the stability of organic carbon. The ratio of bacteria:fungi was higher in wild forest coverage and land abandoned systems, as well as in the soil treated with oat straw. The most intensively managed soils showed higher abundances of bacteria and actinobacteria. Thus, the application of organic matter, such as oats straw, appears to be a sustainable management practice that enhances organic carbon, microbial biomass and activity and fungal abundances, thereby changing the microbial community structure to one more similar to those observed in soils under wild forest coverage.

The importance of humin in soil characterisation: A study on Amazonian soils using different fluorescence techniques.

PubMed

Tadini, Amanda Maria; Nicolodelli, Gustavo; Mounier, Stephane; Montes, Célia Regina; Milori, Débora Marcondes Bastos Pereira

2015-12-15

Soil organic matter (SOM) is a complex mixture of molecules with different physicochemical properties, with humic substances (HS) being the main component as it represents around 20-50% of SOM structure. Soil of the Amazon region is considered one of the larger carbon pools of the world; thus, studies of the humic fractions are important for understanding the dynamics of organic matter (OM) in these soils. The aim of this study was to use laser-induced fluorescence spectroscopy (LIFS) and a combination of excitation-emission matrix (EEM) fluorescence with Parallel Factor Analysis (CP/PARAFAC) to assess the characteristics of humin (HU) extracted from Amazonian soils. The results obtained using LIFS showed that there was an increasing gradient of humification degree with depth, the deeper horizon presenting a higher amount of aromatic groups in the structure of HU. From the EEM, the contribution of two fluorophores with similar behaviour in the structures of HU and whole soil was assessed. Additionally, the results showed that the HU fraction might represent a larger fraction of SOM than previously thought: about 80-93% of some Amazon soils. Therefore, HU is an important humic fraction, thus indicating its role in environmental analysis, mainly in soil analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Visualizing Rhizosphere Soil Structure Around Living Roots

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2008-12-01

The rhizosphere, a thin layer of soil (0 to 2 mm) surrounding a living root, is an important interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 ìm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

Rhizospheric effects on the microbial community of e-waste-contaminated soils using phospholipid fatty acid and isoprenoid glycerol dialkyl glycerol tetraether analyses.

PubMed

Song, Mengke; Cheng, Zhineng; Luo, Chunling; Jiang, Longfei; Zhang, Dayi; Yin, Hua; Zhang, Gan

2018-04-01

We performed the study of rhizospheric effects on soil microbial community structure, including bacteria, fungi, actinomycete, and archaea, at an electronic waste (e-waste) recycling site by analyzing the phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether (GDGT) contents. By comparing PLFA and isoprenoid GDGT profiles of rhizospheric and surrounding bulk soils of 11 crop species, we observed distinct microbial community structures. The total PLFA concentration was significantly higher in rhizospheric soils than in non-rhizospheric soils, whereas no obvious difference was found in the total isoprenoid GDGT concentrations. The microbial community structure was also different, with higher ratios of fungal-to-bacterial PLFAs (F/B) and lower relative abundance of Gram-positive bacteria in rhizospheric soils. The extent of rhizospheric effects varied among plant species, and Colocasia esculenta L. had the greatest positive effects on the total microbial biomass. Dissolved organic carbon and pH were the main environmental factors affecting the microbial community represented by PLFAs, while the archaeal community was influenced by copper and zinc in all soils. These results offer a comprehensive view of rhizospheric effects on microbes in heavy metal and persistent organic pollutant co-contaminated soil, and provide fundamental knowledge regarding microbial ecology in e-waste-contaminated soils.

Soil factors involved in the diversity and structure of soil bacterial communities in commercial organic olive orchards in Southern Spain.

PubMed

Landa, B B; Montes-Borrego, M; Aranda, S; Soriano, M A; Gómez, J A; Navas-Cortés, J A

2014-04-01

Nowadays, there is a tendency in olive production systems to reduce tillage or keep a vegetative cover to reduce soil erosion and degradation. However, there is scarce information on the effects of different soil management systems (SMS) in soil bacterial community composition of olive groves. In this study, we have evaluated the effects of soil type and different SMS implemented to control weeds in the structure and diversity of bacterial communities of 58 soils in the two geographic areas that best represent the organic olive production systems in Spain. Bacterial community composition assessed by frequency and intensity of occurrence of terminal restriction profiles (TRFs) derived from terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified 16S ribosomal deoxyribonucleic acid were strongly correlated with soil type/field site (Eutric/Calcaric) that differed mainly in soil particle size distribution and soil pH, followed by a strong effect of SMS, in that order. Canonical discriminant (CD) analysis of TRFs properly classified all of the olive orchard soils as belonging to their respective soil type or SMS. Furthermore, only a small set of TRFs were enough to clearly and significantly differentiate soil samples according to soil type or SMS. Those specific TRFs could be used as bioindicators to assess the effect of changes in SMS aimed to enhance soil quality in olive production systems. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Impacts of Edaphic Factors on Communities of Ammonia-Oxidizing Archaea, Ammonia-Oxidizing Bacteria and Nitrification in Tropical Soils

PubMed Central

de Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.

2014-01-01

Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 105 to 106 copies archaeal amoA g−1 soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity. PMID:24586878

Profile analysis of microbiomes in soils of solonetz complex in the Caspian Lowland

NASA Astrophysics Data System (ADS)

Chernov, T. I.; Lebedeva, M. P.; Tkhakakhova, A. K.; Kutovaya, O. V.

2017-01-01

The taxonomic structure of the microbiota in two associated soils—solonetz on a microhigh and meadow-chestnut soil in a microlow—was studied in the semidesert of the Caspian Lowland. A highthroughput sequencing of the 16S rRNA gene was used for the soil samples from genetic horizons. A considerable reduction in the bacterial diversity was found in the lower horizons of the solonetz and compact solonetzic horizon with a high content of exchangeable sodium. In the meadow-chestnut soil, the microbial diversity little decreased with the depth. In both soils, a portion of archaea from the Thaumarchaeota group also decreased in the deeper horizons. In the soil horizons with the lower total bacterial diversity, a share of proteobacteria of the Enterobacteriaceae, Pseudomonadaceae, and Sphingomonadaceae families became higher. The difference between the structure of the microbial population in the solonetz and meadow- chestnut soil can be first explained by the different water regimes and soil consistence.

Variation in Vegetation Structure and Soil Properties, and the Relation Between Understory Plants and Environmental Variables Under Different Phyllostachys pubescens Forests in Southeastern China

NASA Astrophysics Data System (ADS)

Zhang, Changshun; Xie, Gaodi; Fan, Shaohui; Zhen, Lin

2010-04-01

Biodiversity maintenance and soil improvement are key sustainable forestry objectives. Research on the effects of bamboo forest management on plant diversity and soil properties are therefore necessary in bamboo-growing regions, such as southeastern China’s Shunchang County, that have not been studied from this perspective. We analyzed the effects of different Phyllostachys pubescens proportions in managed forests on vegetation structure and soil properties using pure Cunninghamia lanceolata forests as a contrast, and analyzed the relation between understory plants and environmental variables (i.e., topography, stand and soil characteristics) by canonical correspondence analysis (CCA). The forest with 80% P. pubescens and 20% hardwoods (such as Phoebe bournei, Jatropha curcas, Schima superba) maintained the highest plant diversity and best soil properties, with significantly higher plant diversity than the C. lanceolata forest, and better soil physicochemical and biological properties. The distribution of understory plants is highly related to environmental factors. Silvicultural disturbance strongly influenced the ability of different bamboo forests to maintain biodiversity and soil quality under extensive management, and the forest responses to management were consistent with the intermediate-disturbance hypothesis (i.e., diversity and soil properties were best at intermediate disturbance levels). Our results suggest that biodiversity maintenance and soil improvement are important management goals for sustainable bamboo management. To achieve those objectives, managers should balance the inputs and outputs of nutrients and protect understory plants by using appropriate fertilizer (e.g., organic fertilizer), adjusting stand structure, modifying utilization model and the harvest time, and controlling the intensity of culms and shoots harvests.

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities.

PubMed

Colin, Y; Nicolitch, O; Turpault, M-P; Uroz, S

2017-03-01

Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. Copyright © 2017 American Society for Microbiology.

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

PubMed Central

Colin, Y.; Nicolitch, O.; Turpault, M.-P.

2016-01-01

ABSTRACT Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. PMID:28003192

Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species

PubMed Central

Zhou, Yang; Zhu, Honghui; Fu, Shenglei; Yao, Qing

2017-01-01

Plants are the essential factors shaping soil microbial community (SMC) structure. When most studies focus on the difference in the SMC structure associated different plant species, the variation in the SMC structure associated with phylogenetically close species is less investigated. Legume (Fabaceae) and grass (Poaceae) are functionally important plant groups; however, their influences on the SMC structure are seldom compared, and the variation in the SMC structure among legume or grass species is largely unknown. In this study, we grew three legume species vs. three grass species in mesocosms, and monitored the soil chemical property, quantified the abundance of bacteria and fungi. The SMC structure was also characterized using PCR-DGGE and Miseq sequencing. Results showed that legume and grass differentially affected soil pH, dissolved organic C, total N content, and available P content, and that legume enriched fungi more greatly than grass. Both DGGE profiling and Miseq-sequencing indicated that the bacterial diversity associated with legume was higher than that associated with grass. When legume increased the abundance of Verrucomicrobia, grass decreased it, and furthermore, linear discriminant analysis identified some group-specific microbial taxa as potential biomarkers of legume or grass. These data suggest that legume and grass differentially select for the SMC. More importantly, clustering analysis based on both DGGE profiling and Miseq-sequencing demonstrated that the variation in the SMC structure associated with three legume species was greater than that associated with three grass species. PMID:28620371

Fractal Feature of Particle-Size Distribution in the Rhizospheres and Bulk Soils during Natural Recovery on the Loess Plateau, China

PubMed Central

Song, Zilin; Zhang, Chao; Liu, Guobin; Qu, Dong; Xue, Sha

2015-01-01

The application of fractal geometry to describe soil structure is an increasingly useful tool for better understanding the performance of soil systems. Only a few studies, however, have focused on the structure of rhizospheric zones, where energy flow and nutrient recycling most frequently occur. We used fractal dimensions to investigate the characteristics of particle-size distribution (PSD) in the rhizospheres and bulk soils of six croplands abandoned for 1, 5, 10, 15, 20, and 30 years on the Loess Plateau of China and evaluated the changes over successional time. The PSDs of the rhizospheres and the fractal dimensions between rhizosphere soil and bulk soils during the natural succession differed significantly due to the influence of plant roots. The rhizospheres had higher sand (0.05–1.00 mm) contents, lower silt (<0.002 mm) contents, and lower fractal dimensions than the bulk soils during the early and intermediate successional stages (1–15 years). The fractal dimensions of the rhizosphere soil and bulk soil ranged from 2.102 to 2.441 and from 2.214 to 2.459, respectively, during the 30-year restoration. Rhizospheric clay and silt contents and fractal dimension tended to be higher and sand content tended to be lower as abandonment age increased, but the bulk soils had the opposite trend. Linear regression analysis indicated that the fractal dimensions of both the rhizospheres and bulk soils were significantly linearly correlated with clay, sand, organic-carbon, and total-nitrogen contents, with R 2 ranging from 0.526 to 0.752 (P<0.001). In conclusion, PSD differed significantly between the rhizosphere soil and bulk soil. The fractal dimension was a sensitive and useful index for quantifying changes in the properties of the different soil zones. This study will greatly aid the application of the fractal method for describing soil structure and nutrient status and the understanding of the performance of rhizospheric zones during ecological restoration. PMID:26368339

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition.

PubMed

Marupakula, Srisailam; Mahmood, Shahid; Jernberg, Johanna; Nallanchakravarthula, Srivathsa; Fahad, Zaenab A; Finlay, Roger D

2017-11-01

Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonized by different fungi and analyzed differences in microbiome structure related to soils from distinct podzol horizons and effects of short-term additions of N, a growth-limiting nutrient commonly applied as a fertilizer, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonizing individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilized soil, but fertilization removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Endophytic fungi and soil microbial community characteristics over different years of phytoremediation in a copper tailings dam of Shanxi, China.

PubMed

Tong, Jia; Miaowen, Cao; Juhui, Jing; Jinxian, Liu; Baofeng, Chai

2017-01-01

We conducted a survey of native grass species infected by endophytic fungi in a copper tailings dam over progressive years of phytoremediation. We investigated how endophytic fungi, soil microbial community structure and soil physiochemical properties and enzymatic activity varied in responses to heavy metal pollution over different stages of phytoremediation. endophyte infection frequency increased with years of phytoremediation. Rates of endophyte infection varied among different natural grass species in each sub-dam. Soil carbon content and soil enzymatic activity gradually increased through the years of phytoremediation. endophyte infection rates of Bothriochloa ischaemum and Festuca rubra were positively related to levels of cadmium (Cd) pollution levels, and fungal endophytes associated with Imperata cylindrical and Elymus dahuricus developed tolerance to lead (Pb). The structure and relative abundance of bacterial communities varied little over years of phytoremediation, but there was a pronounced variation in soil fungi types. Leotiomycetes were the dominant class of resident fungi during the initial phytoremediation period, but Pezizomycetes gradually became dominant as the phytoremediation period progressed. Fungal endophytes in native grasses as well as soil fungi and soil bacteria play different ecological roles during phytoremediation processes. Copyright © 2016 Elsevier B.V. All rights reserved.

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils

PubMed Central

Delgado-Balbuena, Laura; Bello-López, Juan M.; Navarro-Noya, Yendi E.; Rodríguez-Valentín, Analine; Luna-Guido, Marco L.; Dendooven, Luc

2016-01-01

Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the effect of application of carrot residue, earthworms or the surfactant on the bacterial community structure was more accentuated in the arable soil than in the pasture soil. It was found that removal of anthracene was not linked to changes in the bacterial community structure. PMID:27727277

Influence of crop rotation and tillage intensity on soil physical properties and functions

NASA Astrophysics Data System (ADS)

Krümmelbein, Julia

2013-04-01

Soil tillage intensity can vary concerning tillage depth, frequency, power input into the soil and degree of soil turn-over. Conventional tillage systems where a plough is regularly used to turn over the soil can be differentiated from reduced tillage systems without ploughing but with loosening the upper soil and no tillage systems. Between conventional tillage and no tillage is a wide range of more or less reduced tillage systems. In our case the different tillage intensities are not induced by different agricultural machinery or techniques, but result from varying crop rotations with more or less perennial crops and therefore lower or higher tillage frequency. Our experimental area constitutes of quite unstructured substrates, partly heavily compacted. The development of a functioning soil structure and accumulation of nutrients and organic matter are of high importance. Three different crop rotations induce varying tillage intensities and frequencies. The first crop rotation (Alfalfa monoculture) has only experienced seed bed preparation once and subsequently is wheeled once a year to cut and chaff the biomass. The second crop rotation contains perennial and annual crops and has therefore been tilled more often, while the third crop rotation consists only of annual crops with annual seedbed preparation. Our results show that reduced tillage intensity/frequency combined with the intense root growth of Alfalfa creates the most favourable soil physical state of the substrate compared to increased tillage and lower root growth intensity of the other crop rotations. Soil tillage disturbs soil structure development, especially when the substrate is mechanically unstable as in our case. For such problematic locations it is recommendable to reduce tillage intensity and/or frequency to allow the development of soil structure enhanced by root growth and thereby the accumulation of organic matter and nutrients within the rooting zone.

Shifts in bacterial community structure during succession in a glacier foreland of the High Arctic.

PubMed

Kim, Mincheol; Jung, Ji Young; Laffly, Dominique; Kwon, Hye Young; Lee, Yoo Kyung

2017-01-01

Primary succession after glacier retreat has been widely studied in plant communities, but bacterial succession is still poorly understood. In particular, few studies of microbial succession have been performed in the Arctic. We investigated the shifts in bacterial community structure and soil physicochemical properties along a successional gradient in a 100-year glacier foreland of the High Arctic. Multivariate analyses revealed that time after glacier retreat played a key role in associated bacterial community structure during succession. However, environmental filtering (i.e. pH and soil temperature) also accounted for a different, but substantial, proportion of the bacterial community structure. Using the functional trait-based approach, we found that average rRNA operon (rrn) copy number of bacterial communities is high in earlier successional stages and decreased over time. This suggests that soil bacterial taxa with higher rrn copy number have a selective advantage in early successional stages due to their ability of rapidly responding to nutrient inputs in newly exposed soils after glacier retreat. Taken together, our results demonstrate that both deglaciation time and environmental filters play key roles in structuring bacterial communities and soil bacterial groups with different ecological strategies occur in different stages of succession in this glacier foreland. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Mycorrhizas and soil ecosystem function of co-existing woody vegetation islands at the alpine tree line.

PubMed

Wang, Lixia; Otgonsuren, Burenjargal; Godbold, Douglas L

2017-01-01

Picea abies , Pinus mugo and Rhododendron ferrugineum co-exist at the alpine tree line, and can have different mycorrhizal communities. The activity and diversity of mycorrhizal fungi are considered to be important factors in regulation of soil function. At a tree line site and a lower elevation site in the Austrian Alps, the community structure of ectomycorrhiza on Picea abies and Pinus mugo was determined. The activity of surface enzymes was determined on ectomycorrhizal and ericoid mycorrhizal roots. In soils, the activity of a range of enzymes, nitrogen (N) mineralization and biomass decomposition were determined. The community structure of the ectomycorrhizal community of Picea abies and Pinus mugo differed strongly, but the average activity of surface enzymes of the ectomycorrhizal communities was similar. A lower root surface enzyme activity was determined on Rhododendron ferrugineum . Soil N-mineralization under Rhododendron ferrugineum was significantly lower than under Picea abies and Pinus mugo . In soil, the activity of a range of enzymes did not differ at the tree line but differed between the tree line and the lower elevation sites. The different ectomycorrhizal communities on Picea abies and Pinus mugo and ericoid mycorrhizas on Rhododendron ferrugineum support similar ecosystem functions in soil.

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs.

PubMed

Dupont, A Ö C; Griffiths, R I; Bell, T; Bass, D

2016-06-01

A recent large-scale assessment of bacterial communities across a range of UK soil types showed that bacterial community structure was strongly determined by soil pH. We analysed a data set of eukaryotic 454 sequencing 18S rDNA from the surveyed samples and showed significant differences in eukaryotic assemblages according to pH class, mostly between low pH and higher pH soils. Soil eukaryote communities (per sample) differed most at the taxonomic rank approximating to order level. Taxonomies assigned with the Protist Ribosomal Reference and the Silva 119 databases were taxonomically inconsistent, mostly due to differing 18S annotations, although general structure and composition according to pH were coherent. A relatively small number of lineages, mostly putative parasitic protists and fungi, drive most differences between pH classes, with weaker contributions from bacterivores and autotrophs. Overall, soil parasites included a large diversity of alveolates, in particular apicomplexans. Phylogenetic analysis of alveolate lineages demonstrates a large diversity of unknown gregarines, novel perkinsids, coccidians, colpodellids and uncharacterized alveolates. Other novel and/or divergent lineages were revealed across the eukaryote tree of life. Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and reveals novel lineages and insights into their relationships with environmental variables across soil gradients. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Soil-pipe interaction modeling for pipe behavior prediction with super learning based methods

NASA Astrophysics Data System (ADS)

Shi, Fang; Peng, Xiang; Liu, Huan; Hu, Yafei; Liu, Zheng; Li, Eric

2018-03-01

Underground pipelines are subject to severe distress from the surrounding expansive soil. To investigate the structural response of water mains to varying soil movements, field data, including pipe wall strains in situ soil water content, soil pressure and temperature, was collected. The research on monitoring data analysis has been reported, but the relationship between soil properties and pipe deformation has not been well-interpreted. To characterize the relationship between soil property and pipe deformation, this paper presents a super learning based approach combining feature selection algorithms to predict the water mains structural behavior in different soil environments. Furthermore, automatic variable selection method, e.i. recursive feature elimination algorithm, were used to identify the critical predictors contributing to the pipe deformations. To investigate the adaptability of super learning to different predictive models, this research employed super learning based methods to three different datasets. The predictive performance was evaluated by R-squared, root-mean-square error and mean absolute error. Based on the prediction performance evaluation, the superiority of super learning was validated and demonstrated by predicting three types of pipe deformations accurately. In addition, a comprehensive understand of the water mains working environments becomes possible.

Divergent composition but similar function of soil food webs of individual plants: plant species and community effects.

PubMed

Bezemer, T M; Fountain, M T; Barea, J M; Christensen, S; Dekker, S C; Duyts, H; van Hal, R; Harvey, J A; Hedlund, K; Maraun, M; Mikola, J; Mladenov, A G; Robin, C; de Ruiter, P C; Scheu, S; Setälä, H; Smilauer, P; van der Putten, W H

2010-10-01

Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa/groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon mineralization or food web stability. Hence, the composition and structure of entire soil food webs vary at the scale of individual plants and are strongly influenced by the species identity of the plant. However, the ecosystem functions these food webs provide are determined by the identity of the entire plant community.

Ectomycorrhizal fungal diversity and community structure associated with cork oak in different landscapes.

PubMed

Reis, Francisca; Valdiviesso, Teresa; Varela, Carolina; Tavares, Rui M; Baptista, Paula; Lino-Neto, Teresa

2018-05-01

Cork oak (Quercus suber L.) forests play an important ecological and economic role. Ectomycorrhizal fungi (ECMF) are key components for the sustainability and functioning of these ecosystems. The community structure and composition of ECMF associated with Q. suber in different landscapes of distinct Mediterranean bioclimate regions have not previously been compared. In this work, soil samples from cork oak forests residing in different bioclimates (arid, semi-arid, sub-humid, and humid) were collected and surveyed for ectomycorrhizal (ECM) root tips. A global analysis performed on 3565 ECM root tips revealed that the ECMF community is highly enriched in Russula, Tomentella, and Cenoccocum, which correspond to the ECMF genera that mainly contribute to community differences. The ECMF communities from the rainiest and the driest cork oak forests were distinct, with soils from the rainiest climates being more heterogeneous than those from the driest climates. The analyses of several abiotic factors on the ECMF communities revealed that bioclimate, precipitation, soil texture, and forest management strongly influenced ECMF structure. Shifts in ECMF with different hyphal exploration types were also detected among forests, with precipitation, forest system, and soil texture being the main drivers controlling their composition. Understanding the effects of environmental factors on the structuring of ECM communities could be the first step for promoting the sustainability of this threatened ecosystem.

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area.

PubMed

Wu, Zeyan; Haack, Stacey Elizabeth; Lin, Wenxiong; Li, Bailian; Wu, Linkun; Fang, Changxun; Zhang, Zhixing

2015-01-01

Soil microbes play an essential role in the forest ecosystem as an active component. This study examined the hypothesis that soil microbial community structure and metabolic activity would vary with the increasing stand ages in long-term pure plantations of Pinus elliottii. The phospholipid fatty acids (PLFA) combined with community level physiological profiles (CLPP) method was used to assess these characteristics in the rhizospheric soils of P. elliottii. We found that the soil microbial communities were significantly different among different stand ages of P. elliottii plantations. The PLFA analysis indicated that the bacterial biomass was higher than the actinomycic and fungal biomass in all stand ages. However, the bacterial biomass decreased with the increasing stand ages, while the fungal biomass increased. The four maximum biomarker concentrations in rhizospheric soils of P. elliottii for all stand ages were 18:1ω9c, 16:1ω7c, 18:3ω6c (6,9,12) and cy19:0, representing measures of fungal and gram negative bacterial biomass. In addition, CLPP analysis revealed that the utilization rate of amino acids, polymers, phenolic acids, and carbohydrates of soil microbial community gradually decreased with increasing stand ages, though this pattern was not observed for carboxylic acids and amines. Microbial community diversity, as determined by the Simpson index, Shannon-Wiener index, Richness index and McIntosh index, significantly decreased as stand age increased. Overall, both the PLFA and CLPP illustrated that the long-term pure plantation pattern exacerbated the microecological imbalance previously described in the rhizospheric soils of P. elliottii, and markedly decreased the soil microbial community diversity and metabolic activity. Based on the correlation analysis, we concluded that the soil nutrient and C/N ratio most significantly contributed to the variation of soil microbial community structure and metabolic activity in different stand ages of P. elliottii plantations.

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area

PubMed Central

Wu, Zeyan; Haack, Stacey Elizabeth; Lin, Wenxiong; Li, Bailian; Wu, Linkun; Fang, Changxun; Zhang, Zhixing

2015-01-01

Soil microbes play an essential role in the forest ecosystem as an active component. This study examined the hypothesis that soil microbial community structure and metabolic activity would vary with the increasing stand ages in long-term pure plantations of Pinus elliottii. The phospholipid fatty acids (PLFA) combined with community level physiological profiles (CLPP) method was used to assess these characteristics in the rhizospheric soils of P. elliottii. We found that the soil microbial communities were significantly different among different stand ages of P. elliottii plantations. The PLFA analysis indicated that the bacterial biomass was higher than the actinomycic and fungal biomass in all stand ages. However, the bacterial biomass decreased with the increasing stand ages, while the fungal biomass increased. The four maximum biomarker concentrations in rhizospheric soils of P. elliottii for all stand ages were 18:1ω9c, 16:1ω7c, 18:3ω6c (6,9,12) and cy19:0, representing measures of fungal and gram negative bacterial biomass. In addition, CLPP analysis revealed that the utilization rate of amino acids, polymers, phenolic acids, and carbohydrates of soil microbial community gradually decreased with increasing stand ages, though this pattern was not observed for carboxylic acids and amines. Microbial community diversity, as determined by the Simpson index, Shannon-Wiener index, Richness index and McIntosh index, significantly decreased as stand age increased. Overall, both the PLFA and CLPP illustrated that the long-term pure plantation pattern exacerbated the microecological imbalance previously described in the rhizospheric soils of P. elliottii, and markedly decreased the soil microbial community diversity and metabolic activity. Based on the correlation analysis, we concluded that the soil nutrient and C/N ratio most significantly contributed to the variation of soil microbial community structure and metabolic activity in different stand ages of P. elliottii plantations. PMID:26267338

Identification and classification of structural soil conservation measures based on very high resolution stereo satellite data.

PubMed

Eckert, Sandra; Tesfay Ghebremicael, Selamawit; Hurni, Hans; Kohler, Thomas

2017-05-15

Land degradation affects large areas of land around the globe, with grave consequences for those living off the land. Major efforts are being made to implement soil and water conservation measures that counteract soil erosion and help secure vital ecosystem services. However, where and to what extent such measures have been implemented is often not well documented. Knowledge about this could help to identify areas where soil and water conservation measures are successfully supporting sustainable land management, as well as areas requiring urgent rehabilitation of conservation structures such as terraces and bunds. This study explores the potential of the latest satellite-based remote sensing technology for use in assessing and monitoring the extent of existing soil and water conservation structures. We used a set of very high resolution stereo Geoeye-1 satellite data, from which we derived a detailed digital surface model as well as a set of other spectral, terrain, texture, and filtered information layers. We developed and applied an object-based classification approach, working on two segmentation levels. On the coarser level, the aim was to delimit certain landscape zones. Information about these landscape zones is useful in distinguishing different types of soil and water conservation structures, as each zone contains certain specific types of structures. On the finer level, the goal was to extract and identify different types of linear soil and water conservation structures. The classification rules were based mainly on spectral, textural, shape, and topographic properties, and included object relationships. This approach enabled us to identify and separate from other classes the majority (78.5%) of terraces and bunds, as well as most hillside terraces (81.25%). Omission and commission errors are similar to those obtained by the few existing studies focusing on the same research objective but using different types of remotely sensed data. Based on our results, we estimate that the construction of the conservation structures in our study area in Eritrea required over 300,000 person-days of work, which underlines the huge efforts involved in soil and water conservation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rich in life but poor in data: the known knowns and known unknowns of modelling how soil biology drives soil structure

NASA Astrophysics Data System (ADS)

Hallett, Paul; Ogden, Mike

2015-04-01

Soil biology has a fascinating capacity to manipulate pore structure by altering or overcoming hydrological and mechanical properties of soil. Many have postulated, quite rightly, that this capacity of soil biology to 'engineer' its habitat drives its diversity, improves competitiveness and increases resilience to external stresses. A large body of observational research has quantified pore structure evolution accompanied by the growth of organisms in soil. Specific compounds that are exuded by organisms or the biological structures they create have been isolated and found to correlate well with observed changes to pore structure or soil stability. This presentation will provide an overview of basic mechanical and hydrological properties of soil that are affected by biology, and consider missing data that are essential to model how they impact soil structure evolution. Major knowledge gaps that prevent progress will be identified and suggestions will be made of how research in this area should progress. We call for more research to gain a process based understanding of structure formation by biology, to complement observational studies of soil structure before and after imposed biological activity. Significant advancement has already been made in modelling soil stabilisation by plant roots, by combining data on root biomechanics, root-soil interactions and soil mechanical properties. Approaches for this work were developed from earlier materials science and geotechnical engineering research, and the same ethos should be adopted to model the impacts of other biological compounds. Fungal hyphae likely reinforce soils in a similar way to plant roots, with successful biomechanical measurements of these micron diameter structures achieved with micromechanical test frames. Extending root reinforcement models to fungi would not be a straightforward exercise, however, as interparticle bonding and changes to pore water caused by fungal exudates could have a major impact on structure formation and stability. Biological exudates from fungi, bacteria or roots have been found to decrease surface tension and increase viscosity of pore water, with observed impacts to soil strength and water retention. Modelling approaches developed in granular mechanics and geotechnical engineering could be built upon to incorporate biological transformations of hydrological and mechanical properties of soil. With new testing approaches, adapted from materials science, pore scale hydromechanical impacts from biological exudates can be quantified. The research can be complemented with model organisms with differences in biological structures (e.g. root hair mutants), exudation or other properties. Coupled with technological advances that provide 4D imaging of soil structure at relatively rapid capture rates, the potential opportunities to disentangle and model how biology drives soil structure evolution and stability are vast. By quantifying basic soil hydrological and mechanical processes that are driven by soil biology, unknown unknowns may also emerge, providing new insight into how soils function.

Pyrosequencing of microbial community of typical chernozem in contrast land use conditions

NASA Astrophysics Data System (ADS)

Ivanova, Ekaterina; Olga, Kutovaya; Azida, Tkhakakhova

2015-04-01

Chernozems are the principal soil resourse of Russia, so the sustainable use of these fertile soils in the intensive agriculturural production is of great importance, especially in terms of agro-ecological security of the country. The increase in agricultural inputs - intensive cropping, soil fallowing application accompanied with high frequency of mechanical treatment, result in decrease in soil organic matter content as well as soil structure degradation and, finally, lead to the loss of soil fertility. Soil microorganisms can serve as bioindicators of anthropogenic stress experienced by the soil during its agricultural use, so they may be universal indicators of soil quality (soil health) used for optimization and biologization of agricultural systems. The way to study the relationship between the structural status of the soil, its microbial communities and the organic matter content is the comparative analysis of soil aggregates in conditions of different land use practices. The objects of our research were soil samples of soil with permanent wheat cropping (50 years), continuous dead fallow (50 years) soil, and recovering soil (for 18 years under native steppe vegetation, fallowed in previous). The analysis of 16 S rRNA gene amplicon libraries of typical chernozem in conditions of different land use systems revealed that the way of agricultural use is a strong determinant of soil microbiome taxonomic composition. It was shown that the continuous «dead fallowing» application (for 50 years) lead to the establishment of olygothrophic components of microbial community, including spore-forming members of phylum Firmicutes. The increase of Acidobacteria lineages in this variant may be an indicator of some acidification of soil during long-time fallowing application. The variant of continuous wheat cropping lead to increasing in Proteobacteria lineages. The variant of soil under native steppe vegetation was characterized by the highest values of biodiversity indices - species richness and eveness, which can indicate the occurrence of soil recovering. This variant was also characterized by the maximum content of agricultural valuable aggregate fraction of 2-5 mm size. In soil samples from different aggregate fractions the presence of accessory components was revealed. It was determined that Actinobacteria lineages preferred microaggregates (less than 0.25 mm) rather than coarse aggregate fractions (more than 7 mm). The opposite trend was determined for Proteobacteria: the amount was maximum in aggregates more than 7 mm in diameter. The occurrence of specific components in the taxonomic structure of micro-and macro-aggregates may indicate the presence of a certain size fraction in the structure of the investigated soil. The study of soils' metagenome is promising for the development of both soil microbiology, and for the soil processes trends in soils of anthropogenic origin. The study was supported by Russian Scientific Fund (14-26-00079 and 14-26-00094)

Detection of underground structures using UAV and field spectroscopy for defence and security in Cyprus

NASA Astrophysics Data System (ADS)

Melillos, George; Themistocleous, Kyriacos; Prodromou, Maria; Hadjimitsis, Diofantos G.

2017-10-01

The purpose of this paper is to present the results obtained from unmanned aerial vehicle (UAV) and field spectroscopy campaigns for detecting underground structures. Underground structures can affect their surrounding landscapes in different ways, such as soil moisture content, soil composition and vegetation vigor. The last is often observed on the ground as a crop mark; a phenomenon which can be used as a proxy to denote the presence of underground non-visible structures. A number of vegetation indices such as the Normalized Difference Vegetation Index (NDVI), Simple Ratio (SR), Difference Vegetation Index (DVI) and Soil Adjusted Vegetation Index (SAVI) were utilized for the development of a vegetation index-based procedure aiming at the detection of underground military structures by using existing vegetation indices or other in-band algorithms. The measurements were taken at the following test areas such as: (a) vegetation area covered with the vegetation (barley), in the presence of an underground military structure (b) vegetation area covered with the vegetation (barley), in the absence of an underground military structure.

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils.

PubMed

Poli, Anna; Lazzari, Alexandra; Prigione, Valeria; Voyron, Samuele; Spadaro, Davide; Varese, Giovanna Cristina

2016-01-01

Rhizosphere and root-associated microbiota are crucial in determining plant health and in increasing productivity of agricultural crops. To date, research has mainly focused on the bacterial dimension of the microbiota. However, interest in the mycobiota is increasing, since fungi play a key role in soil ecosystems. We examined the effect of plant genotype, soil, and of Fusarium oxysporum f. sp. lycopersici (Fol) on the cultivable component of rhizosphere and root-associated mycobiota of tomato. Resistant and susceptible varieties were cultivated on two different soils (A and B), under glasshouse conditions. Isolated fungi were identified by morphological and molecular approaches. Differences were found between the rhizosphere and the roots, which in general displayed a lower number of species. The structure of the mycobiota was significantly affected by the soil type in the rhizosphere as well as by the plant genotype within the roots (NPERMANOVA, p < 0.05). The addition of Fol changed the community structure, particularly in soil A, where Penicillium spp. and Fusarium spp. were the dominant responding fungi. Overall, the results indicated that i) soil type and plant genotype affect the fungal communities; ii) plant roots select few species from the rhizosphere; and iii) the fungal community structure is influenced by Fol. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Patterns of soil community structure differ by scale and ecosystem type along a large-scale precipitation gradient

USDA-ARS?s Scientific Manuscript database

Climate models predict increased variability in precipitation regimes, which will likely increase frequency/duration of drought. Reductions in soil moisture affect physical and chemical characteristics of the soil habitat and can influence soil organisms such as mites and nematodes. These organisms ...

Soil microbial community structure and target organisms under different fumigation treatments

USDA-ARS?s Scientific Manuscript database

Several high-value crop producers in California rely heavily on soil fumigants to control key diseases, nematodes, weeds and volunteer crops. Fumigants with broad biocidal activity can affect both target and non-target soil organisms. The ability of non-target soil organisms to recover after fumigat...

Effects of the soil pore network architecture on the soil's physical functionalities

NASA Astrophysics Data System (ADS)

Smet, Sarah; Beckers, Eléonore; Léonard, Angélique; Degré, Aurore

2017-04-01

The soil fluid movement's prediction is of major interest within an agricultural or environmental scope because many processes depend ultimately on the soil fluids dynamic. It is common knowledge that the soil microscopic pore network structure governs the inner-soil convective fluids flow. There isn't, however, a general methodthat consider the pore network structure as a variable in the prediction of thecore scale soil's physical functionalities. There are various possible representations of the microscopic pore network: sample scale averaged structural parameters, extrapolation of theoretic pore network, or use of all the information available by modeling within the observed pore network. Different representations implydifferent analyzing methodologies. To our knowledge, few studies have compared the micro-and macroscopic soil's characteristics for the same soil core sample. The objective of our study is to explore the relationship between macroscopic physical properties and microscopic pore network structure. The saturated hydraulic conductivity, the air permeability, the retention curve, and others classical physical parameters were measured for ten soil samples from an agricultural field. The pore network characteristics were quantified through the analyses of X-ray micro-computed tomographic images(micro-CT system Skyscan-1172) with a voxel size of 22 µm3. Some of the first results confirmed what others studies had reported. Then, the comparison between macroscopic properties and microscopic parameters suggested that the air movements depended mostly on the pore connectivity and tortuosity than on the total porosity volume. We have also found that the fractal dimension calculated from the X-ray images and the fractal dimension calculated from the retention curve were significantly different. Our communication will detailthose results and discuss the methodology: would the results be similar with a different voxel size? What are the calculated and measured parameters uncertainties? Sarah Smet, as a research fellow, acknowledges the support of the National Fund for Scientific Research (Brussels, Belgium).

Visualizing the impact of living roots on rhizosphere soil structure using X-ray microtomography

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2009-04-01

The rhizosphere is an interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 μm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

Interactions between soil texture, water, and nutrients control patterns of biocrusts abundance and structure

NASA Astrophysics Data System (ADS)

Young, Kristina; Bowker, Matthew; Reed, Sasha; Howell, Armin

2017-04-01

Heterogeneity in the abiotic environment structures biotic communities by controlling niche space and parameters. This has been widely observed and demonstrated in vascular plant and other aboveground communities. While soil organisms are presumably also strongly influenced by the physical and chemical dimensions of the edaphic environment, there are fewer studies linking the development, structure, productivity or function of surface soil communities to specific edaphic gradients. Here, we use biological soil crusts (biocrusts) as a model system to determine mechanisms regulating community structure of soil organisms. We chose soil texture to serve as an edaphic gradient because of soil texture's influence over biocrust distribution on a landscape level. We experimentally manipulated texture in constructed soil, and simultaneously manipulated two main outcomes of texture, water and nutrient availability, to determine the mechanism underlying texture's influence on biocrust abundance and structure. We grew biocrust communities from a field-sourced inoculum on four different soil textures, sieved from the same parent soil material, manipulating watering levels and nutrient additions across soil textures in a full-factorial design over a 5-month period of time. We measured abundance and structure of biocrusts over time, and measured two metrics of function, N2 fixation rates and soil stabilization, at the conclusion of the experiment. Our results showed finer soil textures resulted in faster biocrust community development and dominance by mosses, whereas coarser textures grew more slowly and had biocrust communities dominated by cyanobacteria and lichen. Additionally, coarser textured soils contained cyanobacterial filaments significantly deeper into the soil profile than fine textured soils. N2-fixation values increased with increasing moss cover and decreased with increasing cyanobacterial cover, however, the rate of change depended on soil texture and water amount. Soil shear resistance was highest on finer textured soil with the highest watering treatment, whereas compression resistance was highest on the coarsest textured soils with the highest watering amounts. Nutrient addition did not influence total cover or biocrust function, but did decrease lichen cover. Taken together, these results suggest that interactions between soil texture, water, and to a lesser degree nutrients, create predictable patterns in biocrust assemblage and offers a mechanistic understanding of edaphic controls over biocrust abundance and structure. These insights add to our increasing understanding of how edaphic gradients structure soil communities.

[Distribution characteristics of soil nematodes in reclaimed land of copper-mine-tailings in different plant associations].

PubMed

Zhu, Yong-heng; Li, Ke-zhong; Zhang, Heng; Han, Fei; Zhou, Ju-hua; Gao, Ting-ting

2015-02-01

A survey was carried out to investigate soil nematode communities in the plant associations of gramineae (Arthraxon lanceolatus, AL; Imperata cylindrica, IC) and leguminosae (Glycine soja, GS) in reclaimed land of copper-mine-tailings and in the plant associations of gramineae (Digitaria chrysoblephara, DC-CK) of peripheral control in Fenghuang Mountain, Tongling City. A total of 1277 nematodes were extracted and sorted into 51 genera. The average individual density of the nematodes was 590 individuals · 100 g(-1) dry soil. In order to analyze the distribution character- istics of soil nematode communities in reclaimed land of copper-mine-tailings, Shannon community diversity index and soil food web structure indices were applied in the research. The results showed that the total number of nematode genus and the Shannon community diversity index of soil nematode in the three plant associations of AL, IC and GS were less than that in the plant associations of DC-CK. Compared with the ecological indices of soil nematode communities among the different plant associations in reclaimed land of copper-mine-tailings and peripheral natural habitat, we found that the structure of soil food web in the plant associations of GS was more mature, with bacterial decomposition being dominant in the soil organic matter decomposition, and that the soil ecosystem in the plant associations of GS was not stable with low interference. This indicated that the soil food web in the plant associations of leguminosae had a greater development potential to improve the ecological stability of the reclaimed land of copper-mine-tailings. On the other hand, the structure of soil food web in the plant associations of AL and IC were relatively stable in a structured state with fungal decomposition being dominant in the decomposition of soil organic matter. This indicated that the soil food web in the plant associations of gramineae was at a poor development level.

Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas.

PubMed

Carbonetto, Belén; Rascovan, Nicolás; Álvarez, Roberto; Mentaberry, Alejandro; Vázquez, Martin P

2014-01-01

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no-tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.

Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas

PubMed Central

Carbonetto, Belén; Rascovan, Nicolás; Álvarez, Roberto; Mentaberry, Alejandro; Vázquez, Martin P.

2014-01-01

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no- tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability. PMID:24923965

Effect of aggregate structure on VOC gas adsorption onto volcanic ash soil.

PubMed

Hamamoto, Shoichiro; Seki, Katsutoshi; Miyazaki, Tsuyoshi

2009-07-15

The understanding of the gaseous adsorption process and the parameters of volatile organic compounds such as organic solvents or fuels onto soils is very important in the analysis of the transport or fate of these chemicals in soils. Batch adsorption experiments with six different treatments were conducted to determine the adsorption of isohexane, a gaseous aliphatic, onto volcanic ash soil (Tachikawa loam). The measured gas adsorption coefficient for samples of Tachikawa loam used in the first three treatments, Control, AD (aggregate destroyed), and AD-OMR (aggregate destroyed and organic matter removed), implied that the aggregate structure of volcanic ash soil as well as organic matter strongly enhanced gas adsorption under the dry condition, whereas under the wet condition, the aggregate structure played an important role in gas adsorption regardless of the insolubility of isohexane. In the gas adsorption experiments for the last three treatments, soils were sieved in different sizes of mesh and were separated into three different aggregate or particle size fractions (2.0-1.0mm, 1.0-0.5mm, and less than 0.5mm). Tachikawa loam with a larger size fraction showed higher gas adsorption coefficient, suggesting the higher contributions of macroaggregates to isohexane gas adsorption under dry and wet conditions.

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities.

PubMed

Uroz, S; Oger, P; Tisserand, E; Cébron, A; Turpault, M-P; Buée, M; De Boer, W; Leveau, J H J; Frey-Klett, P

2016-06-15

The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

PubMed

Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

2014-08-01

The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

Effects of different agricultural managements in soil microbial community structure in a semi-arid Mediterranean region.

NASA Astrophysics Data System (ADS)

García-Orenes, Fuensanta; Morugan, Alicia; Mataix-Solera, Jorge; Scow, Kate

2013-04-01

Agriculture has been practiced in semi-arid Mediterranean regions for 10.000 years and in many cases these practices have been unsuitable causing land degradation for millennium and an important loss of soil quality. The land management can provide solutions to find the best agricultural practices in order to maintain the soil quality and get a sustainable agriculture model. Microbiological properties are the most sensitive and rapid indicators of soil perturbations and land use managements. The study of microbial community and diversity has an important interest as indicators of changes in soil quality. The main objective of this work was to asses the effect of different agricultural management practices in soil microbial community (evaluated as abundance of phospholipid fatty acids, PLFA). Four different treatments were selected, based on the most commonly practices applied by farmers in the study area, "El Teularet Experimental Station", located at the Enguera Range in the southern part of the Valencia province (eastern Spain). These treatments were: a) ploughing, b) herbicides c) mulch, using the types applied by organic farmers to develop a sustainable agriculture, such as oat straw and d) control that was established as plot where the treatment was abandonment after farming. An adjacent area with the same type of soil, but with natural vegetation was used as a standard or reference high quality soil. Soil samples were taken to evaluate the changes in microbial soil structure, analysing the abundance of PLFA. The results showed a major content of total PLFA in soils treated with oats straw, being these results similar to the content of PLFA in the soil with natural vegetation, also these soils were similar in the distribution of abundance of different PLFA studied. However, the herbicide and tillage treatments showed great differences regarding the soil used as reference (soil under natural vegetation).

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 are bacterial dominated with mesofaunal grazing, whereas slowly cycling systems have characteristic higher fungal:bacterial ratios.

[Responses of forest soil carbon pool and carbon cycle to the changes of carbon input].

PubMed

Wang, Qing-kui

2011-04-01

Litters and plant roots are the main sources of forest soil organic carbon (C). This paper summarized the effects of the changes in C input on the forest soil C pool and C cycle, and analyzed the effects of these changes on the total soil C, microbial biomass C, dissoluble organic C, and soil respiration. Different forests in different regions had inconsistent responses to C input change, and the effects of litter removal or addition and of root exclusion or not differed with tree species and regions. Current researches mainly focused on soil respiration and C pool fractions, and scarce were about the effects of C input change on the changes of soil carbon structure and stability as well as the response mechanisms of soil organisms especially soil fauna, which should be strengthened in the future.

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-11-01

Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations

NASA Astrophysics Data System (ADS)

Zhou, Xiaoqi; Guo, Zhiying; Chen, Chengrong; Jia, Zhongjun

2017-04-01

Forest plantations have been recognised as a key strategy management tool for stocking carbon (C) in soils, thereby contributing to climate warming mitigation. However, long-term ecological consequences of anthropogenic forest plantations on the community structure and diversity of soil microorganisms and the underlying mechanisms in determining these patterns are poorly understood. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e. slash pine, hoop pine and kauri pine) and a eucalypt species in subtropical Australia. We investigated the patterns of community structure, and the diversity of soil bacteria and eukaryotes by using high-throughput sequencing of 16S rRNA and 18S rRNA genes. We also measured the potential methane oxidation capacity under different tree species. The results showed that slash pine and Eucalyptus significantly increased the dominant taxa of bacterial Acidobacteria and the dominant taxa of eukaryotic Ascomycota, and formed clusters of soil bacterial and eukaryotic communities, which were clearly different from the clusters under hoop pine and kauri pine. Soil pH and nutrient quality indicators such as C : nitrogen (N) and extractable organic C : extractable organic N were key factors in determining the patterns of soil bacterial and eukaryotic communities between the different tree species treatments. Slash pine and Eucalyptus had significantly lower soil bacterial and eukaryotic operational taxonomical unit numbers and lower diversity indices than kauri pine and hoop pine. A key factor limitation hypothesis was introduced, which gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus. In addition, slash pine and Eucalyptus had a higher soil methane oxidation capacity than the other tree species. These results suggest that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and highlight the importance of soil pH and physiochemical characteristics in microbially mediated ecological processes in forested soils.

Evaluation of soil-foundation-structure interaction effects on seismic response demands of multi-story MRF buildings on raft foundations

NASA Astrophysics Data System (ADS)

Abdel Raheem, Shehata E.; Ahmed, Mohamed M.; Alazrak, Tarek M. A.

2015-03-01

Soil conditions have a great deal to do with damage to structures during earthquakes. Hence the investigation on the energy transfer mechanism from soils to buildings during earthquakes is critical for the seismic design of multi-story buildings and for upgrading existing structures. Thus, the need for research into soil-structure interaction (SSI) problems is greater than ever. Moreover, recent studies show that the effects of SSI may be detrimental to the seismic response of structure and neglecting SSI in analysis may lead to un-conservative design. Despite this, the conventional design procedure usually involves assumption of fixity at the base of foundation neglecting the flexibility of the foundation, the compressibility of the underneath soil and, consequently, the effect of foundation settlement on further redistribution of bending moment and shear force demands. Hence the SSI analysis of multi-story buildings is the main focus of this research; the effects of SSI are analyzed for typical multi-story building resting on raft foundation. Three methods of analysis are used for seismic demands evaluation of the target moment-resistant frame buildings: equivalent static load; response spectrum methods and nonlinear time history analysis with suit of nine time history records. Three-dimensional FE model is constructed to investigate the effects of different soil conditions and number of stories on the vibration characteristics and seismic response demands of building structures. Numerical results obtained using SSI model with different soil conditions are compared to those corresponding to fixed-base support modeling assumption. The peak responses of story shear, story moment, story displacement, story drift, moments at beam ends, as well as force of inner columns are analyzed. The results of different analysis approaches are used to evaluate the advantages, limitations, and ease of application of each approach for seismic analysis.

Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils.

PubMed

Espenberg, Mikk; Truu, Marika; Mander, Ülo; Kasak, Kuno; Nõlvak, Hiie; Ligi, Teele; Oopkaup, Kristjan; Maddison, Martin; Truu, Jaak

2018-03-16

Tropical peatlands, which play a crucial role in the maintenance of different ecosystem services, are increasingly drained for agriculture, forestry, peat extraction and human settlement purposes. The present study investigated the differences between natural and drained sites of a tropical peatland in the community structure of soil bacteria and archaea and their potential to perform nitrogen transformation processes. The results indicate significant dissimilarities in the structure of soil bacterial and archaeal communities as well as nirK, nirS, nosZ, nifH and archaeal amoA gene-possessing microbial communities. The reduced denitrification and N 2 -fixing potential was detected in the drained tropical peatland soil. In undisturbed peatland soil, the N 2 O emission was primarily related to nirS-type denitrifiers and dissimilatory nitrate reduction to ammonium, while the conversion of N 2 O to N 2 was controlled by microbes possessing nosZ clade I genes. The denitrifying microbial community of the drained site differed significantly from the natural site community. The main reducers of N 2 O were microbes harbouring nosZ clade II genes in the drained site. Additionally, the importance of DNRA process as one of the controlling mechanisms of N 2 O fluxes in the natural peatlands of the tropics revealed from the results of the study.

Patterns of Community Change among Ammonia Oxidizers in Meadow Soils upon Long-Term Incubation at Different Temperatures

PubMed Central

Avrahami, Sharon; Conrad, Ralf

2003-01-01

The effect of temperature on the community structure of ammonia-oxidizing bacteria was investigated in three different meadow soils. Two of the soils (OMS and GMS) were acidic (pH 5.0 to 5.8) and from sites in Germany with low annual mean temperature (about 10°C), while KMS soil was slightly alkaline (pH 7.9) and from a site in Israel with a high annual mean temperature (about 22°C). The soils were fertilized and incubated for up to 20 weeks in a moist state and as a buffered (pH 7) slurry amended with urea at different incubation temperatures (4 to 37°C). OMS soil was also incubated with less fertilizer than the other soils. The community structure of ammonia oxidizers was analyzed before and after incubation by denaturing gradient gel electrophoresis (DGGE) of the amoA gene, which codes for the α subunit of ammonia monooxygenase. All amoA gene sequences found belonged to the genus Nitrosospira. The analysis showed community change due to temperature both in moist soil and in the soil slurry. Two patterns of community change were observed. One pattern was a change between the different Nitrosospira clusters, which was observed in moist soil and slurry incubations of GMS and OMS. Nitrosospira AmoA cluster 1 was mainly detected below 30°C, while Nitrosospira cluster 4 was predominant at 25°C. Nitrosospira clusters 3a, 3b, and 9 dominated at 30°C. The second pattern, observed in KMS, showed a community shift predominantly within a single Nitrosospira cluster. The sequences of the individual DGGE bands that exhibited different trends with temperature belonged almost exclusively to Nitrosospira cluster 3a. We conclude that ammonia oxidizer populations are influenced by temperature. In addition, we confirmed previous observations that N fertilizer also influences the community structure of ammonia oxidizers. Thus, Nitrosospira cluster 1 was absent in OMS soil treated with less fertilizer, while Nitrosospira cluster 9 was only found in the sample given less fertilizer. PMID:14532075

The effects of vegetation and soil hydraulic properties on passive microwave sensing of soil moisture: Data report for the 1982 fiels experiments

NASA Technical Reports Server (NTRS)

Oneill, P.; Jackson, T.; Blanchard, B. J.; Vandenhoek, R.; Gould, W.; Wang, J.; Glazar, W.; Mcmurtrey, J., III

1983-01-01

Field experiments to (1) study the biomass and geometrical structure properties of vegetation canopies to determine their impact on microwave emission data, and (2) to verify whether time series microwave data can be related to soil hydrologic properties for use in soil type classification. Truck mounted radiometers at 1.4 GHz and 5 GHz were used to obtain microwave brightness temperatures of bare vegetated test plots under different conditions of soil wetness, plant water content and canopy structure. Observations of soil moisture, soil temperature, vegetation biomass and other soil and canopy parameters were made concurrently with the microwave measurements. The experimental design and data collection procedures for both experiments are documented and the reduced data are presented in tabular form.

Abundance, Composition and Activity of Ammonia Oxidizer and Denitrifier Communities in Metal Polluted Rice Paddies from South China

PubMed Central

Liu, Yuan; Liu, Yongzhuo; Ding, Yuanjun; Zheng, Jinwei; Zhou, Tong; Pan, Genxing; Crowley, David; Li, Lianqing; Zheng, Jufeng; Zhang, Xuhui; Yu, Xinyan; Wang, Jiafang

2014-01-01

While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils. PMID:25058658

The potential of cover crops for improving soil function

NASA Astrophysics Data System (ADS)

Stoate, Chris; Crotty, Felicity

2017-04-01

Cover crops can be grown over the autumn and winter ensuring green cover throughout the year. They have been described as improving soil structure, reducing soil erosion and potentially even a form of grass weed control. These crops retain nutrients within the plant, potentially making them available for future crops, as well as increasing soil organic matter. Over the last three years, we have investigated how different cover crop regimes affect soil quality. Three separate experiments over each autumn/winter period have investigated how different cover crops affect soil biology, physics and chemistry, with each experiment building on the previous one. There have been significant effects of cover crops on soil structure, as well as significantly lower weed biomass and increased yields in the following crop - in comparison to bare stubble. For example, the effect of drilling the cover crops on soil structure in comparison to a bare stubble control that had not been driven on by machinery was quantified, and over the winter period the soil structure of the cover crop treatments changed, with compaction reduced in the cover crop treatments, whilst the bare stubble control remained unchanged. Weeds were found in significantly lower biomass in the cover crop mixes in comparison to the bare stubble control, and significantly lower weed biomass continued to be found in the following spring oat crop where the cover crops had been, indicating a weed suppressive effect that has a continued legacy in the following crop. The following spring oats have shown similar results in the last two years, with higher yields in the previous cover crop areas compared to the bare stubble controls. Overall, these results are indicating that cover crops have the potential to provide improvements to soil quality, reduce weeds and improve yields. We discuss the economic implications.

[Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber].

PubMed

Li, Min; Wu, Feng-zhi

2014-12-01

Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber (Cucumis sativus) were analyzed by conventional chemical method, PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR methods. Pot experiment was carried out in the greenhouse for three consecutive years with cucumber as the main crop, and scallion (Allium fistulosum), wheat (Triticum aestivum) and oilseed rape (Brassica campestri) as catch crops. Results showed that, with the increase of crop planting times, soil urease, neutral phosphatase and invertase activities in the wheat treatment were significantly) higher than in the scallion and oilseed rape treatments, and these enzyme activities in the oilseed rape treatment were significantly higher than in the scallion treatment. PCR-DGGR analysis showed that cucumber rhizosphere bacterial community structures were different among treatments. Scallion and wheat treatments maintained relatively higher diversity indices of bacterial community structure. qPCR results showed that the abundance of soil bacterial community in the wheat treatment was significantly higher than in the scallion and oilseed rape treatments. In conclusion, different catch treatments affected soil enzyme activities and bacteria community and changed the soil environment. Wheat used as summer catch crop could maintain relatively higher soil enzyme activities, bacterial community diversity and abundance.

Modeling the Dynamics of Soil Structure and Water in Agricultural Soil

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2017-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

Influence of different fertilizer types of zucchini (Cucurbita pepo) on the structure of nematode communities.

PubMed

Haytova, D; Bileva, T

2011-01-01

Increasing efficiency of production of vegetable crops is directly related to search for appropriate solution to increase their productivity. Organic amendments have been used for centuries to improve soil fertility and crop yield. Our study suggests that organic amendments can also be used as nematicidal agents. The survey was conducted on Experimental field of Department Horticulture at Agricultural University of Plovdiv, Bulgaria in 2009 on nematode infested sites. Combination with two types of fertilizers was used to investigate their effects on the community of soil nematodes. Characterization and comparative analysis among treatments of soil nematode community structure based on different ecological measures such as total nematode abundance, number of genera, trophic diversity and etc., was made. Changes in the composition and structure of nematode community as result of different fertilizer types were assessed.

Structural composition of organic matter in particle-size fractions of soils along a climo-biosequence in the main range of Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Jafarzadeh-Haghighi, Amir Hossein; Shamshuddin, Jusop; Hamdan, Jol; Zainuddin, Norhazlin

2016-09-01

Information on structural composition of organic matter (OM) in particle-size fractions of soils along a climo-biosequence is sparse. The objective of this study was to examine structural composition and morphological characteristics of OM in particle-size fractions of soils along a climo-biosequence in order to better understand the factors and processes affecting structural composition of soil organic matter. To explore changes in structural composition of OM in soils with different pedogenesis, the A-horizon was considered for further analyses including particle-size fractionation, solid-state 13C nuclear magnetic resonance (NMR) spectroscopy and scanning electron microscopy (SEM). Due to the increase in the thickness of organic layer with increasing elevation, the A-horizon was situated at greater depth in soils of higher elevation. The relationship between relative abundances of carbon (C) structures and particle-size fractions was examined using principal component analysis (PCA). It was found that alkyl C (20.1-73.4%) and O-alkyl C (16.8-67.7%) dominated particle-size fractions. The proportion of alkyl C increased with increasing elevation, while O-alkyl C showed an opposite trend. Results of PCA confirmed this finding and showed the relative enrichment of alkyl C in soils of higher elevation. Increase in the proportion of alkyl C in 250-2000 μm fraction is linked to selective preservation of aliphatic compounds derived from root litter. SEM results showed an increase in root contribution to the 250-2000 μm fraction with increasing elevation. For the <53 μm fraction, pedogenic process of podzolization is responsible for the relative enrichment of alkyl C. This study demonstrates that changes in structural composition of OM in particle-size fractions of soils along the studied climo-biosequence are attributed to site-specific differences in pedogenesis as a function of climate and vegetation.

Determination of phosphorus fertilizer soil reactions by Raman and synchrotron infrared microspectroscopy.

PubMed

Vogel, Christian; Adam, Christian; Sekine, Ryo; Schiller, Tara; Lipiec, Ewelina; McNaughton, Don

2013-10-01

The reaction mechanisms of phosphate-bearing mineral phases from sewage sludge ash-based fertilizers in soil were determined by Raman and synchrotron infrared microspectroscopy. Different reaction mechanisms in wet soil were found for calcium and magnesium (pyro-) phosphates. Calcium orthophosphates were converted over time to hydroxyapatite. Conversely, different magnesium phosphates were transformed to trimagnesium phosphate. Since the magnesium phosphates are unable to form an apatite structure, the plant-available phosphorus remains in the soil, leading to better growth results observed in agricultural pot experiments. The pyrophosphates also reacted very differently. Calcium pyrophosphate is unreactive in soil. In contrast, magnesium pyrophosphate quickly formed plant-available dimagnesium phosphate.

Soil Bacterial Community Response to Differences in Agricultural Management along with Seasonal Changes in a Mediterranean Region

PubMed Central

Bevivino, Annamaria; Paganin, Patrizia; Bacci, Giovanni; Florio, Alessandro; Pellicer, Maite Sampedro; Papaleo, Maria Cristiana; Mengoni, Alessio; Ledda, Luigi; Fani, Renato; Benedetti, Anna; Dalmastri, Claudia

2014-01-01

Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil health and sustainable productivity. PMID:25144665

Soil bacterial community responses to revegetation of moving sand dune in semi-arid grassland.

PubMed

Cao, Chengyou; Zhang, Ying; Cui, Zhenbo; Feng, Shuwei; Wang, Tingting; Ren, Qing

2017-08-01

Grasslands in semi-arid Northern China are widely desertified, thus inducing the formation of a large area of moving sand lands. Revegetation of the sandy land is commonly adopted to restore degraded grasslands. The structure of the soil microbial community might dramatically change during degradation and recovery because microorganisms are one of the major drivers of ecological process through their interactions with plants and soil. Assuming that soil properties are the key determinants of the structure of soil bacterial community within the same soil type, whether the vegetation type causes the significant difference in the structure of soil bacterial community during revegetation and restoration of the degraded grasslands remains poorly understood. Our study aimed to (1) investigate the response of soil bacterial communities to the changes during vegetation degradation and recovery and (2) evaluate whether the soil bacterial communities under plantations return to their native state. We detected the shifts in diversities and compositions of the soil bacterial communities and the relative abundance of dominant bacterial taxa by using the high-throughput Illumina MiSeq sequencing technique in an area covered by 32-year-old Caragana microphylla, Artemisia halodendron, Hedysarum fruticosum, Pinus sylvestris var. mongolica, Populus simonii, and Salix gordejevii sand-fixing plantations and in the native community (NC) dominated by elm, and moving sandy dune (MS). We found that the obtained operational taxonomic units by 16S rRNA gene sequencing and diversity index in MS were all significantly lower than those in NC, and the number and composition of dominant genera were significantly different between NC and MS. Interestingly, the compositions of bacterial communities and the dominant genera in different sand-fixation plantations (C. microphylla, A. halodendron, H. fruticosum, P. sylvestris var. mongolica, P. simonii, and S. gordejevii) were all similar to those of the native soil of NC, suggesting that the plantation type and soil properties exhibit a minimal effect on the compositions of soil microbial communities within a continuous landscape. These results revealed that the structure of the soil bacterial community of degraded sandy grassland (even degenerated into a mobile sand dunes) in semi-arid region can be reversibly restored by planting indigenous shrub or semi-shrub plantation on human time scales.

Cryofacial Analysis of Permafrost Soils

NASA Astrophysics Data System (ADS)

Shur, Y.; Kanevskiy, M.; Jorgenson, M. T.; Fortier, D.

2008-12-01

Cryogenic structure of soils, specifically the patterns formed by ice inclusions and massive ice in permafrost, depends on the genesis of soils and the way they are transformed into a perennially frozen state. Katasonov (1963) recognized that the analysis of relationship between the patterns of cryogenic structure and the processes of permafrost formation (he termed 'cryofacial analysis') is a powerful tool for understanding of genesis of permafrost in relation to different sediment types. He applied cryofacial analysis to Late Pleistocene syngenetic permafrost (yedoma) and to permafrost formed during freezing of thaw bulbs under drained lakes in the continuous permafrost zone. Our long-term studies of cryogenic structure in Alaska and Russia found that cryofacial analysis can be applied to all types of permafrost soil. We described the evolution of cryogenic structure associated with alluvial chronosequences on arctic floodplains in Russia and Alaska and found the differing cryofacies are highly related to patterns of ecosystem development. Cryogenic structure of glacial-lacustrine deposits in several parts of Alaska is similar to cryogenic structure of these deposits in differing permafrost areas in Russia. Cryofacial analysis is extremely useful in recognition of later modifications of permafrost when compared soils are identical in composition. For example, we differentiated original syngenetic permafrost from permafrost modified by thermokarst and thermal erosion in the CRREL permafrost tunnel at Fox, Alaska on the basis of differences in cryogenic structure. We identified unique cryogenic structures associated with the transient zone of the upper permafrost and with the formation of thermokarst-cave ice. Cryofacial analysis showed that parts of permafrost which were previously thawed after fire can be easily distinguished from parts unaffected by thawing. Cryofacial analysis helped in recognizing areas in central and northern Alaska unaffected by the last glaciation. Finally, the study of basal ice under contemporary glaciers makes possible detection of buried glacial ice along the margins of the Arctic Ocean.

Assessment of Bacterial bph Gene in Amazonian Dark Earth and Their Adjacent Soils

PubMed Central

Brossi, Maria Julia de Lima; Mendes, Lucas William; Germano, Mariana Gomes; Lima, Amanda Barbosa; Tsai, Siu Mui

2014-01-01

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry. PMID:24927167

Assessment of bacterial bph gene in Amazonian dark earth and their adjacent soils.

PubMed

Brossi, Maria Julia de Lima; Mendes, Lucas William; Germano, Mariana Gomes; Lima, Amanda Barbosa; Tsai, Siu Mui

2014-01-01

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry.

Effects of drought on forest soil structure and hydrological soil functions

NASA Astrophysics Data System (ADS)

Gimbel, K.; Puhlmann, H.; Weiler, M.

2012-04-01

Climate change is predicted to severely affect precipitation patterns across central Europe. Soil structure is closely linked to the activity of soil microbiota and plant roots, which modify flow pathways along roots, organic matter and water repellence of soils. Through shrinkage and fracturing of soil aggregates, soil structure is also responding to changing climate (in particular drought) conditions. We investigate the possible effects on biogeochemical and hydropedological processes in response to predicted future reduced precipitation, and the interaction of these processes with the biodiversity of the forest understorey and soil biota. The hypotheses of this study are: (i) drought causes a change in soil structure, which affects hydrological soil functions (water infiltration, uptake and redistribution); (ii) changes in rooting patterns and microbial community composition, in response to drought, influence the hydrological soil functions. To test our hypotheses, we built adaptive roofing systems on nine sites in Germany, which allow a flexible reduction of precipitation in order to achieve the long-term minimum precipitation of a site. Here we present first measurements of our repeated measuring/sampling campaign, which will be conducted over a period of three years. The aim of our experiments is to analyze soil pore architecture and related flow and transport behaviour with dye tracer sprinkling experiments, soil column experiments with stable isotope (deuterium, oxygen-18) enriched water, computed tomography at soil monoliths (~70 l) and multi-step outflow experiments with 100 ml soil cores. Finally, we sketch our idea how to relate the observed temporal changes of soil structure and hydrological soil functions to the observed dynamics of hydrometeorological site conditions, soil moisture and desiccation as well as changes in rooting patterns, herb layer and soil microbiotic communities. The results of this study may help to assess future behavior of the plant-soil-water-microbiology-system and may help to adjust models to predict future response to different precipitation patterns as well as help coping with existing and future emerging challenges in forest management.

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

PubMed Central

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. PMID:28611747

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

PubMed

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Energy Transformations of Soil Organic Matter in a Changing World

NASA Astrophysics Data System (ADS)

Herrmann, A. M.; Coucheney, E.; Grice, S. M.; Ritz, K.; Harris, J.

2011-12-01

The role of soils in governing the terrestrial carbon balance is acknowledged as being important but remains poorly understood within the context of climate change. Soils exchange energy with their surroundings and are therefore open systems thermodynamically, but little is known how energy transformations of decomposition processes are affected by temperature. Soil organic matter and the soil biomass can be conceptualised as analogous to the 'fuel' and 'biological engine' of the earth, respectively, and are pivotal in driving the belowground carbon cycle. Thermodynamic principles of soil organic matter decomposition were evaluated by means of isothermal microcalorimetry (TAM Air, TA Instruments, Sollentuna Sweden: (i) Mineral forest soils from the Flakaliden long-term nitrogen fertilisation experiment (Sweden) were amended with a range of different substrates representing structurally simple to complex, ecologically pertinent organic matter and heat signatures were determined at temperatures between 5 and 25°C. (ii) Thermodynamic and resource-use efficiencies of the biomass were determined in arable soils which received contrasting long-term management regimes with respect to organic matter and nitrogen since 1956. The work showed that (i) structurally labile components have higher activation energy and temperature dependence than structurally more complex organic components. This is, however, in contrast to the thermodynamic argument which suggests the opposite that reactions metabolising structurally complex, aromatic components have higher temperature dependence than reactions metabolising structurally more labile components. (ii) Microbial communities exposed to long-term stress by heavy metal and low pH were less thermodynamic efficient and showed a decrease in resource-use efficiency in comparison with conventional input regimes. Differences in efficiencies were mirrored in both the phenotypic and functional profiles of the communities. We will present our findings illustrating the capacity of isothermal microcalorimetry to evaluate temperature dependencies of soil organic matter decomposition, associated energy transformations and thermodynamic principles in soil ecosystems.

Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

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

Hollister, Emily B; Schadt, Christopher Warren; Palumbo, Anthony Vito

In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt tomore » characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.« less

A long-term soil structure observatory for post-compaction soil structure evolution: design and initial soil structure recovery observations

NASA Astrophysics Data System (ADS)

Keller, Thomas; Colombi, Tino; Ruiz, Siul; Grahm, Lina; Reiser, René; Rek, Jan; Oberholzer, Hans-Rudolf; Schymanski, Stanislaus; Walter, Achim; Or, Dani

2016-04-01

Soil compaction due to agricultural vehicular traffic alters the geometrical arrangement of soil constituents, thereby modifying mechanical properties and pore spaces that affect a range of soil hydro-ecological functions. The ecological and economic costs of soil compaction are dependent on the immediate impact on soil functions during the compaction event, and a function of the recovery time. In contrast to a wealth of soil compaction information, mechanisms and rates of soil structure recovery remain largely unknown. A long-term (>10-yr) soil structure observatory (SSO) was established in 2014 on a loamy soil in Zurich, Switzerland, to quantify rates and mechanisms of structure recovery of compacted arable soil under different post-compaction management treatments. We implemented three initial compaction treatments (using a two-axle agricultural vehicle with 8 Mg wheel load): compaction of the entire plot area (i.e. track-by-track), compaction in wheel tracks, and no compaction. After compaction, we implemented four post-compaction soil management systems: bare soil (BS), permanent grass (PG), crop rotation without mechanical loosening (NT), and crop rotation under conventional tillage (CT). BS and PG provide insights into uninterrupted natural processes of soil structure regeneration under reduced (BS) and normal biological activity (PG). The two cropping systems (NT and CT) enable insights into soil structure recovery under common agricultural practices with minimal (NT) and conventional mechanical soil disturbance (CT). Observations include periodic sampling and measurements of soil physical properties, earthworm abundance, crop measures, electrical resistivity and ground penetrating radar imaging, and continuous monitoring of state variables - soil moisture, temperature, CO2 and O2 concentrations, redox potential and oxygen diffusion rates - for which a network of sensors was installed at various depths (0-1 m). Initial compaction increased soil bulk density to about half a metre, decreased gas and water transport functions (air permeability, gas diffusivity, saturated hydraulic conductivity), and increased mechanical impedance. Water infiltration at the soil surface was initially reduced by three orders of magnitude, but significantly recovered within a year. However, within the soil profile, recovery of transport properties is much smaller. Air permeability tended to recover more than gas diffusivity, suggesting that initial post-compaction recovery is initiated by new macropores (e.g. biopores). Tillage recovered topsoil bulk density but not topsoil transport functions. Compaction changed grass species composition in PG, and significantly reduced grass biomass in PG and crop yields in NT and CT.

A tropical freshwater wetland: I Structure, growth, and regeneration

Treesearch

James A. Allen; Ken W. Krauss; Katherine C. Ewel; Bobby D Keeland; Erick E. Waguk

2005-01-01

Forested wetlands dominated by (Terminalia carolinensis) are endemic to Micronesia but common only on the island of Kosrae, Federated States of Micronesia. On Kosrae, these forests occur on Nansepsep, Inkosr, and Sonahnpil soil types, which differ in degree of flooding and soil saturation. We compared forest structure, growth, nutrition, and...

Combined effect of temperature and copper pollution on soil bacterial community: climate change and regional variation aspects.

PubMed

Henriques, Isabel; Araújo, Susana; Pereira, Anabela; Menezes-Oliveira, Vanessa B; Correia, António; Soares, Amadeu M V M; Scott-Fordsmand, Janeck J; Amorim, Mónica J B

2015-01-01

The aim of this study was to assess the combined effects of temperature and copper (Cu) contamination in the structure of soil bacterial community. For this, contaminated or spiked and control soils from two different geographic origins (PT-Portugal and DK-Denmark) were used. The DK soil was from a historically contaminated study field, representing a long-term exposure to Cu while the PT soil was from a clean site and freshly spiked with Cu. Soil bacterial communities were exposed in mesocosms during 84 days to 3 different temperatures based on values typically found in each geographic region and temperature conditions that simulated a warming scenario. Obtained results indicate that Cu stress alters the structure of bacterial community and that this effect is, to some extent, temperature-dependent. Effects on bacterial diversity for both soils were also observed. Differences in the DK and PT communities' response were apparent, with the community from the historically contaminated soil being more resilient to temperature fluctuations. This study presents evidence to support the hypothesis that temperature alters the effect of metals on soils. Further, our results suggest that the definition of soils quality criteria must be based on studies performed under temperatures selected for the specific geographic region. Studies taking into account temperature changes are needed to model and predict risks, this is important to e.g. future adjustments of the maximum permissible levels for soil metal contamination. Copyright © 2014 Elsevier Inc. All rights reserved.

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

PubMed

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

2015-01-01

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

Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.

PubMed

Rampelotto, Pabulo Henrique; de Siqueira Ferreira, Adão; Barboza, Anthony Diego Muller; Roesch, Luiz Fernando Wurdig

2013-10-01

The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.

Community structure and elevational diversity patterns of soil Acidobacteria.

PubMed

Zhang, Yuguang; Cong, Jing; Lu, Hui; Li, Guangliang; Qu, Yuanyuan; Su, Xiujiang; Zhou, Jizhong; Li, Diqiang

2014-08-01

Acidobacteria is one of the most dominant and abundant phyla in soil, and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational diversity patterns. We selected four elevation gradients from 1000 to 2800 m with typical vegetation types of the northern slope of Shennongjia Mountain in central China. The vegetation types were evergreen broadleaved forest, deciduous broadleaved forest, coniferous forest and sub-alpine shrubs. We analyzed the soil acidobacterial community composition, elevational patterns and the relationship between Acidobacteria subdivisions and soil enzyme activities by using the 16S rRNA meta-sequencing technique and multivariate statistical analysis. The result found that 19 known subdivisions as well as an unclassified phylotype were presented in these forest sites, and Subdivision 6 has the highest number of detectable operational taxonomic units (OTUs). A significant single peak distribution pattern (P<0.05) between the OTU number and the elevation was observed. The Jaccard and Bray-Curtis index analysis showed that the soil Acidobacteria compositional similarity significantly decreased (P<0.01) with the increase in elevation distance. Mantel test analysis showed the most of the soil Acidobacteria subdivisions had the significant relationship (P<0.01) with different soil enzymes. Therefore, soil Acidobacteria may be involved in different ecosystem functions in global elemental cycles. Partial Mantel tests and CCA analysis showed that soil pH, soil temperature and plant diversity may be the key factors in shaping the soil Acidobacterial community structure. Copyright © 2014. Published by Elsevier B.V.

Land use influences arbuscular mycorrhizal fungal communities in the farming-pastoral ecotone of northern China.

PubMed

Xiang, Dan; Verbruggen, Erik; Hu, Yajun; Veresoglou, Stavros D; Rillig, Matthias C; Zhou, Wenping; Xu, Tianle; Li, Huan; Hao, Zhipeng; Chen, Yongliang; Chen, Baodong

2014-12-01

We performed a landscape-scale investigation to compare the arbuscular mycorrhizal fungal (AMF) communities between grasslands and farmlands in the farming-pastoral ecotone of northern China. AMF richness and community composition were examined with 454 pyrosequencing. Structural equation modelling (SEM) and multivariate analyses were applied to disentangle the direct and indirect effects (mediated by multiple environmental factors) of land use on AMF. Land use conversion from grassland to farmland significantly reduced AMF richness and extraradical hyphal length density, and these land use types also differed significantly in AMF community composition. SEM showed that the effects of land use on AMF richness and hyphal length density in soil were primarily mediated by available phosphorus and soil structural quality. Soil texture was the strongest predictor of AMF community composition. Soil carbon, nitrogen and soil pH were also significantly correlated with AMF community composition, indicating that these abiotic variables could be responsible for some of the community composition differences among sites. Our study shows that land use has a partly predictable effect on AMF communities across this ecologically relevant area of China, and indicates that high soil phosphorus concentrations and poor soil structure are particularly detrimental to AMF in this fragile ecosystem. © 2014 The Author. New Phytologist © 2014 New Phytologist Trust.

Tellurium Distribution and Speciation in Contaminated Soils from Abandoned Mine Tailings: Comparison with Selenium.

PubMed

Qin, Hai-Bo; Takeichi, Yasuo; Nitani, Hiroaki; Terada, Yasuko; Takahashi, Yoshio

2017-06-06

The distribution and chemical species of tellurium (Te) in contaminated soil were determined by a combination of microfocused X-ray fluorescence (μ-XRF), X-ray diffraction (μ-XRD), and X-ray absorption fine structure (μ-XAFS) techniques. Results showed that Te was present as a mixture of Te(VI) and Te(IV) species, while selenium (Se) was predominantly present in the form of Se(IV) in the soil contaminated by abandoned mine tailings. In the contaminated soil, Fe(III) hydroxides were the host phases for Se(IV), Te(IV), and Te(VI), but Te(IV) could be also retained by illite. The difference in speciation and solubility of Se and Te in soil can result from different structures of surface complexes for Se and Te onto Fe(III) hydroxides. Furthermore, our results suggest that the retention of Te(IV) in soil could be relatively weaker than that of Te(VI) due to structural incorporation of Te(VI) into Fe(III) hydroxides. These findings are of geochemical and environmental significance for better understanding the solubility, mobility, and bioavailability of Te in the surface environment. To the best of our knowledge, this is the first study reporting the speciation and host phases of Te in field soil by the μ-XRF-XRD-XAFS techniques.

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE PAGES

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe; ...

2014-06-16

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

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

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Relationship between gaseous N dynamics and the hydraulic state of hierarchically structured soils

NASA Astrophysics Data System (ADS)

Schlüter, Steffen; Dörsch, Peter; Vogel, Hans-Jörg

2017-04-01

The inherent spatial heterogeneity of soil generates spatially distributed micro-sites with different local N gas (NO, N2O, N2) production and release rates. Moreover, local micro-site conditions and the pathways between them depend on soil moisture which itself is highly dynamic close to the soil surface. These relationships need to be taken into account for a quantitative understanding of soil denitrification and associated N gas dynamics. Soil structure has been recognized as a key factor to understand the high spatial variability of N gas emissions. In particular gaseous N release from soils depends on: i) the total denitrification rate, which is related to the spatial extent and distribution of anaerobic sites and ii) the probability of N2O to escape from the soil without being further reduced to N2. This impact of soil structure is typically ignored in studies with soil slurries or repacked soil. In this project we run well-defined mesocosm experiments on N gas dynamics with hierarchically structured, artificial soils in which the spatial distribution of substrate and denitrifiers is known exactly. Sintered, porous glass pellets are inoculated with strains of Paracoccus denitrificans and/or Agrobacterium tumefaciens and amended with nutrient solution. These pellets are embedded in coarse-grained sand within gas-tight columns under O2/He atmosphere. The pellets are either places in layers or randomly to create different patterns of N gas production sites and diffusion pathways. Denitrification occurs in the anaerobic centers of the porous pellets, while the partially saturated sand matrix controls the diffusive transport of N gases towards the headspace, where all relevant gas concentrations are monitored with gas chromatography. Water saturations are adjusted such that the diffusive pathways are either fully continuous or partially discontinuous. Preliminary results indicate that the water content exert a major control on the magnitude of denitrification, whereas the onset and dynamics are mainly controlled by the position of the substrate and the denitrifiers.

Compositional changes of soil organic matter with cropping time were more profound in subsoils and distinct between Phaeozem and Chernozem in Northeast China

USDA-ARS?s Scientific Manuscript database

Soil organic matter (SOM) contributes to soil processes and is found both in shallow and deep soil layers. Its activity can be affected by its chemical composition, yet knowledge is incomplete of how land use alters the structural composition of SOM throughout the profiles of different soil types. T...

[Effects of sub-watershed landscape patterns at the upper reaches of Minjiang River on soil erosion].

PubMed

Yang, Meng; Li, Xiu-zhen; Yang, Zhao-ping; Hu, Yuan-man; Wen, Qing-chun

2007-11-01

Based on GIS, the spatial distribution of soil loss and sediment yield in Heishui and Zhenjiangguan sub-watersheds at the upper reaches of Minjiang River was simulated by using sediment delivery-distribution (SEDD) model, and the effects of land use/cover types on soil erosion and sediment yield were discussed, based on the simulated results and related land use maps. A landscape index named location-weighted landscape contrast index (LCI) was calculated to evaluate the effects of landscape components' spatial distribution, weight, and structure of land use/cover on soil erosion. The results showed the soil erosion modulus varied with land use pattern, and decreased in the order of bare rock > urban/village > rangeland > farmland > shrub > forest. There were no significant differences in sediment yield modules among different land use/covers. In the two sub-watersheds, the spatial distribution of land use/covers on slope tended to decrease the final sediment load at watershed outlet, hut as related to relative elevation, relative distance, and flow length, the spatial distribution tended to increase sediment yield. The two sub-watersheds had different advantages as related to landscape components' spatial distribution, but, when the land use/cover weight was considered, the advantages of Zhenjiangguan sub-watershed increased. If the land use/cover structure was considered in addition, the landscape pattern of Zhenjiangguan subwatershed was better. Therefore, only the three elements, i.e., landscape components' spatial distribution, land use/cover weight, and land use/cover structure, were considered comprehensively, can we get an overall evaluation on the effects of landscape pattern on soil erosion. The calculation of LCI related to slope suggested that this index couldn' t accurately reflect the effects of land use/cover weight and structure on soil erosion, and thus, needed to be modified.

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

Throughfall-mediated alterations to soil microbial community structure in a forest plot of homogenous soil texture, litter, and plant species composition

NASA Astrophysics Data System (ADS)

Van Stan, John; Rosier, Carl; Moore, Leslie; Gay, Trent; Reichard, James; Wu, Tiehang; Kan, Jinjun

2015-04-01

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to our understanding of patterns in biogeochemical cycling and related ecological services (e.g., plant community structure, water quality, response to environmental change). Since forest canopy structure alters the spatiotemporal patterning of precipitation water and solute supplies to soils (via "throughfall"), is it possible that changes in SMC structure could arise from modifications in canopy elements? Our study investigates this question by monitoring throughfall water and dissolved ion supply to soils beneath a continuum of canopy structure: from large gaps (0% cover), to bare Quercus virginiana Mill. (southern live oak) canopy (~50-70%), to heavy Tillandsia usneoides L. (Spanish moss) canopy (>90% cover). Throughfall water supply diminished with increasing canopy cover, yet increased washoff/leaching of Na+, Cl-, PO43-, and SO42- from the canopy to the soils. Presence of T. usneoides diminished throughfall NO3-, but enhanced NH4+, concentrations supplied to subcanopy soils. The mineral soil horizon (0-10 cm) sampled in triplicate from locations receiving throughfall water and solutes from canopy gaps, bare canopy, and T. usneoides-laden canopy significantly differed in soil chemistry parameters (pH, Ca2+, Mg2+, CEC). Polymerase Chain Reaction-Denaturant Gradient Gel Electrophoresis (PCR-DGGE) banding patterns beneath similar canopy covers (experiencing similar throughfall dynamics) also produced high similarities per ANalyses Of SIMilarity (ANO-SIM), and clustered together when analyzed by Nonmetric Multidimensional Scaling (NMDS). These results suggest that modifications of forest canopy structures are capable of affecting mineral-soil horizon SMC structure via throughfall when canopies' biomass distribution is highly heterogeneous. As SMC structure, in many instances, relates to functional diversity, we suggest that future research seek to identify functional diversity shifts (e.g., nitrogen transformation) in response to canopy structural alterations of throughfall water/solute concentration

Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

PubMed

Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

2014-03-01

Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p < 0.001). Amplicons of AOA from the Nitrososphaera cluster dominated all four ecosystem soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vegetation cover of forest, shrub and pasture strongly influences soil bacterial community structure as revealed by 16S rRNA gene T-RFLP analysis.

PubMed

Chim Chan, On; Casper, Peter; Sha, Li Qing; Feng, Zhi Li; Fu, Yun; Yang, Xiao Dong; Ulrich, Andreas; Zou, Xiao Ming

2008-06-01

Bacterial community structure is influenced by vegetation, climate and soil chemical properties. To evaluate these influences, terminal restriction fragment length polymorphism (T-RFLP) and cloning of the 16S rRNA gene were used to analyze the soil bacterial communities in different ecosystems in southwestern China. We compared (1) broad-leaved forest, shrub and pastures in a high-plateau region, (2) three broad-leaved forests representing a climate gradient from high-plateau temperate to subtropical and tropical regions and (3) the humus and mineral soil layers of forests, shrub lands and pastures with open and restricted grazing activities, having varied soil carbon and nutrient contents. Principal component analysis of the T-RFLP patterns revealed that soil bacterial communities of the three vegetation types were distinct. The broad-leaved forests in different climates clustered together, and relatively minor differences were observed between the soil layers or the grazing regimes. Acidobacteria dominated the broad-leaved forests (comprising 62% of the total clone sequences), but exhibited lower relative abundances in the soils of shrub (31%) and pasture (23%). Betaproteobacteria was another dominant taxa of shrub land (31%), whereas Alpha- (19%) and Gammaproteobacteria (13%) and Bacteriodetes (16%) were major components of pasture. Vegetation exerted more pronounced influences than climate and soil chemical properties.

Composition and structure of aggregates from compacted soil horizons in the southern steppe zone of European Russia

NASA Astrophysics Data System (ADS)

Sorokin, A. S.; Abrosimov, K. N.; Lebedeva, M. P.; Kust, G. S.

2016-03-01

The composition and structure of aggregates from different agrogenic soils in the southern steppe zone of European Russia have been studied. It is shown that the multi-level study (from the macro- to microlevel) of these horizons makes it possible to identify soil compaction caused by different elementary soil processes: solonetz-forming, vertisol-forming, and mechanical (wheel) compaction in the rainfed and irrigated soils. The understanding of the genesis of the compaction of soil horizons (natural or anthropogenic) is important for the economic evaluation of soil degradation. It should enable us to make more exact predictions of the rates of degradation processes and undertake adequate mitigation measures. The combined tomographic and micromorphological studies of aggregates of 1-2 and 3-5 mm in diameter from compacted horizons of different soils have been performed for the first time. Additional diagnostic features of negative solonetz- forming processes (low open porosity of aggregates seen on tomograms and filling of a considerable part of the intraped pores with mobile substance) and the vertisol-forming processes (large amount of fine intraaggregate pores seen on tomograms and a virtual absence of humus-clay plasma in the intraped zone)—have been identified. It is shown that the combination of microtomographic and micromorphological methods is helpful for studying the pore space of compacted horizons in cultivated soils.

Improvements of the Profil Cultural Method for a better Low-tech Field Assessment of Soil Structure under no-till

NASA Astrophysics Data System (ADS)

Roger-Estrade, Jean; Boizard, Hubert; Peigné, Josephine; Sasal, Maria Carolina; Guimaraes, Rachel; Piron, Denis; Tomis, Vincent; Vian, Jean-François; Cadoux, Stephane; Ralisch, Ricardo; Filho, Tavares; Heddadj, Djilali; de Battista, Juan; Duparque, Annie

2016-04-01

In France, agronomists have studied the effects of cropping systems on soil structure, using a field method based on a visual description of soil structure. The "profil cultural" method (Manichon and Gautronneau, 1987) has been designed to perform a field diagnostic of the effects of tillage and compaction on soil structure dynamics. This method is of great use to agronomists improving crop management for a better preservation of soil structure. However, this method was developed and mainly used in conventional tillage systems, with ploughing. As several forms of reduced, minimum and no tillage systems are expanding in many parts of the world, it is necessary to re-evaluate the ability of this method to describe and interpret soil macrostructure in unploughed situations. In unploughed fields, soil structure dynamics of untilled layers is mainly driven by compaction and regeneration by natural agents (climatic conditions, root growth and macrofauna) and it is of major importance to evaluate the importance of these natural processes on soil structure regeneration. These concerns have led us to adapt the standard method and to propose amendments based on a series of field observations and experimental work in different situations of cropping systems, soil types and climatic conditions. We improved the description of crack type and we introduced an index of biological activity, based on the visual examination of clods. To test the improved method, a comparison with the reference method was carried out and the ability of the "profil cultural" method to make a diagnosis was tested on five experiments in France, Brazil and Argentina. Using the improved method, the impact of cropping systems on soil functioning was better assessed when natural processes were integrated into the description.

Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations

PubMed Central

Martins, Guilherme; Lauga, Béatrice; Miot-Sertier, Cécile; Mercier, Anne; Lonvaud, Aline; Soulas, Marie-Louise; Soulas, Guy; Masneuf-Pomarède, Isabelle

2013-01-01

Despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. In this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. Analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. The highest bacteria population counts and the greatest diversity of genera were found in soil samples, followed by bark, grapes and leaves. The identification of isolates revealed that some genera – Pseudomonas, Curtobacterium, and Bacillus – were present in all ecosystems, but in different amounts, while others were ecosystem-specific. About 50% of the genera were common to soil and bark, but absent from leaves and grapes. The opposite was also observed: grape and leaf samples presented 50% of genera in common that were absent from trunk and soil. The bacterial community structure analyzed by T-RFLP indicated similarities between the profiles of leaves and grapes, on the one hand, and bark and soil, on the other, reflecting the number of shared T-RFs. The results suggest an interaction between telluric bacterial communities and the epiphytic bacteria present on the different grapevine parts. PMID:24023666

Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency.

PubMed

Cho, Hyunjun; Kim, Mincheol; Tripathi, Binu; Adams, Jonathan

2017-07-01

Although disturbance is thought to be important in many ecological processes, responses of fungal communities to soil disturbance have been little studied experimentally. We subjected a soil microcosm to physical disturbance, at a range of frequencies designed to simulate ecological disturbance events. We analyzed the fungal community structure using Illumina HiSeq sequencing of the ITS1 region. Fungal diversity was found to decline with the increasing disturbance frequencies, with no sign of the "humpback" pattern found in many studies of larger sedentary organisms. There is thus no evidence of an effect of release from competition resulting from moderate disturbance-which suggests that competition and niche overlap may not be important in limiting soil fungal diversity. Changing disturbance frequency also led to consistent differences in community composition. There were clear differences in OTU-level composition, with different disturbance treatments each having distinct fungal communities. The functional profile of fungal groups (guilds) was changed by the level of disturbance frequency. These predictable differences in community composition suggest that soil fungi can possess different niches in relation to disturbance frequency, or time since last disturbance. Fungi appear to be most abundant relative to bacteria at intermediate disturbance frequencies, on the time scale we studied here.

Impact of roots, mycorrhizas and earthworms on soil physical properties as assessed by shrinkage analysis

NASA Astrophysics Data System (ADS)

Milleret, R.; Le Bayon, R.-C.; Lamy, F.; Gobat, J.-M.; Boivin, P.

2009-07-01

SummarySoil biota such as earthworms, arbuscular mycorrhizal fungi (AMF) and plant roots are known to play a major role in engineering the belowground part of the terrestrial ecosystems, thus strongly influencing the water budget and quality on earth. However, the effect of soil organisms and their interactions on the numerous soil physical properties to be considered are still poorly understood. Shrinkage analysis allows quantifying a large spectrum of soil properties in a single experiment, with small standard errors. The objectives of the present study were, therefore, to assess the ability of the method to quantify changes in soil properties as induced by single or combined effects of leek roots ( Allium porrum), AMF ( Glomus intraradices) and earthworms ( Allolobophora chlorotica). The study was performed on homogenised soil microcosms and the experiments lasted 35 weeks. The volume of the root network and the external fungal hyphae was measured at the end, and undisturbed soil cores were collected. Shrinkage analysis allowed calculating the changes in soil hydro-structural stability, soil plasma and structural pore volumes, soil bulk density and plant available water, and structural pore size distributions. Data analysis revealed different impacts of the experimented soil biota on the soil physical properties. At any water content, the presence of A. chlorotica resulted in a decrease of the specific bulk volume and the hydro-structural stability around 25%, and in a significant increase in the bulk soil density. These changes went with a decrease of the structural pore volumes at any pore size, a disappearing of the thinnest structural pores, a decrease in plant available water, and a hardening of the plasma. On the contrary, leek roots decreased the bulk soil density up to 1.23 g cm -3 despite an initial bulk density of 1.15 g cm -3. This increase in volume was accompanied with a enhanced hydro-structural stability, a larger structural pore volume at any pore size, smaller structural pore radii and an increase in plant available water. Interestingly, a synergistic effect of leek roots and AMF in the absence of the earthworms was highlighted, and this synergistic effect was not observed in presence of earthworms. The structural pore volume generated by root and AMF growth was several orders of magnitude larger than the volume of the organisms. Root exudates as well as other AMF secretion have served as carbon source for bacteria that in turn would enhance soil aggregation and porosity, thus supporting the idea of a self-organization of the soil-plant-microbe complex previously described.

Visualization of physico-chemical properties and microbial distribution in soil and root microenvironments

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2016-04-01

Plant root development is influenced by soil properties and environmental factors. In turn plant roots can also change the physico-chemical conditions in soil resulting in gradients between roots and the root-free bulk soil. By releasing a variety of substances roots facilitate microbial activities in their direct vicinity, the rhizosphere. The related microorganisms are relevant for various ecosystem functions in the root-soil interface such as nutrient cycling. It is therefore important to study the impact and dynamics of microorganisms associated to different compartments in root-soil interfaces on a biologically meaningful micro-scale. The analysis of microorganisms in their habitats requires microscopic observations of the respective microenvironment. This can be obtained by preserving the complex soil structure including the root system by resin impregnation resulting in high quality thin sections. The observation of such sections via fluorescence microscopy, SEM-EDS, and Nano-SIMS will be highlighted in this presentation. In addition, we will discuss the combination of this methodological approach with other imaging techniques such as planar optodes or non-invasive 3D X-ray CT to reveal the entire spatial structure and arrangement of soil particles and roots. When combining the preservation of soil structure via resin impregnation with 16S rRNA targeted fluorescence in situ hybridization (FISH) single microbial cells can be visualized, localized, and quantified in the undisturbed soil matrix including the root-soil interfaces. The simultaneous use of multiple oligonucleotide probes thereby provides information on the spatial distribution of microorganisms belonging to different phylogenetic groups. Results will be shown for paddy soils, where management induced physico-chemical dynamics (flooding and drying) as well as resulting microbial dynamics were visualized via correlative microscopy in resin impregnated samples.

Spatial structure of soil properties at different scales of Mt. Kilimanjaro, Tanzania

NASA Astrophysics Data System (ADS)

Kühnel, Anna; Huwe, Bernd

2013-04-01

Soils of tropical mountain ecosystems provide important ecosystem services like water and carbon storage, water filtration and erosion control. As these ecosystems are threatened by global warming and the conversion of natural to human-modified landscapes, it is important to understand the implications of these changes. Within the DFG Research Unit "Kilimanjaro ecosystems under global change: Linking biodiversity, biotic interactions and biogeochemical ecosystem processes", we study the spatial heterogeneity of soils and the available water capacity for different land use systems. In the savannah zone of Mt. Kilimanjaro, maize fields are compared to natural savannah ecosystems. In the lower montane forest zone, coffee plantations, traditional home gardens, grasslands and natural forests are studied. We characterize the soils with respect to soil hydrology, emphasizing on the spatial variability of soil texture and bulk density at different scales. Furthermore soil organic carbon and nitrogen, cation exchange capacity and the pH-value are measured. Vis/Nir-Spectroscopy is used to detect small scale physical and chemical heterogeneity within soil profiles, as well as to get information of soil properties on a larger scale. We aim to build a spectral database for these soil properties for the Kilimanjaro region in order to get rapid information for geostatistical analysis. Partial least square regression with leave one out cross validation is used for model calibration. Results for silt and clay content, as well as carbon and nitrogen content are promising, with adjusted R² ranging from 0.70 for silt to 0.86 for nitrogen. Furthermore models for other nutrients, cation exchange capacity and available water capacity will be calibrated. We compare heterogeneity within and across the different ecosystems and state that spatial structure characteristics and complexity patterns in soil parameters can be quantitatively related to biodiversity and functional diversity parameters.

The Laboratory Study of Shear Strength of the Overconsolidated and Quasi - Overconsolidated Fine - Grained Soil

NASA Astrophysics Data System (ADS)

Strozyk, Joanna

2017-12-01

The paper presents results of laboratory shear strength test conducted on fine-grained soil samples with different grain size distribution and with different geological age and stress history. The Triaxial Isotopic Consolidation Undrained Tests (TXCIU) were performed under different consolidation stress in normal and overconsolidadion stress state on the samples with natural structure. Soil samples were selected from soil series of different age and geological origins: overconsolidated sensu stricto Miopliocene silty clay (siCl) and quasi overconsolidated Pleistocene clayey silt (clSi). Paper pointed out that overconsolidated sensu stricto and quasi overconsolidated fine-grained soil in same stress and environmental condition could show almost similar behaviour, and in other condition could behave significantly different. The correct evaluation of geotechnical parameters, the possibility of predicting their time-correct ability is only possible with appropriately recognized geological past and past processes that accompanied the soil formation.

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

PubMed

Lan, Mu-ling; Gao, Ming

2015-11-01

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

Microbial mediated soil structure formation under wetting and drying cycles along a climate gradient (arid to humid) on hillslopes in Chile

NASA Astrophysics Data System (ADS)

Bernhard, Nadine; Moskwa, Lisa-Marie; Kühn, Peter; Mueller, Carsten W.; Wagner, Dirk; Scholten, Thomas

2017-04-01

It is well-known that the land surface resistance against erosion is largely controlled by the structure stability of the soil given by its inherent properties. Microbial activity plays a vital role in soil structure development, and thus affecting soil physical parameters. Accordingly the influence of biota shaping the earth's surface has been described through mechanisms such as mineral weathering, formation of ions and biofilms controlling land surface resistance against erosion. However the role of microorganisms for the development of soil stabilizing properties is still unclear and a precise quantitative understanding of the mechanisms under different climate conditions is widely missing. The objectives of our study are to examine to which extend microbiological processes control soil structure formation and stability and whether this is influenced by climate and topographic position. Soil samples were taken along a climate gradient and from different topographic positions of hillslopes in the Chilean Coastal Cordillera in austral autumn 2016. The variables of lithology, human disturbances and relief were held as far as possible constant whereas climate varies along the transect. We implemented 10 wet-dry cycles on air dried and sieved natural and sterile samples to enhance particle aggregation and increase structure stability. Throughout the entire experiment temperature is held constant at 20 °C to avoid changes in microbial activity. Samples are moistened and dried and each kept at the same respective pF-values for the same duration to add the same stress to each sample. Aggregate stability will be measured using wet sieving, ultrasonic dispersion and simulated rainfall. The results will be compared with on-site rainfall simulation experiments on hillslopes in the Chilean Coastal Cordillera to link laboratory results with natural field conditions. The experiment gives first insight into the aggregate formation process over time with and without microorganisms (sterilized samples). Furthermore it allows to qualify and quantify the contribution of biota to soil structure formation and stability.

[Effect of the soil contamination with a potato cyst-forming nematode on the community structure of soil-inhabiting nematodes].

PubMed

Gruzdeva, L I; Suzhchuk, A A

2008-01-01

Nematode community structure of the potato fields with different infection levels of potato cyst-forming nematode (PCN) such as 10, 30 and 214 cysts per 100 g of soil has been investigated. The influence of specialized parasite on nematode fauna and dominance character of different ecological-trophic groups were described. Parasitic nematode genera in natural meadow biocenosis and agrocenoses without PCN are Paratylenchus, Tylenchorhynchus, and Helicotylenchus. It is established, that Paratylenchus nanus was the prevalent species among plant parasites at low infection level. Larvae of Globodera prevailed in the soil with middle and high infection levels and substituted individuals of other genera of parasitic nematodes. The fact of increase in number of hyphal-feeding nematode Aphelenchus avenae was revealed.

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH.

PubMed

Kuramae, Eiko; Gamper, Hannes; van Veen, Johannes; Kowalchuk, George

2011-08-01

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Plant rhizosphere species-specific stoichiometry and regulation of extracellular enzyme and microbial community structure

NASA Astrophysics Data System (ADS)

Bell, C. W.; Calderon, F.; Pendall, E.; Wallenstein, M. D.

2012-12-01

Plant communities affect the activity and composition of soil microbial communities through alteration of the soil environment during root growth; substrate availability through root exudation; nutrient availability through plant uptake; and moisture regimes through transpiration. As a result, positive feedbacks in soil properties can result from alterations in microbial community composition and function in the rhizosphere zone. At the ecosystem-scale, many properties of soil microbial communities can vary between forest stands dominated by different species, including community composition and stoichiometry. However, the influence of smaller individual plants on grassland soils and microbial communities is less well documented. There is evidence to suggest that some plants can modify their soil environment in a manner that favors their persistence. For example, when Bromus tectorum plants invade, soil microbial communities tend to have higher N mineralization rates (in the rhizosphere zone) relative to native plants. If tight linkages between individual plant species and microbial communities inhabiting the rhizosphere exist, we hypothesized that any differences among plant species specific rhizosphere zones could be observed by shifts in: 1) soil -rhizosphere microbial community structure, 2) enzymatic C:N:P acquisition activities, 3) alterations in the soil C chemistry composition in the rhizosphere, and 4) plant - soil - microbial C:N:P elemental stoichiometry. We selected and grew 4 different C3 grasses species including three species native to the Shortgrass Steppe region (Pascopyrum smithii, Koeleria macrantha, and Vulpia octoflora) and one exotic invasive plant species (B. tectorum) in root-boxes that are designed to allow for easy access to the rhizosphere. The field soil was homogenized using a 4mm sieve and mixed 1:1 with sterile sand and seeded as monocultures (24 replicate root - boxes for each species). Plant and soil samples (along with no - plant control soil samples) were collected on day 28, 78, and 148 (N = 4 /sample period/species). Microbial community structure was quantified using the barcoded pyrosequencing protocols. We measured the potential activity of seven hydrolytic soil enzymes to represent the degradation of C, N, and P-rich substrates. Soil microbial C:N biomass responses to specific plant rhizospheres (MBC and MBN) were measured using the chloroform fumigation extraction method followed by DOC & N analysis. Fourier Transform Infrared Spectroscopy was used to assess differences in plant and soil C chemistry. We found that species specific rhizospheres are characteristic of very different soil chemical, edaphic, and microbial properties. These plant species act as gateways that introduce variability into soil C, N, and P ecosystem functional dynamics directly facilitated by rhizosphere - microbe associations. Our results suggest that nutrient stoichiometry within plant species' rhizospheres is a useful tool for identifying intra-ecosystem functional patterns. By identifying what and how specific species rhizospheres differ among the overall plant community, we can better predict how below-ground microbial community function and subsequent ecosystem processes can be influenced by alterations in plant community shifts based on the rhizosphere effects.

Uncovering trophic positions and food resources of soil animals using bulk natural stable isotope composition.

PubMed

Potapov, Anton M; Tiunov, Alexei V; Scheu, Stefan

2018-06-19

Despite the major importance of soil biota in nutrient and energy fluxes, interactions in soil food webs are poorly understood. Here we provide an overview of recent advances in uncovering the trophic structure of soil food webs using natural variations in stable isotope ratios. We discuss approaches of application, normalization and interpretation of stable isotope ratios along with methodological pitfalls. Analysis of published data from temperate forest ecosystems is used to outline emerging concepts and perspectives in soil food web research. In contrast to aboveground and aquatic food webs, trophic fractionation at the basal level of detrital food webs is large for carbon and small for nitrogen stable isotopes. Virtually all soil animals are enriched in 13 C as compared to plant litter. This 'detrital shift' likely reflects preferential uptake of 13 C-enriched microbial biomass and underlines the importance of microorganisms, in contrast to dead plant material, as a major food resource for the soil animal community. Soil organic matter is enriched in 15 N and 13 C relative to leaf litter. Decomposers inhabiting mineral soil layers therefore might be enriched in 15 N resulting in overlap in isotope ratios between soil-dwelling detritivores and litter-dwelling predators. By contrast, 13 C content varies little between detritivores in upper litter and in mineral soil, suggesting that they rely on similar basal resources, i.e. little decomposed organic matter. Comparing vertical isotope gradients in animals and in basal resources can be a valuable tool to assess trophic interactions and dynamics of organic matter in soil. As indicated by stable isotope composition, direct feeding on living plant material as well as on mycorrhizal fungi is likely rare among soil invertebrates. Plant carbon is taken up predominantly by saprotrophic microorganisms and channelled to higher trophic levels of the soil food web. However, feeding on photoautotrophic microorganisms and non-vascular plants may play an important role in fuelling soil food webs. The trophic niche of most high-rank animal taxa spans at least two trophic levels, implying the use of a wide range of resources. Therefore, to identify trophic species and links in food webs, low-rank taxonomic identification is required. Despite overlap in feeding strategies, stable isotope composition of the high-rank taxonomic groups reflects differences in trophic level and in the use of basal resources. Different taxonomic groups of predators and decomposers are likely linked to different pools of organic matter in soil, suggesting different functional roles and indicating that trophic niches in soil animal communities are phylogenetically structured. During last two decades studies using stable isotope analysis have elucidated the trophic structure of soil communities, clarified basal food resources of the soil food web and revealed links between above- and belowground ecosystem compartments. Extending the use of stable isotope analysis to a wider range of soil-dwelling organisms, including microfauna, and a larger array of ecosystems provides the perspective of a comprehensive understanding of the structure and functioning of soil food webs. © 2018 Cambridge Philosophical Society.

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

PubMed

Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

2016-02-01

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Static sampling of dynamic processes - a paradox?

NASA Astrophysics Data System (ADS)

Mälicke, Mirko; Neuper, Malte; Jackisch, Conrad; Hassler, Sibylle; Zehe, Erwin

2017-04-01

Environmental systems monitoring aims at its core at the detection of spatio-temporal patterns of processes and system states, which is a pre-requisite for understanding and explaining their baffling heterogeneity. Most observation networks rely on distributed point sampling of states and fluxes of interest, which is combined with proxy-variables from either remote sensing or near surface geophysics. The cardinal question on the appropriate experimental design of such a monitoring network has up to now been answered in many different ways. Suggested approaches range from sampling in a dense regular grid using for the so-called green machine, transects along typical catenas, clustering of several observations sensors in presumed functional units or HRUs, arrangements of those cluster along presumed lateral flow paths to last not least a nested, randomized stratified arrangement of sensors or samples. Common to all these approaches is that they provide a rather static spatial sampling, while state variables and their spatial covariance structure dynamically change in time. It is hence of key interest how much of our still incomplete understanding stems from inappropriate sampling and how much needs to be attributed to an inappropriate analysis of spatial data sets. We suggest that it is much more promising to analyze the spatial variability of processes, for instance changes in soil moisture values, than to investigate the spatial variability of soil moisture states themselves. This is because wetting of the soil, reflected in a soil moisture increase, is causes by a totally different meteorological driver - rainfall - than drying of the soil. We hence propose that the rising and the falling limbs of soil moisture time series belong essentially to different ensembles, as they are influenced by different drivers. Positive and negative temporal changes in soil moisture need, hence, to be analyzed separately. We test this idea using the CAOS data set as a benchmark. Specifically, we expect the covariance structure of the positive temporal changes of soil moisture to be dominated by the spatial structure of rain- and through-fall and saturated hydraulic conductivity. The covariance in temporarily decreasing soil moisture during radiation driven conditions is expect to be dominated by the spatial structure of retention properties and plant transpiration. An analysis of soil moisture changes has furthermore the advantage that those are free from systematic measurement errors.

Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains.

PubMed

Yang, Guang Li; Hou, Shu Gui; Le Baoge, Ri; Li, Zhi Guo; Xu, Hao; Liu, Ya Ping; Du, Wen Tao; Liu, Yong Qin

2016-11-04

A detailed understanding of microbial ecology in different supraglacial habitats is important due to the unprecedented speed of glacier retreat. Differences in bacterial diversity and community structure between glacial snow and glacial soil on the Chongce Ice Cap were assessed using 454 pyrosequencing. Based on rarefaction curves, Chao1, ACE, and Shannon indices, we found that bacterial diversity in glacial snow was lower than that in glacial soil. Principal coordinate analysis (PCoA) and heatmap analysis indicated that there were major differences in bacterial communities between glacial snow and glacial soil. Most bacteria were different between the two habitats; however, there were some common bacteria shared between glacial snow and glacial soil. Some rare or functional bacterial resources were also present in the Chongce Ice Cap. These findings provide a preliminary understanding of the shifts in bacterial diversity and communities from glacial snow to glacial soil after the melting and inflow of glacial snow into glacial soil.

Assessing the variation in bund structure design and its impact on soil physical properties and hydrology in Koga catchment, Highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Lakew, Walle; Baartman, Jantiene; Fleskens, Luuk; Selassie, Yihenew; Ritsema, Coen

2017-04-01

Prolonged soil drying and severe moisture stress during the dry season, and soil saturation and erosion during the short rainy season are critical problems in the Ethiopian highlands. Large-scale implementation of bund structures has been used as soil and water management (SWM) strategy to fight these problems and establish a sustainable land management (SLM) system. However, many SWM practices are implemented with design flaws or without proper design and maintenance, and do not match conservation requirements. The quality of implementation and effects of bund structures on soil physical properties is not yet documented. Therefore, in this study, field investigations and laboratory analysis were carried out to evaluate the variation in bund structure design and its impact on soil-water retention, bulk density, porosity and soil depth. Results show that the dimensions and stability of bund structures, and consequently, the impacts of bunds varied widely. The widths and heights of bunds, and slope gradients were significantly correlated with infiltration rate and available soil-water content. Water holding capacity was 24% higher compared to that on untreated farms. Bunds with larger dimensions of top width (>85 cm) and height (>75 cm) showed 17 and 18% higher water holding capacity compared to fields with bunds having lower dimensions. In addition, results exhibited that the porosity and soil depth were significantly affected by the dimensions of bund structures and increased with increasing widths and heights of bunds. A 14.2% increase in porosity; a 41.2% increase in infiltration rate; and a 17.5% decrease in bulk density was found in soils of treated farms compared to those of untreated farm plots. Differences in particle size distribution and soil erodibility among widths of the bunds were low. It can be concluded that bund structure design varied substantially throughout the study area, which had impacted soil-water storage and soil physical properties. Bund structure design should be adapted to local biophysical settings at catchment level to enhance on- and offsite impacts.

Effect of rice husk biochar application to soil insect diversity on potato cultivation

NASA Astrophysics Data System (ADS)

Meilin, A.; Rubiana, R.

2018-02-01

High intensity of disease infection and the intensive use of fertilizers and pesticidescause saturated fertilizer and pesticide to the land. Remediation using biochar rice husk is one of the technology to decrease fertilizer and pesticide residue. The diversity of soil insects can be used as bioindicators because of their existence dependsg on soil structure and condition. This study was aimed to study the diversity and structure communities of soil insect in potatoes on difference husk rice biochar application. The sampling of soil insects was done on potato farmer’s land with four treatments i.e control (farmers’ technique), trichokompos without biochar, trichokompos + biochar with dose 1 ton/ha, and trichokompos + biochar with dose 2 ton / ha. At each point a single pitfall trap was installed for two nights and then it was taken for identification. The results showed that biochar application had significant effect on the number of soil insect species (P = 0.037). The soil insect species composition pattern also showed significant differences between the four treatments (R: 0.2306, Pvalue = 0.001). This mean that the application of biochar affects the number of insects species and plays a role in the formation of soil insect diversity beta patterns.

X-ray microtomography analysis of soil structure deformation caused by centrifugation

NASA Astrophysics Data System (ADS)

Schlüter, Steffen; Leuther, Frederic; Vogler, Steffen; Vogel, Hans-Jörg

2016-04-01

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of <-100kPa, macroporosity decreases again because of structure deformation due to compression. While volume changes due to swelling clay minerals are immanent to any drying process, the compaction of soil is a specific drawback of the centrifugation method. A new protocol for digital volume correlation was developed to analyze the spatial heterogeneity of deformation. In both samples the displacement of soil constituents is highest in the top part of the sample and exhibits high lateral variability explained by the spatial distribution of macropores in the sample. Centrifugation should therefore only be applied after the completion of all other hydraulic or thermal experiments, or any other analysis that depends on the integrity of soil structure.

X-ray microtomography analysis of soil structure deformation caused by centrifugation

NASA Astrophysics Data System (ADS)

Schlüter, S.; Leuther, F.; Vogler, S.; Vogel, H.-J.

2016-01-01

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of ψ < -100 kPa, macroporosity decreases again because of structure deformation due to compression. While volume changes due to swelling clay minerals are immanent in any drying process, the compaction of soil is a specific drawback of the centrifugation method. A new protocol for digital volume correlation was developed to analyze the spatial heterogeneity of deformation. In both samples the displacement of soil constituents is highest in the top part of the sample and exhibits high lateral variability explained by the spatial distribution of macropores in the sample. Centrifugation should therefore only be applied after the completion of all other hydraulic or thermal experiments, or any other analysis that depends on the integrity of soil structure.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

PubMed

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2015-03-20

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

Clay:organic-carbon and organic carbon as determinants of the soil physical properties: reassessment of the Complexed Organic Carbon concept

NASA Astrophysics Data System (ADS)

Matter, Adrien; Johannes, Alice; Boivin, Pascal

2016-04-01

Soil Organic Carbon (SOC) is well known to largely determine the soil physical properties and fertility. Total porosity, structural porosity, aeration, structural stability among others are reported to increase linearly with increasing SOC in most studies. Is there an optimal SOC content as target in soil management, or is there no limit in physical fertility improvement with SOC? Dexter et al. (2008) investigated the relation between clay:SOC ratio and the physical properties of soils from different databases. They observed that the R2 of the relation between SOC and the physical properties were maximized when considering the SOC fraction limited to a clay:SOC ratio of 10. They concluded that this fraction of the SOC was complexed, and that the additional SOC was not influencing the physical properties as strongly as the complexed one. In this study, we reassessed this approach, on a database of 180 undisturbed soil samples collected from cambiluvisols of the Swiss Plateau, on an area of 2400 km2, and from different soil uses. The physical properties were obtained with Shrinkage Analysis, which involved the parameters used in Dexter et al., 2008. We used the same method, but detected biases in the statistical approach, which was, therefore, adapted. We showed that the relation between the bulk density and SOC was changing with the score of visual evaluation of the structure (VESS) (Ball et al., 2007). Therefore, we also worked only on the "good" structures according to VESS. All shrinkage parameters were linearly correlated to SOC regardless of the clay:SOC ratio, with R2 ranging from 0.45 to 0.8. Contrarily to Dexter et al. (2008), we did not observed an optimum in the R2 of the relation when considering a SOC fraction based on the clay:SOC ratio. R2 was increasing until a Clay:SOC of about 7, where it reached, and kept, its maximum value. The land use factor was not significant. The major difference with the former study is that we worked on the same soil group, on a large range of texture, with less sandy soils and accounting for structural state. Our results show that, on this soil group, any SOC increase almost linearly increases the physical properties and, therefore, the physical fertility and the ecological functions of the soil, regardless of the clay:SOC ratio. When considering the whole SOC instead of a fraction, we show that the 10 clay:SOC ratio, however corresponds to a good structure according to VESS and optimal physical values. Therefore, we think reaching a clay:SOC ratio of 10 must be considered as an objective for farmers and advisers. Ball, B.C., T. Batey, and L.J. Munkholm. 2007. Field assessment of soil structural quality - a development of the Peerlkamp test. Soil Use Manag. 23(4): 329-337. Dexter, A.R., G. Richard, D. Arrouays, E.A. Czyz, C. Jolivet, and O. Duval. 2008. Complexed organic matter controls soil physical properties. Geoderma 144(3-4): 620-627.

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

PubMed

Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

2010-08-01

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Current advancements and challenges in soil-root interactions modelling

NASA Astrophysics Data System (ADS)

Schnepf, Andrea; Huber, Katrin; Abesha, Betiglu; Meunier, Felicien; Leitner, Daniel; Roose, Tiina; Javaux, Mathieu; Vanderborght, Jan; Vereecken, Harry

2015-04-01

Roots change their surrounding soil chemically, physically and biologically. This includes changes in soil moisture and solute concentration, the exudation of organic substances into the rhizosphere, increased growth of soil microorganisms, or changes in soil structure. The fate of water and solutes in the root zone is highly determined by these root-soil interactions. Mathematical models of soil-root systems in combination with non-invasive techniques able to characterize root systems are a promising tool to understand and predict the behaviour of water and solutes in the root zone. With respect to different fields of applications, predictive mathematical models can contribute to the solution of optimal control problems in plant recourse efficiency. This may result in significant gains in productivity, efficiency and environmental sustainability in various land use activities. Major challenges include the coupling of model parameters of the relevant processes with the surrounding environment such as temperature, nutrient concentration or soil water content. A further challenge is the mathematical description of the different spatial and temporal scales involved. This includes in particular the branched structures formed by root systems or the external mycelium of mycorrhizal fungi. Here, reducing complexity as well as bridging between spatial scales is required. Furthermore, the combination of experimental and mathematical techniques may advance the field enormously. Here, the use of root system, soil and rhizosphere models is presented through a number of modelling case studies, including image based modelling of phosphate uptake by a root with hairs, model-based optimization of root architecture for phosphate uptake from soil, upscaling of rhizosphere models, modelling root growth in structured soil, and the effect of root hydraulic architecture on plant water uptake efficiency and drought resistance.

Current Advancements and Challenges in Soil-Root Interactions Modelling

NASA Astrophysics Data System (ADS)

Schnepf, A.; Huber, K.; Abesha, B.; Meunier, F.; Leitner, D.; Roose, T.; Javaux, M.; Vanderborght, J.; Vereecken, H.

2014-12-01

Roots change their surrounding soil chemically, physically and biologically. This includes changes in soil moisture and solute concentration, the exudation of organic substances into the rhizosphere, increased growth of soil microorganisms, or changes in soil structure. The fate of water and solutes in the root zone is highly determined by these root-soil interactions. Mathematical models of soil-root systems in combination with non-invasive techniques able to characterize root systems are a promising tool to understand and predict the behaviour of water and solutes in the root zone. With respect to different fields of applications, predictive mathematical models can contribute to the solution of optimal control problems in plant recourse efficiency. This may result in significant gains in productivity, efficiency and environmental sustainability in various land use activities. Major challenges include the coupling of model parameters of the relevant processes with the surrounding environment such as temperature, nutrient concentration or soil water content. A further challenge is the mathematical description of the different spatial and temporal scales involved. This includes in particular the branched structures formed by root systems or the external mycelium of mycorrhizal fungi. Here, reducing complexity as well as bridging between spatial scales is required. Furthermore, the combination of experimental and mathematical techniques may advance the field enormously. Here, the use of root system, soil and rhizosphere models is presented through a number of modelling case studies, including image based modelling of phosphate uptake by a root with hairs, model-based optimization of root architecture for phosphate uptake from soil, upscaling of rhizosphere models, modelling root growth in structured soil, and the effect of root hydraulic architecture on plant water uptake efficiency and drought resistance.

Simazine biodegradation and community structures of ammonia-oxidizing microorganisms in bioaugmented soil: impact of ammonia and nitrate nitrogen sources.

PubMed

Wan, Rui; Yang, Yuyin; Sun, Weimin; Wang, Zhao; Xie, Shuguang

2014-02-01

The objective of the present study was to investigate the impact of ammonia and nitrate nitrogen sources on simazine biodegradation by Arthrobacter sp. strain SD1 and the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in non-agricultural soil. Soil microcosms with different treatments were constructed for herbicide biodegradation test. The relative abundance of the strain SD1 and the structures of AOA and AOB communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. The co-existence of two inorganic nitrogen sources (ammonia and nitrate) had certain impact on simazine dissipation by the strain SD1. Bioaugmentation could induce a shift in the community structures of both AOA and AOB, but AOA were more responsive. Nitrogen application had significant impacts on AOA and AOB communities in bioaugmented soils. Moreover, in non-bioaugmented soil, the community structure of AOA, instead of AOB, could be quickly recovered after herbicide application. This study could add some new insights towards the impacts of nitrogen sources on s-triazine bioremediation and ammonia-oxidizing microorganisms in soil ecosystem.

[Effect of pine plantations on soil arthropods in a high Andean forest].

PubMed

León-Gamboa, Alba Lucía; Ramos, Carolina; García, Mary Ruth

2010-09-01

One of the most common problems in the Colombian mountains has been the replacement of native vegetation by pine plantations. Soil arthropods are a fundamental component of forest ecosystem, since they participate in the organic matter fragmentation, previous to decomposition. This role is more valuable in high altitude environments, where low temperatures limit the dynamics of biological processes, where the effects of pine plantations on soil arthropods are still not well-known. In a remnant of high-andean forest (Neusa - Colombia) and a pine plantation of about 50 years-old, it was evaluated the composition, richness and abundance of arthropods at surface (S), organic horizon (O) and mineral horizon (A) of soil, to establish the differences associated to the soil use transformation. It was used "Pitfall" sampling to register the movement of the epigeous fauna, and extraction by funnel Berlese for determining the fauna density from O and A horizons. The Shannon and Simpson indexes estimated the diversity at different places and horizons, and the trophic structure of the community was evaluated. Overall, there were collected 38 306 individuals from forest and 17 386 individuals from pine plantation, mainly distributed in Collembola (42.4%), Acari (27%), Diptera (17.6%) and Coleoptera (4.6%). The most important differences were given in the surface, where the mobilization in forest (86 individuals/day) almost triplicates the one in pine plantation (33 individuals/day). The differences in composition were given in Collembola, Araneae, Hemiptera, Homoptera and Hymenoptera. The dynamics of richness and abundance along the year had significant high values in the native forest than in the pine plantation. The general trophic structure was dominated by saprophagous (75%), followed by predators (14%) and phytophagous (9%), but in two layers of the pine plantation soil (S and O) this structural pattern was not given. Based on the results, it was concluded that pine plantations affect the diversity, composition, community dynamic and trophic structure of soil arthropods. Also, some estimators of soil stability give signals that these effects are reducing the ecosystem function in the region.

Bioindication in Urban Soils in Switzerland

NASA Astrophysics Data System (ADS)

Amossé, J.; Le Bayon, C.; Mitchell, E. A. D.; Gobat, J. M.

2012-04-01

Urban development leads to profound changes in ecosystem structure (e.g. biodiversity) and functioning (e.g. ecosystem services). While above-ground diversity is reasonably well studied much less is known about soil diversity, soil processes and more generally soil health in urban settings. Soil invertebrates are key actors of soil processes at different spatial and temporal scales and provide essential ecosystem services. These functions may be even more vital in stressed environments such as urban ecosystems. Despite the general recognition of the importance of soil organisms in ecosystems, soil trophic food webs are still poorly known and this is especially the case in urban settings. As urban soils are characterised by high fragmentation and stress (e.g. drought, pollution) the structure and functioning of soil communities is likely to be markedly different from that of natural soils. It is for example unclear if earthworms, whose roles in organic matter transformation and soil structuration is well documented in natural and semi-natural soils, are also widespread and active in urban soils. Bioindication is a powerful tool to assess the quality of the environment. It is complementary to classical physicochemical soil analysis or can be used as sole diagnostic tool in cases where these analyses cannot be performed. However little is known about the potential use of bioindicators in urban settings and especially it is unclear if methods developped in agriculture can be applied to urban soils. The development of reliable methods for assessing the quality of urban soils has been identified as a priority for policy making and urban management in Switzerland, a high-urbanized country. We therefore initiated a research project (Bioindication in Urban Soil - BUS). The project is organised around four parts: (i) typology of urban soils in a study Region (Neuchâtel), (ii) sampling of soil fauna and analysis of soil physicochemical properties, (iii) comparison of the functionality of urban soils and alluvial soils, used as a natural reference because of their regular physical perturbation by flooding and associated erosion/sedimentation, (iv) evaluation of soil bioindicators (e.g. earthworm, enchytraeid and testate amoebae) for urban soils. The application objective of my research is to introduce bioindicators and their limit values for the future revision of the legal Ordonnance on soils (OSol), and to develop guidelines to improve or to build urban soils with the aim of reaching a sustainable urban ecosystem development.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.

PubMed

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-07-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

PubMed Central

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-01-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant ‘seed bank'. PMID:25535940

Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils.

PubMed

Dai, Yu; Wu, Zhen; Zhou, Qiheng; Zhao, Qun; Li, Ningning; Xie, Shuguang; Liu, Yong

2015-10-01

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

[Diversity and community structure of soil ammonia-oxidizing bacteria in Hulunbeier Grassland, Inner Mongolia].

PubMed

Wendu, Ri-le; Li, Gang; Yang, Dian-lin; Zhang, Jing-ni; Yi, Jin

2011-04-01

By the methods of polymerase chain reaction-denaturing gradient gel electrophoresis and sequence analysis, a comparative study was conducted on the diversity and community structure of soil ammonia-oxidizing bacteria in the Filifolium sibiricum steppe, Stipa baicalensis steppe, Leymus chinensis steppe, Stipa grandis steppe, and Stipa kryrowi steppe in Hulunbeier Grassland, Inner Mongolia. A significant difference was observed in the community structure of soil ammonia-oxidizing bacteria among the five steppes, with the similarity lower than 50%. The diversity of soil ammonia-oxidizing bacteria was the highest in F. sibiricum steppe, followed by in S. baicalensis steppe, L. chinensis steppe, S. kryrowi steppe, and S. grandis steppe. In the five steppes, Nitrosospira cluster 3 was the dominant group, and the Nitrosospira cluster 1, 2, and 4 as well as Nitrosomonas were also found. The community structure of soil ammonia oxidizing bacteria in F. sibiricum steppe was most complex, while that in L. chinensis steppe and S. grandis steppe was relatively simple. Correlation analysis indicated that there existed significant positive correlations between the diversity of soil ammonia-oxidizing bacteria and the soil moisture, total nitrogen, total organic carbon, and C/N ratio (P<0.05).

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

PubMed

Mendes, Lucas William; Tsai, Siu Mui

2018-01-01

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

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

PubMed

Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

2015-09-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

How Redox Fluctuation Shapes Microbial Community Structure and Mineral-Organic Matter Relationships in a Humid Tropical Forest Soil

NASA Astrophysics Data System (ADS)

Campbell, A.; Bhattacharyya, A.; Lin, Y.; Tfaily, M. M.; Paša-Tolić, L.; Chu, R. K.; Silver, W. L.; Nico, P. S.; Pett-Ridge, J.

2016-12-01

Wet tropical soils can alternate frequently between fully oxygenated and anaerobic conditions, constraining both the metabolism of tropical soil microorganisms, and the mineral-organic matter relationships that regulate many aspects of soil C cycling. Tropical forests are predicted to experience a 2-5°C temperature increase and substantial differences in the amount and timing of rainfall in the coming half century. Yet we have a poor understanding of how soil microbial activity and C cycling in these systems will respond to changes in environmental variability caused by climate change. Using a 44 day redox manipulation and isotope tracing experiment with soils from the Luquillo Experimental Forest, Puerto Rico, we examined patterns of tropical soil microorganisms, metabolites and soil chemistry when soils were exposed to different redox regimes - static oxic, static anoxic, high frequency redox fluctuation (4 days oxic, 4 days anoxic), or low frequency redox fluctuation (8 days oxic, 4 days anoxic). Replicate microcosms were harvested throughout the incubation to understand how changes in redox oscillation frequency altered microbial community structure and activity, organic matter turnover and fate, and soil chemistry. While gross soil respiration was highest in static oxic soils, respiration derived from added litter was highest in static anoxic soils, suggesting that decomposition of preexisting SOM was limited by O2 availability in the anoxic treatment. Microbial communities responded to shifting O2 availability in the different treatments, resulting in significant differences in DOC concentration and molecular composition (measured by FTICR-MS). DOC and Fe2+ concentrations were positively correlated for all four redox treatments, and rapidly increased following oscillation from oxic to anoxic conditions. These results, along with parallel studies of biogeochemical responses (Fe speciation, pH, P availability), suggest a highly responsive microbial and geochemical system, where the frequency of low-redox events controls exchanges of C between mineral-sorbed and aqueous pools.

Future Carbon Dynamics of the Northern Rockies Ecoregion due to Climate Impacts and Fire Effects

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2016-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

Methane production potential and microbial community structure for different forest soils

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate.

PubMed

Niu, Jiaojiao; Chao, Jin; Xiao, Yunhua; Chen, Wu; Zhang, Chao; Liu, Xueduan; Rang, Zhongwen; Yin, Huaqun; Dai, Linjian

2017-01-01

Rotation is an effective strategy to control crop disease and improve plant health. However, the effects of crop rotation on soil bacterial community composition and structure, and crop health remain unclear. In this study, using 16S rRNA gene sequencing, we explored the soil bacterial communities under four different cropping systems, continuous tobacco cropping (control group), tobacco-maize rotation, tobacco-lily rotation, and tobacco-turnip rotation. Results of detrended correspondence analysis and dissimilarity tests showed that soil bacterial community composition and structure changed significantly among the four groups, such that Acidobacteria and Actinobacteria were more abundant in the maize rotation group (16.6 and 11.5%, respectively) than in the control (8.5 and 7.1%, respectively). Compared with the control group (57.78%), maize and lily were effective rotation crops in controlling tobacco bacterial wilt (about 23.54 and 48.67%). On the other hand, tobacco bacterial wilt rate was increased in the turnip rotation (59.62%) relative to the control. Further study revealed that the abundances of several bacterial populations were directly correlated with tobacco bacterial wilt. For example, Acidobacteria and Actinobacteria were significantly negatively correlated to the tobacco bacterial wilt rate, so they may be probiotic bacteria. Canonical correspondence analysis showed that soil pH and calcium content were key factors in determining soil bacterial communities. In conclusion, our study revealed the composition and structure of bacterial communities under four different cropping systems and may unveil molecular mechanisms for the interactions between soil microorganisms and crop health. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

PubMed

Cong, Jing; Liu, Xueduan; Lu, Hui; Xu, Han; Li, Yide; Deng, Ye; Li, Diqiang; Zhang, Yuguang

2015-08-20

Tropical rainforests cover over 50% of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure. Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

The population structure of Escherichia coli isolated from subtropical and temperate soils.

PubMed

Byappanahalli, Muruleedhara N; Yan, Tao; Hamilton, Matthew J; Ishii, Satoshi; Fujioka, Roger S; Whitman, Richard L; Sadowsky, Michael J

2012-02-15

While genotypically-distinct naturalized Escherichia coli strains have been shown to occur in riparian soils of Lake Michigan and Lake Superior watersheds, comparative analyses of E. coli populations in diverse soils across a range of geographic and climatic conditions have not been investigated. The main objectives of this study were to: (a) examine the population structure and genetic relatedness of E. coli isolates collected from different soil types on a tropical island (Hawaii), and (b) determine if E. coli populations from Hawaii and temperate soils (Indiana, Minnesota) shared similar genotypes that may be reflective of biome-related soil conditions. DNA fingerprint and multivariate statistical analyses were used to examine the population structure and genotypic characteristics of the E. coli isolates. About 33% (98 of 293) of the E. coli from different soil types and locations on the island of Oahu, Hawaii, had unique DNA fingerprints, indicating that these bacteria were relatively diverse; the Shannon diversity index for the population was 4.03. Nearly 60% (171 of 293) of the E. coli isolates from Hawaii clustered into two major groups and the rest, with two or more isolates, fell into one of 22 smaller groups, or individual lineages. Multivariate analysis of variance of 89, 21, and 106 unique E. coli DNA fingerprints for Hawaii, Indiana, and Minnesota soils, respectively, showed that isolates formed tight cohesive groups, clustering mainly by location. However, there were several instances of clonal isolates being shared between geographically different locations. Thus, while nearly identical E. coli strains were shared between disparate climatologically- and geographically-distinct locations, a vast majority of the soil E. coli strains were genotypically diverse and were likely derived from separate lineages. This supports the hypothesis that these bacteria are not unique and multiple genotypes can readily adapt to become part of the soil autochthonous microflora. Copyright © 2012 Elsevier B.V. All rights reserved.

The population structure of Escherichia coli isolated from subtropical and temperate soils

USGS Publications Warehouse

Byappanahalli, Muruleedhara N.; Yan, Tao; Hamilton, Matthew J.; Ishii, Satoshi; Fujioka, Roger S.; Whitman, Richard L.; Sadowsky, Michael J.

2012-01-01

While genotypically-distinct naturalized Escherichia coli strains have been shown to occur in riparian soils of Lake Michigan and Lake Superior watersheds, comparative analyses of E. coli populations in diverse soils across a range of geographic and climatic conditions have not been investigated. The main objectives of this study were to: (a) examine the population structure and genetic relatedness of E. coli isolates collected from different soil types on a tropical island (Hawaii), and (b) determine if E. coli populations from Hawaii and temperate soils (Indiana, Minnesota) shared similar genotypes that may be reflective of biome-related soil conditions. DNA fingerprint and multivariate statistical analyses were used to examine the population structure and genotypic characteristics of the E. coli isolates. About 33% (98 of 293) of the E. coli from different soil types and locations on the island of Oahu, Hawaii, had unique DNA fingerprints, indicating that these bacteria were relatively diverse; the Shannon diversity index for the population was 4.03. Nearly 60% (171 of 293) of the E. coli isolates from Hawaii clustered into two major groups and the rest, with two or more isolates, fell into one of 22 smaller groups, or individual lineages. Multivariate analysis of variance of 89, 21, and 106 unique E. coli DNA fingerprints for Hawaii, Indiana, and Minnesota soils, respectively, showed that isolates formed tight cohesive groups, clustering mainly by location. However, there were several instances of clonal isolates being shared between geographically different locations. Thus, while nearly identical E. coli strains were shared between disparate climatologically- and geographically-distinct locations, a vast majority of the soil E. coli strains were genotypically diverse and were likely derived from separate lineages. This supports the hypothesis that these bacteria are not unique and multiple genotypes can readily adapt to become part of the soil autochthonous microflora.

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil.

PubMed

Deng, Linjing; Zeng, Guangming; Fan, Changzheng; Lu, Lunhui; Chen, Xunfeng; Chen, Ming; Wu, Haipeng; He, Xiaoxiao; He, Yan

2015-10-01

Due to the emerging environmental issues related to heavy metals, concern about the soil quality of farming lands near manufacturing district is increasing. Investigating the function of soil microorganisms exposed to long-term heavy metal contamination is meaningful and important for agricultural soil utilization. This article studied the potential influence of several heavy metals on microbial biomass, activity, abundance, and community composition in arable soil near industrial estate in Zhuzhou, Hunan province, China. The results showed that soil organic contents (SOC) were significantly positive correlated with heavy metals, whereas dehydrogenase activity (DHA) was greatly depressed by the heavy metal stress. Negative correlation was found between heavy metals and basal soil respiration (BSR), and no correlation was found between heavy metals and microbial biomass content (MBC). The quantitative PCR (QPCR) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis could suggest that heavy metal pollution has significantly decreased abundance of bacteria and fungi and also changed their community structure. The results could contribute to evaluate heavy metal pollution level in soil. By combining different environmental parameters, it would promote the better understanding of heavy metal effect on the size, structure, and activity of microbial community in arable soil.

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

PubMed

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

2005-01-01

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

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

PubMed Central

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

2014-01-01

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

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

PubMed Central

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

Correlation of soil and sediment organic matter polarity to aqueous sorption of nonionic compounds

USGS Publications Warehouse

Kile, D.E.; Wershaw, R. L.; Chiou, C.T.

1999-01-01

Polarities of the soiL/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment sam pies were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (K(oc)) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxylamide-ester carbons. A plot of the measured partition coefficients (K(oc)) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of K(oc) values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in K(oc) between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with K(oc) illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.Polarities of the soil/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment samples were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (Koc) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxyl-amide-ester carbons. A plot of the measured partition coefficients (Koc) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of Koc values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in Koc between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with Koc illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.

Leaching potential of chlorpyrifos in an Andisol and Entisol: adsorption-desorption and degradation studies

NASA Astrophysics Data System (ADS)

Mosquera-Vivas, Carmen; Walther Hansen, Eddy; Garcia-Santos, Glenda; Obregón-Neira, Nelson; Celis-Ossa, Raul Ernesto; González-Murillo, Carlos Alberto; Juraske, Ronnie; Hellweg, Stefanie; Guerrero-Dallos, Jairo Arturo

2017-04-01

Ecological status of tropical soils like high OC content and microbial activity plays a key role to reduce the leaching of insecticide chlorpyrifos through the soil profile and therefore into groundwater. We found that chlorpyrifos has "transitional" leaching potential (GUS values varied between 1.8 and 2.5) throughout the soil depth, which differs from the "nonleacher" classification for temperate soils as based on surface level t1/2 and Koc values from international databases. These findings provide strong evidence of the importance of estimating the transport parameters and insecticide concentrations in different soil layers, especially when the amount and type of OC content vary throughout the soil profile. We got to such conclusions after studying the soil profile structural composition of soil organic matter and the adsorption/desorption characteristics of the insecticide in two different soil profiles (Andisol and Entisol) under agriculture production using Fourier transform infrared spectroscopy, nuclear magnetic resonance, and batch analysis methods.

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

PubMed

Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

2016-01-01

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Contribution of species-specific chemical signatures to soil organic matter in Kohala, HI.

NASA Astrophysics Data System (ADS)

Stewart, C. E.; Amatangelo, K.; Neff, J. C.

2008-12-01

Soil organic matter (SOM) inherits much of its chemical structure from the dominant vegetation, including phenolic (lignin-derived), aromatic, and aliphatic (cutin and wax-derived) compounds. The Hawaiian fern species Dicranopteris decomposes more slowly than the angiosperm, Cheirodendron due to high concentrations of recalcitrant C compounds. These aliphatic fern leaf waxes are well-preserved and may comprise a large portion of the recalcitrant organic matter in these soils. Our objective was to determine the chemical signature of fern and angiosperm vegetation types and trace the preservation or loss of those compounds into the soil. We collected live tissue, litter, roots, and soil (<53 μm) from five dominant vegetation types including two angiosperms Cheirodendron and Metrosideros, two basal ferns Dicranopteris and Cibotium and a polypod fern Diplazium in Kohala, HI. We characterized them via TMAH-pyrolysis-gas chromatography-mass spectrometry. We found distinct chemical differences between angiosperm and fern vegetation; angiosperm contained more G- and S-derived lignin structures and the fern species contained greater relative abundances of P-derived lignin and tannin-derivatives. There was a general decrease of lignin-derived phenolic compounds from live to litter to soils and an increase in more recalcitrant, aromatic and aliphatic C. Recalcitrant fern-derived cutin and leaf waxes (alkene and alkanes structures) were evident in the soils, but clear species differences were not observed. Although ferns contain distinct lipid and wax-derived compounds, soils developed under fern do not appear to accumulate these compounds in SOM.

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.

Mapping of Soil-Ecological Conditions of a Medium-Size Industrial City (Birobidzhan City, Jewish Autonomous Oblast, FarEast of Russia as an Example)

NASA Astrophysics Data System (ADS)

Kalmanova, V. B.; Matiushkina, L. A.

2018-01-01

The authors analyze soil relations with other elements of the city ecosystem (the position in the landscape, soil-forming rocks and lithology, vegetation and its state) to develop the legend and map of soils in the City of Birobidzhan (scale 1:25 000). The focus of study is the morphological structure of urban soils with different degree of disturbance of these relations under the impact of technical effects, economic and recreational activities of the city population. The soil cover structure is composed of four large ecological groups of soils: natural untransformed, natural with a disturbed surface, anthropogenic soils and technogenic surface formations. Using cartometry of the mapped soil contours the authors created the scheme of soil-ecological city zoning, which in a general way depicts the state of soil ecological functions in the city as well as identified zones of soils with preserved, partially and fully distured ecological functions and zones of local geochemical anomalies at the initial formation stage (environmental risk zones).

Physical parameters of Fluvisols on flooded and non-flooded terraces

NASA Astrophysics Data System (ADS)

Kercheva, Milena; Sokołowska, Zofia; Hajnos, Mieczysław; Skic, Kamil; Shishkov, Toma

2017-01-01

The heterogeneity of soil physical properties of Fluvisols, lack of large pristine areas, and different moisture regimes on non-flooded and flooded terraces impede the possibility to find a soil profile which can serve as a baseline for estimating the impact of natural or anthropogenic factors on soil evolution. The aim of this study is to compare the pore size distribution of pristine Fluvisols on flooded and non-flooded terraces using the method of the soil water retention curve, mercury intrusion porosimetry, nitrogen adsorption isotherms, and water vapour sorption. The pore size distribution of humic horizons of pristine Fluvisols on the non-flooded terrace differs from pore size distribution of Fluvisols on the flooded terrace. The peaks of textural and structural pores are higher in the humic horizons under more humid conditions. The structural characteristics of subsoil horizons depend on soil texture and evolution stage. The peaks of textural pores at about 1 mm diminish with lowering of the soil organic content. Structureless horizons are characterized by uni-modal pore size distribution. Although the content of structural pores of the subsoil horizons of Fluvisols on the non-flooded terrace is low, these pores are represented by biopores, as the coefficient of filtration is moderately high. The difference between non-flooded and flooded profiles is well expressed by the available water storage, volume and mean radius of pores, obtained by mercury intrusion porosimetry and water desorption, which are higher in the surface horizons of frequently flooded Fluvisols.

Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

NASA Astrophysics Data System (ADS)

Cao, Chengyou; Zhang, Ying; Qian, Wei; Liang, Caiping; Wang, Congmin; Tao, Shuang

2017-10-01

The conversion of natural grassland into agricultural fields is an intensive anthropogenic perturbation commonly occurring in semiarid regions, and this perturbation strongly affects soil microbiota. In this study, the influences of land-use conversion on the soil properties and bacterial communities in the Horqin Grasslands in Northeast China were assessed. This study aimed to investigate (1) how the abundances of soil bacteria changed across land-use types, (2) how the structure of the soil bacterial community was altered in each land-use type, and (3) how these variations were correlated with soil physical and chemical properties. Variations in the diversities and compositions of bacterial communities and the relative abundances of dominant taxa were detected in four distinct land-use systems, namely, natural meadow grassland, paddy field, upland field, and poplar plantation, through the high-throughput Illumina MiSeq sequencing technique. The results indicated that land-use changes primarily affected the soil physical and chemical properties and bacterial community structure. Soil properties, namely, organic matter, pH, total N, total P, available N and P, and microbial biomass C, N, and P, influenced the bacterial community structure. The dominant phyla and genera were almost the same among the land-use types, but their relative abundances were significantly different. The effects of land-use changes on the structure of soil bacterial communities were more quantitative than qualitative.

Multifractal analyis of soil invertebrates along a transect under different land uses

NASA Astrophysics Data System (ADS)

Machado Siqueira, Glécio; Alves Silva, Raimunda; Vidal-Vázquez, Eva; Paz-González, Antonio

2017-04-01

Soil fauna play a central role in many essential ecosystem processes. Land use and management can have a dramatic effect upon soil invertebrate community. Indices based on soil invertebrates abundance and diversity are fundamental for soil quality assessment. Many soil properties and attributes have been shown to exhibit spatial variabilityThe aim of this study was to analyze the scaling heterogeneity of the soil invertebrate community sampled using pitfall traps across a transect. The field study was conducted at Mata Roma municipality, Maranhão State, Brazil. Transects were marked under seven different agricultural/forestry land uses (millet, soybean, maize, eucalyptus, pasture, secondary savannah and native savannah). Native vegetation was considered as a reference, whereas the agricultural fields showed a range of soil use intensities. Along these transects 130 pitfall per land use were installed. First, differences in community assemblages and composition under different land use systems were evaluated using classical indices. Then, the spatial distribution of soil fauna trapped by pitfall techniques, characterized through generalized dimension, Dq, and singularity spectra, f(α) - α, showed a well-defined multifractal structure. Differences in scaling heterogeneity and other multifractal characteristics were examined in relation to land use intensification.

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak.

PubMed

Pec, Gregory J; Karst, Justine; Taylor, D Lee; Cigan, Paul W; Erbilgin, Nadir; Cooke, Janice E K; Simard, Suzanne W; Cahill, James F

2017-01-01

Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

[Fractal features of soil aggregate structure in slope farmland with different de-farming patterns in South Sichuan Province of China].

PubMed

Wang, Jing-Yan; Hu, Ting-Xing; Gong, Wei; Gong, Yuan-Bo; Luo, Cheng-De

2010-06-01

By using fractal model, this paper studied the fractal dimension of soil aggregate structure (D) in the slope farmland (CK), its 5-year de-farmed Neosinocalamus affinis plantation (NAP), Bambusa pervariabilis x Dendrocalamopsis oldhami plantation (BDP), Alnus crenastogyne + Neosinocalamus affinis plantation (ANP), and abandoned farmland (AFL) in south Sichuan Province of China, and analyzed the relationships between the D and soil physical and chemical properties. In the de-farmed plantations and abandoned farmland, the contents of > 0.25 mm soil aggregates and water-stable aggregates were increased significantly, compared with those in the slope farmland. The D was 1.377-2.826, being in the order of NAP < BDP < ANP < AFL < CK, and decreased with the increasing contents of > 0.25 mm soil aggregates and water-stable aggregates. Comparing with CK, de-farming increased the soil natural water content, capillary porosity, and contents of soil organic matter, total N, alkali-hydrolysable N, total P, and total K, and decreased soil bulk density, non-capillary porosity, and aeration porosity. There were close relationships between the fractal dimension of soil aggregate structure and the soil physical and chemical properties. All the results suggested that the de-farming of slope farmland was beneficial to the increase of the contents of > 0.25 mm soil aggregates and water-stable aggregates, and the enhancement of soil structure stability. The D could be used as an ideal index to evaluate soil fertility, and planting Neosinocalamus affinis on the de-farming slope farmland was a good measure for the improvement of soil fertility in the research area.

[Effects of different organic manure sources and their combinations with chemical fertilization on soil nematode community structure in a paddy field of East China].

PubMed

Liu, Ting; Ye, Cheng-Long; Chen, Xiao-Yun; Ran, Wei; Shen, Qi-Rong; Hu, Feng; Li, Hui-Xin

2013-12-01

A comparative study was conducted to investigate the effects of different fertilization modes on the soil nematode community structure in a paddy field with paddy rice and wheat rotation in Jintan County (31 degrees 39'41.8" N, 119 degrees 28'23.5" E) of Jiangsu Province, East China. Six treatments were installed, i. e., no fertilization (CK), 100% chemical NPK fertilization (F), pig manure compost plus 50% chemical fertilization (PF), straw returning plus 100% chemical fertilization (SF), pig manure compost and straw returning plus 50% chemical fertilization (PSF), and application of commercial pig manure-inorganic complex fertilizer (PMF). The soil samples were collected from the field after the paddy rice harvested in autumn. The two continuous years study showed that the soil nematode community structure varied with fertilization treatments and years. The combined application of chemical fertilizers and organic manures increased the total number of soil nematodes, decreased the abundance of soil bacterivorous nematodes, and made the abundance of predator- and omnivore nematodes increased significantly. No significant differences were observed in the abundance of soil fungivorous nematodes among all the treatments. Chemical fertilization alone and the application of commercial pig manure-inorganic complex fertilizer had no obvious suppression effect on the soil phytophagous nematodes. The abundance of soil bacteriavorous nematodes under the combined application of chemical fertilizers and organic manures was relatively increased in the second year, as compared with that in the first year, while the abundance of soil phytophagous nematodes (Hirschmanniella) was relatively decreased in the second year. From the aspect of nematode ecological indices, the Margalef diversity index (H) under the combined application of chemical fertilizers and organic manures in the second year had an increasing trend, while the NCR index had less change. The Wasilewka index had a relative increase in the second year, while the plant-parasitic index had a relative decrease. It was suggested that the application of organic manure could increase the abundance of soil microbivorous nematodes, and made the soil environment tend to be healthy.

Key Process Uncertainties in Soil Carbon Dynamics: Comparing Multiple Model Structures and Observational Meta-analysis

NASA Astrophysics Data System (ADS)

Sulman, B. N.; Moore, J.; Averill, C.; Abramoff, R. Z.; Bradford, M.; Classen, A. T.; Hartman, M. D.; Kivlin, S. N.; Luo, Y.; Mayes, M. A.; Morrison, E. W.; Riley, W. J.; Salazar, A.; Schimel, J.; Sridhar, B.; Tang, J.; Wang, G.; Wieder, W. R.

2016-12-01

Soil carbon (C) dynamics are crucial to understanding and predicting C cycle responses to global change and soil C modeling is a key tool for understanding these dynamics. While first order model structures have historically dominated this area, a recent proliferation of alternative model structures representing different assumptions about microbial activity and mineral protection is providing new opportunities to explore process uncertainties related to soil C dynamics. We conducted idealized simulations of soil C responses to warming and litter addition using models from five research groups that incorporated different sets of assumptions about processes governing soil C decomposition and stabilization. We conducted a meta-analysis of published warming and C addition experiments for comparison with simulations. Assumptions related to mineral protection and microbial dynamics drove strong differences among models. In response to C additions, some models predicted long-term C accumulation while others predicted transient increases that were counteracted by accelerating decomposition. In experimental manipulations, doubling litter addition did not change soil C stocks in studies spanning as long as two decades. This result agreed with simulations from models with strong microbial growth responses and limited mineral sorption capacity. In observations, warming initially drove soil C loss via increased CO2 production, but in some studies soil C rebounded and increased over decadal time scales. In contrast, all models predicted sustained C losses under warming. The disagreement with experimental results could be explained by physiological or community-level acclimation, or by warming-related changes in plant growth. In addition to the role of microbial activity, assumptions related to mineral sorption and protected C played a key role in driving long-term model responses. In general, simulations were similar in their initial responses to perturbations but diverged over decadal time scales. This suggests that more long-term soil experiments may be necessary to resolve important process uncertainties related to soil C storage. We also suggest future experiments examine how microbial activity responds to warming under a range of soil clay contents and in concert with changes in litter inputs.

[Responses of soil nematode communities to long-term application of inorganic fertilizers in upland red soil].

PubMed

Zhang, Wei; Liu, Man-Qiang; He, Yuan-Qiu; Fan, Jian-Bo; Chen, Yan

2014-08-01

Soil biota plays a key role in ecosystem functioning of red soil. Based on the long-term inorganic fertilization field experiment (25-year) in an upland red soil, the impacts of different inorganic fertilization managements, including NPK (nitrogen, phosphorus and potassium fertilizers), NPKCaS (NPK plus gypsum fertilizers), NP (nitrogen and phosphorus fertilizers), NK (nitrogen and potassium fertilizers) and PK (phosphorus and potassium fertilizers), on the assemblage of soil nematodes during the growing period of peanut were investigated. Significant differences among the treatments were observed for total nematode abundance, trophic groups and ecological indices (P < 0.01). The total nematode abundance decreased in the order of PK > NPKCaS > NPK > NP > NK. The total number of nematodes was significantly higher in NPKCaS and PK than in NPK, NP and NK except in May. Plant parasitic nematodes were the dominant trophic group in all treatments excepted in NPKCaS, and their proportion ranged between 38% and 65%. The dominant trophic group in NPKCaS was bacterivores and represented 42.1%. Furthermore, the higher values of maturity index, Wasilewska index and structure index in NPKCaS indicated that the combined application of NPK and gypsum could remarkably relieve soil acidification, resulting in a more mature and stable soil food web structure. While, that of the NK had the opposite effect. In conclusion, our study suggested that the application of both gypsum and phosphate is an effective practice to improve soil quality. Moreover, the analysis of nematode assemblage is relevant to reflect the impact of different inorganic fertilizer on the red soil ecosystem.

Compaction of forest soil by logging machinery favours occurrence of prokaryotes.

PubMed

Schnurr-Pütz, Silvia; Bååth, Erland; Guggenberger, Georg; Drake, Harold L; Küsel, Kirsten

2006-12-01

Soil compaction caused by passage of logging machinery reduces the soil air capacity. Changed abiotic factors might induce a change in the soil microbial community and favour organisms capable of tolerating anoxic conditions. The goals of this study were to resolve differences between soil microbial communities obtained from wheel-tracks (i.e. compacted) and their adjacent undisturbed sites, and to evaluate differences in potential anaerobic microbial activities of these contrasting soils. Soil samples obtained from compacted soil had a greater bulk density and a higher pH than uncompacted soil. Analyses of phospholipid fatty acids demonstrated that the eukaryotic/prokaryotic ratio in compacted soils was lower than that of uncompacted soils, suggesting that fungi were not favoured by the in situ conditions produced by compaction. Indeed, most-probable-number (MPN) estimates of nitrous oxide-producing denitrifiers, acetate- and lactate-utilizing iron and sulfate reducers, and methanogens were higher in compacted than in uncompacted soils obtained from one site that had large differences in bulk density. Compacted soils from this site yielded higher iron-reducing, sulfate-reducing and methanogenic potentials than did uncompacted soils. MPN estimates of H2-utilizing acetogens in compacted and uncompacted soils were similar. These results indicate that compaction of forest soil alters the structure and function of the soil microbial community and favours occurrence of prokaryotes.

Quantification of soil structure based on Minkowski functions

NASA Astrophysics Data System (ADS)

Vogel, H.-J.; Weller, U.; Schlüter, S.

2010-10-01

The structure of soils and other geologic media is a complex three-dimensional object. Most of the physical material properties including mechanical and hydraulic characteristics are immediately linked to the structure given by the pore space and its spatial distribution. It is an old dream and still a formidable challenge to relate structural features of porous media to their functional properties. Using tomographic techniques, soil structure can be directly observed at a range of spatial scales. In this paper we present a scale-invariant concept to quantify complex structures based on a limited set of meaningful morphological functions. They are based on d+1 Minkowski functionals as defined for d-dimensional bodies. These basic quantities are determined as a function of pore size or aggregate size obtained by filter procedures using mathematical morphology. The resulting Minkowski functions provide valuable information on the size of pores and aggregates, the pore surface area and the pore topology having the potential to be linked to physical properties. The theoretical background and the related algorithms are presented and the approach is demonstrated for the pore structure of an arable soil and the pore structure of a sand both obtained by X-ray micro-tomography. We also analyze the fundamental problem of limited resolution which is critical for any attempt to quantify structural features at any scale using samples of different size recorded at different resolutions. The results demonstrate that objects smaller than 5 voxels are critical for quantitative analysis.

Spatial and seasonal variations in mercury methylation and microbial community structure in a historic mercury mining area, Yolo County, California

USGS Publications Warehouse

Holloway, J.M.; Goldhaber, M.B.; Scow, K.M.; Drenovsky, R.E.

2009-01-01

The relationships between soil parent lithology, nutrient concentrations, microbial biomass and community structure were evaluated in soils from a small watershed impacted by historic Hg mining. Upland and wetland soils, stream sediments and tailings were collected and analyzed for nutrients (DOC, SO4=, NO3-), Hg, MeHg, and phospholipid fatty acids (PLFA). Stream sediment was derived from serpentinite, siltstone, volcanic rocks and mineralized serpentine with cinnabar, metacinnabar and other Hg phases. Soils from different parent materials had distinct PLFA biomass and community structures that are related to nutrient concentrations and toxicity effects of trace metals including Hg. The formation of MeHg appears to be most strongly linked to soil moisture, which in turn has a correlative relationship with PLFA biomass in wetland soils. The greatest concentrations of MeHg (> 0.5??ng g- 1 MeHg) were measured in wetland soils and soil with a volcanic parent (9.5-37????g g- 1 Hg). Mercury methylation was associated with sulfate-reducing bacteria, including Desulfobacter sp. and Desulfovibrio sp., although these organisms are not exclusively responsible for Hg methylation. Statistical models of the data demonstrated that soil microbial communities varied more with soil type than with season.

Multivariate functions for predicting the sorption of 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-tricyclohexane (RDX) among taxonomically distinct soils.

PubMed

Katseanes, Chelsea K; Chappell, Mark A; Hopkins, Bryan G; Durham, Brian D; Price, Cynthia L; Porter, Beth E; Miller, Lesley F

2016-11-01

After nearly a century of use in numerous munition platforms, TNT and RDX contamination has turned up largely in the environment due to ammunition manufacturing or as part of releases from low-order detonations during training activities. Although the basic knowledge governing the environmental fate of TNT and RDX are known, accurate predictions of TNT and RDX persistence in soil remain elusive, particularly given the universal heterogeneity of pedomorphic soil types. In this work, we proposed a new solution for modeling the sorption and persistence of these munition constituents as multivariate mathematical functions correlating soil attribute data over a variety of taxonomically distinct soil types to contaminant behavior, instead of a single constant or parameter of a specific absolute value. To test this idea, we conducted experiments measuring the sorption of TNT and RDX on taxonomically different soil types that were extensively physical and chemically characterized. Statistical decomposition of the log-transformed, and auto-scaled soil characterization data using the dimension-reduction technique PCA (principal component analysis) revealed a strong latent structure based in the multiple pairwise correlations among the soil properties. TNT and RDX sorption partitioning coefficients (KD-TNT and KD-RDX) were regressed against this latent structure using partial least squares regression (PLSR), generating a 3-factor, multivariate linear functions. Here, PLSR models predicted KD-TNT and KD-RDX values based on attributes contributing to endogenous alkaline/calcareous and soil fertility criteria, respectively, exhibited among the different soil types: We hypothesized that the latent structure arising from the strong covariance of full multivariate geochemical matrix describing taxonomically distinguished soil types may provide the means for potentially predicting complex phenomena in soils. The development of predictive multivariate models tuned to a local soil's taxonomic designation would have direct benefit to military range managers seeking to anticipate the environmental risks of training activities on impact sites. Published by Elsevier Ltd.

Changes of microbial activities and soil aggregation in rhizosphere soil of lettuce plants by drought and the possible influence of inoculation with AM fungi and/or PGPR

NASA Astrophysics Data System (ADS)

Kohler, J.; Caravaca, F.; Roldán, A.

2009-04-01

The effect of different arbuscular mycorrhizal (AM) fungi, Glomus intraradices (Schenk & Smith) or Glomus mosseae (Nicol & Gerd.) Gerd. & Trappe, and plant growth-promoting rhizobacteria (PGPR) (Pseudomonas mendocina Palleroni), alone or in combination, on structural stability and microbial activity in the rhizosphere soil of Lactuca sativa L. was assessed under well-watered conditions and two levels of drought. Desiccation caused an increase in aggregate stability and water-soluble and total carbohydrates but there were no significant differences among treated soils and the control soil. The glomalin-related soil protein (GRSP) levels in both the <2 mm and 0.2-4 mm soil fractions increased with medium water stress, whereas under severe water stress they did not differ with respect to those of well-watered soils. The values of GRSP in soils inoculated with PGPR and AM fungi were higher than in the control or fertilised soil under well-watered and severe-drought conditions, while under medium-drought conditions all soils showed similar GRSP values. Soils inoculated with AM fungi and PGPR generally presented higher dehydrogenase and phosphatase activities than the control soil, independent of the water regime.

Evaluation of dynamic response for monopole and hybrid wind mill tower

NASA Astrophysics Data System (ADS)

Shah, Hemal J.; Desai, Atul K.

2017-07-01

The wind mill towers are constructed using monopoles or lattice type tower. As the height of tower increases it gives more power but it becomes uneconomical, so in the present research work innovative wind mill tower such as combination of monopole and lattice tower is analyzed using FEM software. When the tall structures are constructed on soft soil it becomes dynamically sensitive so 3 types of soil such as hard, medium and soft soil is also modeled and the innovative tower is studied for different operating frequencies of wind turbine. From study it is concluded that the innovative tower will reduce resonance condition considering soil structure interaction.

The effects of multi-walled carbon nanotubes on soil microbial community functional and structural diversity

USDA-ARS?s Scientific Manuscript database

Applications of nanomaterials, including carbon nanotubes (CNTs), are increasing; however, their impact on the environment is still not well understood. A semi-arid soil was treated with multi-walled carbon nanotubes (MWCNTs) at four different concentrations (10-10000 mgMWCNTs kg-1soil), and incubat...

The structure of fungal biomass and diversity of cultivated micromycetes in Antarctic soils (progress and Russkaya Stations)

NASA Astrophysics Data System (ADS)

Marfenina, O. E.; Nikitin, D. A.; Ivanova, A. E.

2016-08-01

The distribution of the fungal biomass and diversity of cultivated microscopic fungi in the profiles of some soils from East (Progress Station, valleys of the Larsemann Hills oasis) and West (Russkaya Station, the Marie Byrd Land) Antarctica regions were studied. The structure of the biomass (spore/mycelium and live cells/dead cells) was analyzed by fluorescence microscopy with staining using a set of coloring agents: calcofluor white, ethidium bromide, and fluorescein diacetate. The species composition of the cultivated microscopic fungi was determined on Czapek's medium. The fungal biomass in the soils studied is not high (on the average, 0.3 mg/g of soil); the greatest biomass (0.6 mg/g) was found in the soil samples with plant residues. The fungal biomass is mainly (to 70%) represented by small (to 2.5 μm) spores. About half of the fungal biomass is composed of living cells. There are differences in the distribution of the fungal biomass within the profiles of different primitive soils. In the soil samples taken under mosses and lichens, the maximal biomass was registered in the top soil horizons. In the soils with the peat horizon under stone pavements, the greatest fungal biomass was registered in the subsurface horizons. Thirty-eight species of cultivated microscopic fungi were isolated from the soils studied. Species of the genus Penicillium and Phoma herbarum predominated.

The influence of exogenous conditions on mobile measured gamma-ray spectrometry

NASA Astrophysics Data System (ADS)

Dierke, C.; Werban, U.; Dietrich, P.

2012-12-01

In the past, gamma ray measurements have been used for geological surveys and exploration using airborne and borehole logging systems. For these applications, the relationships between the measured physical parameter - the concentration of natural gamma emitters 40K, 238U and 232Th - and geological origin or sedimentary developments are well described. Based on these applications and knowledge in combination with adjusted sensor systems, gamma ray measurements are used to derive soil parameters to create detailed soil maps e.g., in digital soil mapping (DSM) and monitoring of soils. Therefore, not only qualitative but also quantitative comparability is necessary. Grain size distribution, type of clay minerals and organic matter content are soil parameters which directly influence the gamma ray emitter concentration. Additionally, the measured concentration is influenced by endogenous processes like soil moisture variation due to raining events, foggy weather conditions, or erosion and deposition of material. A time series of gamma ray measurements was used to observe changes in gamma ray concentration on a floodplain area in Central Germany. The study area is characterised by high variations in grain size distribution and occurrence of flooding events. For the survey, we used a 4l NaI(Tl) detector with GPS connection mounted on a sledge, which is towed across the field sites by a four-wheel-vehicle. The comparison of data from different time steps shows similar structures with minor variation between the data ranges and shape of structures. However, the data measured during different soil moisture contents differ in absolute value. An average increase of soil moisture of 36% leads to a decrease of Th (by 20%), K (by 29%), and U (by 41%). These differences can be explained by higher attenuation of radiation during higher soil moisture content. The different changes in nuclide concentration will also lead to varying ratios. We will present our experiences concerning the measurement under variable field conditions and their impacts on gamma ray data quality. These activities are done within the iSOIL project. iSOIL- Interactions between soil related sciences - Linking geophysics, soil science and digital soil mapping is a Collaborative Project (Grant Agreement number 211386) co-funded by the Research DG of the European Commission within the RTD activities of the FP7 Thematic Priority Environment; iSOIL is one member of the SOIL TECHNOLOGY CLUSTER of Research Projects funded by the EC.

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

PubMed

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

2014-05-01

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

Soil properties and not inputs control carbon, nitrogen, phosphorus ratios in cropped soils in the long-term

NASA Astrophysics Data System (ADS)

Frossard, E.; Buchmann, N.; Bünemann, E. K.; Kiba, D. I.; Lompo, F.; Oberson, A.; Tamburini, F.; Traoré, O. Y. A.

2015-09-01

Stoichiometric approaches have been applied to understand the relationship between soil organic matter dynamics and biological nutrient transformations. However, very few studies explicitly considered the effects of agricultural management practices on soil C : N : P ratio. The aim of this study was to assess how different input types and rates would affect the C : N : P molar ratios of bulk soil, organic matter and microbial biomass in cropped soils in the long-term. Thus, we analysed the C, N and P inputs and budgets as well as soil properties in three long-term experiments established on different soil types: the Saria soil fertility trial (Burkina Faso), the Wagga Wagga rotation/stubble management/soil preparation trial (Australia), and the DOK cropping system trial (Switzerland). In each of these trials, there was a large range of C, N and P inputs which had a strong impact on element concentrations in soils. However, although C : N : P ratios of the inputs were highly variable, they had only weak effects on soil C : N : P ratios. At Saria, a positive correlation was found between the N : P ratio of inputs and microbial biomass, while no relation was observed between the nutrient ratios of inputs and soil organic matter. At Wagga Wagga, the C : P ratio of inputs was significantly correlated to total soil C : P, N : P and C : N ratios, but had no impact on the elemental composition of microbial biomass. In the DOK trial, a positive correlation was found between the C budget and the C to organic P ratio in soils, while the nutrient ratios of inputs were not related to those in the microbial biomass. We argue that these responses are due to differences in soil properties among sites. At Saria, the soil is dominated by quartz and some kaolinite, has a coarse texture, a fragile structure and a low nutrient content. Thus, microorganisms feed on inputs (plant residues, manure). In contrast, the soil at Wagga Wagga contains illite and haematite, is richer in clay and nutrients and has a stable structure. Thus, organic matter is protected from mineralization and can therefore accumulate, allowing microorganisms to feed on soil nutrients and to keep a constant C : N : P ratio. The DOK soil represents an intermediate situation, with high nutrient concentrations, but a rather fragile soil structure, where organic matter does not accumulate. We conclude that the study of C, N, and P ratios is important to understand the functioning of cropped soils in the long-term, but that it must be coupled with a precise assessment of element inputs and budgets in the system and a good understanding of the ability of soils to stabilize C, N and P compounds.

Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)

NASA Astrophysics Data System (ADS)

Kotas, Petr; Šantrůčková, Hana; Elster, Josef; Kaštovská, Eva

2018-03-01

The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS), and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level) were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs). We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects), mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.

Peculiarities of high-altitude landscapes formation in the Small Caucasus mountains

NASA Astrophysics Data System (ADS)

Trifonova, Tatiana

2014-05-01

Various mountain systems differ in character of landscapes and soil. Basic problem of present research: conditions and parameters determining the development of various landscapes and soils in mountain areas. Our research object is the area of Armenia where Small Caucasus, a part of Armenian upland is located. The specific character of the area is defined by the whole variety of all mountain structures like fold, block folding mountain ridges, volcanic upland, individual volcanoes, and intermountain depressions. As for the climate, the area belongs to dry subtropics. We have studied the peculiarities of high-altitude landscapes formation and mountain river basins development. We have used remote sensing data and statistic database of climatic parameters in this research. Field observations and landscape pictures analysis of space images allow distinguishing three types of mountain geosystems clearly: volcanic massifs, fold mountainous structures and closed high mountain basins - area of the lakes. The distribution of precipitation according to altitude shows some peculiarities. It has been found that due to this factor the investigated mountain area may be divided into three regions: storage (fold) mountainous area; Ararat volcanic area (southern macro exposure); closed high mountainous basin-area of the lake Sevan. The mountainous nature-climatic vertical landscapes appear to be horizontally oriented and they are more or less equilibrium (stable) geosystems, where the stable functional relationship between the landscape components is formed. Within their limits, definite bioclimatic structure of soil is developed. Along the slopes of fold mountains specific landscape shapes like litho-drainage basins are formed. They are intensively developing like relatively independent vertical geosystems. Mechanism of basin formation is versatile resulting in formation of the polychronous soil mantle structure. Landscapes and soils within the basin are of a different age, since the permanent exogenic processes favor regular rejuvenation of the slope soils. The basin structure determines the soilscape, and morphological elements of the basin are also different. The factors playing the significant part in the formation of soil-mantle composition in the basin can be identified. It is shown that landscapes formation and soil structure in mountains are controlled by two superimposed natural processes, i.e. the formation of vertical zonality and the development of river lithodrainage basins. References Trifonova T.A., 2008. River drainage basin as self-regulated natural geosistem. Izv. Russian of Academy of Sciences, Series on geography, 1: 28-36. Trifonova T.A., 2005. Development of basin approach in pedological and ecological studies. Eurasian Soil Science, 9: 931-937

A tropical freshwater wetlands: I. Structure, growth, and regeneration

USGS Publications Warehouse

Allen, J.A.; Krauss, K.W.; Ewel, K.C.; Keeland, B.D.; Waguk, E.E.

2005-01-01

Forested wetlands dominated by Terminalia carolinensis are endemic to Micronesia but common only on the island of Kosrae, Federated States of Micronesia. On Kosrae, these forests occur on Nansepsep, Inkosr, and Sonahnpil soil types, which differ in degree of flooding and soil saturation. We compared forest structure, growth, nutrition, and regeneration on two sites each on Nansepsep and Inkosr soils and one site on the much less common Sonahnpil soil type. Terminalia tree sizes were similar on all three soil types, but forests differed in total basal area, species of smaller trees, and total plant species diversity. Terminalia regeneration was found only on the Inkosr soil type, which had the highest water table levels. Other Terminalia species are relatively light demanding, and T. carolinensis exhibited similar characteristics. It is therefore likely that Terminalia requires periodic, but perhaps naturally rare, stand-replacing disturbances (e.g., typhoons) in order to maintain its dominanace, except on the wettest sites, where competition from other species is reduced. Terminalia swamps in the Nansepsep soil type appeared to be at the greatest risk of conversion to other uses, but swamps on all three types may face reater pressure as Kosrae's population increases and the island's infrastrucure becomes more developed.

Root carbon decomposition and microbial biomass response at different soil depths

NASA Astrophysics Data System (ADS)

Rumpel, C.

2012-12-01

The relationship between root litter addition and soil organic matter (SOM) formation in top- versus subsoils is unknown. The aim of this study was to investigate root litter decomposition and stabilisation in relation to microbial parameters in different soil depths. Our conceptual approach included incubation of 13C-labelled wheat roots at 30, 60 and 90 cm soil depth for 36 months under field conditions. Quantitative root carbon contribution to SOM was assessed, changes of bulk root chemistry studied by solid-state 13C NMR spectroscopy and lignin content and composition was assessed after CuO oxidation. Compound-specific isotope analysis allowed to assess the role of root lignin for soil C storage in the different soil depths. Microbial biomass and community structure was determined after DNA extraction. After three years of incubation, O-alkyl C most likely assigned to polysaccharides decreased in all soil depth compared to the initial root material. The degree of root litter decomposition assessed by the alkyl/O-alkyl ratio decreased with increasing soil depth, while aryl/O-alkyl ratio was highest at 60 cm depth. Root-derived lignin showed depth specific concentrations (30 < 90 < 60 cm). Its composition was soil depth independent suggesting that microbial communities in all three soil depths had similar degradation abilities. Microbial biomass C and fungi contribution increased after root litter addition. Their community structure changed after root litter addition and showed horizon specific dynamics. Our study shows that root litter addition can contribute to C storage in subsoils but did not influence C storage in topsoil. We conclude that specific conditions of single soil horizons have to be taken into account if root C dynamics are to be fully understood.

Colonization and community structure of arbuscular mycorrhizal fungi in maize roots at different depths in the soil profile respond differently to phosphorus inputs on a long-term experimental site.

PubMed

Wang, Chao; White, Philip J; Li, Chunjian

2017-05-01

Effects of soil depth and plant growth stages on arbuscular mycorrhizal fungal (AMF) colonization and community structure in maize roots and their potential contribution to host plant phosphorus (P) nutrition under different P-fertilizer inputs were studied. Research was conducted on a long-term field experiment over 3 years. AMF colonization was assessed by AM colonization rate and arbuscule abundances and their potential contribution to host P nutrition by intensity of fungal alkaline phosphatase (ALP)/acid phosphatase (ACP) activities and expressions of ZmPht1;6 and ZmCCD8a in roots from the topsoil and subsoil layer at different growth stages. AMF community structure was determined by specific amplification of 18S rDNA. Increasing P inputs up to 75-100 kg ha -1  yr -1 increased shoot biomass and P content but decreased AMF colonization and interactions between AMF and roots. AM colonization rate, intensity of fungal ACP/ALP activities, and expression of ZmPht1;6 in roots from the subsoil were greater than those from topsoil at elongation and silking but not at the dough stage when plants received adequate or excessive P inputs. Neither P input nor soil depth influenced the number of AMF operational taxonomic units (OTUs) present in roots, but P-fertilizer input, in particular, influenced community composition and relative AMF abundance. In conclusion, although increasing P inputs reduce AMF colonization and influence AMF community structure, AMF can potentially contribute to plant P nutrition even in well-fertilized soils, depending on the soil layer in which roots are located and the growth stage of host plants.

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.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

PubMed Central

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D.; Zhou, Jizhong

2015-01-01

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0–5 cm and 5–15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems. PMID:25791904

Root uptake of 137Cs by natural and semi-natural grasses as a function of texture and moisture of soils.

PubMed

Grytsyuk, N; Arapis, G; Davydchuk, V

2006-01-01

This work studies the dependence of 137Cs root uptake on the structure of landscape, especially on texture and moisture of soils, under natural conditions, on abandoned radiopolluted lands in Northern Ukraine. Researches were carried out on a wide range of landscape conditions, at various levels of 137Cs contamination (from 20 up to 5000 kBqm(-2)), with different types of soils (approx. 20 soil varieties), which differ in texture, granulometric composition, degrees of gleyization and water regime, and anthropogenic transformation. The results showed that transfer factor (TF) values of 137Cs differ 50 times for the natural grassy coenoses and 8 times for the semi-natural ones. The lowest 137Cs TF values were measured in the herbages of dry meadows at automorphous loamy soils, while the highest were observed in wetland meadows at organic soils. Finally, the correlation between 137Cs TF values and granulometric composition of soil was determined for both automorphic and hydromorphic mineral soils.

Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota.

PubMed

Leiva, Diego; Clavero-León, Claudia; Carú, Margarita; Orlando, Julieta

2016-11-01

Definition of lichens has evolved from bi(tri)partite associations to multi-species symbioses, where bacteria would play essential roles. Besides, although soil bacterial communities are known to be affected by edaphic factors, when lichens grow upon them these could become less preponderant. We hypothesized that the structure of both the lichen microbiota and the microbiota in the soil underneath lichens is shaped by lichen intrinsic and extrinsic factors. In this work, intrinsic factors corresponded to mycobiont and cyanobiont identities of Peltigera lichens, metabolite diversity and phenoloxidase activity and extrinsic factors involved the site of the forest where lichens grow. Likewise, the genetic and metabolic structure of the lichen and soil bacterial communities were analyzed by fingerprinting. Among the results, metabolite diversity was inversely related to the genetic structure of bacterial communities of lichens and soils, highlighting the far-reaching effect of these substances; while phenoloxidase activity was inversely related to the metabolic structure only of the lichen bacterial microbiota, presuming a more limited effect of the products of these enzymes. Soil bacterial microbiota was different depending on the site and, strikingly, according to the cyanobiont present in the lichen over them, which could indicate an influence of the photobiont metabolism on the availability of soil nutrients. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Research on filling scheme and deformation properties of wide subgrade of foamed lightweight soil on soft ground

NASA Astrophysics Data System (ADS)

Zhang, Faru; Yang, Deguang; Zhang, Liujun

2018-01-01

The wide subgrade on soft soil ground has the significantly different transverse settlement curve characteristics and the lacation of the maximum asymmetrical transverse settlement compared with ordinary subgrade. Especially when the subgrade filled with materials of different densities, the synergism deformation of ground-subgrade-pavement and the pavement structure stress become more complex. Combining with the engineering example, the settlement deformation characteristics of wide subgrade adopting the different filling scheme and the stress distribution of pavement structure are analyzed. Results show that the settlement curve of wide subgrade has a shape of flat middle with steep sides, and the maximum transverse asymmetrical settlement locates in close to the shoulder position. The maximum stress within the pavement structure is also in close to the shoulder position. Regarding the wide subgrade composed of main road and relief road, the post-construction settlement can be greatly reduced when both roads are filled with foamed lightweight soil.

CHANGES IN EARTHWORM DENSITY AND COMMUNITY STRUCTURE DURING SECONDARY SUCCESSION IN ABANDONED TROPICAL PASTURES

Treesearch

Xiaoming Zou; Grizelle Gonzalez

1997-01-01

Plant community succession alters the quantity and chemistry of organic inputs to soils. These differences in organic input may trigger changes in soil fertility and fauna1 activity. We examined earthworm density and community structure along a successional sequence of plant communities in abandoned tropical pastures in Puerto Rico. The chronological sequence of these...

Reflecting on the structure of soil classification systems: insights from a proposal for integrating subsoil data into soil information systems

NASA Astrophysics Data System (ADS)

Dondeyne, Stefaan; Juilleret, Jérôme; Vancampenhout, Karen; Deckers, Jozef; Hissler, Christophe

2017-04-01

Classification of soils in both World Reference Base for soil resources (WRB) and Soil Taxonomy hinges on the identification of diagnostic horizons and characteristics. However as these features often occur within the first 100 cm, these classification systems convey little information on subsoil characteristics. An integrated knowledge of the soil, soil-to-substratum and deeper substratum continuum is required when dealing with environmental issues such as vegetation ecology, water quality or the Critical Zone in general. Therefore, we recently proposed a classification system of the subsolum complementing current soil classification systems. By reflecting on the structure of the subsoil classification system which is inspired by WRB, we aim at fostering a discussion on some potential future developments of WRB. For classifying the subsolum we define Regolite, Saprolite, Saprock and Bedrock as four Subsolum Reference Groups each corresponding to different weathering stages of the subsoil. Principal qualifiers can be used to categorize intergrades of these Subsoil Reference Groups while morphologic and lithologic characteristics can be presented with supplementary qualifiers. We argue that adopting a low hierarchical structure - akin to WRB and in contrast to a strong hierarchical structure as in Soil Taxonomy - offers the advantage of having an open classification system avoiding the need for a priori knowledge of all possible combinations which may be encountered in the field. Just as in WRB we also propose to use principal and supplementary qualifiers as a second level of classification. However, in contrast to WRB we propose to reserve the principal qualifiers for intergrades and to regroup the supplementary qualifiers into thematic categories (morphologic or lithologic). Structuring the qualifiers in this manner should facilitate the integration and handling of both soil and subsoil classification units into soil information systems and calls for paying attention to these structural issues in future developments of WRB.

The structure of bacterial communities in natural and anthropogenic brown forest soils of the Botanical Garden on Murav'eva-Amurskogo Peninsula

NASA Astrophysics Data System (ADS)

Kovaleva, G. V.; Dobrovol'Skaya, T. G.; Golovacheva, A. V.

2007-05-01

The microbiological characterization of the brown forest soils in the territory of the Botanical Garden-Institute of the Far East Division of the Russian Academy of Sciences in southern Primor’e is given. The high humus content and weakly acid reaction of these soils were shown to provide the optimal conditions for the development of bacteria. In the brown forest soils differing in the thickness of the humus horizons, all the ecologic-trophic groups of bacteria were present and the bacterial communities were highly diverse. The structure of the bacterial communities was identical in all the organomineral horizons of the soils and varied greatly by the seasons. In the anthropogenically disturbed soils, the share of corynebacteria, which are resistant to stress and capable of the destruction of xenobiotics, decreased.

Analysis of soils - Part II: Determination of oligosaccharides in soils by MALDI-time-of-flight mass spectrometry

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

Schuerch, S.; Howald, M.; Schlunegger, U.P.

1995-12-31

Polysaccharides are the most abundant organic compounds in nature. Decomposition of plant and animal residues leads to a high polysaccharide content in soils. The decomposition of carbohydrates and subsequent mineralization of the products are part of the cycle of life on earth. In extracts of soils collected in the Valle Onsernone (Ticino, Switzerland), oligosaccharides of different size and structure have been identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The selected soils show identical climatic parameters and pedological factors, whereas the age of fallow land is the only varying factor. Identification and structure elucidation of the oligosaccharides is performedmore » by substrate-specific enzymatic hydrolysis. Moreover the appearance and the distribution of the oligosaccharides is correlated to soil genesis.« less

High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils

PubMed Central

Chiri, Eleonora; Nauer, Philipp A.; Rainer, Edda-Marie; Zeyer, Josef

2017-01-01

ABSTRACT Glacier forefield soils can provide a substantial sink for atmospheric CH4, facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH4 oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH4 flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH4 uptake rates ranging from −3.7 to −0.03 mg CH4 m−2 day−1. Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH4 emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH4 flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH4 sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH4 inventories. IMPORTANCE Oxidation of methane (CH4) in well-drained, “upland” soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH4 oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH4 oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH4 in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH4 oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH4 inventories. PMID:28687652

High temporal and spatial variability of atmospheric-methane oxidation in Alpine glacier-forefield soils.

PubMed

Chiri, Eleonora; Nauer, Philipp A; Rainer, Edda-Marie; Zeyer, Josef; Schroth, Martin H

2017-07-07

Glacier-forefield soils can provide a substantial sink for atmospheric CH 4 , facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, location in different forefield landforms, and temporal fluctuations in soil-physical parameters. We assessed spatial and temporal variability of atmospheric CH 4 oxidation in an Alpine glacier forefield during the snow-free season 2013. We quantified CH 4 flux in soils of increasing age and in different landforms (sandhill, terrace, floodplain) using soil-gas-profile and static flux-chamber methods. To determine MOB abundance and community structure, we employed pmoA -gene-based quantitative PCR and targeted-amplicon sequencing. Uptake of CH 4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH 4 uptake ranging from -0.03- -3.7 mg CH 4 m -2 d -1 Floodplain and terrace soils exhibited smaller uptake and even intermittent CH 4 emissions. Linear mixed-effect models indicated that soil age and landform were dominating factors shaping CH 4 flux, followed by cumulative rainfall (weighted sum ≤ 4 d prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with Upland Soil Clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical, but differed significantly from highly variable sandhill-soil communities. We conclude that soil age and landform modulate the soil CH 4 sink strength in glacier forefields, and recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH 4 inventories. Importance Oxidation of methane (CH 4 ) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric CH 4 oxidation in mature upland soils, little is known about this important function in young, developing soils such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat.In this field-based study we investigated spatial and temporal variability of atmospheric CH 4 oxidation and associated MOB communities in Alpine glacier-forefield soils, aiming at better understanding factors that shape the sink for atmospheric CH 4 in this young soil ecosystem. The study contributes to the knowledge on the dynamics of atmospheric CH 4 oxidation in developing upland soils, and represents a further step towards the inclusion of Alpine glacier-forefield soils in global CH 4 inventories. Copyright © 2017 American Society for Microbiology.

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

PubMed Central

Pereira e Silva, Michele C.; Dias, Armando Cavalcante Franco; van Elsas, Jan Dirk; Salles, Joana Falcão

2012-01-01

Background Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities. PMID:23284712

Influence of edaphic and management factors on the diversity and abundance of ammonia-oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars.

PubMed

Bertagnolli, Anthony D; Meinhardt, Kelley A; Pannu, Manmeet; Brown, Sally; Strand, Stuart; Fransen, Steven C; Stahl, David A

2015-04-01

Ammonia-oxidizing thaumarcheota (AOA) and ammonia-oxidizing bacteria (AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene (amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass (Panicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. Nitrosotalea-like and Nitrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with Nitrososphaera and Nitrosospira cluster 3A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high-throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India

PubMed Central

2012-01-01

Background Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO2 dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content. Results In cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac. Conclusion This study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the three sites, probably because of differences in salinity, carbon and sulphur contents. The cbbL form IA-containing sulphide-oxidizing chemolithotrophs were found only in high saline soil clone library, thus giving the indication of sulphide availability in this soil ecosystem. This is the first comparative study of the community structure and diversity of chemolithoautotrophic bacteria in coastal agricultural and saline barren soils using functional (cbbL) and phylogenetic (16S rDNA) marker genes. PMID:22834535

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

PubMed

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

2017-05-01

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

Field-Scale Transplantation Experiment To Investigate Structures of Soil Bacterial Communities at Pioneering Sites▿†

PubMed Central

Lazzaro, Anna; Gauer, Andreas; Zeyer, Josef

2011-01-01

Studies on the effect of environmental conditions on plants and microorganisms are a central issue in ecology, and they require an adequate experimental setup. A strategy often applied in geobotanical studies is based on the reciprocal transplantation of plant species at different sites. We adopted a similar approach as a field-based tool to investigate the relationships of soil bacterial communities with the environment. Soil samples from two different (calcareous and siliceous) unvegetated glacier forefields were reciprocally transplanted and incubated for 15 months between 2009 and 2010. Controls containing local soils were included. The sites were characterized over time in terms of geographical (bedrock, exposition, sunlight, temperature, and precipitation) and physicochemical (texture, water content, soluble and nutrients) features. The incubating local (“home”) and transplanted (“away”) soils were monitored for changes in extractable nutrients and in the bacterial community structure, defined through terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. Concentrations of soluble ions in most samples were more significantly affected by seasons than by the transplantation. For example, NO3− showed a seasonal pattern, increasing from 1 to 3 μg NO3− (g soil dry weight)−1 after the melting of snow but decreasing to <1 μg NO3− (g soil dry weight)−1 in autumn. Seasons, and in particular strong precipitation events occurring in the summer of 2010 (200 to 300 mm of rain monthly), were also related to changes of bacterial community structures. Our results show the suitability of this approach to compare responses of bacterial communities to different environmental conditions directly in the field. PMID:21965395

Spatial Variability of PAHs and Microbial Community Structure in Surrounding Surficial Soil of Coal-Fired Power Plants in Xuzhou, China

PubMed Central

Ma, Jing; Zhang, Wangyuan; Chen, Yi; Zhang, Shaoliang; Feng, Qiyan; Hou, Huping; Chen, Fu

2016-01-01

This work investigated the spatial profile and source analysis of polycyclic aromatic hydrocarbons (PAHs) in soil that surrounds coal-fired power plants in Xuzhou, China. High-throughput sequencing was employed to investigate the composition and structure of soil bacterial communities. The total concentration of 15 PAHs in the surface soils ranged from 164.87 to 3494.81 μg/kg dry weight. The spatial profile of PAHs was site-specific with a concentration of 1400.09–3494.81 μg/kg in Yaozhuang. Based on the qualitative and principal component analysis results, coal burning and vehicle emission were found to be the main sources of PAHs in the surface soils. The phylogenetic analysis revealed differences in bacterial community compositions among different sampling sites. Proteobacteria was the most abundant phylum, while Acidobacteria was the second most abundant. The orders of Campylobacterales, Desulfobacterales and Hydrogenophilales had the most significant differences in relative abundance among the sampling sites. The redundancy analysis revealed that the differences in bacterial communities could be explained by the organic matter content. They could also be explicated by the acenaphthene concentration with longer arrows. Furthermore, OTUs of Proteobacteria phylum plotted around particular samples were confirmed to have a different composition of Proteobacteria phylum among the sample sites. Evaluating the relationship between soil PAHs concentration and bacterial community composition may provide useful information for the remediation of PAH contaminated sites. PMID:27598188

Spatial Variability of PAHs and Microbial Community Structure in Surrounding Surficial Soil of Coal-Fired Power Plants in Xuzhou, China.

PubMed

Ma, Jing; Zhang, Wangyuan; Chen, Yi; Zhang, Shaoliang; Feng, Qiyan; Hou, Huping; Chen, Fu

2016-09-02

This work investigated the spatial profile and source analysis of polycyclic aromatic hydrocarbons (PAHs) in soil that surrounds coal-fired power plants in Xuzhou, China. High-throughput sequencing was employed to investigate the composition and structure of soil bacterial communities. The total concentration of 15 PAHs in the surface soils ranged from 164.87 to 3494.81 μg/kg dry weight. The spatial profile of PAHs was site-specific with a concentration of 1400.09-3494.81 μg/kg in Yaozhuang. Based on the qualitative and principal component analysis results, coal burning and vehicle emission were found to be the main sources of PAHs in the surface soils. The phylogenetic analysis revealed differences in bacterial community compositions among different sampling sites. Proteobacteria was the most abundant phylum, while Acidobacteria was the second most abundant. The orders of Campylobacterales, Desulfobacterales and Hydrogenophilales had the most significant differences in relative abundance among the sampling sites. The redundancy analysis revealed that the differences in bacterial communities could be explained by the organic matter content. They could also be explicated by the acenaphthene concentration with longer arrows. Furthermore, OTUs of Proteobacteria phylum plotted around particular samples were confirmed to have a different composition of Proteobacteria phylum among the sample sites. Evaluating the relationship between soil PAHs concentration and bacterial community composition may provide useful information for the remediation of PAH contaminated sites.

Microbial community structure and density under different tree species in an acid forest soil (Morvan, France).

PubMed

Lejon, David P H; Chaussod, Rémi; Ranger, Jacques; Ranjard, Lionel

2005-11-01

Overexploitation of forests to increase wood production has led to the replacement of native forest by large areas of monospecific tree plantations. In the present study, the effects of different monospecific tree cover plantations on density and composition of the indigenous soil microbial community are described. The experimental site of "Breuil-Chenue" in the Morvan (France) was the site of a comparison of a similar mineral soil under Norway spruce (Picea abies), Douglas fir (Pseudotuga menziesii), oak (Quercus sessiflora), and native forest [mixed stand dominated by oak and beech (Fagus sylvatica)]. Sampling was performed during winter (February) at three depths (0-5, 5-10, and 10-15 cm). Abundance of microorganisms was estimated via microbial biomass measurements, using the fumigation-extraction method. The genetic structure of microbial communities was investigated using the bacterial- and fungal-automated ribosomal intergenic spacer analysis (B-ARISA and F-ARISA, respectively) DNA fingerprint. Only small differences in microbial biomass were observed between tree species, the highest values being recorded under oak forest and the lowest under Douglas fir. B- and F-ARISA community profiles of the different tree covers clustered separately, but noticeable similarities were observed for soils under Douglas fir and oak. A significant stratification was revealed under each tree species by a decrease in microbial biomass with increasing depths and by distinct microbial communities for each soil layer. Differences in density and community composition according to tree species and depth were related to soil physicochemical characteristics and organic matter composition.

Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

NASA Technical Reports Server (NTRS)

Franklin, Rima B.; Mills, Aaron L.

2003-01-01

To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties. c2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem.

PubMed

Gibbons, Sean M; Lekberg, Ylva; Mummey, Daniel L; Sangwan, Naseer; Ramsey, Philip W; Gilbert, Jack A

2017-01-01

Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West. Each invader had a unique impact on soil physicochemical properties. We found that invasions drove shifts in the abundances of specific microbial taxa, while overall belowground community structure and functional potential were fairly constant. Forb invaders were generally enriched in copiotrophic bacteria with higher 16S rRNA gene copy numbers and showed greater microbial carbohydrate and nitrogen metabolic potential. Older invasions had stronger effects on abiotic soil properties, indicative of multiyear successions. Overall, we show that plant invasions are idiosyncratic in their impact on soils and are directly responsible for driving reproducible shifts in the soil environment over multiyear time scales. IMPORTANCE In this study, we show how invasive plant species drive rapid shifts in the soil environment from surrounding native communities. Each of the three plant invaders had different but consistent effects on soils. Thus, there does not appear to be a one-size-fits-all strategy for how plant invaders alter grassland soil environments. This work represents a crucial step toward understanding how invaders might be able to prevent or impair native reestablishment by changing soil biotic and abiotic properties.

Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing

PubMed Central

Penton, C. Ryan; Gupta, V. V. S. R.; Tiedje, James M.; Neate, Stephen M.; Ophel-Keller, Kathy; Gillings, Michael; Harvey, Paul; Pham, Amanda; Roget, David K.

2014-01-01

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils ‘suppressive’ or ‘non-suppressive’ for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. PMID:24699870

Investigation of Pb species in soils, celery and duckweed by synchrotron radiation X-ray absorption near-edge structure spectrometry

NASA Astrophysics Data System (ADS)

Luo, Liqiang; Shen, Yating; Liu, Jian; Zeng, Yuan

2016-08-01

The Pb species play a key role in its translocation in biogeochemical cycles. Soils, sediments and plants were collected from farmlands around Pb mines, and the Pb species in them was identified by X-ray absorption near-edge structure spectrometry. In soils, Pb5(PO4)3Cl and Pb3(PO4)2 were detected, and in sediments, Pb-fulvic acids (FAs) complex was identified. A Pb complex with FA fragments was also detected in celery samples. We found that (1) different Pb species were present in soils and sediments; (2) the Pb species in celery, which was grown in sediments, was different from the species present in duckweed, which grew in water; and (3) a Pb-FA-like compound was present in celery roots. The newly identified Pb species, the Pb-FA-like compound, may play a key role in Pb tolerance and translocation within plants.

An objective and reproducible landform and topography description approach based on digital terrain analysis used for soil profile site characteristics

NASA Astrophysics Data System (ADS)

Gruber, Fabian E.; Baruck, Jasmin; Hastik, Richard; Geitner, Clemens

2015-04-01

All major soil description and classification systems, including the World Reference Base (WRB) and the German Soil description guidelines (KA5), require the characterization of landform and topography for soil profile sites. This is commonly done at more than one scale, for instance at macro-, meso- and micro scale. However, inherent when humans perform such a task, different surveyors will reach different conclusions due to their subjective perception of landscape structure, based on their individual mind-model of soil-landscape structure, emphasizing different aspects and scales of the landscape. In this study we apply a work-flow using the GRASS GIS extension module r.geomorphon to make use of high resolution digital elevation models (DEMs) to characterize the landform elements and topography of soil profile sites at different scales, and compare the results with a large number of soil profile site descriptions performed during the course of forestry surveys in South and North Tyrol (Italy and Austria, respectively). The r.geomorphon extension module for the open source geographic information system GRASS GIS applies a pattern recognition algorithm to delineate landform elements based on an input DEM. For each raster cell it computes and characterizes the visible neighborhood using line-of-sight calculations and then applies a lookup-table to classify the raster cell into one of ten landform elements (flat, peak, ridge, shoulder, slope, spur, hollow, footslope, valley and pit). The input parameter search radius (L) represents the maximum number of pixels for line-of-sight calculation, resulting in landforms larger than L to be split into landform components. The use of these visibility calculations makes this landform delineation approach suitable for comparison with the landform descriptions of soil surveyors, as their spatial perception of the landscape surrounding a soil profile site certainly influences their classification of the landform on which the profile is situated (aided by additional information such as topographic maps and aerial images). Variation of the L-value furthermore presents the opportunity to mimic the different scales at which surveyors describe soil profile locations. We first illustrate the use of r.geomorphon for site descriptions using exemplary artificial elevation profiles resembling typic catenas at different scales (L-values). We then compare the results of a landform element map computed with r.geomorphon to the relief descriptions in the test dataset. We link the surveyors' landform classification to the computed landform elements. Using a multi-scale approach we characterize raster cell locations in a way similar to the micro-, meso- and macroscale definitions used in soil survey, resulting in so-called geomorphon-signatures, such as "pit (meso-scale) located on a ridge (macro-scale)". We investigate which ranges of L-values best represent the different observation-scales as noted by soil surveyors and discuss the impacts of using a large dataset of profile location descriptions performed by different surveyors. Issues that arise are possible individual differences in landscape structure perception, but also questions regarding the accuracy of position and resulting topographic measurements in soil profile site description.

Seismic behavior of breakwaters on complex ground by numerical tests: Liquefaction and post liquefaction ground settlements

NASA Astrophysics Data System (ADS)

Gu, Linlin; Zhang, Feng; Bao, Xiaohua; Shi, Zhenming; Ye, Guanlin; Ling, Xianzhang

2018-04-01

A large number of breakwaters have been constructed along coasts to protect humans and infrastructures from tsunamis. There is a risk that foundation soils of these structures may liquefy, or partially liquefy during the earthquake preceding a tsunami, which would greatly reduce the structures' capacity to resist the tsunami. It is necessary to consider not only the soil's liquefaction behavior due to earthquake motions but also its post-liquefaction behavior because this behavior will affect the breakwater's capacity to resist an incoming tsunami. In this study, numerical tests based on a sophisticated constitutive model and a soil-water coupled finite element method are used to predict the mechanical behavior of breakwaters and the surrounding soils. Two real breakwaters subjected to two different seismic excitations are examined through numerical simulation. The simulation results show that, earthquakes affect not only the immediate behavior of breakwaters and the surrounding soils but also their long-term settlements due to post-earthquake consolidation. A soil profile with thick clayey layers beneath liquefied soil is more vulnerable to tsunami than a soil profile with only sandy layers. Therefore, quantitatively evaluating the seismic behavior of breakwaters and surrounding soils is important for the design of breakwater structures to resist tsunamis.

Distinct soil microbial diversity under long-term organic and conventional farming

PubMed Central

Hartmann, Martin; Frey, Beat; Mayer, Jochen; Mäder, Paul; Widmer, Franco

2015-01-01

Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms. PMID:25350160

Parental material and cultivation determine soil bacterial community structure and fertility.

PubMed

Sun, Li; Gao, Jusheng; Huang, Ting; Kendall, Joshua R A; Shen, Qirong; Zhang, Ruifu

2015-01-01

Microbes are the key components of the soil environment, playing important roles during soil development. Soil parent material provides the foundation elements that comprise the basic nutritional environment for the development of microbial community. After 30 years artificial maturation of cultivation, the soil developments of three different parental materials were evaluated and bacterial community compositions were investigated using the high-throughput sequencing approach. Thirty years of cultivation increased the soil fertility and soil microbial biomass, richness and diversity, greatly changed the soil bacterial communities, the proportion of phylum Actinobacteria decreased significantly, while the relative abundances of the phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Armatimonadetes and Nitrospira were significantly increased. Soil bacterial communities of parental materials were separated with the cultivated ones, and comparisons of different soil types, granite soil and quaternary red clay soil were similar and different with purple sandy shale soil in both parental materials and cultivated treatments. Bacterial community variations in the three soil types were affected by different factors, and their alteration patterns in the soil development also varied with soil type. Soil properties (except total potassium) had a significant effect on the soil bacterial communities in all three soil types and a close relationship with abundant bacterial phyla. The amounts of nitrogen-fixing bacteria as well as the abundances of the nifH gene in all cultivated soils were higher than those in the parental materials; Burkholderia and Rhizobacte were enriched significantly with long-term cultivation. The results suggested that crop system would not deplete the nutrients of soil parental materials in early stage of soil maturation, instead it increased soil fertility and changed bacterial community, specially enriched the nitrogen-fixing bacteria to accumulate nitrogen during soil development. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effect of soil properties, heavy metals and emerging contaminants in the soil nematodes diversity.

PubMed

Gutiérrez, Carmen; Fernández, Carlos; Escuer, Miguel; Campos-Herrera, Raquel; Beltrán Rodríguez, Mª Eulalia; Carbonell, Gregoria; Rodríguez Martín, Jose Antonio

2016-06-01

Among soil organisms, nematodes are seen as the most promising candidates for bioindications of soil health. We hypothesized that the soil nematode community structure would differ in three land use areas (agricultural, forest and industrial soils), be modulated by soil parameters (N, P, K, pH, SOM, CaCO3, granulometric fraction, etc.), and strongly affected by high levels of heavy metals (Cd, Pb, Zn, Cr, Ni, Cu, and Hg) and emerging contaminants (pharmaceuticals and personal care products, PPCPs). Although these pollutants did not significantly affect the total number of free-living nematodes, diversity and structure community indices vastly altered. Our data showed that whereas nematodes with r-strategy were tolerant, genera with k-strategy were negatively affected by the selected pollutants. These effects diminished in soils with high levels of heavy metals given their adaptation to the historical pollution in this area, but not to emerging pollutants like PPCPs. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Effect of flooding time on community structure and abundance of Geobacteraceae in paddy soil].

PubMed

You, Jiaohua; Xia, Shuhong; Wang, Baoli; Qu, Dong

2011-06-01

The dynamic characteristics of community structure and relative abundance of Geobacteraceae were investigated to understand their response to microbial iron (III) reducing in flooded paddy soil. The paddy soil was incubated anaerobically and the amount of Fe(II) was determined during the flooding incubation. We retrieved Geobacteraceae sequences from clone libraries constructed for different time points (1 h and day 1, 5, 10, 20 and 30) after flooding of the paddy soil. The diversity and community structure were analyzed by using RFLP method, and the relative abundance of Geobacteraceae was detected by real-time PCR. Microbial reduction of iron (III) changed greatly in early time and was stable after incubated for 20 d in paddy soil. The largest iron reduction potential was 10.16 mg/g with a Vmax of 1.064 mg/(g x d) at the time of 4.84 d whereas this process achieved plateau after 20 days flooding. Diversity of Geobacteraceae, given by alpha indices, fluctuated during the flooding incubation. Two peaks of diversity were observed in treatments of 5 d and 20 d respectively, while significant low diversity appeared in samples of 10 d and 30 d. Beta indices described the differences between community structures of Geobacteraceae and hence reflected the variation of the flooding situation over time. In all samples, 10 RFLP-based preponderant types were found, which fell into clade 1 and clade 2 of Geobacteraceae. The relative abundance of Geobacteraceae was the lowest in 1 d (1.20% ) and the highest in 20 d (4.54%). The dynamic variation of Geobacteraceae diversity, community structure and abundance are closely related to microbial iron (III) reducing in flooding paddy soil.

pH rather than nitrification and urease inhibitors determines the community of ammonia oxidizers in a vegetable soil.

PubMed

Xi, Ruijiao; Long, Xi-En; Huang, Sha; Yao, Huaiying

2017-12-01

Nitrification inhibitors and urease inhibitors, such as nitrapyrin and N-(n-butyl) thiophosphoric triamide (NBPT), can improve the efficiencies of nitrogen fertilizers in cropland. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across different soil pH levels are still unclear. In the present work, vegetable soils at four pH levels were tested to determine the impacts of nitrification and urease inhibitors on the nitrification activities, abundances and diversities of ammonia oxidizers at different pHs by real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and clone sequence analysis. The analyses of the abundance of ammonia oxidizers and net nitrification rate suggested that AOA was the dominate ammonia oxidizer and the key driver of nitrification in acidic soil. The relationships between pH and ammonia oxidizer abundance indicated that soil pH dominantly controlled the abundance of AOA but not that of AOB. The T-RFLP results suggested that soil pH could significantly affect the AOA and AOB community structure. Nitrapyrin decreased the net nitrification rate and inhibited the abundance of bacterial amoA genes in this vegetable soil, but exhibited no effect on that of the archaeal amoA genes. In contrast, NBPT just lagged the hydrolysis of urea and kept low NH 4 + -N levels in the soil at the early stage. It exhibited no or slight effects on the abundance and community structure of ammonia oxidizers. These results indicated that soil pH, rather than the application of urea, nitrapyrin and NBPT, was a critical factor influencing the abundance and community structure of AOA and AOB.

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

BiodivERsA project VineDivers: Analysing interlinkages between soil biota and biodiversity-based ecosystem services in vineyards across Europe

NASA Astrophysics Data System (ADS)

Zaller, Johann G.; Winter, Silvia; Strauss, Peter; Querner, Pascal; Kriechbaum, Monika; Pachinger, Bärbel; Gómez, José A.; Campos, Mercedes; Landa, Blanca; Popescu, Daniela; Comsa, Maria; Iliescu, Maria; Tomoiaga, Liliana; Bunea, Claudiu-Ioan; Hoble, Adela; Marghitas, Liviu; Rusu, Teodor; Lora, Ángel; Guzmán, Gema; Bergmann, Holger

2015-04-01

Essential ecosystem services provided by viticultural landscapes result from diverse communities of above- and belowground organisms and their interactions. For centuries traditional viticulture was part of a multifunctional agricultural system including low-input grasslands and fruit trees resulting in a high functional biodiversity. However, in the last decades intensification and mechanisation of vineyard management caused a separation of production and conservation areas. As a result of management intensification including frequent tilling and/or use of pesticides several ecosystem services are affected leading to high rates of soil erosion, degradation of soil structure and fertility, contamination of groundwater and high levels of agricultural inputs. In this transdisciplinary BiodivERsA project we will examine to what extent differently intensive managed vineyards affect the activity and diversity of soil biota (e.g. earthworms, collembola, soil microorganisms) and how this feed back on aboveground biodiversity (e.g. weeds, pollinators). We will also investigate ecosystem services associated with soil faunal activity and biodiversity such as soil structure, the formation of stable soil aggregates, water infiltration, soil erosion as well as grape quality. These effects will become increasingly important as more extreme precipitation events are predicted with climate change. The socio-economic part of the project will investigate the role of diversely structured, species-rich viticultural landscapes as a cultural heritage providing aesthetic values for human well-being and recreation. The project objectives will be analysed at plot, field (vineyard) and landscape scales in vineyards located in Spain, France, Romania and Austria. A detailed engagement and dissemination plan for stakeholder at the different governance levels will accompany scientific research and will contribute to the implementation of best-practice recommendations for policy and farmers.

Geomorphology, disturbance, and the soil and vegetation of two subtropical wet steepland watersheds of Puerto Rico.

Treesearch

Ariel E. Lugo F.N. Scatena

1995-01-01

Relationships between landforms, soil nutrients, forest structure, and the relative importance of different disturbances were quantified in two subtropical wet steepland watersheds in Puerto Rico. Ridges had fewer landslides and treefall gaps, more above-ground biomass, older aged stands, and greater species richness than other landscape positions. Ridge soils had...

Microbial community biomass and structure in saline and non-saline soils associated with salt, boran tolerant poplar clones grown for the phytoremediation of selenium

USDA-ARS?s Scientific Manuscript database

The effect of naturally-occurring salts, boron (B), and selenium (Se) on soil microbial community composition associated with plants during different growing seasons used in bioremediation strategies is not known. This information is needed for developing sustainable remediation practices as soil mi...

Changes in the structure of bacterial complexes of vegetable crops in the course of their growth on a cultivated soddy-podzolic soil

NASA Astrophysics Data System (ADS)

Dobrovol'skaya, T. G.; Khusnetdinova, K. A.

2017-11-01

The dynamics of population density and taxonomic structure of epiphytic bacterial communities on the leaves and roots of potatoes, carrots, and beets have been studied. Significant changes take place in the ontogenesis of these vegetables with substitution of hydrolytic bacteria for eccrisotrophic bacteria feeding on products of plant exosmosis. The frequency of domination of representatives of different taxa of epiphytic bacteria on the studied plants has been determined for the entire period of their growth. Bacteria of different genera have been isolated from the aboveground and underground organs of vegetables; their functions are discussed. It is shown that the taxonomic structure of bacterial communities in the soil under studied plants is not subjected to considerable changes and is characterized by the domination of typical soil bacteria— Arthrobacter and bacilli—with the appearance of Rhodococcus as a codominant at the end of the season (before harvesting).

Effects of soil structure destruction on methane production and carbon partitioning between methanogenic pathways in tropical rain forest soils

NASA Astrophysics Data System (ADS)

Teh, Yit Arn; Silver, Whendee L.

2006-03-01

Controls on methanogenesis are often determined from laboratory incubations of soils converted to slurries. Destruction of soil structure during slurry conversion may disrupt syntrophic associations, kill methanogens, and/or alter the microsite distribution of methanogenic activity, suppressing CH4 production. The effects of slurry conversion on methanogenesis were investigated to determine if disruption of aggregate structure impacted methanogenesis, substrate utilization, and C partitioning between methanogenic pathways. Soils were collected from the tropical rain forest life zone of the Luquillo Experimental Forest, Puerto Rico, and exposed to different physical disturbances, including flooding and physical homogenization. Slurry conversion negatively impacted methanogenesis. Rates of CH4 production declined by a factor of 17 after well-aggregated soils were converted to slurries. Significantly more 13C-acetate was recovered in CO2 compared to CH4 after slurry conversion, suggesting that methanogens consumed less acetate after slurry conversion and may have competed less effectively with other anaerobes for acetate. Isotopic data indicate that the relative partitioning of C between aceticlastic and hydrogenotrophic pathways was unchanged after slurry conversion. These data suggest that experiments which destroy soil structure may significantly underestimate methanogenesis and overestimate the potential for other microorganisms to compete with methanogens for organic substrates. Current knowledge of the factors that regulate methanogenesis in soil may be biased by the findings of slurry-based experiments, that do not accurately represent the complex, spatially heterogeneous conditions found in well-aggregated soils.

[Research on soil bacteria under the impact of sealed CO2 leakage by high-throughput sequencing technology].

PubMed

Tian, Di; Ma, Xin; Li, Yu-E; Zha, Liang-Song; Wu, Yang; Zou, Xiao-Xia; Liu, Shuang

2013-10-01

Carbon dioxide Capture and Storage has provided a new option for mitigating global anthropogenic CO2 emission with its unique advantages. However, there is a risk of the sealed CO2 leakage, bringing a serious threat to the ecology system. It is widely known that soil microorganisms are closely related to soil health, while the study on the impact of sequestered CO2 leakage on soil microorganisms is quite deficient. In this study, the leakage scenarios of sealed CO2 were constructed and the 16S rRNA genes of soil bacteria were sequenced by Illumina high-throughput sequencing technology on Miseq platform, and related biological analysis was conducted to explore the changes of soil bacterial abundance, diversity and structure. There were 486,645 reads for 43,017 OTUs of 15 soil samples and the results of biological analysis showed that there were differences in the abundance, diversity and community structure of soil bacterial community under different CO, leakage scenarios while the abundance and diversity of the bacterial community declined with the amplification of CO2 leakage quantity and leakage time, and some bacteria species became the dominant bacteria species in the bacteria community, therefore the increase of Acidobacteria species would be a biological indicator for the impact of sealed CO2 leakage on soil ecology system.

Microbial Ecology of Soil Aggregation in Agroecosystems

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

2017-12-01

Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences in the abundance of chemical classes in clay loams compared to sandy loams. Together our data demonstrate that the potential for aggregation and C storage is strongly influenced by soil mineralogy with important implications for plant-microbe interactions that mediate C biogeochemistry.

Do anaerobic digestates promote dispersion, acidification and water repellency in soils?

NASA Astrophysics Data System (ADS)

Voelkner, Amrei; Holthusen, Dörthe; Horn, Rainer

2014-05-01

Digestates are used as organic fertilizer on agricultural land due to their high amounts of nutrients (e.g. potassium, sodium). It is commonly expected that the application of sludge derived from anaerobic digestion can influence the soil structure and soil stability. Due to the fact that digestates contain large quantities of monovalent salts and long-chained fatty acids, the consequence of sludge amendment can be soil degradation caused by acidification, dispersion and increased water-repellency. Thus, water infiltration can be impeded which results in a preservation of stable soil aggregates. However, a diminished water infiltration can support water erosion and preferential flow of easy soluble nutrients into the groundwater. Our research was conducted with different digestates derived from maize, wheat and sugar beet to examine occurring processes in soils of two different textures after the application of anaerobic sludges. Particularly, we focused on the wetting properties of the soil. For this purpose, the wetting behavior was investigated by determining the sorptivity-based Repellency Index with moist samples and the contact angle with homogenized, air-dried soil material. Further surveys were carried out to assess the flow behavior of digestates application and the deformation of the particle-to-particle association by microscaled shearing. Additionally, the acidification process in the soil as a result of sludge application was investigated. To account for the dispersive impact of digestates, the turbidity of soil suspensions was ascertained. We summarize from the results that the digestates have a clear impact on the water repellency of the soil. We recognized a shift to more hydrophobic conditions. Partially, the pH remains on a high level due to the alkaline digestate, but several samples show a decline of pH, depending on the soil texture, respectively. However, soil structure was weakened as was shown by an increase of turbidity. As a conclusion, we point out the necessity to take into account the impact which anaerobic digestates might have on soil structure and stability in addition to their fertilizing effect to sustain the soil in a good state.

Cryptogamic community structure as a bioindicator of soil condition along a pollution gradient.

PubMed

Rola, Kaja; Osyczka, Piotr

2014-09-01

This study aims to determine changes in the structure of cryptogamic vegetation of poor psammophilous grassland along a pollution gradient near a zinc smelter to evaluate the potential of species assemblages as bioindicators of soil condition. Lichens and bryophytes were examined in study plots along six transects in four distance zones, and the physicochemical properties of corresponding soil samples were analysed. Four different responses of species to substrate contamination were identified, with a distinct group of species resistant to and favoured by metal contamination. Although species richness decreases as one approaches the smelter, the gradual replacement of certain sensitive species by resistant ones was observed along the pollution gradient. The results enabled us to develop a useful tool to diagnose strongly polluted sites. Two different cryptogamic assemblages of well-recognised key species characteristic for strongly polluted and lightly polluted sites were distinguished. We conclude that cryptogamic community structure clearly corresponds to the degree of soil contamination, thus demonstrating high bioindicative value. The study confirmed the high relevance of the community approach in metal pollution biomonitoring.

Physicochemical and microbiological effects of long- and short-term winery wastewater application to soils.

PubMed

Mosse, K P M; Patti, A F; Smernik, R J; Christen, E W; Cavagnaro, T R

2012-01-30

Application of winery wastewaters to soils for irrigation of various crops or landscapes is a common practice in the wine industry. In this study, we sought to investigate the effects of this practice, by comparing the physicochemical and microbiological soil properties in paired sites that differed in having had a history of winery waste application or not. We also compared the effects of a single application of untreated winery wastewater, to application of treated winery wastewater (sequencing batch reactor) and pure water to eliminate the effects of wetting alone. Long-term application of winery wastes was found to have significant impacts on soil microbial community structure, as determined by phospholipid fatty acid analysis, as well as on many physicochemical properties including pH, EC, and cation concentrations. (13)C NMR revealed only slight differences in the nature of the carbon present at each of the paired sites. A single application of untreated winery wastewater was shown to have significant impacts upon soil respiration, nitrogen cycling and microbial community structure, but the treated wastewater application showed no significant differences to wetting alone. Results are discussed in the context of sustainable winery wastewater disposal. Copyright © 2011 Elsevier B.V. All rights reserved.

Soil processes and functions across an international network of Critical Zone Observatories: Introduction to experimental methods and initial results

NASA Astrophysics Data System (ADS)

Banwart, Steven; Menon, Manoj; Bernasconi, Stefano M.; Bloem, Jaap; Blum, Winfried E. H.; Souza, Danielle Maia de; Davidsdotir, Brynhildur; Duffy, Christopher; Lair, Georg J.; Kram, Pavel; Lamacova, Anna; Lundin, Lars; Nikolaidis, Nikolaos P.; Novak, Martin; Panagos, Panos; Ragnarsdottir, Kristin Vala; Reynolds, Brian; Robinson, David; Rousseva, Svetla; de Ruiter, Peter; van Gaans, Pauline; Weng, Liping; White, Tim; Zhang, Bin

2012-11-01

Growth in human population and demand for wealth creates ever-increasing pressure on global soils, leading to soil losses and degradation worldwide. Critical Zone science studies the impact linkages between these pressures, the resulting environmental state of soils, and potential interventions to protect soil and reverse degradation. New research on soil processes is being driven by the scientific hypothesis that soil processes can be described along a life cycle of soil development. This begins with formation of new soil from parent material, development of the soil profile, and potential loss of the developed soil functions and the soil itself under overly intensive anthropogenic land use, thus closing the cycle. Four Critical Zone Observatories in Europe have been selected focusing research at sites that represent key stages along the hypothetical soil life cycle; incipient soil formation, productive use of soil for farming and forestry, and decline of soil due to longstanding intensive agriculture. Initial results from the research show that soil develops important biogeochemical properties on the time scale of decades and that soil carbon and the development of favourable soil structure takes place over similar time scales. A new mathematical model of soil aggregate formation and degradation predicts that set-aside land at the most degraded site studied can develop substantially improved soil structure with the accumulation of soil carbon over a period of several years. Further results demonstrate the rapid dynamics of soil carbon; how quickly it can be lost, and also demonstrate how data from the CZOs can be used to determine parameter values for models at catchment scale. A structure for a new integrated Critical Zone model is proposed that combines process descriptions of carbon and nutrient flows, a simplified description of the soil food web, and reactive transport; all coupled with a dynamic model for soil structure and soil aggregation. This approach is proposed as a methodology to analyse data along the soil life cycle and test how soil processes and rates vary within, and between, the CZOs representing different life cycle stages. In addition, frameworks are discussed that will help to communicate the results of this science into a more policy relevant format using ecosystem service approaches.

Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest

PubMed Central

Hu, Yanqiu; Su, Zhiyao; Li, Wenbin; Li, Jingpeng; Ke, Xiandong

2015-01-01

We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1) forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2) soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3) a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting. PMID:26317523

Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest.

PubMed

Hu, Yanqiu; Su, Zhiyao; Li, Wenbin; Li, Jingpeng; Ke, Xiandong

2015-01-01

We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1) forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2) soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3) a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting.

Ectomycorrhizal Community Structure and Soil Characteristics of Mature Lodgepole Pine (Pinus Contorta) and Adjacent Stands of Old Growth Mixed Conifer in Yellowstone National Park, Wyoming USA

NASA Technical Reports Server (NTRS)

Douglas, Robert B.; Parker, V. Thomas; Cullings, Kenneth W.; Sun, Sidney (Technical Monitor)

2003-01-01

Forest development patterns following disturbance are known to influence the physical and chemical attributes of soils at different points in time. Changes in soil resources are thought to have a corresponding effect on ectomycorrhizal (ECM) community structure. We used molecular methods to compare below-ground ECM species richness, composition, and abundance between adjacent stands of homogenous lodgepole pine and old growth mixed conifer in Yellowstone National Park (YNP). In each stand-type we collected soil cores to both identify mycorrhizae and assess soil chemistry. Although no statistical difference was observed in the mean number of ECM root tips per core between stand types, the total number of species identified (85 versus 35) and the mean number of species per core (8.8 +/- 0.6 versus 2.5 +/- 0.3) were significantly higher in lodgepole pine. Differences between the actual and estimated species richness levels indicated that these forest types support a high number of ECM species and that undersampling was severe. Species compositions were widely disparate between stands where only four species were shared out of a total of 116. Soil analysis also revealed that mixed conifer was significantly lower in pH, but higher in organic matter, potassium, phosphorus, and ammonium when compared to lodgepole pine stands. Species richness per core was correlated with these chemical data, however, analysis of covariance indicated that stand type was the only statistically significant factor in the observed difference in species richness. Our data suggest that ECM fungal richness increases as homogenous lodgepole pine stands grow and mature, but declines after Engelmann spruce and subalpine fir colonize. Despite difficulties linking species composition with soil chemistry, there are a variety of physical and chemical factors that could be influencing ECM community structure. Future field experiments are necessary to test some of the mechanisms potentially operating within this system.

Soil porosity correlation and its influence in percolation dynamics

NASA Astrophysics Data System (ADS)

Rodriguez, Alfredo; Capa-Morocho, Mirian; Ruis-Ramos, Margarita; Tarquis, Ana M.

2016-04-01

The prediction of percolation in natural soils is relevant for modeling root growth and optimizing infiltration of water and nutrients. Also, it would improve our understanding on how pollutants as pesticides, and virus and bacteria (Darnault et al., 2003) reach significant depths without being filtered out by the soil matrix (Beven and Germann, 2013). Random walk algorithms have been used successfully to date to characterize the dynamical characteristics of disordered media. This approach has been used here to describe how soil at different bulk densities and with different threshold values applied to the 3D gray images influences the structure of the pore network and their implications on particle flow and distribution (Ruiz-Ramos et al., 2009). In order to do so first we applied several threshold values to each image analyzed and characterized them through Hurst exponents, then we computed random walks algorithms to calculate distances reached by the particles and speed of those particles. At the same time, 3D structures with a Hurst exponent of ca 0.5 and with different porosities were constructed and the same random walks simulations were replicated over these generated structures. We have found a relationship between Hurst exponents and the speed distribution of the particles reaching percolation of the total soil depth. REFERENCES Darnault, C.J. G., P. Garnier, Y.J. Kim, K.L. Oveson, T.S. Steenhuis, J.Y. Parlange, M. Jenkins, W.C. Ghiorse, and P. Baveye (2003), Preferential transport of Cryptosporidium parvum oocysts in variably saturated subsurface environments, Water Environ. Res., 75, 113-120. Beven, Keith and Germann, Peter. 2013. Macropores and water flow in soils revisited. Water Resources Research, 49(6), 3071-3092. DOI: 10.1002/wrcr.20156. Ruiz-Ramos, M., D. del Valle, D. Grinev, and A.M. Tarquis. 2009. Soil hydraulic behaviour at different bulk densities. Geophysical Research Abstracts, 11, EGU2009-6234.

Spatial variability structure of soil CO2 emission and soil physical and chemical properties characterized by fractal dimension in sugarcane areas

NASA Astrophysics Data System (ADS)

Bicalho, E. S.; Teixeira, D. B.; Panosso, A. R.; Perillo, L. I.; Iamaguti, J. L.; Pereira, G. T.; La Scala, N., Jr.

2012-04-01

Soil CO2 emission (FCO2) is influenced by chemical, physical and biological factors that affect the production of CO2 in the soil and its transport to the atmosphere, varying in time and space depending on environmental conditions, including the management of agricultural area. The aim of this study was to investigate the structure of spatial variability of FCO2 and soil properties by using fractal dimension (DF), derived from isotropic variograms at different scales, and construction of fractograms. The experimental area consisted of a regular grid of 60 × 60 m on sugarcane area under green management, containing 141 points spaced at minimum distances ranging from 0.5 to 10 m. Soil CO2 emission, soil temperature and soil moisture were evaluated over a period of 7 days, and soil chemical and physical properties were determined by sampling at a depth of 0.0 to 0.1 m. FCO2 showed an overall average of 1.51 µmol m-2 s-1, correlated significantly (p < 0.05) with soil physical factors such as soil bulk density, air-filled pore space, macroporosity and microporosity. Significant DF values were obtained in the characterization of FCO2 in medium and large scales (from 20 m). Variations in DF with the scale, which is the fractogram, indicate that the structure of FCO2 variability is similar to that observed for the soil temperature and total pore volume, and reverse for the other soil properties, except for macroporosity, sand content, soil organic matter, carbon stock, C/N ratio and CEC, which fractograms were not significantly correlated to the FCO2 fractogram. Thus, the structure of spatial variability for most soil properties, characterized by fractogram, presents a significant relationship with the structure of spatial variability of FCO2, generally with similar or dissimilar behavior, indicating the possibility of using the fractogram as tool to better observe the behavior of the spatial dependence of the variables along the scale.

The Effect of Vegetation on Soil Water Infiltration and Retention Capacity by Improving Soil Physiochemical Property in Semi-arid Grassland

NASA Astrophysics Data System (ADS)

A, Y.; Wang, G.

2017-12-01

Water shortage is the main limiting factor for semi-arid grassland development. However, the grassland are gradually degraded represented by species conversion, biomass decrease and ecosystem structure simplification under the influence of human activity. Soil water characteristics such as moisture, infiltration and conductivity are critical variables affecting the interactions between soil parameters and vegetation. In this study, Cover, Height, Shannon-Wiener diversity index, Pielou evenness index and Richness index are served as indexes of vegetation productivity and community structure. And saturated hydraulic conductivity (Ks) and soil moisture content are served as indexes of soil water characters. The interaction between vegetation and soil water is investigated through other soil parameters, such as soil organic matter content at different vertical depths and in different degradation area (e.g., initial, transition and degraded plots). The results show that Ks significantly controlled by soil texture other than soil organic matter content. So the influence of vegetation on Ks through increasing soil organic content (SOM) might be slight. However, soil moisture content (SMC) appeared significantly positive relationship with SOM and silt content and negative relationship with sand content at all depth, significantly. This indicated that capacity of soil water storage was influenced both by soil texture and organic matter. In addition, the highest correlation coefficient of SMC was with SOM at the sub-surficial soil layer (20 40 cm). At the depth of 20 40 cm, the soil water content was relatively steady which slightly influenced by precipitation and evaporation. But it significantly influenced by soil organic matter content which related to vegetation. The correlation coefficient between SOM and SMC at topsoil layer (0 20 cm) was lowest (R2=0.36, p<0.01), which indicated the influence of vegetation on soil water content not only by soil organic matter content but also the other influential factors, such as the root water uptake, precipitation and evaporation.

Study of microarthopod communities to assess soil quality in different managed vineyards

NASA Astrophysics Data System (ADS)

Gagnarli, E.; Goggioli, D.; Tarchi, F.; Guidi, S.; Nannelli, R.; Vignozzi, N.; Valboa, G.; Lottero, M. R.; Corino, L.; Simoni, S.

2015-01-01

Land use influences the abundance and diversity of soil arthropods. The evaluation of the impact of different management strategies on soil quality is increasingly requested. The determination of communities' structures of edaphic fauna can represent an efficient tool. In this study, in some vineyards in Piedmont (Italy), the effects of two different management systems, organic and integrated pest management (IPM), on soil biota were evaluated. As microarthropods living in soil surface are an important component of soil ecosystem interacting with all the other system components, a multi disciplinary approach was adopted by characterizing also some soil physical and chemical characteristics (soil texture, soil pH, total organic carbon, total nitrogen, calcium carbonate). Soil samplings were carried out on Winter 2011 and Spring 2012. All specimens were counted and determined up to the order level. The biological quality of the soil was defined through the determination of ecological indices, such as QBS-ar, species richness and indices of Shannon-Weaver, Pielou, Margalef and Simpson. The mesofauna abundance was affected by both the type of management and the soil texture. The analysis of microarthropod communities by QBS-ar showed higher values in organic than in IPM managed vineyards; in particular, the values registered in organic vineyards were similar to those characteristic of preserved soils.

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

PubMed

Ji, Li; Yang, Li Xue

2017-12-01

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

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

PubMed

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

2018-04-01

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

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities

PubMed Central

Iffis, Bachir; St-Arnaud, Marc; Hijri, Mohamed

2017-01-01

Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the PHPs present in the soil. PMID:28848583

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities.

PubMed

Iffis, Bachir; St-Arnaud, Marc; Hijri, Mohamed

2017-01-01

Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species ( Solidago canadensis, Populus balsamifera , and Lycopus europaeus ) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the PHPs present in the soil.

Relative Roles of Soil Moisture, Nutrient Supply, Depth, and Mechanical Impedance in Determining Composition and Structure of Wisconsin Prairies

PubMed Central

Wernerehl, Robert W.; Givnish, Thomas J.

2015-01-01

Ecologists have long classified Midwestern prairies based on compositional variation assumed to reflect local gradients in moisture availability. The best known classification is based on Curtis’ continuum index (CI), calculated using the presence of indicator species thought centered on different portions of an underlying moisture gradient. Direct evidence of the extent to which CI reflects differences in moisture availability has been lacking, however. Many factors that increase moisture availability (e.g., soil depth, silt content) also increase nutrient supply and decrease soil mechanical impedance; the ecological effects of the last have rarely been considered in any ecosystem. Decreased soil mechanical impedance should increase the availability of soil moisture and nutrients by reducing the root costs of retrieving both. Here we assess the relative importance of soil moisture, nutrient supply, and mechanical impedance in determining prairie composition and structure. We used leaf δ13C of C3 plants as a measure of growing-season moisture availability, cation exchange capacity (CEC) x soil depth as a measure of mineral nutrient availability, and penetrometer data as a measure of soil mechanical impedance. Community composition and structure were assessed in 17 remnant prairies in Wisconsin which vary little in annual precipitation. Ordination and regression analyses showed that δ13C increased with CI toward “drier” sites, and decreased with soil depth and % silt content. Variation in δ13C among remnants was 2.0‰, comparable to that along continental gradients from ca. 500–1500 mm annual rainfall. As predicted, LAI and average leaf height increased significantly toward “wetter” sites. CI accounted for 54% of compositional variance but δ13C accounted for only 6.2%, despite the strong relationships of δ13C to CI and CI to composition. Compositional variation reflects soil fertility and mechanical impedance more than moisture availability. This study is the first to quantify the effects of soil mechanical impedance on community ecology. PMID:26368936

Identification of Bacterial Groups Preferentially Associated with Mycorrhizal Roots of Medicago truncatula▿

PubMed Central

Offre, P.; Pivato, B.; Siblot, S.; Gamalero, E.; Corberand, T.; Lemanceau, P.; Mougel, C.

2007-01-01

The genetic structures of bacterial communities associated with Medicago truncatula Gaertn. cv. Jemalong line J5 (Myc+ Nod+) and its symbiosis-defective mutants TRV48 (Myc+ Nod−) and TRV25 (Myc− Nod−) were compared. Plants were cultivated in a fertile soil (Châteaurenard, France) and in soil from the Mediterranean basin showing a low fertility (Mas d'Imbert, France). Plant growth, root architecture, and the efficiency of root symbiosis of the three plant genotypes were characterized in the two soils. Structures of the bacterial communities were assessed by automated-ribosomal intergenic spacer analysis (A-RISA) fingerprinting from DNA extracted from the rhizosphere soil and root tissues. As expected, the TRV25 mutant did not develop endomycorrhizal symbiosis in any of the soils, whereas mycorrhization of line J5 and the TRV48 mutant occurred in both soils but at a higher intensity in the Mas d'Imbert (low fertility) than in the Châteaurenard soil. However, modifications of plant growth and root architecture, between mycorrhizal (J5 and TRV48) and nonmycorrhizal (TRV25) plants, were recorded only when cultivated in the Mas d'Imbert soil. Similarly, the genetic structures of bacterial communities associated with mycorrhizal and nonmycorrhizal plants differed significantly in the Mas d'Imbert soil but not in the Châteaurenard soil. Multivariate analysis of the patterns allowed the identification of molecular markers, explaining these differences, and markers were further sequenced. Molecular marker analysis allowed the delineation of 211 operational taxonomic units. Some of those belonging to the Comamonadaceae and Oxalobacteraceae (β-Proteobacteria) families were found to be significantly more represented within bacterial communities associated with the J5 line and the TRV48 mutant than within those associated with the TRV25 mutant, indicating that these bacterial genera were preferentially associated with mycorrhizal roots in the Mas d'Imbert soil. PMID:17142371

Relative Roles of Soil Moisture, Nutrient Supply, Depth, and Mechanical Impedance in Determining Composition and Structure of Wisconsin Prairies.

PubMed

Wernerehl, Robert W; Givnish, Thomas J

2015-01-01

Ecologists have long classified Midwestern prairies based on compositional variation assumed to reflect local gradients in moisture availability. The best known classification is based on Curtis' continuum index (CI), calculated using the presence of indicator species thought centered on different portions of an underlying moisture gradient. Direct evidence of the extent to which CI reflects differences in moisture availability has been lacking, however. Many factors that increase moisture availability (e.g., soil depth, silt content) also increase nutrient supply and decrease soil mechanical impedance; the ecological effects of the last have rarely been considered in any ecosystem. Decreased soil mechanical impedance should increase the availability of soil moisture and nutrients by reducing the root costs of retrieving both. Here we assess the relative importance of soil moisture, nutrient supply, and mechanical impedance in determining prairie composition and structure. We used leaf δ13C of C3 plants as a measure of growing-season moisture availability, cation exchange capacity (CEC) x soil depth as a measure of mineral nutrient availability, and penetrometer data as a measure of soil mechanical impedance. Community composition and structure were assessed in 17 remnant prairies in Wisconsin which vary little in annual precipitation. Ordination and regression analyses showed that δ13C increased with CI toward "drier" sites, and decreased with soil depth and % silt content. Variation in δ13C among remnants was 2.0‰, comparable to that along continental gradients from ca. 500-1500 mm annual rainfall. As predicted, LAI and average leaf height increased significantly toward "wetter" sites. CI accounted for 54% of compositional variance but δ13C accounted for only 6.2%, despite the strong relationships of δ13C to CI and CI to composition. Compositional variation reflects soil fertility and mechanical impedance more than moisture availability. This study is the first to quantify the effects of soil mechanical impedance on community ecology.

Spatial variability of isoproturon mineralizing activity within an agricultural field: geostatistical analysis of simple physicochemical and microbiological soil parameters.

PubMed

El Sebai, T; Lagacherie, B; Soulas, G; Martin-Laurent, F

2007-02-01

We assessed the spatial variability of isoproturon mineralization in relation to that of physicochemical and biological parameters in fifty soil samples regularly collected along a sampling grid delimited across a 0.36 ha field plot (40 x 90 m). Only faint relationships were observed between isoproturon mineralization and the soil pH, microbial C biomass, and organic nitrogen. Considerable spatial variability was observed for six of the nine parameters tested (isoproturon mineralization rates, organic nitrogen, genetic structure of the microbial communities, soil pH, microbial biomass and equivalent humidity). The map of isoproturon mineralization rates distribution was similar to that of soil pH, microbial biomass, and organic nitrogen but different from those of structure of the microbial communities and equivalent humidity. Geostatistics revealed that the spatial heterogeneity in the rate of degradation of isoproturon corresponded to that of soil pH and microbial biomass.

Carbon and nitrogen inputs affect soil microbial community structure and function

NASA Astrophysics Data System (ADS)

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

2016-12-01

Climate change has been projected to increase energy and nutrient inputs to soils, affecting soil organic matter (SOM) decomposition (priming effect) and microbial communities. However, many important questions remain: how do labile C and/or N inputs affect priming and microbial communities? What is the relationship between them? To address these questions, we applied N (NH4NO3 ; 100 µg N g-1 wk-1), C (13C glucose; 1000 µg C g-1 wk-1), C+N to four different soils for five weeks. We found: 1) N showed no effect, whereas C induced the greatest priming, and C+N had significantly lower priming than C. 2) C and C+N additions increased the relative abundance of actinobacteria, proteobacteria, and firmicutes, but reduced relative abundance of acidobacteria, chloroflexi, verrucomicrobia, planctomycetes, and gemmatimonadetes. 3) Actinobacteria and proteobacteria increased relative abundance over time, but most others decreased over time. 4) substrate additions (N, C, C+N) significantly reduced microbial alpha diversity, which also decreased over time. 5) For beta diversity, C and C+N formed significantly different communities compare to the control and N treatments. Overtime, microbial community structure significantly altered. Four soils have drastically different community structures. These results indicate amounts of substrate C were determinant factors in modulating the rate of SOM decomposition and microbial communities. Variable responses of different microbial communities to labile C and N inputs indicate that complex relationships between priming and microbial functions. In general, we demonstrate that energy inputs can quickly accelerate SOM decomposition whereas extra N input can slow this process, though both had similar microbial community responses.

The impact of cotton growing practices on soil microbiology and its relation to plant and soil health

NASA Astrophysics Data System (ADS)

Pereg, Lily

2013-04-01

Crop production and agricultural practices heavily impact the soil microbial communities, which differ among varying types of soils and environmental conditions. Soil-borne microbial communities in cotton production systems, as in every other cropping system, consist of microbial populations that may either be pathogenic, beneficial or neutral with respect to the cotton crop. Crop production practices have major roles in determining the composition of microbial communities and function of microbial populations in soils. The structure and function of any given microbial community is determined by various factors, including those that are influenced by farming and those not controlled by farming activities. Examples of the latter are environmental conditions such as soil type, temperature, daylight length and UV radiation, air humidity, atmospheric pressure and some abiotic features of the soil. On the other hand, crop production practices may determine other abiotic soil properties, such as water content, density, oxygen levels, mineral and elemental nutrient levels and the load of other crop-related soil amendments. Moreover, crop production highly influences the biotic properties of the soil and has a major role in determining the fate of soil-borne microbial communities associated with the crop plant. Various microbial strains react differently to the presence of certain plants and plant exudates. Therefore, the type of plant and crop rotations are important factors determining microbial communities. In addition, practice management, e.g. soil cultivation versus crop stubble retention, have a major effect on the soil conditions and, thus, on microbial community structure and function. All of the above-mentioned factors can lead to preferential selection of certain microbial population over others. It may affect not only the composition of microbial communities (diversity and abundance of microbial members) but also the function of the community (the ability of different microbes to perform certain activities). Therefore, agricultural practices may determine the ability of beneficial microbes to realise their plant growth promoting potential or the pathogenic expression of others. This presentation will review the current knowledge about the impact of cotton growing practices on microbial communities and soil health in different environments as well as endeavour to identify gaps worthwhile exploring in future research for promoting plant growth in healthy soils.

Soil Type Has a Stronger Role than Dipterocarp Host Species in Shaping the Ectomycorrhizal Fungal Community in a Bornean Lowland Tropical Rain Forest

PubMed Central

Essene, Adam L.; Shek, Katherine L.; Lewis, J. D.; Peay, Kabir G.; McGuire, Krista L.

2017-01-01

The role that mycorrhizal fungal associations play in the assembly of long-lived tree communities is poorly understood, especially in tropical forests, which have the highest tree diversity of any ecosystem. The lowland tropical rain forests of Southeast Asia are characterized by high levels of species richness within the family Dipterocarpaceae, the entirety of which has been shown to form obligate ectomycorrhizal (ECM) fungal associations. Differences in ECM assembly between co-occurring species of dipterocarp have been suggested, but never tested in adult trees, as a mechanism for maintaining the coexistence of closely related tree species in this family. Testing this hypothesis has proven difficult because the assembly of both dipterocarps and their ECM associates co-varies with the same edaphic variables. In this study, we used high-throughput DNA sequencing of soils and Sanger sequencing of root tips to evaluate how ECM fungi were structured within and across a clay–sand soil nutrient ecotone in a mixed-dipterocarp rain forest in Malaysian Borneo. We compared assembly patterns of ECM fungi in bulk soil to ECM root tips collected from three ecologically distinct species of dipterocarp. This design allowed us to test whether ECM fungi are more strongly structured by soil type or host specificity. As with previous studies of ECM fungi on this plot, we observed that clay vs. sand soil type strongly structured both the bulk soil and root tip ECM fungal communities. However, we also observed significantly different ECM communities associated with two of the three dipterocarp species evaluated on this plot. These results suggest that ECM fungal assembly on these species is shaped by a combination of biotic and abiotic factors, and that the soil edaphic niche occupied by different dipterocarp species may be mediated by distinct ECM fungal assemblages. PMID:29163567

Detecting Below-Ground Processes, Diversity, and Ecosystem Function in a Savanna Ecosystem Using Spectroscopy Across Different Vegetation Layers

NASA Astrophysics Data System (ADS)

Cavender-Bares, J.; Schweiger, A. K.; Madritch, M. D.; Gamon, J. A.; Hobbie, S. E.; Montgomery, R.; Townsend, P. A.

2017-12-01

Above-and below-ground plant traits are important for substrate input to the rhizosphere. The substrate composition of the rhizosphere, in turn, affects the diversity of soil organisms, influences soil biochemistry, and water content, and resource availability for plant growth. This has substantial consequences for ecosystem functions, such as above-ground productivity and stability. Above-ground plant chemical and structural traits can be linked to the characteristics of other plant organs, including roots. Airborne imaging spectroscopy has been successfully used to model and predict chemical and structural traits of the above-ground vegetation. However, remotely sensed images capture, almost exclusively, signals from the top of the canopy, providing limited direct information about understory vegetation. Here, we use a data set collected in a savanna ecosystem consisting of spectral measurements gathered at the leaf, the whole plant, and vegetation canopy level to test for hypothesized linkages between above- and below-ground processes that influence root biomass, soil biochemistry, and the diversity of the soil community. In this environment, consisting of herbaceous vegetation intermixed with shrubs and trees growing at variable densities, we investigate the contribution of different vegetation strata to soil characteristics and test the ability of imaging spectroscopy to detect these in plant communities with contrasting vertical structure.

Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River

PubMed Central

Wang, Wenhui; Wang, Hui; Feng, Youzhi; Wang, Lei; Xiao, Xingji; Xi, Yunguan; Luo, Xue; Sun, Ruibo; Ye, Xianfeng; Huang, Yan; Zhang, Zhengguang; Cui, Zhongli

2016-01-01

Soil microorganisms play a crucial role in the biogeochemical cycling of nutrient elements and maintaining soil health. We aimed to investigate the response of bacteria communities to organic farming over different crops (rice, tea and vegetable) along the middle and lower reaches of the Yangtze River of China. Compared with conventional farming, organic farming significantly increased soil nutrients, soil enzyme activities, and bacterial richness and diversity. A Venn diagram and principal component analysis revealed that the soils with 3 different crops under organic farming have more number and percent of shared OTUs (operational taxonomic units), and shared a highly similar microbial community structure. Under organic farming, several predominant guilds and major bacterial lineages (Rhizobiales, Thiotrichaceae, Micromonosporaceae, Desulfurellaceae and Myxococcales) contributing to nutrient (C, N, S and P) cycling were enriched, whereas the relative abundances of acid and alkali resistant microorganisms (Acidobacteriaceae and Sporolactobacillaceae) were increased under conventional farming practices. Our results indicated that, for all three crops, organic farming have a more stable microflora and the uniformity of the bacterial community structure. Organic agriculture significantly increased the abundance of some nutrition-related bacteria, while reducing some of the abundance of acid and alkali resistant bacteria. PMID:27725750

Rapid Shifts in Soil and Forest Floor Microbial Communities with Changes in Vegetation during Secondary Tropical Forest Succession

NASA Astrophysics Data System (ADS)

Smith, A.; Marin-Spiotta, E.; Balser, T. C.

2012-12-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. In order to predict how disturbance affects belowground carbon storage, it is important to understand how the forest floor and soil microbial community respond to changes in land cover, and the consequences on SOM formation and stabilization. We are measuring microbial functional diversity and activity across a long-term successional chronosequence of secondary forests regrowing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Here we report intra- and interannual data on soil and litter microbial community composition (via phospholipid fatty acid analysis, PLFA) and microbial activity (via extracellular enzyme activity) from active pastures, secondary forests aged 20, 30, 40, 70, and 90-years, and primary forests. Microbial community composition and extracellular enzyme activity differed significantly by season in these wet subtropical ecosystems, even though differences in mean monthly precipitation between the middle of the dry season (January) and the wet season (July) is only 30mm. Despite seasonal differences, there was a persistent strong effect of land cover type and forest successional stage, or age, on overall microbial community PLFA structure. Using principal component analysis, we found differences in microbial community structure among active pastures, early, and late successional forests. The separation of soil microbes into early and late successional communities parallels the clustering of tree composition data. While the successional patterns held across seasons, the importance of different microbial groups driving these patterns differed seasonally. Biomarkers for gram-positive and actinobacteria (i15:0 and 16:0 10Me) were associated with early (20, 30 & 40 year old) secondary forests in the dry season. These younger forest communities were identified by the biomarker for anaerobic gram-negative bacteria (c19:0) in the wet season, which suggests the presence of anaerobic microsites in these very clayey Oxisols. Enzymatic activity did not differ with succession but was highest in the dry season. We expect this may be due to decreased turnover of enzymes with low soil moisture. Interannual sampling has revealed a very rapid microbial response to changes in aboveground cover. Within a year following woody biomass encroachment, we detected a shift in the soil microbial community from a pasture-associated community to an early secondary forest community in one of our replicate pasture sites. This very rapid response in the belowground microbial community structure to changes in vegetation has not been strongly documented in the literature. This data supports a direct link between aboveground and belowground biotic community structures and highlights the importance of long-term repeated sampling of microbial communities in dynamic ecosystems. Our findings have implications for predicting rapid ecological responses to land-cover change.

Aggregate Stability and Erodibility of Purple Soil on Sloping Farmland as affected by different Soil Thickness

NASA Astrophysics Data System (ADS)

Huang, Xinjun; Zhang, Qingwen; Chen, Shanghong; Dong, Yuequn; Xiao, Meijia; Hamed, Lamy Mamdoh Mohamed

2017-04-01

Soil thickness is basic limiting condition for purple soil, not only due to its effect on crop production, but also its effect on soil structure. Steady-state of soil thickness will be achieved over time, as result the soil aggregate which the key factor of soil erodibility can be enhanced as well. However, the effect of soil thickness on aggregates stability and the characteristics of soil erodibility in sloping land have not yet fully understood.A field survey was conducted in hilly area of Sichuan region located in southeast China to study the relationship between soil aggregate stability and soil erodibility on sloping farmland under different four thickness (100cm, 80cm, 60cm, 30cm) of purple soil. Based on two different sieving methods (Dry and Wet sieving), we analyzed soil aggregate stability and its effect on soil erodibility within depth of 0-30cm soil layers. The results indicated that: Water stable aggregate on sloping farmland was ranged between 37.9% to 58.6%, where it increased with increasing the soil thickness. Moreover, fractal dimension calculated from dry-sieving and wet-sieving was 2.06-2.49 and 2.70-2.85 respectively, where it decreased with decreasing the soil thickness. The overall soil erodibility was 0.05-1.00 and a negative significant correlation was found between soil aggregate stability and erodibility(P<0.01). Moreover, farmland with thick soil profile tended to be high in soil erodibility within the top soil layer (0-30cm). The results reveal that soil thickness can affect soil aggregate stability as well as erodibility. As soil thickness increased, the top soil became more stable and less erodible. Keywords：purple soil; soil thickness; soil aggregate；soil erodibility

Small scale variability of soil parameters in different land uses on the southern slopes of Mount Kilimanjaro

NASA Astrophysics Data System (ADS)

Bogner, Christina; Kühnel, Anna; Hepp, Johannes; Huwe, Bernd

2016-04-01

The Kilimanjaro region in Tanzania constitutes a particularity compared to other areas in the country. Because enough water is available the population grows rapidly and large areas are converted from natural ecosystems to agricultural areas. Therefore, the southern slopes of Mt. Kilimanjaro encompass a complex mosaic of different land uses like coffee plantations, maize, agroforestry or natural savannah. Coffee is an important cash crop in the region and is owned mostly by large companies. In contrast, the agroforestry is a traditional way of agriculture and has been sustained by the Chagga tribe for centuries. These so called homegardens are organised as multi-level systems and contain a mixture of different crops. Correlations in soil and vegetation data may serve as indicators for crop and management impacts associated to different types of land use. We hypothesize that Chagga homegardens, for example, show a more pronounced spatial autocorrelation compared to coffee plantations due to manifold above and belowground crop structures, whereas the degree of anisotropy is assumed to be higher in the coffee sites due to linear elements in management. Furthermore, we hypothesize that the overall diversity of soil parameters in homegardens on a larger scale is higher, as individual owners manage their field differently, whereas coffee plantation management often follows general rules. From these general hypotheses we derive two specific research questions: a) Are there characteristic differences in the spatial organisation of soil physical parameters of different land uses? b) Is there a recognizable relationship between vegetation structure and soil physical parameters of topsoils? We measured soil physical parameters in the topsoil (bulk density, stone content, texture, soil moisture and penetration resistance). Additionally, we took spectra of soil samples with a portable VIS-NIR spectrometer to determine C and N and measured leaf area index and troughfall as an indicator of vegetation patterns. First results support our general hypotheses. In the coffee plantation anisotropic variation of soil parameters clearly showed the anthropogenic influence like compaction due to agricultural machinery. However, soil bulk density and penetration resistance in the homegarden were also quite variable at the sites. The larger variability of throughfall in the homegarden is reflected in the patterns of soil moisture. Regarding the larger scale, where we compared different homegardens and coffee plantations along the southern slope of the mountain, soil parameters of the coffee plots were less diverse than those of the homegardens.

Soil properties and not inputs control carbon : nitrogen : phosphorus ratios in cropped soils in the long term

NASA Astrophysics Data System (ADS)

Frossard, Emmanuel; Buchmann, Nina; Bünemann, Else K.; Kiba, Delwende I.; Lompo, François; Oberson, Astrid; Tamburini, Federica; Traoré, Ouakoltio Y. A.

2016-02-01

Stoichiometric approaches have been applied to understand the relationship between soil organic matter dynamics and biological nutrient transformations. However, very few studies have explicitly considered the effects of agricultural management practices on the soil C : N : P ratio. The aim of this study was to assess how different input types and rates would affect the C : N : P molar ratios of bulk soil, organic matter and microbial biomass in cropped soils in the long term. Thus, we analysed the C, N, and P inputs and budgets as well as soil properties in three long-term experiments established on different soil types: the Saria soil fertility trial (Burkina Faso), the Wagga Wagga rotation/stubble management/soil preparation trial (Australia), and the DOK (bio-Dynamic, bio-Organic, and "Konventionell") cropping system trial (Switzerland). In each of these trials, there was a large range of C, N, and P inputs which had a strong impact on element concentrations in soils. However, although C : N : P ratios of the inputs were highly variable, they had only weak effects on soil C : N : P ratios. At Saria, a positive correlation was found between the N : P ratio of inputs and microbial biomass, while no relation was observed between the nutrient ratios of inputs and soil organic matter. At Wagga Wagga, the C : P ratio of inputs was significantly correlated to total soil C : P, N : P, and C : N ratios, but had no impact on the elemental composition of microbial biomass. In the DOK trial, a positive correlation was found between the C budget and the C to organic P ratio in soils, while the nutrient ratios of inputs were not related to those in the microbial biomass. We argue that these responses are due to differences in soil properties among sites. At Saria, the soil is dominated by quartz and some kaolinite, has a coarse texture, a fragile structure, and a low nutrient content. Thus, microorganisms feed on inputs (plant residues, manure). In contrast, the soil at Wagga Wagga contains illite and haematite, is richer in clay and nutrients, and has a stable structure. Thus, organic matter is protected from mineralization and can therefore accumulate, allowing microorganisms to feed on soil nutrients and to keep a constant C : N : P ratio. The DOK soil represents an intermediate situation, with high nutrient concentrations, but a rather fragile soil structure, where organic matter does not accumulate. We conclude that the study of C, N, and P ratios is important to understand the functioning of cropped soils in the long term, but that it must be coupled with a precise assessment of element inputs and budgets in the system and a good understanding of the ability of soils to stabilize C, N, and P compounds.

Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter.

PubMed

Sun, Ruibo; Dsouza, Melissa; Gilbert, Jack A; Guo, Xisheng; Wang, Daozhong; Guo, Zhibin; Ni, Yingying; Chu, Haiyan

2016-12-01

Organic matter application is a widely used practice to increase soil carbon content and maintain soil fertility. However, little is known about the effect of different types of organic matter, or the input of exogenous species from these materials, on soil fungal communities. In this study, fungal community composition was characterized from soils amended with three types of organic matter over a 30-year fertilization experiment. Chemical fertilization significantly changed soil fungal community composition and structure, which was exacerbated by the addition of organic matter, with the direction of change influenced by the type of organic matter used. The addition of organic matter significantly increased soil fungal richness, with the greatest richness achieved in soils amended with pig manure. Importantly, following addition of cow and pig manure, fungal taxa associated with these materials could be found in the soil, suggesting that these exogenous species can augment soil fungal composition. Moreover, the addition of organic matter decreased the relative abundance of potential pathogenic fungi. Overall, these results indicate that organic matter addition influences the composition and structure of soil fungal communities in predictable ways. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Rheological properties of soil: a review

NASA Astrophysics Data System (ADS)

Zhu, Guangli; Zhu, Long; Yu, Chao

2017-05-01

Recently rheological methods have been applied to investigate the mechanical properties of soil micro-structure. Rheological techniques have a number of quantitative physically based measurements and offer a better understanding of how soil micro-structure behaves when subject to stress. Rheological material is refers to deformation properties similar to the solid and flow properties similar to the liquid of bound water and colloidal substances under stress. Soil rheology is divided into fluid rheology and plasticity rheology. Fluid rheology is produced by rheological material. Plasticity rheology mainly refers to the sliding and peristaltic between soil solid particles under shear stress. It is generally believed that the soft soil rheology mainly belongs to fluid rheology, while the rheology of sand and other coarse grained soil mainly belongs to plasticity rheology. Thus, rheology mechanisms of soft soil and sand are different. This paper introduces the methods of the research progress on the rheology of soil, in the soil rheological mechanism, rheological model and rheological numerical aspects of the research at home and abroad were summarized and analysed, discussed the problems existed in related research, and puts forward some suggestions for the future study on the rheology of soil.

ORGANIC VS CONVENTIONAL: SOIL NEMATODE COMMUNITY STRUCTURE AND FUNCTION.

PubMed

Kapp, C; Storey, S G; Malan, A P

2014-01-01

Global increases in human population are creating an ever-greater need for food production. Poor soil management practices have degraded soil to such an extent that rapidly improved management practices is the only way to ensure future food demands. In South Africa, deciduous fruit producers are realising the need for soil health, and for an increased understanding of the benefits of soil ecology, to ensure sustainable fruit production. This depends heavily on improved orchard management. Conventional farming relies on the addition of artificial fertilizers, and the application of chemicals, to prevent or minimise, the effects of the soil stages of pest insects, and of plant-parasitic nematodes. Currently, there is resistance toward conventional farming practices, which, it is believed, diminishes biodiversity within the soil. The study aimed to establish the soil nematode community structure and function in organically, and conventionally, managed deciduous fruit orchards. This was done by determining the abundance, the diversity, and the functionality of the naturally occurring free-living, and plant-parasitic, nematodes in deciduous fruit orchards in the Western Cape province of South Africa. The objective of the study was to form the basis for the use of nematodes as future indicators of soil health in deciduous fruit orchards. Orchards from neighbouring organic, and conventional, apricot farms, and from an organic apple orchard, were studied. All the nematodes were quantified, and identified, to family level. The five nematode-classified trophic groups were found at each site, while 14 families were identified in each orchard, respectively. Herbivores were dominant in all the orchards surveyed. Organic apples had the fewest herbivores and fungivores, with the highest number of carnivores. When comparing organic with conventional apricot orchards, higher numbers of plant-parasitic nematodes were found in the organic apricot orchards. The Maturity Index (MI) indicated that all orchard soils had values below 1.5, indicating disturbed conditions. The conventionally managed apricot orchard had the highest MI value, of 1.48. The Plant Parasitic Index (PPI) value was highest in the organically managed apricot orchard. In order to determine the existing enrichment, structural, and basal conditions, the nematode faunal analysis was applied to each site. All the sites indicated enriched and structured conditions. Regarding the diversity, the richness, and the evenness of the distribution, soil from the conventional apricot orchard had the highest species richness, whereas the organic apple orchard soil had the most even distribution of families. Different management practices in fruit orchards did not show marked differences in terms of community composition and structure.

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Partitioning of habitable pore space in earthworm burrows.

PubMed

Gorres, Josef H; Amador, Jose A

2010-03-01

Earthworms affect macro-pore structure of soils. However, some studies suggest that earthworm burrow walls and casts themselves differ greatly in structure from surrounding soils, potentially creating habitat for microbivorours nematodes which accelerate the decomposition and C and N mineralization. In this study aggregates were sampled from the burrow walls of the anecic earthworm Lumbricus terrestris and bulk soil (not altered by earthworms) from mesocosm incubated in the lab for 0, 1, 3, 5 and 16 weeks. Pore volumes and pore sizes were measured in triplicate with Mercury Intrusion Porosimetry (MIP). This method is well suited to establish pore size structure in the context of habitat, because it measures the stepwise intrusion of mercury from the outside of the aggregate into ever smaller pores. The progress of mercury into the aggregate interior thus resembles potential paths of a nematode into accessible habitable pore spaces residing in an aggregate. Total specific pore volume, V(s), varied between 0.13 and 0.18 mL/g and increased from 3 to 16 weeks in both burrow and bulk soil. Differences between total V(s) of bulk and burrow samples were not significant on any sampling date. However, differences were significant for pore size fractions at the scale of nematode body diameter.

Partitioning of habitable pore space in earthworm burrows

PubMed Central

Amador, Jose A.

2010-01-01

Earthworms affect macro-pore structure of soils. However, some studies suggest that earthworm burrow walls and casts themselves differ greatly in structure from surrounding soils, potentially creating habitat for microbivorours nematodes which accelerate the decomposition and C and N mineralization. In this study aggregates were sampled from the burrow walls of the anecic earthworm Lumbricus terrestris and bulk soil (not altered by earthworms) from mesocosm incubated in the lab for 0, 1, 3, 5 and 16 weeks. Pore volumes and pore sizes were measured in triplicate with Mercury Intrusion Porosimetry (MIP). This method is well suited to establish pore size structure in the context of habitat, because it measures the stepwise intrusion of mercury from the outside of the aggregate into ever smaller pores. The progress of mercury into the aggregate interior thus resembles potential paths of a nematode into accessible habitable pore spaces residing in an aggregate. Total specific pore volume, Vs, varied between 0.13 and 0.18 mL/g and increased from 3 to 16 weeks in both burrow and bulk soil. Differences between total Vs of bulk and burrow samples were not significant on any sampling date. However, differences were significant for pore size fractions at the scale of nematode body diameter. PMID:22736839

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters.

PubMed

Johnson, Riegardt M; Ramond, Jean-Baptiste; Gunnigle, Eoin; Seely, Mary; Cowan, Don A

2017-03-01

The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan). Permutational multivariate analysis of variance indicated that the nine soil niches presented significantly different physicochemistries (R 2  = 0.8306, P ≤ 0.0001) and that bacterial, fungal and archaeal populations were soil niche specific (R 2  ≥ 0.64, P ≤ 0.001). However, the abiotic drivers of community structure were Domain-specific (P < 0.05), with P, clay and sand fraction, and NH 4 influencing bacterial, fungal and archaeal communities, respectively. Soil physicochemistry and soil niche explained over 50% of the variation in community structure, and communities displayed strong non-random patterns of co-occurrence. Taken together, these results demonstrate that in central Namib Desert soil microbial communities, assembly is principally driven by deterministic processes.

Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil.

PubMed

Uhlik, Ondrej; Musilova, Lucie; Ridl, Jakub; Hroudova, Miluse; Vlcek, Cestmir; Koubek, Jiri; Holeckova, Marcela; Mackova, Martina; Macek, Tomas

2013-10-01

The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites have a strong effect on the bacterial community structure, activity, and associated degradative ability.

Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field.

PubMed

Cretoiu, Mariana Silvia; Korthals, Gerard W; Visser, Johnny H M; van Elsas, Jan Dirk

2013-09-01

A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment.

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

PubMed Central

Cretoiu, Mariana Silvia; Korthals, Gerard W.; Visser, Johnny H. M.

2013-01-01

A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment. PMID:23811512

Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community.

PubMed

Wang, Yi; Li, Chunyue; Tu, Cong; Hoyt, Greg D; DeForest, Jared L; Hu, Shuijin

2017-12-31

Intensive tillage and high inputs of chemicals are frequently used in conventional agriculture management, which critically depresses soil properties and causes soil erosion and nonpoint source pollution. Conservation practices, such as no-tillage and organic farming, have potential to enhance soil health. However, the long-term impact of no-tillage and organic practices on soil microbial diversity and community structure has not been fully understood, particularly in humid, warm climate regions such as the southeast USA. We hypothesized that organic inputs will lead to greater microbial diversity and a more stable microbial community, and that the combination of no-tillage and organic inputs will maximize soil microbial diversity. We conducted a long-term experiment in the southern Appalachian mountains of North Carolina, USA to test these hypotheses. The results showed that soil microbial diversity and community structure diverged under different management regimes after long term continuous treatments. Organic input dominated the effect of management practices on soil microbial properties, although no-tillage practice also exerted significant impacts. Both no-tillage and organic inputs significantly promoted soil microbial diversity and community stability. The combination of no-tillage and organic management increased soil microbial diversity over the conventional tillage and led to a microbial community structure more similar to the one in an adjacent grassland. These results indicate that effective management through reducing tillage and increasing organic C inputs can enhance soil microbial diversity and community stability. Copyright © 2017 Elsevier B.V. All rights reserved.

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

PubMed

Su, Jian-Qiang; Ding, Long-Jun; Xue, Kai; Yao, Huai-Ying; Quensen, John; Bai, Shi-Jie; Wei, Wen-Xue; Wu, Jin-Shui; Zhou, Jizhong; Tiedje, James M; Zhu, Yong-Guan

2015-01-01

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions. © 2014 John Wiley & Sons Ltd.

Distinct Soil Bacterial Communities Revealed under a Diversely Managed Agroecosystem

PubMed Central

Shange, Raymon S.; Ankumah, Ramble O.; Ibekwe, Abasiofiok M.; Zabawa, Robert; Dowd, Scot E.

2012-01-01

Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture) on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC) values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH) also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of pyrosequencing along with traditional analysis of soil physiochemical properties may provide insight into the ecology of descending taxonomic groups in bacterial communities. PMID:22844402

Distinct soil bacterial communities revealed under a diversely managed agroecosystem.

PubMed

Shange, Raymon S; Ankumah, Ramble O; Ibekwe, Abasiofiok M; Zabawa, Robert; Dowd, Scot E

2012-01-01

Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture) on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC) values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH) also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of pyrosequencing along with traditional analysis of soil physiochemical properties may provide insight into the ecology of descending taxonomic groups in bacterial communities.

Evidence for Different Reaction Pathways for Liquid and Granular Micronutrients in a Calcareous Soil

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

Hettiarachchi, Ganga M.; McLaughlin, Mike J.; Scheckel, Kirk G.

2008-06-16

The benefits of Mn and Zn fluid fertilizers over conventional granular products in calcareous sandy loam soils have been agronomically demonstrated. We hypothesized that the differences in the effectiveness between granular and fluid Mn and Zn fertilizers is due to different Mn and Zn reaction processes in and around fertilizer granules and fluid fertilizer bands. We used a combination of several synchrotron-based x-ray techniques, namely, spatially resolved micro-x-ray fluorescence (?-XRF), micro-x-ray absorption near edge structure spectroscopy (?-XANES), and bulk-XANES and -extended x-ray absorption fine structure (EXAFS) spectroscopy, along with several laboratory-based x-ray techniques to speciate different fertilizer-derived Mn and Znmore » species in highly calcareous soils to understand the chemistry underlying the observed differential behavior of fluid and granular micronutrient forms. Micro-XRF mapping of soil-fertilizer reactions zones indicated that the mobility of Mn and Zn from liquid fertilizer was greater than that observed for equivalent granular sources of these micronutrients in soil. After application of these micronutrient fertilizers to soil, Mn and Zn from liquid fertilizers were found to remain in comparatively more soluble solid forms, such as hydrated Mn phosphate-like, Mn calcite-like, adsorbed Zn-like, and Zn silicate-like phases, whereas Mn and Zn from equivalent granular sources tended to transform into comparatively less soluble solid forms such as Mn oxide-like, Mn carbonate-like, and Zn phosphate-like phases.« less

Soil physical and X-ray computed tomographic measurements to investigate small-scale structural differences under strip tillage compared to mulch till and no-till

NASA Astrophysics Data System (ADS)

Pöhlitz, Julia; Rücknagel, Jan; Schlüter, Steffen; Vogel, Hans-Jörg

2017-04-01

In recent years there has been an increasing application of conservation tillage techniques where the soil is no longer turned, but only loosened or left completely untilled. Dead plant material remains on the soil surface, which provides environmental and economic benefits such as the conservation of water, preventing soil erosion and saving time during seedbed preparation. There is a variety of conservation tillage systems, e.g. mulch till, no-till and strip tillage, which is a special feature. In strip tillage, the seed bed is divided into a seed zone (strip-till within the seed row: STWS) and a soil management zone (strip-till between the seed row: STBS). However, each tillage application affects physical soil properties and processes. Here, the combined application of classical soil mechanical and computed tomographic methods is used on a Chernozem (texture 0-30 cm: silt loam) to show small-scale structural differences under strip tillage (STWS, STBS) compared to no-till (NT) and mulch till (MT). In addition to the classical soil physical parameters dry bulk density and saturated conductivity (years: 2012, 2014, 2015) at soil depths 2-8 and 12-18 cm, stress-strain tests were carried out to map mechanical behavior. The stress-strain tests were performed for a load range from 5-550 kPa at 12-18 cm depth (year 2015). Mechanical precompression stress was determined on the stress-dry bulk density curves. Further, CT image cross sections and computed tomographic examinations (average pore size, porosity, connectivity, and anisotropy) were used from the same soil samples. For STBS and NT, a significant increase in dry bulk density was observed over the course of time compared to STWS and MT, which was more pronounced at 2-8 cm than at 12-18 cm depth. Despite higher dry bulk density, STBS displayed higher saturated conductivity in contrast to STWS, which can be attributed to higher earthworm abundance. In strip tillage, structural differences were identified. Mechanical precompression stress was significantly higher for STBS (141 kPa) than STWS (38 kPa). In addition, the CT image cross sections and the computed tomographic parameters confirmed the mechanically more stable soil structure observed under STBS with a higher initial average pore size but lower porosity and connectivity values compared to STWS. The reason for this is the lack of tillage. On the other hand, tillage at STWS created a loosened, porous and connective substrate. For all variants, the increasing load application led to progressive homogenization processes of the soil structure. At the same time, as stress application increased in all variants, the increase in dry bulk density led to a decrease in average pore size, porosity, and connectivity, while anisotropy increased. It was possible to confirm that strip tillage combines the advantages of no-till and a deeper conservation primary tillage, since on the one hand MT and STWS and on the other hand STBS and NT showed very similar soil structures. The computed tomographic parameters therefore provide valuable information about the impact of tillage on microscopic pore space attributes that improve our understanding about soil functional behavior at much larger scales.

Form and function in hillslope hydrology: in situ imaging and characterization of flow-relevant structures

NASA Astrophysics Data System (ADS)

Jackisch, Conrad; Angermann, Lisa; Allroggen, Niklas; Sprenger, Matthias; Blume, Theresa; Tronicke, Jens; Zehe, Erwin

2017-07-01

The study deals with the identification and characterization of rapid subsurface flow structures through pedo- and geo-physical measurements and irrigation experiments at the point, plot and hillslope scale. Our investigation of flow-relevant structures and hydrological responses refers to the general interplay of form and function, respectively. To obtain a holistic picture of the subsurface, a large set of different laboratory, exploratory and experimental methods was used at the different scales. For exploration these methods included drilled soil core profiles, in situ measurements of infiltration capacity and saturated hydraulic conductivity, and laboratory analyses of soil water retention and saturated hydraulic conductivity. The irrigation experiments at the plot scale were monitored through a combination of dye tracer, salt tracer, soil moisture dynamics, and 3-D time-lapse ground penetrating radar (GPR) methods. At the hillslope scale the subsurface was explored by a 3-D GPR survey. A natural storm event and an irrigation experiment were monitored by a dense network of soil moisture observations and a cascade of 2-D time-lapse GPR trenches. We show that the shift between activated and non-activated state of the flow paths is needed to distinguish structures from overall heterogeneity. Pedo-physical analyses of point-scale samples are the basis for sub-scale structure inference. At the plot and hillslope scale 3-D and 2-D time-lapse GPR applications are successfully employed as non-invasive means to image subsurface response patterns and to identify flow-relevant paths. Tracer recovery and soil water responses from irrigation experiments deliver a consistent estimate of response velocities. The combined observation of form and function under active conditions provides the means to localize and characterize the structures (this study) and the hydrological processes (companion study Angermann et al., 2017, this issue).

Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models

DOE PAGES

Wieder, William R.; Hartman, Melannie D.; Sulman, Benjamin N.; ...

2017-11-09

Emerging insights into factors responsible for soil organic matter stabilization and decomposition are being applied in a variety of contexts, but new tools are needed to facilitate the understanding, evaluation, and improvement of soil biogeochemical theory and models at regional to global scales. To isolate the effects of model structural uncertainty on the global distribution of soil carbon stocks and turnover times we developed a soil biogeochemical testbed that forces three different soil models with consistent climate and plant productivity inputs. The models tested here include a first-order, microbial implicit approach (CASA-CNP), and two recently developed microbially explicit models thatmore » can be run at global scales (MIMICS and CORPSE). When forced with common environmental drivers, the soil models generated similar estimates of initial soil carbon stocks (roughly 1,400 Pg C globally, 0–100 cm), but each model shows a different functional relationship between mean annual temperature and inferred turnover times. Subsequently, the models made divergent projections about the fate of these soil carbon stocks over the 20th century, with models either gaining or losing over 20 Pg C globally between 1901 and 2010. Single-forcing experiments with changed inputs, tem- perature, and moisture suggest that uncertainty associated with freeze-thaw processes as well as soil textural effects on soil carbon stabilization were larger than direct temper- ature uncertainties among models. Finally, the models generated distinct projections about the timing and magnitude of seasonal heterotrophic respiration rates, again reflecting structural uncertainties that were related to environmental sensitivities and assumptions about physicochemical stabilization of soil organic matter. Here, by providing a computationally tractable and numerically consistent framework to evaluate models we aim to better understand uncertainties among models and generate insights about fac- tors regulating the turnover of soil organic matter.« less

Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models

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

Wieder, William R.; Hartman, Melannie D.; Sulman, Benjamin N.

Emerging insights into factors responsible for soil organic matter stabilization and decomposition are being applied in a variety of contexts, but new tools are needed to facilitate the understanding, evaluation, and improvement of soil biogeochemical theory and models at regional to global scales. To isolate the effects of model structural uncertainty on the global distribution of soil carbon stocks and turnover times we developed a soil biogeochemical testbed that forces three different soil models with consistent climate and plant productivity inputs. The models tested here include a first-order, microbial implicit approach (CASA-CNP), and two recently developed microbially explicit models thatmore » can be run at global scales (MIMICS and CORPSE). When forced with common environmental drivers, the soil models generated similar estimates of initial soil carbon stocks (roughly 1,400 Pg C globally, 0–100 cm), but each model shows a different functional relationship between mean annual temperature and inferred turnover times. Subsequently, the models made divergent projections about the fate of these soil carbon stocks over the 20th century, with models either gaining or losing over 20 Pg C globally between 1901 and 2010. Single-forcing experiments with changed inputs, tem- perature, and moisture suggest that uncertainty associated with freeze-thaw processes as well as soil textural effects on soil carbon stabilization were larger than direct temper- ature uncertainties among models. Finally, the models generated distinct projections about the timing and magnitude of seasonal heterotrophic respiration rates, again reflecting structural uncertainties that were related to environmental sensitivities and assumptions about physicochemical stabilization of soil organic matter. Here, by providing a computationally tractable and numerically consistent framework to evaluate models we aim to better understand uncertainties among models and generate insights about fac- tors regulating the turnover of soil organic matter.« less

Using semi-variogram analysis for providing spatially distributed information on soil surface condition for land surface modeling

NASA Astrophysics Data System (ADS)

Croft, Holly; Anderson, Karen; Kuhn, Nikolaus J.

2010-05-01

The ability to quantitatively and spatially assess soil surface roughness is important in geomorphology and land degradation studies. Soils can experience rapid structural degradation in response to land cover changes, resulting in increased susceptibility to erosion and a loss of Soil Organic Matter (SOM). Changes in soil surface condition can also alter sediment detachment, transport and deposition processes, infiltration rates and surface runoff characteristics. Deriving spatially distributed quantitative information on soil surface condition for inclusion in hydrological and soil erosion models is therefore paramount. However, due to the time and resources involved in using traditional field sampling techniques, there is a lack of spatially distributed information on soil surface condition. Laser techniques can provide data for a rapid three dimensional representation of the soil surface at a fine spatial resolution. This provides the ability to capture changes at the soil surface associated with aggregate breakdown, flow routing, erosion and sediment re-distribution. Semi-variogram analysis of the laser data can be used to represent spatial dependence within the dataset; providing information about the spatial character of soil surface structure. This experiment details the ability of semi-variogram analysis to spatially describe changes in soil surface condition. Soil for three soil types (silt, silt loam and silty clay) was sieved to produce aggregates between 1 mm and 16 mm in size and placed evenly in sample trays (25 x 20 x 2 cm). Soil samples for each soil type were exposed to five different durations of artificial rainfall, to produce progressively structurally degraded soil states. A calibrated laser profiling instrument was used to measure surface roughness over a central 10 x 10 cm plot of each soil state, at 2 mm sample spacing. The laser data were analysed within a geostatistical framework, where semi-variogram analysis quantitatively represented the change in soil surface structure during crusting. The laser data were also used to create digital surface models (DSM) of the soil states for visual comparison. This research has shown that aggregate breakdown and soil crusting can be shown quantitatively by a decrease in sill variance (silt soil: 11.67 (control) to 1.08 (after 90 mins rainfall)). Features present within semi-variograms were spatially linked to features at the soil surface, such as soil cracks, tillage lines and areas of deposition. Directional semi-variograms were used to provide a spatially orientated component, where the directional sill variance associated with a soil crack was shown to increase from 7.95 to 19.33. Periodicity within semi-variogram was also shown to quantify the spatial scale of soil cracking networks and potentially surface flowpaths; an average distance between soil cracks of 37 mm closely corresponded to the distance of 38 mm shown in the semi-variogram. The results provide a strong basis for the future retrieval of spatio-temporal variations in soil surface condition. Furthermore, the presence of process-based information on hydrological pathways within semi-variograms may work towards an inclusion of geostatisically-derived information in land surface models and the understanding of complex surface processes at different spatial scales.

Directional reflectance factors for monitoring spatial changes in soil surface structure and soil organic matter erosion in agricultural systems

NASA Astrophysics Data System (ADS)

Croft, H.; Anderson, K.

2012-04-01

Soils can experience rapid structural degradation in response to land cover changes, resulting in reduced soil productivity, increased erodibility and a loss of soil organic matter (SOM). The breakdown of soil aggregates through slaking and raindrop impact is linked to organic matter turnover, with subsequently eroded material often displaying proportionally more SOM. A reduction in aggregate stability is reflected in a decline in soil surface roughness (SSR), indicating that a soil structural change can be used to highlight soil vulnerability to SOM loss through mineralisation or erosion. Accurate, spatially-continuous measurements of SSR are therefore needed at a variety of spatial and temporal scales to understand the spatial nature of SOM erosion and deposition. Remotely-sensed data can provide a cost-effective means of monitoring changes in soil surface condition over broad spatial extents. Previous work has demonstrated the ability of directional reflectance factors to monitor soil crusting within a controlled laboratory experiment, due to changes in the levels of self-shadowing effects by soil aggregates. However, further research is needed to test this approach in situ, where other soil variables may affect measured reflectance factors and to investigate the use of directional reflectance factors for monitoring soil erosion processes. This experiment assesses the potential of using directional reflectance factors to monitor changes in SSR, aggregate stability and soil organic carbon (SOC) content for two agricultural conditions. Five soil plots representing tilled and seedbed soils were subjected to different durations of natural rainfall, producing a range of different levels of SSR. Directional reflectance factors were measured concomitantly with sampling for soil structural and biochemical tests at each soil plot. Soil samples were taken to measure aggregate stability (wet sieving), SOC (loss on ignition) and soil moisture (gravimetric method). SSM values varied from 8.70 to 20.05% and SOC from 1.33 to 1.05%, across all soil plots. Each plot was characterised using a close-range laser scanning device with a 2 mm sampling interval. The point laser data were geostatistically analysed to provide a spatially-distributed measure of SSR, giving sill variance values from 3.15 to 22.99. Reflectance factors from the soil states were measured using a ground-based hyperspectral spectroradiometer (400-2500 nm) attached to an A-frame device. This method allowed measurement at a range of viewing zenith angles from extreme forwardscatter (-60°) to extreme backscatter (+60°) at a 10° sampling resolution in the solar principal plane. Reflectance measurements were compared to geostatistically-derived indicators of SSR from the laser profile data. Forward-scattered reflectance factors exhibited a very strong relationship to SSR (R2 = 0.84 at -60°; p< 0.05), demonstrating the operational potential of directional reflectance for providing SSR measurements, despite conflicting variation in SSM. SSM also presented an interesting directional signal (R2 = 0.99 at +20°; p< 0.01). Furthermore, the results showed an important link between SRR decline as measured using directional reflectance, with a decline in aggregate stability and SOC content. These findings provide an empirical and theoretical basis for the future retrieval of spatially-continuous assessments of soil surface structure and carbon turnover within a landscape context.

The effect of water harvesting techniques on runoff, sedimentation, and soil properties.

PubMed

Al-Seekh, Saleh H; Mohammad, Ayed G

2009-07-01

This study addressed the hydrological processes of runoff and sedimentation, soil moisture content, and properties under the effect of different water harvesting techniques (treatments). The study was conducted at three sites, representing environmental condition gradients, located in the southern part of the West Bank. For each treatment, the study evaluated soil chemical and physical properties, soil moisture at 30 cm depth, surface runoff and sedimentation at each site. Results showed that runoff is reduced by 65-85% and sedimentation by 58-69% in stone terraces and semi-circle bunds compared to the control at the semi-humid site. In addition, stone terraces and contour ridges significantly reduced the amount of total runoff by 80% and 73%, respectively, at the arid site. Soil moisture content was significantly increased by water harvesting techniques compared to the control in all treatments at the three study sites. In addition, the difference between the control and the water harvesting structures were higher in the arid and semi-arid areas than in the semi-humid area. Soil and water conservation, via utilization of water harvesting structures, is an effective principle for reducing the negative impact of high runoff intensity and subsequently increasing soil moisture storage from rainfall. Jessour systems in the valley and stone terraces were effective in increasing soil moisture storage, prolonging the growing season for natural vegetation, and decreasing the amount of supplemental irrigation required for growing fruit trees.

Can organic matter hide from decomposers in the labyrinth of soil aggregates? Micro-engineered Soil Chips challenging foraging fungi

NASA Astrophysics Data System (ADS)

Hammer, Edith C.; Aleklett, Kristin; Arellano Caicedo, Carlos G.; Bengtsson, Martin; Micaela Mafla Endara, Paola; Ohlsson, Pelle

2017-04-01

From the point of view of microorganisms, the soil environment is an enormously complex labyrinth with paths and dead-end streets, where resources and shelters are unevenly distributed. We study foraging strategies of soil organisms, especially fungi, and the possibility of physio-spatial stabilization of organic matter by "hiding" in occluded soil spaces. We manipulate growth habitat microstructure with lab-on-a-chip techniques, where we designed complex environments with channels and obstacle at dimensions of the size of hyphae, and construct them in the transparent, gas-permeable polymer PDMS. We fill those with different nutrient solutions or combine with mineral nutrient gradients, and inoculate them with soil organisms. We analyze organisms and substrates with microscopy, fluorescence microscopy and analytical chemistry. We compared different soil litter decomposers and an arbuscular mycorrhizal fungus for their ability to forage through complex air-gap structures and attempt to classify them into functional traits concerning their mycelium directionality, space-exploring approach and ability to grow through acute angles and narrow constrictions. We identified structures which are very difficult to penetrate for most species, and compounds located behind such features may thus be spatially unavailable for decomposers. We discuss our approach in comparison to soil pore space tomographic analyses and findings we made in the pore space of colonized wood biochar.

The Effect of Water Harvesting Techniques on Runoff, Sedimentation, and Soil Properties

NASA Astrophysics Data System (ADS)

Al-Seekh, Saleh H.; Mohammad, Ayed G.

2009-07-01

This study addressed the hydrological processes of runoff and sedimentation, soil moisture content, and properties under the effect of different water harvesting techniques (treatments). The study was conducted at three sites, representing environmental condition gradients, located in the southern part of the West Bank. For each treatment, the study evaluated soil chemical and physical properties, soil moisture at 30 cm depth, surface runoff and sedimentation at each site. Results showed that runoff is reduced by 65-85% and sedimentation by 58-69% in stone terraces and semi-circle bunds compared to the control at the semi-humid site. In addition, stone terraces and contour ridges significantly reduced the amount of total runoff by 80% and 73%, respectively, at the arid site. Soil moisture content was significantly increased by water harvesting techniques compared to the control in all treatments at the three study sites. In addition, the difference between the control and the water harvesting structures were higher in the arid and semi-arid areas than in the semi-humid area. Soil and water conservation, via utilization of water harvesting structures, is an effective principle for reducing the negative impact of high runoff intensity and subsequently increasing soil moisture storage from rainfall. Jessour systems in the valley and stone terraces were effective in increasing soil moisture storage, prolonging the growing season for natural vegetation, and decreasing the amount of supplemental irrigation required for growing fruit trees.

Streptomyces communities in soils polluted with heavy metals

NASA Astrophysics Data System (ADS)

Grishko, V. N.; Syshchikova, O. V.

2009-02-01

The contents of differently mobile heavy metal compounds and their influence on the formation of microbial cenoses (particularly, streptomyces communities) in technogenically disturbed soils are considered. Elevated concentrations of mobile Cu, Zn, Ni, Cd, and Fe compounds are shown to determine structural-functional changes in microbial cenoses that are displayed in a decreasing number of microorganisms and a narrower spectrum of the streptomyces species. Some specific features of the formation of streptomyces communities in technogenic soils were revealed on the basis of the analysis of their species structure with the use of the Margalef, Berger-Parker, and Sorensen indices of biodiversity.

How to interpret rheometry, an innovative technique in soil physicochemistry, correctly - explained by critical users

NASA Astrophysics Data System (ADS)

Holthusen, Dörthe; Paulus, Eloi; Pértile, Patricia; Reichert, José Miguel; José Reinert, Dalvan; Horn, Rainer

2015-04-01

In soil physics some new methods were developed in the past years, e.g. with regard to observe soil structure non-invasively by means of micro-computed tomography, while the range of methods that investigate a soil's behavior in motion, e.g. under the impact of mechanic stresses, was enlarged by rheometry. The adjustment to the specific conditions of soil as a relatively dry and heterogeneous media opened a new field compared to the materials under investigations till then, like concrete or clay dispersions. The potential of this methodology is not fully appreciated yet which we would like to change with the help of our findings and the deduced guidelines. Rheology itself has been making part of soil science already for many years; however, the technical investigation was mostly done at a large scale, by means of triaxial shear or shear frame or compression tests etc. The corresponding measuring device, the rheometer, hence was tested and developed by and for the industries of food, cosmetics, paintings and coatings and only quite recently found to be applicable to soil also. The most interesting aspect was the possibility to combine soil physics with soil chemistry, namely to relate the behavior of soil under mechanical stresses to chemical interactions like e.g. particle charge and friction between single particles by means of an amplitude sweep test. Meanwhile, many different soils of different texture, organic matter and oxides and hydroxides content, and fertilization levels have been investigated at different matric potentials and allowed for a comparatively broad classification system. Therewith, the microstructural stability of a given soil by means of stiffness degradation during an amplitude sweep test can be categorized as a function of texture and matric potential. The micro scale soil stability furthermore influences the processes and thus soil structural stability at larger scales, which supports the investigations of relationships between different scales. Transferability to field situations is given due to the character of the mechanic stress which equals those appearing e.g. under a tractor tire exerting vibrating, compressing and shearing forces. Unfortunately, the multiple results of this single test can impede the use of rheometry as their interpretation requires intensive data analysis. By pointing out the single results and their meaning for soil structure, we aim at facilitating the use of rheometry. We also suggest moderate alterations to take into account more strongly the vertical compression of soil for a more comprehensive implementation of a micro shear test. Additionally, we point out further uses of a rheometer in soil physics, which is the viscosity, i. e. the ability of a fluid to penetrate into a porous system and to be relocated within. Herewith, quite complex fluid characteristics, e.g. of animal manure, anaerobic digestates, but also pesticides in aqueous solution, root mucilage etc. can be determined and applied as improved, because more detailed, model parameters in soil water transport. As a conclusion, our contribution aims at further promoting a promising method for investigating the fundamentals of soil physics at the interface to soil chemistry.

Comparative study of soil erodibility and critical shear stress between loess and purple soils

NASA Astrophysics Data System (ADS)

Xing, Hang; Huang, Yu-han; Chen, Xiao-yan; Luo, Bang-lin; Mi, Hong-xing

2018-03-01

Loess and purple soils are two very important cultivated soils, with the former in the loess region and the latter in southern sub-tropical region of China, featured with high-risks of erosion, considerable differences of soil structures due to differences in mineral and nutrient compositions. Study on soil erodibility (Kr) and critical shear stress (τc) of these two soils is beneficial to predict soil erosion with such models as WEPP. In this study, rill erosion experimental data sets of the two soils are used for estimating their Kr and τc before they are compared to understand their differences of rill erosion behaviors. The maximum detachment rates of the loess and purple soils are calculated under different hydrodynamic conditions (flow rates: 2, 4, 8 L/min; slope gradients: 5°, 10°, 15°, 20°, 25°) through analytical and numerical methods respectively. Analytical method used the derivative of the function between sediment concentration and rill length to estimate potential detachment rates, at the rill beginning. Numerical method estimated potential detachment rates with the experimental data, at the rill beginning and 0.5 m location. The Kr and τc of these two soils are determined by the linear equation based on experimental data. Results show that the methods could well estimate the Kr and τc of these two soils as they remain basically unchanged under different hydrodynamic conditions. The Kr value of loess soil is about twice of the purple soil, whereas the τc is about half of that. The numerical results have good correlations with the analytical values. These results can be useful in modeling rill erosion processes of loess and purple soils.

Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

PubMed Central

Shi, Yu; Xiang, Xingjia; Shen, Congcong; Neufeld, Josh D.; Walker, Virginia K.

2014-01-01

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H′) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. PMID:25362064

Vegetation-associated impacts on arctic tundra bacterial and microeukaryotic communities.

PubMed

Shi, Yu; Xiang, Xingjia; Shen, Congcong; Chu, Haiyan; Neufeld, Josh D; Walker, Virginia K; Grogan, Paul

2015-01-01

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H') were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau.

PubMed

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Zhou, Huakun; Ganjurjav, Hasbagan; Wang, Xuexia

2016-08-15

Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, <10% variations of microbial diversity was explained by soil properties; and the soil microbial communities among different treatments were similar. The soil microbial community in the cultivated grassland was varied from it in native grasslands. Over 50% variations of soil microbial communities among different treatments were explained by soil nutrients and moisture in each grassland type. Our results suggest that climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

Non-invasive localization of organic matter in soil aggregates using SR-μCT

NASA Astrophysics Data System (ADS)

Peth, Stephan; Mordhorst, Anneka; Chenu, Claire; Uteau Puschmann, Daniel; Garnier, Patricia; Nunan, Naoise; Pot, Valerie; Beckmann, Felix; Ogurreck, Malte

2014-05-01

Knowledge of the location of soil organic matter (SOM) and its spatial association to soil structure is an important step in improving modeling approaches for simulating organic matter turnover processes. Advanced models for carbon mineralization are able to account for the 3D distribution of SOM which is assumed to influence mineralisation. However, their application is still limited by the fact that no method exists to non-invasively determine the 3D spatial distribution of SOM in structured soils. SR-based X-ray microtomography (SR-µCT) is an advanced and promising tool in gaining knowledge on the 3-dimensional organization of soil phases (minerals, organic matter, water, air) which on a voxel level could be implemented into spatially explicit models. However, since the contrast of linear attenuation coefficients of soil organic matter on the one hand and mineral components and water on the other hand are relatively low, especially when materials are finely dispersed, organic matter within the soil pore space is often not resolved in ordinary X-ray absorption contrast imaging. To circumvent this problem we have developed a staining procedure for organic matter using Osmium-tetroxide since Osmium is an element with an absorption edge at a higher X-ray energy level. Osmium is known from transmission electron microscopy analysis (TEM) to stain organic matter specifically and irreversibly while having an absorption edge at approximately 74 keV. We report on the application of a novel Osmium vapor staining method to analyze differences in organic matter content and identify small scale spatial distribution of SOM in soil aggregates. To achieve this we have taken soil aggregate samples (6-8 mm across) obtained from arable soils differing in soil management. Aggregate samples were investigated by synchrotron-based X-ray microtomography (SR-µCT) after staining the sample with Osmium-tetroxide (OsO4) vapor. We utilized the monochromatic X-ray beam to locate osmium bound to SOM in the stained soil aggregate samples by scanning the aggregates at different photon energies: 30 keV at which the attenuation contrast is optimal for distinguishing other soil constituents, 70 keV (below the absorption of osmium) and 78 keV (above the absorption edge of osmium). The results suggest that particulate organic matter, which was not visibly by scanning samples at energy levels optimal for resolving soil structure (30 keV), was identified after osmium staining and scanning the samples at energy levels just below (70 keV) and above (78 keV) the absorption edge of Osmium. Subtracting the images below from the images above the osmium edged we were able to isolate stained particulate organic matter which otherwise would have been wrongly interpreted as pore space without staining. Combining both pore space and organic matter distribution we are able to investigate the association of SOM with soil structure.

Microbiological indicators for assessing ecosystem soil quality and changes in it at degraded sites treated with compost

NASA Astrophysics Data System (ADS)

Ancona, Valeria; Barra Caracciolo, Anna; Grenni, Paola; Di Lenola, Martina; Calabrese, Angelantonio; Campanale, Claudia; Felice Uricchio, Vito

2014-05-01

Soil quality is defined as the capacity of a soil to function as a vital system, within natural or managed ecosystem boundaries, sustain plant and animal health and productivity, maintain or enhance air and water environment quality and support human health and habitation. Soil organisms are extremely diverse and contribute to a wide range of ecosystem services that are essential to the sustainable functioning of natural and managed ecosystems. In particular, microbial communities provide several ecosystem services, which ensure soil quality and fertility. In fact, they adapt promptly to environmental changes by varying their activity and by increasing the reproduction of populations that have favourable skills. The structure (e.g. cell abundance) and functioning (e.g. viability and activity) of natural microbial communities and changes in them under different environmental conditions can be considered useful indicators of soil quality state. In this work we studied the quality state of three different soils, located in Taranto Province (Southern Italy), affected by land degradation processes, such as organic matter depletion, desertification and contamination (PCB and metals). Moreover, compost, produced from selected organic waste, was added to the soils studied in order to improve their quality state. Soil samples were collected before and after compost addition and both microbial and chemical analyses were performed in order to evaluate the soil quality state at each site at different times. For this purpose, the microbiological indicators evaluated were bacterial abundance (DAPI counts), cell viability (Live/Dead method), dehydrogenase activity (DHA) and soil respiration. At the same time, the main physico-chemical soil characteristics (organic carbon, available phosphorous, total nitrogen, carbonate and water content, texture and pH) were also measured. Moreover, in the contaminated soil samples PCB and inorganic (e.g. Pb, Se, Sn, Zn) contaminants were analysed respectively by GC-MS and ICP-MS. The overall results showed that the bacterial structure and functioning were affected in different ways by the organic carbon availability and quality, and contaminant occurrence (organic or inorganic compounds). The compost treatment contributed to improve soil fertility and to increase cell number and activity after 7 months in the two low organic carbon content soils. At the polluted site a general increase in bacterial activity after compost addition was also observed and this might be related to a decrease in inorganic and organic contamination levels.

Abundance and diversity of Archaea in heavy-metal-contaminated soils.

PubMed

Sandaa, R A; Enger, O; Torsvik, V

1999-08-01

The impact of heavy-metal contamination on archaean communities was studied in soils amended with sewage sludge contaminated with heavy metals to varying extents. Fluorescent in situ hybridization showed a decrease in the percentage of Archaea from 1.3% +/- 0.3% of 4', 6-diamidino-2-phenylindole-stained cells in untreated soil to below the detection limit in soils amended with heavy metals. A comparison of the archaean communities of the different plots by denaturing gradient gel electrophoresis revealed differences in the structure of the archaean communities in soils with increasing heavy-metal contamination. Analysis of cloned 16S ribosomal DNA showed close similarities to a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species.

Microbiological assessment of the application of quicklime and limestone as a measure to stabilize the structure of compaction-prone soils

NASA Astrophysics Data System (ADS)

Deltedesco, Evi; Bauer, Lisa-Maria; Unterfrauner, Hans; Peticzka, Robert; Zehetner, Franz; Keiblinger, Katharina Maria

2014-05-01

Compaction of soils is caused by increasing mechanization of agriculture and forestry, construction of pipelines, surface mining and land recultivation. This results in degradation of aggregate stability and a decrease of pore space, esp. of macropores. It further impairs the water- and air permeability, and restricts the habitat of soil organisms. A promising approach to stabilize the structure and improve the permeability of soils is the addition of polyvalent ions like Ca2+ which can be added in form of quicklime (CaO) and limestone (CaCO3). In this study, we conducted a greenhouse pot experiment using these two different sources of calcium ions in order to evaluate their effect over time on physical properties and soil microbiology. We sampled silty and clayey soils from three different locations in Austria and incubated them with and without the liming materials (application 12.5 g) for 3 months in four replicates. In order to assess short-term and medium-term effects, soil samples were taken 2 days, 1 month and 3 months after application of quicklime and limestone, respectively. For these samples, we determined pH, bulk density, aggregate stability and water retention characteristics. Further, we measured microbiological parameters, such as potential enzyme activities (cellulase, phosphatase, chitinase, protease, phenoloxidase and peroxidase activity), PLFAs, microbial biomass carbon and nitrogen, dissolved organic carbon and nitrogen, nitrate nitrogen and ammonium nitrogen. In contrast to limestone, quicklime significantly improved soil aggregate stability in all tested soils only 2 days after application. Initially, soil pH was strongly increased by quicklime; however, after the second sampling (one month) the pH values of all tested soils returned to levels comparable to the soils treated with limestone. Our preliminary microbiological results show an immediate inhibition effect of quicklime on most potential hydrolytic enzyme activities and an increase in oxidative enzyme activities. These effects seem to be less pronounced in the medium term. In summary our results indicate, that the application of quicklime is a feasible measure for immediate stabilization of the structure of compaction-prone soils, showing only short-term impact on most microbial parameters.

Scaling methane oxidation: From laboratory incubation experiments to landfill cover field conditions

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

Abichou, Tarek, E-mail: abichou@eng.fsu.edu; Mahieu, Koenraad; Chanton, Jeff

2011-05-15

Evaluating field-scale methane oxidation in landfill cover soils using numerical models is gaining interest in the solid waste industry as research has made it clear that methane oxidation in the field is a complex function of climatic conditions, soil type, cover design, and incoming flux of landfill gas from the waste mass. Numerical models can account for these parameters as they change with time and space under field conditions. In this study, we developed temperature, and water content correction factors for methane oxidation parameters. We also introduced a possible correction to account for the different soil structure under field conditions.more » These parameters were defined in laboratory incubation experiments performed on homogenized soil specimens and were used to predict the actual methane oxidation rates to be expected under field conditions. Water content and temperature corrections factors were obtained for the methane oxidation rate parameter to be used when modeling methane oxidation in the field. To predict in situ measured rates of methane with the model it was necessary to set the half saturation constant of methane and oxygen, K{sub m}, to 5%, approximately five times larger than laboratory measured values. We hypothesize that this discrepancy reflects differences in soil structure between homogenized soil conditions in the lab and actual aggregated soil structure in the field. When all of these correction factors were re-introduced into the oxidation module of our model, it was able to reproduce surface emissions (as measured by static flux chambers) and percent oxidation (as measured by stable isotope techniques) within the range measured in the field.« less

Effect of Sugarcane Burning or Green Harvest Methods on the Brazilian Cerrado Soil Bacterial Community Structure

PubMed Central

Rachid, Caio T. C. C.; Santos, Adriana L.; Piccolo, Marisa C.; Balieiro, Fabiano C.; Coutinho, Heitor L. C.; Peixoto, Raquel S.; Tiedje, James M.; Rosado, Alexandre S.

2013-01-01

Background The Brazilian Cerrado is one of the most important biodiversity reservoirs in the world. The sugarcane cultivation is expanding in this biome and necessitates the study of how it may impact the soil properties of the Cerrado. There is a lack of information especially about the impacts of different sugarcane management on the native bacterial communities of Cerrado soil. Therefore, our objective was to evaluate and compare the soil bacterial community structure of the Cerrado vegetation with two sugarcane systems. Methods We evaluated samples under native vegetation and the impact of the two most commonly used management strategies for sugarcane cultivation (burnt cane and green cane) on this diversity using pyrosequencing and quantitative PCR of the rrs gene (16S rRNA). Results and Conclusions Nineteen different phyla were identified, with Acidobacteria (≈35%), Proteobacteria (≈24%) and Actinobacteria (≈21%) being the most abundant. Many of the sequences were represented by few operational taxonomic units (OTUs, 3% of dissimilarity), which were found in all treatments. In contrast, there were very strong patterns of local selection, with many OTUs occurring only in one sample. Our results reveal a complex bacterial diversity, with a large fraction of microorganisms not yet described, reinforcing the importance of this biome. As possible sign of threat, the qPCR detected a reduction of the bacterial population in agricultural soils compared with native Cerrado soil communities. We conclude that sugarcane cultivation promoted significant structural changes in the soil bacterial community, with Firmicutes phylum and Acidobacteria classes being the groups most affected. PMID:23533619

Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure.

PubMed

Rachid, Caio T C C; Santos, Adriana L; Piccolo, Marisa C; Balieiro, Fabiano C; Coutinho, Heitor L C; Peixoto, Raquel S; Tiedje, James M; Rosado, Alexandre S

2013-01-01

The Brazilian Cerrado is one of the most important biodiversity reservoirs in the world. The sugarcane cultivation is expanding in this biome and necessitates the study of how it may impact the soil properties of the Cerrado. There is a lack of information especially about the impacts of different sugarcane management on the native bacterial communities of Cerrado soil. Therefore, our objective was to evaluate and compare the soil bacterial community structure of the Cerrado vegetation with two sugarcane systems. We evaluated samples under native vegetation and the impact of the two most commonly used management strategies for sugarcane cultivation (burnt cane and green cane) on this diversity using pyrosequencing and quantitative PCR of the rrs gene (16S rRNA). Nineteen different phyla were identified, with Acidobacteria (≈35%), Proteobacteria (≈24%) and Actinobacteria (≈21%) being the most abundant. Many of the sequences were represented by few operational taxonomic units (OTUs, 3% of dissimilarity), which were found in all treatments. In contrast, there were very strong patterns of local selection, with many OTUs occurring only in one sample. Our results reveal a complex bacterial diversity, with a large fraction of microorganisms not yet described, reinforcing the importance of this biome. As possible sign of threat, the qPCR detected a reduction of the bacterial population in agricultural soils compared with native Cerrado soil communities. We conclude that sugarcane cultivation promoted significant structural changes in the soil bacterial community, with Firmicutes phylum and Acidobacteria classes being the groups most affected.

Simazine biodegradation in soil: analysis of bacterial community structure by in situ hybridization.

PubMed

Caracciolo, Anna Barra; Grenni, Paola; Ciccoli, Roberto; Di Landa, Giuseppe; Cremisini, Carlo

2005-09-01

Pesticide and nitrate contamination of soil and groundwater from agriculture is an environmental and public health concern worldwide. Simazine, 6-chloro-N2,N4-diethyl-1,3,5-triazine-2,4-diamine, is a triazine herbicide used in agriculture for selective weed control with several types of crops and it is frequently applied to soils receiving N-fertilizers. Degradation experiments were performed in the laboratory to assess whether the biodegradation of simazine in soil may be influenced by the presence of urea. Simazine degradation rates under different experimental conditions (presence/absence of urea, microbiologically active/sterilized soil) were assessed together with the formation, degradation and transformation of its main metabolites in soil. Simazine degradation was affected by the presence of urea, in terms both of a smaller half-life (t(1/2)) and of a higher amount of desethyl-simazine formed. The soil bacterial community was also studied. Microbial abundances were determined by epifluorescence direct counting. Moreover in situ hybridization with rRNA-targeted fluorescent oligonucleotide probes was used to analyze the bacterial community structure. Fluorescent in situ hybridization (FISH) was used to detect specific groups of bacteria such as the alpha,beta,gamma-subdivisions of Proteobacteria, Gram-positive bacteria with a high G + C DNA content, Planctomycetes, Betaproteobacterial ammonia-oxidizing bacteria and nitrifying bacteria. The presence of the herbicide and/or urea affected the bacterial community structure, showing that FISH is a valuable tool for determining the response of bacterial populations to different environmental conditions. Copyright 2005 Society of Chemical Industry

The role of Soil Water Retention Curve in slope stability analysis in unsaturated and heterogeneous soils.

NASA Astrophysics Data System (ADS)

Antinoro, Chiara; Arnone, Elisa; Noto, Leonardo V.

2015-04-01

The mechanisms of rainwater infiltration causing slope instability had been analyzed and reviewed in many scientific works. Rainwater infiltration into unsaturated soil increases the degree of saturation, hence affecting the shear strength properties and thus the probability of slope failure. It has been widely proved that the shear strength properties change with the soil water suction in unsaturated soils; therefore, the accuracy to predict the relationship between soil water content and soil water suction, parameterized by the soil-water characteristic curve, has significant effects on the slope stability analysis. The aim of this study is to investigate how the characterization of SWRC of differently structured unsaturated soils affects the slope stability on a simple infinite slope. In particular, the unimodal and bimodal distributions of the soil pore size were compared. Samples of 40 soils, highly different in terms of structure and texture, were collected and used to calibrate two bimodal SWRCs, i.e. Ross and Smettem (1993) and Dexter et al., (2008). The traditional unimodal van Genuchten (1980) model was also applied for comparison. Slope stability analysis was conducted in terms of Factor of Safety (FS) by applying the infinite slope model for unsaturated soils. In the used formulation, the contribution of the suction effect is tuned by a parameter 'chi' in a rate proportional to the saturation conditions. Different parameterizations of this term were also compared and analyzed. Results indicated that all three SWRC models showed good overall performance in fitting the sperimental SWRCs. Both the RS and DE models described adequately the water retention data for soils with a bimodal behavior confirmed from the analysis of pore size distribution, but the best performance was obtained by DE model confirmed. In terms of FS, the tree models showed very similar results as soil moisture approached to the saturated condition; however, within the residual zone, the DE model denoted an anomalous behavior depending on the used formulation for the 'chi' parameter, with decreasing FS as soil moisture decreases.

Manure Refinement Affects Apple Rhizosphere Bacterial Community Structure: A Study in Sandy Soil

PubMed Central

Zhang, Qiang; Sun, Jian; Liu, Songzhong; Wei, Qinping

2013-01-01

We used DNA-based pyrosequencing to characterize the bacterial community structure of the sandy soil of an apple orchard with different manure ratios. Five manure percentages (5%, 10%, 15%, 20% and 25%) were examined. More than 10,000 valid reads were obtained for each replicate. The communities were composed of five dominant groups (Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Bacteroidetes), of which Proteobacteria content gradually decreased from 41.38% to 37.29% as manure ratio increased from 0% to 25%, respectively. Redundancy analysis showed that 37 classes were highly correlated with manure ratio, 18 of which were positively correlated. Clustering revealed that the rhizosphere samples were grouped into three components: low manure (control, 5%) treatment, medium manure (10%, 15%) treatment and high manure (20%, 25%) treatment. Venn analysis of species types of these three groups revealed that the bacteria community difference was primarily reflected by quantity ratio rather than species variety. Although greater manure content led to higher soil organic matter content, the medium manure improved soil showed the highest urease activity and saccharase activity, while 5% to 20% manure ratio improvement also resulted in higher bacteria diversity than control and 25% manure ratio treatment. Our experimental results suggest that the use of a proper manure ratio results in significantly higher soil enzyme activity and different bacteria community patterns, whereas the use of excessive manure amounts has negative effect on soil quality. PMID:24155909

Enzymology under global change: organic nitrogen turnover in alpine and sub-Arctic soils.

PubMed

Weedon, James T; Aerts, Rien; Kowalchuk, George A; van Bodegom, Peter M

2011-01-01

Understanding global change impacts on the globally important carbon storage in alpine, Arctic and sub-Arctic soils requires knowledge of the mechanisms underlying the balance between plant primary productivity and decomposition. Given that nitrogen availability limits both processes, understanding the response of the soil nitrogen cycle to shifts in temperature and other global change factors is crucial for predicting the fate of cold biome carbon stores. Measurements of soil enzyme activities at different positions of the nitrogen cycling network are an important tool for this purpose. We review a selection of studies that provide data on potential enzyme activities across natural, seasonal and experimental gradients in cold biomes. Responses of enzyme activities to increased nitrogen availability and temperature are diverse and seasonal dynamics are often larger than differences due to experimental treatments, suggesting that enzyme expression is regulated by a combination of interacting factors reflecting both nutrient supply and demand. The extrapolation from potential enzyme activities to prediction of elemental nitrogen fluxes under field conditions remains challenging. Progress in molecular '-omics' approaches may eventually facilitate deeper understanding of the links between soil microbial community structure and biogeochemical fluxes. In the meantime, accounting for effects of the soil spatial structure and in situ variations in pH and temperature, better mapping of the network of enzymatic processes and the identification of rate-limiting steps under different conditions should advance our ability to predict nitrogen fluxes.

Treatability of volatile chlorinated hydrocarbon-contaminated soils of different textures along a vertical profile by mechanical soil aeration: A laboratory test.

PubMed

Ma, Yan; Shi, Yi; Hou, Deyi; Zhang, Xi; Chen, Jiaqi; Wang, Zhifen; Xu, Zhu; Li, Fasheng; Du, Xiaoming

2017-04-01

Mechanical soil aeration is a simple, effective, and low-cost soil remediation technology that is suitable for sites contaminated with volatile chlorinated hydrocarbons (VCHs). Conventionally, this technique is used to treat the mixed soil of a site without considering the diversity and treatability of different soils within the site. A laboratory test was conducted to evaluate the effectiveness of mechanical soil aeration for remediating soils of different textures (silty, clayey, and sandy soils) along a vertical profile at an abandoned chloro-alkali chemical site in China. The collected soils were artificially contaminated with chloroform (TCM) and trichloroethylene (TCE). Mechanical soil aeration was effective for remediating VCHs (removal efficiency >98%). The volatilization process was described by an exponential kinetic function. In the early stage of treatment (0-7hr), rapid contaminant volatilization followed a pseudo-first order kinetic model. VCH concentrations decreased to low levels and showed a tailing phenomenon with very slow contaminant release after 8hr. Compared with silty and sandy soils, clayey soil has high organic-matter content, a large specific surface area, a high clay fraction, and a complex pore structure. These characteristics substantially influenced the removal process, making it less efficient, more time consuming, and consequently more expensive. Our findings provide a potential basis for optimizing soil remediation strategy in a cost-effective manner. Copyright © 2016. Published by Elsevier B.V.

THE EFFECT OF NITROGEN OVER-ENRICHMENT ON SOME PLANT-SOIL RELATIONSHIPS AND MICROBIAL PROCESSES

EPA Science Inventory

Salt marshes of similar geomorphology and hydrology with varying watershed nitrogen loads were examined for differences in plant structure, soil characteristics, and
denitrification. We observed landward encroachment of the low marsh Spartina alterniflora, and the displacement...

Soil aggregate and organic carbon distribution at dry land soil and paddy soil: the role of different straws returning.

PubMed

Huang, Rong; Lan, Muling; Liu, Jiang; Gao, Ming

2017-12-01

Agriculture wastes returning to soil is one of common ways to reuse crop straws in China. The returned straws are expected to improve the fertility and structural stability of soil during the degradation of straw it selves. The in situ effect of different straw (wheat, rice, maize, rape, and broad bean) applications for soil aggregate stability and soil organic carbon (SOC) distribution were studied at both dry land soil and paddy soil in this study. Wet sieving procedures were used to separate soil aggregate sizes. Aggregate stability indicators including mean weight diameter, geometric mean diameter, mean weight of specific surface area, and the fractal dimension were used to evaluate soil aggregate stability after the incubation of straws returning. Meanwhile, the variation and distribution of SOC in different-sized aggregates were further studied. Results showed that the application of straws, especially rape straw at dry land soil and rice straw at paddy soil, increased the fractions of macro-aggregate (> 0.25 mm) and micro-aggregate (0.25-0.053 mm). Suggesting the nutrients released from straw degradation promotes the growing of soil aggregates directly and indirectly. The application of different straws increased the SOC content at both soils and the SOC mainly distributed at < 0.53 mm aggregates. However, the contribution of SOC in macro- and micro-aggregates increased. Straw-applied paddy soil have a higher total SOC content but lower SOC contents at > 0.25 and 0.25-0.053 mm aggregates with dry land soil. Rape straw in dry land and rice straw in paddy field could stabilize soil aggregates and increasing SOC contents best.

Influence of humic substances and iron and aluminum ions on the sorption of acetamiprid to an arable soil.

PubMed

Murano, Hirotatsu; Suzuki, Katsuhiro; Kayada, Saori; Saito, Mitsuhiko; Yuge, Naoya; Arishiro, Takuji; Watanabe, Akira; Isoi, Toshiyuki

2018-02-15

Humic substances (HS) in soil and sediments, and surface water influence the behavior of organic xenobiotics in the environment. However, our knowledge of the effects of specific HS fractions, i.e., humic acids (HAs), fulvic acids (FAs), and humin (HM), on the sorption of organic xenobiotics is limited. The neonicotinoid insecticide acetamiprid is thought to contribute to the collapse of honeybee colonies. To understand the role that soil organic matter plays in the fate of acetamiprid, interactions between acetamiprid and the above HS fractions were examined. Batch experiments were conducted using various combinations of a field soil sample and the above 3 HS fractions prepared from the same soil, and differences in isotherm values for acetamiprid sorption were investigated based on the structural differences among the HS fractions. The sorption of acetamiprid to soil minerals associated with HM (MHM) (Freundlich isotherm constant, K f : 6.100) was reduced when HAs or FAs were added (K f : 4.179 and 4.756, respectively). This can be attributed to hydrophobic interactions between HM and HAs or FAs in which their dissociated carboxyl and phenolic groups become oriented to face the soil solution. The amount of acetamiprid that was adsorbed to (MHM+HA) or (MHM+FA) increased when aluminum ions were added (K f : 6.933 and 10.48, respectively), or iron ions were added (K f : 7.303 and 11.29, respectively). Since acetamiprid has no affinity for inorganic components in soil, the formation of HS-metal complexes by cation bridging may have oriented the hydrophobic moieties in the HAs or FAs to face the soil solution and may also have resulted in the formation of dense structures, resulting in an increase in the amount of acetamiprid that becomes adsorbed to these structures. These results highlight the importance of interactions among soil components in the pedospheric diffusion of acetamiprid. Copyright © 2017 Elsevier B.V. All rights reserved.

Fungal colonization in soils with different management histories: modeling growth in three-dimensional pore volumes.

PubMed

Kravchenko, Alexandra; Falconer, Ruth E; Grinev, Dmitri; Otten, Wilfred

2011-06-01

Despite the importance of fungi in soil functioning they have received comparatively little attention, and our understanding of fungal interactions and communities is lacking. This study aims to combine a physiologically based model of fungal growth with digitized images of internal pore volume of samples of undisturbed soil from contrasting management practices to determine the effect of physical structure on fungal growth dynamics. We quantified pore geometries of the undisturbed-soil samples from two contrasting agricultural practices, conventionally plowed (chisel plow) (CT) and no till (NT), and from native-species vegetation land use on land that was taken out of production in 1989 (NS). Then we modeled invasion of a fungal species within the soil samples and evaluated the role of soil structure on the progress of fungal colonization of the soil pore space. The size of the studied pores was > or =110 microm. The dynamics of fungal invasion was quantified through parameters of a mathematical model fitted to the fungal invasion curves. Results indicated that NT had substantially lower porosity and connectivity than CT and NS soils. For example, the largest connected pore volume occupied 79% and 88% of pore space in CT and NS treatments, respectively, while it only occupied 45% in NT. Likewise, the proportion of pore space available to fungal colonization was much greater in NS and CT than in NT treatment, and the dynamics of the fungal invasion differed among the treatments. The relative rate of fungal invasion at the onset of simulation was higher in NT samples, while the invasion followed a more sigmoidal pattern with relatively slow invasion rates at the initial time steps in NS and CT samples. Simulations allowed us to elucidate the contribution of physical structure to the rates and magnitudes of fungal invasion processes. It appeared that fragmented pore space disadvantaged fungal invasion in soils under long-term no-till, while large connected pores in soils under native vegetation or in tilled agriculture promoted the invasion.

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

Kuperman, R.G.

Soil macroinvertebrate communities were studied in ecologically analogous oak-hickory forests across a three-state atmospheric pollution gradient in Illinois, Indiana, and Ohio. The goal was to investigate changes in the community structure of soil fauna in study sites receiving different amounts of acidic deposition for several decades and the possible relationships between these changes and physico-chemical properties of soil. The study revealed significant differences in the numbers of soil animals among the three study sites. The sharply differentiated pattern of soil macroinvertebrate fauna seems closely linked to soil chemistry. Significant correlations of the abundance of soil macroinvertebrates with soil parameters suggestmore » that their populations could have been affected by acidic deposition in the region. Abundance of total soil macroinvertebrates decreased with the increased cumulative loading of acidic deposition. Among the groups most sensitive to deposition were: earthworms gastropods, dipteran larvae, termites, and predatory beetles. The results of the study support the hypothesis that chronic long-term acidic deposition could aversely affect the soil decomposer community which could cause lower organic matter turnover rates leading to an increase in soil organic matter content in high deposition sites.« less

[Soil infiltration characteristics under main vegetation types in Anji County of Zhejiang Province].

PubMed

Liu, Dao-Ping; Chen, San-Xiong; Zhang, Jin-Chi; Xie, Li; Jiang, Jiang

2007-03-01

The study on the soil infiltration under different main vegetation types in Anji County of Zhejiang Province showed that the characteristics of soil infiltration differed significantly with land use type, and the test eight vegetation types could be classified into four groups, based on soil infiltration capability. The first group, deciduous broadleaved forest, had the strongest soil infiltration capability, and the second group with a stronger soil infiltration capability was composed of grass, pine forest, shrub community and tea bush. Bamboo and evergreen broadleaved forest were classified into the third group with a relatively strong soil infiltration capability, while bare land belonged to the fourth group because of the bad soil structure and poorest soil infiltration capability. The comprehensive parameters of soil infiltration (alpha) and root (beta) were obtained by principal component analysis, and the regression model of alpha and beta could be described as alpha = 0. 1708ebeta -0. 3122. Soil infiltration capability was greatly affected by soil physical and chemical characteristics and root system. Fine roots (< or = 1 mm in diameter) played effective roles on the improvement of soil physical and chemical properties, and the increase of soil infiltration capability was closely related to the amount of the fine roots.

Thermal Conductivity Prediction of Soil in Complex Plant Soil System using Artificial Neural Networks

NASA Astrophysics Data System (ADS)

Wardani, A. K.; Purqon, A.

2016-08-01

Thermal conductivity is one of thermal properties of soil in seed germination and plants growth. Different soil types have different thermal conductivity. One of soft-computing promising method to predict thermal conductivity of soil types is Artificial Neural Network (ANN). In this study, we estimate the thermal conductivity of soil prediction in a soil-plant complex systems using ANN. With a feed-forward multilayer trained with back-propagation with 4, 10 and 1 on the input, hidden and output layers respectively. Our input are heating time, temperature and thermal resistance with thermal conductivity of soil as a target. ANN prediction demonstrates a good agreement with Mean Squared Error-testing (MSEte) of 9.56 x 10-7 for soils with green beans and those of bare soils is 7.00 × 10-7 respectively Green beans grow only on black-clay soil with a thermal conductivity of 0.7 W/m K with a sufficient water content. Our results demonstrate that temperature, moisture content, colour, texture and structure of soil are greatly affect to the thermal conductivity of soil in seed germination and plant growth. In future, it is potentially applied to estimate more complex compositions of plant-soil systems.

Ground Penetrating Radar For Estimating Root Biomass Through Empirical Analysis

NASA Astrophysics Data System (ADS)

Wolfe, M.; Dobreva, I. D.; Delgado, A.; Hays, D. B.; Bishop, M. P.; Huo, D.; Wang, X.; Teare, B. L.; Burris, S.

2017-12-01

Variability in soil carbon storage due to agricultural practices is an important component of the carbon cycle. Enhancing soil organic content is a means for restoring degraded soils and for improving soil quality, but also for carbon sequestration. In particular, accurate estimates of soil organic content are essential for quantifying carbon sequestration capabilities of agricultural systems. This project aims to advance the technological and analytical capabilities of Ground Penetrating Radar (GPR) for diagnoses of the soil carbon storage occurring due to the perennial grasses which are often utilized as biofuels. A new GPR processing workflow applied via a prototype software was tested on simulated GPR data of roots with different densities and depths to determine the sensitivity and capability of this technology to quantify these parameters. Field experiments were also conducted in long-term trials of different genotypes of perennial grasses over field sites in Texas to determine the application in authentic environments. GPR scans and soil samples were collected, and root dry biomass was obtained. Evaluation of pre-processing techniques was conducted to provide optimal resolution for assessment. The novel backscatter spatial structure workflow was implemented, and empirical relationships between root biomass and GPR derived observations were developed. Preliminary results suggest that the backscatter spatial structure changes in the presence of high density root biomass conditions, and these variations are indicative of root zone depth and density. Our results illustrate promising applications in root detection, and therefore, the soil organic content accumulation that is pertinent to a healthy soil system.

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

PubMed Central

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

2015-01-01

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

A soil alteration index based on phospholipid fatty acids.

PubMed

Puglisi, Edoardo; Nicelli, Marco; Capri, Ettore; Trevisan, Marco; Del Re, Attilio A M

2005-12-01

Phospholipid fatty acid (PLFA) analysis has gained great importance in the study of soil microbial community structure. This structure can give indication of the soil status. Purpose of the present paper is to analyse PLFA patterns in altered agricultural soils in order to develop a soil status alteration index. Soils subjected either to intensive agricultural exploitation, or to overflow by municipal and industrial wastes, or to irrigation with saline waters were analysed for PLFA content and compared to adjacent untreated soils by means of different statistical techniques. Principal component analysis separated PLFAs in three groups: unsaturated PLFAs (first axis, 48% of total variance), monounsaturated and cyclopropane PLFAs (second axis, 28% of total variance) and polyunsaturated PLFAs (third axis, 24% of total variance). By means of canonical discriminant analysis, a soil alteration index (SAI) was produced from 15 PLFAs using two data sets. A third data set was used to test the SAI general validity together with other data sets reported in literature. The index validity was confirmed in most cases: SAI gave higher scores for control soils and was generally able to classify soils according to their reported degree of alteration.

Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

NASA Astrophysics Data System (ADS)

Ricketts, Michael P.; Poretsky, Rachel S.; Welker, Jeffrey M.; Gonzalez-Meler, Miquel A.

2016-09-01

Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snow fence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of expected ecosystem response to climate change. Soil was collected from three pre-established treatment zones representing varying degrees of snow accumulation, where deep snow ˜ 100 % and intermediate snow ˜ 50 % increased snowpack relative to the control, and low snow ˜ 25 % decreased snowpack relative to the control. Soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C concentration, nitrogen (N) concentration, and pH. Soil microbial community DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla (ranging from 82 to 96 % of total detected phyla per sample) and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (% C, % N, C : N, pH); however, a single predictor was not identified, suggesting that each bacterial phylum responds differently to soil characteristics. Overall, bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties. Bacterial functional potential was inferred using ancestral state reconstruction to approximate functional gene abundance, revealing a decreased abundance of genes required for soil organic matter (SOM) decomposition in the organic layers of the deep snow accumulation zones. These results suggest that predicted climate change scenarios may result in altered soil bacterial community structure and function, and indicate a reduction in decomposition potential, alleviated temperature limitations on extracellular enzymatic efficiency, or both. The fate of stored C in Arctic soils ultimately depends on the balance between these mechanisms.

Biological and physical factors controlling aggregate stability under different climatic conditions in Southern Spain.

NASA Astrophysics Data System (ADS)

Ángel Gabarrón-Galeote, Miguel; Damián Ruiz-Sinoga, Jose; Francisco Martinez-Murillo, Juan; Lavee, Hanoch

2013-04-01

Soil aggregation is a key factor determining the soil structure. The presence of stable aggregates is essential to maintain a good soil structure, that in turn plays an important role in sustaining agricultural productivity and preserving environmental quality. A wide range of physical and biological soil components are involved in the aggregate formation and stabilization, namely clay mineral content; the quantity and quality of organic matter, that can be derived from plants, fungal hyphae, microorganism and soil animals; and the soil water content. Climatic conditions, through their effect on soil water content, vegetation cover and organic matter content, are supposed to affect soil aggregation. Thus the main objective of this research is to analyse the effect of organic matter, clay content and soil water content on aggregate stability along a climatic transect in Southern Spain. This study was conducted in four catchments along a pluviometric gradient in the South of Spain (rainfall depth decreases from west to east from more than 1000 mm year-1 to less than 300 mm year-1) and was based on a methodology approximating the climatic gradient in Mediterranean conditions. The selected sites shared similar conditions of geology, topography and soil use, which allowed making comparisons among them and relating the differences to the pluviometric conditions. In February 2007, 250 disturbed and undisturbed samples from the first 5cm of the soil were collected along the transect. We measured the aggregate stability, organic matter, clay content and bulk density of every sample. In the field we measured rainfall, air temperature, relative humidity, wind speed, wind direction, solar radiation, potential evapotranspiration, soil water content, vegetation cover and presence of litter. Our results suggest that aggregate stability is a property determined by a great number of highly variable factors, which can make extremely difficult to predict its behavior taking in account only a few of them. The climate exerted a great influence in aggregate stability and could determine by itself the soil structure along the climate transect. As a result, properties unrelated in a specific point of the climate transect became highly associated if we took it into account completely. Along the climate transect analyzed could be defined two areas, separated by a threshold located between 573.6 mm y-1 and 335.9 mm y-1. In the wettest part soil structure was mainly determined by biotic factors and in the driest part was highly probable that abiotic factors play a key role determining aggregate stability.

Role of model structure on the response of soil biogeochemistry to hydro-climatic fluctuations

NASA Astrophysics Data System (ADS)

Manzoni, S.; Porporato, A.

2005-05-01

Soil carbon and nutrient cycles are strongly affected by hydro-climatic variability, which interacts with the internal ecosystem structure. Here we test the implications of biogeochemical model structure on such dynamics by extending an existing model by the authors and coworkers. When forced by hydro-climatic fluctuations, the different model structures induce specific preferential nutrient paths among the soil pools, which in turn affect nutrient distribution and availability to microbes and plants. In particular, if it is assumed that microbes can directly assimilate organic nitrogen, plants tend to be inferior competitors for nutrients even in well-watered conditions, while if a certain amount of organic nitrogen is assumed to be mineralized without being first incorporated into microbial cells, vegetation can be advantaged over a wide range of soil moisture values. We also investigate the intensification of competition for nutrients (e.g., nitrogen) between plant and soil microbial communities under extreme hydrologic conditions, such as droughts and intense storms. Frequent rainfall events may determine ideal soil moisture conditions for plant uptake, enhancing nitrogen leaching while lowering oxygen concentration and inhibiting microbial activity. During droughts, the soil water potential often drops to the point of hampering the plant nutrient uptake while still remaining high enough for microbial decomposition and nitrogen immobilization. The interplay of microbe and vegetation water stress is investigated in depth as it controls the ability of one community (e.g., plants or soil microbes) to establish competitive advantage on the other. The long-term effects of these dynamics of competition and nutrient allocation are explored under steady-state and stochastic soil moisture conditions to analyze the feedbacks between soil organic matter and vegetation dynamics.

Community structures and activity of denitrifying microbes in a forested catchment in central Japan: survey using nitrite reductase genes

NASA Astrophysics Data System (ADS)

Ohte, N.; Aoki, M.; Katsuyama, C.; Suwa, Y.; Tange, T.

2012-12-01

To elucidate the mechanisms of denitrification processes in the forested catchment, microbial ecological approaches have been applied in an experimental watershed that has previously investigated its hydrological processes. The study catchment is located in the Chiba prefecture in central Japan under the temperate Asian monsoon climate. Potential activities of denitrification of soil samples were measured by incubation experiments under anoxic condition associated with Na15NO3 addition. Existence and variety of microbes having nitrite reductase genes were investigated by PCR amplification, cloning and sequencings of nirK and nirS fragments after DNA extraction. Contrary to our early expectation that the potential denitrification activity was higher at deeper soil horizon with consistent groundwater residence than that in the surface soil, denitrification potential was higher in shallower soil horizons than deeper soils. This suggested that the deficiency of NO3- as a respiratory substrate for denitrifier occurred in deeper soils especially in the summer. However, high denitrification activity and presence of microbes having nirK and nirS in surface soils usually under aerobic condition was explainable by the fact that the majority of denitrifying bacteria have been recognized as a facultative anaerobic bacterium. This also suggests the possibility of that denitrification occurs even in the surface soils if the wet condition is provided by rainwater during and after a storm event. Community structures of microbes having nirK were different between near surface and deeper soil horizons, and ones having nirS was different between saturated zone (under groundwater table) and unsaturated soil horizons. These imply that microbial communities with nisK are sensitive to the concentration of soil organic matters and ones with nirS is sensitive to soil moisture contents.

Influence of soil development on the geomorphic evolution of landscapes: An example from the Transverse Ranges of California

NASA Astrophysics Data System (ADS)

Eppes, M. C.; McFadden, L. D.; Matti, J.; Powell, R.

2002-03-01

Soil development can significantly influence the topographic evolution of a tectonically deforming mountain piedmont. Faults and folds associated with the North Frontal thrust system deform piedmont sediments of variable compositions along the north flank of the San Bernardino Mountains. The topographic expressions of folds with similar structural characteristics diverge appreciably, primarily as a function of differences in sediment composition and associated soil development. Soils with petrocalcic horizons in limestone- rich deposits are resistant to erosion, and anticlinal folds form prominent ridges. Folds forming in granite-derived deposits with argillic soil horizons are eroded and/or buried and are therefore topographically less pronounced. We propose that these landform contrasts can be explained by differences in soil-controlled hydrologic and erosion characteristics of deposits without calling upon changes in tectonic style along the mountain front.

Community structure of grassland ground-dwelling arthropods along increasing soil salinities.

PubMed

Pan, Chengchen; Feng, Qi; Liu, Jiliang; Li, Yulin; Li, Yuqiang; Yu, Xiaoya

2018-03-01

Ground-dwelling arthropod communities are influenced by numerous biotic and abiotic factors. Little is known, however, about the relative importance of vegetation structure and abiotic environmental factors on the patterns of ground-dwelling arthropod community across a wide range of soil salinities. Here, a field survey was conducted to assess the driving forces controlling ground-dwelling arthropod community in the salinized grasslands in the Hexi Corridor, Gansu Province, China. The data were analyzed by variance partitioning with canonical correspondence analysis (CCA). We found that vegetation structure and edaphic factors were at least of similar importance to the pattern of the whole ground-dwelling arthropod community. However, when all collected ground-dwelling arthropods were categorized into three trophic guilds (predators, herbivores, and decomposers), as these groups use different food sources, their populations were controlled by different driving forces. Predators and decomposers were mainly determined by biotic factors such as vegetation cover and aboveground plant biomass and herbivores by plant density and vegetation cover. Abiotic factors were also major determinants for the variation occurring in these guilds, with predators strongly affected by soil electrical conductivity (EC) and the content of fine particles (silt + clay, CS), herbivores by soil N:P, EC, and CS, and decomposers by soil EC and organic matter content (SOM). Since plant cover, density, and aboveground biomass can indicate resource availability, which are mainly constrained by soil N:P, EC, CS, and SOM, we consider that the ground-dwelling arthropod community in the salinized grasslands was mainly influenced by resource availability.

Influence of Vinasse Application in the Structure and Composition of the Bacterial Community of the Soil under Sugarcane Cultivation

PubMed Central

de Camargo, André Ferreira; Goulart, Karla Cristina Stropa; Lemos, Eliana Gertrudes de Macedo

2016-01-01

Although the use of vinasse as a waste helps replenish soil nutrients and improves the quality of the sugarcane crop, it is known that vinasse residues alter the diversity of bacteria naturally present in the soil. The actual impacts of vinasse application on the selection of bacterial taxa are not understood because no studies have addressed this phenomenon directly. Analysis of 16S rRNA gene clone sequences from four soil types showed that the soil planted with sugarcane and fertilized with vinasse has a high diversity of bacteria compared to other biomes, where Acidobacteria were the second most abundant phylum. Although the composition and structure of bacterial communities differ significantly in the four environments (Libshuff's test), forest soils and soil planted with sugarcane without vinasse fertilizer were similar to each other because they share at least 28 OTUs related to Rhizobiales, which are important agents involved in nitrogen fixation. OTUs belonging to Actinomycetales were detected more often in the soil that had vinasse applied, indicating that these groups are more favored by this type of land management. PMID:27528875

Reappraisal of soil C storage processes. The controversy on structural diversity of humic substances as biogeochemical driver for soil C fluxes

NASA Astrophysics Data System (ADS)

Almendros, Gonzalo; Gonzalez-Vila, Francisco J.; Gonzalez-Perez, Jose Antonio; Knicker, Heike

2016-04-01

The functional relationships between the macromolecular structure of the humic substances (HS) and a series of biogeochemical processes related with the C sequestration performance in soils have been recently questioned. In this communication we collect recent data from a wide array of different ecosystems where the C storage in soils has been studied and explained as a possible cause-to-effect relationship or has been found significantly correlated (multivariate statistical models) with a series of structural characteristics of humic materials. The study of humic materials has methodological analytical limitations that are derived from its complex, chaotic and not completely understood structure, that reflects its manifold precursors as well as the local impact of environmental/depositional factors. In this work we attempt to design an exploratory, multiomic approach based on the information provided by the molecular characterization of the soil organic matter (SOM). Massive data harvesting was carried out of statistical variables, to infer biogeochemical proxies (spectroscopic, chromatographic, mass spectrometric quantitative descriptors). The experimental data were acquired from advanced instrumental methodologies, viz, analytical pyrolysis, compound-specific stable isotope analysis (CSIA), derivative infrared (FTIR) spectroscopy, solid-state C-13 and N-15 nuclear magnetic resonance (NMR) and mass spectrometry (MS) data after direct injection (thermoevaporation), previous pyrolysis, or ion averaging of specific m/z ranges from classical GC/MS chromatograms. In the transversal exploratory analysis of the multianalytical information, the data were coded for on-line processing in a stage in which there is no need for interpretation, in molecular or structural terms, of the quantitative data consisting of e.g., peak intensities, signal areas, chromatographic (GC) total abundances, etc. A series of forecasting chemometric approaches (aiming to express SOM biodegradability, or soil C resilience as a function of intrinsic molecular characteristics of the SOM) were especially successful in the case of: a) linear multiple regression models (LMR) with automatic backward variable selection, b) supervised removal of internal redundancy of the variables based on multidimensional scaling (MDS), and c) partial least squares (PLS) regression to obtain the variable importance for projection (VIP) which is useful to identify new environmental proxies. At least the results obtained from differing continental Mediterranean soils showed that a large influence of local (soil-dependant) abiotic factors in the final variance (of the total soil C quality and quantity) was explained by the SOM molecular structure. This conclusion is relevant as regards the recent (in our opinion hermeneutic and speculative) controversy disregarding the importance of the structural features of HS in biogeochemical and environmental processes controlling C sequestration in soils.

Life cycle performances of log wood applied for soil bioengineering constructions

NASA Astrophysics Data System (ADS)

Kalny, Gerda; Strauss-Sieberth, Alexandra; Strauss, Alfred; Rauch, Hans Peter

2016-04-01

Nowadays there is a high demand on engineering solutions considering not only technical aspects but also ecological and aesthetic values. Soil bioengineering is a construction technique that uses biological components for hydraulic and civil engineering solutions. Soil bioengineering solutions are based on the application of living plants and other auxiliary materials including among others log wood. This kind of construction material supports the soil bioengineering system as long as the plants as living construction material overtake the stability function. Therefore it is important to know about the durability and the degradation process of the wooden logs to retain the integral performance of a soil bio engineering system. These aspects will be considered within the framework of the interdisciplinary research project „ELWIRA Plants, wood, steel and concrete - life cycle performances as construction materials". Therefore field investigations on soil bioengineering construction material, specifically European Larch wood logs, of different soil bioengineering structures at the river Wien have been conducted. The drilling resistance as a parameter for particular material characteristics of selected logs was measured and analysed. The drilling resistance was measured with a Rinntech Resistograph instrument at different positions of the wooden logs, all surrounded with three different backfills: Fully surrounded with air, with earth contact on one side and near the water surface in wet-dry conditions. The age of the used logs ranges from one year old up to 20 year old. Results show progress of the drilling resistance throughout the whole cross section as an indicator to assess soil bioengineering construction material. Logs surrounded by air showed a higher drilling resistance than logs with earth contact and the ones exposed to wet-dry conditions. Hence the functional capability of wooden logs were analysed and discussed in terms of different levels of degradation. The results contribute to a sustainable and resource conserving handling with building materials in frame of construction and maintenance works of soil bioengineering structures.

Organic matter composition of soil macropore surfaces under different agricultural management practices

NASA Astrophysics Data System (ADS)

Glæsner, Nadia; Leue, Marin; Magid, Jacob; Gerke, Horst H.

2016-04-01

Understanding the heterogeneous nature of soil, i.e. properties and processes occurring specifically at local scales is essential for best managing our soil resources for agricultural production. Examination of intact soil structures in order to obtain an increased understanding of how soil systems operate from small to large scale represents a large gap within soil science research. Dissolved chemicals, nutrients and particles are transported through the disturbed plow layer of agricultural soil, where after flow through the lower soil layers occur by preferential flow via macropores. Rapid movement of water through macropores limit the contact between the preferentially moving water and the surrounding soil matrix, therefore contact and exchange of solutes in the water is largely restricted to the surface area of the macropores. Organomineral complex coated surfaces control sorption and exchange properties of solutes, as well as availability of essential nutrients to plant roots and to the preferentially flowing water. DRIFT (Diffuse Reflectance infrared Fourier Transform) Mapping has been developed to examine composition of organic matter coated macropores. In this study macropore surfaces structures will be determined for organic matter composition using DRIFT from a long-term field experiment on waste application to agricultural soil (CRUCIAL, close to Copenhagen, Denmark). Parcels with 5 treatments; accelerated household waste, accelerated sewage sludge, accelerated cattle manure, NPK and unfertilized, will be examined in order to study whether agricultural management have an impact on the organic matter composition of intact structures.

Arbuscular Mycorrhizal Fungi Community Structure, Abundance and Species Richness Changes in Soil by Different Levels of Heavy Metal and Metalloid Concentration

PubMed Central

Krishnamoorthy, Ramasamy; Kim, Chang-Gi; Subramanian, Parthiban; Kim, Ki-Yoon; Selvakumar, Gopal; Sa, Tong-Min

2015-01-01

Arbuscular Mycorrhizal Fungi (AMF) play major roles in ecosystem functioning such as carbon sequestration, nutrient cycling, and plant growth promotion. It is important to know how this ecologically important soil microbial player is affected by soil abiotic factors particularly heavy metal and metalloid (HMM). The objective of this study was to understand the impact of soil HMM concentration on AMF abundance and community structure in the contaminated sites of South Korea. Soil samples were collected from the vicinity of an abandoned smelter and the samples were subjected to three complementary methods such as spore morphology, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) for diversity analysis. Spore density was found to be significantly higher in highly contaminated soil compared to less contaminated soil. Spore morphological study revealed that Glomeraceae family was more abundant followed by Acaulosporaceae and Gigasporaceae in the vicinity of the smelter. T-RFLP and DGGE analysis confirmed the dominance of Funneliformis mosseae and Rhizophagus intraradices in all the study sites. Claroideoglomus claroideum, Funneliformis caledonium, Rhizophagus clarus and Funneliformis constrictum were found to be sensitive to high concentration of soil HMM. Richness and diversity of Glomeraceae family increased with significant increase in soil arsenic, cadmium and zinc concentrations. Our results revealed that the soil HMM has a vital impact on AMF community structure, especially with Glomeraceae family abundance, richness and diversity. PMID:26035444

Fate and transport of selected estrogen compounds in Hawaii soils: effect of soil type and macropores.

PubMed

D'Alessio, Matteo; Vasudevan, Dharni; Lichwa, Joseph; Mohanty, Sanjay K; Ray, Chittaranjan

2014-10-01

The fate and transport of estrogen compounds in the environment is of increasing concern due to their potential impact on freshwater organisms, ecosystems and human health. The behavior of these compounds in batch experiments suggests low mobility, while field studies indicate the persistence of estrogen compounds in the soil with the possibility of migration to surface water as well as groundwater. To better understand the movement of these chemicals through soils, we examined their transport in three different Hawaiian soils and two aqueous matrices. The three different soils used were an Oxisol, a Mollisol and a cinder, characterized by different mineralogical properties and collected at depths of 60-90 cm and 210-240 cm. Two liquid matrices were used; deionized (DI) water containing calcium chloride (CaCl2), and recycled water collected from a wastewater treatment facility. The experiments were conducted in packed and structured columns. Non-equilibrium conditions were observed during the study, especially in the structured soil. This is believed to be primarily related to the presence of macropores in the soil. The presence of macropores resulted in reduced contact time between soil and estrogens, which facilitated their transport. We found that the organic carbon content and mineralogical composition of the soils had a profound effect on the transport of the estrogens. The mobility of estrone (E1) and 17β-estradiol (E2) was greater in cinder than in the other soils. In column experiments with recycled water, earlier breakthrough peaks and longer tails of estrogens were produced compared to those observed using DI water. The use of recycled water for agricultural purposes and the siting of septic tanks and cesspools should be critically reviewed in light of these findings, especially in areas where groundwater is the primary source of potable water, such as Hawaii. Copyright © 2014 Elsevier B.V. All rights reserved.

Fate and transport of selected estrogen compounds in Hawaii soils: Effect of soil type and macropores

NASA Astrophysics Data System (ADS)

D'Alessio, Matteo; Vasudevan, Dharni; Lichwa, Joseph; Mohanty, Sanjay K.; Ray, Chittaranjan

2014-10-01

The fate and transport of estrogen compounds in the environment is of increasing concern due to their potential impact on freshwater organisms, ecosystems and human health. The behavior of these compounds in batch experiments suggests low mobility, while field studies indicate the persistence of estrogen compounds in the soil with the possibility of migration to surface water as well as groundwater. To better understand the movement of these chemicals through soils, we examined their transport in three different Hawaiian soils and two aqueous matrices. The three different soils used were an Oxisol, a Mollisol and a cinder, characterized by different mineralogical properties and collected at depths of 60-90 cm and 210-240 cm. Two liquid matrices were used; deionized (DI) water containing calcium chloride (CaCl2), and recycled water collected from a wastewater treatment facility. The experiments were conducted in packed and structured columns. Non-equilibrium conditions were observed during the study, especially in the structured soil. This is believed to be primarily related to the presence of macropores in the soil. The presence of macropores resulted in reduced contact time between soil and estrogens, which facilitated their transport. We found that the organic carbon content and mineralogical composition of the soils had a profound effect on the transport of the estrogens. The mobility of estrone (E1) and 17β-estradiol (E2) was greater in cinder than in the other soils. In column experiments with recycled water, earlier breakthrough peaks and longer tails of estrogens were produced compared to those observed using DI water. The use of recycled water for agricultural purposes and the siting of septic tanks and cesspools should be critically reviewed in light of these findings, especially in areas where groundwater is the primary source of potable water, such as Hawaii.

Organic carbon, water repellency and soil stability to slaking at aggregate and intra-aggregate scales

NASA Astrophysics Data System (ADS)

Jordán López, Antonio; García-Moreno, Jorge; Gordillo-Rivero, Ángel J.; Zavala, Lorena M.; Cerdà, Artemi; Alanís, Nancy; Jiménez-Compán, Elizabeth

2015-04-01

Water repellency (WR) is a property of some soils that inhibits or delays water infiltration between a few seconds and days or weeks. Inhibited or delayed infiltration contributes to ponding and increases runoff flow generation, often increasing soil erosion risk. In water-repellent soils, water infiltrates preferentially through cracks or macropores, causing irregular soil wetting patterns, the development of preferential flow paths and accelerated leaching of nutrients. Although low inputs of hydrophobic organic substances and high mineralization rates lead to low degrees of WR in cropped soils, it has been reported that conservative agricultural practices may induce soil WR. Although there are many studies at catchment, slope or plot scales very few studies have been carried out at particle or aggregate scale. Intra-aggregate heterogeneity of physical, biological and chemical properties conditions the transport of substances, microbial activity and biochemical processes, including changes in the amount, distribution and chemical properties of organic matter. Some authors have reported positive relationships between soil WR and aggregate stability, since it may delay the entry of water into aggregates, increase structural stability and contribute to reduce soil erosion risk. Organic C (OC) content, aggregate stability and WR are therefore strongly related parameters. In the case of agricultural soils, where both the type of management as crops can influence all these parameters, it is important to evaluate the interactions among them and their consequences. Studies focused on the intra-aggregate distribution of OC and WR are necessary to shed light on the soil processes at a detailed scale. It is extremely important to understand how the spatial distribution of OC in soil aggregates can protect against rapid water entry and help stabilize larger structural units or lead to preferential flow. The objectives of this research are to study [i] the OC content and the intensity of WR in aggregates of different sizes. [ii] the intra-aggregate distribution of OC and the intensity of WR and [iii] the structural stability of soil aggregates relative to the OC content and the intensity of WR in soils under different crops (apricot, citrus and wheat) and different treatments (conventional tilling and mulching). Soil samples were collected from an experimental area (Luvic Calcisols and Calcic Luvisols) in the province of Sevilla (Southern Spain) under different crops (apricot, citrus and wheat) and different management types (conventional tillage with moldboard plow) and mulching (no-tilling and addition of wheat residues at rates varying between 5 and 8 Mg/ha/year). At each sampling site, soil blocks (50 cm long × 50 cm wide × 10 cm deep) were carefully collected to avoid disturbance of aggregates as much as possible and transported to the laboratory. At field moist condition, undisturbed soil aggregates were separated by hand. In order to avoid possible interferences due to disturbance by handling, aggregates broken during this process were discarded. Individual aggregates were arranged in paper trays and air-dried during 7 days under laboratory standard conditions. After air-drying, part of each sample was carefully divided for different analyses: [i] part of the original samples was sieved (2 mm) to eliminate coarse soil particles and homogenized for characterization of OC and N contents, C/N ratio and texture; [ii] part of the aggregates were dry-sieved (0.25-0.5, 0.5-1 and 1-2 mm) or measured with a caliper (2-5, 5-10 and 10-15 mm) and separated in different sieve-size classes for determination of WR and OC content; [iii] aggregates 10-15 mm in size were selected for obtaining aggregate layers using a soil aggregate erosion (SAE) apparatus and WR and OC content were determined at each layer; finally, [iv] in order to study the relation between stability to slaking, WR and OC, these properties were determined in 90 air-dried aggregates (about 10 mm in size) selected per treatment (mulched or conventional tillage) and crop (apricot, citrus and wheat). In this case, every set of aggregates was randomly divided in three groups (n = 30) for assessing stability to slaking, WR and OC, respectively. OC content in the fine earth fraction of soils under different crops did not show important variations, although it increased significantly from conventionally tilled to mulched soils. The distribution of OC content in aggregates with different size varied among soils under different crops, generally increasing with decreasing size. At the intra-aggregate level, OC concentrated preferably in the exterior layer of differently sized aggregates and of aggregate coatings and interior from conventionally tilled soils, probably because of recent organic inputs or leachates. In the case of mulched soils, higher concentrations were observed, but no significant differences among aggregate regions were found. The intensity of water repellency, determined by the ethanol method, did not show great variations among differently sized aggregates under different crops in the 0-10 cm layer, but increased significantly from conventionally tilled to mulched soils. Coarser aggregates were generally wettable, while finer aggregates showed slight water repellency. Regardless of variations in the distribution of OC in different layers of aggregate from conventionally tilled soils, great or significant differences in the distribution of water repellency at the intra-aggregate level were not found. In case of mulched soils such differences were not significant. Finally, the intensity of water repellency was much more important than the concentration of OC in the stability to slaking of aggregates.

Stabilities of ant nests and their adjacent soils

NASA Astrophysics Data System (ADS)

Echezona, B. C.; Igwe, C. A.

2012-10-01

Nests habour ants and termites and protect them from harsh environmental conditions. The structural stabilities of nests were studied to ascertain their relative vulnerability to environmental stresses. Arboreal-ant nests were pried from different trees, while epigeous-termite nests were excavated from soil surface within the sample area. Soils without any visible sign of ant or termite activity were also sampled 6 m away from the nests as control. Laboratory analysis result showed that irrespective of the tree hosts, the aggregate stabilities of the ant nests were lower than those of the ground termite, with nests formed on Cola nitida significantly showing lower aggregate stability (19.7%) than other antnest structures. Clay dispersion ratio, moisture content, water stable aggregate class <0.25mm and sand mass were each negatively correlated with aggregate stability, while water stable aggregate class1.00-0.50 mm gave a positive correlation. Nest structures were dominated more by water stable aggregate class >2.00 mm but path analysis demonstrated that water stable aggregate class <0.25 mm contributed most to the higher aggregate stability of the termite nest than the other nest. Nest aggregates had greater structural stability compared to the control soil. The higher structural stability of termite nests over other nest and soil was considered a better adaptive mechanism against body desiccation.

Evaluation of conceptual models of natural organic matter (humus) from a consideration of the chemical and biochemical processes of humification

USGS Publications Warehouse

Wershaw, Robert L.

2004-01-01

Natural organic matter (NOM) has been studied for more than 200 years because of its importance in enhancing soil fertility, soil structure, and water-holding capacity and as a carbon sink in the global carbon cycle. Two different types of models have been proposed for NOM: (1) the humic polymer models and (2) the molecular aggregate models. In the humic polymer models, NOM molecules are depicted as large (humic) polymers that have unique chemical structures that are different from those of the precursor plant degradation products. In the molecular aggregate models, NOM is depicted as being composed of molecular aggregates (supramolecular aggregates) of plant degradation products held together by non-covalent bonds. The preponderance of evidence favors the supramolecular aggregate models. These models were developed by studying the properties of NOM extracted from soils and natural waters, and as such, they provide only a very generalized picture of the structure of NOM aggregates in soils and natural waters prior to extraction. A compartmental model, in which the structure of the NOM in each of the compartments is treated separately, should provide a more accurate representation of NOM in soil and sediment systems. The proposed NOM compartments are: (1) partially degraded plant tissue, (2) biomass from microorganisms, (3) organic coatings on mineral grains, (4) pyrolytic carbon, (5) organic precipitates, and (6) dissolved organic matter (DOM) in interstitial water. Within each of these compartments there are NOM supramolecular aggregates that will be dissolved by the solvent systems that are used by researchers for extraction of NOM from soils and sediments. In natural water systems DOM may be considered as existing in two subcompartments: (1) truly dissolved DOM and (2) colloidal DOM.

Dissecting the multi-scale spatial relationship of earthworm assemblages with soil environmental variability.

PubMed

Jiménez, Juan J; Decaëns, Thibaud; Lavelle, Patrick; Rossi, Jean-Pierre

2014-12-05

Studying the drivers and determinants of species, population and community spatial patterns is central to ecology. The observed structure of community assemblages is the result of deterministic abiotic (environmental constraints) and biotic factors (positive and negative species interactions), as well as stochastic colonization events (historical contingency). We analyzed the role of multi-scale spatial component of soil environmental variability in structuring earthworm assemblages in a gallery forest from the Colombian "Llanos". We aimed to disentangle the spatial scales at which species assemblages are structured and determine whether these scales matched those expressed by soil environmental variables. We also tested the hypothesis of the "single tree effect" by exploring the spatial relationships between root-related variables and soil nutrient and physical variables in structuring earthworm assemblages. Multivariate ordination techniques and spatially explicit tools were used, namely cross-correlograms, Principal Coordinates of Neighbor Matrices (PCNM) and variation partitioning analyses. The relationship between the spatial organization of earthworm assemblages and soil environmental parameters revealed explicitly multi-scale responses. The soil environmental variables that explained nested population structures across the multi-spatial scale gradient differed for earthworms and assemblages at the very-fine- (<10 m) to medium-scale (10-20 m). The root traits were correlated with areas of high soil nutrient contents at a depth of 0-5 cm. Information on the scales of PCNM variables was obtained using variogram modeling. Based on the size of the plot, the PCNM variables were arbitrarily allocated to medium (>30 m), fine (10-20 m) and very fine scales (<10 m). Variation partitioning analysis revealed that the soil environmental variability explained from less than 1% to as much as 48% of the observed earthworm spatial variation. A large proportion of the spatial variation did not depend on the soil environmental variability for certain species. This finding could indicate the influence of contagious biotic interactions, stochastic factors, or unmeasured relevant soil environmental variables.

Rhizosphere biophysics and root water uptake

NASA Astrophysics Data System (ADS)

Carminati, Andrea; Zarebanadkouki, Mohsen; Ahmed, Mutez A.; Passioura, John

2016-04-01

The flow of water into the roots and the (putative) presence of a large resistance at the root-soil interface have attracted the attention of plant and soil scientists for decades. Such resistance has been attributed to a partial contact between roots and soil, large gradients in soil matric potential around the roots, or accumulation of solutes at the root surface creating a negative osmotic potential. Our hypothesis is that roots are capable of altering the biophysical properties of the soil around the roots, the rhizosphere, facilitating root water uptake in dry soils. In particular, we expect that root hairs and mucilage optimally connect the roots to the soil maintaining the hydraulic continuity across the rhizosphere. Using a pressure chamber apparatus we measured the relation between transpiration rate and the water potential difference between soil and leaf xylem during drying cycles in barley mutants with and without root hairs. The samples were grown in well structured soils. At low soil moistures and high transpiration rates, large drops in water potential developed around the roots. These drops in water potential recovered very slowly, even after transpiration was severely decreased. The drops in water potential were much bigger in barley mutants without root hairs. These mutants failed to sustain high transpiration rates in dry conditions. To explain the nature of such drops in water potential across the rhizosphere we performed high resolution neutron tomography of the rhizosphere of the barleys with and without root hairs growing in the same soil described above. The tomograms suggested that the hydraulic contact between the soil structures was the highest resistance for the water flow in dry conditions. The tomograms also indicate that root hairs and mucilage improved the hydraulic contact between roots and soil structures. At high transpiration rates and low water contents, roots extracted water from the rhizosphere, while the bulk soil, due its low unsaturated conductivity, failed to compensate root water uptake. We conclude that root hairs are functional to increase the contact area between the roots and the soil structures and mucilage maintains wet the soil region between root hairs. These observations demonstrate the importance of the biophysical processes in the rhizosphere in modulating root water uptake.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Main factors controlling microbial community structure, growth and activity after reclamation of a tailing pond with aided phytostabilization

NASA Astrophysics Data System (ADS)

Zornoza, Raúl; Acosta, José A.; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

2015-04-01

Reclamation on bare tailing ponds has the potential to represent soil genesis in Technosols favoring the understanding of the changes of microbial communities and function. In this study we used phytostabilization aided with calcium carbonate and pig slurry/manure to reclaim an acidic bare tailing pond with the aim of investigating the effect of amending and different species on microbial community structure and function. We sampled after two years of amending and planting: unamended tailing soil (UTS), non-rhizospheric amended tailing soil (ATS), rhizospheric soil from four species, and non-rhizospheric native forest soil (NS), which acted as reference. The application of amendments increased pH up to neutrality, organic carbon (Corg), C/N and aggregate stability, while decreased salinity and heavy metals availability. No effect of rhizosphere was observed on physicochemical properties, metals immobilization and microbial community structure and function. To account for confounding effects due to soil organic matter, microbial properties were expressed per Corg. The high increments in pH and Corg have been the main factors driving changes in microbial community structure and function. Bacterial biomass was higher in UTS, without significant differences among the rest of soils. Fungal biomass followed the trend UTS < ATS = rhizospheric soils < NS. Bacterial growth increased and fungal growth decreased with increasing pH, despite the high availability of metals at low pH. Enzyme activities were lower in UTS, being β-glucosidase and β-glucosaminidase activities highly correlated with bacterial growth. Microbial activities were not correlated with the exchangeable fraction of heavy metals, indicating that microbial function is not strongly affected by these metals, likely due to the efficiency of the reclamation procedure to reduce metals toxicity. Changes in microbial community composition were largely explained by changes in pH, heavy metals availability and Corg, with increments in fungal and actinobacterial proportions with soil amending. Acknowledgements R. Zornoza acknowledges the financial support to Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia (Spain).

Community structures and antagonistic activities of the bacteria associated with surface-sterilized pepper plants grown in different field soils.

PubMed

Kang, Sin Ae; Han, Jae Woo; Kim, Beom Seok

2016-12-01

Endophytic bacteria may act individually or in consortia in controlling certain plant diseases. In this study, pepper plants (Capsicum annuum L. cv. Nokkwang) were cultivated in glasshouse conditions using field soils collected from two different geographic locations, Deokso (DS) and Gwangyang (GY) in Korea. Community structure and antifungal activity of pepper endophytic bacteria were analyzed using culture-independent (PCR-DGGE) and culture-dependent (plating) methods, respectively. Dissimilarities were observed between DGGE profiles of DS and GY samples at all plant tissues. However, sequencing of the major DGGE bands revealed an enrichment of Firmicutes in the leaves of plants propagated in either soil. Similar results were observed with the culturable assays. Firmicutes dominated the isolates from both leaf samples, DS leaf (100 %) and GY leaf (83.3 %), although the genus compositions of DS leaf and GY leaf isolates were different. We assessed the antifungal activity of each isolate recovered to better understand the potential role that these endophytic bacteria may play. Of the 27 representative isolates from DS plant samples, 17 isolates (63.0 %) had antagonistic activity against at least one of the fungi tested. Seventeen isolates from GY plant samples (58.6 %) displayed antagonistic properties. The results show that the endophytic communities differ in the same plant species when propagated in different soils. Exploring the internal tissues of plants growing in diverse soil environments could be a way to find potential candidates for biocontrol agents.

Effects of heavy metal pollution of highway origin on soil nematode guilds in North Shenyang, China.

PubMed

Han, Dechang; Zhang, Xiaoke; Tomar Vijay Vikram, Singh; Li, Qi; Wen, Dazhong; Liang, Wenju

2009-01-01

Soil samples were collected with distance at 5, 20, 40, 80, 160, and 320 m from the Shen-Ha (Shenyang-Harbin) Highway, Northeast China, to investigate the effect of heavy metals of highway origin on soil nematode guilds. The contents of soil Pb, Cu, Zn, and the nematode community structure were analyzed. The results showed that the contents of total and available Pb, Cu, Zn varied significantly with the different distances from the highway. Pb was the main pollutant in the soils in the vicinity of Shen-Ha Highway. The zone from 20 to 40 m away from the highway was the most polluted area. The highest abundance of soil nematodes was found at 5 m while the lowest at 20 m away from the highway. Thirty six genera of nematodes belonging to 23 families were identified. Nematode guilds having different responses to soil heavy metals were classified into four types. Soil nematode guilds may act as a prominent indicator to heavy metal pollution of highway origin.

Effects of haze pollution on microbial community changes and correlation with chemical components in atmospheric particulate matter.

PubMed

Sun, Yujiao; Xu, Shangwei; Zheng, Danyang; Li, Jie; Tian, Hezhong; Wang, Yong

2018-05-10

In this study, particulate matter (PM) with aerodynamic diameters of ≤2.5 and ≤10 μm (PM 2.5 and PM 10 , respectively), which was found at different concentrations in spring, was collected in Beijing. The chemical composition and bacterial community diversity of PM were determined, and the relationship between them was studied by 16S rRNA sequencing and mathematical statistics. Chemical composition analysis revealed greater relative percentages of total organic compounds (TOC) and secondary ions (NO 3 - , SO 4 2- , and NH 4 + ). The concentrations of Ca 2+ , Na + , Mg 2+ , K + and SO 4 2- increased in high-concentration PM, which was associated with the contribution of soil, dust and soot. Microbiological analysis revealed 1191 operational taxonomic units. Microbial community structure was stable at the phylum level. The most abundant phyla were Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Community clustering analysis at the genus level showed that the difference in bacterial community structure between different PM concentrations (clean air vs. smog) was greater than that between different particle sizes. The dominant genera varied in different concentrations of PM. An unclassified genus of Cyanobacteria and Comamonadaceae were most abundant in low- and high-concentration PM, respectively. The microbial community structure was dynamic at the genus level due to different environmental factors. The dominant bacteria in high-concentration PM were widely distributed in soils, indicating that the soil contributed more to the increase in the PM. The individual microbes that were detected did not increase significantly as the PM concentration increased. The bacterial community structure was strongly correlated with K + , Ca 2+ , Na + , Mg 2+ , SO 4 2- and TOC in high-concentration PM and had a good correlation with NO 3 - , Cl - , NH 4 + and TIC in low-concentration PM. Soil and dust contributed to the increase in the concentration of the particles, and the relevant chemical components also produced differences in the bacterial community structure in different concentrations of PM. Copyright © 2018. Published by Elsevier B.V.

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships.

PubMed

Zhao, Jun; Zhou, Xing; Jiang, Anqi; Fan, Juanzi; Lan, Tao; Zhang, Jinbo; Cai, Zucong

2018-06-21

Soil disinfestation is an important agricultural practice to conquer soil-borne diseases and thereby ensure crop productivity. Reductive soil disinfestation (RSD) had been developed as an environmentally friendly alternative to chemical soil disinfestation (CSD). However, the differences between CSD and RSD on soil-borne pathogen suppression and fungal community structure remain poorly understood. In this work, five treatments, i.e., untreated soil (CK), CSD with 0.5 t ha -1 dazomet (DZ), RSD with 10 t ha -1 ethanol (ET), 15 t ha -1 sugarcane bagasse (SB), and 15 t ha -1 bean dregs (BD), were performed to investigate their influences on disinfestation efficiency, fungal abundance, diversity, and community structure via quantitative PCR and high-throughput sequencing. RSD-related treatments, especially the BD treatment, effectively alleviated soil acidification and salinization. The fungal abundance and microbial activity considerably increased in the BD treatment and significantly declined in the DZ treatment as compared to the CK treatment. Moreover, both CSD and RSD-related treatments significantly inhibited the population of Fusarium oxysporum and the relative abundance of genus Fusarium. Fungal community structure was notably altered by CSD and RSD practices. Furthermore, both CSD and RSD harbored a distinct unique microbiome, with the DZ treatment dominated by the genus Mortierella and BD treatment predominated by the genera Zopfiella, Chaetomium, and Penicillium. Taken together, these results indicate that the BD treatment could considerably alleviate the soil deterioration, improve soil microbial activity, and reassemble a non-pathogen unique microbiome that have more disease-suppressive agents and thus might be a promising disinfestation practice to control soil-borne disease in monoculture system.

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

PubMed

Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

2017-05-01

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Removal of volatile organic compounds in soils by soil vapor extraction (SVE)].

PubMed

Yin, Fu-xiang; Zhang, Sheng-tian; Zhao, Xin; Feng, Ke; Lin, Yu-suo

2011-05-01

An experiment study has been carried out to investigate effects of the diameter of soil columns, the size of soil particulate and different contaminants on efficiency of simulated soil vapor extraction (SVE). Experiments with benzene, toluene, ethylbenzene and n-propylbenzene contaminated soils showed that larger bottom area/soil height (S/H) of the columns led to higher efficiency on removal of contaminants. Experiments with contaminated soils of different particulate size showed that the efficiency of SVE decreased with increases in soil particulate size, from 10 mesh to between 20 mesh and 40 mesh and removal of contaminants in soils became more difficult. Experiments with contaminated soils under different ventilation rates suggested that soil vapor extraction at a ventilation rate of 0.10 L x min(-1) can roughly remove most contaminants from the soils. Decreasing of contaminants in soils entered tailing stages after 12 h, 18 h and 48 h for benzene, toluene and ethylbenzene, respectively. Removal rate of TVOCs (Total VOCs) reached a level as high as 99.52%. The results of the experiment have indicated that molecule structure and properties of the VOCs are also important factors which have effects on removal rates of the contaminants. Increases in carbon number on the benzene ring, decreases in vapor pressure and volatile capability resulted in higher difficulties in soil decontamination. n-propylbenzene has a lower vapor pressure than toluene and ethylbenzene which led to a significant retard effect on desorption and volatilization of benzene and ethylbenzene.

Impact of land management on soil structure and soil hydraulic properties

NASA Astrophysics Data System (ADS)

Kodesova, Radka; Jirku, Veronika; Nikodem, Antonin; Muhlhanselova, Marcela; Zigova, Anna

2010-05-01

Study is focused on a comparison of a soil structure and soil hydraulic properties within soil profiles of a same soil type under different land management. Study was performed in Haplic Luvisol in Hnevceves the Czech Republic. Two soil profiles, which were in close distance from each other, were chosen: 1. under the conventional tillage, 2. under the permanent (30 years) grass cover. Soil sampling and field experiments were carried out immediately after the harvest of winter barley in 2008. The micromorphological images were used to evaluate the soil structure of all Ap, Bt1, Bt2 and C diagnostic horizons. The hydraulic properties of the diagnostic horizons were studied in the laboratory using multistep outflow experiments performed on the undisturbed 100-cm3 soil samples. A tension disc infiltrometer (with a disc radius of 10 cm) and minidisc tension infiltrometers (with a disc radius of 2.2 cm) were used to measure cumulative water infiltration under unsaturated conditions created using a pressure head of -2 cm. Measurements were performed at a depths of 5, 45, 75 and 110 cm, which corresponded to the Ap, Bt1, Bt2 and C horizons of studied Haplic Luvisol at both locations. The Guelph permeameter was used to measure cumulative water flux under surface ponding conditions. The depth of the drilled well was 10, 50, 80 and 115 cm, the well radius was 3 cm, and the well ponding depth was 5 cm. Both tests were used to evaluate hydraulic conductivity (K for h=-2cm, and Ks) values. Results showed, that while properties in the Bt2 and C horizons of both soil profiles were relatively similar, properties in the Ap and Bt1 horizons were different. The fraction of gravitational pores (which may cause preferential flow) in the Ap and Bt1 horizons of the soil profile under the convectional tillage was large than those in the Ap and Bt1 horizons of the soil profile under the permanent grass. This influenced for instance the Ks values measured using the Guelph permeametr. The Ks values were higher and more variable in the soil profile under the convectional tillage than those in the soil profile under the permanent grass. On the other hand, due to the periodical tillage and consequent soil structure breakdown, the fraction of the large capillary pores were smaller in the Ap horizon of the soil profile under the convectional tillage than that in the Ap horizon of the soil profile under the permanent grass. As result the K (h=-2cm) values measured using the tension infiltrometer in the soil profile under the permanent grass was higher than those in the soil profile under the convectional tillage. However, the fraction of the large capillary pores and K (h=-2cm) values were similar in the Bt1 horizons of both soil profiles. Thus the land management impacted both macropores and matrix pores in the Ap horizon and macropores (prismatic structure and biopores) in the Bt1 horizon. Acknowledgement: Authors acknowledge the financial support of the Grant Agency of the Czech Republic (grant No. GA CR 526/08/0434) and the Ministry of Education, Youth and Sports of the Czech Republic (grant No. MSM 6046070901).

Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce.

PubMed

Schreiter, Susanne; Ding, Guo-Chun; Heuer, Holger; Neumann, Günter; Sandmann, Martin; Grosch, Rita; Kropf, Siegfried; Smalla, Kornelia

2014-01-01

The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for 10 years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected 3 and 7 weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas, and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three soils. The number of rhizosphere responders was highest 3 weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce.

Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce

PubMed Central

Schreiter, Susanne; Ding, Guo-Chun; Heuer, Holger; Neumann, Günter; Sandmann, Martin; Grosch, Rita; Kropf, Siegfried; Smalla, Kornelia

2014-01-01

The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for 10 years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected 3 and 7 weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas, and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three soils. The number of rhizosphere responders was highest 3 weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce. PMID:24782839

CO2 efflux from soil under influence of cadmium and glucose

NASA Astrophysics Data System (ADS)

Gilmullina, Aliia; Galitskaya, Polina; Selivanovskaya, Svetlana

2017-04-01

Soil is the largest pool of organic carbon. Any anthropogenic activity may change the soil organic carbon stock resulting in the atmospheric carbon concentration increase. Organic wastes and sewage sludge are often used for soil fertilization. These amendments often contain not only organic compounds stimulating soil microflora but also toxic compounds e.g. metals inhibiting them. The question about the influence of such amendments on soil carbon stock still remains open. The aim of this study was to evaluate individual glucose and cadmium (Cd) additions and their combined effects on carbon mineralization and microbial community structure in forest soil sampled from different depths (0-20 cm, 20-40 cm and 40-60 cm). We incubated soil samples for 14 days after the addition of: glucose (10000 mg kg-1), Cd (300 mg kg-1) and their mixture. CO2 efflux was measured by CO2 trapping in NaOH, at the 3rd, 7th and 14th days of incubation DNA was extracted from soil samples for assessment of microbial community structure via real-time PCR and Illumina sequencing. Glucose addition induced the increase of soil respiration and fungal-bacterial ratio. However, bacterial alpha-biodiversity decreased as glucose addition caused the dominance of Proteobacteria (0-20 cm, 20-40 cm and 40-60 cm), Actinobacteria (20-40 cm) and Acidobacteria (40-60 cm) phyla. Single Cd addition did not have any effect on parameters studied. In case of simultaneous addition of glucose and Cd, soil respiration and microbial community structure mainly depended more on glucose amendment as compared with metal.

Photothermal Beam Deflection Spectroscopy for the Determination of Thermal Diffusivity of Soils and Soil Aggregates

NASA Astrophysics Data System (ADS)

Proskurnin, M. A.; Korte, D.; Rogova, O. B.; Volkov, D. S.; Franko, M.

2018-07-01

Photothermal beam deflection spectroscopy (BDS) with a red He-Ne laser (632.8 nm, 35 mW) as an excitation beam source and a green He-Ne laser (543.1 nm, 2 mW) as a probe was used for estimating thermal diffusivity of several types of soil samples and individual soil aggregates with small surfaces (2 × 2 mm). It is shown that BDS can be used on demand for studies of changes in properties of soil entities of different hierarchical levels under the action of agrogenesis. It is presented that BDS clearly distinguishes between thermal diffusivities of different soil types: Sod-podzolic [Umbric Albeluvisols, Abruptic], 29 ± 3; Chernozem typical [Voronic Chernozems, Pachic], 9.9 ± 0.9; and Light Chestnut [Haplic Kastanozems, Chromic], 9.7 ± 0.9 cm2·h-1. Aggregates of chernozem soil show a significantly higher thermal diffusivity compared to the bulk soil. Thermal diffusivities of aggregates of Chernozem for virgin and bare fallow samples differ, 53 ± 4 cm2·h-1 and 45 ± 4 cm2·h-1, respectively. Micromonoliths of different Sod-podzolic soil horizons within the same profile (topsoil, depth 10-14 cm, and a parent rock with Fe illuviation, depth 180-185 cm) also show a significant difference, thermal diffusivities are 9.5 ± 0.8 cm2·h-1 and 27 ± 2 cm2·h-1, respectively. For soil micromonoliths, BDS is capable to distinguish the difference in thermal diffusivity resulting from the changes in the structure of aggregates.

Exploring the spatial variability of soil properties in an Alfisol Catena

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

Rosemary, F.; Vitharana, U. W. A.; Indraratne, S. P.

Detailed digital soil maps showing the spatial heterogeneity of soil properties consistent with the landscape are required for site-specific management of plant nutrients, land use planning and process-based environmental modeling. We characterized the short-scale spatial heterogeneity of soil properties in an Alfisol catena in a tropical landscape of Sri Lanka. The impact of different land-uses (paddy, vegetable and un-cultivated) was examined to assess the impact of anthropogenic activities on the variability of soil properties at the catenary level. Conditioned Latin hypercube sampling was used to collect 58 geo-referenced topsoil samples (0–30 cm) from the study area. Soil samples were analyzedmore » for pH, electrical conductivity (EC), organic carbon (OC), cation exchange capacity (CEC) and texture. The spatial correlation between soil properties was analyzed by computing crossvariograms and subsequent fitting of theoretical model. Spatial distribution maps were developed using ordinary kriging. The range of soil properties, pH: 4.3–7.9; EC: 0.01–0.18 dS m –1 ; OC: 0.1–1.37%; CEC: 0.44– 11.51 cmol (+) kg –1 ; clay: 1.5–25% and sand: 59.1–84.4% and their coefficient of variations indicated a large variability in the study area. Electrical conductivity and pH showed a strong spatial correlation which was reflected by the cross-variogram close to the hull of the perfect correlation. Moreover, cross-variograms calculated for EC and Clay, CEC and OC, CEC and clay and CEC and pH indicated weak positive spatial correlation between these properties. Relative nugget effect (RNE) calculated from variograms showed strongly structured spatial variability for pH, EC and sand content (RNE < 25%) while CEC, organic carbon and clay content showed moderately structured spatial variability (25% < RNE < 75%). Spatial dependencies for examined soil properties ranged from 48 to 984 m. The mixed effects model fitting followed by Tukey's post-hoc test showed significant effect of land use on the spatial variability of EC. Our study revealed a structured variability of topsoil properties in the selected tropical Alfisol catena. Except for EC, observed variability was not modified by the land uses. Investigated soil properties showed distinct spatial structures at different scales and magnitudes of strength. Our results will be useful for digital soil mapping, site specific management of soil properties, developing appropriate land use plans and quantifying anthropogenic impacts on the soil system.« less

Impact of endochitinase-transformed white spruce on soil fungal communities under greenhouse conditions.

PubMed

Lamarche, Josyanne; Stefani, Franck O P; Séguin, Armand; Hamelin, Richard C

2011-05-01

Chitinase genes isolated from plants, bacteria or fungi have been widely used in genetic engineering to enhance the resistance of crops and trees to fungal pathogens. However, there are concerns about the possible effect of chitinase-transformed plants on nontarget fungi. This study aimed at evaluating the impact of endochitinase-transformed white spruce on soil fungal communities. Endochitinase-expressing white spruce and untransformed controls were transplanted in soils from two natural forests and grown for 8 months in a greenhouse. Soil fungal biomass and diversity, estimated through species richness and Shannon and Rao diversity indices, were not different between transgenic and control tree rhizospheres. The fungal phylogenetic community structure was the same in soil samples from control and transgenic white spruces after 8 months. Soil type and presence of seedlings had a much more significant impact on fungal community structure than the insertion and expression of the ech42 transgene within the white spruce genome. The results suggest that the insertion and constitutive expression of the ech42 gene in white spruce did not significantly affect soil fungal biomass, diversity and community structure. © 2011 Her Majesty the Queen in Right of Canada FEMS Microbiology Ecology © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.

Nematode diversity, abundance and community structure 50 years after the formation of the volcanic island of Surtsey

NASA Astrophysics Data System (ADS)

Ilieva-Makulec, K.; Bjarnadottir, B.; Sigurdsson, B. D.

2014-10-01

The soil nematode fauna can give important insights into soil development and other habitat changes that occur during primary succession. We investigated the generic composition, density, distribution and community structure of nematodes 50 years after the formation of a pristine volcanic island, Surtsey, Iceland. Part of the island has received additional nutrient inputs from seagulls breeding there since 1985, while the reminder has been much less affected and is at present found at a different successional sere. In total, 25 genera of nematodes were identified, of which 14 were reported on Surtsey for the first time. Nematode communities were more diverse in the more infertile area outside the gull colony, where 24 genera were found, compared to 18 inside. The trophic structure of the nematode communities showed relatively higher abundance of fungal feeders in the infertile areas, but relatively more bacterial- and plant-feeders inside the colony. Nematode abundance in surface soil was, however, significantly higher within the gull colony, with 16.7 ind. cm-2 compared to 3.6 ind. cm-2 outside. A multivariate analysis indicated that the nematode abundance and distribution on Surtsey were most strongly related to the soil C : N ratio, soil acidity, plant cover and biomass, soil temperature and soil depth.

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

PubMed

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

2018-01-01

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

Bacterial community structure in the rhizosphere of a Cry1Ac Bt-brinjal crop and comparison to its non-transgenic counterpart in the tropical soil.

PubMed

Singh, Amit Kishore; Rai, Govind Kumar; Singh, Major; Dubey, Suresh Kumar

2013-11-01

To elucidate whether the transgenic crop alters the rhizospheric bacterial community structure, a 2-year study was performed with Cry1Ac gene-inserted brinjal crop (Bt) and their near isogenic non-transformed trait (non-Bt). The event of Bt crop (VRBT-8) was screened using an insect bioassay and enzyme-linked immunosorbent assay. Soil moisture, NH4 (+)-N, NO3 (-)-N, and PO4 (-)-P level had non-significant variation. Quantitative polymerase chain reaction revealed that abundance of bacterial 16S rRNA gene copies were lower in soils associated with Bt brinjal. Microbial biomass carbon (MBC) showed slight reduction in Bt brinjal soils. Higher MBC values in the non-Bt crop soil may be attributed to increased root activity and availability of readily metabolizable carbon compounds. The restriction fragment length polymorphism of PCR-amplified rRNA gene fragments detected 13 different bacterial groups with the exclusive presence of β-Proteobacteria, Chloroflexus, Planctomycetes, and Fusobacteria in non-Bt, and Cyanobacteria and Bacteroidetes in Bt soils, respectively, reflecting minor changes in the community structure. Despite the detection of Cry1Ac protein in the rhizospheric soil, the overall impact of Cry1Ac expressing Bt brinjal was less compared to that due to seasonal changes.

Fluorescence lifetime evaluation of whole soils from the Amazon rainforest.

PubMed

Nicolodelli, Gustavo; Tadini, Amanda Maria; Nogueira, Marcelo Saito; Pratavieira, Sebastião; Mounier, Stephane; Huaman, Jose Luis Clabel; Dos Santos, Cléber Hilário; Montes, Célia Regina; Milori, Débora Marcondes Bastos Pereira

2017-08-20

Time-resolved fluorescence spectroscopy (TRFS) is a new tool that can be used to investigate processes of interaction between metal ions and organic matter (OM) in soils, providing a specific analysis of the structure and dynamics of macromolecules. To the best of our knowledge, there are no studies in the literature reporting the use of this technique applied to whole/non-fractionated soil samples, making it a potential method for use in future studies. This work describes the use of TRFS to evaluate the fluorescence lifetimes of OM of whole soils from the Amazon region. Analysis was made of pellets of soils from an oxisol-spodosol system, collected in São Gabriel da Cachoeira (Amazonas, Brazil). The fluorescence lifetimes in the oxisol-spodosol system were attributed to two different fluorophores. One was related to complexation of an OM fraction with metals, resulting in a shorter fluorophore lifetime. A short fluorescence lifetime (2-12 ns) could be associated with simpler structures of the OM, while a long lifetime (19-66 ns) was associated with more complex OM structures. This new TRFS technique for analysis of the fluorescence lifetime in whole soil samples complies with the principles of green chemistry.

Influence of the Soil Genesis on Physical and Mechanical Properties

PubMed Central

Marschalko, Marian; Yilmaz, Işık; Fojtová, Lucie; Kubečka, Karel; Bouchal, Tomáš; Bednárik, Martin

2013-01-01

The paper deals with the influence of soil genesis on the physical-mechanical properties. The presented case study was conducted in the region of the Ostrava Basin where there is a varied genetic composition of the Quaternary geological structure on the underlying Neogeneous sediments which are sediments of analogous granulometry but different genesis. In this study, 7827 soil samples of an eolian, fluvial, glacial, and deluvial origin and their laboratory analyses results were used. The study identified different values in certain cases, mostly in coarser-grained foundation soils, such as sandy loam S4 (MS) and clayey sand F4 (CS). The soils of the fluvial origin manifest different values than other genetic types. Next, based on regression analyses, dependence was proved neither on the deposition depth (depth of samples) nor from the point of view of the individual foundation soil classes or the genetic types. The contribution of the paper is to point at the influence of genesis on the foundation soil properties so that engineering geologists and geotechnicians pay more attention to the genesis during engineering-geological and geotechnical investigations. PMID:23844398

Molecular aspects of aromatic C additions to soils: Implications of char quality for ecosystem functionality

NASA Astrophysics Data System (ADS)

Keiluweit, M.; Nico, P. S.; Johnson, M. G.; Kleber, M.

2009-12-01

Solid residues of incomplete combustion (biochar or char) are continuously being added to soils due to natural vegetation fires in many ecosystems. However, new strategies for carbon sequestration in soils are likely to include the active addition of biochar to soils. Since biochar is a highly aromatic organic material such additions will modify the native molecular structure of soil organic matter and thus alter interactions with the global atmosphere and hydrosphere. Here we present a molecular level assessment of the physical organization and chemical complexity of biomass-derived chars and, specifically, that of aromatic carbon in char structures. Differences among wood and grass charred at temperatures from 100 to 700°C are investigated. BET-N2 surface area, X-ray diffraction (XRD), synchrotron-based Near-edge X-ray Absorption Fine Structure (NEXAFS) and Fourier transform infrared (FT-IR) spectroscopy results demonstrate how the two plant precursor materials undergo analogous, but quantitatively different physical-chemical transitions as charring intensity increases. These changes suggest the existence of four distinct physical and chemical categories of char. We find that each category of char consists of a unique mixture of chemical phases and physical states: (i) in transition chars the crystalline character of the precursor materials is preserved, (ii) in amorphous chars the heat-altered molecules and incipient aromatic polycondensates are randomly mixed, (iii) composite chars consist of poorly ordered graphene stacks embedded in amorphous phases, and (iv) turbostratic chars are dominated by turbostratic (disordered) graphitic crystallites. There is wide variation in both the chemical and the physical nature of aromatic carbon among these char categories. In this presentation we will point out how molecular variations among the aromatic components of the different char categories translate into differences in their ability to: (i) persist in the environment, (ii) function as environmental sorbents, and (iii) to enable the soil to provide environmental services.

Effect of Activated Carbon Amendment on Bacterial Community Structure and Functions in a PAH Impacted Urban Soil

PubMed Central

2012-01-01

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. PMID:22455603

Complex Forms of Soil Organic Phosphorus-A Major Component of Soil Phosphorus.

PubMed

McLaren, Timothy I; Smernik, Ronald J; McLaughlin, Mike J; McBeath, Therese M; Kirby, Jason K; Simpson, Richard J; Guppy, Christopher N; Doolette, Ashlea L; Richardson, Alan E

2015-11-17

Phosphorus (P) is an essential element for life, an innate constituent of soil organic matter, and a major anthropogenic input to terrestrial ecosystems. The supply of P to living organisms is strongly dependent on the dynamics of soil organic P. However, fluxes of P through soil organic matter remain unclear because only a minority (typically <30%) of soil organic P has been identified as recognizable biomolecules of low molecular weight (e.g., inositol hexakisphosphates). Here, we use (31)P nuclear magnetic resonance spectroscopy to determine the speciation of organic P in soil extracts fractionated into two molecular weight ranges. Speciation of organic P in the high molecular weight fraction (>10 kDa) was markedly different to that of the low molecular weight fraction (<10 kDa). The former was dominated by a broad peak, which is consistent with P bound by phosphomonoester linkages of supra-/macro-molecular structures, whereas the latter contained all of the sharp peaks that were present in unfractionated extracts, along with some broad signal. Overall, phosphomonoesters in supra-/macro-molecular structures were found to account for the majority (61% to 73%) of soil organic P across the five diverse soils. These soil phosphomonoesters will need to be integrated within current models of the inorganic-organic P cycle of soil-plant terrestrial ecosystems.

Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil.

PubMed

Meynet, Paola; Hale, Sarah E; Davenport, Russell J; Cornelissen, Gerard; Breedveld, Gijs D; Werner, David

2012-05-01

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. © 2012 American Chemical Society

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

Soil organic matter is a key attribute of soil fertility. The pool of soil organic C can be increased, either by mineral fertilisers or by adding organic amendments such as sewage sludge. Sewage sludge has positive effects on agricultural soils through the supply of organic matter and essential plant nutrients, but sludge may also contain unwanted heavy metals, xenobiotic substances and pathogens. One obvious effect of long-term sewage sludge addition is a decrease in soil pH, caused by N mineralisation followed by nitrification, sulphate formation and presence of organic acids with the organic matter added. The objective of this study was to investigate the effect of sewage sludge on the microbial biomass and community structure. Materials and methods We analysed soil samples from four sites where sewage sludge has been repeatedly applied in long-term field experiments situated in different parts of Sweden; Ultuna (59°49'N, 17°39'E, started 1956), Lanna (58°21'N, 13°06'E, started 1997-98), Petersborg (55°32'N, 13°00'E, started 1981) and Igelösa (55°45'N, 13°18'E, started 1981). In these four experiments, at least one sewage sludge treatment is included in the experimental design. In the Ultuna experiment, all organic fertilisers, including sewage sludge, are applied every second year, corresponding to 4 ton C ha-1. The Lanna experiment has a similar design, with 8 ton dry matter ha-1 applied every second year. Lanna also has an additional treatment in which metal salts (Cd, Cu, Ni and Zn) are added together with sewage sludge. At Petersborg and Igelösa, two levels of sewage sludge (4 or 12 ton dry matter ha-1 every 4th year) are compared with three levels of NPK fertiliser (0 N, ½ normal N and normal N). Topsoil samples (0-20 cm depth) from the four sites were analysed for total C, total N, pH and PLFAs (phospholipid fatty acids). In addition, crop yields were recorded. Results At all four sites, sewage sludge has had a positive effect on crop yields 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.

Measurements of pH and redox potential distributions in TNT-contaminated plant-soil systems using microelectrode techniques

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

Pang, H.; Zhang, T.C.

1997-12-31

The pH and redox potential profiles in TNT-contaminated soils with and without plants were investigated using microelectrode techniques. The new pH cocktail and double-barreled structure greatly improved the performance of the pH microelectrode. For soil without plants, there is almost no pH difference at different locations with different heights; while for the TNT-contaminated soils with plants there exist pH profiles. The soil immediately near the root of the plant has the lowest pH value. The pH value increases as the distance between the measuring point and the plant roots increases. The pH gradient (the increased pH value over the unitmore » distance) decreases with an increase of the distance between the measuring point and the plant roots. These results show that the plant presence can greatly affect the pH distribution. In vegetated soil, the redox potentials in the layer nearest the plant roots are higher than those in the bulk soil without plants. The redox potentials in the central part of the plant are lower than those in the soil around the plant and soil without the plant. The redox potentials in the soil without plants decrease with an increase of depth.« less

Selenium speciation in seleniferous agricultural soils under different cropping systems using sequential extraction and X-ray absorption spectroscopy.

PubMed

Qin, Hai-Bo; Zhu, Jian-Ming; Lin, Zhi-Qing; Xu, Wen-Po; Tan, De-Can; Zheng, Li-Rong; Takahashi, Yoshio

2017-06-01

Selenium (Se) speciation in soil is critically important for understanding the solubility, mobility, bioavailability, and toxicity of Se in the environment. In this study, Se fractionation and chemical speciation in agricultural soils from seleniferous areas were investigated using the elaborate sequential extraction and X-ray absorption near-edge structure (XANES) spectroscopy. The speciation results quantified by XANES technique generally agreed with those obtained by sequential extraction, and the combination of both approaches can reliably characterize Se speciation in soils. Results showed that dominant organic Se (56-81% of the total Se) and lesser Se(IV) (19-44%) were observed in seleniferous agricultural soils. A significant decrease in the proportion of organic Se to the total Se was found in different types of soil, i.e., paddy soil (81%) > uncultivated soil (69-73%) > upland soil (56-63%), while that of Se(IV) presented an inverse tendency. This suggests that Se speciation in agricultural soils can be significantly influenced by different cropping systems. Organic Se in seleniferous agricultural soils was probably derived from plant litter, which provides a significant insight for phytoremediation in Se-laden ecosystems and biofortification in Se-deficient areas. Furthermore, elevated organic Se in soils could result in higher Se accumulation in crops and further potential chronic Se toxicity to local residents in seleniferous areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

National Soil Information System in Turkey

NASA Astrophysics Data System (ADS)

Emrah Erdogan, Hakki; Sahin, Mehmet; Sahin, Yuksel

2013-04-01

Land consolidation (LC) represents complexity if management, legal, economic and technical procedures realized in order to adjust the land structure according to actual human preferences and needs. It includes changes in ownership rights to land and other real estate property, exchange of parcels among owners, changes in parcel borders, parcel size and shape, joining and dividing of parcels, changes in land use, construction works as roads, bridges, water changes etc.. Since the subject of LC is agricultural lands, the quality of consolidation depends on the quality of soil data. General Directorate of Agrarian Reform (GDAR) is the responsible institution on land consolidation whole of Turkey. Under GDAR, National Soil Information System (NSIS) has been build up with base soil data in relevant scale (1:5000). NSIS contain detailed information on soil chemical and physical properties, current land use, parent material, land capability class, Storie Index Values. SI were used on land consolidation, land use planning and farm development services. LCC was used for land distribution, rental land; define of village settlement, consolidation, expropriation, reconstruction, reclamation, non-agricultural usage. LCC were also specified to subclasses in four different limited factors as i) flow and erosion risk ii) requirement of drainage and soil moisture iii) Limits of soil tillage and root (shallow soils, low water retention capacity, stony, salty .etc) iv) climatic limits. In this study, digital soil survey and mapping project located in Yumurtalik, Adana is presented as an example of NSIS data structure. The project cover an area of 45709 ha that include crop lands as an area of 28528 ha and other land use (urban, roads..etc) as an area of 17181 ha. Soil profiles were described in 45 different points and totally 1279 soil samples were collected in field study and the check bore hole were made in 3170 points.

[Community structure and seasonal change of soil micro-arthropodes in the Lower Reaches of Liaohe River Plain under different land utilization].

PubMed

Ke, Xin; Liang, Wenju; Yu, Wantai; Xie, Rongdong; Weng, Chaolian; Yang, Yiming; Yin, Wenying

2004-04-01

The data on the soil micro-arthropodes under four land utilization types (fallow, forest, upland field and paddy) in the Lower Reaches of Liaohe River Plain were collected in a period from October 2000 to October 2001. Using the community parameters of population density, group richness, diversity index and evenness, the community structure and its seasonal changes were described. There were 12 groups of soil micro-arthropodes in this region, and of the groups, Collembola and Acarina were dominant, and Diptera, Coleoptera and Hymenoptera were often seen in fallow, forest and upland field, while Collembola, Acarina and Diptera were dominant in paddy. Both land utilization and seasonal change influenced the population density, group richness and diversity index of soil micro-arthropodes. The vertical distribution in both density and group number of arthropods in soil was in the order of surface > middle > bottom.

Observing and modeling links between soil moisture, microbes and CH4 fluxes from forest soils

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Levy-Booth, David; Barker, Jason; Prescott, Cindy; Grayston, Sue

2017-04-01

Soil moisture is a key driver of methane (CH4) fluxes in forest soils, both of the net uptake of atmospheric CH4 and emission from the soil. Climate and land use change will alter spatial patterns of soil moisture as well as temporal variability impacting the net CH4 exchange. The impact on the resultant net CH4 exchange however is linked to the underlying spatial and temporal distribution of the soil microbial communities involved in CH4 cycling as well as the response of the soil microbial community to environmental changes. Significant progress has been made to target specific CH4 consuming and producing soil organisms, which is invaluable in order to understand the microbial regulation of the CH4 cycle in forest soils. However, it is not clear as to which extent soil moisture shapes the structure, function and abundance of CH4 specific microorganisms and how this is linked to observed net CH4 exchange under contrasting soil moisture regimes. Here we report on the results from a research project aiming to understand how the CH4 net exchange is shaped by the interactive effects soil moisture and the spatial distribution CH4 consuming (methanotrophs) and producing (methanogens). We studied the growing season variations of in situ CH4 fluxes, microbial gene abundances of methanotrophs and methanogens, soil hydrology, and nutrient availability in three typical forest types across a soil moisture gradient in a temperate rainforest on the Canadian Pacific coast. Furthermore, we conducted laboratory experiments to determine whether the net CH4 exchange from hydrologically contrasting forest soils responded differently to changes in soil moisture. Lastly, we modelled the microbial mediation of net CH4 exchange along the soil moisture gradient using structural equation modeling. Our study shows that it is possible to link spatial patterns of in situ net exchange of CH4 to microbial abundance of CH4 consuming and producing organisms. We also show that the microbial community responds different to environmental change dependent on the soil moisture regime. These results are important to include in future modeling efforts to predict changes in soil-atmosphere exchange of CH4 under global change.

A Model for Partitioning CO2 Flux and Calculating Transformation of Soil C Fractions

NASA Astrophysics Data System (ADS)

Zhang, S.; Noormets, A.; Tu, C.; King, J.

2011-12-01

It has been recognized that mechanistic understanding of soil organic carbon (SOC) mineralization requires partitioning of SOM to different sub-pools, whose turnover kinetics differ. Different fractionation methods have been developed to separate and analyze SOC fractions with different turnover rates, but some recent studies have called to questions earlier assumptions about chemical structure of C compounds and their recalcitrance to decomposition. To our knowledge, there is also no model that would bring together the information on various indicators of recalcitrance in a kinetic model framework . Here we deploy an analytical framework to partition soil net CO2 emissions to three density fractions (F1, F2, and F3, in the order of increasing density) in a peat soil and follow mineralization-related transformations (from lighter to heavier fractions). We followed the changes in total C content [C] and 13C of each three density fractions through a 3-month incubation study. We partitioned the CO2 produced by the soil between the different fractions using 13C and [C] change data. Applying this approach to a factorial experiment, we found that partitioning of CO2 emission and transformation rates among fractions differed between the organic top soil and deeper sandy soil. At depth of 45-75cm, almost no C was released through CO2 emission for all three fractions, while at 0-30cm, emission reached 0.2 g C/g soil over the incubation period, an average of 99% of which was from F2. Mineralization-related transformation rate at 45-75cm was 0.02 g soil/g soil with no significant differences among fractions. At 0-30cm, out of one gram of initial bulk soil, an average of 0.31g F1 transformed to F2, whereas no F2 was transformed to F3. Although the current study was carried out on a high-organic soil, the partitioning method is applicable to all soil types.

Aspect has a greater impact on alpine soil bacterial community structure than elevation.

PubMed

Wu, Jieyun; Anderson, Barbara J; Buckley, Hannah L; Lewis, Gillian; Lear, Gavin

2017-03-01

Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of < 1000 m, bacterial community composition was more closely related to the aspect of a site than its elevation. However, despite large differences in climate and resource-availability factors across elevation- and aspect-related gradients, bacterial community composition and richness were most strongly correlated with soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Responses of soil N-fixing bacteria communities to invasive plant species under different types of simulated acid deposition

NASA Astrophysics Data System (ADS)

Wang, Congyan; Zhou, Jiawei; Jiang, Kun; Liu, Jun; Du, Daolin

2017-06-01

Biological invasions have incurred serious threats to native ecosystems in China, and soil N-fixing bacteria communities (SNB) may play a vital role in the successful plant invasion. Meanwhile, anthropogenic acid deposition is increasing in China, which may modify or upgrade the effects that invasive plant species can cause on SNB. We analyzed the structure and diversity of SNB by means of new generation sequencing technology in soils with different simulated acid deposition (SAD), i.e., different SO4 2- to NO3 - ratios, and where the invasive ( Amaranthus retroflexus L.) and the native species ( Amaranthus tricolor L.) grew mixed or isolated for 3 months. A. retroflexus itself did not exert significant effects on the diversity and richness of SNB but did it under certain SO4 2- to NO3 - ratios. Compared to soils where the native species grew isolated, the soils where the invasive A. retroflexus grew isolated showed lower relative abundance of some SNB classes under certain SAD treatments. Some types of SAD can alter soil nutrient content which in turn could affect SNB diversity and abundance. Specifically, greater SO4 2- to NO3 - ratios tended to have more toxic effects on SNB likely due to the higher exchange capacity of hydroxyl groups (OH-) between SO4 2- and NO3 -. As a conclusion, it can be expected a change in the structure of SNB after A. retroflexus invasion under acid deposition rich in sulfuric acid. This change may create a plant soil feedback favoring future A. retroflexus invasions.

[Effects of legume-oat intercropping on abundance and community structure of soil N2-fixing bacteria].

PubMed

Yang, Ya Dong; Feng, Xiao Min; Hu, Yue Gao; Ren, Chang Zhong; Zeng, Zhao Hai

2017-03-18

In this study, real-time PCR and high-throughput sequencing approaches were employed to investigate the abundance and community structure of N 2 -fixing bacteria in a field experiment with three planting patterns (Oat monoculture, O; Soybean-oat intercropping, OSO; Mung bean-oat intercropping, OMO). The results showed that soil chemical properties varied significantly in different soil samples (P＜0.05). The abundance of nifH gene varied from 1.75×10 10 to 7.37×10 10 copies·g -1 dry soil in all soil samples. The copy numbers of nifH gene in OSO and OMO were 2.18, 2.64, and 1.92, 2.57 times as much as that in O at jointing and mature stages, with a significant decline from jointing to mature stage for all treatments (P＜0.05). Rarefaction curve and cove-rage results proved the nifH gene sequencing results were reliable, and the diversity index showed that the N 2 -fixing bacteria diversity of OSO was much higher than that of O. Azohydromonas, Azotobacter, Bradyrhizobium, Skermanella and other groups that could not be classified are the dominant genera, with significant differences in proportion of these dominant groups observed among all soil samples (P＜0.05). Venn and PCA analysis indicated that there were greater differences of nifH gene communities between jointing and mature stages; however, the OSO and OMO had similar communities in both stages. All these results confirmed that legume-oat intercropping significantly increased the abundance and changed the community composition of N 2 -fixing bacteria in oat soils.

Various forms of organic and inorganic P fertilizers did not negatively affect soil- and root-inhabiting AM fungi in a maize-soybean rotation system.

PubMed

Beauregard, M S; Gauthier, M-P; Hamel, C; Zhang, T; Welacky, T; Tan, C S; St-Arnaud, M

2013-02-01

Arbuscular mycorrhizal (AM) fungi are key components of most agricultural ecosystems. Therefore, understanding the impact of agricultural practices on their community structure is essential to improve nutrient mobilization and reduce plant stress in the field. The effects of five different organic or mineral sources of phosphorus (P) for a maize-soybean rotation system on AM fungal diversity in roots and soil were assessed over a 3-year period. Total DNA was extracted from root and soil samples collected at three different plant growth stages. An 18S rRNA gene fragment was amplified and taxa were detected and identified using denaturing gradient gel electrophoresis followed by sequencing. AM fungal biomass was estimated by fatty acid methyl ester analysis. Soil P fertility parameters were also monitored and analyzed for possible changes related with fertilization or growth stages. Seven AM fungal ribotypes were detected. Fertilization significantly modified soil P flux, but had barely any effect on AM fungi community structure or biomass. There was no difference in the AM fungal community between plant growth stages. Specific ribotypes could not be significantly associated to P treatment. Ribotypes were associated with root or soil samples with variable detection frequencies between seasons. AM fungal biomass remained stable throughout the growing seasons. This study demonstrated that roots and soil host distinct AM fungal communities and that these are very temporally stable. The influence of contrasting forms of P fertilizers was not significant over 3 years of crop rotation.

Responses of soil N-fixing bacteria communities to invasive plant species under different types of simulated acid deposition.

PubMed

Wang, Congyan; Zhou, Jiawei; Jiang, Kun; Liu, Jun; Du, Daolin

2017-06-01

Biological invasions have incurred serious threats to native ecosystems in China, and soil N-fixing bacteria communities (SNB) may play a vital role in the successful plant invasion. Meanwhile, anthropogenic acid deposition is increasing in China, which may modify or upgrade the effects that invasive plant species can cause on SNB. We analyzed the structure and diversity of SNB by means of new generation sequencing technology in soils with different simulated acid deposition (SAD), i.e., different SO 4 2- to NO 3 - ratios, and where the invasive (Amaranthus retroflexus L.) and the native species (Amaranthus tricolor L.) grew mixed or isolated for 3 months. A. retroflexus itself did not exert significant effects on the diversity and richness of SNB but did it under certain SO 4 2- to NO 3 - ratios. Compared to soils where the native species grew isolated, the soils where the invasive A. retroflexus grew isolated showed lower relative abundance of some SNB classes under certain SAD treatments. Some types of SAD can alter soil nutrient content which in turn could affect SNB diversity and abundance. Specifically, greater SO 4 2- to NO 3 - ratios tended to have more toxic effects on SNB likely due to the higher exchange capacity of hydroxyl groups (OH - ) between SO 4 2- and NO 3 - . As a conclusion, it can be expected a change in the structure of SNB after A. retroflexus invasion under acid deposition rich in sulfuric acid. This change may create a plant soil feedback favoring future A. retroflexus invasions.

Soil Bacterial Community Structure Responses to Precipitation Reduction and Forest Management in Forest Ecosystems across Germany

PubMed Central

Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E.; Ellerbrock, Ruth; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

2015-01-01

Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season. PMID:25875835

Soil bacterial community structure responses to precipitation reduction and forest management in forest ecosystems across Germany.

PubMed

Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E; Ellerbrock, Ruth; Bruelheide, Helge; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

2015-01-01

Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season.

Effects of land use pattern on soil water in revegetation watersheds in semi-arid Chinese Loess Plateau

NASA Astrophysics Data System (ADS)

Yang, Lei; Chen, Liding; Wei, Wei

2017-04-01

Soil water stored below rainfall infiltration depth is a reliable water resource for plant growth in arid and semi-arid regions. For decreasing serious soil erosion, large-scale human-introduced vegetation restoration was initiated in Chinese Loess Plateau in late 1990s. However, these activities may result in excessive water consumption and soil water deficit if no appropriate scientific guidance were offered. This in turn impacts the regional ecological restoration and sustainable management of water resources. In this study, soil water content data in depth of 0-5 m was obtained by long-term field observation and geostatistical method in 6 small watersheds covered with different land use pattern. Profile characteristics and spatial-temporal patterns of soil water were compared between different land use types, hillslopes, and watersheds. The results showed that: (1) Introduced vegetation consumed excessive amount of water when compared with native grassland and farmland, and induced temporally stable soil desiccation in depth of 0-5 m. The introduced vegetation decreased soil water content to levels lower than the reference value representing no human impact in all soil layers. (2) The analysis of differences in soil water at hillslope and watershed scales indicated that land use determined the spatial and temporal variability of soil water. Soil water at watershed scale increased with the increasing area of farmland, and decreased with increasing percentage of introduced vegetation. Land use structure determined the soil water condition and land use pattern determined the spatial-temporal variability of soil water at watershed scale. (3) Large-scale revegetation with introduced vegetation diminished the spatial heterogeneity of soil water at different scales. Land use pattern adjustment could be used to improve the water resources management and maintain the sustainability of vegetation restoration.

[Study on mechanism of SOM stabilization of paddy soils under long-term fertilizations].

PubMed

Luo, Lu; Zhou, Ping; Tong, Cheng-Li; Shi, Hui; Wu, Jin-Shui; Huang, Tie-Ping

2013-02-01

Fourier transform infrared spectroscopy (FTIR) was applied to study the structure of soil organic matter (SOM) of paddy soils under long-term different fertilization treatments. The aim was to clarify the different distribution of SOM between different fertilization methods and between topsoil and subsoil, and to explore the stability mechanism of SOM under different fertilization treatments. The results showed that the content of topsoil organic carbon (SOC) was the highest under organic-inorganic fertilizations, with the increment of SOC by 18.5%, 12.9% and 18.4% under high organic manure (HOM), low organic manure (LOM) and straw returning (STW) respectively compared with no fertilization treatment (CK). The long-term fertilizations also changed the chemical structure of SOM. As compared with CK, different fertilization treatments increased the functional group absorbing intensity of chemical resistance compounds (aliphatic, aromaticity), carbohydrate and organo-silicon compounds, which was the most distinctive under treatments of HOM, LOM and STW. For example, the absorbing intensity of alkyl was 0.30, 0.25 and 0.29 under HOM, LOM and STW, respectively. These values were increased by 87% , 56% and 81% as compared with that under CK treatment. The functional group absorbing intensity of SOM in the topsoil was stronger than that in the subsoil, with the most distinctive difference under HOM, LOM and STW treatments. The present research indicated that the enhanced chemical resistance of functional group of SOM may contribute to the high contents of SOC in the paddy soils under long-term organic-inorganic fertilizations, which also suggested a chemical stabilization mechanism of SOM in the paddy soils.

Impact of postfire logging on soil bacterial and fungal communities and soil biogeochemistry in a mixed-conifer forest in central Oregon

Treesearch

Tara N. Jennings; Jane E. Smith; Kermit Cromack; Elizabeth W. Sulzman; Donaraye McKay; Bruce A. Caldwell; Sarah I. Beldin

2012-01-01

Postfire logging recoups the economic value of timber killed by wildfire, but whether such forest management activity supports or impedes forest recovery in stands differing in structure from historic conditions remains unclear. The aim of this study was to determine the impact of mechanical logging after wildfire on soil bacterial and fungal communities and other...

Microorganisms in small patterned ground features and adjacent vegetated soils along topographic and climatic gradients in the High Arctic, Canada

Treesearch

G. Gonzalez; F.J. Rivera-Figueroa; W. Gould; S.A. Cantrell; J.R. Pérez-Jiménez

2014-01-01

In this study, we determine differences in total biomass of soil microorganisms and community structure (using the most probable number of bacteria (MPN) and the number of fungal genera) in patterned ground features (PGF) and adjacent vegetated soils (AVS) in mesic sites from three High Arctic islands in order to characterize microbial dynamics as affected by...

[Characteristics of soil macrofaunal community structure in secondary forest and forest plantations in western Qinling Mountains of Northwest China].

PubMed

Liu, Ji-Liang; Cao, Jing; Li, Shi-Jie; Pan, Chun-Lin; Pan, Cheng-Chen

2012-09-01

Long-term disturbance of human beings on secondary forest ecosystem would have profound impacts on belowground ecological processes, whereas the community structure and functional diversity of soil fauna would be sensitive to the changes of belowground ecological processes, with significance as an indicator of the changes. In this study, the method of hand-sorting was adopted to investigate the density of soil macrofaunal community in a secondary forest and the Pinus tabulaeformis, Larix kaempferi, Picea abie, and Picea asperata plantations of nearly 30 years old in Xiaolongshan forest area of western Qinling Mountains, and the PCA ordination and one-way ANOVA analysis were applied to analyze the community structure and trophic group composition of soil macrofauna in the five forest types. In the P. tabulaeformis and L. kaempferi plantations, the density of soil macrofaunal community was 3.0 and 2.1 times of that in the secondary forest, respectively, and the consumers/decomposers ratio of the community was obviously higher than that in the secondary forest. Among the plantations, P. tabulaeformis and L. kaempferi plantations had a significantly higher consumers/decomposers ratio of soil macrofaunal community than P. abies and P. asperata plantations. There was an obvious difference in community structure of soil macrofauna among the four plantations. The density of soil macrofaunal community in P. tabulaeformis and L. kaempferi plantations was 3.5 and 2.1 times higher than that in P. asperata plantation, respectively, whereas the group richness of soil macrofaunal community in P. tabulaeformis plantation was 1.5 times of that in P. abies and P. asperata plantations.

Spatial distribution of vanadium and microbial community responses in surface soil of Panzhihua mining and smelting area, China.

PubMed

Cao, Xuelong; Diao, Muhe; Zhang, Baogang; Liu, Hui; Wang, Song; Yang, Meng

2017-09-01

Spatial distribution of vanadium in surface soils from different processing stages of vanadium-bearing titanomagnetite in Panzhihua mining and smelting area (China) as well as responses of microbial communities including bacteria and fungi to vanadium were investigated by fieldwork and laboratory incubation experiment. The vanadium contents in this region ranged from 149.3 to 4793.6 mg kg -1 , exceeding the soil background value of vanadium in China (82 mg kg -1 ) largely. High-throughput DNA sequencing results showed bacterial communities from different manufacturing locations were quite diverse, but Bacteroidetes and Proteobacteria were abundant in all samples. The contents of organic matter, available P, available S and vanadium had great influences on the structures of bacterial communities in soils. Bacterial communities converged to similar structure after long-term (240 d) cultivation with vanadium containing medium, dominating by bacteria which can tolerate or reduce toxicities of heavy metals. Fungal diversities decreased after cultivation, but Ascomycota and Ciliophora were still the most abundant phyla as in the original soil samples. Results in this study emphasize the urgency of investigating vanadium contaminations in soils and provide valuable information on how vanadium contamination influences bacterial and fungal communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Basidiomycete fungal communities in Australian sclerophyll forest soil are altered by repeated prescribed burning.

PubMed

Anderson, Ian C; Bastias, Brigitte A; Genney, David R; Parkin, Pamela I; Cairney, John W G

2007-04-01

Soil basidiomycetes play key roles in forest nutrient and carbon cycling processes, yet the diversity and structure of below ground basidiomycete communities remain poorly understood. Prescribed burning is a commonly used forest management practice and there is evidence that single fire events can have an impact on soil fungal communities but little is known about the effects of repeated prescribed burning. We have used internal transcribed spacer (ITS) terminal restriction fragment length polymorphism (T-RFLP) analysis to investigate the impacts of repeated prescribed burning every two or four years over a period of 30 years on soil basidiomycete communities in an Australian wet sclerophyll forest. Detrended correspondence analysis of ITS T-RFLP profiles separated basidiomycete communities in unburned control plots from those in burned plots, with those burned every two years being the most different from controls. Burning had no effect on basidiomycete species richness, thus these differences appear to be due to changes in community structure. Basidiomycete communities in the unburned control plots were vertically stratified in the upper 20 cm of soil, but no evidence was found for stratification in the burned plots, suggesting that repeated prescribed burning results in more uniform basidiomycete communities. Overall, the results demonstrate that repeated prescribed burning alters soil basidiomycete communities, with the effect being greater with more frequent burning.

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.

Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China.

PubMed

Li, Guangyu; Wu, Cifang

2017-08-14

Set-aside farmland can effectively improve the self-rehabilitation of arable soil. Long-term set-asides however cannot satisfy provisionment, therefore the use of short-term set-asides to restore cultivated soil is a better option. Few studies have compared short-term set-aside patterns, and the effects of set-asides on soil microbial community and enzyme enzymes. We analyzed the bacterial structure, microbial biomass carbon/nitrogen and enzyme activity of farmland soil under different set-aside regimes in the Yellow River Delta of China. Bacterial alpha diversity was relatively lower under only irrigation, and farmyard manure applications showed clear advantages. Set-asides should consider their influence on soil organic carbon and nitrogen, which were correlated with microbial community structure. Nitrospira (0.47-1.67%), Acidobacteria Gp6 (8.26-15.91%) and unclassified Burkholderiales (1.50-2.81%) were significantly altered ( p < 0.01). Based on functions of these genera, some set-aside patterns led to a relative balance in nitrogen and carbon turnover. Partial treatments showed a deficiency in organic matter. In addition, farmyard manure may lead to the increased consumption of organic matter, with the exception of native plants set-asides. Conventional farming (control group) displayed a significant enzyme activity advantage. Set-aside management practices guided soil microbial communities to different states. Integrated soil microbiota and the content of carbon and nitrogen, native plants with farmyard manure showed an equilibrium state relatively, which would be helpful to improve land quality in the short-term.

Uncertainty in the fate of soil organic carbon: A comparison of three conceptually different soil decomposition models

USGS Publications Warehouse

He, Yujie; Yang, Jinyan; Zhuang, Qianlai; McGuire, A. David; Zhu, Qing; Liu, Yaling; Teskey, Robert O.

2014-01-01

Conventional Q10 soil organic matter decomposition models and more complex microbial models are available for making projections of future soil carbon dynamics. However, it is unclear (1) how well the conceptually different approaches can simulate observed decomposition and (2) to what extent the trajectories of long-term simulations differ when using the different approaches. In this study, we compared three structurally different soil carbon (C) decomposition models (one Q10 and two microbial models of different complexity), each with a one- and two-horizon version. The models were calibrated and validated using 4 years of measurements of heterotrophic soil CO2 efflux from trenched plots in a Dahurian larch (Larix gmelinii Rupr.) plantation. All models reproduced the observed heterotrophic component of soil CO2 efflux, but the trajectories of soil carbon dynamics differed substantially in 100 year simulations with and without warming and increased litterfall input, with microbial models that produced better agreement with observed changes in soil organic C in long-term warming experiments. Our results also suggest that both constant and varying carbon use efficiency are plausible when modeling future decomposition dynamics and that the use of a short-term (e.g., a few years) period of measurement is insufficient to adequately constrain model parameters that represent long-term responses of microbial thermal adaption. These results highlight the need to reframe the representation of decomposition models and to constrain parameters with long-term observations and multiple data streams. We urge caution in interpreting future soil carbon responses derived from existing decomposition models because both conceptual and parameter uncertainties are substantial.

The Response of Soil Carbon Stocks to Changing Atmospheric Carbon Dioxide Concentrations are Soil-Type-Dependent

NASA Astrophysics Data System (ADS)

Hockaday, W. C.; Gallagher, M. E.; Masiello, C. A.; Pyle, L. A.; Polley, W. H.; Baldock, J.

2010-12-01

Global soil C stocks (2 × 1018 gC) are large enough that a minor climate-induced change in the cycling of the soil C pool would constitute a major climate feedback. The responses of soil carbon stocks to experimental manipulations of atmospheric carbon dioxide concentration ([CO2]) and temperature vary widely in direction and magnitude across different ecosystems. The mechanisms for differences soil C cycle response to climate change are not well understood. In particular, little is known about the potential role of soil genetic factors such as mineralogy and structure in the climate response. To address this, we examined [CO2]-induced changes in soil organic matter (SOM) quantity and quality at the USDA lysimeter CO2 gradient facility (in Temple, TX), which comprises 3 major soil orders (Mollisol, Alfisol, and Vertisol). Temperature, precipitation, and vegetation type are controlled variables across the soil orders. We used 13C nuclear magnetic resonance to study the chemical structure and composition of SOM under a native tallgrass prairie community exposed to CO2 concentrations ranging from 250 to 500 ppm. A mixing model (Baldock et al., 2004) was used to estimate soil biochemical stocks. The relative magnitude of biochemical inputs (from grassland roots and shoots) follows the order: carbohydrates >> lignins > proteins = lipids. However, the relative chemical abundances in the soil C pool are: carbohydrates = protein > lipid > lignin > charcoal. These discrepancies in the relative magnitude of the biochemical fluxes and stocks highlight the selectivity of SOM preservation and show that increased primary production (mainly carbohydrate synthesis) in response to elevated [CO2] may not lead to long-term soil C storage unless a carbohydrate preservation mechanism exists in the soil. Indeed, carbohydrate stocks in the Alfisol and Vertisol decreased despite greater inputs at high [CO2]. Only the Mollisol exhibited a capacity to store additional carbohydrate C at high atmospheric CO2 levels. Soil protein stocks in the Mollisol, and lignin stocks in the Alfisol, doubled in response to the doubling of atmospheric [CO2]. Soil lipids decreased with increasing [CO2] in all 3 soil orders. These [CO2]-induced changes in the soil biochemical stocks suggest that soil genetic factors could play an important role in the soil C storage potential under different climate regimes. The molecular basis for C preservation in soils of distinct genetic origin should inform efforts to model C cycle-climate feedbacks.

The potential roles of biological soil crusts in dryland hydrologic cycles

USGS Publications Warehouse

Belnap, J.

2006-01-01

Biological soil crusts (BSCs) are the dominant living cover in many drylands of the world. They possess many features that can influence different aspects of local hydrologic cycles, including soil porosity, absorptivity, roughness, aggregate stability, texture, pore formation, and water retention. The influence of biological soil crusts on these factors depends on their internal and external structure, which varies with climate, soil, and disturbance history. This paper presents the different types of biological soil crusts, discusses how crust type likely influences various aspects of the hydrologic cycle, and reviews what is known and not known about the influence of biological crusts on sediment production and water infiltration versus runoff in various drylands around the world. Most studies examining the effect of biological soil crusts on local hydrology are done by comparing undisturbed sites with those recently disturbed by the researchers. Unfortunately, this greatly complicates interpretation of the results. Applied disturbances alter many soil features such as soil texture, roughness, aggregate stability, physical crusting, porosity, and bulk density in ways that would not necessarily be the same if crusts were not naturally present. Combined, these studies show little agreement on how biological crusts affect water infiltration or runoff. However, when studies are separated by biological crust type and utilize naturally occurring differences among these types, results indicate that biological crusts in hyperarid regions reduce infiltration and increase runoff, have mixed effects in and regions, and increase infiltration and reduce runoff in semiarid cool and cold drylands. However, more studies are needed before broad generalizations can be made on how biological crusts affect infiltration and runoff. We especially need studies that control for sub-surface soil features such as bulk density, micro- and macropores, and biological crust structure. Unlike the mixed effects of biological crusts on infiltration and runoff among regions, almost all studies show that biological crusts reduce sediment production, regardless of crust or dryland type.

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, such as significant changes in water availability.

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, such as significant changes in water availability. PMID:27486444

The potential roles of biological soil crusts in dryland hydrologic cycles

NASA Astrophysics Data System (ADS)

Belnap, Jayne

2006-10-01

Biological soil crusts (BSCs) are the dominant living cover in many drylands of the world. They possess many features that can influence different aspects of local hydrologic cycles, including soil porosity, absorptivity, roughness, aggregate stability, texture, pore formation, and water retention. The influence of biological soil crusts on these factors depends on their internal and external structure, which varies with climate, soil, and disturbance history. This paper presents the different types of biological soil crusts, discusses how crust type likely influences various aspects of the hydrologic cycle, and reviews what is known and not known about the influence of biological crusts on sediment production and water infiltration versus runoff in various drylands around the world. Most studies examining the effect of biological soil crusts on local hydrology are done by comparing undisturbed sites with those recently disturbed by the researchers. Unfortunately, this greatly complicates interpretation of the results. Applied disturbances alter many soil features such as soil texture, roughness, aggregate stability, physical crusting, porosity, and bulk density in ways that would not necessarily be the same if crusts were not naturally present. Combined, these studies show little agreement on how biological crusts affect water infiltration or runoff. However, when studies are separated by biological crust type and utilize naturally occurring differences among these types, results indicate that biological crusts in hyperarid regions reduce infiltration and increase runoff, have mixed effects in arid regions, and increase infiltration and reduce runoff in semiarid cool and cold drylands. However, more studies are needed before broad generalizations can be made on how biological crusts affect infiltration and runoff. We especially need studies that control for sub-surface soil features such as bulk density, micro- and macropores, and biological crust structure. Unlike the mixed effects of biological crusts on infiltration and runoff among regions, almost all studies show that biological crusts reduce sediment production, regardless of crust or dryland type.

Root controls on soil microbial community structure in forest soils.

PubMed

Brant, Justin B; Myrold, David D; Sulzman, Elizabeth W

2006-07-01

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0-10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.

Tundra fire disturbance homogonizes belowground food web structure, function and dynamics

NASA Astrophysics Data System (ADS)

Moore, J. C.; Pressler, Y.; Koltz, A.; Asmus, A.; Simpson, R.

2016-12-01

Tundra fires on Alaska's North Slope are on the rise due to increased lightning strikes since 2000. On July 16, 2007 lightning ignited the Anaktuvuk River fire, burning a 40-by-10 mile swath of tundra about 24 miles north of Toolik Field Station. The fire burned 401 square miles, was visible from space, and released more than 2.3 million tons of carbon into the atmosphere. A large amount of the organic layer of the soil was burned, changing the over all composition of the site and exposing deeper soil horizons. Due to fundamental transitions in soil characteristics and vegetation we hypothesized that the belowground food web community would be affected both in terms of biomass and location within the soil profile. Microbial biomass was reduced with burn severity. In the lower organic horizon there was a significant reduction in fungal biomass but we did not observe this effect in the upper organic soil. We did not observe a significant effect of burn severity on individual group biomass within higher trophic levels. Canonical Discriminant Analysis using the biomass estimates of the functional groups in the food webs found that the webs are becoming increasingly homogenized in the severely burned site compared to the moderately burned and unburned sites. The unburned soils differed significantly from soil at both burn sites; the greatest effects on food web structure were at the lower organic depth, whereas. We modeled the effects of the fire on soil organic matter processing rates and energy flow through the three food webs. The model estimated a decrease in C and N mineralization with fire severity, due in large part to the loss of organic material. While the organic horizon at the unburned site had 12 times greater C and N mineralization than the mineral soils, we observed little to no difference in C and N mineralization between the organic and mineral soil horizons in the moderately and severely burned sites. Our results show that the fire significantly altered the trophic structure of the soil food web, with loss of trophic complexity with increasing fire severity, which correlated strongly with C and N processing and food web stability.

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Science.gov Websites

, through soil-structure interaction, to structural response. New computer simulation tools are necessary to of structures and soils to investigate challenging problems in soil-structure-foundation interaction including foundations and soils is used to study the effects of soil liquefaction and permanent

Experimental sensitivity analysis of subsoil-slab behaviour regarding degree of fibre-concrete slab reinforcement

NASA Astrophysics Data System (ADS)

Hrubesova, E.; Lahuta, H.; Mohyla, M.; Quang, T. B.; Phi, N. D.

2018-04-01

The paper is focused on the sensitivity analysis of behaviour of the subsoil – foundation system as regards the variant properties of fibre-concrete slab resulting into different relative stiffness of the whole cooperating system. The character of slab and its properties are very important for the character of external load transfer, but the character of subsoil cannot be neglected either because it determines the stress-strain behaviour of the all system and consequently the bearing capacity of structure. The sensitivity analysis was carried out based on experimental results, which include both the stress values in soil below the foundation structure and settlements of structure, characterized by different quantity of fibres in it. Flat dynamometers GEOKON were used for the stress measurements below the observed slab, the strains inside slab were registered by tensometers, the settlements were monitored geodetically. The paper is focused on the comparison of soil stresses below the slab for different quantity of fibres in structure. The results obtained from the experimental stand can contribute to more objective knowledge of soil – slab interaction, to the evaluation of real carrying capacity of the slab, to the calibration of corresponding numerical models, to the optimization of quantity of fibres in the slab, and finally, to higher safety and more economical design of slab.

Influence of biochar on the physical, chemical and retention properties of an amended sandy soil

NASA Astrophysics Data System (ADS)

Baiamonte, Giorgio; De Pasquale, Claudio; Parrino, Francesco; Crescimanno, Giuseppina

2017-04-01

Soil porosity plays an important role in soil-water retention and water availability to crops, potentially affecting both agricultural practices and environmental sustainability. The pore structure controls fluid flow and transport through the soil, as well as the relationship between the properties of individual minerals and plants. Moreover, the anthropogenic pressure on soil properties has produced numerous sites with extensive desertification process close to residential areas. Biochar (biologically derived charcoal) is produced by pyrolysis of biomasses under low oxygen conditions, and it can be applied for recycling organic waste in soils and increase soil fertility, improving soil structure and enhancing soil water storage and soil water movement. Soil application of biochar might have agricultural, environmental and sustainability advantages over the use of organic manures or compost, as it is a porous material with a high inner surface area. The main objectives of the present study were to investigate the possible application of biochar from forest residues, derived from mechanically chipped trunks and large branches of Abies alba M., Larix decidua Mill., Picea excelsa L., Pinus nigra A. and Pinus sylvestris L. pyrolysed at 450 °C for 48h, to improve soil structural and hydraulic properties (achieving a stabilization of soil). Different amount of biochar were added to a desertic sandy soil, and the effect on soil porosity water retention and water available to crops were investigated. The High Energy Moisture Characteristic (HEMC) technique was applied to investigate soil-water retention at high-pressure head levels. The adsorption and desorption isotherms of N2 on external surfaces were also determined in order to investigate micro and macro porosity ratio. Both the described model of studies on adsorption-desorption experiments with the applied isotherms model explain the increasing substrate porosity with a particular attention to the macro and micro porosity, respectively.

Spatio-temporal variability of soil water content on the local scale in a Mediterranean mountain area (Vallcebre, North Eastern Spain). How different spatio-temporal scales reflect mean soil water content

NASA Astrophysics Data System (ADS)

Molina, Antonio J.; Latron, Jérôme; Rubio, Carles M.; Gallart, Francesc; Llorens, Pilar

2014-08-01

As a result of complex human-land interactions and topographic variability, many Mediterranean mountain catchments are covered by agricultural terraces that have locally modified the soil water content dynamic. Understanding these local-scale dynamics helps us grasp better how hydrology behaves on the catchment scale. Thus, this study examined soil water content variability in the upper 30 cm of the soil on a Mediterranean abandoned terrace in north-east Spain. Using a dataset of high spatial (regular grid of 128 automatic TDR probes at 2.5 m intervals) and temporal (20-min time step) resolution, gathered throughout a 84-day period, the spatio-temporal variability of soil water content at the local scale and the way that different spatio-temporal scales reflect the mean soil water content were investigated. Soil water content spatial variability and its relation to wetness conditions were examined, along with the spatial structuring of the soil water content within the terrace. Then, the ability of single probes and of different combinations of spatial measurements (transects and grids) to provide a good estimate of mean soil water content on the terrace scale was explored by means of temporal stability analyses. Finally, the effect of monitoring frequency on the magnitude of detectable daily soil water content variations was studied. Results showed that soil water content spatial variability followed a bimodal pattern of increasing absolute variability with increasing soil water content. In addition, a linear trend of decreasing soil water content as the distance from the inner part of the terrace increased was identified. Once this trend was subtracted, resulting semi-variograms suggested that the spatial resolution examined was too high to appreciate spatial structuring in the data. Thus, the spatial pattern should be considered as random. Of all the spatial designs tested, the 10 × 10 m mesh grid (9 probes) was considered the most suitable option for a good, time-stable estimate of mean soil water content, as no improvement was obtained with the 5 × 5 m mesh grid (30 probes). Finally, the results of temporal aggregation showed that decreasing the monitoring frequency down to 8 h during wetting-up periods and to 1 day during drying-down ones did not result in a loss of information on daily soil water content variations.

Soil Aggregates and Organic Carbon Distribution in Red Soils after Long-term Fertilization with Different Fertilizer Treatments

NASA Astrophysics Data System (ADS)

Tang, J.; Wang, Y.

2013-12-01

Red soils, a typical Udic Ferrosols, widespread throughout the subtropical and tropical region in southern China, support the majority of grain production in this region. The red soil is naturally low in pH values, cation exchange capacity, fertility, and compaction, resulting in low organic matter contents and soil aggregation. Application of chemical fertilizers and a combination of organic-chemical fertilizers are two basic approaches to improve soil structure and organic matter contents. We studied the soil aggregation and the distribution of aggregate-associated organic carbon in red soils with a long-term fertilization experiment during 1988-2009. We established treatments including 1) NPK and NK in the chemical fertilizer plots, 2) CK (Control), and 3) CK+ Peanut Straw (PS), CK+ Rice Straw (RS), CK+ Fresh Radish (FR), and CK + Pig Manure (PM) in the organic-chemical fertilizer plots. Soil samples were fractionated into 6 different sized aggregate particles through the dry-wet sieving method according to the hierarchical model of aggregation. Organic carbon in the aggregate/size classes was analyzed. The results showed that the distribution of mechanically stable aggregates in red soils after long-term fertilization decreased with the size, from > 5mm, 5 ~ 2 mm, 2 ~ 1 mm, 1~ 0.25 mm, to < 0.25 mm, but the distribution of water-stable aggregates did not follow this pattern. Compared with the chemical fertilizer application alone, the addition of pig manure and green manure can significantly improve the distribution of aggregates in the 5-2 mm, 2-1 mm and 1-0.25 mm classes. The organic carbon (OC) contents in red soils were all increased after the long-term fertilization. Compared with Treatment NK, soil OC in Treatment NPK was increased by 45.4%. Compared with Treatment CK (low chemical fertilizer), organic fertilizer addition increased soil OC. The OC in the different particle of water-stable aggregates were all significantly increased after long-term fertilization. OC mainly existed in the macroaggregate (> 0.25 mm) of red soils after the long-term fertilization, and the organic matter was the most important colloid material for macroaggregates. We conclude that the long-term, appropriate application of chemical fertilizer and the combination with organic manure were the most effective measures to improve soil structure and organic carbon contents in red soil regions.

Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses.

PubMed

Ben-David, Eric A; Zaady, Eli; Sher, Yoni; Nejidat, Ali

2011-06-01

Arid and semi-arid ecosystems are often characterized by vegetation patchiness and variable availability of resources. Phospholipid fatty acid (PLFA) and 16S rRNA gene fragment analyses were used to compare the bulk soil microbial community structure at patchy arid and semi-arid landscapes. Multivariate analyses of the PLFA data and the 16S rRNA gene fragments were in agreement with each other, suggesting that the differences between bulk soil microbial communities were primarily related to shrub vs intershrub patches, irrespective of climatic or site differences. This suggests that the mere presence of a living shrub is the dominant driving factor for the differential adaptation of the microbial communities. Lipid markers suggested as indicators of Gram-positive bacteria were higher in soils under the shrub canopies, while markers suggested as indicators of cyanobacteria and anaerobic bacteria were elevated in the intershrub soils. Secondary differences between soil microbial communities were associated with intershrub characteristics and to a lesser extent with the shrub species. This study provides an insight into the multifaceted nature of the factors that shape the microbial community structure in patchy desert landscapes. It further suggests that these drivers not only act in concert but also in a way that is dependent on the aridity level. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Contribution of soil fauna to soil functioning in degraded environments: a multidisciplinary approach

NASA Astrophysics Data System (ADS)

Gargiulo, Laura; Mele, Giacomo; Moradi, Jabbar; Kukla, Jaroslav; Jandová, Kateřina; Frouz, Jan

2016-04-01

The restoration of the soil functions is essential for the recovery of highly degraded sites and, consequently, the study of the soil fauna role in the soil development in such environments has great potential from a practical point of view. The soils of the post-mining sites represent unique models for the study of the natural ecological succession because mining creates similar environments characterized by the same substrate, but by different ages according to the year of closure of mines. The aim of this work was to assess the contribution of different species of macrofauna on the evolution of soil structure and on the composition and activity of the microbial community in soil samples subjected to ecological restoration or characterized by spontaneous ecological succession. For this purpose, an experimental test was carried out in two sites characterized by different post-mining conditions: 1) natural succession, 2) reclamation with planting trees. These sites are located in the post-mining area of Sokolov (Czech Republic). For the experimental test repacked soil cores were prepared in laboratory with sieved soil sampled from the two sites. The soil cores were prepared maintaining the sequence of soil horizons present in the field. These samples were inoculated separately with two genera of earthworms (Lumbricus and Aporrectodea) and two of centipedes (Julida and Polydesmus). In particular, based on their body size, were inoculated for each cylinder 2 individuals of millipedes, 1 individual of Lumbricus and 4 individuals of Aporrectodea. For each treatment and for control samples 5 replicates were prepared and all samples were incubated in field for 1 month in the two original sampling sites. After the incubation the samples were removed from the field and transported in laboratory in order to perform the analysis of microbial respiration, of PLFA (phospholipid-derived fatty acids) and ergosterol contents and finally for the characterization of soil structure. All replicates were subjected to soil respiration measurement by means of chemical titration method. Then some replicates were destructively analyzed for PLFA and ergosterol and others were used for the 3D soil image analysis of the soil pore system. The soil cores were imaged using X-ray microtomography and three-dimensional image processing was performed in order to obtain 3D reconstructions and preliminary analysis of the identified biopores. The experimental approach used in this multidisciplinary study showed a promising potential to provide new useful information about the widely differentiated contribution of many types of macrofauna to the formation of the soil pore system and to the development of the soil microbial functions in different types of environments.

Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils.

PubMed

Frey, Beat; Niklaus, Pascal A; Kremer, Johann; Lüscher, Peter; Zimmermann, Stephan

2011-09-01

Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH(4) consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release.

Geochemical soil sampling for deeply-buried mineralized breccia pipes, northwestern Arizona

USGS Publications Warehouse

Wenrich, K.J.; Aumente-Modreski, R. M.

1994-01-01

Thousands of solution-collapse breccia pipes crop out in the canyons and on the plateaus of northwestern Arizona; some host high-grade uranium deposits. The mineralized pipes are enriched in Ag, As, Ba, Co, Cu, Mo, Ni, Pb, Sb, Se, V and Zn. These breccia pipes formed as sedimentary strata collapsed into solution caverns within the underlying Mississippian Redwall Limestone. A typical pipe is approximately 100 m (300 ft) in diameter and extends upward from the Redwall Limestone as much as 1000 m (3000 ft). Unmineralized gypsum and limestone collapses rooted in the Lower Permian Kaibab Limestone or Toroweap Formation also occur throughout this area. Hence, development of geochemical tools that can distinguish these unmineralized collapse structures, as well as unmineralized breccia pipes, from mineralized breccia pipes could significantly reduce drilling costs for these orebodies commonly buried 300-360 m (1000-1200 ft) below the plateau surface. Design and interpretation of soil sampling surveys over breccia pipes are plagued with several complications. (1) The plateau-capping Kaibab Limestone and Moenkopi Formation are made up of diverse lithologies. Thus, because different breccia pipes are capped by different lithologies, each pipe needs to be treated as a separate geochemical survey with its own background samples. (2) Ascertaining true background is difficult because of uncertainties in locations of poorly-exposed collapse cones and ring fracture zones that surround the pipes. Soil geochemical surveys were completed on 50 collapse structures, three of which are known mineralized breccia pipes. Each collapse structure was treated as an independent geochemical survey. Geochemical data from each collapse feature were plotted on single-element geochemical maps and processed by multivariate factor analysis. To contrast the results between geochemical surveys (collapse structures), a means of quantifying the anomalousness of elements at each site was developed. This degree of anomalousness, named the "correlation value", was used to rank collapse features by their potential to overlie a deeply-buried mineralized breccia pipe. Soil geochemical results from the three mineralized breccia pipes (the only three of the 50 that had previously been drilled) show that: (1) Soils above the SBF pipe contain significant enrichment of Ag, Al, As, Ba, Ga, K, La, Mo, Nd, Ni, Pb, Sc, Th, U and Zn, and depletion in Ca, Mg and Sr, in contrast to soils outside the topographic and structural rim; (2) Soils over the inner treeless zone of the Canyon pipe show Mo and Pb enrichment anf As and Ga depletion, in contrast to soils from the surrounding forest; and (3) The soil survey of the Mohawk Canyon pipe was a failure because of the rocky terrane and lack of a B soil horizon, or because the pipe plunges. At least 11 of the 47 other collapse structures studied contain anomalous soil enrichments similar to the SBF uranium ore-bearing pipe, and thus have good potential as exploration targets for uranium. One of these 11, #1102, does contain surface mineralized rock. These surveys suggest that soil geochemical sampling is a useful tool for the recognition of many collapse structures with underlying ore-bearing breccia pipes. ?? 1994.

Microbial Communities in Cerrado Soils under Native Vegetation Subjected to Prescribed Fires and Under Pasture

EPA Science Inventory

The objective of this work was to evaluate the effects of fire regimes and vegetation cover on the structure and dynamics of soil microbial communities, through phospholipid fatty acid (PLFA) analysis. Comparisons were made between native areas with different woody covers ("cerra...

Response of Nitrifier and Denitrifier Abundance and Microbial Community Structure to Experimental Warming in an Agricultural Ecosystem

PubMed Central

Waghmode, Tatoba R.; Chen, Shuaimin; Li, Jiazhen; Sun, Ruibo; Liu, Binbin; Hu, Chunsheng

2018-01-01

Soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, the response of the soil nitrifier and denitrifier communities to climate warming is poorly understood. A long-term field warming experiment has been conducted for 8 years at Luancheng Experimental Farm Station on the North China Plain; we used this field to examine how soil microbial community structure, nitrifier, and denitrifier abundance respond to warming under regular irrigation (RI) and high irrigation (HI) at different soil depths (0–5, 5–10, and 10–20 cm). Nitrifier, denitrifier, and the total bacterial abundance were assessed by quantitative polymerase chain reaction of the functional genes and 16S rRNA gene, respectively. Bacterial community structure was studied through high throughput sequencing of the 16S rRNA gene. Under RI, warming significantly (P < 0.05) increased the potential nitrification rate and nitrate concentration and decreased the soil moisture. In most of the samples, warming increased the ammonia-oxidizing bacteria abundance but decreased the ammonia-oxidizing archaea (AOA) and denitrifier (nirK, nirS, and nosZ genes) abundance. Under HI, there was a highly increased AOA and 16S rRNA gene abundance and a slightly higher denitrifier abundance compared with RI. Warming decreased the bacterial diversity and species richness, and the microbial community structure differed greatly between the warmed and control plots. The decrease in bacterial diversity was higher in RI than HI and at the 0–5 cm depths than at the 5–10 and 10–20 cm soil depths. Warming led to an increase in the relative abundance of Actinobacteria, Bacteroidetes, and TM7 but a decrease in Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Nitrospira, and Planctomycetes. The greater shift in microbial community structure was observed only in RI at the 0–5 cm soil depth. This study provides new insight into our understanding of the nitrifier and denitrifier activity and microbial community response to climate warming in agricultural ecosystems. PMID:29593703

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

PubMed Central

Narr, Anja; Nawaz, Ali; Wick, Lukas Y.; Harms, Hauke; Chatzinotas, Antonis

2017-01-01

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors. PMID:29067022

Soil bacterial diversity in degraded and restored lands of Northeast Brazil.

PubMed

Araújo, Ademir Sérgio Ferreira; Borges, Clovis Daniel; Tsai, Siu Mui; Cesarz, Simone; Eisenhauer, Nico

2014-11-01

Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.

Ectomycorrhizal fungal associates of Pinus contorta in soils associated with a hot spring in Norris Geyser Basin, Yellowstone National Park, Wyoming

NASA Technical Reports Server (NTRS)

Cullings, K.; Makhija, S.

2001-01-01

Molecular methods and comparisons of fruiting patterns (i.e., presence or absence of fungal fruiting bodies in different soil types) were used to determine ectomycorrhizal (EM) associates of Pinus contorta in soils associated with a thermal soil classified as ultra-acidic to extremely acidic (pH 2 to 4). EM were sampled by obtaining 36 soil cores from six paired plots (three cores each) of both thermal soils and forest soils directly adjacent to the thermal area. Fruiting bodies (mushrooms) were collected for molecular identification and to compare fruiting body (above-ground) diversity to below-ground diversity. Our results indicate (i) that there were significant decreases in both the level of EM infection (130 +/- 22 EM root tips/core in forest soil; 68 +/- 22 EM root tips/core in thermal soil) and EM fungal species richness (4.0 +/- 0.5 species/core in forest soil; 1.2 +/- 0.2 species/core in thermal soil) in soils associated with the thermal feature; (ii) that the EM mycota of thermal soils was comprised of a small set of dominant species and included very few rare species, while the EM mycota of forest soils contained a few dominant species and several rare EM fungal species; (iii) that Dermocybe phoenecius and a species of Inocybe, which was rare in forest soils, were the dominant EM fungal species in thermal soils; (iv) that other than the single Inocybe species, there was no overlap in the EM fungal communities of the forest and thermal soils; and (v) that the fungal species forming the majority of the above-ground fruiting structures in thermal soils (Pisolithus tinctorius, which is commonly used in remediation of acid soils) was not detected on a single EM root tip in either type of soil. Thus, P. tinctorius may have a different role in these thermal soils. Our results suggest that this species may not perform well in remediation of all acid soils and that factors such as pH, soil temperature, and soil chemistry may interact to influence EM fungal community structure. In addition, we identified at least one new species with potential for use in remediation of hot acidic soil.

Metagenomic Insights of Microbial Feedbacks to Elevated CO2 (Invited)

NASA Astrophysics Data System (ADS)

Zhou, J.; Tu, Q.; Wu, L.; He, Z.; Deng, Y.; Van Nostrand, J. D.

2013-12-01

Understanding the responses of biological communities to elevated CO2 (eCO2) is a central issue in ecology and global change biology, but its impacts on the diversity, composition, structure, function, interactions and dynamics of soil microbial communities remain elusive. In this study, we first examined microbial responses to eCO2 among six FACE sites/ecosystems using a comprehensive functional gene microarray (GeoChip), and then focused on details of metagenome sequencing analysis in one particular site. GeoChip is a comprehensive functional gene array for examining the relationships between microbial community structure and ecosystem functioning and is a very powerful technology for biogeochemical, ecological and environmental studies. The current version of GeoChip (GeoChip 5.0) contains approximately 162,000 probes from 378,000 genes involved in C, N, S and P cycling, organic contaminant degradation, metal resistance, antibiotic resistance, stress responses, metal homeostasis, virulence, pigment production, bacterial phage-mediated lysis, soil beneficial microorganisms, and specific probes for viruses, protists, and fungi. Our experimental results revealed that both ecosystem and CO2 significantly (p < 0.05) affected the functional composition, structure and metabolic potential of soil microbial communities with the ecosystem having much greater influence (~47%) than CO2 (~1.3%) or CO2 and ecosystem (~4.1%). On one hand, microbial responses to eCO2 shared some common patterns among different ecosystems, such as increased abundances for key functional genes involved in nitrogen fixation, carbon fixation and degradation, and denitrification. On the other hand, more ecosystem-specific microbial responses were identified in each individual ecosystem. Such changes in the soil microbial community structure were closely correlated with geographic distance, soil NO3-N, NH4-N and C/N ratio. Further metagenome sequencing analysis of soil microbial communities in one particular site showed eCO2 altered the overall structure of soil microbial communities with ambient CO2 samples retaining a higher functional gene diversity than eCO2 samples. Also the taxonomic diversity of functional genes decreased at eCO2. Random matrix theory (RMT)-based network analysis showed that the identified networks under ambient and elevated CO2 were substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher order organization (meta-modules), topological roles of individual nodes, and network hubs, indicating that elevated CO2 dramatically altered the network interactions among different phylogenetic and functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen content, indicating the potential importance of network interactions in ecosystem functioning. Taken together, this study indicates that eCO2 may decrease the overall functional and taxonomic diversity of soil microbial communities, but such effects appeared to be ecosystem-specific, which makes it more challenging for predicting global or regional terrestrial ecosystems responses to eCO2.

Differences in the Activities of Eight Enzymes from Ten Soil Fungi and Their Possible Influences on the Surface Structure, Functional Groups, and Element Composition of Soil Colloids

PubMed Central

Wang, Wenjie; Li, Yanhong; Wang, Huimei; Zu, Yuangang

2014-01-01

How soil fungi function in soil carbon and nutrient cycling is not well understood by using fungal enzymatic differences and their interactions with soil colloids. Eight extracellular enzymes, EEAs (chitinase, carboxymethyl cellulase, β-glucosidase, protease, acid phosphatase, polyphenol oxidase, laccase, and guaiacol oxidase) secreted by ten fungi were compared, and then the fungi that showed low and high enzymatic activity were co-cultured with soil colloids for the purpose of finding fungi-soil interactions. Some fungi (Gomphidius rutilus, Russula integra, Pholiota adiposa, and Geastrum mammosum) secreted 3–4 enzymes with weak activities, while others (Cyathus striatus, Suillus granulate, Phallus impudicus, Collybia dryophila, Agaricus sylvicola, and Lactarius deliciosus) could secret over 5 enzymes with high activities. The differences in these fungi contributed to the alterations of functional groups (stretching bands of O-H, N-H, C-H, C = O, COO- decreased by 11–60%, while P = O, C-O stretching, O-H bending and Si-O-Si stretching increased 9–22%), surface appearance (disappearance of adhesive organic materials), and elemental compositions (11–49% decreases in C1s) in soil colloids. Moreover, more evident changes were generally in high enzymatic fungi (C. striatus) compared with low enzymatic fungi (G. rutilus). Our findings indicate that inter-fungi differences in EEA types and activities might be responsible for physical and chemical changes in soil colloids (the most active component of soil matrix), highlighting the important roles of soil fungi in soil nutrient cycling and functional maintenance. PMID:25398013

Differences in the activities of eight enzymes from ten soil fungi and their possible influences on the surface structure, functional groups, and element composition of soil colloids.

PubMed

Wang, Wenjie; Li, Yanhong; Wang, Huimei; Zu, Yuangang

2014-01-01

How soil fungi function in soil carbon and nutrient cycling is not well understood by using fungal enzymatic differences and their interactions with soil colloids. Eight extracellular enzymes, EEAs (chitinase, carboxymethyl cellulase, β-glucosidase, protease, acid phosphatase, polyphenol oxidase, laccase, and guaiacol oxidase) secreted by ten fungi were compared, and then the fungi that showed low and high enzymatic activity were co-cultured with soil colloids for the purpose of finding fungi-soil interactions. Some fungi (Gomphidius rutilus, Russula integra, Pholiota adiposa, and Geastrum mammosum) secreted 3-4 enzymes with weak activities, while others (Cyathus striatus, Suillus granulate, Phallus impudicus, Collybia dryophila, Agaricus sylvicola, and Lactarius deliciosus) could secret over 5 enzymes with high activities. The differences in these fungi contributed to the alterations of functional groups (stretching bands of O-H, N-H, C-H, C = O, COO- decreased by 11-60%, while P = O, C-O stretching, O-H bending and Si-O-Si stretching increased 9-22%), surface appearance (disappearance of adhesive organic materials), and elemental compositions (11-49% decreases in C1s) in soil colloids. Moreover, more evident changes were generally in high enzymatic fungi (C. striatus) compared with low enzymatic fungi (G. rutilus). Our findings indicate that inter-fungi differences in EEA types and activities might be responsible for physical and chemical changes in soil colloids (the most active component of soil matrix), highlighting the important roles of soil fungi in soil nutrient cycling and functional maintenance.

Mapping fields of 137Cs contamination in soils in the context of their stability and hierarchical spatial structure

NASA Astrophysics Data System (ADS)

Korobova, E.; Romanov, S.

2009-04-01

Technogenic radioisotopes now dispersed in the environment are involved in natural and technogenic processes forming specific geochemical fields and serving as tracers of modern mass migration and geofield transformation. Cs-137 radioisotopes having a comparatively long life time are known for a fast fixation by the top soil layer; radiocesium activity can be measured in the surface layer in field conditions. This makes 137Cs rather convenient for the study and modeling a behavior of toxic elements in soils [1-3, 5] and for the investigation of relative stability and hierarchical fractal structures of the soil contamination of the atmospheric origin [2]. The objective of the experimental study performed on the test site in Bryansk region was to find and prove polycentric regularities in the structure of 137Cs contamination field formed after the Chernobyl accident in natural conditions. Such a character of spatial variability can be seen on the maps showing different soil parameters and chemical element distribution measured in grids [3-5]. The research was undertaken to support our idea of the regular patterns in the contamination field structure that enables to apply a mathematical theory of the field to the geochemical fields modeling on the basis of a limited number of direct measurements sufficient to reproduce the configuration and main parameters of the geochemical field structure on the level of the elementary landscape geochemical system (top-slope-bottom). Cs-137 field measurements were verified by a direct soil sampling. Soil cores dissected into subsamples with increments of 2, 5 and 10 cm, were taken to the depth of 40 cm at points with various surface activity located at different elements of relief. According to laboratory measurements 137Cs inventory in soils varied from 344 to 3448 kBq/m2 (983 kBq/m2 on the average). From 95,1% to 98,0% to of the total inventory was retained in the top 20-cm soil layer. This confirmed that field gamma spectrometry could be used to investigate patterns of 137Cs spatial redistribution in the top soil layers. The portion of 137Cs conserved in top layers corresponded to the meso- and micro relief elements. The character and stability of 137Cs spatial structure was studied by measuring its activity within nested plots with different steps of 5, 2, 1 and 0,2 m (the latter was a minimum resolution step for the field NaI detector). Performed measurements showed that the contamination field of 137Cs had a regular structure of polycentric character and exhibited a decrease in spatial variability of contamination with the decrease of the measured area. Repeated measurements of soil contamination in successive years of 2005-2008 along and cross the slopes provided with topographic survey proved the stability of contamination field (r=0, 915, n=121, r=0,912, n=30) and its relation to the meso- and microrelief features. Variation 137Cs activity in lateral direction (along the slopes and thalweg of the hollow)showed a regular character also. In our opinion the regularity in 137Cs spatial structure in the soil cover may result from radionuclide redistribution with the surface and subsurface water flow highly sensitive to the changes in elevation of different scale, and to the slope length and inclination. Cs-137 lateral distribution pattern was likely to reflect alternation of lateral and vertical water mass migration along the slopes. The performed study showing regularity in 137Cs redistribution seems to open new possibilities to develop the deterministic strategy in the study of contamination fields and modeling toxic elements spatial distribution in the soil cover on different scales. The authors are much obliged to Dr. V. Samsonov and Dr. F. Moiseenko for participation in the field work and to S. Kirov for the performance of the laboratory measurement of the soil and plant samples. References 1. Khomutinin, Yu.V., Kashparov, V.A., Zhebrovskaya, E.I., 2001. Optimization of sampling and measurement of the specimen for radioecological monitoring. UkrNIISKHR, Kiev. 2. Korobova, E.M., Romanov, S.L., Samsonov, V.L., Kirov, S.S., 2006. Experimental study of spatial 137Cs redistribution in paragenetic elementary landscapes, in: Kasimov, N.S. et al (Eds.), Geochemistry of biosphere (devoted to 90-th anniversary of A.I. Perelman), MSU, IGEM, RFFI, Moscow-Smolensk, pp.157-159. 3. Linnik, V.G., Saveliev, A.A., Govorun, A.P., Ivanitsky, O.M., Sokolov, A.V., 2006. Analysis of the Cs-137 contamination field on micro-landscape scale within the virgin meadows in the western part of the Bryansk region, in: Kasimov, N.S. et al (Eds.), Geochemistry of biosphere (devoted to 90-th anniversary of A.I. Perelman), MSU, IGEM, RFFI, Moscow-Smolensk, pp. 201-204. 4. Samsonova V.P. Spatial variability of the soil parameters. On example of soddy-podozolic soils. Moscow, LKI, 2008, 156 p. 5.Shcheglov, A.I., Tsvetnova, O.B., Klyashtorin, A.I., 2001. Biogeochemical migration of technogenic radionuclides in forest ecosystems. Nauka, Moscow.

An experimental investigation to characterise soil macroporosity under different land use and land covers of northeast India

NASA Astrophysics Data System (ADS)

Shougrakpam, Sangeeta; Sarkar, Rupak; Dutta, Subashisa

2010-10-01

Saturated macropore flow is the dominant hydrological process in tropical and subtropical hilly watersheds of northeast India. The process of infiltration into saturated macroporous soils is primarily controlled by size, network, density, connectivity, saturation of surrounding soil matrix, and depthwise distribution of macropores. To understand the effects of local land use, land cover and management practices on soil macroporosity, colour dye infiltration experiments were conducted with ten soil columns (25 × 25 × 50 cm) collected from different watersheds of the region under similar soil and agro-climatic zones. The sampling sites included two undisturbed forested hillslopes, two conventionally cultivated paddy fields, two forest lands abandoned after Jhum cultivation, and two paddy fields, one pineapple plot and one banana plot presently under active cultivation stage of the Jhum cycle. Digital image analyses of the obtained dye patterns showed that the infiltration patterns differed significantly for different sites with varying land use, land cover, and cultivation practices. Undisturbed forest soils showed high degree of soil macroporosity throughout the soil profile, paddy fields revealed sealing of macropores at the topsoil due to hard pan formation, and Jhum cultivated plots showed disconnected subsoil macropores. The important parameters related to soil macropores such as maximum and average size of macropores, number of active macropores, and depthwise distribution of macropores were estimated to characterise the soil macroporosity for the sites. These experimentally derived quantitative data of soil macroporosity can have wide range of applications in the region such as water quality monitoring and groundwater pollution assessment due to preferential leaching of solutes and pesticides, study of soil structural properties and infiltration behaviour of soils, investigation of flash floods in rivers, and hydrological modelling of the watersheds.

Relationships between soil organic matter, nutrients, bacterial community structure, and the performance of microbial fuel cells.

PubMed

Dunaj, Sara J; Vallino, Joseph J; Hines, Mark E; Gay, Marcus; Kobyljanec, Christine; Rooney-Varga, Juliette N

2012-02-07

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful renewable resource: soil organic carbon. We analyzed bacterial community structure, MFC performance, and soil characteristics in different microhabitats within MFCs constructed from agricultural or forest soils in order to determine how soil type and bacterial dynamics influence MFC performance. 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. Bacterial community profile data indicate that the bacterial 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 results suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic bacterial communities, while the quality of available organic matter may have played a significant role in supporting high performing bacterial communities.

Carbon stabilization and microbial growth in acidic mine soils after addition of different amendments for soil reclamation

NASA Astrophysics Data System (ADS)

Zornoza, Raúl; Acosta, Jose; Ángeles Muñoz, María; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

2016-04-01

The extreme soil conditions in metalliferous mine soils have a negative influence on soil biological activity and therefore on soil carbon estabilization. Therefore, amendments are used to increase organic carbon content and activate microbial communities. In order to elucidate some of the factors controlling soil organic carbon stabilization in reclaimed acidic mine soils and its interrelationship with microbial growth and community structure, we performed an incubation experiment with four amendments: pig slurry (PS), pig manure (PM) and biochar (BC), applied with and without marble waste (MW; CaCO3). Results showed that PM and BC (alone or together with MW) contributed to an important increment in recalcitrant organic C, C/N ratio and aggregate stability. Bacterial and fungal growths were highly dependent on pH and labile organic C. PS supported the highest microbial growth; applied alone it stimulated fungal growth, and applied with MW it stimulated bacterial growth. BC promoted the lowest microbial growth, especially for fungi, with no significant increase in fungal biomass. MW+BC increased bacterial growth up to values similar to PM and MW+PM, suggesting that part of the biochar was degraded, at least in short-term mainly by bacteria rather than fungi. PM, MW+PS and MW+PM supported the highest microbial biomass and a similar community structure, related with the presence of high organic C and high pH, with immobilization of metals and increased soil quality. BC contributed to improved soil structure, increased recalcitrant organic C, and decreased metal mobility, with low stimulation of microbial growth.

Heterotrophic Soil Respiration in Warming Experiments: Using Microbial Indicators to Partition Contributions from Labile and Recalcitrant Soil Organic Carbon. Final Report

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

Bradford, M A; Melillo, J M; Reynolds, J F

2010-06-10

The central objective of the proposed work was to develop a genomic approach (nucleic acid-based) that elucidates the mechanistic basis for the observed impacts of experimental soil warming on forest soil respiration. The need to understand the mechanistic basis arises from the importance of such information for developing effective adaptation strategies for dealing with projected climate change. Specifically, robust predictions of future climate will permit the tailoring of the most effective adaptation efforts. And one of the greatest uncertainties in current global climate models is whether there will be a net loss of carbon from soils to the atmosphere asmore » climate warms. Given that soils contain approximately 2.5 times as much carbon as the atmosphere, a net loss could lead to runaway climate warming. Indeed, most ecosystem models predict that climate warming will stimulate microbial decomposition of soil carbon, producing such a positive feedback to rising global temperatures. Yet the IPCC highlights the uncertainty regarding this projected feedback. The uncertainty arises because although warming-experiments document an initial increase in the loss of carbon from soils, the increase in respiration is short-lived, declining to control levels in a few years. This attenuation could result from changes in microbial physiology with temperature. We explored possible microbial responses to warming using experiments and modeling. Our work advances our understanding of how soil microbial communities and their activities are structured, generating insight into how soil carbon might respond to warming. We show the importance of resource partitioning in structuring microbial communities. Specifically, we quantified the relative abundance of fungal taxa that proliferated following the addition of organic substrates to soil. We added glycine, sucrose, cellulose, lignin, or tannin-protein to soils in conjunction with 3-bromo-deoxyuridine (BrdU), a nucleotide analog. Active microbes absorb BrdU from the soil solution; if they multiply in response to substrate additions, they incorporate the BrdU into their DNA. After allowing soils to incubate, we extracted BrdU-labeled DNA and sequenced the ITS regions of fungal rDNA. Fungal taxa that proliferated following substrate addition were likely using the substrate as a resource for growth. We found that the structure of active fungal communities varied significantly among substrates. The active fungal community under glycine was significantly different from those under other conditions, while the active communities under sucrose and cellulose were marginally different from each other and the control. These results indicate that the overall community structure of active fungi was altered by the addition of glycine, sucrose, and cellulose and implies that some fungal taxa respond to changes in resource availability. The community composition of active fungi is also altered by experimental warming. We found that glycine-users tended to increase under warming, while lignin-, tannin/protein-, and sucrose-users declined. The latter group of substrates requires extracellular enzymes for use, but glycine does not. It is possible that warming selects for fungal species that target, in particular, labile substrates. Linking these changes in microbial communities and resource partitioning to soil carbon dynamics, we find that substrate mineralization rates are, in general, significantly lower in soils exposed to long-term warming. This suggests that microbial use of organic substrates is impaired by warming. Yet effects are dependent on substrate identity. There are fundamental differences in the metabolic capabilities of the communities in the control and warmed soils. These differences might relate to the changes in microbial community composition, which appeared to be associated with groups specialized on different resources. We also find that functional responses indicate temperature acclimation of the microbial community. There are distinct seasonal patterns and to long-term soil warming, with higher-temperature optima for soils exposed to warmer temperatures. To relate these changes within the microbial community to potential positive feedbacks between climate warming and soil respiration, we develop a microbial-enzyme model to simulate the responses of soil carbon to warming. We find that declines in microbial biomass and degradative enzymes can explain the observed attenuation of soil-carbon emissions in response to warming. Specifically, reduced carbon-use efficiency limits the biomass of microbial decomposers and mitigates loss of soil carbon. However, microbial adaptation or a change in microbial communities could lead to an upward adjustment of the efficiency of carbon use, counteracting the decline in microbial biomass and accelerating soil-carbon loss. We conclude that the soil-carbon response to climate warming depends on the efficiency of soil microbes in using carbon.« less

13C NMR spectroscopy characterization of particle-size fractionated soil organic carbon in subalpine forest and grassland ecosystems.

PubMed

Shiau, Yo-Jin; Chen, Jenn-Shing; Chung, Tay-Lung; Tian, Guanglong; Chiu, Chih-Yu

2017-12-01

Soil organic carbon (SOC) and carbon (C) functional groups in different particle-size fractions are important indicators of microbial activity and soil decomposition stages under wildfire disturbances. This research investigated a natural Tsuga forest and a nearby fire-induced grassland along a sampling transect in Central Taiwan with the aim to better understand the effect of forest wildfires on the change of SOC in different soil particle scales. Soil samples were separated into six particle sizes and SOC was characterized by solid-state 13 C nuclear magnetic resonance spectroscopy in each fraction. The SOC content was higher in forest than grassland soil in the particle-size fraction samples. The O-alkyl-C content (carbohydrate-derived structures) was higher in the grassland than the forest soils, but the alkyl-C content (recalcitrant substances) was higher in forest than grassland soils, for a higher humification degree (alkyl-C/O-alkyl-C ratio) in forest soils for all the soil particle-size fractions. High humification degree was found in forest soils. The similar aromaticity between forest and grassland soils might be attributed to the fire-induced aromatic-C content in the grassland that offsets the original difference between the forest and grassland. High alkyl-C content and humification degree and low C/N ratios in the fine particle-size fractions implied that undecomposed recalcitrant substances tended to accumulate in the fine fractions of soils.

Methods, Computational Platform, Verification, and Application of Earthquake-Soil-Structure-Interaction Modeling and Simulation

NASA Astrophysics Data System (ADS)

Tafazzoli, Nima

Seismic response of soil-structure systems has attracted significant attention for a long time. This is quite understandable with the size and the complexity of soil-structure systems. The focus of three important aspects of ESSI modeling could be on consistent following of input seismic energy and a number of energy dissipation mechanisms within the system, numerical techniques used to simulate dynamics of ESSI, and influence of uncertainty of ESSI simulations. This dissertation is a contribution to development of one such tool called ESSI Simulator. The work is being done on extensive verified and validated suite for ESSI Simulator. Verification and validation are important for high fidelity numerical predictions of behavior of complex systems. This simulator uses finite element method as a numerical tool to obtain solutions for large class of engineering problems such as liquefaction, earthquake-soil-structure-interaction, site effect, piles, pile group, probabilistic plasticity, stochastic elastic-plastic FEM, and detailed large scale parallel models. Response of full three-dimensional soil-structure-interaction simulation of complex structures is evaluated under the 3D wave propagation. Domain-Reduction-Method is used for applying the forces as a two-step procedure for dynamic analysis with the goal of reducing the large size computational domain. The issue of damping of the waves at the boundary of the finite element models is studied using different damping patterns. This is used at the layer of elements outside of the Domain-Reduction-Method zone in order to absorb the residual waves coming out of the boundary layer due to structural excitation. Extensive parametric study is done on dynamic soil-structure-interaction of a complex system and results of different cases in terms of soil strength and foundation embedment are compared. High efficiency set of constitutive models in terms of computational time are developed and implemented in ESSI Simulator. Efficiency is done based on simplifying the elastic-plastic stiffness tensor of the constitutive models. Almost in all the soil-structure systems, there are interface zones in contact with each other. These zones can get detached during the loading or can slip on each other. In this dissertation the frictional contact element is implemented in ESSI Simulator. Extended verification has been done on the implemented element. The interest here is the effect of slipping and gap opening at the interface of soil and concrete foundation on the soil-structure system behavior. In fact transferring the loads to structure is defined based on the contact areas which will affect the response of the system. The effect of gap openings and sliding at the interfaces are shown through application examples. In addition, dissipation of the seismic energy due to frictional sliding of the interface zones are studied. Application Programming Interface (API) and Domain Specific Language (DSL) are being developed to increase developer's and user's modeling and simulation capabilities. API describes software services developed by developers that are used by users. A domain-specific language (DSL) is a small language which usually focuses on a particular problem domain in software. In general DSL programs are translated to a common function or library which can be viewed as a tool to hide the details of the programming, and make it easier for the user to deal with the commands.

Linking Microbial Community Structure to β-Glucosidic Function in Soil Aggregates

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

Bailey, Vanessa L.; Fansler, Sarah J.; Stegen, James C.

2013-10-01

To link microbial community 16S structure to a measured function in a natural soil we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-glucosidase activity was assayed in 450 individual aggregates which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differencesmore » in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be that observed functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to presence or absence of particular taxonomic groups.« less

Genetic structure of traditional varieties of bitter manioc in three soils in Central Amazonia.

PubMed

Alves-Pereira, Alessandro; Peroni, Nivaldo; Abreu, Aluana Gonçalves; Gribel, Rogério; Clement, Charles R

2011-10-01

Manioc is the most important food crop that originated in Amazonia. Many studies have increased our understanding of its evolutionary dynamics under cultivation. However, most of them focused on manioc cultivation in environments with low soil fertility, generally Oxisols. Recent ethnobotanical observations showed that bitter manioc also performs well in high fertility soils, such as Amazonian dark earths (ADE) and the floodplain. We used 10 microsatellite loci to investigate the genetic diversity and structure of bitter manioc varieties grown in different soil types in communities of smallholder farmers along the middle Madeira River in Central Amazonia. The genetic diversity of some sweet varieties and seedlings was also evaluated. Adult individuals showed higher levels of genetic diversity and smaller inbreeding coefficients (A ( R ) = 5.52, H ( O ) = 0.576, f = 0.086) than seedlings (A ( R ) = 4.39, H ( O ) = 0.421, f = 0.242). Bitter manioc varieties from the floodplain showed higher levels of genetic diversity (A ( R ) = 5.19, H ( O ) = 0.606) than those from ADE (A ( R ) = 4.45, H ( O ) = 0.538) and from Oxisols (A ( R ) = 4.15, H ( O ) = 0.559). The varieties grown in the floodplain were strongly differentiated from the varieties grown in Oxisols (F ( ST ) = 0.093) and ADE (F ( ST ) = 0.108), suggesting important genetic structuring among varieties grown in the floodplain and upland soils (ADE and Oxisols). This is the first time that genetic divergence of bitter manioc varieties in cultivation in different Amazonian soils in a small geographic area is reported.

Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments▿

PubMed Central

Yergeau, Etienne; Arbour, Mélanie; Brousseau, Roland; Juck, David; Lawrence, John R.; Masson, Luke; Whyte, Lyle G.; Greer, Charles W.

2009-01-01

High-Arctic soils have low nutrient availability, low moisture content, and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at the Canadian high-Arctic stations of Alert (ex situ approach) and Eureka (in situ approach). Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as quantitative reverse transcriptase PCR targeting key functional genes. The results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon-ring-hydroxylating dioxygenases were observed 1 month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e., ex situ versus in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. PMID:19684169

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils.

PubMed

Walker, Jennifer K M; Egger, Keith N; Henry, Gregory H R

2008-09-01

Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils

PubMed Central

Torres, Maria Pilar; Montesinos-Navarro, Alicia; Roldán, Antonio

2016-01-01

ABSTRACT We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. IMPORTANCE Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions. PMID:27016567