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Sample records for total soil microbial

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

    Science.gov (United States)

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

    2017-10-01

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

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

    DEFF Research Database (Denmark)

    Cao, Haichuan; Chen, Ruirui; Wang, Libing

    2016-01-01

    Considering the extensive functional redundancy in microbial communities and great difficulty in elucidating it based on taxonomic structure, studies on the biogeography of soil microbial activity at large spatial scale are as important as microbial community structure. Eighty-four soil samples...... scaling clearly revealed that soil microbial activities showed distinct differentiation at different sites over a regional spatial scale, which were strongly affected by soil pH, total P, rainfall, temperature, soil type and location. In addition, microbial community structure was greatly influenced...... scales. There are common (distance, climate, pH and soil type) but differentiated aspects (TP, SOC and N) in the biogeography of soil microbial community structure and activity....

  3. 11 Soil Microbial Biomass

    African Journals Online (AJOL)

    186–198. Insam H. (1990). Are the soil microbial biomass and basal respiration governed by the climatic regime? Soil. Biol. Biochem. 22: 525–532. Insam H. D. and Domsch K. H. (1989). Influence of microclimate on soil microbial biomass. Soil Biol. Biochem. 21: 211–21. Jenkinson D. S. (1988). Determination of microbial.

  4. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

    Czech Academy of Sciences Publication Activity Database

    Baldrian, Petr; Kolařík, Miroslav; Štursová, Martina; Kopecký, J.; Valášková, Vendula; Větrovský, Tomáš; Žifčáková, Lucia; Šnajdr, Jaroslav; Rídl, Jakub; Vlček, Čestmír; Voříšková, Jana

    2012-01-01

    Roč. 6, č. 2 (2012), s. 248-258 ISSN 1751-7362 R&D Projects: GA ČR GA526/08/0751; GA MŠk LC06066 Institutional research plan: CEZ:AV0Z50200510; CEZ:AV0Z50520514 Keywords : cellulose decomposition * bacteria * forest soil Subject RIV: EE - Microbiology, Virology Impact factor: 8.951, year: 2012

  5. Soil Microbes and soil microbial proteins: interactions with clay minerals

    International Nuclear Information System (INIS)

    Spence, A.; Kelleher, B. P.

    2009-01-01

    Bacterial enumeration in soil environments estimates that the population may reach approximately 10 1 0 g - 1 of soil and comprise up to 90% of the total soil microbial biomass. Bacteria are present in soils as single cells or multicell colonies and often strongly adsorb onto mineral surfaces such as sand and clay. The interactions of microbes and microbial biomolecules with these minerals have profound impacts on the physical, chemical and biological properties of soils. (Author)

  6. Soil microbial activities and its relationship with soil chemical ...

    African Journals Online (AJOL)

    The fields assessed are organically managed Soils (OMS), Inorganically Managed Soils (IMS) and an Uncultivated Land having grass coverage (ULS). Soil Microbial Respiration (SMR), Microbial Biomass Carbon (MBC), Microbial Biomass Nitrogen (MBN) and Microbial Biomass Phosphorus (MBP) were analyzed.

  7. Seasonal variation and distribution of total and active microbial community of beta-glucosidase encoding genes in coniferous forest soil

    Czech Academy of Sciences Publication Activity Database

    Pathan, S.I.; Žifčáková, Lucia; Ceccherini, M.T.; Pantani, O.L.; Větrovský, Tomáš; Baldrian, Petr

    2017-01-01

    Roč. 105, February (2017), s. 71-80 ISSN 0038-0717 R&D Projects: GA ČR(CZ) GA16-08916S Grant - others:Transbiodiverse(CZ) 7. RP Marie Curie ITN FP7/2007e2013 project 289949 Institutional support: RVO:61388971 Keywords : Beta-Glucosidases * Forest soil * Bacteria Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 4.857, year: 2016

  8. Microbial communities in blueberry soils

    Science.gov (United States)

    Microbial communities thrive in the soil of the plant root zone and it is clear that these communities play a role in plant health. Although blueberry fields can be productive for decades, yields are sometimes below expectations and fields that are replanted sometimes underperform and/or take too lo...

  9. Soil microbial community response to land use and various soil ...

    African Journals Online (AJOL)

    Soil microbial community response to land use and various soil elements in a city landscape of north China. ... African Journal of Biotechnology ... Legumes played an important role in stimulating the growth and reproduction of various soil microbial populations, accordingly promoting the microbial catabolic activity.

  10. Microbial population changes in tropical agricultural soil ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-17

    Dec 17, 2008 ... Microbial degradation is known to be an efficient process in the in ..... exhibited a great impact on the ecology of the soil by causing drastic ... city of the soil (Dibble and Bartha, 1979). Hydrocarbon .... Atlas RM (1991). Microbial ...

  11. Soil microbial biomass in an agroforestry system of Northeast Brazil

    Directory of Open Access Journals (Sweden)

    Rosane C. Rodrigues

    2015-01-01

    Full Text Available Agroforestry systems (AFS are considered alternative land use options to help prevent soil degradation and improve soil microbial biomass and organic C status. However, it is unclear how different densities of babassu palm [Attalea speciosa (syn. Orbignya phalerata], which is an important tree in Northeast Brazil, affect the soil microbial biomass. We investigated the soil microbial biomass C and activity under AFS with different densities of babassu palm associated with Brachiaria brizantha grass. Soil microbial biomass C (MBC, soil microbial biomass N (MBN, MBC:total organic C ratio, fluorescein diacetate hydrolysis and dehydrogenase activity showed highest values in plots with high density of babassu palm. On the other hand, the respiratory quotient (qCO2 was significantly greater in plots without babassu palm. Brachiaria brizantha in monoculture may promote C losses from the soil, but AFS with high density of babassu palm may increase the potential of soils to accumulate C.Keywords: Enzyme activity, tropical soil, babassu palm, silvopastoral system, soil quality.DOI: 10.17138/TGFT(341-48

  12. A Compilation of Global Soil Microbial Biomass Carbon, Nitrogen, and Phosphorus Data

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides the concentrations of soil microbial biomass carbon (C), nitrogen (N) and phosphorus (P), soil organic carbon, total nitrogen, and total...

  13. Microbial Ecology of Soil Aggregation in Agroecosystems

    Science.gov (United States)

    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

  14. Developing and using artificial soils to analyze soil microbial processes

    Science.gov (United States)

    Gao, X.; Cheng, H. Y.; Boynton, L.; Masiello, C. A.; Silberg, J. J.

    2017-12-01

    Microbial diversity and function in soils are governed by soil characteristics such as mineral composition, particles size and aggregations, soil organic matter (SOM), and availability of nutrients and H2O. The spatial and temporal heterogeneity of soils creates a range of niches (hotspots) differing in the availability of O2, H2O, and nutrients, which shapes microbial activities at scales ranging from nanometer to landscape. Synthetic biologists often examine microbial response trigged by their environment conditions in nutrient-rich aqueous media using single strain microbes. While these studies provided useful insight in the role of soil microbes in important soil biogeochemical processes (e.g., C cycling, N cycling, etc.), the results obtained from the over-simplified model systems are often not applicable natural soil systems. On the contrary, soil microbiologists examine microbial processes in natural soils using longer incubation time. However, due to its physical, chemical and biological complexity of natural soils, it is often difficult to examine soil characteristics independently and understand how each characteristic influences soil microbial activities and their corresponding soil functioning. Therefore, it is necessary to bridge the gap and develop a model matrix to exclude unpredictable influences from the environment while still reliably mimicking real environmental conditions. The objective of this study is to design a range of ecologically-relevant artificial soils with varying texture (particle size distribution), structure, mineralogy, SOM content, and nutrient heterogeneity. We thoroughly characterize the artificial soils for pH, active surface area and surface morphology, cation exchange capacity (CEC), and water retention curve. We demonstrate the effectiveness of the artificial soils as useful matrix for microbial processes, such as microbial growth and horizontal gene transfer (HGT), using the gas-reporting biosensors recently developed in

  15. Soil microbial diversity in the vicinity of desert shrubs.

    Science.gov (United States)

    Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

    2013-04-01

    Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.

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

    Science.gov (United States)

    Maharjan, M.

    2016-12-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  18. Spectral Characteristics of Salinized Soils during Microbial Remediation Processes.

    Science.gov (United States)

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

    2015-09-01

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

  19. Microbial population changes in tropical agricultural soil ...

    African Journals Online (AJOL)

    Impacts of crude petroleum pollution on the soil environment and microbial population dynamics as well as recovery rates of an abandoned farmland was monitored for seven months spanning the two major seasons in Nigeria with a ... The physico-chemistry of the control and contaminated soils differed just significantly (P ...

  20. Feedbacks Between Soil Structure and Microbial Activities in Soil

    Science.gov (United States)

    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

  1. The effects of boron management on soil microbial population and ...

    African Journals Online (AJOL)

    Soil microorganisms directly influence boron content of soil as maximum boron release corresponds with the highest microbial activity. The objective of this study is to determine the effects of different levels of boron fertilizer on microbial population, microbial respiration and soil enzyme activities in different soil depths in ...

  2. Non-microbial methane emissions from soils

    Science.gov (United States)

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

    2013-12-01

    Traditionally, methane (CH4) is anaerobically formed by methanogenic archaea. However, non-microbial CH4 can also be produced from geologic processes, biomass burning, animals, plants, and recently identified soils. Recognition of non-microbial CH4 emissions from soils remains inadequate. To better understand this phenomenon, a series of laboratory incubations were conducted to examine effects of temperature, water, and hydrogen peroxide (H2O2) on CH4 emissions under both aerobic and anaerobic conditions using autoclaved (30 min, 121 °C) soils and aggregates (>2000 μm, A1; 2000-250 μm, A2; 250-53 μm, M1; and A2 > A1 > M2 and C-based emission an order of M2 > M1 > A1 > A2, demonstrating that both organic carbon quantity and property are responsible for CH4 emissions from soils at the scale of aggregate. Whole soil-based order of A2 > A1 > M1 > M2 suggests that non-microbial CH4 release from forest soils is majorly contributed by macro-aggregates (i.e., >250 μm). The underlying mechanism is that organic matter through thermal treatment, photolysis, or reactions with free radicals produce CH4, which, in essence, is identical with mechanisms of other non-microbial sources, indicating that non-microbial CH4 production may be a widespread phenomenon in nature. This work further elucidates the importance of non-microbial CH4 formation which should be distinguished from the well-known microbial CH4 formation in order to define both roles in the atmospheric CH4 global budget.

  3. Microbial biomass carbon and enzyme activities of urban soils in Beijing.

    Science.gov (United States)

    Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

    2011-07-01

    To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p urban soils influenced the nature and activities of the microbial communities.

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

    Science.gov (United States)

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

    2018-07-15

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

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

    Science.gov (United States)

    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 soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p 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.

  6. Soil-borne microbial functional structure across different land uses.

    Science.gov (United States)

    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.

  7. Soil-Borne Microbial Functional Structure across Different Land Uses

    Directory of Open Access Journals (Sweden)

    Eiko E. Kuramae

    2014-01-01

    Full Text Available 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.

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

    Science.gov (United States)

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

    2016-04-22

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

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

    Science.gov (United States)

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

    2011-12-01

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

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

    Science.gov (United States)

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

    2016-01-15

    Afforestation may alter soil microbial community structure and function, and further affect soil carbon (C) and nitrogen (N) dynamics. Here we investigated soil microbial carbon and nitrogen (MBC and MBN) and microbial community [e.g. bacteria (B), fungi (F)] derived from phospholipid fatty acids (PLFAs) analysis in afforested (implementing woodland and shrubland plantations) and adjacent croplands in central China. Relationships of microbial properties with biotic factors [litter, fine root, soil organic carbon (SOC), total nitrogen (TN) and inorganic N], abiotic factors (soil temperature, moisture and pH), and major biological processes [basal microbial respiration, microbial metabolic quotient (qCO2), net N mineralization and nitrification] were developed. Afforested soils had higher mean MBC, MBN and MBN:TN ratios than the croplands due to an increase in litter input, but had lower MBC:SOC ratio resulting from low-quality (higher C:N ratio) litter. Afforested soils also had higher F:B ratio, which was probably attributed to higher C:N ratios in litter and soil, and shifts of soil inorganic N forms, water, pH and disturbance. Alterations in soil microbial biomass and community structure following afforestation were associated with declines in basal microbial respiration, qCO2, net N mineralization and nitrification, which likely maintained higher soil carbon and nitrogen storage and stability. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Microbial hotspots and hot moments in soil

    Science.gov (United States)

    Kuzyakov, Yakov; Blagodatskaya, Evgenia

    2015-04-01

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

  12. Dynamics of culturable soil microbial communities during ...

    African Journals Online (AJOL)

    Ecological zones impacted significantly (P < 0.05) on bacterial proliferation, but not on fungal growth. Sampling period significantly (P < 0.05) affected microbial density and the semi-arid agroecozone was more supportive of microbial proliferation than the arid zone. A total of nine predominant fungal species belonging to ...

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

    Science.gov (United States)

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

    2012-11-15

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

  14. Microbial community composition affects soil fungistasis.

    Science.gov (United States)

    de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J A; Kowalchuk, George A; van Veen, Johannes A

    2003-02-01

    Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

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

    Science.gov (United States)

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

    2016-06-15

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

  16. Effect of pesticides on soil microbial community.

    Science.gov (United States)

    Lo, Chi-Chu

    2010-07-01

    According to guidelines for the approval of pesticides, information about effects of pesticides on soil microorganisms and soil fertility are required, but the relationships of different structures of pesticides on the growth of various groups of soil microorganisms are not easily predicted. Some pesticides stimulate the growth of microorganisms, but other pesticides have depressive effects or no effects on microorganisms. For examples, carbofuran stimulated the population of Azospirillum and other anaerobic nitrogen fixers in flooded and non-flooded soil, but butachlor reduced the population of Azospirillum and aerobic nitrogen fixers in non-flooded soil. Diuron and chlorotoluron showed no difference between treated and nontreated soil, and linuron showed a strong difference. Phosphorus(P)-contains herbicides glyphosate and insecticide methamidophos stimulated soil microbial growth, but other P-containing insecticide fenamiphos was detrimental to nitrification bacteria. Therefore, the following review presents some data of research carried out during the last 20 years. The effects of twenty-one pesticides on the soil microorganisms associated with nutrient and cycling processes are presented in section 1, and the applications of denaturing gradient gel electrophoresis (DGGE) for studying microbial diversity are discussed in section 2.

  17. Impact of (+/-)-catechin on soil microbial communities.

    Science.gov (United States)

    Inderjit; Kaur, Rajwant; Kaur, Surinder; Callaway, Ragan M

    2009-01-01

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

  18. Soil microbial toxicity of eight polycyclic aromatic compounds: effects on nitrification, the genetic diversity of bacteria, and the total number of protozoans

    DEFF Research Database (Denmark)

    Sverdrup, Line Emilie; Ekelund, Flemming; Krogh, Paul Henning

    2002-01-01

    mg/kg. For effects on nitrification, toxicity (NOEC values) expressed as soil pore-water concentrations (log10(micromol/L)) showed a significant inverse relationship with lipophilicity (log octanol-water partition coefficient) of the substances (r2 = 0.69, p = 0.011, n = 8). This finding could...

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

    Science.gov (United States)

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

    2017-12-01

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

  20. Alterations in soil microbial community composition and biomass following agricultural land use change.

    Science.gov (United States)

    Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

    2016-11-04

    The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

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

    Science.gov (United States)

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

    2014-12-01

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

  2. Effects of simulated acid rain on microbial characteristics in a lateritic red soil.

    Science.gov (United States)

    Xu, Hua-qin; Zhang, Jia-en; Ouyang, Ying; Lin, Ling; Quan, Guo-ming; Zhao, Ben-liang; Yu, Jia-yu

    2015-11-01

    A laboratory experiment was performed to examine the impact of simulated acid rain (SAR) on nutrient leaching, microbial biomass, and microbial activities in a lateritic red soil in South China. The soil column leaching experiment was conducted over a 60-day period with the following six SAR pH treatments (levels): 2.5, 3.0, 3.5, 4.0, 4.5, and 5.0 and one control treatment (pH = 7). Compared with the control treatment, the concentrations of soil organic matter, total nitrogen, total phosphorus, total potassium, soil microbial biomass carbon (MBC), soil microbial biomass nitrogen (MBN), and average well color density (AWCD) in the Ecoplates were all significantly decreased by leaching with SAR at different pH levels. The decrease in MBC and MBN indicated that acid rain reduced the soil microbial population, while the decrease in AWCD revealed that acid rain had a negative effect on soil bacterial metabolic function. Soil basal respiration increased gradually from pH 4.0 to 7.0 but decreased dramatically from pH 2.5 to 3.0. The decrease in soil nutrient was the major reason for the change of soil microbial functions. A principal component analysis showed that the major carbon sources used by the bacteria were carbohydrates and carboxylic acids.

  3. Evaluation of methyl bromide alternatives efficacy against soil-borne pathogens, nematodes and soil microbial community.

    Directory of Open Access Journals (Sweden)

    Hongwei Xie

    Full Text Available Methyl bromide (MB and other alternatives were evaluated for suppression of Fusarium spp., Phytophthora spp., and Meloidogyne spp. and their influence on soil microbial communities. Both Fusarium spp. and Phytophthora spp. were significantly reduced by the MB (30.74 mg kg-1, methyl iodide (MI: 45.58 mg kg-1, metham sodium (MS: 53.92 mg kg-1 treatments. MS exhibited comparable effectiveness to MB in controlling Meloidogyne spp. and total nematodes, followed by MI at the tested rate. By contrast, sulfuryl fluoride (SF: 33.04 mg kg-1 and chloroform (CF: 23.68 mg kg-1 showed low efficacy in controlling Fusarium spp., Phytophthora spp., and Meloidogyne spp. MB, MI and MS significantly lowered the abundance of different microbial populations and microbial biomass in soil, whereas SF and CF had limited influence on them compared with the control. Diversity indices in Biolog studies decreased in response to fumigation, but no significant difference was found among treatments in PLFA studies. Principal component and cluster analyses of Biolog and PLFA data sets revealed that MB and MI treatments greatly influenced the soil microbial community functional and structural diversity compared with SF treatment. These results suggest that fumigants with high effectiveness in suppressing soil-borne disease could significantly influence soil microbial community.

  4. Degradation and impact of phthalate plasticizers on soil microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Cartwright, C.D.; Thompson, I.P.; Burns, R.G.

    2000-05-01

    To assess the impact of phthalates on soil microorganisms and to supplement the environmental risk assessment for these xenobiotics, soil was treated with diethyl phthalate (DEP) or di (2-ethyl hexyl) phthalate (DEHP) at 0.1 to 100 mg/g. Bioavailability and membrane disruption were proposed as the characteristics responsible for the observed fate and toxicity of both compounds. Diethyl phthalate was biodegraded rapidly in soil with a half-life of 0.75 d at 20 C, and was not expected to persist in the environment. The DEHP, although biodegradable in aqueous solution, was recalcitrant in soil, because of poor bioavailability and was predicted to account for the majority of phthalate contamination in the environment. Addition of DEP or DEHP to soil at a concentration similar to that detected in nonindustrial environments had no impact on the structural diversity or functional diversity (BIOLOG) of the microbial community. At concentrations representative of a phthalate spill, DEP reduced numbers of both total culturable bacteria and pseudomonads within 1 d. This was due to disruption of membrane fluidity by the lipophilic phthalate, a mechanism not previously attributed to phthalates. However, DEHP had no effect on the microbial community or membrane fluidity, even at 100 mg/g, and was predicted to have no impact on microbial communities in the environment.

  5. A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Xiaofeng [ORNL; Thornton, Peter E [ORNL; Post, Wilfred M [ORNL

    2013-01-01

    Soil microbes play a pivotal role in regulating land-atmosphere interactions; the soil microbial biomass carbon (C), nitrogen (N), phosphorus (P) and C:N:P stoichiometry are important regulators for soil biogeochemical processes; however, the current knowledge on magnitude, stoichiometry, storage, and spatial distribution of global soil microbial biomass C, N, and P is limited. In this study, 3087 pairs of data points were retrieved from 281 published papers and further used to summarize the magnitudes and stoichiometries of C, N, and P in soils and soil microbial biomass at global- and biome-levels. Finally, global stock and spatial distribution of microbial biomass C and N in 0-30 cm and 0-100 cm soil profiles were estimated. The results show that C, N, and P in soils and soil microbial biomass vary substantially across biomes; the fractions of soil nutrient C, N, and P in soil microbial biomass are 1.6% in a 95% confidence interval of (1.5%-1.6%), 2.9% in a 95% confidence interval of (2.8%-3.0%), and 4.4% in a 95% confidence interval of (3.9%-5.0%), respectively. The best estimates of C:N:P stoichiometries for soil nutrients and soil microbial biomass are 153:11:1, and 47:6:1, respectively, at global scale, and they vary in a wide range among biomes. Vertical distribution of soil microbial biomass follows the distribution of roots up to 1 m depth. The global stock of soil microbial biomass C and N were estimated to be 15.2 Pg C and 2.3 Pg N in the 0-30 cm soil profiles, and 21.2 Pg C and 3.2 Pg N in the 0-100 cm soil profiles. We did not estimate P in soil microbial biomass due to data shortage and insignificant correlation with soil total P and climate variables. The spatial patterns of soil microbial biomass C and N were consistent with those of soil organic C and total N, i.e. high density in northern high latitude, and low density in low latitudes and southern hemisphere.

  6. Tillage and manure effect on soil microbial biomass and respiration ...

    African Journals Online (AJOL)

    The objective of this study was to determine the influence of both tillage and liquid pig manure application on soil microbial biomass, enzyme activities and microbial respiration in a meadow soil. The results obtained did not show any significant effect of tillage and manure on microbial biomass carbon (C) and nitrogen (N) ...

  7. Microbial content of abattoir wastewater and its contaminated soil in ...

    African Journals Online (AJOL)

    Microbial content of wastewater in two abattoirs and the impact on microbial population of receiving soil was studied in Agege and Ojo Local Government Areas in Lagos State, Nigeria. Wastewater samples were collected from each of the abattoirs over three months period and examined for microbial content. Soil samples ...

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

    Science.gov (United States)

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

    2015-06-01

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

  9. Microbial Mechanisms Enhancing Soil C Storage

    Energy Technology Data Exchange (ETDEWEB)

    Zak, Donald [Univ. of Michigan, Ann Arbor, MI (United States)

    2015-09-24

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

  10. Soil microbial effects of smelter induced heavy metal contamination

    Energy Technology Data Exchange (ETDEWEB)

    Nordgren, A

    1986-01-01

    The soil concentrations of Cu and Zn at the secondary smelter were 20 00 mu g/g dry soil. Close to the primary smelter the soil was contaminated with more than ten elements including Pb, Zn, Cu and As at levels ranging between 6000 and 1000 mu g/g dry soil. The correlations between the concentrations of the metals were high at both smelters. Soil respiration rate decreased by about 75% close to both smelters. Total and fluorescein diacetate stained mycelial lengths decrease with increasing heavy metal pollution at the secondary but not at the primary smelter. The fungal community structure was strongly affected by the contamination. General common in coniferous forest soils such as Penicillium and Oidiodendron virtually vanished, while less frequent species like Paecilomyces farinosus and Geomyces pannorum dominated the site close to the smelter. Colony forming units of a number of functional groups of bacteria were found to be very sensitive to metal contamination. The urease activity of the soil was inhibited. Multivariate statistical analyses showed that the metal contamination was the major environmental influence on the microbiotain the soils studied. A study of about 200 decomposition curves resulting from glutamic acid additions to the different soils produced four microbially related parameters: basal respiration rate, initial respiration rate after the addition of the glutamic acid, specific respiration rate during the exponential increase of the respiration rate and the lag time before the exponential phase. With 53 refs.

  11. Relationships among Contrasting Measurements of Microbial Dynamics in Pasture and Organic Farm Soils

    International Nuclear Information System (INIS)

    Edenborn, S.L; Sexstone, A.J; Sutanto, Y; Chapman, J.A

    2011-01-01

    Soil bacteria exhibit short-term variations in community structure, providing an indication of anthropogenic disturbances. In this study, microbial biomass carbon (MBC), potentially mineralizable nitrogen (PMN), community level physiological profiling (CLPP), and culture-dependent DGGE (CD DGGE) fingerprinting of the 16 S r RNA gene were used to compare microbial communities in organic farm and pasture soils subjected to differing agronomic treatments. Correlation analyses revealed significant relationships between MBC, PMN, and data derived from microbial community analyses. All measures separated soil types but varied in their ability to distinguish among treatments within a soil type. Overall, MBC, PMN, and CLPP were most responsive to compost and manure amendments, while CD DGGE resolved differences in legume cropping and inorganic fertilization. The results support the hypothesis that culturable soil bacteria are a responsive fraction of the total microbial community, sensitive to agronomic perturbations and amenable to further studies aimed at linking community structure with soil functions.

  12. Soil Microbial Activity in Conventional and Organic Agricultural Systems

    Directory of Open Access Journals (Sweden)

    Romero F.V. Carneiro

    2009-06-01

    Full Text Available The aim of this study was to evaluate microbial activity in soils under conventional and organic agricultural system management regimes. Soil samples were collected from plots under conventional management (CNV, organic management (ORG and native vegetation (AVN. Soil microbial activity and biomass was significantly greater in ORG compared with CNV. Soil bulk density decreased three years after adoption of organic system. Soil organic carbon (SOC was higher in the ORG than in the CNV. The soil under organic agricultural system presents higher microbial activity and biomass and lower bulk density than the conventional agricultural system.

  13. Monomethylhydrazine degradation and its effect on carbon dioxide evolution and microbial populations in soil

    International Nuclear Information System (INIS)

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

    1988-01-01

    Monomethylhydrazine (MMH), along with hydrazine and 1,1-dimethylhydrazine are the main components of hydrazine fuels. Information on the fate of MMH in soil and its overall effect on soil microbial activity is not known, though MMH is known to be toxic to a number of soil bacteria. Despite the fact that axenic bacterial cultures are inhibited by the three hydrazines, Ou and Street reported that soil respiration, and total bacterial and fungal populations in soil, were not inhibited by hydrazine at concentrations of 100 μg/g and lower. Even at 500 μg/g, only total bacterial populations in soil were inhibited by the presence of hydrazine. They also reported that hydrazine rapidly disappeared in soil. The authors initiated this study to investigate the effect of MMH on soil microbial activity and on degradation of the chemical in soil

  14. Radiocesium storage in soil microbial biomass of undisturbed alpine meadow soils and its relation to 137Cs soil-plant transfer

    International Nuclear Information System (INIS)

    Stemmer, Michael; Hromatka, Angelika; Lettner, Herbert; Strebl, Friederike

    2005-01-01

    This study focuses on radiocesium storage in soil microbial biomass of undisturbed alpine meadow sites and its relation to the soil-to-plant transfer. Soil and plant samples were taken in August 1999 from an altitude transect (800-1600 m.a.s.l.) at Gastein valley, Austria. Soil samples were subdivided into 3-cm layers for analyses of total, K 2 SO 4 -extractable and microbially stored 137 Cs. Microbial biomass was measured by the fumigation extraction method, and fungal biomass was quantified using ergosterol as biomarker molecule. In general, the quantity of 137 Cs stored in the living soil microbial biomass was relatively small. At the high-altitude meadows, showing high amounts of fungal biomass, microbially stored 137 Cs amounted to 0.64 ± 0.14 kBq m -2 which corresponds to about 1.2-2.7% of the total 137 Cs soil inventory. At lower altitudes, microbial 137 Cs content was distinctly smaller and in most cases not measurable at all using the fumigation extraction method. However, a positive correlation between the observed soil-to-plant aggregated transfer factor, microbially stored 137 Cs and fungal biomass was found, which indicates a possible role of fungal biomass in the storage and turnover of 137 Cs in soils and in the 137 Cs uptake by plants

  15. Long-term oil contamination causes similar changes in microbial communities of two distinct soils.

    Science.gov (United States)

    Liao, Jingqiu; Wang, Jie; Jiang, Dalin; Wang, Michael Cai; Huang, Yi

    2015-12-01

    Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of

  16. Variations in soil microbial community structure induced by the conversion from paddy fields to upland fields

    Science.gov (United States)

    Dai, X.

    2015-12-01

    Land-use conversion is an important factor influencing the carbon and nitrogen gas exchange between land and atmosphere, and soil microorganisms is main driver of soil carbon and nitrogen gas production. Understanding the effect of land-use conversion on soil microbial communities and its influencing factor is important for greenhouse gas emission reduction and soil organic carbon and nitrogen sequestration and stability. The influence of land use conversion on soil process was undergoing a dynamic change, but little research has been done to understand the effect on soil microbial communities during the initial years after land conversion. In the study, the influences of land-use conversion from double rice cropping (RR) to maize-maize (MM) and soybean-peanut (SP) double cropping systems on soil physical and chemical properties, and microbial community structure was studied after two years of the conversion in southern China. The results showed that land use conversion significantly changed soil properties, microbial communities and biomass. Soil pH significantly decreased by 0.50 and 0.52 after conversion to MM and SP, respectively. Soil TN and NH4-N also significantly decreased by 9%-15% and 60% after conversion to upland fields, respectively. The total PLFAs, bacterial, gram-positive bacterial (G+), gram-negative bacterial (G-) and actinomycetic PLFAs decreased significantly. The ng g-1 soil concentration of monounsaturated chain PLFAs 16:1ω7c and 18:1ω9t were significantly higher at paddy fields than at upland fields. No significant differences in soil properties, microbial communities and biomass were found between conversed MM and SP. Our results indicated that land use conversion, not crop type conversed had a significant effects on soil properties and microbial communities at the initial of land conversion. And soil pH was the key factor regulating the variations in soil microbial community structure after land use conversion from paddy to upland fields.

  17. [Soil Microbial Respiration Under Different Soil Temperature Conditions and Its Relationship to Soil Dissolved Organic Carbon and Invertase].

    Science.gov (United States)

    Wu, Jing; Chen, Shu-tao; Hu, Zheng-hua; Zhang, Xu

    2015-04-01

    In order to investigate the soil microbial respiration under different temperature conditions and its relationship to soil dissolved organic carbon ( DOC) and invertase, an indoor incubation experiment was performed. The soil samples used for the experiment were taken from Laoshan, Zijinshan, and Baohuashan. The responses of soil microbial respiration to the increasing temperature were studied. The soil DOC content and invertase activity were also measured at the end of incubation. Results showed that relationships between cumulative microbial respiration of different soils and soil temperature could be explained by exponential functions, which had P values lower than 0.001. The coefficient of temperature sensitivity (Q10 value) varied from 1.762 to 1.895. The Q10 value of cumulative microbial respiration decreased with the increase of soil temperature for all soils. The Q10 value of microbial respiration on 27 days after incubation was close to that of 1 day after incubation, indicating that the temperature sensitivity of recalcitrant organic carbon may be similar to that of labile organic carbon. For all soils, a highly significant ( P = 0.003 ) linear relationship between cumulative soil microbial respiration and soil DOC content could be observed. Soil DOC content could explain 31.6% variances of cumulative soil microbial respiration. For the individual soil and all soils, the relationship between cumulative soil microbial respiration and invertase activity could be explained by a highly significant (P soil microbial respiration.

  18. Microbial response of an acid forest soil to experimental soil warming

    Science.gov (United States)

    S.S. Arnold; I.J. Fernandez; L.E. Rustad; L.M. Zibilske

    1999-01-01

    Effects of increased soil temperature on soil microbial biomass and dehydrogenase activity were examined on organic (O) horizon material in a low-elevation spruce-fir ecosystem. Soil temperature was maintained at 5 °C above ambient during the growing season in the experimental plots, and soil temperature, moisture, microbial biomass, and dehydrogenase activity were...

  19. Effects of heavy metals on soil microbial community

    Science.gov (United States)

    Chu, Dian

    2018-02-01

    Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.

  20. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

    Science.gov (United States)

    Zhang, Yuguang; Cong, Jing; Lu, Hui; Yang, Caiyun; Yang, Yunfeng; Zhou, Jizhong; Li, Diqiang

    2014-01-01

    Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (PThe regression analysis showed that a strong positive (Pthe soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (Pthe relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

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

    Science.gov (United States)

    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.

  2. Microbial Remediation of Metals in Soils

    Science.gov (United States)

    Hietala, K. A.; Roane, T. M.

    Of metal-contaminated systems, metal-contaminated soils present the greatest challenge to remediation efforts because of the structural, physical, chemical, and biological heterogeneities encountered in soils. One of the confounding issues surrounding metal remediation is that metals can be readily re-mobilized, requiring constant monitoring of metal toxicity in sites where metals are not removed. Excessive metal content in soils can impact air, surface water, and groundwater quality. However, our understanding of how metals affect organisms, from bacteria to plants and animals, and our ability to negate the toxicity of metals are in their infancies. The ubiquity of metal contamination in developing and industrialized areas of the world make remediation of soils via removal, containment, and/or detoxification of metals a primary concern. Recent examples of the health and environmental consequences of metal contamination include arsenic in drinking water (Wang and Wai 2004), mercury levels in fish (Jewett and Duffy 2007), and metal uptake by agricultural crops (Howe et al. 2005). The goal of this chapter is to summarize the traditional approaches and recent developments using microorganisms and microbial products to address metal toxicity and remediation.

  3. Soil-Borne Microbial Functional Structure across Different Land Uses

    NARCIS (Netherlands)

    Kuramae, E.E.; Zhou, J.Z.; Kowalchuk, G.A.; van Veen, J.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

  4. Soil-borne microbial functional structure across different land uses

    NARCIS (Netherlands)

    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

  5. Organic contaminants in soil : desorption kinetics and microbial degradation

    NARCIS (Netherlands)

    Schlebaum, W.

    1999-01-01

    The availability of organic contaminants in soils or sediments for microbial degradation or removal by physical means (e.g.) soil washing or soil venting) depends on the desorption kinetics of these contaminants from the soil matrix. When the organic contaminants desorb very slow from the

  6. Effect of four herbicides on microbial population, soil organic matter ...

    African Journals Online (AJOL)

    The effect of four herbicides (atrazine, primeextra, paraquat and glyphosate) on soil microbial population, soil organic matter and dehydrogenase activity was assessed over a period of six weeks. Soil samples from cassava farms were treated with herbicides at company recommended rates. Soil dehydrogenase activity was ...

  7. Production of Microbial Protease from Selected Soil Fungal Isolates ...

    African Journals Online (AJOL)

    Production of Microbial Protease from Selected Soil Fungal Isolates. ... Nigerian Journal of Biotechnology ... and 500C. The optimal pH on the enzyme production was observed to be between pH 3.5 and 5.5 for the organisms. Keywords: Soil microorganism, fungal isolate, incubation period, microbial enzyme. Nig J. Biotech.

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

    Science.gov (United States)

    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.

  9. Nutrient limitation of soil microbial activity during the earliest stages of ecosystem development.

    Science.gov (United States)

    Castle, Sarah C; Sullivan, Benjamin W; Knelman, Joseph; Hood, Eran; Nemergut, Diana R; Schmidt, Steven K; Cleveland, Cory C

    2017-11-01

    A dominant paradigm in ecology is that plants are limited by nitrogen (N) during primary succession. Whether generalizable patterns of nutrient limitation are also applicable to metabolically and phylogenetically diverse soil microbial communities, however, is not well understood. We investigated if measures of N and phosphorus (P) pools inform our understanding of the nutrient(s) most limiting to soil microbial community activities during primary succession. We evaluated soil biogeochemical properties and microbial processes using two complementary methodological approaches-a nutrient addition microcosm experiment and extracellular enzyme assays-to assess microbial nutrient limitation across three actively retreating glacial chronosequences. Microbial respiratory responses in the microcosm experiment provided evidence for N, P and N/P co-limitation at Easton Glacier, Washington, USA, Puca Glacier, Peru, and Mendenhall Glacier, Alaska, USA, respectively, and patterns of nutrient limitation generally reflected site-level differences in soil nutrient availability. The activities of three key extracellular enzymes known to vary with soil N and P availability developed in broadly similar ways among sites, increasing with succession and consistently correlating with changes in soil total N pools. Together, our findings demonstrate that during the earliest stages of soil development, microbial nutrient limitation and activity generally reflect soil nutrient supply, a result that is broadly consistent with biogeochemical theory.

  10. Microbial responses to carbon and nitrogen supplementation in an Antarctic dry valley soil

    DEFF Research Database (Denmark)

    Dennis, P. G.; Sparrow, A. D.; Gregorich, E. G.

    2013-01-01

    The soils of the McMurdo Dry Valleys are exposed to extremely dry and cold conditions. Nevertheless, they contain active biological communities that contribute to the biogeochemical processes. We have used ester-linked fatty acid (ELFA) analysis to investigate the effects of additions of carbon...... and nitrogen in glucose and ammonium chloride, respectively, on the soil microbial community in a field experiment lasting three years in the Garwood Valley. In the control treatment, the total ELFA concentration was small by comparison with temperate soils, but very large when expressed relative to the soil...... organic carbon concentration, indicating efficient conversion of soil organic carbon into microbial biomass and rapid turnover of soil organic carbon. The ELFA concentrations increased significantly in response to carbon additions, indicating that carbon supply was the main constraint to microbial...

  11. Microbial diversity in soil : Selection of microbial populations by plant and soil type and implications for disease suppressiveness

    NARCIS (Netherlands)

    Garbeva, P; van Veen, JA; van Elsas, JD

    2004-01-01

    An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil

  12. Soil Microbial Community Structure Evolution along Halophyte Succession in Bohai Bay Wetland

    Directory of Open Access Journals (Sweden)

    Mingyang Cong

    2014-01-01

    Full Text Available It is urgent to recover Bohai Bay costal wetland ecosystem because of covering a large area of severe saline-alkali soil. To explore the relationship between halophyte herbaceous succession and microbial community structure, we chose four local communities which played an important role in improving soil microenvironment. We performed phospholipid fatty acid analysis, measured soil parameters, and evaluated shifts of microbial community structure. Results showed that microbial community structure changed significantly along succession and bacteria community was dominant. Total phospholipid fatty acid content increased in different successional stages but decreased with depth, with similar variations in bacterial and fungal biomass. Soil organic carbon and especially total nitrogen were positively correlated with microbial biomass. Colonization of pioneering salt-tolerant plants Suaeda glauca in saline-alkali bare land changed total soil microorganism content and composition. These results showed that belowground processes were strongly related with aboveground halophyte succession. Fungal/bacterial ratio, Gram-negative/Gram-positive bacteria ratio, total microbial biomass, and fungi and bacteria content could indicate the degree of succession stages in Bohai Bay wetland ecosystem. And also these findings demonstrated that microbial community biomass and composition evolved along with vegetation succession environmental variables.

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

    Science.gov (United States)

    Ravindran, Anita; Yang, Shang-Shyng

    2015-08-01

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

  14. Imidacloprid application changes microbial dynamics and enzymes in rice soil.

    Science.gov (United States)

    Mahapatra, Bibhab; Adak, Totan; Patil, Naveen K B; Pandi G, Guru P; Gowda, G Basana; Jambhulkar, N N; Yadav, Manoj Kumar; Panneerselvam, P; Kumar, Upendra; Munda, Sushmita; Jena, Mayabini

    2017-10-01

    Extensive use of imidacloprid in rice ecosystem may alter dynamics of microorganisms and can change soil biochemical properties. The objective of this study was to assess the effect of imidacloprid on growth and activities of microbes in tropical rice soil ecosystem. Four treatments, namely, recommended dose (at 25g a.i. ha -1 , RD), double the recommended dose (at 50g a.i. ha -1 , 2RD), five times the recommended dose (at 125g a.i. ha -1 , 5RD) & ten times the recommended dose (at 250g a.i. ha -1 , 10RD) along with control were imposed under controlled condition. Dissipation half lives of imidacloprid in soil were 19.25, 20.38, 21.65 and 33.00 days for RD, 2RD, 5RD and 10RD, respectively. In general bacteria, actinomycetes, fungi and phosphate solubilising bacteria population were disturbed due to imidacloprid application. Changes in diversity indices within bacterial community confirmed that imidacloprid application significantly affected distribution of bacteria. Total soil microbial biomass carbon content was reduced on imidacloprid application. Except dehydrogenase and alkaline phosphatase activities, all other soil enzymes namely, β-glycosidase, fluorescien diacetate hydrolase, acid phosphatase and urease responded negatively to imidacloprid application. The extent of negative effect of imidacloprid depends on dose and exposure time. This study concludes imidacloprid application had transient negative effects on soil microbes. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2014-05-01

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

  16. Survival of a microbial soil community under Martian conditions

    Science.gov (United States)

    Hansen, A. A.; Noernberg, P.; Merrison, J.; Lomstein, B. Aa.; Finster, K. W.

    2003-04-01

    Because of the similarities between Earth and Mars early history the hypothesis was forwarded that Mars is a site where extraterrestrial life might have and/or may still occur(red). Sample-return missions are planned by NASA and ESA to test this hypothesis. The enormous economic costs and the logistic challenges of these missions make earth-based model facilities inevitable. The Mars simulation system at University of Aarhus, Denmark allows microbiological experiments under Mars analogue conditions. Thus detailed studies on the effect of Mars environmental conditions on the survival and the activity of a natural microbial soil community were carried out. Changes in the soil community were determined with a suite of different approaches: 1) total microbial respiration activity was investigated with 14C-glucose, 2) the physiological profile was investigated by the EcoLog-system, 3) colony forming units were determined by plate counts and 4) the microbial diversity on the molecular level was accessed with Denaturing Gradient Gel Electrophoresis. The simulation experiments showed that a part of the bacterial community survived Martian conditions corresponding to 9 Sol. These and future simulation experiments will contribute to our understanding of the possibility for extraterrestrial and terrestrial life on Mars.

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

    Directory of Open Access Journals (Sweden)

    Sreejata Bandopadhyay

    2018-04-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Science.gov (United States)

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

    2014-05-01

    The implementation of olive cultivation techniques in Greece has not been systematically tested under the prevailing Mediterranean conditions. A LIFE+ project was initiated (oLIVE-CLIMA; LIFE 11/ENV/000942) aiming to introduce new management practices in olive tree crops that lead to increased carbon dioxide uptake by plants as well as carbon sequestration from the atmosphere and reverse the trend of soil organic matter decline, erosion and desertification. This paper presents data on soil organic matter and microbial activity from a soil campaign in a pilot region in Greece, and particularly in the area of Chora, prefecture of Messinia, South west Peloponnese. The soil campaign took place during the period December 2012-February 2013. Twelve soil parcels of olive groves were selected (6 irrigated and 6 rainfed) and in each soil parcel six composite soil samples were taken from 0-10 cm depth at equal intervals along a straight line of the trunk of the tree to the middle of the distance from the nearest tree of the next tree series. The first three samples were under olive tree canopy. An additional composite sample was taken at depth of 10-40 cm. Soil samples were analyzed for soil physicochemical and biological properties. In this study results for total organic carbon (TOC), soil basal microbial respiration (BR), microbial biomass C (MB-C) from the region of Messinia, are presented. Organic matter was determined by dichromate oxidation. The microbial activity was measured by the amount of CO2 evolution, while microbial biomass C was determined by substrate-induced respiration, after the addition of glucose. The results showed considerable differences in TOC, BR and MB-C associated with the sampling position and soil depth. The higher TOC, BR and MB-C values, in most cases, were determined in samples taken from points under the canopy, but not close to the tree trunk compared to the sampling points outside the canopy. This indicates the positive effect of

  20. Microbial diversity of septic tank effluent and a soil biomat.

    Science.gov (United States)

    Tomaras, Jill; Sahl, Jason W; Siegrist, Robert L; Spear, John R

    2009-05-01

    Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.

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

    Science.gov (United States)

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

  2. Measurement and characteristics of microbial biomass in forest soils

    International Nuclear Information System (INIS)

    Vance, E.D.

    1986-01-01

    The soil microbial biomass is the primary agent responsible for the breakdown and mineralization of soil organic matter and plays a major role in regulating nutrient availability to plants. In this study, methods for measuring biomass in soil were compared and tested in forest soils ranging in pH from 3.2 to 7.2. A good relationship between biomass C measured using the chloroform fumigation-incubation method and soil ATP or microbial biomass C by direct microscopy was found in soils at or above pH 4.2. The fumigation-incubation method consistently underestimated biomass C in soils below pH 4.2, however. Hypotheses for the breakdown of the fumigation-incubation method in strongly acid soils were tested by using an alterative fumigant, measuring the proportion of added 14 C labelled fungi and bacteria decomposed in fumigated soils (k/sub C/), and by studying the effect of large, non-fumigated soil inocula on the flush of respiration following fumigation. These studies indicated that the failure of the method in strongly acid soils was due to inhibited decomposition of non-microbial soil organic matter by the microbial recolonizing population following fumigation. A modified method for measuring biomass C by fumigation-incubation in acid soils is proposed

  3. Linking diagnostic features to soil microbial biomass and respiration in agricultural grassland soil

    NARCIS (Netherlands)

    Richter, A.; Huallacháin, D.O.; Doyle, E.; Clipson, N.; Leeuwen, Van J.P.; Heuvelink, G.B.; Creamer, R.E.

    2018-01-01

    The functional potential of soil ecosystems can be predicted from the activity and abundance of the microbial community in relation to key soil properties. When describing microbial community dynamics, soil physicochemical properties have traditionally been used. The extent of correlations between

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  5. Microbial biomass, microbial diversity, soil carbon storage, and stability after incubation of soil from grass-clover pastures of different age

    DEFF Research Database (Denmark)

    Müller-Stöver, Dorette Sophie; Hauggaard-Nielsen, Henrik; Eriksen, Jørgen

    2012-01-01

    A laboratory incubation study with clover grass pasture soils of seven different ages (0, 1, 2, 3, 4, 5, and 16 production years) was carried out to determine initial soil carbon (C) and nitrogen (N) stocks and potentials for greenhouse gas emissions (N2O and CO2). Compared with the soil from...... the recently established pasture, an increase of total soil C and N was observed along with pasture age. Greenhouse gas emissions were low and not significantly different among the soils from younger pastures (0-5 years), but especially N2O emissions increased markedly in the soil from 16-year-old grass......-clover. Low emissions might mainly be due to an early C limitation occurring in the soils from younger pastures, which was also corroborated by decreasing levels of cold water-extractable C and early shifts within the microbial community. However, higher emissions from the old pasture soil were offset by its...

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

    Science.gov (United States)

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

    2018-01-01

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

  7. The Effect of Long Term Mercury Pollution on the Soil Microbial Community

    DEFF Research Database (Denmark)

    Müller, A.K.; Westergaard, K.; Christensen, Søren

    2001-01-01

    The effect of long-term exposure to mercury on the soil microbial community was investigated in soil from three different sites along a pollution gradient. The amount of total and bioavailable mercury was negatively correlated to the distance from the center of contamination. The size...... of the bacterial and protozoan populations was reduced in the most contaminated soil, whereas there was no significant difference in fungal biomass measured as chitinase activity. Based on the number of colony morphotypes, moreover, the culturable bacterial population was structurally less diverse and contained...... of the number and abundance of bands. The functional potential of the microbial population measured as sole carbon source utilization by Ecoplates® differed between the soils, but there was no change in the number of substrates utilized. The observed changes in the different soil microbial populations...

  8. The effect of glyphosate application on soil microbial activities in ...

    African Journals Online (AJOL)

    In this study, glyphosate effects as N, P and C nutrient sources on microbial population and the effect of different concentration of it on dehydrogenease activity and soil respiration were investigated. The results show that in a soil with a long historical use of glyphosate (soil 1), the hetrotrophic bacterial population was ...

  9. Lead Contamination and Microbial Lead Tolerance in Soils at Major ...

    African Journals Online (AJOL)

    Devika

    ABSTRACT: Lead pollution and lead tolerance levels of microbes in soil at major road junctions in Benin. City were investigated. Results revealed that distance from the road junctions affected the concentrations of lead in soil, as well as the microbial population density and types of microbes present in the soil. The highest ...

  10. Lead Contamination and Microbial Lead Tolerance in Soils at Major ...

    African Journals Online (AJOL)

    Lead pollution and lead tolerance levels of microbes in soil at major road junctions in Benin City were investigated. Results revealed that distance from the road junctions affected the concentrations of lead in soil, as well as the microbial population density and types of microbes present in the soil. The highest concentrations ...

  11. Microbial Contribution to Organic Carbon Sequestration in Mineral Soil

    Science.gov (United States)

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

  12. Seasonal variability of microbial biomass phosphorus in urban soils.

    Science.gov (United States)

    Halecki, W; Gąsiorek, M

    2015-01-01

    Urban soils have been formed through human activities. Seasonal evaluation with time-control procedure are essential for plant, and activity of microorganisms. Therefore, these processes are crucial in the urban area due to geochemical changes in the past years. The purpose of this study was to investigate the changes of content of microbial biomass phosphorus (P) in the top layer of soils throughout the season. In this research, the concentration of microbial biomass P ranged from 0.01 to 6.29 mg·kg(-1). We used single-factor repeated-measure analysis of variance to test the effect of season on microbial biomass P content of selected urban soils. We found no statistically significant differences between the concentration of microbial biomass P in the investigated urban and sub-urban soils during the growing season. This analysis explicitly recognised that environmental urban conditions are steady. Specifically, we have studied how vegetation seasonality and ability of microbial biomass P are useful for detecting quality deviations, which affect the equilibrium of urban soil. In conclusion, seasonal variability of the stringency of assurance across the different compounds of soil reveals, as expected, the stable condition of the urban soils. Seasonal responses in microbial biomass P under urban soil use should establish a framework as a reference to the activity of the microorganisms. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2007-12-01

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

  14. Exploring Microbial Iron Oxidation in Wetland Soils

    Science.gov (United States)

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

    2009-04-01

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

  15. Carbono orgânico, nitrogênio total, biomassa e atividade microbiana do solo em duas cronosseqüências de reabilitação após a mineração de bauxita Soil organic carbon, total nitrogen, microbial biomass and activity in two rehabilitation chronosequences after bauxite mining

    Directory of Open Access Journals (Sweden)

    Marco Aurélio Carbone Carneiro

    2008-04-01

    reas de referência a partir do primeiro ano, enquanto para o CO e o Nt estes só foram alcançados de modo consistente em períodos mais longos de reabilitação (18 anos. O coeficiente metabólico (qCO2 foi indicativo do estresse provocado pela mineração, mas não diferenciou os diferentes tempos de reabilitação. Os resultados deste estudo mostram que os atributos essenciais ao funcionamento adequado do solo são recuperáveis pela revegetação.Mining is a human activity with a harsh impact on ecosystems. The degradation degree depends on the intensity of soil impact, exploited soil volume and amount of mine spoil. Soil microbial activities are responsible for key functions in ecosystems and can indicate the degree of rehabilitation of mined areas. The purpose of this study was to evaluate the impact of bauxite mining in two chronosequences with different rehabilitation strategies (revegetation on the following soil attributes: organic carbon (C org, total nitrogen (Nt, microbial biomass and respiration, and enzymatic activities. The study was developed in mining areas owned by Alcoa S/A in two different environments: (a areas originally covered by a tropical prairie vegetation called "campo", at elevations up to 1,000 masl, and (b in hilly areas, on the plateau top, including remnants of the native vegetation cover, represented by a subtropical decidous forest, at elevations about 1.600 masl, called "serra". Rehabilitation differed depending on strategies and time, varying from recent mining to 19 years of rehabilitation. Composite samples were collected in eight "campo" and nine "serra" areas, in two layers (0-10 and 10-20 cm in the winter as well as in the summer, in three replicates. Bauxite mining caused a negative impact on org C, Nt and microbial biomass (C, N and P. The values of these attributes were reduced by up to 99 % in comparison with those in reference areas (native vegetation. In both "campo" and "serra", the C org, Nt, microbial biomass and

  16. Formation and Stability of Microbially Derived Soil Organic Matter

    Science.gov (United States)

    Waldrop, M. P.; Creamer, C.; Foster, A. L.; Lawrence, C. R.; Mcfarland, J. W.; Schulz, M. S.

    2017-12-01

    Soil carbon is vital to soil health, food security, and climate change mitigation, but the underlying mechanisms controlling the stabilization and destabilization of soil carbon are still poorly understood. There has been a conceptual paradigm shift in how soil organic matter is formed which now emphasizes the importance of microbial activity to build stable (i.e. long-lived) and mineral-associated soil organic matter. In this conceptual model, the consumption of plant carbon by microorganisms, followed by subsequent turnover of microbial bodies closely associated with mineral particles, produces a layering of amino acid and lipid residues on the surfaces of soil minerals that remains protected from destabilization by mineral-association and aggregation processes. We tested this new model by examining how isotopically labeled plant and microbial C differ in their fundamental stabilization and destabilization processes on soil minerals through a soil profile. We used a combination of laboratory and field-based approaches to bridge multiple spatial scales, and used soil depth as well as synthetic minerals to create gradients of soil mineralogy. We used Raman microscopy as a tool to probe organic matter association with mineral surfaces, as it allows for the simultaneous quantification and identification of living microbes, carbon, minerals, and isotopes through time. As expected, we found that the type of minerals present had a strong influence on the amount of C retained, but the stabilization of new C critically depends on growth, death, and turnover of microbial cells. Additionally, the destabilization of microbial residue C on mineral surfaces was little affected by flushes of DOC relative to wet-dry cycles alone. We believe this new insight into microbial mechanisms of C stabilization in soils will eventually lead to new avenues for measuring and modeling SOM dynamics in soils, and aid in the management of soil C to mediate global challenges.

  17. Charcoal Increases Microbial Activity in Eastern Sierra Nevada Forest Soils

    Directory of Open Access Journals (Sweden)

    Zachary W. Carter

    2018-02-01

    Full Text Available Fire is an important component of forests in the western United States. Not only are forests subjected to wildfires, but fire is also an important management tool to reduce fuels loads. Charcoal, a product of fire, can have major impacts on carbon (C and nitrogen (N cycling in forest soils, but it is unclear how these effects vary by dominant vegetation. In this study, soils collected from Jeffrey pine (JP or lodgepole pine (LP dominated areas and amended with charcoal derived from JP or LP were incubated to assess the importance of charcoal on microbial respiration and potential nitrification. In addition, polyphenol sorption was measured in unamended and charcoal-amended soils. In general, microbial respiration was highest at the 1% and 2.5% charcoal additions, but charcoal amendment had limited effects on potential nitrification rates throughout the incubation. Microbial respiration rates decreased but potential nitrification rates increased over time across most treatments. Increased microbial respiration may have been caused by priming of native organic matter rather than the decomposition of charcoal itself. Charcoal had a larger stimulatory effect on microbial respiration in LP soils than JP soils. Charcoal type had little effect on microbial processes, but polyphenol sorption was higher on LP-derived than JP-derived charcoal at higher amendment levels despite surface area being similar for both charcoal types. The results from our study suggest that the presence of charcoal can increase microbial activity in soils, but the exact mechanisms are still unclear.

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

    Science.gov (United States)

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

    2011-09-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  20. Accounting for microbial habitats in modeling soil organic matter dynamics

    Science.gov (United States)

    Chenu, Claire; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Raynaud, Xavier; Vieublé, Laure; Otten, Wilfred; Falconer, Ruth; Monga, Olivier

    2017-04-01

    The extreme heterogeneity of soils constituents, architecture and inhabitants at the microscopic scale is increasingly recognized. Microbial communities exist and are active in a complex 3-D physical framework of mineral and organic particles defining pores of various sizes, more or less inter-connected. This results in a frequent spatial disconnection between soil carbon, energy sources and the decomposer organisms and a variety of microhabitats that are more or less suitable for microbial growth and activity. However, current biogeochemical models account for C dynamics at the macroscale (cm, m) and consider time- and spatially averaged relationships between microbial activity and soil characteristics. Different modelling approaches have intended to account for this microscale heterogeneity, based either on considering aggregates as surrogates for microbial habitats, or pores. Innovative modelling approaches are based on an explicit representation of soil structure at the fine scale, i.e. at µm to mm scales: pore architecture and their saturation with water, localization of organic resources and of microorganisms. Three recent models are presented here, that describe the heterotrophic activity of either bacteria or fungi and are based upon different strategies to represent the complex soil pore system (Mosaic, LBios and µFun). These models allow to hierarchize factors of microbial activity in soil's heterogeneous architecture. Present limits of these approaches and challenges are presented, regarding the extensive information required on soils at the microscale and to up-scale microbial functioning from the pore to the core scale.

  1. Agroforestry management in vineyards: effects on soil microbial communities

    Science.gov (United States)

    Montagne, Virginie; Nowak, Virginie; Guilland, Charles; Gontier, Laure; Dufourcq, Thierry; Guenser, Josépha; Grimaldi, Juliette; Bourgade, Emilie; Ranjard, Lionel

    2017-04-01

    Some vineyard practices (tillage, chemical weeding or pest management) are generally known to impact the environment with particular negative effects on the diversity and the abundance of soil microorganisms, and cause water and soil pollutions. In an agro-ecological context, innovative cropping systems have been developed to improve ecosystem services. Among them, agroforestry offers strategies of sustainable land management practices. It consists in intercropping trees with annual/perennial/fodder crop on the same plot but it is weakly referenced with grapevine. The present study assesses the effects of intercropped and neighbouring trees on the soil of three agroforestry vineyards, in south-western France regions. More precisely soils of the different plots were sampled and the impact of the distance to the tree or to the neighbouring trees (forest) on soil microbial community has been considered. Indigenous soil microbial communities were characterized by a metagenomic approach that consisted in extracting the molecular microbial biomass, then in calculating the soil fungi/bacteria ratio - obtained by qPCR - and then in characterizing the soil microbial diversity - through Illumina sequencing of 16S and 18S regions. Our results showed a significant difference between the soil of agroforestry vineyards and the soil sampled in the neighbouring forest in terms of microbial abundance and diversity. However, only structure and composition of bacterial community seem to be influenced by the implanted trees in the vine plots. In addition, the comparison of microbial co-occurrence networks between vine and forest plots as well as inside vine plots according to distance to the tree allow revealing a more sensitive impact of agroforestry practices. Altogether, the results we obtained build up the first references for concerning the soil of agroforestry vineyards which will be interpreted in terms of soil quality, functioning and sustainability.

  2. Effects of sodium hypochlorite and high pH buffer solution in electrokinetic soil treatment on soil chromium removal and the functional diversity of soil microbial community

    International Nuclear Information System (INIS)

    Cang Long; Zhou Dongmei; Alshawabkeh, Akram N.; Chen Haifeng

    2007-01-01

    Effects of sodium hypochlorite (NaClO), applied as an oxidant in catholyte, and high pH buffer solution on soil Cr removal and the functional diversity of soil microbial community during enhanced electrokinetic treatments of a chromium (Cr) contaminated red soil are evaluated. Using pH control system to maintain high alkalinity of soil together with the use of NaClO increased the electrical conductivities of soil pore liquid and electroosmotic flux compared with the control (Exp-01). The pH control and NaClO improved the removal of Cr(VI) and total Cr from the soil. The highest removal percentages of soil Cr(VI) and total Cr were 96 and 72%, respectively, in Exp-04 when the pH value of the anolyte was controlled at 10 and NaClO was added in the catholyte. The alkaline soil environment and introduction of NaClO in the soil enhanced the desorption of Cr(VI) from the soil and promoted Cr(III) oxidation to mobile Cr(VI), respectively. However, the elevated pH and introduction of NaClO in the soil, which are necessary for improving the removal efficiency of soil Cr, resulted in a significantly adverse impact on the functional diversity of soil microbial community. It suggests that to assess the negative impact of extreme conditions for enhancing the extraction efficiencies of Cr on the soil properties and function is necessary

  3. The survival strategy of the soil microbial biomass

    Science.gov (United States)

    Brookes, Philip; Kemmitt, Sarah; Dungait, Jennifer; Xu, Jianming

    2014-05-01

    The soil microbial biomass (biomass) is defined as the sum of the masses of all soil microorganisms > 5000 µm3 (e.g. fungi, bacteria, protozoa, yeasts, actinomycetes and algae). Typically comprising about 1 to 3 % of total soil organic matter (SOM), the biomass might be though to live in a highly substrate-rich environment. However, the SOM is, normally, only exceedingly slowly available to the biomass. However the biomass can survive for months or even years on this meagre energy source. Not surprisingly, therefore, the biomass exhibits many features typical of a dormant or resting population. These include a very low rate of basal and specific respiration, a slow rate of cell division (about once every six months on average) and slow turnover rate. These are clearly adaptations to existing in an environment where substrate availability is very low. Yet, paradoxically, the biomass, in soils worldwide, has an adenosine triphosphate (ATP) concentration (around 10 to 12 µmol ATP g-1 biomass C), and an Adenylate Energy Charge (AEC = [(ATP) + (0.5 ADP)]/[(ATP)+(ADP) + (AMP)]) which are typical of microorganisms growing exponentially in a chemostat. This sets us several questions. Firstly, under the condition of extremely limited substrate availability in soil, why does the biomass not mainly exist as spores, becoming active, by increasing both its ATP concentration and AEC, when substrate (plant and animal residues) becomes available? We surmise that a spore strategy may put organisms at a competitive disadvantage, compared to others which are prepared to invest energy, maintaining high ATP and ATP, to take advantage of a 'food event' as soon as it becomes available. Secondly, since SOM is available (although only very slowly) to the biomass, why have some groups not evolved the ability to mineralize it faster, obtain more energy, and so gain a competitive advantage? We believe that the reason why organisms do not use this strategy is, simply, that they cannot. Our

  4. Soil microbial community response to aboveground vegetation and ...

    African Journals Online (AJOL)

    lenovo

    2011-11-21

    Nov 21, 2011 ... magnitude, activity, structure and function of soil microbial community may .... CaO were quantified by inductively coupled plasmaatomic emission spectroscopy ...... Validation of signature polarlipid fatty acid biomarkers for ...

  5. Microbial Fuel Cells for Organic-Contaminated Soil Remedial Applications

    NARCIS (Netherlands)

    Li, Xiaojing; Wang, Xin; Weng, Liping; Zhou, Qixing; Li, Yongtao

    2017-01-01

    Efficient noninvasive techniques are desired for repairing organic-contaminated soils. Bioelectrochemical technology, especially microbial fuel cells (MFCs), has been widely used to promote a polluted environmental remediation approach, and applications include wastewater, sludge, sediment, and

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

    Science.gov (United States)

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

    2013-01-01

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

  7. Effect of pesticide applications on soil microbial activity and on 14C-methyl parathion dissipation

    International Nuclear Information System (INIS)

    Peres, Terezinha Bonanho

    2000-01-01

    Some crops, as cotton, need different pesticide application to control pests and diseases. These compounds reach soil and may affect the soil microbial activity. As the microorganisms play important role on the nutrient cycling, changes in their activities may affect the soil fertility. The influence of several pesticides on soil microbial activity of the 0-15 cm and 15-30 cm depth of the soil profile, and the 14 C-methyl parathion dissipation was studied under influence of other pesticide applications. The influence of pesticides on the microorganisms was followed in an experimental area of the Instituto Biologico, that was divided in two subareas, both under cotton crop. Columns of PVC was buried in both subareas and a solution of 14 C-methyl parathion diluted in the technical compound was applied on the soil surface of each column. One subarea received all the recommended pesticides for the cotton crop besides the 14 C-methyl parathion. The other subarea received only 14 C-methyl parathion solution on the columns soil surface. The soil microbial activity of both subareas was estimated by measurements of dehydrogenase, arylsulfatase and arginine deaminase enzymes. Further, the availability of total nitrogen in the soil was also measured. The dissipation of 14 C-methyl parathion was studied by radiocarbon recovery in soil extracts and combustion of extracted soil and quantification by radiometric techniques. (author)

  8. Microbial characteristics of soils on a latitudinal transect in Siberia

    Czech Academy of Sciences Publication Activity Database

    Šantrůčková, Hana; Bird, M. I.; Kalaschnikov, Y. N.; Grund, M.; Elhottová, Dana; Šimek, Miloslav; Grigoryev, S.; Gleixner, G.; Arneth, A.; Schulze, E.D.; Lloyd, J.

    2003-01-01

    Roč. 9, - (2003), s. 1106-1117 ISSN 1354-1013 R&D Projects: GA ČR GA526/99/P033 Institutional research plan: CEZ:AV0Z6066911 Keywords : latitudial transect * microbial net growth rate * soil microbial activity Subject RIV: EH - Ecology, Behaviour Impact factor: 4.152, year: 2003

  9. Multivariate analyses in soil microbial ecology : a new paradigm

    OpenAIRE

    Thioulouse, J.; Prin, Y.; Duponnois, Robin

    2012-01-01

    Mycorrhizal symbiosis is a key component of a sustainable soil-plant system, governing the cycles of major plant nutrients and vegetation cover. The mycorrhizosphere includes plants roots, the mycorrhizal fungi, and a complex microbial compartment. A large number of methods have been used to characterize the genetic and functional diversity of these soil microbial communities. We present here a review of the multivariate data analysis methods that have been used in 16 research articles publis...

  10. Interactions between selected PAHs and the microbial community in rhizosphere of a paddy soil.

    Science.gov (United States)

    Su, Yu H; Yang, Xue Y

    2009-01-15

    This study investigated the interaction of three polycyclic aromatic hydrocarbons (PAHs), i.e., naphthalene (NAP), phenanthrene (PHN), and pyrene (PYR), with the microbial community in the rhizosphere of a paddy soil and the influence of the rice (Oryza sativa) rhizosphere on the microbial community structure. A range of initial NAP, PHN and PYR levels in soil (50-200, 18-72, and 6.6-26.6 mg kg(-1), respectively) were prepared and the soil samples were then aged for 4 months (to yield PAH concentrations at 1.02-1.42, 1.32-4.77, and 2.98-18.5 mg kg(-)(1), respectively) before the soil samples were planted with rice seedlings. The microbial phospholipid-fatty-acid (PLFA) patterns in PAH-contaminated soils were analyzed to elucidate the changes of the microbial biomass and community composition. Results indicated that at the applied concentrations the PAHs were not toxic to rice seedlings, as evidenced by no growth inhibition during the 8-week planting period. However, the microbial biomass, as revealed by PLFAs, decreased significantly with increasing PAH concentration in both rhizospheric and non-rhizospheric soils. The PAHs in soils were obviously toxic to microorganisms, and the toxicity of PHN was greater than PYR due likely to the higher PHN bioavailability. Total PLFAs in rhizospheric soils were profoundly higher than those in non-rhizospheric soils, suggesting that the inhibitive effect of PAHs on microbial activities was alleviated by the rice roots. The principal component analysis (PCA) of the PLFA signatures revealed pronounced changes in PLFA pattern in rhizospheric and non-rhizospheric soils with or without spiked PAHs. Using the PLFA patterns as a biomarker, it was found that Gram-positive bacteria were more sensitive to PAHs than Gram-negative bacteria, and the rhizosphere of rice roots stimulated the growth of aerobic bacteria.

  11. [Soil organic pollution characteristics and microbial properties in coal mining areas of Mentougou].

    Science.gov (United States)

    Jia, Jian-Li; Zhang, Yue; Wang, Chen; Li, Dong; Liu, Bo-Wen; Liu, Ying; Zhao, Le; Yang, Si-Qi

    2011-03-01

    Soil micro-ecosystem including organic pollution characteristics, basic physicochemical parameters, and microbial properties was analyzed which contaminated with organic pollutants in coal mining area. Results showed that the organic pollution level in coal mining area soils distributed from 0.4 to 1.5 mg/g dry soil, which was 1. 5-6 times as much as the background sample. Furthermore, the column chromatography and GC-MS analysis revealed that content of lightly components including saturated and aromatic hydrocarbons exceeded 40%, specifically was alkenes (> C15), hydrocarbon derivatives, and a small amount aromatic hydrocarbons. Totally, the components of organic pollutants extracted in soils were similar to which in coal gangue samples, illustrating the source of soil pollution to a certain extent in coal mining areas. The physicochemical factors such as nutrient level and moisture contents were not conducive to the growth and reproduction of microbe except pH level, which might show inhibition to microbial activities. Microbial density of pollutant soils in coal mining areas was totally low, with specific amount 10(4)-10(5) cell/g dry soil and FDA activity 2.0-2.9 mg/(g x min). Generally, the microbial density and activity were decreased as the enhancing pollution level. However, in-depth analysis was needed urgently because of the complex impact of environmental conditions like pH, moisture, and nutrition.

  12. Long-term application of winery wastewater - Effect on soil microbial populations and soil chemistry

    Science.gov (United States)

    Mosse, Kim; Patti, Antonio; Smernik, Ron; Cavagnaro, Timothy

    2010-05-01

    The ability to reuse winery wastewater (WWW) has potential benefits both with respect to treatment of a waste stream, as well as providing a beneficial water resource in water limited regions such as south-eastern Australia, California and South Africa. Over an extended time period, this practice leads to changes in soil chemistry, and potentially, also to soil microbial populations. In this study, we compared the short term effects of WWW (both treated and untreated) application on soil biology and chemistry in two adjacent paired sites with the same soil type, one of which had received WWW for approximately 30 years, and the other which had not. The paired sites were treated with an industrially relevant quantity of WWW, and the soil microbial activity (measured as soil CO2 efflux) and common soil physicochemical properties were monitored over a 16-day period. In addition, Solid State 13C NMR was employed on whole soil samples from the two sites, to measure and compare the chemical nature of the soil organic matter at the paired sites. The acclimatised soil showed a high level of organic matter and a greater spike in microbial activity following WWW addition, in comparison with the non-acclimatised soil, suggesting differences in soil chemistry and soil microbial communities between the two sites. Soil nitrate and phosphorus levels showed significant differences between WWW treatments; these differences likely to be microbially mediated.

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

    Science.gov (United States)

    Spohn, Marie; Chodak, Marcin

    2015-04-01

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

  14. Microbial Biofertilizer Decreases Nicotine Content by Improving Soil Nitrogen Supply.

    Science.gov (United States)

    Shang, Cui; Chen, Anwei; Chen, Guiqiu; Li, Huanke; Guan, Song; He, Jianmin

    2017-01-01

    Biofertilizers have been widely used in many countries for their benefit to soil biological and physicochemical properties. A new microbial biofertilizer containing Phanerochaete chrysosporium and Bacillus thuringiensis was prepared to decrease nicotine content in tobacco leaves by regulating soil nitrogen supply. Soil NO 3 - -N, NH 4 + -N, nitrogen supply-related enzyme activities, and nitrogen accumulation in plant leaves throughout the growing period were investigated to explore the mechanism of nicotine reduction. The experimental results indicated that biofertilizer can reduce the nicotine content in tobacco leaves, with a maximum decrement of 16-18 % in mature upper leaves. In the meantime, the total nitrogen in mature lower and middle leaves increased with the application of biofertilizer, while an opposite result was observed in upper leaves. Protein concentration in leaves had similar fluctuation to that of total nitrogen in response to biofertilizer. NO 3 - -N content and nitrate reductase activity in biofertilizer-amended soil increased by 92.3 and 42.2 %, respectively, compared to those in the control, whereas the NH 4 + -N and urease activity decreased by 37.8 and 29.3 %, respectively. Nitrogen uptake was improved in the early growing stage, but this phenomenon was not observed during the late growth period. Nicotine decrease is attributing to the adjustment of biofertilizer in soil nitrogen supply and its uptake in tobacco, which result in changes of nitrogen content as well as its distribution in tobacco leaves. The application of biofertilizer containing P. chrysosporium and B. thuringiensis can reduce the nicotine content and improve tobacco quality, which may provide some useful information for tobacco cultivation.

  15. Viral impacts on microbial carbon cycling in thawing permafrost soils

    Science.gov (United States)

    Trubl, G. G.; Roux, S.; Bolduc, B.; Jang, H. B.; Emerson, J. B.; Solonenko, N.; Li, F.; Solden, L. M.; Vik, D. R.; Wrighton, K. C.; Saleska, S. R.; Sullivan, M. B.; Rich, V. I.

    2017-12-01

    Permafrost contains 30-50% of global soil carbon (C) and is rapidly thawing. While the fate of this C is unknown, it will be shaped in part by microbes and their associated viruses, which modulate host activities via mortality and metabolic control. To date, viral research in soils has been outpaced by that in aquatic environments, due to the technical challenges of accessing viruses as well as the dramatic physicochemical heterogeneity in soils. Here, we describe advances in soil viromics from our research on permafrost-associated soils, and their implications for associated terrestrial C cycling. First, we optimized viral resuspension-DNA extraction methods for a range of soil types. Second, we applied cutting-edge viral-specific informatics methods to recover viral populations, define their gene content, connect them to potential hosts, and analyze their relationships to environmental parameters. A total of 781 viral populations were recovered from size-fractionated virus samples of three soils along a permafrost thaw gradient. Ecological analyses revealed endemism as recovered viral populations were largely unique to each habitat and unlike those in aquatic communities. Genome- and network-based classification assigned these viruses into 226 viral clusters (VCs; genus-level taxonomy), 55% of which were novel. This increases the number of VCs by a third and triples the number of soil viral populations in the RefSeq database (currently contains 256 VCs and 316 soil viral populations). Genomic analyses revealed 85% of the genes were functionally unknown, though 5% of the annotatable genes contained C-related auxiliary metabolic genes (AMGs; e.g. glycoside hydrolases). Using sequence-based features and microbial population genomes, we were able to in silico predict hosts for 30% of the viral populations. The identified hosts spanned 3 phyla and 6 genera but suggested these viruses have species-specific host ranges as >80% of hosts for a given virus were in the same

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

    Science.gov (United States)

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

    2015-01-01

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

  17. Permissiveness of soil microbial communities towards broad host range plasmids

    DEFF Research Database (Denmark)

    Klümper, Uli

    . Plasmids are implicated in the rapid spread of antibiotic resistance and the emergence of multi-resistant pathogenic bacteria, making it crucial to be able to quantify, understand, and, ideally, control plasmid transfer in mixed microbial communities. The fate of plasmids in microbial communities...... of microbial communities may be directly interconnected through transfer of BHR plasmids at a so far unrecognized level. The developed method furthermore enabled me to explore how agronomic practices may affect gene transfer in soil microbial communities. I compared bacterial communities extracted from plots...

  18. Habitat constraints on the functional significance of soil microbial communities

    Science.gov (United States)

    Nunan, Naoise; Leloup, Julie; Ruamps, Léo; Pouteau, Valérie; Chenu, Claire

    2017-04-01

    An underlying assumption of most ecosystem models is that soil microbial communities are functionally equivalent; in other words, that microbial activity under given set of conditions is not dependent on the composition or diversity of the communities. Although a number of studies have suggested that this assumption is incorrect, ecosystem models can adequately describe ecosystem processes, such as soil C dynamics, without an explicit description of microbial functioning. Here, we provide a mechanistic basis for reconciling this apparent discrepancy. In a reciprocal transplant experiment, we show that microbial communities are not always functionally equivalent. The data suggest that when the supply of substrate is restricted, then the functioning of different microbial communities cannot be distinguished, but when the supply is less restricted, the intrinsic functional differences among communities can be expressed. When the supply of C is restricted then C dynamics are related to the properties of the physical and chemical environment of the soil. We conclude that soil C dynamics may depend on microbial community structure or diversity in environments such as the rhizosphere or the litter layer, but are less likely to do so in oligotrophic environments such as the mineral layers of soil.

  19. Effects of uranium on soil microbial biomass carbon, enzymes, plant biomass and microbial diversity in yellow soils

    International Nuclear Information System (INIS)

    Yan, X.; Zhang, Y.; Luo, X.; Yu, L.

    2016-01-01

    We conducted an experiment to investigate the effects of uranium (U) on soil microbial biomass carbon (MBC), enzymes, plant biomass and microbial diversity in yellow soils under three concentrations: 0 mg kg"-"1 (T1, control), 30 mg kg"-"1 (T2) and 60 mg kg"-"1 (T3). Under each treatment, elevated U did not reduce soil MBC or plant biomass, but inhibited the activity of the soil enzymes urease (UR), dehydrogenase (DH) and phosphatase (PHO). The microbial diversity was different, with eight dominant phyla in T1 and six in T2 and T3. Furthermore, Proteobacteria and material X were both detected in each treatment site (T1, T2 and T3). Pseudomonas sp. was the dominant strain, followed by Acidiphilium sp. This initial study provided valuable data for further research toward a better understanding of U contamination in yellow soils in China. (authors)

  20. Integrating microbial diversity in soil carbon dynamic models parameters

    Science.gov (United States)

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

    2015-04-01

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

  1. Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau.

    Science.gov (United States)

    Zhang, Yuguang; Lu, Zhenmei; Liu, Shanshan; Yang, Yunfeng; He, Zhili; Ren, Zuohua; Zhou, Jizhong; Li, Diqiang

    2013-03-29

    GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes. High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were

  2. Overview: Microbial amendment of remediated soils for effective recycling

    Directory of Open Access Journals (Sweden)

    Kim Soo-Bin

    2017-01-01

    Full Text Available In recent years, various methods are being considered with appropriate amendments, not with conventional reclamation to recycle deteriorated soils after remediation as agricultural addition, backfilling and construction materials etc. Among these amendments, microbial amendments with effective microorganism(EMs are known to improve soil qualities such as fertility, strength and toxicity to be recycled into possible utilizations. This study indicates the possibility of recycling the remediated soils by using these EMs most efficiently. Soil samples will be collected from contaminated sites with either heavy metals or petroleum and will be remediated by bench-scale soil washing and thermal desorption. And then the remediated soils will be treated with easily obtainable inocula, substrates (culture media near our life and they are compared with commercial EM products in terms of the cost and efficiency. Also, after treating with a number of mixing ratios, soil properties of (1 fresh, (2 contaminated, (3 remediated (4 amended soils will be evaluated based on soil quality indicators depending on demands and the optimal mixing ratios which are effective than commercial EM products will be determined. The ratio derived from pre-tests could be applied on the remediated soils with pilot-scale in order to assess suitability for recycling and characterize correlation between soil properties and microbial amendments regarding contaminants and remediation, and furthermore for modelling. In conclusion, application of the established models on recycling remediated soils may help to dispose the remediated soils in future, including environmental and ecological values as well as economical values.

  3. Microbial ecology and biogeochemistry of continental Antarctic soils

    Directory of Open Access Journals (Sweden)

    Don A Cowan

    2014-04-01

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

  4. Microbial ecology and biogeochemistry of continental Antarctic soils.

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2017-08-01

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

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

    Science.gov (United States)

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

    2016-03-01

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

  8. Active microbial soil communities in different agricultural managements

    Science.gov (United States)

    Landi, S.; Pastorelli, R.

    2009-04-01

    We studied the composition of active eubacterial microflora by RNA extraction from soil (bulk and rhizosphere) under different environmental impact managements, in a hilly basin in Gallura (Sardinia). We contrasted grassy vineyard, in which the soil had been in continuous contact with plant roots for a long period of time, with traditional tilled vineyard. Moreover, we examined permanent grassland, in which plants had been present for some years, with temporary grassland, in which varying plants had been present only during the respective growing seasons. Molecular analysis of total population was carried out by electrophoretic separation by Denaturing Gradient Gel Electrophoresis (DGGE) of amplified cDNA fragments obtained from 16S rRNA. In vineyards UPGMA (Unweighted Pair Group Mathematical Average) analysis made up separate clusters depending on soil management. In spring both clusters showed similarity over 70%, while in autumn the similarity increased, 84% and 90% for grassy and conventional tilled vineyard respectively. Permanent and temporary grassland joined in a single cluster in spring, while in autumn a partial separation was evidenced. The grassy vineyard, permanent and temporary grassland showed higher richness and diversity Shannon-Weiner index values than vineyard with conventional tillage although no significant. In conclusion the expected effect of the rhizosphere was visible: the grass cover influenced positively the diversity of active microbial population.

  9. Response of soil microbial activities and microbial community structure to vanadium stress.

    Science.gov (United States)

    Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

    2017-08-01

    High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2016-03-01

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

  11. Long-Term Effects of Legacy Copper Contamination on Microbial Activity and Soil Physical Properties

    DEFF Research Database (Denmark)

    Arthur, Emmanuel; Møldrup, Per; Holmstrup, Martin

    Soils heavily contaminated with copper (Cu) are considered unsuitable for agricultural use due to adverse impacts on microbial activity, soil physical properties, and direct toxicity to crops. This study investigated effects of Cu pollution from timber preservation activities between 1911 and 1924...... on soil micro-organisms and subsequent effects on physical properties of a sandy loam soil. Tillage operations over the last 70 years have caused spreading of the initially localized contamination and have created a Cu concentration gradient from 20 to 3800 mg kg-1 across an agricultural field in Hygum......, Denmark. Soil samples obtained from the fallow field were used to determine total microbial activity using fluorescein diacetate and dehydrogenase assays. The physical properties measured included water-dispersible clay, bulk density, air permeability and air-filled porosity. Significant differences...

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

    Directory of Open Access Journals (Sweden)

    Zhuofei Xu

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

  13. Correlation between Soil Organic Matter, Total Organic Matter and ...

    African Journals Online (AJOL)

    A total of four sites distributed in different soils of Kelantan State, Malaysia was identified for the study. Soils were collected by depth interval of 0-10cm, 10-20cm and 20-30cm. The correlation of soil organic matter (SOM) content, total organic carbon (TOC) content, water content and soils texture for industrial area at ...

  14. Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER

    2005-01-01

    Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P < 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P < 0.05). There were also significant decreases (P < 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.

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

    Science.gov (United States)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2010-12-01

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

  18. Impact of repeated insecticide application on soil microbial activity

    International Nuclear Information System (INIS)

    Xu Bujin; Zhang Yongxi; Chen Meici; Zhu Nanwen; Ming Hong

    2001-01-01

    The effects of repeated insecticide application on soil microbial activity were studied both in a cotton field and in the laboratory. The results of experiment show that there are some effects on soil microbial activities, such as the population of soil microorganisms, soil respiration, dehydrogenase activity and nitrogen fixation. The degree of effects depends on the chemical dosage. Within the range of 0.5-10.0 μg/g air-dry-soil, the higher the concentration, the stronger effect. In this experiment, the effect disappeared within 4, 8 or 16 days after treatment, depending on the dose applied. In field conditions, the situation is more complex and the data of field experiment show greater fluctuation. (author)

  19. Seasonal Development of Microbial Activity in Soils of Northern Norway

    Institute of Scientific and Technical Information of China (English)

    M. B(O)LTER; N. SOETHE; R. HORN; C. UHLIG

    2005-01-01

    Seasonal development of soil microbial activity and bacterial biomass in sub-polar regions was investigated to determine the impacts of biotic and abiotic factors, such as organic matter content, temperature and moisture. The study was performed during spring thaw from three cultivated meadows and two non-cultivated forest sites near Alta, in northern Norway. Samples from all five sites showed increasing respiration rates directly after the spring thaw with soil respiration activity best related to soil organic matter content. However, distributions of bacterial biomass showed fewer similarities to these two parameters. This could be explained by variations of litter exploitation through the biomass. Microbial activity started immediately after the thaw while root growth had a longer time lag. An influence of root development on soil microbes was proposed for sites where microorganisms and roots had a tight relationship caused by a more intensive root structure. Also a reduction of microbial activity due to soil compaction in the samples from a wheel track could not be observed under laboratory conditions. New methodological approaches of differential staining for live and dead organisms were applied in order to follow changes within the microbial community. Under laboratory conditions freeze and thaw cycles showed a damaging influence on parts of the soil bacteria. Additionally, different patterns for active vs.non-active bacteria were noticeable after freeze-thaw cycles.

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

    Science.gov (United States)

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

    2008-08-15

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

  1. Long-term application of bioorganic fertilizers improved soil biochemical properties and microbial communities of an apple orchard soil

    Directory of Open Access Journals (Sweden)

    Wang Lei

    2016-11-01

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

  2. Microbial community composition affects soil fungistasis

    NARCIS (Netherlands)

    De Boer, W.; Verheggen, P.; Klein Gunnewiek, P.J.A.; Kowalchuk, G.A.; Van Veen, J.A.

    2003-01-01

    Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis)

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

    Science.gov (United States)

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

    2015-01-01

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

  4. Soil microbial community responses to antibiotic-contaminated manure under different soil moisture regimes.

    Science.gov (United States)

    Reichel, Rüdiger; Radl, Viviane; Rosendahl, Ingrid; Albert, Andreas; Amelung, Wulf; Schloter, Michael; Thiele-Bruhn, Sören

    2014-01-01

    Sulfadiazine (SDZ) is an antibiotic frequently administered to livestock, and it alters microbial communities when entering soils with animal manure, but understanding the interactions of these effects to the prevailing climatic regime has eluded researchers. A climatic factor that strongly controls microbial activity is soil moisture. Here, we hypothesized that the effects of SDZ on soil microbial communities will be modulated depending on the soil moisture conditions. To test this hypothesis, we performed a 49-day fully controlled climate chamber pot experiments with soil grown with Dactylis glomerata (L.). Manure-amended pots without or with SDZ contamination were incubated under a dynamic moisture regime (DMR) with repeated drying and rewetting changes of >20 % maximum water holding capacity (WHCmax) in comparison to a control moisture regime (CMR) at an average soil moisture of 38 % WHCmax. We then monitored changes in SDZ concentration as well as in the phenotypic phospholipid fatty acid and genotypic 16S rRNA gene fragment patterns of the microbial community after 7, 20, 27, 34, and 49 days of incubation. The results showed that strongly changing water supply made SDZ accessible to mild extraction in the short term. As a result, and despite rather small SDZ effects on community structures, the PLFA-derived microbial biomass was suppressed in the SDZ-contaminated DMR soils relative to the CMR ones, indicating that dynamic moisture changes accelerate the susceptibility of the soil microbial community to antibiotics.

  5. Soil structure and microbial activity dynamics in 20-month field-incubated organic-amended soils

    DEFF Research Database (Denmark)

    Arthur, Emmanuel; Schjønning, Per; Møldrup, Per

    2014-01-01

    to determine compressive strength. During incubation, the amount of WDC depended on soil carbon content while the trends correlated with moisture content. Organic amendment only yielded modest decreases (mean of 14% across all sampling times and soils) in WDC, but it was sufficient to stimulate the microbial......Soil structure formation is essential to all soil ecosystem functions and services. This study aims to quantify changes in soil structure and microbial activity during and after field incubation and examine the effect of carbon, organic amendment and clay on aggregate characteristics. Five soils...... community (65–100% increase in FDA). Incubation led to significant macroaggregate formation (>2 mm) for all soils. Friability and strength of newly-formed aggregates were negatively correlated with clay content and carbon content, respectively. Soil workability was best for the kaolinite-rich soil...

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

    Science.gov (United States)

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

    2016-12-01

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

  7. [Soil microbial community structure of two types of forests in the mid-subtropics of China].

    Science.gov (United States)

    Han, Shi-zhong; Gao, Ren; Li, Ai-ping; Ma, Hong-liang; Yin, Yun-feng; Si, You-tao; Chen, Shi-dong; Zheng, Qun-rui

    2015-07-01

    Soil microbial community structures were analyzed by biomarker method of phospholipid fatty acid (PLFA) for a natural forest dominated by Castanopsis fabri (CF) and an adjacent plantation of Cunninghamia lanceolata (CL) in the mid-subtropics of China. The results showed that the amounts of total PLFAs, bacterial PLFAs, fungal PLFAs, gram-positive bacterial PLFAs and gramnegative bacterial PLFAs in the 0-10 cm soil layer were higher than in the 10-20 cm soil layer, and each type of PLFAs in CF were higher than in CL. In either soil layer of the two forest types, the contents of bacterial PLFAs were significantly higher than those of fungal PLFAs. In the two forests, the contents of bacterial PLFAs accounted for 44%-52% of total PLFAs, while the contents of fungal PLFAs just accounted for 6%-8%, indicating the bacteria were dominant in the soils of the two vegetation types. Principal component analysis showed that the influence of vegetation types was greater than soil depth on the microbial community structures. Correlation analysis showed that gram-negative bacterial PLFAs, gram-positive bacterial PLFAs and bacterial PLFAs were significantly negatively correlated with pH, positively with water content, and the PLFAs of main soil microorganism groups were significantly positively correlated with soil total nitrogen, organic carbon, C/N and ammonium.

  8. Assessment of Soil Health in Urban Agriculture: Soil Enzymes and Microbial Properties

    Directory of Open Access Journals (Sweden)

    Avanthi Deshani Igalavithana

    2017-02-01

    Full Text Available Urban agriculture has been recently highlighted with the increased importance for recreation in modern society; however, soil quality and public health may not be guaranteed because of continuous exposure to various pollutants. The objective of this study was to evaluate the soil quality of urban agriculture by soil microbial assessments. Two independent variables, organic and inorganic fertilizers, were considered. The activities of soil enzymes including dehydrogenase, β-glucosidase, arylsulfatase, urease, alkaline and acid phosphatases were used as indicators of important microbial mediated functions and the soil chemical properties were measured in the soils applied with organic or inorganic fertilizer for 10 years. Fatty acid methyl ester analysis was applied to determine the soil microbial community composition. Relatively higher microbial community richness and enzyme activities were found in the organic fertilizers applied soils as compared to the inorganic fertilizers applied soils. Principal component analysis explained the positive influence of organic fertilizers on the microbial community. The application of organic fertilizers can be a better alternative compared to inorganic fertilizers for the long-term health and security of urban agriculture.

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

    Science.gov (United States)

    Mykhailova, Larysa; Fischer, Thomas; Iurchenko, Valentina

    2015-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Terence L. Marsh

    2004-05-26

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

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

    Science.gov (United States)

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

    2017-12-01

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

  12. Microbial degradation and impact of Bracken toxin ptaquiloside on microbial communities in soil

    DEFF Research Database (Denmark)

    Engel, Pernille; Brandt, Kristian Koefoed; Rasmussen, Lars Holm

    2007-01-01

    ), but not in the NZ soil (weak acid loamy Entisol). In the DK soil PTA turnover was predominantly due to microbial degradation (biodegradation); chemical hydrolysis was occurring mainly in the uppermost A horizon where pH was very low (3.4). Microbial activity (basal respiration) and growth ([3H]leucine incorporation...... assay) increased after PTA exposure, indicating that the Bracken toxin served as a C substrate for the organotrophic microorganisms. On the other hand, there was no apparent impact of PTA on community size as measured by substrate-induced respiration or composition as indicated by community......-level physiological profiles. Our results demonstrate that PTA stimulates microbial activity and that microorganisms play a predominant role for rapid PTA degradation in Bracken-impacted soils....

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

    Science.gov (United States)

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

    2013-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Darine Trabelsi

    2013-01-01

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

  15. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

    Science.gov (United States)

    Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

    2011-03-01

    To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

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

    Science.gov (United States)

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

    2016-05-01

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

  17. Response of soil microbial activity and biodiversity in soils polluted with different concentrations of cypermethrin insecticide.

    Science.gov (United States)

    Tejada, Manuel; García, Carlos; Hernández, Teresa; Gómez, Isidoro

    2015-07-01

    We performed a laboratory study into the effect of cypermethrin insecticide applied to different concentrations on biological properties in two soils [Typic Xerofluvent (soil A) and Xerollic Calciorthid (soil B)]. Two kg of each soil were polluted with cypermethrin at a rate of 60, 300, 600, and 1,200 g ha(-1) (C1, C2, C3, and C4 treatments). A nonpolluted soil was used as a control (C0 treatment). For all treatments and each experimental soil, soil dehydrogenase, urease, β-glucosidase, phosphatase, and arylsulphatase activities and soil microbial community were analysed by phospholipid fatty acids, which were measured at six incubation times (3, 7, 15, 30, 60, and 90 days). The behavior of the enzymatic activities and microbial population were dependent on the dose of insecticide applied to the soil. Compared with the C0 treatment, in soil A, the maximum inhibition of the enzymatic activities was at 15, 30, 45, and 90 days for the C1, C2, C3, and C4 treatments, respectively. However, in soil B, the maximum inhibition occurred at 7, 15, 30, and 45 days for the C1, C2, C3, and C4 treatments, respectively. These results suggest that the cypermethrin insecticide caused a negative effect on soil enzymatic activities and microbial diversity. This negative impact was greater when a greater dose of insecticide was used; this impact was also greater in soil with lower organic matter content. For both soils, and from these respective days onward, the enzymatic activities and microbial populations progressively increased by the end of the experimental period. This is possibly due to the fact that the insecticide or its breakdown products and killed microbial cells, subsequently killed by the insecticide, are being used as a source of energy or as a carbon source for the surviving microorganisms for cell proliferation.

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

    Science.gov (United States)

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

    2009-05-15

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

  19. Assessment of Cu applications in two contrasting soils-effects on soil microbial activity and the fungal community structure.

    Science.gov (United States)

    Keiblinger, Katharina M; Schneider, Martin; Gorfer, Markus; Paumann, Melanie; Deltedesco, Evi; Berger, Harald; Jöchlinger, Lisa; Mentler, Axel; Zechmeister-Boltenstern, Sophie; Soja, Gerhard; Zehetner, Franz

    2018-03-01

    Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community. Two contrasting agricultural soils, an acidic sandy loam and an alkaline silt loam, were used for an eco-toxicological greenhouse pot experiment. The soils were spiked with a Cu-based fungicide in seven concentrations (0-5000 mg Cu kg -1 soil) and alfalfa was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test Cu toxicity effects on total microbial biomass, basal respiration and enzyme activities. Fungal abundance was analysed by ergosterol at both samplings, and for the second sampling, fungal community structure was evaluated via ITS amplicon sequences. Soil microbial biomass C as well as microbial respiration rate decreased with increasing Cu concentrations, with EC 50 ranging from 76 to 187 mg EDTA-extractable Cu kg -1 soil. Oxidative enzymes showed a trend of increasing activity at the first sampling, but a decline in peroxidase activity was observed for the second sampling. We found remarkable Cu-induced changes in fungal community abundance (EC 50 ranging from 9.2 to 94 mg EDTA-extractable Cu kg -1 soil) and composition, but not in diversity. A large number of diverse fungi were able to thrive under elevated Cu concentrations, though within the order of Hypocreales several species declined. A remarkable Cu-induced change in the community composition was found, which depended on the soil properties and, hence, on Cu availability.

  20. Effects of litter addition and warming on soil carbon, nutrient pools and microbial communities in a subarctic heath ecosystem

    DEFF Research Database (Denmark)

    Rinnan, Riikka; Michelsen, Anders; Jonasson, Sven Evert

    2008-01-01

    in the uppermost 5 cm soil, while decreasing the pool of total P per unit area of the organic profile and having no significant effects on N concentrations or pools. Microbial biomass C and N were unaffected by the treatments, while the microbial biomass P increased significantly with litter addition. Soil...... proportion of biomarkers for Gram-positive bacteria. The combined warming plus litter addition treatment decreased the soil water content in the uppermost 5 cm soil, which was a likely reason for many interactions between the effects of warming and litter addition. The soil organic matter quality...... of the combined treatment was also clearly different from the control based on a near-infrared reflectance (NIR) spectroscopic analysis, implying that the treatment altered the composition of soil organic matter. However, it appears that the biological processes and the microbial community composition responded...

  1. Effect of monospecific and mixed sea-buckthorn (Hippophae rhamnoides plantations on the structure and activity of soil microbial communities.

    Directory of Open Access Journals (Sweden)

    Xuan Yu

    Full Text Available 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.

  2. Effects of different soil management practices on soil properties and microbial diversity

    Science.gov (United States)

    Gajda, Anna M.; Czyż, Ewa A.; Dexter, Anthony R.; Furtak, Karolina M.; Grządziel, Jarosław; Stanek-Tarkowska, Jadwiga

    2018-01-01

    The effects of different tillage systems on the properties and microbial diversity of an agricultural soil was investigated. In doing so, soil physical, chemical and biological properties were analysed in 2013-2015, on a long-term field experiment on a loamy sand at the IUNG-PIB Experimental Station in Grabów, Poland. Winter wheat was grown under two tillage treatments: conventional tillage using a mouldboard plough and traditional soil tillage equipment, and reduced tillage based on soil crushing-loosening equipment and a rigid-tine cultivator. Chopped wheat straw was used as a mulch on both treatments. Reduced tillage resulted in increased water content throughout the whole soil profile, in comparison with conventional tillage. Under reduced tillage, the content of readily dispersible clay was also reduced, and, therefore, soil stability was increased in the toplayers, compared with conventional tillage. In addition, the beneficial effects of reduced tillage were reflected in higher soil microbial activity as measured with dehydrogenases and hydrolysis of fluorescein diacetate, compared with conventional tillage. Moreover, the polimerase chain reaction - denaturing gradient gel electrophoresis analysis showed that soil under reduced till-age had greater diversity of microbial communities, compared with conventionally-tilled soil. Finally, reduced tillage increased organic matter content, stability in water and microbial diversity in the top layer of the soil.

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

    Science.gov (United States)

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

    2015-01-01

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

  4. Towards a methodology for removing and reconstructing soil protists with intact soil microbial communities

    Science.gov (United States)

    Hu, Junwei; Tsegaye Gebremikael, Mesfin; Salehi Hosseini, Pezhman; De Neve, Stefaan

    2017-04-01

    Soil ecological theories on the role of soil fauna groups in soil functions are often tested in highly artificial conditions, i.e. on completely sterilized soils or pure quartz sand re-inoculated with a small selection of these fauna groups. Due to the variable sensitivity of different soil biota groups to gamma irradiation, the precise doses that can be administered, and the relatively small disturbance of soil physical and chemical properties (relative to e.g. autoclaving, freezing-thawing and chemical agents), gamma irradiation has been employed to selectively eliminate soil organisms. In recent research we managed to realistically estimate on the contribution of the entire nematode communities to C and N mineralization in soil, by selective removal of nematodes at 5 kGy gamma irradiation doses followed by reinoculation. However, we did not assess the population dynamics of protozoa in response to this irradiation, i.e. we could not assess the potential contribution of protists to the mineralization process. Selective removal of protists from soils with minimal disturbance of the soil microflora has never been attempted and constitutes a highly challenging but potentially groundbreaking technique in soil ecology. Accordingly, the objective of this research is to modify the successful methodology of selective elimination of nematodes, to selectively eliminate soil fauna including nematodes and protists with minimal effects on the soil microbial community and reconstruct soil protists and microbial communities in completely sterilized soil. To this end, we here compared two different approaches: 1) remove nematodes and protists while keeping the microbial community intact (through optimizing gamma irradiation doses); 2) reconstruct protists and microbial communities in sterilized soil (through adding multicellular fauna free pulverized soil). The experiment consists of 7 treatments with soil collected from 0 to 15 cm layer of an organically managed agricultural

  5. The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil

    International Nuclear Information System (INIS)

    Kirk, Jennifer L.; Klironomos, John N.; Lee, Hung; Trevors, Jack T.

    2005-01-01

    Enhanced rhizosphere degradation uses plants to stimulate the rhizosphere microbial community to degrade organic contaminants. We measured changes in microbial communities caused by the addition of two species of plants in a soil contaminated with 31,000 ppm of total petroleum hydrocarbons. Perennial ryegrass and/or alfalfa increased the number of rhizosphere bacteria in the hydrocarbon-contaminated soil. These plants also increased the number of bacteria capable of petroleum degradation as estimated by the most probable number (MPN) method. Eco-Biolog plates did not detect changes in metabolic diversity between bulk and rhizosphere samples but denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified partial 16S rDNA sequences indicated a shift in the bacterial community in the rhizosphere samples. Dice coefficient matrices derived from DGGE profiles showed similarities between the rhizospheres of alfalfa and perennial ryegrass/alfalfa mixture in the contaminated soil at week seven. Perennial ryegrass and perennial ryegrass/alfalfa mixture caused the greatest change in the rhizosphere bacterial community as determined by DGGE analysis. We concluded that plants altered the microbial population; these changes were plant-specific and could contribute to degradation of petroleum hydrocarbons in contaminated soil. - Plant-specific changes in microbial populations on roots affect degradation of petroleum hydrocarbons in contaminated soil

  6. Chloride concentration affects soil microbial community

    Czech Academy of Sciences Publication Activity Database

    Gryndler, Milan; Rohlenová, Jana; Kopecký, Jan; Matucha, Miroslav

    2008-01-01

    Roč. 71, č. 7 (2008), s. 1401-1408 ISSN 0045-6535 R&D Projects: GA ČR GA526/05/0636 Institutional research plan: CEZ:AV0Z50200510; CEZ:AV0Z50380511 Keywords : soil chloride * terminal restriction fragments * soil microorganisms Subject RIV: EE - Microbiology, Virology Impact factor: 3.054, year: 2008

  7. Interactions between microbial-feeding and predatory soil fauna trigger N2O emissions

    NARCIS (Netherlands)

    Thakur, M.P.; Groenigen, van J.W.; Kuiper, I.; Deyn, de G.B.

    2014-01-01

    Recent research has shown that microbial-feeding invertebrate soil fauna species can significantly contribute to N2O emissions. However, in soil food webs microbial-feeding soil fauna interact with each other and with their predators, which affects microbial activity. To date we lack empirical tests

  8. Impact of simulated acid rain on soil microbial community function in Masson pine seedlings

    Directory of Open Access Journals (Sweden)

    Lin Wang

    2014-09-01

    Conclusion: The results obtained indicated that the higher acid load decreased the soil microbial activity and no effects on soil microbial diversity assessed by Biolog of potted Masson pine seedlings. Simulated acid rain also changed the metabolic capability of the soil microbial community.

  9. Soil microbial community of abandoned sand fields

    Czech Academy of Sciences Publication Activity Database

    Elhottová, Dana; Szili-Kovács, T.; Tříska, Jan

    2002-01-01

    Roč. 47, č. 4 (2002), s. 435-440 ISSN 0015-5632 R&D Projects: GA ČR GA526/99/P033 Grant - others:OTKA(HU) T25739 Institutional research plan: CEZ:AV0Z6066911 Keywords : microbial community * abandoned fields Subject RIV: EH - Ecology, Behaviour Impact factor: 0.979, year: 2002

  10. Measures of Microbial Biomass for Soil Carbon Decomposition Models

    Science.gov (United States)

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

    2014-12-01

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

  11. Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

    Science.gov (United States)

    Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

    2015-01-01

    The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession

  12. Soil microbial responses to nitrogen addition in arid ecosystems

    Directory of Open Access Journals (Sweden)

    Robert L Sinsabaugh

    2015-08-01

    Full Text Available The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts. We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg ha-1 yr-1 from March 2012 to March 2013. In March 2013, biocrust (0-0.5 cm and bulk soils (0-10 cm were collected beneath Ambrosia canopies and in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities (EEA and rates of N transformation. By most measures, nutrient availability, microbial biomass and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N.

  13. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

    Kaur, Rajwant; Kaur, Surinder

    2009-01-01

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

  15. Evaluation of soil microbial communities as influenced by crude oil ...

    African Journals Online (AJOL)

    Impact of petroleum pollution in a vulnerable Niger Delta ecosystem was investigated to assess interactions in a first-generation phytoremediation site of a crude oil freshly-spilled agricultural soil. Community-level approach for assessing patterns of sole carbon-source utilization by mixed microbial samples was employed to ...

  16. Effects of PAH-Contaminated Soil on Rhizosphere Microbial Communities

    DEFF Research Database (Denmark)

    Pritchina, Olga; Ely, Cairn; Smets, Barth F.

    2011-01-01

    Bacterial associations with plant roots are thought to contribute to the success of phytoremediation. We tested the effect of addition of a polycyclic aromatic hydrocarbon contaminated soil on the structure of the rhizosphere microbial communities of wheat (Triticum aestivum), lettuce (Lactuca...

  17. Microbial Genetic Memory to Study Heterogeneous Soil Processes

    Science.gov (United States)

    Fulk, E. M.; Silberg, J. J.; Masiello, C. A.

    2017-12-01

    Microbes can be engineered to sense environmental conditions and produce a detectable output. These microbial biosensors have traditionally used visual outputs that are difficult to detect in soil. However, recently developed gas-producing biosensors can be used to noninvasively monitor complex soil processes such as horizontal gene transfer or cell-cell signaling. While these biosensors report on the fraction of a microbial population exposed to a process or chemical signal at the time of measurement, they do not record a "memory" of past exposure. Synthetic biologists have recently developed a suite of genetically encoded memory circuits capable of reporting on historical exposure to the signal rather than just the current state. We will provide an overview of the microbial memory systems that may prove useful to studying microbial decision-making in response to environmental conditions. Simple memory circuits can give a yes/no report of any past exposure to the signal (for example anaerobic conditions, osmotic stress, or high nitrate concentrations). More complicated systems can report on the order of exposure of a population to multiple signals or the experiences of spatially distinct populations, such as those in root vs. bulk soil. We will report on proof-of-concept experiments showing the function of a simple permanent memory system in soil-cultured microbes, and we will highlight additional applications. Finally, we will discuss challenges still to be addressed in applying these memory circuits for biogeochemical studies.

  18. Soil Characteristics, Microbial Compostion of Plot, Leaf Count and ...

    African Journals Online (AJOL)

    Soil Characteristics, Microbial Compostion of Plot, Leaf Count and Sprout Studies of Cocoyam ( Colocasia [Schott] and Xanthosoma [Schott], Araceae) Collected in Edo State, ... Science, Technology and Arts Research Journal ... Government Areas (LGA) in Edo state and describe them based on leaf count and sprout

  19. Microbial conversion of hymexazol in soil

    International Nuclear Information System (INIS)

    Nakanishi, Toshiro; Takahi, Yukiyoshi; Tomita, Kazuo

    1974-01-01

    The metabolism of hymexazol (3-hydroxy-5-methylisoxazole) in soil was studied by using 14 C-labeled chemical ( 14 C-labeled at the 3 position on the isoxazole ring) to obtain fundamental information on its persistence in disease controlling activity and on residue analysis. Radioactive hymexazol was degraded in the unsterilized soil, and three radioactive metabolites were identified with carbon dioxide, acetoacetamide, and 5-methyl-2(3H)-oxazolone. The amount of 14 CO 2 evolved from radioactive hymexazol treated soil increased with time, whereas those of the other metabolites decreased. The breakdown of hymexazol in unsterilized soil is biological, since only a trace of 14 CO 2 was evolved from the sterilized soil. Production of 14 CO 2 was remarkable in submerged condition compared to that in moist one. The amount of 14 CO 2 evolved from radioactive hymexazol treated soil increased with increasing temperature levels from 15C to 35C. Hymexazol was also degraded to CO 2 , acetoacetamide, and 5-methyl-2(3H)-oxazolone in the soil infested with Bacillus subtilis, Streptomyces griseus, Aspergillus niger, Arthrinium sp., or Penicillium sp. A certain portion of hymexazol and/or its metabolites were so tightly adsorbed by the soil that it could not be removed by extraction with 1N HCl and subsequent elution with 1N NaOH or methanol. Since acetoacetamide and 5-methyl-2(3H)-oxazolone were found to be less effective than hymexazol against Fusarium wilt of cucumber, the metabolism of hymexazol in soil can be considered as a detoxication step. (auth.)

  20. Methane production potential and microbial community structure for different forest soils

    Science.gov (United States)

    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

  1. Arctic Tundra Soils: A Microbial Feast That Shrubs Will Cease

    Science.gov (United States)

    Machmuller, M.; Calderon, F.; Cotrufo, M. F.; Lynch, L.; Paul, E. A.; Wallenstein, M. D.

    2016-12-01

    Rapid climate warming may already be driving rapid decomposition of the vast stocks of carbon in Arctic tundra soils. However, stimulated decomposition may also release nitrogen and support increased plant productivity, potentially counteracting soil carbon losses. At the same time, these two processes interact, with plant derived carbon potentially fueling soil microbes to attack soil organic matter (SOM) to acquire nitrogen- a process known as priming. Thus, differences in the physiology, stoichiometry and microbial interactions among plant species could affect climate-carbon feedbacks. To reconcile these interactive mechanisms, we examined how vegetation type (Betula nana and Eriophorum vaginatum) and fertilization (short-term and long-term) influenced the decomposition of native SOM after labile carbon and nutrient addition. We hypothesized that labile carbon inputs would stimulate the loss of native SOM, but the magnitude of this effect would be indirectly related to soil nitrogen concentrations (e.g. SOM priming would be highest in N-limited soils). We added isotopically enriched (13C) glucose and ammonium nitrate to soils under shrub (B. nana) and tussock (E. vaginatum) vegetation. We found that nitrogen additions stimulated priming only in tussock soils, characterized by lower nutrient concentrations and microbial biomass (p20yrs. Rather, we found that long-term fertilization shifted SOM chemistry towards a greater abundance of recalcitrant SOM, lower microbial biomass, and decreased SOM respiration (p<0.05). Our results suggest that, in the short-term, the magnitude of SOM priming is dependent on vegetation and soil nitrogen concentrations, but this effect may not persist if shrubs increase in abundance under climate warming. Therefore, including nitrogen as a control on SOM decomposition and priming is critical to accurately model the effects of climate change on arctic carbon storage.

  2. Soil fauna communities and microbial respiration in high Arctic tundra soils at Zackenberg, Northeast Greenland

    DEFF Research Database (Denmark)

    Sørensen, Louise I.; Holmstrup, Martin; Maraldo, Kristine

    2006-01-01

    The soil fauna communities were described for three dominant vegetation types in a high arctic site at Zackenberg, Northeast Greenland. Soil samples were extracted to quantify the densities of mites, collembolans, enchytraeids, diptera larvae, nematodes and protozoa. Rates of microbial respiration...... densities (naked amoeba and heterotrophic flagellates) were equal. Respiration rate of unamended soil was similar in soil from the three plots. However, a higher respiration rate increase in carbon + nutrient amended soil and the higher densities of soil fauna (with the exception of mites and protozoa...

  3. Soil microbial respiration beneath Stipa tenacissima L. and in surrounding bare soil

    Directory of Open Access Journals (Sweden)

    Irena Novosádová

    2011-01-01

    Full Text Available Open steppes dominated by Stipa tenacissima L. constitute one of the most representative ecosystems of the semi-arid zones of Eastern Mediterranean Basin (Iberian Peninsula, North of Africa. Ecosystem functioning of these steppes is strongly related to the spatial pattern of grass tussocks. Soils beneath Stipa tenacissima L. grass show different fertility and different microclimatic conditions than in surrounding bare soil. The objective of this study was to assess the effect of Stipa tenacissima L. on the key soil microbial activities under controlled incubation conditions (basal and potential respiration. Basal and potential microbial respirations in the soils beneath Stipa tenacissima L. were, in general, not significantly different from the bare soils. The differences were less than 10%. Significantly less ethylene produced by microbial activity in soils beneath Stipa tenacissima L. after the addition of glucose could indicate the dependence of rhizospheric microbial communities on available carbon compounds. It can be concluded, that the soil respiration in semi-arid Mediterranean ecosystems is not necessarily associated with the patchy plant distribution and that some microbial activities characteristics can be unexpectedly homogenous.

  4. Correlations between soil microbial and physicochemical variations ...

    Indian Academy of Sciences (India)

    Prakash

    Changes in soil quality can be detected by observing community-level ... School of Environment, Resources and Development, Asian Institute of Technology,. Klong Luang .... version 3.3 (International Institute for Geo-Information. Science and ...

  5. Elevated atmospheric CO2 increases microbial growth rates and enzymes activity in soil

    Science.gov (United States)

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Dorodnikov, Maxim; Kuzyakov, Yakov

    2010-05-01

    Increasing the belowground translocation of assimilated carbon by plants grown under elevated CO2 can cause a shift in the structure and activity of the microbial community responsible for the turnover of organic matter in soil. We investigated the long-term effect of elevated CO2 in the atmosphere on microbial biomass and specific growth rates in root-free and rhizosphere soil. The experiments were conducted under two free air carbon dioxide enrichment (FACE) systems: in Hohenheim and Braunschweig, as well as in the intensively managed forest mesocosm of the Biosphere 2 Laboratory (B2L) in Oracle, AZ. Specific microbial growth rates (μ) were determined using the substrate-induced respiration response after glucose and/or yeast extract addition to the soil. We evaluated the effect of elevated CO2 on b-glucosidase, chitinase, phosphatase, and sulfatase to estimate the potential enzyme activity after soil amendment with glucose and nutrients. For B2L and both FACE systems, up to 58% higher μ were observed under elevated vs. ambient CO2, depending on site, plant species and N fertilization. The μ-values increased linearly with atmospheric CO2 concentration at all three sites. The effect of elevated CO2 on rhizosphere microorganisms was plant dependent and increased for: Brassica napus=Triticum aestivumyeast extract then for those growing on glucose, i.e. the effect of elevated CO2 was smoothed on rich vs. simple substrate. So, the r/K strategies ratio can be better revealed by studying growth on simple (glucose) than on rich substrate mixtures (yeast extract). After adding glucose, enzyme activities under elevated CO2 were 1.2-1.9-fold higher than under ambient CO2. This indicates the increased activity of microorganisms, which leads to accelerated C turnover in soil under elevated CO2. Our results clearly showed that the functional characteristics of the soil microbial community (i.e. specific growth rates and enzymes activity) rather than total microbial biomass

  6. Resistance and Resilience of Soil Microbial Communities Exposed to Petroleum-Derived Compounds

    DEFF Research Database (Denmark)

    Modrzynski, Jakub Jan

    Functioning of soil microbial communities is generally considered resilient to disturbance, including chemical stress. Activities of soil microbial communities are often sustained in polluted environments due to exceptional plasticity of microbial communities and functional redundancy. Pollution......-induced community tolerance (PICT) often develops following chemical stress. Nonetheless, environmental pollution may severely disturb functioning of soil microbial communities, thereby threatening provision of important ecosystem services provided by microorganisms. Pollution with petroleum and petroleum......-derived compounds (PDCs) is a significant environmental problem on a global scale. Research addressing interactions between microorganisms and PDC pollution is dominated by studies of biodegradation, with less emphasis on microbial ecotoxicology. Soil microbial communities are generally considered highly resilient...

  7. Soil fauna communities and microbial respiration in high Arctic tundra soils at Zackenberg, Northeast Greenland

    DEFF Research Database (Denmark)

    Sørensen, Louise I.; Holmstrup, Martin; Maraldo, Kristine

    2006-01-01

    The soil fauna communities were described for three dominant vegetation types in a high arctic site at Zackenberg, Northeast Greenland. Soil samples were extracted to quantify the densities of mites, collembolans, enchytraeids, diptera larvae, nematodes and protozoa. Rates of microbial respiration...... densities (naked amoeba and heterotrophic flagellates) were equal. Respiration rate of unamended soil was similar in soil from the three plots. However, a higher respiration rate increase in carbon + nutrient amended soil and the higher densities of soil fauna (with the exception of mites and protozoa...... were also assessed. Collembolans were found in highest densities in dry heath soil, about 130,000 individuals m-2, more than twice as high as in mesic heath soils. Enchytraeids, diptera larvae and nematodes were also more abundant in the dry heath soil than in mesic heath soils, whereas protozoan...

  8. The effect of the herbicide diuron on soil microbial activity.

    Science.gov (United States)

    Prado, A G; Airoldi, C

    2001-07-01

    The inhibitory effect of the herbicide diuron [3-(3,4-dichlorophenyl)-1,1-dimethylurea] on microbial activity in red Latosol soil was followed using microcalorimetry. The activity of the micro-organisms in 1.50 g of soil sample was stimulated by addition of 6.0 mg of glucose and 6.0 mg of ammonium sulfate under 35% controlled humidity at 298.15 (+/- 0.02) K. This activity was determined by power-time curves that were recorded for increasing amounts of diuron, varying from zero to 333.33 micrograms g-1 soil. An increase in the amount of diuron in soil caused a decrease of the original thermal effect, to reach a null value above 333.33 micrograms g-1 of herbicide. The power-time curve showed that the lag-phase period and peak time increased with added herbicide. The decrease of the thermal effect evolved by micro-organisms and the increase of the lag-phase period are associated with the death of microbial populations caused by diuron, which strongly affects soil microbial communities.

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

    Science.gov (United States)

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

    2014-03-06

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

  10. Microbial activity in Alaskan taiga soils contaminated by crude oil in 1976

    International Nuclear Information System (INIS)

    Monroe, E.M.; Lindstrom, J.E.; Brown, E.J.; Raddock, J.F.

    1995-01-01

    Biodegradation, often measured via microbial activity, includes destruction of environmental pollutants by living microorganisms and is dependent upon many physical and chemical factors. Effects of mineral nutrients and organic matter on biodegradation of Prudhoe Bay crude oil were investigated at a nineteen-year-old oil spill site in Alaskan taiga. Microcosms of two different soil types from the spill site; one undeveloped soil with forest litter and detritus (O horizon) and one more developed with lower organic content (A horizon), were treated with various nitrogen and phosphorus amendments, and incubated for up to six weeks. Each microcosm was sampled periodically and assayed for hydrocarbon mineralization potential using radiorespirometry, for total carbon dioxide respired using gas chromatography, and for numbers of hydrocarbon-degrading bacteria and heterotrophic bacteria using most probable number counting techniques. Organic matter in the O horizon soil along with combinations of mineral nutrients were found to stimulate microbial activity. No combination of mineral nutrient additions to the A horizon soil stimulated any of the parameters above those measured in control microcosms. The results of this study indicate that adding mineral nutrients and tilling the O horizon into the A horizon of subarctic soils contaminated with crude oil, would stimulate microbial activity, and therefore the biodegradation potential, ultimately increasing the rate of destruction of crude oil in these soils

  11. Microbial assemblages in soil microbial succession after glacial retreat in Svalbard (High Arctic)

    Czech Academy of Sciences Publication Activity Database

    Kaštovská, Klára; Elster, Josef; Stibal, Marek; Šantrůčková, H.

    2005-01-01

    Roč. 50, č. 3 (2005), s. 396-407 ISSN 0095-3628 Institutional research plan: CEZ:AV0Z6005908 Keywords : microbial assemblages * deglaciated soil * Svalbard Subject RIV: EF - Botanics Impact factor: 2.674, year: 2005

  12. Assessment of tillage systems in organic farming: influence of soil structure on microbial biomass. First results

    OpenAIRE

    Vian, Jean François; Peigné, Joséphine; Chaussod, Rémi; Roger-Estrade, Jean

    2007-01-01

    Soil tillage modifies environmental conditions of soil microorganisms and their ability to release nitrogen. We compare the influence of reduced tillage (RT) and mouldboard ploughing (MP) on the soil microbial functioning in organic farming. In order to connect soil structure generated by these tillage systems on the soil microbial biomass we adopt a particular sampling scheme based on the morphological characterisation of the soil structure by the description of the soil profile. This method...

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

    Science.gov (United States)

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

    2018-06-01

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

  14. Influence of soil zinc concentrations on zinc sensitivity and functional diversity of microbial communities

    International Nuclear Information System (INIS)

    Lock, K.; Janssen, C.R.

    2005-01-01

    Pollution induced community tolerance (PICT) is based on the phenomenon that toxic effects reduce survival of the most sensitive organisms, thus increasing community tolerance. Community tolerance for a contaminant is thus a strong indicator for the presence of that contaminant at the level of adverse concentrations. Here we assessed PICT in 11 soils contaminated with zinc runoff from galvanised electricity pylons and 11 reference soils sampled at 10 m distance from these pylons. Using PICT, the influence of background concentration and bioavailability of zinc on zinc sensitivity and functional diversity of microbial communities was assessed. Zinc sensitivity of microbial communities decreased significantly with increasing zinc concentrations in pore water and calcium chloride extracted fraction while no significant relationship was found with total zinc concentration in the soil. It was also found that functional diversity of microbial communities decreased with increasing zinc concentrations, indicating that increased tolerance is indeed an undesirable phenomenon when environmental quality is considered. The hypothesis that zinc sensitivity of microbial communities is related to background zinc concentration in pore water could not be confirmed. - Zinc sensitivity of microbial communities and functional diversity decrease with increasing zinc concentration in the pore water

  15. Soil inoculation with microbial communities - can this become a useful tool in soil remediation?

    Science.gov (United States)

    Krug, Angelika; Wang, Fang; Dörfler, Ulrike; Munch, Jean Charles; Schroll, Reiner

    2010-05-01

    We artificially loaded different type of agricultural soils with model 14C-labelled chemicals, and we inoculated such soils with different microbial communities as well as isolated strains to enhance the mineralization of such chemicals. Inocula were introduced by different approaches: (i) soil inocula, (ii) application of isolated strain as well as microbial community via media, (iii) isolated strain as well as microbial community attached to a carrier material. Most of the inoculation experiments were conducted in laboratory but we also tested one of these approaches under real environmental conditions in lysimeters and we could show that the approach was successful. We already could show that inoculating soils with microbial communities attached on a specific carrier material shows the highest mineralization effectiveness and also the highest sustainability. Microbes attached on clay particles preserved their function over a long time period even if the specific microbial substrate was already degraded or at least not detectable any more. Additionally we already could show that in specific cases some soil parameters might reduce the effectiveness of such an approach. Results on isoproturon as a model for phenylurea-herbicides and 1,2,4-trichlorobenzene as an example for an industrially used chemical as well as the corresponding chemicals` degrading microbial communities and isolated strain will be presented.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

  18. Microbial control on decomposition of radionuclides-containing oily waste in soil

    Science.gov (United States)

    Selivanovskaya, Svetlana; Galitskaya, Polina

    2014-05-01

    The oily wastes are formed annually during extraction, refinement, and transportation of the oil and may cause pollution of the environment. These wastes contain different concentrations of waste oil (40-60%), waste water (30-90%), and mineral particles (5-40%). Some oily wastes also contain naturally occurring radionuclides which were incorporated by water that was pumped up with the oil. For assessment of the hazard level of waste treated soil, not only measurements of contaminants content are needed, because bioavailability of oily components varies with hydrocarbon type, and soil properties. As far as namely microbial communities control the decomposition of organic contaminants, biological indicators have become increasingly important in hazard assessment and the efficiency of remediation process. In this study the decomposition of radionuclides-containing oily waste by soil microbial communities were estimated. Waste samples collected at the Tikchonovskii petroleum production yard (Tatarstan, Russia) were mixed with Haplic greyzem soil at ratio 1:4 and incubated for 120 days. During incubation period, the total hydrocarbon content of the soil mixed with the waste reduced from 156 ± 48 g kg-1 to 54 ± 8 g kg-1 of soil. The concentrations of 226Ra and 232Th were found to be 643 ± 127, 254 ± 56 Bq kg-1 and not changed significantly during incubation. Waste application led to a soil microbial biomass carbon decrease in comparison to control (1.9 times after 1 day and 1.3 times after 120 days of incubation). Microbial respiration increased in the first month of incubation (up to 120% and 160% of control after 1 and 30 days, correspondingly) and decreased to the end of incubation period (74% of control after 120 days). Structure of bacterial community in soil and soil/waste mixture was estimated after 120 days of incubation using SSCP method. The band number decreased in contaminated soil in comparison to untreated soil. Besides, several new dominant DNA

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

    Science.gov (United States)

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

    2013-01-01

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

  20. Rain-induced changes in soil CO2 flux and microbial community composition in a tropical forest of China.

    Science.gov (United States)

    Deng, Qi; Hui, Dafeng; Chu, Guowei; Han, Xi; Zhang, Quanfa

    2017-07-17

    Rain-induced soil CO 2 pulse, a rapid excitation in soil CO 2 flux after rain, is ubiquitously observed in terrestrial ecosystems, yet the underlying mechanisms in tropical forests are still not clear. We conducted a rain simulation experiment to quantify rain-induced changes in soil CO 2 flux and microbial community composition in a tropical forest. Soil CO 2 flux rapidly increased by ~83% after rains, accompanied by increases in both bacterial (~51%) and fungal (~58%) Phospholipid Fatty Acids (PLFA) biomass. However, soil CO 2 flux and microbial community in the plots without litters showed limited response to rains. Direct releases of CO 2 from litter layer only accounted for ~19% increases in soil CO 2 flux, suggesting that the leaching of dissolved organic carbon (DOC) from litter layer to the topsoil is the major cause of rain-induced soil CO 2 pulse. In addition, rain-induced changes in soil CO 2 flux and microbial PLFA biomass decreased with increasing rain sizes, but they were positively correlated with litter-leached DOC concentration rather than total DOC flux. Our findings reveal an important role of litter-leached DOC input in regulating rain-induced soil CO 2 pulses and microbial community composition, and may have significant implications for CO 2 losses from tropical forest soils under future rainfall changes.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Karolina Oszust

    2014-06-01

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

  3. Microbial degradation of metalaxyl in soil

    International Nuclear Information System (INIS)

    Musumeci, M.R.; Ruegg, E.F.

    1984-01-01

    The behaviour of the fungicide metalaxyl in purple latosol soil was investigated using a ring - 14 C labelled compound under laboratory conditions. In nonsterile soil samples under aerobic conditions, metalaxyl was degrated into two metabolites. After 60 days, 60% of the radiocarbon on TLC plates corresponded to the parent fungicide, 22% to its metabolite N-(2-methoxyacetyl)-N-(2,6-xylyl)-DL-alanine, and 2.7% to a second and unidentified metabolite. The U.V. absorbance value of metalaxyl decreased after seven days incubation with a soil microorganisms suspension. Incubation of 14 C-metalaxyl for 50 days with a bacterium or a fungus isolated from that suspension resulted in metalaxyl gradual disappearance from the medium, but not metabolites were detected during this period. (Author) [pt

  4. Microbial degradation of metalaxyl in soil

    Energy Technology Data Exchange (ETDEWEB)

    Musumeci, M.R.; Ruegg, E.F. (Instituto Biologico, Sao Paulo (Brazil). Centro de Radioisotopos)

    1984-10-01

    The behaviour of the fungicide metalaxyl in purple latosol soil was investigated using a ring - /sup 14/C labelled compound under laboratory conditions. In nonsterile soil samples under aerobic conditions, metalaxyl was degraded into two metabolites. After 60 days, 60% of the radiocarbon on TLC plates corresponded to the parent fungicide, 22% to its metabolite N-(2-methoxyacetyl)-N-(2,6-xylyl)-DL-alanine, and 2.7% to a second and unidentified metabolite. The U.V. absorbance value of metalaxyl decreased after seven days incubation with a soil microorganisms suspension. Incubation of /sup 14/C-metalaxyl for 50 days with a bacterium or a fungus isolated from that suspension resulted in metalaxyl gradual disappearance from the medium, but not metabolites were detected during this period.

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

    Science.gov (United States)

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

    2016-06-01

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

  6. Soil Temperature and Moisture Effects on Soil Respiration and Microbial Community Abundance

    Science.gov (United States)

    2015-04-13

    Bárcenas-Moreno, G., M. Gómez-Brandón, J. Rousk, and E. Bååth. 2009. Adaptation of soil microbial communities to temperature: Comparison of fungi and...ER D C/ CR RE L TR -1 5- 6 ERDC 6.2 Geospatial Research and Engineering (GRE) ARTEMIS TSP-SA Soil Temperature and Moisture Effects on... Soil Respiration and Microbial Community Abundance Co ld R eg io ns R es ea rc h an d En gi ne er in g La bo ra to ry Robyn A. Barbato

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

    Science.gov (United States)

    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

  8. Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities

    NARCIS (Netherlands)

    Epelde, L.; Becerril, J.M.; Kowalchuk, G.A.; Deng, Y.; Zhou, J.N.; Garbisu, C.

    2010-01-01

    Soil microorganisms drive critical functions in plant-soil systems. As such, various microbial properties have been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses

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

    Science.gov (United States)

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

    2016-04-01

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

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

    Science.gov (United States)

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

    2010-05-01

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

  11. Effects of forest conversion on soil microbial communities depend on soil layer on the eastern Tibetan Plateau of China.

    Directory of Open Access Journals (Sweden)

    Ruoyang He

    Full Text Available Forest land-use changes have long been suggested to profoundly affect soil microbial communities. However, how forest type conversion influences soil microbial properties remains unclear in Tibetan boreal forests. The aim of this study was to explore variations of soil microbial profiles in the surface organic layer and subsurface mineral soil among three contrasting forests (natural coniferous forest, NF; secondary birch forest, SF and spruce plantation, PT. Soil microbial biomass, activity and community structure of the two layers were investigated by chloroform fumigation, substrate respiration and phospholipid fatty acid analysis (PLFA, respectively. In the organic layer, both NF and SF exhibited higher soil nutrient levels (carbon, nitrogen and phosphorus, microbial biomass carbon and nitrogen, microbial respiration, PLFA contents as compared to PT. However, the measured parameters in the mineral soils often did not differ following forest type conversion. Irrespective of forest types, the microbial indexes generally were greater in the organic layer than in the mineral soil. PLFAs biomarkers were significantly correlated with soil substrate pools. Taken together, forest land-use change remarkably altered microbial community in the organic layer but often did not affect them in the mineral soil. The microbial responses to forest land-use change depend on soil layer, with organic horizons being more sensitive to forest conversion.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2014-01-01

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

  14. Estimating Soil Bulk Density and Total Nitrogen from Catchment ...

    African Journals Online (AJOL)

    Even though data on soil bulk density (BD) and total nitrogen (TN) are essential for planning modern farming techniques, their data availability is limited for many applications in the developing word. This study is designed to estimate BD and TN from soil properties, land-use systems, soil types and landforms in the ...

  15. Microbial Diversity in Cerrado Biome (Neotropical Savanna Soils.

    Directory of Open Access Journals (Sweden)

    Alinne Pereira de Castro

    Full Text Available The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture.

  16. Effect of Soil Amendments on Microbial Resilience Capacity of Acid Soil Under Copper Stress.

    Science.gov (United States)

    Mounissamy, Vassanda Coumar; Kundu, Samaresh; Selladurai, Rajendiran; Saha, Jayanta Kumar; Biswas, Ashish Kumar; Adhikari, Tapan; Patra, Ashok Kumar

    2017-11-01

    An incubation study was undertaken to study microbial resilience capacity of acid soil amended with farmyard manure (FYM), charcoal and lime under copper (Cu) perturbation. Copper stress significantly reduced enzymatic activities and microbial biomass carbon (MBC) in soil. Percent reduction in microbial activity of soil due to Cu stress was 74.7% in dehydrogenase activity, 59.9% in MBC, 48.2% in alkaline phosphatase activity and 15.1% in acid phosphatase activity. Soil treated with FYM + charcoal showed highest resistance index for enzymatic activities and MBC. Similarly, the highest resilience index for acid phosphatase activity was observed in soil amended with FYM (0.40), whereas FYM + charcoal-treated soil showed the highest resilience indices for alkaline, dehydrogenase activity and MBC: 0.50, 0.22 and 0.25, respectively. This investigation showed that FYM and charcoal application, either alone or in combination, proved to be better than lime with respect to microbial functional resistance and resilience of acid soil under Cu perturbation.

  17. Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

    Science.gov (United States)

    Dey, Samrat; Tribedi, Prosun

    2018-03-01

    Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both

  18. Profile Changes in the Soil Microbial Community When Desert Becomes Oasis.

    Directory of Open Access Journals (Sweden)

    Chen-hua Li

    Full Text Available The conversion of virgin desert into oasis farmland creates two contrasting types of land-cover. During oasis formation with irrigation and fertilizer application, however, the changes in the soil microbial population, which play critical roles in the ecosystem, remain poorly understood. We applied high-throughput pyrosequencing to investigate bacterial and archaeal communities throughout the profile (0-3 m in an experimental field, where irrigation and fertilization began in 1990 and cropped with winter wheat since then. To assess the effects of cultivation, the following treatments were compared with the virgin desert: CK (no fertilizer, PK, NK, NP, NPK, NPKR, and NPKM (R: straw residue; M: manure fertilizer. Irrigation had a greater impact on the overall microbial community than fertilizer application. The greatest impact occurred in topsoil (0-0.2 m, e.g., Cyanobacteria (25% total abundance were most abundant in desert soil, while Actinobacteria (26% were most abundant in oasis soil. The proportions of extremophilic and photosynthetic groups (e.g., Deinococcus-Thermus and Cyanobacteria decreased, while the proportions of R-strategy (e.g., Gammaproteobacteria including Xanthomonadales, nitrifying (e.g., Nitrospirae, and anaerobic bacteria (e.g., Anaerolineae increased throughout the oasis profile. Archaea occurred only in oasis soil. The impact of fertilizer application was mainly reflected in the non-dominant communities or finer taxonomic divisions. Oasis formation led to a dramatic shift in microbial community and enhanced soil enzyme activities. The rapidly increased soil moisture and decreased salt caused by irrigation were responsible for this shift. Furthermore, difference in fertilization and crop growth altered the organic carbon contents in the soil, which resulted in differences of microbial communities within oasis.

  19. Biochemical and microbial soil functioning after application of the insecticide imidacloprid.

    Science.gov (United States)

    Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2015-01-01

    Imidacloprid is one of the most commonly used insecticides in agricultural practice, and its application poses a potential risk for soil microorganisms. The objective of this study was to assess whether changes in the structure of the soil microbial community after imidacloprid application at the field rate (FR, 1mg/kg soil) and 10 times the FR (10× FR, 10mg/kg soil) may also have an impact on biochemical and microbial soil functioning. The obtained data showed a negative effect by imidacloprid applied at the FR dosage for substrate-induced respiration (SIR), the number of total bacteria, dehydrogenase (DHA), both phosphatases (PHOS-H and PHOS-OH), and urease (URE) at the beginning of the experiment. In 10× FR treated soil, decreased activity of SIR, DHA, PHOS-OH and PHOS-H was observed over the experimental period. Nitrifying and N2-fixing bacteria were the most sensitive to imidacloprid. The concentration of NO3(-) decreased in both imidacloprid-treated soils, whereas the concentration of NH4(+) in soil with 10× FR was higher than in the control. Analysis of the bacterial growth strategy revealed that imidacloprid affected the r- or K-type bacterial classes as indicated also by the decreased eco-physiological (EP) index. Imidacloprid affected the physiological state of culturable bacteria and caused a reduction in the rate of colony formation as well as a prolonged time for growth. Principal component analysis showed that imidacloprid application significantly shifted the measured parameters, and the application of imidacloprid may pose a potential risk to the biochemical and microbial activity of soils. Copyright © 2014. Published by Elsevier B.V.

  20. Engineering soil organic matter quality: Biodiesel Co-Product (BCP) stimulates exudation of nitrogenous microbial biopolymers

    Science.gov (United States)

    Redmile-Gordon, Marc A.; Evershed, Richard P.; Kuhl, Alison; Armenise, Elena; White, Rodger P.; Hirsch, Penny R.; Goulding, Keith W.T.; Brookes, Philip C.

    2015-01-01

    Biodiesel Co-Product (BCP) is a complex organic material formed during the transesterification of lipids. We investigated the effect of BCP on the extracellular microbial matrix or ‘extracellular polymeric substance’ (EPS) in soil which is suspected to be a highly influential fraction of soil organic matter (SOM). It was hypothesised that more N would be transferred to EPS in soil given BCP compared to soil given glycerol. An arable soil was amended with BCP produced from either 1) waste vegetable oils or 2) pure oilseed rape oil, and compared with soil amended with 99% pure glycerol; all were provided with 15N labelled KNO3. We compared transfer of microbially assimilated 15N into the extracellular amino acid pool, and measured concomitant production of exopolysaccharide. Following incubation, the 15N enrichment of total hydrolysable amino acids (THAAs) indicated that intracellular anabolic products had incorporated the labelled N primarily as glutamine and glutamate. A greater proportion of the amino acids in EPS were found to contain 15N than those in the THAA pool, indicating that the increase in EPS was comprised of bioproducts synthesised de novo. Moreover, BCP had increased the EPS production efficiency of the soil microbial community (μg EPS per unit ATP) up to approximately double that of glycerol, and caused transfer of 21% more 15N from soil solution into EPS-amino acids. Given the suspected value of EPS in agricultural soils, the use of BCP to stimulate exudation is an interesting tool to consider in the theme of delivering sustainable intensification. PMID:26635420

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

    Science.gov (United States)

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

    2014-12-01

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

  2. The influence of soil organic carbon on interactions between microbial parameters and metal concentrations at a long-term contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Muhlbachova, G. [Crop Research Institute, Drnovska 507, 161 06 Prague 6, Ruzyne (Czech Republic); Sagova-Mareckova, M., E-mail: sagova@vurv.cz [Crop Research Institute, Drnovska 507, 161 06 Prague 6, Ruzyne (Czech Republic); Omelka, M. [Charles University, Faculty of Mathematics and Physics, Dept. of Probability and Mathematical Statistics, Prague 8, Karlin (Czech Republic); Szakova, J.; Tlustos, P. [Czech University of Life Sciences, Department of Agroenvironmental Chemistry and Plant Nutrition, Prague 6, Suchdol (Czech Republic)

    2015-01-01

    The effects of lead, zinc, cadmium, arsenic and copper deposits on soil microbial parameters were investigated at a site exposed to contamination for over 200 years. Soil samples were collected in triplicates at 121 sites differing in contamination and soil organic carbon (SOC). Microbial biomass, respiration, dehydrogenase activity and metabolic quotient were determined and correlated with total and extractable metal concentrations in soil. The goal was to analyze complex interactions between toxic metals and microbial parameters by assessing the effect of soil organic carbon in the relationships. The effect of SOC was significant in all interactions and changed the correlations between microbial parameters and metal fractions from negative to positive. In some cases, the effect of SOC was combined with that of clay and soil pH. In the final analysis, dehydrogenase activity was negatively correlated to total metal concentrations and acetic acid extractable metals, respiration and metabolic quotient were to ammonium nitrate extractable metals. Dehydrogenase activity was the most sensitive microbial parameter correlating most frequently with contamination. Total and extractable zinc was most often correlated with microbial parameters. The large data set enabled robust explanation of discrepancies in organic matter functioning occurring frequently in analyzing of contaminated soil processes. - Highlights: • Soil organic carbon affected all interactions between metals and microorganisms. • Soil organic carbon adjustment changed correlations from positive to negative. • Ammonium nitrate extractable metals were the most influencing fraction. • Dehydrogenase activity was the most affected soil parameter. • Zinc was the most toxic metal among studied metals.

  3. The influence of soil organic carbon on interactions between microbial parameters and metal concentrations at a long-term contaminated site

    International Nuclear Information System (INIS)

    Muhlbachova, G.; Sagova-Mareckova, M.; Omelka, M.; Szakova, J.; Tlustos, P.

    2015-01-01

    The effects of lead, zinc, cadmium, arsenic and copper deposits on soil microbial parameters were investigated at a site exposed to contamination for over 200 years. Soil samples were collected in triplicates at 121 sites differing in contamination and soil organic carbon (SOC). Microbial biomass, respiration, dehydrogenase activity and metabolic quotient were determined and correlated with total and extractable metal concentrations in soil. The goal was to analyze complex interactions between toxic metals and microbial parameters by assessing the effect of soil organic carbon in the relationships. The effect of SOC was significant in all interactions and changed the correlations between microbial parameters and metal fractions from negative to positive. In some cases, the effect of SOC was combined with that of clay and soil pH. In the final analysis, dehydrogenase activity was negatively correlated to total metal concentrations and acetic acid extractable metals, respiration and metabolic quotient were to ammonium nitrate extractable metals. Dehydrogenase activity was the most sensitive microbial parameter correlating most frequently with contamination. Total and extractable zinc was most often correlated with microbial parameters. The large data set enabled robust explanation of discrepancies in organic matter functioning occurring frequently in analyzing of contaminated soil processes. - Highlights: • Soil organic carbon affected all interactions between metals and microorganisms. • Soil organic carbon adjustment changed correlations from positive to negative. • Ammonium nitrate extractable metals were the most influencing fraction. • Dehydrogenase activity was the most affected soil parameter. • Zinc was the most toxic metal among studied metals

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

    Science.gov (United States)

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

    2014-09-15

    There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils.

    Science.gov (United States)

    Wagner, Robert; Zona, Donatella; Oechel, Walter; Lipson, David

    2017-08-01

    While there is no doubt that biogenic methane production in the Arctic is an important aspect of global methane emissions, the relative roles of microbial community characteristics and soil environmental conditions in controlling Arctic methane emissions remains uncertain. Here, relevant methane-cycling microbial groups were investigated at two remote Arctic sites with respect to soil potential methane production (PMP). Percent abundances of methanogens and iron-reducing bacteria correlated with increased PMP, while methanotrophs correlated with decreased PMP. Interestingly, α-diversity of the methanogens was positively correlated with PMP, while β-diversity was unrelated to PMP. The β-diversity of the entire microbial community, however, was related to PMP. Shannon diversity was a better correlate of PMP than Simpson diversity across analyses, while rarefied species richness was a weak correlate of PMP. These results demonstrate the following: first, soil pH and microbial community structure both probably control methane production in Arctic soils. Second, there may be high functional redundancy in the methanogens with regard to methane production. Third, iron-reducing bacteria co-occur with methanogens in Arctic soils, and iron-reduction-mediated effects on methanogenesis may be controlled by α- and β-diversity. And finally, species evenness and rare species abundances may be driving relationships between microbial groups, influencing Arctic methane production. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

    Directory of Open Access Journals (Sweden)

    Franck O P Stefani

    Full Text Available Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA with culture-dependent (isolation using seven different growth media techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

  7. Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

    Science.gov (United States)

    Stefani, Franck O P; Bell, Terrence H; Marchand, Charlotte; de la Providencia, Ivan E; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed

    2015-01-01

    Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

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

    Science.gov (United States)

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

    2012-07-01

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

  9. Effect of acid rain on soil microbial processes

    International Nuclear Information System (INIS)

    Myrold, D.D.; Nason, G.E.

    1992-01-01

    Acid rain is real; the pH of precipitation in many areas of the world is below its normal equilibrium value, and concentrations of inorganic N and S are elevated above background. The impact of acid rain on soil microbial processes is less clear. This is largely because of the chemical buffering of the soil ecosystem and the inherent resiliency and redundancy of soil microorganisms. Microorganisms have an amazing capacity to adapt to new situations, which is enhanced by their ability to evolve under selection pressure. Their resilience is a function of both the large number of microorganisms present in a given volume of soil and their high growth rate relative to macroorganisms. This suggests that microorganisms are likely to be able to adapt more quickly to acidification than plants or animals, which may be one reason why symbiotic associations, such as ectomycorrhizae, are more susceptible to acid inputs than their saprophytic counterparts

  10. Microbial utilization of rice straw and its derived biochar in a paddy soil

    International Nuclear Information System (INIS)

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

    2016-01-01

    The application of straw and biochar to soil has received great attention because of their potential benefits such as fertility improvement and carbon (C) sequestration. The abiotic effects of these materials on C and nitrogen (N) cycling in the soil ecosystem have been previously investigated, however, the effects of straw or its derived biochar on the soil microbial community structure and function are not well understood. For this purpose, a short-term incubation experiment was conducted using 13 C-labeled rice straw and its derived biochar ( 13 C-labeled biochar) to deepen our understanding about soil microbial community dynamics and function in C sequestration and greenhouse gas emission in the acidic paddy soil amended with these materials. Regarding microbial function, biochar and straw applications increased CO 2 emission in the initial stage of incubation and reached the highest level (0.52 and 3.96 mg C kg −1 soil h −1 ) at 1 d and 3 d after incubation, respectively. Straw amendment significantly (p < 0.01) increased respiration rate, total phospholipid fatty acids (PLFAs) and 13 C-PLFA as compared to biochar amendment and the control. The amount and percent of Gram positive bacteria, fungi and actinomycetes were also significantly (p < 0.05) higher in 13 C-labeled straw amended soil than the 13 C-labeled biochar amended soil. According to the 13 C data, 23 different PLFAs were derived from straw amended paddy soil, while only 17 PLFAs were derived from biochar amendments. The profile of 13 C-PLFAs derived from straw amendment was significantly (p < 0.01) different from biochar amendment. The PLFAs 18:1ω7c and cy17:0 (indicators of Gram negative bacteria) showed high relative abundances in the biochar amendment, while 10Me18:0, i17:0 and 18:2ω6,9c (indicators of actinomycetes, Gram positive bacteria and fungi, respectively) showed high relative abundance in the straw amendments. Our results suggest that the function, size and structure of the

  11. Microbial utilization of rice straw and its derived biochar in a paddy soil

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Fuxia [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo 315800 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Yaying [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo 315800 (China); Chapman, Stephen James [The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH (United Kingdom); Khan, Sardar [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Department of Environmental Science, University of Peshawar (Pakistan); Yao, Huaiying, E-mail: hyyao@iue.ac.cn [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo 315800 (China)

    2016-07-15

    The application of straw and biochar to soil has received great attention because of their potential benefits such as fertility improvement and carbon (C) sequestration. The abiotic effects of these materials on C and nitrogen (N) cycling in the soil ecosystem have been previously investigated, however, the effects of straw or its derived biochar on the soil microbial community structure and function are not well understood. For this purpose, a short-term incubation experiment was conducted using {sup 13}C-labeled rice straw and its derived biochar ({sup 13}C-labeled biochar) to deepen our understanding about soil microbial community dynamics and function in C sequestration and greenhouse gas emission in the acidic paddy soil amended with these materials. Regarding microbial function, biochar and straw applications increased CO{sub 2} emission in the initial stage of incubation and reached the highest level (0.52 and 3.96 mg C kg{sup −1} soil h{sup −1}) at 1 d and 3 d after incubation, respectively. Straw amendment significantly (p < 0.01) increased respiration rate, total phospholipid fatty acids (PLFAs) and {sup 13}C-PLFA as compared to biochar amendment and the control. The amount and percent of Gram positive bacteria, fungi and actinomycetes were also significantly (p < 0.05) higher in {sup 13}C-labeled straw amended soil than the {sup 13}C-labeled biochar amended soil. According to the {sup 13}C data, 23 different PLFAs were derived from straw amended paddy soil, while only 17 PLFAs were derived from biochar amendments. The profile of {sup 13}C-PLFAs derived from straw amendment was significantly (p < 0.01) different from biochar amendment. The PLFAs 18:1ω7c and cy17:0 (indicators of Gram negative bacteria) showed high relative abundances in the biochar amendment, while 10Me18:0, i17:0 and 18:2ω6,9c (indicators of actinomycetes, Gram positive bacteria and fungi, respectively) showed high relative abundance in the straw amendments. Our results suggest

  12. Empirical evidence that soil carbon formation from plant inputs is positively related to microbial growth

    Science.gov (United States)

    Mark A. Bradford; Ashley D. Keiser; Christian A. Davies; Calley A. Mersmann; Michael S. Strickland

    2012-01-01

    Plant-carbon inputs to soils in the form of dissolved sugars, organic acids and amino acids fuel much of heterotrophic microbial activity belowground. Initial residence times of these compounds in the soil solution are on the order of hours, with microbial uptake a primary removal mechanism. Through microbial biosynthesis, the dissolved compounds become dominant...

  13. Soil microbial community responses to acid exposure and neutralization treatment.

    Science.gov (United States)

    Shin, Doyun; Lee, Yunho; Park, Jeonghyun; Moon, Hee Sun; Hyun, Sung Pil

    2017-12-15

    Changes in microbial community induced by acid shock were studied in the context of potential release of acids to the environment due to chemical accidents. The responses of microbial communities in three different soils to the exposure to sulfuric or hydrofluoric acid and to the subsequent neutralization treatment were investigated as functions of acid concentration and exposure time by using 16S-rRNA gene based pyrosequencing and DGGE (Denaturing Gradient Gel Electrophoresis). Measurements of soil pH and dissolved ion concentrations revealed that the added acids were neutralized to different degrees, depending on the mineral composition and soil texture. Hydrofluoric acid was more effectively neutralized by the soils, compared with sulfuric acid at the same normality. Gram-negative ß-Proteobacteria were shown to be the most acid-sensitive bacterial strains, while spore-forming Gram-positive Bacilli were the most acid-tolerant. The results of this study suggest that the Gram-positive to Gram-negative bacterial ratio may serve as an effective bio-indicator in assessing the impact of the acid shock on the microbial community. Neutralization treatments helped recover the ratio closer to their original values. The findings of this study show that microbial community changes as well as geochemical changes such as pH and dissolved ion concentrations need to be considered in estimating the impact of an acid spill, in selecting an optimal remediation strategy, and in deciding when to end remedial actions at the acid spill impacted site. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    Mitchell, Jeffrey; Scow, Kate

    2018-01-01

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

  15. Biochar alters microbial community and carbon sequestration potential across different soil pH.

    Science.gov (United States)

    Sheng, Yaqi; Zhu, Lizhong

    2018-05-01

    Biochar application to soil has been proposed for soil carbon sequestration and global warming mitigation. While recent studies have demonstrated that soil pH was a main factor affecting soil microbial community and stability of biochar, little information is available for the microbiome across different soil pH and the subsequently CO 2 emission. To investigate soil microbial response and CO 2 emission of biochar across different pH levels, comparative incubation studies on CO 2 emission, degradation of biochar, and microbial communities in a ferralsol (pH5.19) and a phaeozems (pH7.81) with 4 biochar addition rates (0.5%, 1.0%, 2.0%, 5.0%) were conducted. Biochar induced higher CO 2 emission in acidic ferralsol, largely due to the higher biochar degradation, while the more drastic negative priming effect (PE) of SOC resulted in decreased total CO 2 emission in alkaline phaeozems. The higher bacteria diversity, especially the enrichment of copiotrophic bacteria such as Bacteroidetes, Gemmatimonadetes, and decrease of oligotrophic bacteria such as Acidobacteria, were responsible for the increased CO 2 emission and initial positive PE of SOC in ferralsol, whereas biochar did not change the relative abundances of most bacteria at phylum level in phaeozems. The relative abundances of other bacterial taxa (i.e. Actinobacteria, Anaerolineae) known to degrade aromatic compounds were also elevated in both soils. Soil pH was considered to be the dominant factor to affect CO 2 emission by increasing the bioavailability of organic carbon and abundance of copiotrophic bacteria after biochar addition in ferralsol. However, the decreased bioavailability of SOC via adsorption of biochar resulted in higher abundance of oligotrophic bacteria in phaeozems, leading to the decrease in CO 2 emission. Copyright © 2017. Published by Elsevier B.V.

  16. Assessing toxic levels of hydrocarbons on microbial degrader communities in vadose zone fill soils

    International Nuclear Information System (INIS)

    Schoenberg, T.H.; Long, S.C.

    1995-01-01

    Authentic fill samples were collected from the vadose zone at a highway travel plaza. The contamination at the site is a combination of gasoline, diesel, and waste oil resulting from leaking underground storage tanks. Microbial assessments including plate counts and specific-degrader enumerations were performed to establish the presence of degrader microbial communities, and thus bioremediation potential. Contaminant levels were estimated in samples by quantifying headspace VOCs in collection jars. Physical soil characteristics including soil grain size distribution and moisture content were measured to evaluate the potential ecological variables that would affect implementation of a bioremediation technology. Toxicity screening using the Microtox trademark acute toxicity assay was used to compare the level of toxicity present among samples. These analyses were used to assess the potential for using in situ bioventing remediation to clean-up the leaking underground storage tank spill study site. High contaminant levels appear to have exerted a toxic effect and resulted in smaller total microbial community sizes in highly contaminated areas (thousands of ppmv) of the site. Microtox trademark EC50 results generally corroborated with the trends of the enumeration experiments. Microbial characterization results indicate that in situ bioremediation would be possible at the study site. Soil heterogeneity appears to pose the greatest challenges to the design and implementation of bioremediation at this site

  17. Root systems and soil microbial biomass under no-tillage system

    Directory of Open Access Journals (Sweden)

    Venzke Filho Solismar de Paiva

    2004-01-01

    Full Text Available Some root parameters such as distribution, length, diameter and dry matter are inherent to plant species. Roots can influence microbial population during vegetative cycle through the rhizodeposits and, after senescence, integrating the soil organic matter pool. Since they represent labile substrates, especially regarding nitrogen, they can determine the rate of nutrient availability to the next crop cultivated under no-tillage (NT. The root systems of two crop species: maize (Zea mays L. cultivar Cargill 909 and soybean [Glycine max (L. Merr.] cultivar Embrapa 59, were compared in the field, and their influence on spatial distribution of the microbial C and N in a clayey-textured Typic Hapludox cultivated for 22 years under NT, at Tibagi, State of Paraná (PR, Brazil, was determined. Digital image processing and nail-plate techniques were used to evaluate 40 plots of a 80 ´ 50 ´ 3 cm soil profile. It was observed that 36% and 30% of the maize and soybeans roots, respectively, are concentrated in the 0 to 10 cm soil layer. The percent distribution of root dry matter was similar for both crops. The maize roots presented a total of 1,324 kg C ha-1 and 58 kg N ha-1, with higher root dry matter density and more roots in decomposition in the upper soil layer, decreasing with depth. The soybean roots (392 kg C ha-1 and 21 kg N ha-1 showed higher number of thinner roots and higher density per length unity compared to the maize. The maize roots enhanced microbial-C down to deeper soil layers than did the soybean roots. The microbial N presented a better correlation with the concentration of thin active roots and with roots in decomposition or in indefinite shape, possibly because of higher concentration of C and N easily assimilated by soil microorganisms.

  18. Divergent surface and total soil moisture projections under global warming

    Science.gov (United States)

    Berg, Alexis; Sheffield, Justin; Milly, Paul C.D.

    2017-01-01

    Land aridity has been projected to increase with global warming. Such projections are mostly based on off-line aridity and drought metrics applied to climate model outputs but also are supported by climate-model projections of decreased surface soil moisture. Here we comprehensively analyze soil moisture projections from the Coupled Model Intercomparison Project phase 5, including surface, total, and layer-by-layer soil moisture. We identify a robust vertical gradient of projected mean soil moisture changes, with more negative changes near the surface. Some regions of the northern middle to high latitudes exhibit negative annual surface changes but positive total changes. We interpret this behavior in the context of seasonal changes in the surface water budget. This vertical pattern implies that the extensive drying predicted by off-line drought metrics, while consistent with the projected decline in surface soil moisture, will tend to overestimate (negatively) changes in total soil water availability.

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

    Science.gov (United States)

    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

  20. Response of soil microbial communities and microbial interactions to long-term heavy metal contamination.

    Science.gov (United States)

    Li, Xiaoqi; Meng, Delong; Li, Juan; Yin, Huaqun; Liu, Hongwei; Liu, Xueduan; Cheng, Cheng; Xiao, Yunhua; Liu, Zhenghua; Yan, Mingli

    2017-12-01

    Due to the persistence of metals in the ecosystem and their threat to all living organisms, effects of heavy metal on soil microbial communities were widely studied. However, little was known about the interactions among microorganisms in heavy metal-contaminated soils. In the present study, microbial communities in Non (CON), moderately (CL) and severely (CH) contaminated soils were investigated through high-throughput Illumina sequencing of 16s rRNA gene amplicons, and networks were constructed to show the interactions among microbes. Results showed that the microbial community composition was significantly, while the microbial diversity was not significantly affected by heavy metal contamination. Bacteria showed various response to heavy metals. Bacteria that positively correlated with Cd, e.g. Acidobacteria_Gp and Proteobacteria_thiobacillus, had more links between nodes and more positive interactions among microbes in CL- and CH-networks, while bacteria that negatively correlated with Cd, e.g. Longilinea, Gp2 and Gp4 had fewer network links and more negative interactions in CL and CH-networks. Unlike bacteria, members of the archaeal domain, i.e. phyla Crenarchaeota and Euryarchaeota, class Thermoprotei and order Thermoplasmatales showed only positive correlation with Cd and had more network interactions in CH-networks. The present study indicated that (i) the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, (ii) archaea were resistant to heavy metal contamination and may contribute to the adaption to heavy metals. It was proposed that the contribution might be achieved either by improving environment conditions or by cooperative interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.

    Science.gov (United States)

    Bissett, Andrew; Fitzgerald, Anna; Meintjes, Thys; Mele, Pauline M; Reith, Frank; Dennis, Paul G; Breed, Martin F; Brown, Belinda; Brown, Mark V; Brugger, Joel; Byrne, Margaret; Caddy-Retalic, Stefan; Carmody, Bernie; Coates, David J; Correa, Carolina; Ferrari, Belinda C; Gupta, Vadakattu V S R; Hamonts, Kelly; Haslem, Asha; Hugenholtz, Philip; Karan, Mirko; Koval, Jason; Lowe, Andrew J; Macdonald, Stuart; McGrath, Leanne; Martin, David; Morgan, Matt; North, Kristin I; Paungfoo-Lonhienne, Chanyarat; Pendall, Elise; Phillips, Lori; Pirzl, Rebecca; Powell, Jeff R; Ragan, Mark A; Schmidt, Susanne; Seymour, Nicole; Snape, Ian; Stephen, John R; Stevens, Matthew; Tinning, Matt; Williams, Kristen; Yeoh, Yun Kit; Zammit, Carla M; Young, Andrew

    2016-01-01

    Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'. Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.

  2. Effects of Nitrogen and Water on Soil Enzyme Activity and Soil Microbial Biomass in Stipa baicalensis Steppe,Inner Mongolia of North China

    Directory of Open Access Journals (Sweden)

    WANG Jie

    2014-06-01

    Full Text Available In this paper, eight nitrogen treatments were applied at 0 g·m -2(N0, 1.5 g·m -2(N15, 3.0 g·m -2(N30, 5.0 g·m -2(N50, 10.0 g·m -2(N100, 15.0 g·m -2(N150, 20.0 g·m -2(N200, 30.0 g·m -2(N300 as NH 4 NO 3 and adding water to simulate summer rainfall of 100 mm, the interactive experiment was set to explore the effects of nitrogen and water addition in Stipa baicalensis steppe on soil nutrients, enzyme activities and soil microbial biomass. The results showed that the nitrogen and water addition changed soil physico-chemical factors obviously, the content of soil total organic carbon, total nitrogen, nitrate nitrogen and ammonium nitrogen increased along with the increasing of application rate of nitrogen, on the contrary, the soil pH value had decreasing trend. Appropriate application of nitrogen could enhance the activity of urease and catalase but decreased the activity of polyphenol oxidase. Nitrogen and water addition had significant effect on soil microbial biomass C and N. Higher level of N fertilizer significantly reduced microbial biomass C, and the microbial biomass N was on the rise with the application rate of nitrogen. The addition of water could slow the inhibition of nitrogen to microorganism and increase the microbial biomass C and N. A closed relationship existed in soil nutrient, activities of soil enzyme and soil microbial biomass C and N. The significantly positive correlation existed between total N, organic C, nitrate N and catalase, significantly negative correlation between nitrate N, ammonium N, total N and polyphenol oxidase. Microbial biomass N was significantly positive correlated with total N, nitrate N, ammonium N, catalase, phosphatase, and was negative correlated with polyphenol oxidase. Microbial biomass C was significantly positive correlated with polyphenol oxidase, and was negative correlated with catalase.

  3. A meta-analysis of soil microbial biomass responses to forest disturbances

    Directory of Open Access Journals (Sweden)

    Sandra Robin Holden

    2013-06-01

    Full Text Available Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm and biotic (insect, pathogen disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7%, 19.1%, and 41.7% reductions in microbial biomass, respectively. In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics.

  4. Agroforestry systems, nutrients in litter and microbial activity in soils cultivated with coffee at high altitude

    Directory of Open Access Journals (Sweden)

    Krystal de Alcantara Notaro

    2014-04-01

    Full Text Available Agroforestry systems are an alternative option for sustainable production management. These systems contain trees that absorb nutrients from deeper layers of the soil and leaf litter that help improve the soil quality of the rough terrain in high altitude areas, which are areas extremely susceptible to environmental degradation. The aim of this study was to characterize the stock and nutrients in litter, soil activity and the population of microorganisms in coffee (Coffea arabica L. plantations under high altitude agroforestry systems in the semi-arid region of the state of Pernambuco, Brazil. Samples were collected from the surface litter together with soil samples taken at two depths (0-10 and 10-20 cm from areas each subject to one of the following four treatments: agroforestry system (AS, native forest (NF, biodynamic system (BS and coffee control (CT.The coffee plantation had been abandoned for nearly 15 years and, although there had been no management or harvesting, still contained productive coffee plants. The accumulation of litter and mean nutrient content of the litter, the soil nutrient content, microbial biomass carbon, total carbon, total nitrogen, C/N ratio, basal respiration, microbial quotient, metabolic quotient and microbial populations (total bacteria, fluorescent bacteria group, total fungi and Trichoderma spp. were all analyzed. The systems thatwere exposed to human intervention (A and BS differed in their chemical attributes and contained higher levels of nutrients when compared to NF and CT. BS for coffee production at high altitude can be used as a sustainable alternative in the high altitude zones of the semi-arid region in Brazil, which is an area that is highly susceptible to environmental degradation.

  5. Colonization patterns of soil microbial communities in the Atacama Desert.

    Science.gov (United States)

    Crits-Christoph, Alexander; Robinson, Courtney K; Barnum, Tyler; Fricke, W Florian; Davila, Alfonso F; Jedynak, Bruno; McKay, Christopher P; Diruggiero, Jocelyne

    2013-11-20

    The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life. Analyses of high throughput DNA sequence data revealed that bacterial communities from six geographic locations in the hyper-arid core and along a North-South moisture gradient were structurally and phylogenetically distinct (ANOVA test for observed operating taxonomic units at 97% similarity (OTU0.03), P microbial communities' diversity metrics (least squares linear regression for observed OTU0.03 and air RH and soil conductivity, P PCoA Spearman's correlation for air RH and soil conductivity, P <0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples, with increased rates in soils from the southern locations. Our results suggest that microorganisms in the driest soils of the Atacama Desert are in a state of stasis for most of the time, but can potentially metabolize if presented with liquid water for a sufficient duration. Over geological time, rare rain events and physicochemical factors potentially played a major role in selecting micro-organisms that are most adapted to extreme desiccating conditions.

  6. Microbial Community Structure of Casing Soil During Mushroom Growth

    Institute of Scientific and Technical Information of China (English)

    CAI Wei-Ming; YAO Huai-Ying; FENG Wei-Lin; JIN Qun-Li; LIU Yue-Yan; LI Nan-Yi; ZHENG Zhong

    2009-01-01

    The culturable bacterial population and phospholipid fatty acid (PLFA)profile of casing soil were investigated at different mushroom (Agaricus bisporusI cropping stages.The change in soil bacterial PLFAs was always accompanied by a change in the soil culturable bacterial population in the first flush.Comparatively higher culturable bacterial population and bacterial PLFAs were found in the casing soil at the primordia formation stage of the first flush.There was a significant increase in the ratio of fungal to bacterial PLFAs during mushroom growth.Multivariate analysis of PLFA data demonstrated that the mushroom cropping stage could considerably affect the microbial community structure of the casing soil.The bacterial population increased significantly from casing soil application to the primordia formation stage of the first flush.Casing soil application resulted in an increase in the ratio of gram-negative bacterial PLFAs to gram-positive bacterial PLFAs,suggesting that some gram-negative bacteria might play an important role in mushroom sporophore initiation.

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

    Energy Technology Data Exchange (ETDEWEB)

    Šimek, Miloslav, E-mail: misim@upb.cas.cz [Biology Centre AS CR, v. v. i., Institute of Soil Biology, 370 05 České Budějovice (Czech Republic); University of South Bohemia, Faculty of Science, 370 05 České Budějovice (Czech Republic); Virtanen, Seija; Simojoki, Asko [Department of Food and Environmental Sciences, University of Helsinki, FI-00014 Helsinki (Finland); Chroňáková, Alica; Elhottová, Dana; Krištůfek, Václav [Biology Centre AS CR, v. v. i., Institute of Soil Biology, 370 05 České Budějovice (Czech Republic); Yli-Halla, Markku [Department of Food and Environmental Sciences, University of Helsinki, FI-00014 Helsinki (Finland)

    2014-01-01

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

  8. In situ phytoremediation of PAH-contaminated soil by intercropping alfalfa (Medicago sativa L.) with tall fescue (Festuca arundinacea Schreb.) and associated soil microbial activity

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Mingming; Fu, Dengqiang; Teng, Ying; Shen, Yuanyuan; Luo, Yongming; Li, Zhengao [Chinese Academy of Sciences, Nanjing (China). Key Laboratory of Soil Environment and Pollution Remediation; Christie, Peter [Agri-Food and Biosciences Institute, Belfast (United Kingdom). Agri-Environment Branch

    2011-09-15

    Purpose: A 7-month field experiment was conducted to investigate the polycyclic aromatic hydrocarbon (PAH) remediation potential of two plant species and changes in counts of soil PAH-degrading bacteria and microbial activity. Materials and methods: Alfalfa and tall fescue were grown in monoculture and intercropped for 7 months in contaminated field soil. Soil and plant samples were analyzed for PAHs. Plant biomass, densities of PAH-degradation soil bacteria, soil microbial biomass C and N, enzyme activities, and the physiological profile of the soil microbial community were determined. Results and discussion: Average removal percentage of total PAHs in intercropping (30.5%) was significantly higher than in monoculture (19.9%) or unplanted soil (-0.6%). About 7.5% of 3-ring, 12.3% of 4-ring, and 17.2% of 5(+6)-ring PAHs were removed from the soil by alfalfa, with corresponding values of 25.1%, 10.4%, and 30.1% for tall fescue. Intercropping significantly enhanced the remediation efficiency. About 18.9% of 3-ring, 30.9% of 4-ring, and 33.4% of 5(+6)-ring PAHs were removed by the intercropping system. Higher counts of soil culturable PAH-degrading bacteria and elevated microbial biomass and enzyme activities were found after intercropping. Soil from intercropping showed significantly higher (p < 0.05) average well-color development obtained by the BIOLOG Ecoplate assay and Shannon-Weaver index compared with monoculture. Conclusions: Cropping promoted the dissipation of soil PAHs. Tall fescue gave greater removal of soil PAHs than alfalfa, and intercropping was more effective than monoculture. Intercropping of alfalfa and tall fescue may be a promising in situ bioremediation strategy for PAH-contaminated soils. (orig.)

  9. Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

    Energy Technology Data Exchange (ETDEWEB)

    Firestone, Mary [Univ. of California, Berkeley, CA (United States)

    2015-03-31

    It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbon decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.

  10. Selective progressive response of soil microbial community to wild oat roots

    Energy Technology Data Exchange (ETDEWEB)

    DeAngelis, K.M.; Brodie, E.L.; DeSantis, T.Z.; Andersen, G.L.; Lindow, S.E.; Firestone, M.K.

    2008-10-01

    Roots moving through soil enact physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. Use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies previously reported compositional changes, including increases in chitinase and protease specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change in 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA T-RFLP analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared to bulk soil, but then increased in older root zones. Quantitative PCR revealed {beta}-Proteobacteria and Actinobacteria present at about 10{sup 8} copies of 16S rRNA genes g{sup -1} soil, with Nitrospira having about 10{sup 5} copies g{sup -1} soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in function in progressively more mature rhizosphere zones.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2017-08-22

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

  13. [Effects of biochar on microbial ecology in agriculture soil: a review].

    Science.gov (United States)

    Ding, Yan-Li; Liu, Jie; Wang, Ying-Ying

    2013-11-01

    Biochar, as a new type of soil amendment, has been obtained considerable attention in the research field of environmental sciences worldwide. The studies on the effects of biochar in improving soil physical and chemical properties started quite earlier, and already covered the field of soil microbial ecology. However, most of the studies considered the soil physical and chemical properties and the microbial ecology separately, with less consideration of their interactions. This paper summarized and analyzed the interrelationships between the changes of soil physical and chemical properties and of soil microbial community after the addition of biochar. Biochar can not only improve soil pH value, strengthen soil water-holding capacity, increase soil organic matter content, but also affect soil microbial community structure, and alter the abundance of soil bacteria and fungi. After the addition of biochar, the soil environment and soil microorganisms are interacted each other, and promote the improvement of soil microbial ecological system together. This review was to provide a novel perspective for the in-depth studies of the effects of biochar on soil microbial ecology, and to promote the researches on the beneficial effects of biochar to the environment from ecological aspect. The methods to improve the effectiveness of biochar application were discussed, and the potential applications of biochar in soil bioremediation were further analyzed.

  14. Microbial populations and activities of mangrove, restinga and Atlantic forest soils from Cardoso Island, Brazil.

    Science.gov (United States)

    Pupin, B; Nahas, E

    2014-04-01

    Mangroves provide a distinctive ecological environment that differentiates them from other ecosystems. This study deal to evaluate the frequency of microbial groups and the metabolic activities of bacteria and fungi isolated from mangrove, restinga and Atlantic forest soils. Soil samples were collected during the summer and winter at depths of 0-2, 2-5 and 5-10 cm. Except for fungi, the counts of the total, sporulating, Gram-negative, actinomycetes, nitrifying and denitrifying bacteria decreased significantly in the following order: Atlantic forest >mangrove > restinga. The counts of micro-organisms decreased by 11 and 21% from the surface to the 2-5 and 5-10 cm layers, but denitrifying bacteria increased by 44 and 166%, respectively. A larger growth of micro-organisms was verified in the summer compared with the winter, except for actinomycetes and fungi. The average frequency of bacteria isolated from mangrove, restinga and Atlantic forest soils was 95, 77 and 78%, and 93, 90 and 95% for fungi, respectively. Bacteria were amylolytic (33%), producers of acid phosphatase (79%) and solubilizers (18%) of inorganic phosphate. The proportions of fungi were 19, 90 and 27%. The mangrove soil studied had higher chemical characteristics than the Atlantic forest, but the high salinity may have restricted the growth of microbial populations. Estimates of the microbial counts and activities were important to elucidate the differences of mangrove ecosystem from restinga and Atlantic forest. © 2013 The Society for Applied Microbiology.

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

    Science.gov (United States)

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

    2013-04-01

    Paddy soils are characterised by interchanging cycles of anaerobic and aerobic conditions. Such fluctuations cause continuous changes in soil solution chemistry as well as in the composition and physiological responses of the microbial community. Temporary deficiency in oxygen creates conditions favourable to facultative or obligates anaerobic bacteria, while aerobic communities can thrive in the period of water absence. These alterations can strongly affect soil processes, in particular organic matter (OM) accumulation and mineralization. In submerged soils, lignin generally constitutes a major portion of the total OM because of hampered degradation under anoxic conditions. The alternating redox cycles resulting from paddy soil management might promote both degradation and preservation of lignin, affecting the overall composition and reactivity of total and dissolved OM. We sampled soils subjected to cycles of anoxic (rice growing period) and oxic (harvest and growth of other crops) conditions since 700 and 2000 years. We incubated suspended Ap material, sampled from the two paddy plus two corresponding non-paddy control soils under oxic and anoxic condition, for 3 months, interrupted by a short period of three weeks (from day 21 to day 43) with reversed redox conditions. At each sampling time (day 2, 21, 42, 63, 84), we determined lignin-derived phenols (by CuO oxidation) as well as phospholipids fatty acids contents and composition. We aimed to highlight changes in lignin decomposition as related to the potential rapid changes in microbial community composition. Since the studied paddy soils had a long history of wet rice cultivation, the microbial community should be well adapted to interchanging oxic and anoxic cycles, therefore fully expressing its activity at both conditions. In non-paddy soil changes in redox conditions caused modification of quantity and composition of the microbial community. On the contrary, in well-established paddy soils the microbial

  16. Microbial community responses in forest mineral soil to compaction, organic matter removal, and vegetation control

    Science.gov (United States)

    Matt D. Busse; Samual E. Beattie; Robert F. Powers; Filpe G. Sanchez; Allan E. Tiarks

    2006-01-01

    We tested three disturbance hypotheses in young conifer plantations: H1: soil compaction and removal of surface organic matter produces sustained changes in microbial community size, activity, and structure in mineral soil; H2: microbial community characteristics in mineral soil are linked to the recovery of plant diversity...

  17. [Microbial biomass and growth kinetics of microorganisms in chernozem soils under different farm land use modes].

    Science.gov (United States)

    Blagodatskiĭ, S A; Bogomolova, I N; Blagodatskaia, E V

    2008-01-01

    The carbon content of microbial biomass and the kinetic characteristics of microbial respiration response to substrate introduction have been estimated for chernozem soils of different farm lands: arable lands used for 10, 46, and 76 years, mowed fallow land, non-mowed fallow land, and woodland. Microbial biomass and the content of microbial carbon in humus (Cmic/Corg) decreased in the following order: soils under forest cenoses-mowed fallow land-10-year arable land-46- and 75-year arable land. The amount of microbial carbon in the long-plowed horizon was 40% of its content in the upper horizon of non-mowed fallow land. Arable soils were characterized by a lower metabolic diversity of microbial community and by the highest portion of microorganisms able to grow directly on glucose introduced into soil. The effects of different scenarios of carbon sequestration in soil on the reserves and activity of microbial biomass are discussed.

  18. Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient

    Science.gov (United States)

    Chapman, Eric; Cadillo-Quiroz, Hinsby; Childers, Daniel L.; Turetsky, Merritt R.; Waldrop, Mark P.

    2017-01-01

    Climate change is modifying global biogeochemical cycles. Microbial communities play an integral role in soil biogeochemical cycles; knowledge about microbial composition helps provide a mechanistic understanding of these ecosystem-level phenomena. Next generation sequencing approaches were used to investigate changes in microbial functional groups during ecosystem development, in response to climate change, in northern boreal wetlands. A gradient of wetlands that developed following permafrost degradation was used to characterize changes in the soil microbial communities that mediate C cycling: a bog representing an “undisturbed” system with intact permafrost, and a younger bog and an older bog that formed following the disturbance of permafrost thaw. Reference 16S rRNA databases and several diversity indices were used to assess structural differences among these communities, to assess relationships between soil microbial community composition and various environmental variables including redox potential and pH. Rates of potential CO2 and CH4 gas production were quantified to correlate sequence data with gas flux. The abundance of organic C degraders was highest in the youngest bog, suggesting higher rates of microbial processes, including potential CH4 production. In addition, alpha diversity was also highest in the youngest bog, which seemed to be related to a more neutral pH and a lower redox potential. These results could potentially be driven by increased niche differentiation in anaerobic soils. These results suggest that ecosystem structure, which was largely driven by changes in edaphic and plant community characteristics between the “undisturbed” permafrost bog and the two bogs formed following permafrost thaw, strongly influenced microbial function.

  19. Relating soil microbial activity to water content and tillage-induced differences in soil structure

    DEFF Research Database (Denmark)

    Schjønning, Per; Thomsen, Ingrid Kaag; Petersen, Søren O

    2011-01-01

    Several studies have identified optima in soil water content for aerobic microbial activity, and this has been ascribed to a balance between gas and solute diffusivity as limiting processes. We investigated the role of soil structure, as created by different tillage practices (moldboard ploughing......, MP, or shallow tillage, ST), in regulating net nitrification, applied here as an index of aerobic microbial activity. Intact soil cores were collected at 0–4 and 14–18 cm depth from a fine sandy (SAND) and a loamy (LOAM) soil. The cores were drained to one of seven matric potentials ranging from − 15...... content to a maximum and then decreased. This relationship was modelled with a second order polynomium. Model parameters did not show any tillage effect on the optimum water content, but the optimum coincided with a lower matric potential in ST (SAND: − 140 to –197 hPa; LOAM: − 37 to − 65 hPa) than in MP...

  20. Soil microbial population and nitrogen fixation in peanut under fly ash and sewage sludge

    International Nuclear Information System (INIS)

    Sarkar, S.; Khan, A.R.

    2002-06-01

    such as C, N, S, and P in the biosphere (Wong and Wong, 1986). Addition of such wastes to agricultural lands is likely to alter the nutrient cycling processes particularly for leguminous crops, where nodulation, N 2 fixation and N uptake is mainly governed by a group of microorganisms (McGrath et al., 1988). It is therefore imperative to study the effect of different doses and combination of wastes on changes in microbial population and its impact on overall performance of a crop. The objective of this study is thus, to investigate the implications of industrial wastes (Fly Ash) and urban sewage sludge (treated City Waste) application at different rates and frequencies of application on the total soil microbial population, Rhizobium population, nodulation, N-uptake, N-accumulation and yield of peanut crop in lateritic sandy loam soil of eastern India

  1. Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity

    Directory of Open Access Journals (Sweden)

    Binu M Tripathi

    2016-04-01

    Full Text Available There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

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

    Science.gov (United States)

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

    2012-10-01

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

  3. Changes in microbial and soil organic matter following amendment ...

    African Journals Online (AJOL)

    user

    The amendment of the soil with untreated OMW improved the soil carbon content (2.18 ... Total solids (g l-1). 52 ± 2.98 ... Untreated olive mill wastewater was taken from a three-phase discontinuous extraction factory located in Sfax, Tunisia. ..... Effect of bioaugmentation of activated sludge with white-rot fungi on olive mill.

  4. Nitrogen fractions in the microbial biomass in soils of southern Brazil

    Directory of Open Access Journals (Sweden)

    F. A.O. Camargo

    1999-03-01

    Full Text Available The reaction of nitrogen compounds with ninhydrin can be used as an indicator of cytoplasmic materials released from microbial cells killed by fumigation. Total-N, ninhydrin-reactive-N (NR-N, ammonium-N (A-N, and α-amino-N in the microbial biomass of soils from the State of Rio Grande do Sul, Brazil, were determined, in 1996, in 0.5 mol L-1 K2SO4 extracts of fumigated and non-fumigated soils. Total-N varied from 20.3 to 104.4 mg kg-1 and the ninhydrin-reactive-N corresponded, in average, to 27% of this. The ninhydrin-reactive-N was made up of 67% ammonium-N and 33% aminoacids with the amino group at the α-carbon position. It was concluded that colorimetric analysis of NR-N and A-N may be used as a direct measure of microbial N in soil. This simple and rapid procedure is adequate for routine analyses.

  5. Electronic Nose Technology to Measure Soil Microbial Activity and Classify Soil Metabolic Status

    OpenAIRE

    Fabrizio De Cesare; Elena Di Mattia; Simone Pantalei; Emiliano Zampetti; Vittorio Vinciguerra; Antonella Macagnano

    2011-01-01

    The electronic nose (E-nose) is a sensing technology that has been widely used to monitor environments in the last decade. In the present study, the capability of an E-nose, in combination with biochemical and microbiological techniques, of both detecting the microbial activity and estimating the metabolic status of soil ecosystems, was tested by measuring on one side respiration, enzyme activities and growth of bacteria in natural but simplified soil ecosystems over 23 days of incubation thr...

  6. Separating rhizosphere respiration from total soil respiration in two larch plantations in northeastern China.

    Science.gov (United States)

    Jiang, Lifen; Shi, Fuchen; Li, Bo; Luo, Yiqi; Chen, Jiquan; Chen, Jiakuan

    2005-09-01

    The potential capacity of soil to sequester carbon in response to global warming is strongly regulated by the ratio of rhizosphere respiration to respiration by soil microbial decomposers, because of their different temperature sensitivities. To quantify relative contributions of rhizosphere respiration to total soil respiration as influenced by forest stand development, we conducted a trenching study in two larch (Larix gmelini (Rupr.) Rupr.) plantations, aged 17 and 31 years, in northeastern China. Four plots in each plantation were randomly selected and trenched in early May 2001. Soil surface CO2 effluxes both inside and outside the plots were measured from May 2001 to August 2002. Soil respiration (i.e., the CO2 effluxes outside the trenched plots) varied similarly in the two plantations from 0.8 micromol m(-2) s(-1) in winter to 6.0 micromol m(-2) s(-1) in summer. Rhizosphere respiration (i.e., CO2 efflux outside the trenched plots minus that inside the plots) varied from 0.2 to 2.0 micromol m(-2) s(-1) in the old forest and from 0.3 to 4.0 micromol m(-2) s(-1) in the young forest over the seasons. Rhizosphere respiration, on average, accounted for 25% of soil respiration in the old forest and 65% in the young forest. Rhizosphere and soil respiration were significantly correlated with soil temperature but not with soil water content. We conclude that the role forests play in regulating climate change may depend on their age.

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

    Directory of Open Access Journals (Sweden)

    Camila O. Martinez

    2010-03-01

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

  8. Long Term Monitoring of Microbial Induced Soil Strengthening Processes

    Science.gov (United States)

    Saneiyan, S.; Ntarlagiannis, D.; Werkema, D. D., Jr.; Colwell, F. S.; Ohan, J.

    2016-12-01

    Soil strengthening/stabilization processes are used to address some of soil quality issues. Microbial induced calcite precipitation (MICP) is a promising soil stabilization process that could offer long term solution by overcoming problems of commonly used methods (e.g. injecting cement slurry). MICP can be applied in larger spatial scales, allowing the enhanced soils to be maintained in an economic sustainable and environmental friendly way. Methods are sought for the long term monitoring of MICP enhanced soils. The spectral induced polarization (SIP) method is one promising method due to sensitivity on such processes and the ability for long term, even autonomous, operation as well as cost effectiveness. Previous laboratory tests showed the sensitivity of the SIP method on soil strengthening as a result of abiotic calcite precipitation. We extended this work to biotic calcite precipitation through MICP. Early results suggest that the MICP formed calcite is denser and could provide improved strengthening capabilities. Our results are supported by geophysical (SIP and shear-wave velocity), geo-chemical and microbiological monitoring. Destructive analysis and visualization (scanning electron imaging - SEM) is expected to provide conclusive evidence on the MICP long term effectiveness.

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

    Science.gov (United States)

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

    2017-08-15

    New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation ( cbbL-R [ cbbL gene, red-like subunit] and apsA ), nitrogen cycling ( noxZ and amoA ), and contaminant degradation ( bphA ); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a

  10. Microbial activities in soil near natural gas leaks

    Energy Technology Data Exchange (ETDEWEB)

    Adamse, A D; Hoeks, J; de Bont, J A.M.; van Kessel, J F

    1972-01-01

    From the present experiments it may be concluded that in the surroundings of natural gas leaks, methane, ethane and possibly some other components of the natural gas are oxidized by microbial activities as long as oxygen is available. This is demonstrated by an increased oxygen consumption and carbon dioxide production, as well as by increased numbers of different types of bacteria. The resulting deficiency of oxygen, the excess of carbon dioxide, and perhaps the formation of inhibitory amounts of ethylene, are considered to be mainly responsible for the death of trees near natural gas leaks. Also the long period of time needed by the soil to recover, may be due to prolonged microbial activities, as well as to the presence of e.g. ethylene. The present experiments suggest that especially methane-oxidizing bacteria of the Methylosinus trichosporium type were present in predominating numbers and consequently have mainly been responsible for the increased oxygen consumption. However, some fungi oxidizing components of natural gas, including methane and ethane may also have contributed to the increased microbial activities in the soil. The same will be true of a possible secondary microflora on products derived from microorganisms oxidizing natural gas components. 12 references, 9 figures, 7 tables.

  11. Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine.

    Science.gov (United States)

    Chao, Yuanqing; Liu, Wenshen; Chen, Yanmei; Chen, Wenhui; Zhao, Lihua; Ding, Qiaobei; Wang, Shizhong; Tang, Ye-Tao; Zhang, Tong; Qiu, Rong-Liang

    2016-11-01

    Mining activity for rare earth elements (REEs) has caused serious environmental pollution, particularly for soil ecosystems. However, the effects of REEs on soil microbiota are still poorly understood. In this study, soils were collected from abandoned sites of a REEs mine, and the structure, diversity, and co-occurrence patterns of soil microbiota were evaluated by Illumina high-throughput sequencing targeting 16S rRNA genes. Although microbiota developed significantly along with the natural restoration, the microbial structure on the site abandoned for 10 years still significantly differed from that on the unmined site. Potential plant growth promoting bacteria (PGPB) were identified by comparing 16S sequences against a self-constructed PGPB database via BLAST, and it was found that siderophore-producing and phosphorus-solubilizing bacteria were more abundant in the studied soils than in reference soils. Canonical correspondence analysis indicated that species richness of plant community was the prime factor affecting microbial structure, followed by limiting nutrients (total carbon and total nitrogen) and REEs content. Further co-occurring network analysis revealed nonrandom assembly patterns of microbiota in the studied soils. These results increase our understanding of microbial variation and assembly pattern during natural restoration in REE contaminated soils.

  12. Impact of electrokinetic remediation on microbial communities within PCP contaminated soil

    International Nuclear Information System (INIS)

    Lear, G.; Harbottle, M.J.; Sills, G.; Knowles, C.J.; Semple, K.T.; Thompson, I.P.

    2007-01-01

    Electrokinetic techniques have been used to stimulate the removal of organic pollutants within soil, by directing contaminant migration to where remediation may be more easily achieved. The effect of this and other physical remediation techniques on the health of soil microbial communities has been poorly studied and indeed, largely ignored. This study reports the impact on soil microbial communities during the application of an electric field within ex situ laboratory soil microcosms contaminated with pentachlorophenol (PCP; 100 mg kg -1 oven dry soil). Electrokinetics reduced counts of culturable bacteria and fungi, soil microbial respiration and carbon substrate utilisation, especially close to the acidic anode where PCP accumulated (36 d), perhaps exacerbated by the greater toxicity of PCP at lower soil pH. There is little doubt that a better awareness of the interactions between soil electrokinetic processes and microbial communities is key to improving the efficacy and sustainability of this remediation strategy. - Electrokinetics negatively impacted soil

  13. The Effect of Re-Planting Trees on Soil Microbial Communities in a Wildfire-Induced Subalpine Grassland

    Directory of Open Access Journals (Sweden)

    Ed-Haun Chang

    2017-10-01

    Full Text Available Wildfire often causes tremendous changes in ecosystems, particularly in subalpine and alpine areas, which are vulnerable due to severe climate conditions such as cold temperature and strong wind. This study aimed to clarify the effect of tree re-planting on ecosystem services such as the soil microbial community after several decades. We compared the re-planted forest and grassland with the mature forest as a reference in terms of soil microbial biomass C and N (Cmic and Nmic, enzyme activities, phospholipid fatty acids (PLFA composition, and denaturing gradient gel electrophoresis (DGGE. The Cmic and Nmic did not differ among the grassland, re-planted forest and mature forest soil; however, ratios of Cmic/Corg and Nmic/Ntot decreased from the grassland to re-planted forest and mature forest soil. The total PLFAs and those attributed to bacteria and Gram-positive and Gram-negative bacteria did not differ between the re-planted forest and grassland soil. Principle component analysis of the PLFA content separated the grassland from re-planted forest and mature forest soil. Similarly, DGGE analysis revealed changes in both bacterial and fungal community structures with changes in vegetation. Our results suggest that the microbial community structure changes with the re-planting of trees after a fire event in this subalpine area. Recovery of the soil microbial community to the original state in a fire-damaged site in a subalpine area may require decades, even under a re-planted forest.

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

    Science.gov (United States)

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

    2015-04-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

  16. Effects of Monoculture, Crop Rotation, and Soil Moisture Content on Selected Soil Physicochemical and Microbial Parameters in Wheat Fields

    Directory of Open Access Journals (Sweden)

    A. Marais

    2012-01-01

    Full Text Available Different plants are known to have different soil microbial communities associated with them. Agricultural management practices such as fertiliser and pesticide addition, crop rotation, and grazing animals can lead to different microbial communities in the associated agricultural soils. Soil dilution plates, most-probable-number (MPN, community level physiological profiling (CLPP, and buried slide technique as well as some measured soil physicochemical parameters were used to determine changes during the growing season in the ecosystem profile in wheat fields subjected to wheat monoculture or wheat in annual rotation with medic/clover pasture. Statistical analyses showed that soil moisture had an over-riding effect on seasonal fluctuations in soil physicochemical and microbial populations. While within season soil microbial activity could be differentiated between wheat fields under rotational and monoculture management, these differences were not significant.

  17. Comparative Study of Crude Oil Contamination Effect on Industrial and Forest Soil Microbial Community

    Directory of Open Access Journals (Sweden)

    Nasrin Ansari

    2017-02-01

    Full Text Available Introduction: Petroleum hydrocarbons are widespread pollutant that enters to soil by some pathwayssuch as: Transportation of crude oil, conservation of oil compounds, crude oil spill and treatment process on refineries. Oil pollution has some ecological effect on soil that disturbed composition and diversity of microbial community. Also this pollution has some effects on microbial activity and enzymes of soil. Forests ecosystems may be polluted with petroleum hydrocarbons via different ways such as transportation and spill of crude oil from resource of petroleum storage. Industrial soil defined as the soils that located in industrial area such as petrochemical plant, mine, chemical factories and etc. These soils always contaminated to many pollutant such as: oil, diesel and heavy metals. These pollutants have some effects on the texture of the soil and microbial community. The aim of this research is to understand the effect of oil pollution on two different soils. Material and Methods: In order to evaluate the effect of crude oil on soil microbial community, two different soil samples were collected from industrial and forest soils. Six microcosms were designed in this experiment. Indeed each soil sample examined inthree microcosms asunpolluted microcosm, polluted microcosm, and polluted microcosm with nutrient supply of Nitrogen and PhosphorusSome factors were assayed in each microcosm during 120 days of experiment. The included study factors were: total heterotrophic bacteria, total crude oil degrading bacteria, dehydrogenase enzyme and crude oil biodegradation. For enumeration of heterotrophic bacteria nutrient agar medium was used. In this method serial dilutions were done from each soil and spread on nutrient agar medium then different colonies were counted. For enumeration of degrading bacteria Bushnel-Hass (BH medium were used. The composition of this medium was (g/lit: 1 gr KH2PO4, 1gr K2HPO4, 0.2 gr MgSO4.7H2O, 0.02 gr CaCl2, 1 gr NH4

  18. Mineralogical controls on microbial biomass accumulation on two tropical soils

    Science.gov (United States)

    Block, K. A.; Pena, S. A.; Katz, A.; Gottlieb, P.; Volta, A.

    2017-12-01

    The characteristics of soil organic matter (SOM) generated by microbes and associated with minerals are not well defined. This information is critical to reducing uncertainty in climate models related to C cycling and ecosystem feedbacks. The resistance to degradation of mineral-associated SOM is influenced by aggregate structure, mineral chemistry and microbial community. In this work we examine the influence of mineral composition, including amorphous coatings on the biomass yield and aggregate structure through thermogravimetric analysis, X-ray diffraction and electron microscopy. Two soil organisms, Pseudomonas phaseolicola, and Streptomyces griseosporus, were each incubated over a 72-hour period in minimal media with the cultured under the same conditions. In all samples, approximately half of the sample mass loss occurred between 175 ºC - 375 ºC, which we attribute to biomolecules accumulated on the mineral surfaces. We observed a slightly larger mass loss in the Inceptisol than in the Oxisol, most of which corresponded to compounds that underwent pyrolysis at 300 ºC. HRTEM micrographs and TEM-EDS image maps showing the spatial relationship of microbial necromass to soil minerals will be reported.

  19. Soil Microbial Community Contribution to Small Headwater Stream Metabolism.

    Science.gov (United States)

    Clapcott, J. E.; Gooderham, J. P.; Barmuta, L. A.; Davies, P. E.

    2005-05-01

    The temporal dynamics of sediment respiration were examined in seven small headwater streams in forested catchments in 2004. A strong seasonal response was observed with higher respiration rates in depositional zones than in gravel runs. The data were also examined in the context of proportional habitat distributions that highlighted the importance of high flow events in shaping whole stream metabolic budgets. This study specifically examines the question of terrestrial soil respiration contribution to whole stream metabolism by the controlled inundation of terrestrial soils. The experiment included six experimentally inundated terrestrial zones, six terrestrial controls, and six in-stream depositional zones. Sediment bacterial respiration was measured using 14C leucine incorporation and cotton strip bioassays were also employed to provide an indicative measure of sediment microbial activity. Despite high variability and exhibiting significantly lower bacterial activity than in-stream sediments, modelling using flow data and habitat mapping illustrated the important contribution of terrestrial soil respiration to the whole stream metabolic budgets of small headwater streams. In addition, microbial community composition examined using phospholipid fatty acid analysis clearly differentiated between terrestrial and aquatic communities. Freshly inundated terrestrial communities remained similar to un-inundated controls after 28 days.

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

    Science.gov (United States)

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

    2009-12-01

    Woody plant encroachment (WPE) into savannas and grasslands is a global phenomenon that alters soil organic matter (SOM) dynamics through changes in litter quality and quantity, soil structure, microbial ecology, and soil hydrology. To elucidate the controls upon microbial accessibility to SOM, bulk soils from a chronosequence of progressive WPE into native grasslands at the Texas A&M Agricultural Experimental Station La Copita Research Area were incubated for one year. The quantity and stable carbon isotope composition of respired CO2, plant biopolymer chemistry in SOM, and microbial community structure were tracked. Respiration rates declined steadily over the course of the experiment with 15-25% of the total CO2 respired released in the first month of incubation. Between 8 and 18% of the total carbon was mineralized to CO2 throughout the incubation. After day 84 a significantly (p evidence of enhanced carbon stabilization in these respiration experiments. In fact, a greater proportion of total carbon was lost from the soil of mature woody stands than from young stands, suggesting carbon accumulation observed with WPE may be due to greater input rates or microbial dynamics not captured in the laboratory incubation. A cluster approximately 34 years in age represents a transition point in WPE where respiration dynamics become distinct between grassland and wooded elements. By day 84 of the incubation CO2 respired from all soils was depleted with respect to bulk SOM (1.5 to 5‰) and this pattern remained for the rest of the incubation. As the depletion of CO2 relative to bulk SOM was observed in grassland and cluster soils, we hypothesized the depleted signature resulted from the utilization of depleted biopolymers, specifically lignin, cutin and suberin, as hypothesized by others. Quantitative and isotopic comparisons of these monomers prior to and following the incubation will determine if selective compound utilization is a reason for this depletion. The results

  1. Short-term utilization of carbon by the soil microbial community under future climatic conditions in a temperate heathland

    DEFF Research Database (Denmark)

    Reinsch, Sabine; Michelsen, Anders; Sárossy, Zsuzsa

    2014-01-01

    An in-situ13C pulse-labeling experiment was carried out in a temperate heath/grassland to study the impacts of elevated CO2 concentration (510ppm), prolonged summer droughts (annual exclusion of 7.6±0.8%) and increased temperature (~1°C) on belowground carbon (C) utilization. Recently assimilated C...... (13C from the pulse-label) was traced into roots, soil and microbial biomass 1, 2 and 8 days after pulse-labeling. The importance of the microbial community in C utilization was investigated using 13C enrichment patterns in different microbial functional groups on the basis of phospholipid fatty acid...... (PLFA) biomarker profiles. Climate treatments did not affect microbial abundance in soil or rhizosphere fractions in terms of total PLFA-C concentration. Elevated CO2 significantly reduced the abundance of gram-negative bacteria (17:0cy), but did not affect the abundance of decomposers (fungi...

  2. Microbial Diversity in Soil Treatment Systems for Wastewater

    Science.gov (United States)

    Van Cuyk, S.; Spear, J.; Siegrist, R.; Pace, N.

    2002-05-01

    There is an increasing awareness and concern over land based wastewater system performance with respect to the removal of bacteria and virus. The goal of this work is to describe and identify the organismal composition of the microbiota in the applied wastewater effluent, the rich biomat that develops at the infiltrative surface, and in the soil percolate in order to aid in the understanding of bacterial and virus purification in soil treatment systems. The traditional reliance on pure culture techniques to describe microbiota is circumvented by the employment of a molecular approach. Microbial community characterization is underway based on cloning and sequencing of 16S rRNA genes for phylogenetic analyses, to determine the nature and quantity of microbiota that constitute these ecosystems. Knowledge of the organisms naturally present can influence the design and treatment capacity of these widely used land based systems. Laboratory, intermediate and field scale systems are currently under study. Since human pathogens are known to exist in sewage effluents, their removal in wastewater infiltration systems and within the underlying soil are in need of a more fundamental understanding. The relationship between design parameters and environmental conditions, including a microbial characterization, is essential for the prevention of contamination in groundwater sources. Preliminary results indicate the presence of uncultured organisms and phylogenetic kinds that had not been detected in these systems using other methods. Acinetobacter johnsonii and Acrobacter cryaerophilus were the two dominant species found in septic tank effluent, comprising 20% and 11% of the library respectively. In soil samples collected from the infiltrative surface of a column dosed with STE, there was no dominant bacterial species present. Percolate samples collected from the outflow of the column showed that a tuber borchii symbiont, a common soil microorganism, dominated the bacterial

  3. Temporal dynamics in microbial soil communities at anthrax carcass sites.

    Science.gov (United States)

    Valseth, Karoline; Nesbø, Camilla L; Easterday, W Ryan; Turner, Wendy C; Olsen, Jaran S; Stenseth, Nils Chr; Haverkamp, Thomas H A

    2017-09-26

    Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing. The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species. Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be

  4. Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

    Science.gov (United States)

    Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

    2016-11-01

    Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.

  5. Impact of treated wastewater for irrigation on soil microbial communities.

    Science.gov (United States)

    Ibekwe, A M; Gonzalez-Rubio, A; Suarez, D L

    2018-05-01

    The use of treated wastewater (TWW) for irrigation has been suggested as an alternative to use of fresh water because of the increasing scarcity of fresh water in arid and semiarid regions of the world. However, significant barriers exist to widespread adoption due to some potential contaminants that may have adverse effects on soil quality and or public health. In this study, we investigated the abundance and diversity of bacterial communities and the presence of potential pathogenic bacterial sequences in TWW in comparison to synthetic fresh water (SFW) using pyrosequencing. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity and abundance of different bacterial groups in TWW irrigated soils to soils treated with SFW. Shannon diversity index values (H') suggest that microbial diversity was not significantly different (P<0.086) between soils with TWW and SFW. Pyrosequencing detected sequences of 17 bacterial phyla with Proteobacteria (32.1%) followed by Firmicutes (26.5%) and Actinobacteria (14.3%). Most of the sequences associated with nitrifying bacteria, nitrogen-fixing bacteria, carbon degraders, denitrifying bacteria, potential pathogens, and fecal indicator bacteria were more abundant in TWW than in SFW. Therefore, TWW effluent may contain bacterial that may be very active in many soil functions as well as some potential pathogens. Published by Elsevier B.V.

  6. Impact of long term pesticide usage on soil microbial activities and 14C-monocrotophos degradation

    International Nuclear Information System (INIS)

    Tayaputch, N.; Pimpan, P.; Phaikaew, Y.; Chukiatwatana, L.

    2001-01-01

    The effects of long term pesticide usage on soil microbial activities and degradation of 14 C-monocrotophos was observed under cotton field conditions. The experimental field was divided into treated and untreated plots. Pesticides were applied to treated plots at weekly intervals as in common practice in Thailand. The total numbers of applications were 11, 16 and 16 for first, second and third crop seasons, during the three years from 1996 to 1998. Soil samples at depths of 0-15 cm and 15-30 cm were sampled before and after pesticide application for the first two crops, while in the third crop season only the surface layer of soil was taken. The samples were assessed for CO 2 from respiration, soil microbial population, iron reduction capacity, and rates of nitrification. Soil biomass and microbial activities as measured from respiration and iron reduction decreased in the treated plots at both depths after each pesticide application over the three crop seasons, whereas samples from untreated plots at both depths did not show decreases. Repeated application of pesticides did not show any effect on nitrification rates of the first crop but there was inhibition in the second and third crops. Soil columns, treated with 14 C-monocrotophos one week after last pesticide application, were harvested after 0, 3, 6, 9, 18, 24 and 30 months. Extractable residues of 14 C were found only in the 0-15 cm layer. In treated and untreated plots, residues declined from 80.17 and 85.68 to 0.44% of the applied 14 C within 6 months. The long term usage of pesticides did not affect the half-life of 14 C-monocrotophos. Bound residues of 14 C were found at the highest concentrations, 18.94 and 12.58% of that applied, at 6 months in treated and untreated plots, thereafter the binding decreased to 4.68 and 2.74% within 30 months. (author)

  7. Effects of Carbon in Flooded Paddy Soils: Implications for Microbial Activity and Arsenic Mobilization

    Science.gov (United States)

    Avancha, S.; Boye, K.

    2014-12-01

    In the Mekong delta in Cambodia, naturally occurring arsenic (originating from erosion in the Himalaya Mountains) in paddy soils is mobilized during the seasonal flooding. As a consequence, rice grown on the flooded soils may take up arsenic and expose people eating the rice to this carcinogenic substance. Microbial activity will enhance or decrease the mobilization of arsenic depending on their metabolic pathways. Among the microbes naturally residing in the soil are denitrifying bacteria, sulfate reducers, metal reducers (Fe, Mn), arsenic reducers, methanogens, and fermenters, whose activity varies based on the presence of oxygen. The purpose of the experiment was to assess how different amendments affect the microbial activity and the arsenic mobilization during the transition from aerobic to anaerobic metabolism after flooding of naturally contaminated Cambodian soil. In a batch experiment, we investigated how the relative metabolic rate of naturally occurring microbes could vary with different types of organic carbon. The experiment was designed to measure the effects of various sources of carbon (dried rice straw, charred rice straw, manure, and glucose) on the microbial activity and arsenic release in an arsenic-contaminated paddy soil from Cambodia under flooded conditions. All amendments were added based on the carbon content in order to add 0.036 g of carbon per vial. The soil was flooded with a 10mM TRIS buffer solution at pH 7.04 in airtight 25mL serum vials and kept at 25 °C. We prepared 14 replicates per treatment to sample both gas and solution. On each sampling point, the solution replicates were sampled destructively. The gas replicates continued on and were sampled for both gas and solution on the final day of the experiment. We measured pH, total arsenic, methane, carbon dioxide, and nitrous oxide at 8 hours, 1.5 days, 3.33 days, and 6.33 days from the start of the experiment.

  8. Microbial biomass, community structure and metal tolerance of a naturally Pb-enriched forest soil.

    Science.gov (United States)

    Bååth, E; Díaz-Raviña, M; Bakken, L R

    2005-11-01

    The effect of long-term elevated soil Pb levels on soil microbiota was studied at a forest site in Norway, where the soil has been severely contaminated with Pb since the last period of glaciation (several thousand years). Up to 10% Pb (total amount, w/w) has been found in the top layer. The microbial community was drastically affected, as judged from changes in the phospholipid fatty acid (PLFA) pattern. Specific PLFAs that were high in Pb-enriched soil were branched (especially br17:0 and br18:0), whereas PLFAs common in eukaryotic organisms such as fungi (18:2omega6,9 and 20:4) were low compared with levels at adjacent, uncontaminated sites. Congruent changes in the PLFA pattern were found upon analyzing the culturable part of the bacterial community. The high Pb concentrations in the soil resulted in increased tolerance to Pb of the bacterial community, measured using both thymidine incorporation and plate counts. Furthermore, changes in tolerance were correlated to changes in the community structure. The bacterial community of the most contaminated soils showed higher specific activity (thymidine and leucine incorporation rates) and higher culturability than that of control soils. Fungal colony forming units (CFUs) were 10 times lower in the most Pb-enriched soils, the species composition was widely different from that in control soils, and the isolated fungi had high Pb tolerance. The most commonly isolated fungus in Pb-enriched soils was Tolypocladium inflatum. Comparison of isolates from Pb-enriched soil and isolates from unpolluted soils showed that T. inflatum was intrinsically Pb-tolerant, and that the prolonged conditions with high Pb had not selected for any increased tolerance.

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

    Science.gov (United States)

    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).

  10. Dynamics of soil organic carbon and microbial activity in treated wastewater irrigated agricultural soils along soil profiles

    Science.gov (United States)

    Jüschke, Elisabeth; Marschner, Bernd; Chen, Yona; Tarchitzky, Jorge

    2010-05-01

    Treated wastewater (TWW) is an important source for irrigation water in arid and semiarid regions and already serves as an important water source in Jordan, the Palestinian Territories and Israel. Reclaimed water still contains organic matter (OM) and various compounds that may effect microbial activity and soil quality (Feigin et al. 1991). Natural soil organic carbon (SOC) may be altered by interactions between these compounds and the soil microorganisms. This study evaluates the effects of TWW irrigation on the quality, dynamics and microbial transformations of natural SOC. Priming effects (PE) and SOC mineralization were determined to estimate the influence of TWW irrigation on SOC along soil profiles of agricultural soils in Israel and the Westbank. The used soil material derived from three different sampling sites allocated in Israel and The Palestinian Authority. Soil samples were taken always from TWW irrigated sites and control fields from 6 different depths (0-10, 10-20, 20-30, 30-50, 50-70, 70-100 cm). Soil carbon content and microbiological parameters (microbial biomass, microbial activities and enzyme activities) were investigated. In several sites, subsoils (50-160 cm) from TWW irrigated plots were depleted in soil organic matter with the largest differences occurring in sites with the longest TWW irrigation history. Laboratory incubation experiments with additions of 14C-labelled compounds to the soils showed that microbial activity in freshwater irrigated soils was much more stimulated by sugars or amino acids than in TWW irrigated soils. The lack of such "priming effects" (Hamer & Marschner 2005) in the TWW irrigated soils indicates that here the microorganisms are already operating at their optimal metabolic activity due to the continuous substrate inputs with soluble organic compounds from the TWW. The fact that PE are triggered continuously due to TWW irrigation may result in a decrease of SOC over long term irrigation. Already now this could be

  11. Accelerated decay rates drive soil organic matter persistence and storage in temperate forests via greater mineral stabilization of microbial residues.

    Science.gov (United States)

    Phillips, R.; Craig, M.; Turner, B. L.; Liang, C.

    2017-12-01

    Climate predicts soil organic matter (SOM) stocks at the global scale, yet controls on SOM stocks at finer spatial scales are still debated. A current hypothesis predicts that carbon (C) and nitrogen (N) storage in soils should be greater when decomposition is slow owing to microbial competition for nutrients or the recalcitrance of organic substrates (hereafter the `slow decay' hypothesis). An alternative hypothesis predicts that soil C and N storage should be greater in soils with rapid decomposition, owing to the accelerated production of microbial residues and their stabilization on soil minerals (hereafter the `stabilization hypothesis'). To test these alternative hypotheses, we quantified soil C and N to 1-m depth in temperate forests across the Eastern and Midwestern US that varied in their biotic, climatic, and edaphic properties. At each site, we sampled (1) soils dominated by arbuscular mycorrhizal (AM) tree species, which typically have fast decay rates and accelerated N cycling, (2) soils dominated by ectomycorrhizal (ECM) tree species, which generally have slow decay rates and slow N cycling, and (3) soils supporting both AM and ECM trees. To the extent that trees and theor associated microbes reflect and reinforce soil conditions, support for the slow decay hypothesis would be greater SOM storage in ECM soils, whereas support for the stabilization hypothesis would be greater SOM storage in AM soils. We found support for both hypotheses, as slow decomposition in ECM soils increased C and N storage in topsoil, whereas fast decomposition in AM soils increased C and N storage in subsoil. However, at all sites we found 57% greater total C and N storage in the entire profile in AM- soils (P stabilization hypothesis. Amino sugar biomarkers (an indicator of microbial necromass) and particle size fractionation revealed that the greater SOM storage in AM soils was driven by an accumulation of microbial residues on clay minerals and metal oxides. Taken together

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

    Science.gov (United States)

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

    2016-10-01

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

  13. Effect of elevated CO2 on chlorpyriphos degradation and soil microbial activities in tropical rice soil.

    Science.gov (United States)

    Adak, Totan; Munda, Sushmita; Kumar, Upendra; Berliner, J; Pokhare, Somnath S; Jambhulkar, N N; Jena, M

    2016-02-01

    Impact of elevated CO2 on chlorpyriphos degradation, microbial biomass carbon, and enzymatic activities in rice soil was investigated. Rice (variety Naveen, Indica type) was grown under four conditions, namely, chambered control, elevated CO2 (550 ppm), elevated CO2 (700 ppm) in open-top chambers and open field. Chlorpyriphos was sprayed at 500 g a.i. ha(-1) at maximum tillering stage. Chlorpyriphos degraded rapidly from rice soils, and 88.4% of initially applied chlorpyriphos was lost from the rice soil maintained under elevated CO2 (700 ppm) by day 5 of spray, whereas the loss was 80.7% from open field rice soil. Half-life values of chlorpyriphos under different conditions ranged from 2.4 to 1.7 days with minimum half-life recorded with two elevated CO2 treatments. Increased CO2 concentration led to increase in temperature (1.2 to 1.8 °C) that played a critical role in chlorpyriphos persistence. Microbial biomass carbon and soil enzymatic activities specifically, dehydrogenase, fluorescien diacetate hydrolase, urease, acid phosphatase, and alkaline phosphatase responded positively to elevated CO2 concentrations. Generally, the enzyme activities were highly correlated with each other. Irrespective of the level of CO2, short-term negative influence of chlorpyriphos was observed on soil enzymes till day 7 of spray. Knowledge obtained from this study highlights that the elevated CO2 may negatively influence persistence of pesticide but will have positive effects on soil enzyme activities.

  14. Monitoring the Perturbation of Soil and Groundwater Microbial Communities Due to Pig Production Activities

    KAUST Repository

    Hong, Pei-Ying; Yannarell, A. C.; Dai, Q.; Ekizoglu, M.; Mackie, R. I.

    2013-01-01

    This study aimed to determine if biotic contaminants originating from pig production farms are disseminated into soil and groundwater microbial communities. A spatial and temporal sampling of soil and groundwater in proximity to pig production farms

  15. Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities.

    NARCIS (Netherlands)

    Epelde, L.; Becerril, J.M.; Kowalchuk, G.A.; Deng, Y.; Zhou, J.; Garbisu, C.

    2010-01-01

    been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts

  16. Bioremediation of soil heavily contaminated with crude oil and its products: composition of the microbial consortium

    Directory of Open Access Journals (Sweden)

    JELENA S. MILIĆ

    2009-04-01

    Full Text Available Bioremediation, a process that utilizes the capability of microorganism to degrade toxic waste, is emerging as a promising technology for the treatment of soil and groundwater contamination. The technology is very effective in dealing with petroleum hydrocarbon contamination. The aim of this study was to examine the composition of the microbial consortium during the ex situ experiment of bioremediation of soil heavily contaminated with crude oil and its products from the Oil Refinery Pančevo, Serbia. After a 5.5-month experiment with biostimulation and bioventilation, the concentration of the total petroleum hydrocarbons (TPH had been reduced from 29.80 to 3.29 g/kg (89 %. In soil, the dominant microorganism population comprised Gram-positive bacteria from actinomycete-Nocardia group. The microorganisms which decompose hydrocarbons were the dominant microbial population at the end of the process, with a share of more than 80 % (range 107 CFU/g. On the basis of the results, it was concluded that a stable microbial community had been formed after initial fluctuations.

  17. Seasonal Variations in Sugar Contents and Microbial Community Behavior in a Ryegrass Soil

    Science.gov (United States)

    Medeiros, P. M.; Fernandes, M. F.; Dick, R. P.; Simoneit, B. R.

    2004-12-01

    Soil is a complex mixture of numerous inorganic and organic constituents that vary in size, shape, chemical constitution and reactivity, and hosts numerous organisms. Total sugars have been estimated to constitute 10% (average) of soil organic matter, occurring in living and decaying organisms, as well as in extracellular materials. The role of sugars in soils is attributed to their influence on soil structure, chemical processes, plant nutrition and microbial activity. The sources of sugars in soils are: a) plants (the primary source); b) animals (the minor source), and c) microorganisms (fungi, bacteria, algae), which decompose the primary plant and animal material, and synthesize the major part of soil carbohydrates. A particular soil sample provides a momentary glimpse into a dynamic system (continuous addition, degradation and synthesis) that might, except for seasonal variations, be in equilibrium. The purpose of this study is to identify and quantify the major sugars in a grass soil and characterize the relationship between their concentration variations and soil microbial behavior over an annual cycle. Soil samples were collected monthly in a ryegrass field close to Corvallis, Oregon, and analyzed by gas chromatography-mass spectrometry as total silylated extracts for sugar composition, and by gas chromatography-flame ionization as fatty acid methyl esters derived from phospholipids and neutral lipids (PLFA and NLFA, respectively). The preliminary results of the first six-month experiment (from January to June, 2004) show that as the ambient temperatures increase the sugar concentrations (glucose, fructose, sucrose and trehalose) also tend to increase in the soil. A decrease is observed in March when precipitation was low during the whole month. The same trend is observed for the active biomass of fungi and bacteria estimated by their fatty acids derived from phospholipids. Fatty acids 18:2ω 6c and 18:3ω 6c are used as fungal biomarkers. Branched (15:0i

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

    DEFF Research Database (Denmark)

    Modrzyński, Jakub J.; Christensen, Jan H.; Mayer, Philipp

    2016-01-01

    During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial...... functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial...... microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient...

  19. Effect of Pulp mill sludge on soil characteristics, microbial diversity and vegetal production of Lollium perene

    Energy Technology Data Exchange (ETDEWEB)

    Gallardo, F.; Cea, M.; Diez, M. C.

    2009-07-01

    The Chemical properties of the sludge (High organic matter content, pH, buffer capacity, nitrogen and phosphorous level, and low concentration of trace heavy metals and organic pollutants) suggest that this material may represent a valuable resource as soil amendment, improving soil characteristics, microbial diversity and vegetal production of mill sludge addition to volcanic soil (Andisol) on soil characteristics, microbial diversity and vegetal production of Lollium perenne, in field assays. (Author)

  20. Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils

    OpenAIRE

    Hamamura, Natsuko; Olson, Sarah H.; Ward, David M.; Inskeep, William P.

    2006-01-01

    Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-14C]hexadecane. Microbial populat...

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

    Science.gov (United States)

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

    2016-10-01

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

  2. Changes in Soil Enzyme Activities and Microbial Biomass after Revegetation in the Three Gorges Reservoir, China

    Directory of Open Access Journals (Sweden)

    Qingshui Ren

    2018-05-01

    Full Text Available Soil enzymes and microbes are central to the decomposition of plant and microbial detritus, and play important roles in carbon, nitrogen, and phosphorus biogeochemistry cycling at the ecosystem level. In the present study, we characterized the soil enzyme activity and microbial biomass in revegetated (with Taxodium distichum (L. Rich. and Cynodon dactylon (L. Pers. versus unplanted soil in the riparian zone of the Three Gorges Dam Reservoir (TGDR, in order to quantify the effect of revegetation on the edaphic microenvironment after water flooding in situ. After revegetation, the soil physical and chemical properties in revegetated soil showed significant differences to those in unplanted soil. The microbial biomass carbon and phosphorus in soils of T. distichum were significantly higher than those in C. dactylon and unplanted soils, respectively. The microbial biomass nitrogen in revegetated T. distichum and C. dactylon soils was significantly increased by 273% and 203%, respectively. The enzyme activities of T. distichum and C. dactylon soils displayed no significant difference between each other, but exhibited a great increase compared to those of the unplanted soil. Elements ratio (except C/N (S did not vary significantly between T. distichum and C. dactylon soils; meanwhile, a strong community-level elemental homeostasis in the revegetated soils was found. The correlation analyses demonstrated that only microbial biomass carbon and phosphorus had a significantly positive relationship with soil enzyme activities. After revegetation, both soil enzyme activities and microbial biomasses were relatively stable in the T. distichum and C. dactylon soils, with the wooded soil being more superior. The higher enzyme activities and microbial biomasses demonstrate the C, N, and P cycling and the maintenance of soil quality in the riparian zone of the TGDR.

  3. Soil Microbial Biomass, Basal Respiration and Enzyme Activity of Main Forest Types in the Qinling Mountains

    Science.gov (United States)

    Cheng, Fei; Peng, Xiaobang; Zhao, Peng; Yuan, Jie; Zhong, Chonggao; Cheng, Yalong; Cui, Cui; Zhang, Shuoxin

    2013-01-01

    Different forest types exert essential impacts on soil physical-chemical characteristics by dominant tree species producing diverse litters and root exudates, thereby further regulating size and activity of soil microbial communities. However, the study accuracy is usually restricted by differences in climate, soil type and forest age. Our objective is to precisely quantify soil microbial biomass, basal respiration and enzyme activity of five natural secondary forest (NSF) types with the same stand age and soil type in a small climate region and to evaluate relationship between soil microbial and physical-chemical characters. We determined soil physical-chemical indices and used the chloroform fumigation-extraction method, alkali absorption method and titration or colorimetry to obtain the microbial data. Our results showed that soil physical-chemical characters remarkably differed among the NSFs. Microbial biomass carbon (Cmic) was the highest in wilson spruce soils, while microbial biomass nitrogen (Nmic) was the highest in sharptooth oak soils. Moreover, the highest basal respiration was found in the spruce soils, but mixed, Chinese pine and spruce stands exhibited a higher soil qCO2. The spruce soils had the highest Cmic/Nmic ratio, the greatest Nmic/TN and Cmic/Corg ratios were found in the oak soils. Additionally, the spruce soils had the maximum invertase activity and the minimum urease and catalase activities, but the maximum urease and catalase activities were found in the mixed stand. The Pearson correlation and principle component analyses revealed that the soils of spruce and oak stands obviously discriminated from other NSFs, whereas the others were similar. This suggested that the forest types affected soil microbial properties significantly due to differences in soil physical-chemical features. PMID:23840671

  4. Radionuclides distribution, properties, and microbial diversity of soils in uranium mill tailings from southeastern China

    International Nuclear Information System (INIS)

    Yan, Xun; Luo, Xuegang

    2015-01-01

    Objective: To collect the radioactive contamination data for environmental rehabilitation in uranium mill tailings in southeastern China. Method: The sample areas were divided into high, moderate and low concentration areas, according to the uranium concentration. For every area, 3 soil samples were collected at 0–15 cm, 15–30 cm and 30–45 cm depth respectively, with 5 repetitions for each. Total 45 (3 × 5 × 3) soil samples were collected. Physicochemical properties and enzyme activities of soils were determined as described by references. The concentrations of the radionuclides 238 U, 232 Th, 226 Ra and 40 K in soils were determined by using HPGe gamma-ray spectrometer. Soil microbial diversity was analyzed via denaturing gradient gel electrophoresis (DGGE). Results: Soil samples were all acidic. Physicochemical properties, like pH, content of total/available N, P and K, as well as enzyme activities were all increased along with decreased uranium concentration. The 232 Th concentration was increased with the decreased uranium concentration and was not influenced by the depth of sample sites. However, uranium concentration and depth of sample showed no significant influence on the concentrations of 226 Ra and 40 K. The concentration of 232 Th was significantly correlated with that of 226 Ra and 40 K, while the concentrations of 226 Ra and 40 K were significantly correlated. However, Pearson correlation coefficients between 238 U and other radionuclides were not significant. The microbial population in different concentration areas was different with four domain strains in low area, and two for both moderate and high areas. Furthermore, in each sample site, Proteobacteria was the most dominant flora, while environmental samples were the second according to GenBank database. Moreover, Serratia sp. of Proteobacteria was the dominant strain. Conclusion: Radionuclides distribution in the uranium mill tailing showed a profound influence on soil properties and

  5. Microbial Activity in Forest Soil Under Beech, Spruce, Douglas Fir and Fir

    Directory of Open Access Journals (Sweden)

    Hajnal-Jafari Timea

    2016-08-01

    Full Text Available The aim of this research was to investigate the microbial activity in forest soil from different sites under deciduous and coniferous trees in Serbia. One site on Stara planina was under beech trees (Fagus sp. while another under mixture of spruce (Picea sp. and Douglas fir (Pseudotsuga sp.. The site on Kopaonik was under mixture of beech (Fagus sp. and spruce (Picea sp. trees. The site on Tara was dominantly under fir (Abies sp., beech (Fagus sp. and spruce (Picea sp.. The total number of bacteria, the number of actinobacteria, fungi and microorganisms involved in N and C cycles were determined using standard method of agar plates. The activities of dehydrogenase and ß-glucosidase enzymes were measured by spectrophotometric methods. The microbial activity was affected by tree species and sampling time. The highest dehydrogenase activity, total number of bacteria, number of actinobacteria, aminoheterotrophs, amylolytic and cellulolytic microorganisms were determined in soil under beech trees. The highest total number of fungi and number of pectinolytic microorganisms were determined in soil under spruce and Douglas fir trees. The correlation analyses proved the existence of statistically significant interdependency among investigated parameters.

  6. Soil biochemical properties and microbial resilience in agroforestry systems: effects on wheat growth under controlled drought and flooding conditions.

    Science.gov (United States)

    Rivest, David; Lorente, Miren; Olivier, Alain; Messier, Christian

    2013-10-01

    Agroforestry is increasingly viewed as an effective means of maintaining or even increasing crop and tree productivity under climate change while promoting other ecosystem functions and services. This study focused on soil biochemical properties and resilience following disturbance within agroforestry and conventional agricultural systems and aimed to determine whether soil differences in terms of these biochemical properties and resilience would subsequently affect crop productivity under extreme soil water conditions. Two research sites that had been established on agricultural land were selected for this study. The first site included an 18-year-old windbreak, while the second site consisted in an 8-year-old tree-based intercropping system. In each site, soil samples were used for the determination of soil nutrient availability, microbial dynamics and microbial resilience to different wetting-drying perturbations and for a greenhouse pot experiment with wheat. Drying and flooding were selected as water stress treatments and compared to a control. These treatments were initiated at the beginning of the wheat anthesis period and maintained over 10 days. Trees contributed to increase soil nutrient pools, as evidenced by the higher extractable-P (both sites), and the higher total N and mineralizable N (tree-based intercropping site) found in the agroforestry compared to the conventional agricultural system. Metabolic quotient (qCO2) was lower in the agroforestry than in the conventional agricultural system, suggesting higher microbial substrate use efficiency in agroforestry systems. Microbial resilience was higher in the agroforestry soils compared to soils from the conventional agricultural system (windbreak site only). At the windbreak site, wheat growing in soils from agroforestry system exhibited higher aboveground biomass and number of grains per spike than in conventional agricultural system soils in the three water stress treatments. At the tree

  7. Evidence for a soil microbial terroir in the Chianti Classico district in Tuscany (Italy)

    Science.gov (United States)

    Mocali, Stefano; Priori, Simone; Valboa, Giuseppe; Fabiani, Arturo; Pellegrini, Sergio; Puccioni, Sergio; Zombardo, Alessandra; Storchi, Paolo; Costantini, Edoardo

    2017-04-01

    Originally developed for wine, the terroir concept is becoming popular throughout agri-environmental sciences in many parts of the world, linking the uniqueness and quality of agricultural products to the environment where they are produced. Even thought it is well known that geology, morphology and microclimate influence and diversify the wine characters within a wine district (macro-terroir), recent literature suggests that different soil features can drive wine characters also within the same macro-terroir, at both farm and vineyard scale. However, the drivers beyond these differences remain elusive, and the potential contribution of soil microbes has been ignored until recently. Therefore, in this multidisciplinary work we have tried to assess the possible role of soil microbial communities in vineyards on defining the quality of the wine produced. Soils from 4 different macro-terroir areas located within the Barone Ricasoli farm in Brolio (SI), Tuscany (Central Italy), characterized by different geology and cultivated with the grapevine cultivar Sangiovese, were collected: Fattoio (feldspathic sandstone), Leccio (marine sands), Agresto (limestone), and Ceni (fluvial deposits). Within each terroir, two areas homogeneous for soil features were delimited (Basic terroir unit, BTU) and monitored over 3 years for the soil physico-chemical and biological parameters as well as viticultural parameters. In this work we report the results of the analysis of microbial communities in the 8 BTUs, determined through molecular (PCR-DGGE), metabolic (BIOLOG) and biochemical (microbial respiration, biomass C) techniques. The results showed that each vineyard is characterized by a well defined bacterial community whose structure varies both as a function of different BTUs and terroir areas, depending on soil features. In fact, the vineyards Fattoio 1 and 2 exhibit a very similar bacterial composition between them and stable over time, even for the low total organic matter

  8. Temperature sensitivity of soil respiration rates enhanced by microbial community response.

    Science.gov (United States)

    Karhu, Kristiina; Auffret, Marc D; Dungait, Jennifer A J; Hopkins, David W; Prosser, James I; Singh, Brajesh K; Subke, Jens-Arne; Wookey, Philip A; Agren, Göran I; Sebastià, Maria-Teresa; Gouriveau, Fabrice; Bergkvist, Göran; Meir, Patrick; Nottingham, Andrew T; Salinas, Norma; Hartley, Iain P

    2014-09-04

    Soils store about four times as much carbon as plant biomass, and soil microbial respiration releases about 60 petagrams of carbon per year to the atmosphere as carbon dioxide. Short-term experiments have shown that soil microbial respiration increases exponentially with temperature. This information has been incorporated into soil carbon and Earth-system models, which suggest that warming-induced increases in carbon dioxide release from soils represent an important positive feedback loop that could influence twenty-first-century climate change. The magnitude of this feedback remains uncertain, however, not least because the response of soil microbial communities to changing temperatures has the potential to either decrease or increase warming-induced carbon losses substantially. Here we collect soils from different ecosystems along a climate gradient from the Arctic to the Amazon and investigate how microbial community-level responses control the temperature sensitivity of soil respiration. We find that the microbial community-level response more often enhances than reduces the mid- to long-term (90 days) temperature sensitivity of respiration. Furthermore, the strongest enhancing responses were observed in soils with high carbon-to-nitrogen ratios and in soils from cold climatic regions. After 90 days, microbial community responses increased the temperature sensitivity of respiration in high-latitude soils by a factor of 1.4 compared to the instantaneous temperature response. This suggests that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.

  9. Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO).

    Science.gov (United States)

    Touceda-González, M; Prieto-Fernández, Á; Renella, G; Giagnoni, L; Sessitsch, A; Brader, G; Kumpiene, J; Dimitriou, I; Eriksson, J; Friesl-Hanl, W; Galazka, R; Janssen, J; Mench, M; Müller, I; Neu, S; Puschenreiter, M; Siebielec, G; Vangronsveld, J; Kidd, P S

    2017-12-01

    Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg -1 soil, respiration increased from 7.4 to 40.1 mg C-CO 2 kg -1 soil d -1 , and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Variation in soil physical, chemical and microbial parameters under different land uses in bagrot valley, gilgit, pakistan

    International Nuclear Information System (INIS)

    Ali, S.

    2017-01-01

    Soil degradation due to unsustainable land use is a global problem and the biggest challenge for sustainability in mountain areas due to their ecological and socio-economic impacts. The study aims to evaluate the variation in the physical, chemical and microbial parameters of soil across various land uses in the Bagrot valley, Central Karakoram National Park (CKNP), Gilgit-Baltistan. Soil samples from 0-20 cm were collected from three land uses such as arable land, pasture, and adjacently located forest. The variables investigated were soil bulk density, total porosity, saturation percentage, sand, silt, clay, pH, electric conductivity, CaCO/sub 3/, organic matter, TN, available P, K, Fe, Mn, Cu and Zn and microbial parameters (16SrRNA and ITS copies number and fungi-to-bacterial ratio). A sigificant varriation in all parameters were found accross the land uses (ANOVA, p < 0.01). Similarly, the highest bulk density, sand, pH, EC, CaCO/sub 3/ were found in arable land, with the lowest values in forest. In contrast, soil under forest showed a higher total porosity, percent saturation, clay, OM, macro and micronutrients, microbial abundance and fungi-to-bacterial ratio than for other land uses. The differences in soil parameters across the land uses indicated detrimental impacts of agricultural activities on soil health. Soil pH and organic matter are the main controlling factors for microbial indicators as well as physical and chemical parameters. The results suggest that restoration of natural vegetation in degraded land and decrease in intensity of land use could improve soil properties in the study area, as well as other similar mountainous regions. (author)

  11. Predicting Soluble Nickel in Soils Using Soil Properties and Total Nickel.

    Science.gov (United States)

    Zhang, Xiaoqing; Li, Jumei; Wei, Dongpu; Li, Bo; Ma, Yibing

    2015-01-01

    Soil soluble nickel (Ni) concentration is very important for determining soil Ni toxicity. In the present study, the relationships between soil properties, total and soluble Ni concentrations in soils were developed in a wide range of soils with different properties and climate characteristics. The multiple regressions showed that soil pH and total soil Ni concentrations were the most significant parameters in predicting soluble Ni concentrations with the adjusted determination coefficients (Radj2) values of 0.75 and 0.68 for soils spiked with soluble Ni salt and the spiked soils leached with artificial rainwater to mimic field conditions, respectively. However, when the soils were divided into three categories (pH 8), they obtained better predictions with Radj2 values of 0.78-0.90 and 0.79-0.94 for leached and unleached soils, respectively. Meanwhile, the other soil properties, such as amorphous Fe and Al oxides and clay, were also found to be important for determining soluble Ni concentrations, indicating that they were also presented as active adsorbent surfaces. Additionally, the whole soil speciation including bulk soil properties and total soils Ni concentrations were analyzed by mechanistic speciation models WHAM VI and Visual MINTEQ3.0. It was found that WHAM VI provided the best predictions for the soils with pH 8. The Visual MINTEQ3.0 could provide better estimation for pH 8. These results indicated the possibility and applicability of these models to predict soil soluble Ni concentration by soil properties.

  12. Effects of Conservation Agriculture and Fertilization on Soil Microbial Diversity and Activity

    Directory of Open Access Journals (Sweden)

    Johan Habig

    2015-07-01

    Full Text Available Soil microbial communities perform critical functions in ecosystem processes. These functions can be used to assess the impact of agricultural practices on sustainable crop production. In this five-year study, the effect of various agricultural practices on soil microbial diversity and activity was investigated in a summer rainfall area under South African dryland conditions. Microbial diversity and activity were measured in the 0–15 cm layer of a field trial consisting of two fertilizer levels, three cropping systems, and two tillage systems. Using the Shannon–Weaver and Evenness diversity indices, soil microbial species richness and abundance were measured. Microbial enzymatic activities: β-glucosidase, phosphatase and urease, were used to evaluate ecosystem functioning. Cluster analysis revealed a shift in soil microbial community diversity and activity over time. Microbial diversity and activity were higher under no-till than conventional tillage. Fertilizer levels seemed to play a minor role in determining microbial diversity and activity, whereas the cropping systems played a more important role in determining the activity of soil microbial communities. Conservation agriculture yielded the highest soil microbial diversity and activity in diversified cropping systems under no-till.

  13. Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

    Science.gov (United States)

    Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

    2017-02-15

    Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

  14. The importance of anabolism in microbial control over soil carbon storage

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Chao; Schimel, Joshua P.; Jastrow, Julie D.

    2017-07-25

    Studies of the decomposition, transformation and stabilization of soil organic matter (SOM) have dramatically increased in recent years owing to growing interest in studying the global carbon (C) cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic C reservoir in soils depends upon microbial involvement, as soil C dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microorganism-mediated processes lead to soil C stabilization. Here, we define two pathways—ex vivo modification and in vivo turnover—which jointly explain soil C dynamics driven by microbial catabolism and/or anabolism. Accordingly, we use the conceptual framework of the soilmicrobial carbon pump’ (MCP) to demonstrate how microorganisms are an active player in soil C storage. The MCP couples microbial production of a set of organic compounds to their further stabilization, which we define as the entombing effect. This integration captures the cumulative long-term legacy of microbial assimilation on SOM formation, with mechanisms (whether via physical protection or a lack of activation energy due to chemical composition) that ultimately enable the entombment of microbial-derived C in soils. We propose a need for increased efforts and seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil C dynamics to the responses of the terrestrial C cycle under global change.

  15. Tropical forest soil microbial communities couple iron and carbon biogeochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Dubinsky, E.A.; Silver, W.L.; Firestone, M.K.

    2009-10-15

    We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500 - 5000 mm yr-1) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 x 10{sup 9} cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction of iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44 % of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron-reducers. the coexistence of large populations of ironreducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states, and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH4 production in these upland tropical forests.

  16. Perturbation of an arctic soil microbial community by metal nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Niraj [Department of Biology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada); Shah, Vishal [Department of Biology, Dowling College, Oakdale, NY 11769 (United States); Walker, Virginia K., E-mail: walkervk@queensu.ca [Department of Biology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada); Department of Biology, School of Environmental Studies and Department of Microbiology and Immunology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada)

    2011-06-15

    Highlights: {yields} Silver, copper and silica nanoparticles had an impact on arctic soil {yields} A microbial community toxicity indicator was developed {yields} Community surveys using pyrosequencing confirmed a shift in bacterial biodiversity {yields} Troublingly, silver nanoparticles were highly toxic to a plant beneficial bacterium - Abstract: Technological advances allowing routine nanoparticle (NP) manufacture have enabled their use in electronic equipment, foods, clothing and medical devices. Although some NPs have antibacterial activity, little is known about their environmental impact and there is no information on the influence of NPs on soil in the possibly vulnerable ecosystems of polar regions. The potential toxicity of 0.066% silver, copper or silica NPs on a high latitude (>78{sup o}N) soil was determined using community level physiological profiles (CLPP), fatty acid methyl ester (FAME) assays and DNA analysis, including sequencing and denaturing gradient gel electrophoresis (DGGE). The results of these different investigations were amalgamated in order to develop a community toxicity indicator, which revealed that of the three NPs examined, silver NPs could be classified as highly toxic to these arctic consortia. Subsequent culture-based studies confirmed that one of the community-identified plant-associating bacteria, Bradyrhizobium canariense, appeared to have a marked sensitivity to silver NPs. Thus, NP contamination of arctic soils particularly by silver NPs is a concern and procedures for mitigation and remediation of such pollution should be a priority for investigation.

  17. Perturbation of an arctic soil microbial community by metal nanoparticles

    International Nuclear Information System (INIS)

    Kumar, Niraj; Shah, Vishal; Walker, Virginia K.

    2011-01-01

    Highlights: → Silver, copper and silica nanoparticles had an impact on arctic soil → A microbial community toxicity indicator was developed → Community surveys using pyrosequencing confirmed a shift in bacterial biodiversity → Troublingly, silver nanoparticles were highly toxic to a plant beneficial bacterium - Abstract: Technological advances allowing routine nanoparticle (NP) manufacture have enabled their use in electronic equipment, foods, clothing and medical devices. Although some NPs have antibacterial activity, little is known about their environmental impact and there is no information on the influence of NPs on soil in the possibly vulnerable ecosystems of polar regions. The potential toxicity of 0.066% silver, copper or silica NPs on a high latitude (>78 o N) soil was determined using community level physiological profiles (CLPP), fatty acid methyl ester (FAME) assays and DNA analysis, including sequencing and denaturing gradient gel electrophoresis (DGGE). The results of these different investigations were amalgamated in order to develop a community toxicity indicator, which revealed that of the three NPs examined, silver NPs could be classified as highly toxic to these arctic consortia. Subsequent culture-based studies confirmed that one of the community-identified plant-associating bacteria, Bradyrhizobium canariense, appeared to have a marked sensitivity to silver NPs. Thus, NP contamination of arctic soils particularly by silver NPs is a concern and procedures for mitigation and remediation of such pollution should be a priority for investigation.

  18. Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

    Science.gov (United States)

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Anderson, Traute-Heidi; Kuzyakov, Yakov

    2014-01-01

    Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)–the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed. PMID:24722409

  19. Erratum: potential microbial contamination during sampling of permafrost soil assessed by tracers

    DEFF Research Database (Denmark)

    Bang-Andreasen, Toke; Schostag, Morten Dencker; Priemé, Anders

    2017-01-01

    Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial b...

  20. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    Energy Technology Data Exchange (ETDEWEB)

    He, Yujie [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Yang, Jinyan [Univ. of Georgia, Athens, GA (United States). Warnell School of Forestry and Natural Resources; Northeast Forestry Univ., Harbin (China). Center for Ecological Research; Zhuang, Qianlai [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Purdue Univ., West Lafayette, IN (United States). Dept. of Agronomy; Harden, Jennifer W. [U.S. Geological Survey, Menlo Park, CA (United States); McGuire, Anthony D. [Alaska Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, Univ. of Alaska, Fairbanks, AK (United States). U.S. Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit; Liu, Yaling [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Wang, Gangsheng [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Climate Change Science Inst. and Environmental Sciences Division; Gu, Lianhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division

    2015-11-20

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here in this study we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil RH (7.5 ± 2.4 PgCyr-1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil RH with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  1. Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

    Science.gov (United States)

    Cartwright, Jennifer M.; Advised by Dzantor, E. Kudjo

    2015-01-01

    Limestone cedar glades are a type of rock outcrop ecosystem characterized by shallow soil and extreme hydrologic conditions—seasonally ranging from xeric to saturated—that support a number of plant species of conservation concern. Although a rich botanical literature exists on cedar glades, soil biochemical processes and the ecology of soil microbial communities in limestone cedar glades have largely been ignored. This investigation documents the abiotic stress regime of this ecosystem (shallow soil, extreme hydrologic fluctuations and seasonally high soil surface temperatures) as well as soil physical and chemical characteristics, and relates both types of information to ecological structures and functions including vegetation, soil respiration, and soil microbial community metabolic profiles and diversity. Methods used in this investigation include field observations and measurements of soil physical and chemical properties and processes, laboratory analyses, and microbiological assays of soil samples.

  2. Comparison of model microbial allocation parameters in soils of varying texture

    Science.gov (United States)

    Hagerty, S. B.; Slessarev, E.; Schimel, J.

    2017-12-01

    The soil microbial community decomposes the majority of carbon (C) inputs to the soil. However, not all of this C is respired—rather, a substantial portion of the carbon processed by microbes may remain stored in the soil. The balance between C storage and respiration is controlled by microbial turnover rates and C allocation strategies. These microbial community properties may depend on soil texture, which has the potential to influence both the nature and the fate of microbial necromass and extracellular products. To evaluate the role of texture on microbial turnover and C allocation, we sampled four soils from the University of California's Hastings Reserve that varied in texture (one silt loam, two sandy loam, and on clay soil), but support similar grassland plant communities. We added 14C- glucose to the soil and measured the concentration of the label in the carbon dioxide (CO2), microbial biomass, and extractable C pools over 7 weeks. The labeled biomass turned over the slowest in the clay soil; the concentration of labeled biomass was more than 1.5 times the concentration of the other soils after 8 weeks. The clay soil also had the lowest mineralization rate of the label, and mineralization slowed after two weeks. In contrast, in the sandier soils mineralization rates were higher and did not plateau until 5 weeks into the incubation period. We fit the 14C data to a microbial allocation model and estimated microbial parameters; assimilation efficiency, exudation, and biomass specific respiration and turnover for each soil. We compare these parameters across the soil texture gradient to assess the extent to which models may need to account for variability in microbial C allocation across soils of different texture. Our results suggest that microbial C turns over more slowly in high-clay soils than in sandy soils, and that C lost from microbial biomass is retained at higher rates in high-clay soils. Accounting for these differences in microbial allocation

  3. Build your own soil: exploring microfluidics to create microbial habitat structures

    Science.gov (United States)

    Aleklett, Kristin; Kiers, E Toby; Ohlsson, Pelle; Shimizu, Thomas S; Caldas, Victor EA; Hammer, Edith C

    2018-01-01

    Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats. PMID:29135971

  4. Microbial colonisation in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

    Science.gov (United States)

    Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

    2014-09-01

    Colonisation of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focusing on settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associate vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soils types on the surface of the island. Total viable bacterial counts were performed with plate count at 22, 30 and 37 °C for all soils samples and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms aerobic and anaerobic bacteria. The deep subsurface biosphere was investigated by collecting liquid subsurface samples from a 182 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between N deficits and the number of microorganisms in surface soils samples. The lowest number of bacteria (1 × 104-1 × 105 g-1) was detected in almost pure pumice but the count was significant higher (1 × 106-1 × 109 g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 m and 172 m depth at 80 °C and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

  5. Microbial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

    Science.gov (United States)

    Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

    2015-02-01

    Colonization of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focused on the settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associated vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soil types on the surface of the island. Total viable bacterial counts were performed with the plate count method at 22, 30 and 37 °C for all soil samples, and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms and aerobic and anaerobic bacteria. The subsurface biosphere was investigated by collecting liquid subsurface samples from a 181 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between nutrient deficits and the number of microorganisms in surface soil samples. The lowest number of bacteria (1 × 104-1 × 105 cells g-1) was detected in almost pure pumice but the count was significantly higher (1 × 106-1 × 109 cells g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated samples and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 and 172 m depth at 80 and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

  6. Responses of microbial community from tropical pristine coastal soil to crude oil contamination

    Directory of Open Access Journals (Sweden)

    Daniel Morais

    2016-02-01

    Full Text Available Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg−1, in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.

  7. Functional soil microbial diversity across Europe estimated by EEA, MicroResp and BIOLOG

    DEFF Research Database (Denmark)

    Winding, Anne; Rutgers, Michiel; Creamer, Rachel

    consisting of 81 soil samples covering five Biogeograhical Zones and three land-uses in order to test the sensitivity, ease and cost of performance and biological significance of the data output. The techniques vary in how close they are to in situ functions; dependency on growth during incubation......Soil microorganisms are abundant and essential for the bio-geochemical processes of soil, soil quality and soil ecosystem services. All this is dependent on the actual functions the microbial communities are performing in the soil. Measuring soil respiration has for many years been the basis...... of estimating soil microbial activity. However, today several techniques are in use for determining microbial functional diversity and assessing soil biodiversity: Methods based on CO2 development by the microbes such as substrate induced respiration (SIR) on specific substrates have lead to the development...

  8. Soil microbial and physical properties and their relations along a steep copper gradient

    DEFF Research Database (Denmark)

    Arthur, Emmanuel; Møldrup, Per; Holmstrup, Martin

    2012-01-01

    years; from background concentrations up to 3837 mg Cu kg–1) on soil microbial enzyme activity, physical properties and resilience to compression. Soil samples and cores were taken from a fallow sandy loam field in Denmark. Microbial activity was quantified using fluorescein diacetate (FDA...

  9. Inclusion of caraway in the ryegrass-red clover mixture modifies soil microbial community composition

    DEFF Research Database (Denmark)

    Cong, Wenfeng; Jing, Jingying; Søegaard, Karen

    -containing grass-clover mixtures may potentially affect soil microbial community structure, biomass and associated ecosystem functions, but it is yet to be elucidated. We hypothesized that inclusion of plantain in the grass-clover mixture would enhance soil microbial biomas and functions through its high biomass...

  10. Fire vs. Metal: A Laboratory Study Demonstrating Microbial Responses to Soil Disturbances

    Science.gov (United States)

    Stromberger, Mary E.

    2005-01-01

    Incubation studies are traditionally used in soil microbiology laboratory classes to demonstrate microbial respiration and N mineralization-immobilization processes. Sometimes these exercises are done to calculate a N balance in N fertilizer-amended soils. However, examining microbial responses to environmental perturbations would appeal to soil…

  11. Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

    NARCIS (Netherlands)

    Kraigher, Barbara; Stres, Blaz; Hacin, Janez; Ausec, Luka; Mahne, Ivan; van Elsas, Jan D.; Mandic-Mulec, Ines

    Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled

  12. The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

    Science.gov (United States)

    Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

    2016-01-01

    Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

  13. Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

    OpenAIRE

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

    2011-01-01

    Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mini...

  14. Glyphosate toxicity and the effects of long-term vegetation control on soil microbial communities

    Science.gov (United States)

    Matt D. Busse; Alice W. Ratcliff; Carol J. Stestak; Robert F. Powers

    2001-01-01

    We assessed the direct and indirect effect of the herbicide glyphosate on soil microbial communities from soil bioassays at glyphosate concentrations up to 100-fold greater than expected following a single field application. Indirect effects on microbial biomass, respiration, and metabolic diversity (Biolog and catabolic response profile) were compared seasonally after...

  15. Monitoring the Perturbation of Soil and Groundwater Microbial Communities Due to Pig Production Activities

    KAUST Repository

    Hong, Pei-Ying

    2013-02-08

    This study aimed to determine if biotic contaminants originating from pig production farms are disseminated into soil and groundwater microbial communities. A spatial and temporal sampling of soil and groundwater in proximity to pig production farms was conducted, and quantitative PCR (Q-PCR) was utilized to determine the abundances of tetracycline resistance genes (i.e., tetQ and tetZ) and integrase genes (i.e., intI1 and intI2). We observed that the abundances of tetZ, tetQ, intI1, and intI2 in the soils increased at least 6-fold after manure application, and their abundances remained elevated above the background for up to 16 months. Q-PCR further determined total abundances of up to 5.88 × 109 copies/ng DNA for tetZ, tetQ, intI1, and intI2 in some of the groundwater wells that were situated next to the manure lagoon and in the facility well used to supply water for one of the farms. We further utilized 16S rRNA-based pyrosequencing to assess the microbial communities, and our comparative analyses suggest that most of the soil samples collected before and after manure application did not change significantly, sharing a high Bray-Curtis similarity of 78.5%. In contrast, an increase in Bacteroidetes and sulfur-oxidizing bacterial populations was observed in the groundwaters collected from lagoon-associated groundwater wells. Genera associated with opportunistic human and animal pathogens, such as Acinetobacter, Arcobacter, Yersinia, and Coxiella, were detected in some of the manure-treated soils and affected groundwater wells. Feces-associated bacteria such as Streptococcus, Erysipelothrix, and Bacteroides were detected in the manure, soil, and groundwater ecosystems, suggesting a perturbation of the soil and groundwater environments by invader species from pig production activities.

  16. Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination.

    Science.gov (United States)

    Wu, Manli; Li, Wei; Dick, Warren A; Ye, Xiqiong; Chen, Kaili; Kost, David; Chen, Liming

    2017-02-01

    Bioremediation of hydrocarbon degradation in petroleum-polluted soil is carried out by various microorganisms. However, little information is available for the relationships between hydrocarbon degradation rates in petroleum-contaminated soil and microbial population and activity in laboratory assay. In a microcosm study, degradation rate and efficiency of total petroleum hydrocarbons (TPH), alkanes, and polycyclic aromatic hydrocarbons (PAH) in a petroleum-contaminated soil were determined using an infrared photometer oil content analyzer and a gas chromatography mass spectrometry (GC-MS). Also, the populations of TPH, alkane, and PAH degraders were enumerated by a modified most probable number (MPN) procedure, and the hydrocarbon degrading activities of these degraders were determined by the Biolog (MT2) MicroPlates assay. Results showed linear correlations between the TPH and alkane degradation rates and the population and activity increases of TPH and alkane degraders, but no correlation was observed between the PAH degradation rates and the PAH population and activity increases. Petroleum hydrocarbon degrading microbial population measured by MPN was significantly correlated with metabolic activity in the Biolog assay. The results suggest that the MPN procedure and the Biolog assay are efficient methods for assessing the rates of TPH and alkane, but not PAH, bioremediation in oil-contaminated soil in laboratory. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming.

    Science.gov (United States)

    Feng, Wenting; Liang, Junyi; Hale, Lauren E; Jung, Chang Gyo; Chen, Ji; Zhou, Jizhong; Xu, Minggang; Yuan, Mengting; Wu, Liyou; Bracho, Rosvel; Pegoraro, Elaine; Schuur, Edward A G; Luo, Yiqi

    2017-11-01

    Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon-climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming. Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the

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

    Science.gov (United States)

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

    2009-01-01

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

  19. Soil plus root respiration and microbial biomass following water, nitrogen, and phosphorus application at a high arctic semi desert

    DEFF Research Database (Denmark)

    Illeris, Lotte; Michelsen, Anders; Jonasson, Sven Evert

    2003-01-01

    CO2 emmision, Decomposition, Microbial biomass carbon, Soil organic matter, Tundra, Water and nutrient limitation......CO2 emmision, Decomposition, Microbial biomass carbon, Soil organic matter, Tundra, Water and nutrient limitation...

  20. The impact of zero-valent iron nanoparticles upon soil microbial communities is context dependent.

    Science.gov (United States)

    Pawlett, Mark; Ritz, Karl; Dorey, Robert A; Rocks, Sophie; Ramsden, Jeremy; Harris, Jim A

    2013-02-01

    Nanosized zero-valent iron (nZVI) is an effective land remediation tool, but there remains little information regarding its impact upon and interactions with the soil microbial community. nZVI stabilised with sodium carboxymethyl cellulose was applied to soils of three contrasting textures and organic matter contents to determine impacts on soil microbial biomass, phenotypic (phospholipid fatty acid (PLFA)), and functional (multiple substrate-induced respiration (MSIR)) profiles. The nZVI significantly reduced microbial biomass by 29 % but only where soil was amended with 5 % straw. Effects of nZVI on MSIR profiles were only evident in the clay soils and were independent of organic matter content. PLFA profiling indicated that the soil microbial community structure in sandy soils were apparently the most, and clay soils the least, vulnerable to nZVI suggesting a protective effect imparted by clays. Evidence of nZVI bactericidal effects on Gram-negative bacteria and a potential reduction of arbuscular mycorrhizal fungi are presented. Data imply that the impact of nZVI on soil microbial communities is dependent on organic matter content and soil mineral type. Thereby, evaluations of nZVI toxicity on soil microbial communities should consider context. The reduction of AM fungi following nZVI application may have implications for land remediation.

  1. Effect of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil.

    Science.gov (United States)

    Kim, Seong-Hye; Han, Hyo-Yeol; Lee, You-Jin; Kim, Chul Woong; Yang, Ji-Won

    2010-07-15

    Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. Copyright 2010 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2017-08-01

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

  3. Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites

    NARCIS (Netherlands)

    Thomson, Bruce C.; Tisserant, Emilie; Plassart, Pierre; Uroz, Stéphane; Griffiths, Rob I.; Hannula, S. Emilia; Buée, Marc; Mougel, Christophe; Ranjard, Lionel; Van Veen, Johannes A.; Martin, Francis; Bailey, Mark J.; Lemanceau, Philippe

    2015-01-01

    Abstract Intensive land use practices necessary for providing food and raw materials are known to have a deleterious effect on soil. However, the effects such practices have on soil microbes are less well understood. To investigate the effects of land use intensification on soil microbial

  4. The Effects of Rice Straw and Biochar Applications on the Microbial Community in a Soil with a History of Continuous Tomato Planting History

    Directory of Open Access Journals (Sweden)

    Yiming Zhang

    2018-05-01

    Full Text Available Soil microbial abundance and diversity change constantly in continuous cropping systems, resulting in the prevalence of soil-borne pathogens and a decline in crop yield in solar greenhouses. To investigate the effects of rice straw and biochar on soil microbial abundance and diversity in soils with a history of continuous planting, three treatments were examined: mixed rice straw and biochar addition (RC, rice straw addition (R, and biochar addition (C. The amount of C added in each treatment group was 3.78 g kg−1 soil. Soil without rice straw and biochar addition was treated as a control (CK. Results showed that RC treatment significantly increased soil pH, available nitrogen (AN, available phosphorus (AP, and potassium (AK by 40.3%, 157.2%, and 24.2%, respectively, as compared to the CK soil. The amount of soil labile organic carbon (LOC, including readily oxidizable organic carbon (ROC, dissolved organic carbon (DOC, and light fraction organic carbon (LFOC, was significantly greater in the RC, R, and C treatment groups as compared to CK soil. LOC levels with RC treatment were higher than with the other treatments. Both rice straw and biochar addition significantly increased bacterial and total microbial abundance, whereas rice straw but not biochar addition improved soil microbial carbon metabolism and diversity. Thus, the significant effects of rice straw and biochar on soil microbial carbon metabolism and diversity were attributed to the quantity of DOC in the treatments. Therefore, our results indicated that soil microbial diversity is directly associated with DOC. Based on the results of this study, mixed rice straw and biochar addition, rather than their application individually, might be key to restoring degraded soil.

  5. Plutonium interactions with soil microbial metabolites: effect on plutonium sorption by soil

    International Nuclear Information System (INIS)

    Wildung, R.E.; Garland, T.R.; Rogers, J.E.

    1987-01-01

    To develop an understanding of the mechanisms of plutonium (Pu) complexation and solubilization by soil microorganisms, a broad range of bacteria and fungi were isolated in pure cultures from soil on the basis of metal tolerance and carbon requirements. The organisms were then used in investigations to examine Pu cellular transport, Pu complexation by extracellular metabolites, and the effects of complexation on Pu valence state, chemical form, and solubility in soil. Of the 239 bacteria and 250 fungi isolated from soil, 19 bacteria and 60 fungi were selected for detailed study. Of these organisms, 15 bacteria and 18 fungi grew to form extracellular Pu complexes that increased the concentration of Pu in soil column eluates relative to controls. Elution through soil effectively removed positively charged Pu complexes. Increased Pu mobility in soil resulted from the formation of neutral and negatively charged Pu complexes, which differed with organism type. In the presence of known microbial metabolites and synthetic ligands (DTPA, EDTA, EDDHA), Pu(VI) was reduced to Pu(IV) before complexation, suggesting that Pu(IV) would be the dominant valence state associated with organic complexes in soils. Studies on selected organisms indicated that both active Pu transport and Pu sorption on the cell occurred, and these phenomena, as well as complexation by extracellular metabolites of Pu, were a function of the form of Pu supplied, the organism type and growth characteristics, and the ability of the organism to alter extracellular pH. 18 references, 6 figures, 7 tables

  6. Microbial control of soil organic matter mineralization responses to labile carbon in subarctic climate change treatments.

    Science.gov (United States)

    Rousk, Kathrin; Michelsen, Anders; Rousk, Johannes

    2016-12-01

    Half the global soil carbon (C) is held in high-latitude systems. Climate change will expose these to warming and a shift towards plant communities with more labile C input. Labile C can also increase the rate of loss of native soil organic matter (SOM); a phenomenon termed 'priming'. We investigated how warming (+1.1 °C over ambient using open top chambers) and litter addition (90 g m -2  yr -1 ) treatments in the subarctic influenced the susceptibility of SOM mineralization to priming, and its microbial underpinnings. Labile C appeared to inhibit the mineralization of C from SOM by up to 60% within hours. In contrast, the mineralization of N from SOM was stimulated by up to 300%. These responses occurred rapidly and were unrelated to microbial successional dynamics, suggesting catabolic responses. Considered separately, the labile C inhibited C mineralization is compatible with previously reported findings termed 'preferential substrate utilization' or 'negative apparent priming', while the stimulated N mineralization responses echo recent reports of 'real priming' of SOM mineralization. However, C and N mineralization responses derived from the same SOM source must be interpreted together: This suggested that the microbial SOM-use decreased in magnitude and shifted to components richer in N. This finding highlights that only considering SOM in terms of C may be simplistic, and will not capture all changes in SOM decomposition. The selective mining for N increased in climate change treatments with higher fungal dominance. In conclusion, labile C appeared to trigger catabolic responses of the resident microbial community that shifted the SOM mining to N-rich components; an effect that increased with higher fungal dominance. Extrapolating from these findings, the predicted shrub expansion in the subarctic could result in an altered microbial use of SOM, selectively mining it for N-rich components, and leading to a reduced total SOM-use. © 2016 John Wiley

  7. Factors for Microbial Carbon Sources in Organic and Mineral Soils from Eastern United States Deciduous Forests

    Energy Technology Data Exchange (ETDEWEB)

    Stitt, Caroline R. [Mills College, Oakland, CA (United States)

    2013-09-16

    Forest soils represent a large portion of global terrestrial carbon; however, which soil carbon sources are used by soil microbes and respired as carbon dioxide (CO2) is not well known. This study will focus on characterizing microbial carbon sources from organic and mineral soils from four eastern United States deciduous forests using a unique radiocarbon (14C) tracer. Results from the dark incubation of organic and mineral soils are heavily influenced by site characteristics when incubated at optimal microbial activity temperature. Sites with considerable differences in temperature, texture, and location differ in carbon source attribution, indicating that site characteristics play a role in soil respiration.

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

    Science.gov (United States)

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

    2013-04-01

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

  9. Bioremediation of oil sludge contaminated soil using bulking agent mixture enriched consortia of microbial inoculants based by irradiated compost

    International Nuclear Information System (INIS)

    Tri Retno, D.L.; Mulyana, N.

    2013-01-01

    Bulking agent mixture enriched consortia of microbial inoculants based by irradiated compost was used on bioremediation of microcosm scale contaminated by hydrocarbon soil. Bioremediation composting was carried out for 42 days. Composting was done with a mixture of bulking agent (sawdust, residual sludge biogas and compost) by 30%, mud petroleum (oil sludge) by 20% and 50% of soil. Mixture of 80% soil and 20% oil sludge was used as a control. Irradiated compost was used as a carrier for consortia of microbial inoculants (F + B) which biodegradable hydrocarbons. Treatment variations include A1, A2, B1, B2, C1, C2, D1 and D2. Process parameters were observed to determine the optimal conditions include: temperature, pH, water content, TPC (Total Plate Count) and degradation of % TPH (Total Petroleum Hydrocarbon). Optimal conditions were achieved in the remediation of oil sludge contamination of 20% using the B2 treatment with the addition consortia of microbial inoculants based by irradiated compost of sawdust (bulking agentby 30% at concentrations of soil by 50% with TPH degradation optimal efficiency of 81.32%. The result of GC-MS analysis showed that bioremediation for 42 days by using a sawdust as a mixture of bulking agents which enriched consortia of microbial inoculants based by irradiated compost is biodegradeable, so initial hydrocarbons with the distribution of the carbon chain C-7 to C-54 into final hydrocarbons with the distribution of carbon chain C-6 to C-8. (author)

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

    Science.gov (United States)

    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.

  11. Microbial carbon pump and its significance for carbon sequestration in soils

    Science.gov (United States)

    Liang, Chao

    2017-04-01

    Studies of the decomposition, transformation and stabilization of soil organic carbon have dramatically increased in recent years due to growing interest in studying the global carbon cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic carbon reservoir in soils depends upon microbial involvement because soil carbon dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microbe-mediated processes lead to soil carbon stabilization. Here, two pathways, ex vivo modification and in vivo turnover, were defined to jointly explain soil carbon dynamics driven by microbial catabolism and/or anabolism. Accordingly, a conceptual framework consisting of the raised concept of the soil "microbial carbon pump" (MCP) was demonstrated to describe how microbes act as an active player in soil carbon storage. The hypothesis is that the long-term microbial assimilation process may facilitate the formation of a set of organic compounds that are stabilized (whether via protection by physical interactions or a reduction in activation energy due to chemical composition), ultimately leading to the sequestration of microbial-derived carbon in soils. The need for increased efforts was proposed to seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil carbon dynamics to the responses of the terrestrial carbon cycle under global change.

  12. Microbial functional diversity and enzymatic activity of soil degraded by sulphur mining reclaimed with various waste

    Science.gov (United States)

    Joniec, Jolanta; Frąc, Magdalena

    2017-10-01

    The aim of the study was to evaluate microbial functional diversity based on community level physiological profiling and β-glucosidase activity changes in soil degraded by sulphur mining and subjected to reclamation with various waste. The experiment was set up in the area of the former `Jeziórko' Sulphur Mine (Poland), on a soilless substrate with a particle size distribution of slightly loamy sand. The experimental variants included the application of post-flotation lime, sewage sludge and mineral wool. The analyses of soil samples included the assessment of the following microbiological indices: β-glucosidase activity and functional diversity average well color development and richness). The results indicate that sewage sludge did not exert a significant impact on the functional diversity of microorganisms present in the reclaimed soil. In turn, the application of other types of waste contributed to a significant increase in the parameters of total metabolic activity and functional diversity of the reclaimed soil. However, the temporal analysis of the metabolic profile of soil microorganisms demonstrated that a single application of waste did not yield a durable, stable metabolic profile in the reclaimed soil. Still, there was an increase in β-glucosidase activity, especially in objects treated with sewage sludge.

  13. Soil Microbial Communities and Gas Dynamics Contribute to Arbuscular Mycorrhizal Nitrogen Uptake and Transfer to Plants

    Science.gov (United States)

    Hestrin, R.; Harrison, M. J.; Lehmann, J.

    2016-12-01

    Arbuscular mycorrhizal fungi (AMF) associate with most terrestrial plants and influence ecosystem ecology and biogeochemistry. There is evidence that AMF play a role in soil nitrogen cycling, in part by taking up nitrogen and transferring it to plants. However, many aspects of this process are poorly understood, including the factors that control fungal access to nitrogen stored in soil organic matter. In this study, we used stable isotopes and root exclusion to track nitrogen movement from organic matter into AMF and host plants. AMF significantly increased total plant biomass and nitrogen content, but both AMF and other soil microbes seemed to compete with plants for nitrogen. Surprisingly, gaseous nitrogen species also contributed significantly to plant nitrogen content under alkaline soil conditions. Our current experiments investigate whether free-living microbial communities that have evolved under a soil nitrogen gradient influence AMF access to soil organic nitrogen and subsequent nitrogen transfer to plants. This research links interactions between plants, mycorrhizal symbionts, and free-living microbes with terrestrial carbon and nitrogen dynamics.

  14. Comparative effects of application of coated and non-coated urea in clayey and sandy paddy soil microcosms examined by the 15N tracer technique. 2. Effects on soil microbial biomass N and microbial 15N immobilization

    International Nuclear Information System (INIS)

    Acquaye, Solomon; Inubushi, Kazuyuki

    2004-01-01

    Nitrogen fertilizer and soil types exert an impact on plant and soil microbial biomass (SMB). A 15 N tracer experiment was conducted to compare the effects of the application of controlled-release coated urea (CRCU) and urea on SMB in gley (clayey) and sandy paddy soils. The fertilizers were applied at the rate of 8 g N m -2 for CRCU as deep-side placement and 10 g N m -2 for urea mixed into soil or applied into floodwater. The soil type and soil layer (surface: few millimeter depth of surface soil to include benthic algae; subsurface: 1 to 20 cm depth), but not the fertilizer type, affected the amount of microbial biomass N (B N ). On an area basis, subsurface soil layers contained about 2-3 times the amount of B N in the surface layers. The seasonal average B N amount i.e. at 1 to 20 cm depth, in the gley soil was 1.67 g N m -2 , compared to 1.20 g N m -2 for the sandy soil. The proportion of B N in total soil N was significantly influenced by the soil type and soil layer, and was higher for the surface layers of both soils and subsurface layer of the sandy soil than for the subsurface layer of gley soil. Soil type, soil layer, and fertilizer type significantly influenced the amount of microbial biomass 15 N (B 15N ). Unlike B N , the amount of B 15N was significantly higher in the surface (11.9-177.3 mg N m -2 ) than in the subsurface soil layers (4.8-83.6 mg N m -2 ), especially with urea application between 60 and 120 DAT (days after transplanting). At 30 DAT, the subsurface layer of the sandy soil showed a higher B 15N (218 mg N m -2 ) amount than the surface layer (133.4 mg N m -2 ). Sandy soil (4.8-218 mg N m -2 ) and urea (6.2-218 mg N m -2 ) induced a larger increase of the amount of B 15 N than the gley soil (6.2-83.6 mg N m -2 ) and CRCU (4.8-40 mg Nm -2 ). Again, the sandy soil, surface soil layers, and urea induced a higher proportion (%) of B 15N in B N than the gley soil, subsurface soil layers, and CRCU, respectively. The soil type affected B N

  15. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    Science.gov (United States)

    He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, A. David; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

    2015-01-01

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4–0.6) in the simulated spatial pattern of soil RHwith both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = −0.43 to −0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  16. Diffuse Reflectance Spectroscopy for Total Carbon Analysis of Hawaiian Soils

    Science.gov (United States)

    McDowell, M. L.; Bruland, G. L.; Deenik, J. L.; Grunwald, S.; Uchida, R.

    2010-12-01

    Accurate assessment of total carbon (Ct) content is important for fertility and nutrient management of soils, as well as for carbon sequestration studies. The non-destructive analysis of soils by diffuse reflectance spectroscopy (DRS) is a potential supplement or alternative to the traditional time-consuming and costly combustion method of Ct analysis, especially in spatial or temporal studies where sample numbers are large. We investigate the use of the visible to near-infrared (VNIR) and mid-infrared (MIR) spectra of soils coupled with chemometric analysis to determine their Ct content. Our specific focus is on Hawaiian soils of agricultural importance. Though this technique has been introduced to the soil community, it has yet to be fully tested and used in practical applications for all soil types, and this is especially true for Hawaii. In short, DRS characterizes and differentiates materials based on the variation of the light reflected by a material at certain wavelengths. This spectrum is dependent on the material’s composition, structure, and physical state. Multivariate chemometric analysis unravels the information in a set of spectra that can help predict a property such as Ct. This study benefits from the remarkably diverse soils of Hawaii. Our sample set includes 216 soil samples from 145 pedons from the main Hawaiian Islands archived at the National Soil Survey Center in Lincoln, NE, along with more than 50 newly-collected samples from Kauai, Oahu, Molokai, and Maui. In total, over 90 series from 10 of the 12 soil orders are represented. The Ct values of these samples range from < 1% - 55%. We anticipate that the diverse nature of our sample set will ensure a model with applicability to a wide variety of soils, both in Hawaii and globally. We have measured the VNIR and MIR spectra of these samples and obtained their Ct values by dry combustion. Our initial analyses are conducted using only samples obtained from the Lincoln archive. In this

  17. Evolution of microbial communities during electrokinetic treatment of antibiotic-polluted soil.

    Science.gov (United States)

    Li, Hongna; Li, Binxu; Zhang, Zhiguo; Zhu, Changxiong; Tian, Yunlong; Ye, Jing

    2018-02-01

    The evolution of microbial communities during the electrokinetic treatment of antibiotic-polluted soil (EKA) was investigated with chlortetracycline (CTC), oxytetracycline (OTC) and tetracycline (TC) as template antibiotics. The total population of soil microorganisms was less affected during the electrokinetic process, while living anti-CTC, anti-OTC, anti-TC and anti-MIX bacteria were inactivated by 10.48%, 31.37%, 34.76%, and 22.08%, respectively, during the 7-day treatment compared with antibiotic-polluted soil without an electric field (NOE). Accordingly, samples with NOE treatment showed a higher Shannon index than those with EKA treatment, indicating a reduction of the microbial community diversity after electrokinetic processes. The major taxonomic phyla found in the samples of EKA and NOE treatment were Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. And the distribution of Actinobacteria, Cyanobacteria, and Chloroflexi was greatly decreased compared with blank soil. In the phylum Proteobacteria, the abundance of Alphaproteobacteria was greatly reduced in the soils supplemented with antibiotics (from 13.40% in blank soil to 6.43-10.16% after treatment); while Betaproteobacteria and Deltaproteobacteria showed a different trend with their abundance increased compared to blank soil, and Gammaproteobacteria remained unchanged for all treatments (2.36-2.78%). The varied trends for different classes indicated that the major bacterial groups changed with the treatments due to their different adaptability to the antibiotics as well as to the electric field. SulI being an exception, the reduction ratio of the observed antibiotic resistance genes (ARGs) including tetC, tetG, tetW, tetM, intI1, and sulII in the 0-2cm soil sampled with EKA versus NOE treatment reached 55.17%, 3.59%, 99.26%, 89.51%, 30.40%, and 27.92%, respectively. Finally, correlation analysis was conducted between antibiotic-resistant bacteria, ARGs and taxonomic bacterial classes. It

  18. Total mercury, methyl mercury, and carbon in fresh and burned plants and soil in Northwestern Ontario

    International Nuclear Information System (INIS)

    Mailman, M.; Bodaly, R.A.

    2005-01-01

    Terrestrial plants and soil contain substantial amounts of organic carbon (C) and mercury. Flooding terrestrial areas stimulates microbial methyl mercury (MeHg) production and fish obtain elevated MeHg concentrations. Our purpose was to determine the loss of C, total mercury (THg), and MeHg from boreal plants and soil after burning to assess the potential of burning before flooding to lower MeHg. Fresh plants contained 4 to 52 ng g -1 dry weight (dw) of THg and 0.1 to 1.3 ng g -1 dw of MeHg. Upland soils contained 162±132 ng g -1 dw of THg and 0.6±0.6 ng g -1 dw of MeHg. Complete burning caused plants to lose 96, 98, 97, and 94% of the mass, C, THg, and MeHg, respectively. Upland soil lost 27, 95, 79, and 82% of the mass, C, THg, and MeHg, respectively. Our results demonstrated that a substantial loss of C, THg, and MeHg was caused by burning. - Burning terrestrial vegetation and soil causes substantial losses of organic carbon, total mercury, and methyl mercury

  19. Total mercury, methyl mercury, and carbon in fresh and burned plants and soil in Northwestern Ontario

    Energy Technology Data Exchange (ETDEWEB)

    Mailman, M. [Department of Zoology, University of Manitoba, Winnipeg, Man. R3T 2N2 (Canada); Freshwater Institute, 501 University Crescent, Winnipeg, Man. R3T 2N6 (Canada)]. E-mail: mailmanma@dfo-mpo.gc.ca; Bodaly, R.A. [Department of Zoology, University of Manitoba, Winnipeg, Man. R3T 2N2 (Canada); Freshwater Institute, 501 University Crescent, Winnipeg, Man. R3T 2N6 (Canada)

    2005-11-15

    Terrestrial plants and soil contain substantial amounts of organic carbon (C) and mercury. Flooding terrestrial areas stimulates microbial methyl mercury (MeHg) production and fish obtain elevated MeHg concentrations. Our purpose was to determine the loss of C, total mercury (THg), and MeHg from boreal plants and soil after burning to assess the potential of burning before flooding to lower MeHg. Fresh plants contained 4 to 52 ng g{sup -1} dry weight (dw) of THg and 0.1 to 1.3 ng g{sup -1} dw of MeHg. Upland soils contained 162{+-}132 ng g{sup -1} dw of THg and 0.6{+-}0.6 ng g{sup -1} dw of MeHg. Complete burning caused plants to lose 96, 98, 97, and 94% of the mass, C, THg, and MeHg, respectively. Upland soil lost 27, 95, 79, and 82% of the mass, C, THg, and MeHg, respectively. Our results demonstrated that a substantial loss of C, THg, and MeHg was caused by burning. - Burning terrestrial vegetation and soil causes substantial losses of organic carbon, total mercury, and methyl mercury.

  20. Terrestrial exposure of oilfield flowline additives diminish soil structural stability and remediative microbial function

    International Nuclear Information System (INIS)

    George, S.J.; Sherbone, J.; Hinz, C.; Tibbett, M.

    2011-01-01

    Onshore oil production pipelines are major installations in the petroleum industry, stretching many thousands of kilometres worldwide which also contain flowline additives. The current study focuses on the effect of the flowline additives on soil physico-chemical and biological properties and quantified the impact using resilience and resistance indices. Our findings are the first to highlight deleterious effect of flowline additives by altering some fundamental soil properties, including a complete loss of structural integrity of the impacted soil and a reduced capacity to degrade hydrocarbons mainly due to: (i) phosphonate salts (in scale inhibitor) prevented accumulation of scale in pipelines but also disrupted soil physical structure; (ii) glutaraldehyde (in biocides) which repressed microbial activity in the pipeline and reduced hydrocarbon degradation in soil upon environmental exposure; (iii) the combinatory effects of these two chemicals synergistically caused severe soil structural collapse and disruption of microbial degradation of petroleum hydrocarbons. - Highlights: → Effects of flowline additives on soil structure and microbial function highlighted. → Phosphonate salts (in scale inhibitor) were found to disrupt soil physical structure. → Glutaraldehyde (in biocides) caused significant reduction of hydrocarbon degradation in soil. → Flowline additive chemicals synergistically affects soil structure and remediative microbial function. - Scale inhibitor and biocide oilfield flowline additives interactively affect soil physical and microbial properties

  1. Microbial activities in soil near natural gas leaks

    Energy Technology Data Exchange (ETDEWEB)

    Adamse, A D; Hoeks, J; de Bont, J A.M.

    1971-01-01

    Gas leaks cause the death of more than half the trees that perish in the streets since natural gas has been distributed in the Netherlands. Measurements performed in pot experiments, in which a sandy soil was supplied with a constant stream of a mixture of natural gas and air, proved that gas components, such as methane (81.6%), ethane (2.7%), propane (0.37%), were oxidized. Consumption of methane and oxygen, and production of carbon dioxide could be clearly demonstrated. Oxidation of methane started after an extended lag phase during which propane and ethane were found to be consumed. Methane oxidation was demonstrated by a sharp rise of the oxygen-consumption curve, followed by a fall until it became rather constant. After the gas supply had been stopped, a long recovery period was found to be needed for restoring the normal oxygen consumption of the soil. The rate of oxidation was subject to seasonal differences in temperature. Counts of bacteria in soil were carried out using Oxiod membrane filters on Whatman paper discs soaked with a basic salts solutions according to Leadbetter and Foster (1958) or on soil-extract agar plates. Incubation temperature was 30C. The presence of natural gas in soil resulted in an adaptation of the aerobic microflora to this substrate. Moreover, it stimulated the total aerobic microflora as counted on soil-extract agar plates.

  2. Total Nitrogen and Available Phosphorus Dynamics in Soils ...

    African Journals Online (AJOL)

    Total nitrogen and available phosphorus concentration of soils in three secondary forest fields aged 1, 5 and 10 years of age regenerating from degraded abandoned rubber plantation (Hevea brasiliensis) and a mature forest in the west African Rainforest belt in southern Nigeria were investigated in order to determine the ...

  3. Comparison of seasonal soil microbial process in snow-covered temperate ecosystems of northern China.

    Directory of Open Access Journals (Sweden)

    Xinyue Zhang

    Full Text Available More than half of the earth's terrestrial surface currently experiences seasonal snow cover and soil frost. Winter compositional and functional investigations in soil microbial community are frequently conducted in alpine tundra and boreal forest ecosystems. However, little information on winter microbial biogeochemistry is known from seasonally snow-covered temperate ecosystems. As decomposer microbes may differ in their ability/strategy to efficiently use soil organic carbon (SOC within different phases of the year, understanding seasonal microbial process will increase our knowledge of biogeochemical cycling from the aspect of decomposition rates and corresponding nutrient dynamics. In this study, we measured soil microbial biomass, community composition and potential SOC mineralization rates in winter and summer, from six temperate ecosystems in northern China. Our results showed a clear pattern of increased microbial biomass C to nitrogen (N ratio in most winter soils. Concurrently, a shift in soil microbial community composition occurred with higher fungal to bacterial biomass ratio and gram negative (G- to gram positive (G+ bacterial biomass ratio in winter than in summer. Furthermore, potential SOC mineralization rate was higher in winter than in summer. Our study demonstrated a distinct transition of microbial community structure and function from winter to summer in temperate snow-covered ecosystems. Microbial N immobilization in winter may not be the major contributor for plant growth in the following spring.

  4. Total and Available Heavy Metal Concentrations and Assessment of Soil Pollution Indices in Selected Soils of Zanjan

    Directory of Open Access Journals (Sweden)

    M. Taheri

    2017-01-01

    Full Text Available Introduction: Soil is a hardly renewable natural resource. Although soil degradation, caused by either human activities and natural processes is a relatively slow procedure, but its effects are long lasting and most often, irreversible in the time scale of man's life. Among the most significant soil contaminants resulting from both natural and human sources, heavy metals are more important due to their long- term toxicity effects. For evaluating soil's enrichment rate by heavy metals, a wide and full study of soils background values, including total and available fractions of heavy metal contents should be done. Zanjan province has some great mines and concentrating industries of lead and zinc especially in Angoran, Mahneshan. Unfortunately produced waste materials of these industries spread over the adjacent areas. Investigations showed that accumulation of some heavy metals in vegetables and crops planted in this region had occurred. Therefore, performing some investigations in these polluted areas and assessing pollution rate and heavy metals distribution in arable lands had prime importance. Our goals were: 1 determining the total and available amounts of Cu, Pb, Zn and Cd in the soils of arable lands in polluted areas of Zanjan city, 2 producing the distribution map for the metals mentioned above and 3 calculating pollution indices in the soils. Materials and Methods: The study area was in south west of Zanjan city. For soil sampling, a 1 Km by 1 Km grid defined in ArcGIS software on landuse layer and totally 144 points that placed on agricultural lands, due to our goals, were sampled. For sampling, in a 5m radius around the point we collected some subsamples from depth of 0 - 15 cm, and after mixing the subsamples, finally a 1Kg soil sample prepared and sent to the laboratory. Sampled soils were air dried and were passed through a 2mm sieve. Soils organic matter (OM content and texture were determined by Walkely-Black and Bouyoucos

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

    Science.gov (United States)

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

    2017-01-01

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

  6. Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

    Science.gov (United States)

    Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

    2016-09-01

    Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

  7. Microbial metabolism and community structure in response to bioelectrochemically enhanced remediation of petroleum hydrocarbon-contaminated soil.

    Science.gov (United States)

    Lu, Lu; Huggins, Tyler; Jin, Song; Zuo, Yi; Ren, Zhiyong Jason

    2014-04-01

    This study demonstrates that electrodes in a bioelectrochemical system (BES) can potentially serve as a nonexhaustible electron acceptor for in situ bioremediation of hydrocarbon contaminated soil. The deployment of BES not only eliminates aeration or supplement of electron acceptors as in contemporary bioremediation but also significantly shortens the remediation period and produces sustainable electricity. More interestingly, the study reveals that microbial metabolism and community structure distinctively respond to the bioelectrochemically enhanced remediation. Tubular BESs with carbon cloth anode (CCA) or biochar anode (BCA) were inserted into raw water saturated soils containing petroleum hydrocarbons for enhancing in situ remediation. Results show that total petroleum hydrocarbon (TPH) removal rate almost doubled in soils close to the anode (63.5-78.7%) than that in the open circuit positive controls (37.6-43.4%) during a period of 64 days. The maximum current density from the BESs ranged from 73 to 86 mA/m(2). Comprehensive microbial and chemical characterizations and statistical analyses show that the residual TPH has a strongly positive correlation with hydrocarbon-degrading microorganisms (HDM) numbers, dehydrogenase activity, and lipase activity and a negative correlation with soil pH, conductivity, and catalase activity. Distinctive microbial communities were identified at the anode, in soil with electrodes, and soil without electrodes. Uncommon electrochemically active bacteria capable of hydrocarbon degradation such as Comamonas testosteroni, Pseudomonas putida, and Ochrobactrum anthropi were selectively enriched on the anode, while hydrocarbon oxidizing bacteria were dominant in soil samples. Results from genus or phylum level characterizations well agree with the data from cluster analysis. Data from this study suggests that a unique constitution of microbial communities may play a key role in BES enhancement of petroleum hydrocarbons

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

    Science.gov (United States)

    Tate, Robert, III; Mikita, Robyn

    2010-05-01

    Wildfires are common disturbances that will increase in frequency and intensity as a result of conditions associated with the changing climate. In turn, forest fires exacerbate climate conditions by increasing carbon and atmospheric aerosols, and changing the surface albedo. Fires have significant economic, environmental, and ecological repercussions; however, we have a limited understanding on the effect of severe wildfires on the composition, diversity, and function of belowground microorganisms. The objective of this research was to examine the shift of the forest soil microbial community as a result of a severe wildfire in the New Jersey Pinelands. Over the span of two years following the fire, soil samples from the organic and mineral layers of the severely burned sites were collected six times. Samples were also collected twice from an unburned control site. It was hypothesized that soil microbial communities from severely burned samples collected shortly after the fire would be significantly different from (1) the unburned samples that serve as controls and (2) the severely burned samples collected more than a year after the fire. Microbial community composition was analyzed by principal component analysis and multivariate analysis of variance of molecular fingerprint data from denaturing gradient gel electrophoresis of bacterial and archaeal-specific amplicons. Bacterial community composition was significantly different among all the organic and mineral layer samples collected 2, 5, 13, and 17 months following the fire. This indicated a shift in the bacterial communities with time following the fire. Common phylotypes from the burned organic layer samples collected 2 months after the fire related closely to members of the phyla Cyanobacteria and Acidobacteria, whereas those from later samples (5, 13, and 17 months following the fire) were closely related to members of the genus Mycobacteria. Canonical correlation analysis was used to determine connections

  9. Functional patterns of microbial communities of rhizospheric soils across the development stages of a young mangrove in French Guiana.

    Science.gov (United States)

    Luglia, Mathieu; Criquet, Stéven; Sarrazin, Max; Ziarelli, Fabio; Guiral, Daniel

    2014-02-01

    The functional patterns of microbial communities (microbial respiration, enzyme activities, functional diversity) and the relevant physico-chemical characteristics of rhizospheric soils were studied during the process of mudflat colonization by mangrove. The study site is a fringe mangrove stand located in Montabo Bay at Cayenne (French Guiana). It is characterized by different vegetation development stages dominated by an assemblage of Avicennia germinans and Laguncularia racemosa. Rhizospheric and surface soils were collected from three stations based on successional stages of mangrove colonization: pioneer (P), coppice (C), and young forest (F). The microbial functional patterns showed significant progressive shifts along the mangrove vegetation profile. The P stages, those most influenced by tide currents, were macroscopically characterized by hydro-sedimentary instability and micro-phytobenthic colonization of mudflat. This stage, characterized by low total organic carbon (TOC) content and quality, showed the lowest extracellular enzymatic activities and the highest functional metabolic diversities. TOC quality analyses by (13)C CPMAS NMR provided evidence of progressive TOC enrichment and an increasing imprint of aboveground vegetation on C quality as succession occurs. These differences in the origin, amount, and quality of soil organic matter (SOM) of older stages exerted both a quantitative and qualitative control over microbial functional responses. This indicated the enhancement of aboveground-belowground functional linkages, leading to the expression of high decomposition activities and a functional loss and specialization of rhizospheric microbial communities.

  10. Microbial life in volcanic/geothermal areas: how soil geochemistry shapes microbial communities

    Science.gov (United States)

    Gagliano, Antonina Lisa; D'Alessandro, Walter; Franzetti, Andrea; Parello, Francesco; Tagliavia, Marcello; Quatrini, Paola

    2015-04-01

    Extreme environments, such as volcanic/geothermal areas, are sites of complex interactions between geosphere and biosphere. Although biotic and abiotic components are strictly related, they were separately studied for long time. Nowadays, innovative and interdisciplinary approaches are available to explore microbial life thriving in these environments. Pantelleria island (Italy) hosts a high enthalpy geothermal system characterized by high CH4 and low H2S fluxes. Two selected sites, FAV1 and FAV2, located at Favara Grande, the main exhalative area of the island, show similar physical conditions with a surface temperature close to 60° C and a soil gas composition enriched in CH4, H2 and CO2. FAV1 soil is characterized by harsher conditions (pH 3.4 and 12% of H2O content); conversely, milder conditions were recorded at site FAV2 (pH 5.8 and 4% of H2O content). High methanotrophic activity (59.2 nmol g-1 h-1) and wide diversity of methanotrophic bacteria were preliminary detected at FAV2, while no activity was detected at FAV1(1). Our aim was to investigate how the soil microbial communities of these two close geothermal sites at Pantelleria island respond to different geochemical conditions. Bacterial and Archaeal communities of the sites were investigated by MiSeq Illumina sequencing of hypervariable regions of the 16S rRNA gene. More than 33,000 reads were obtained for Bacteria and Archaea from soil samples of the two sites. At FAV1 99% of the bacterial sequences were assigned to four main phyla (Proteobacteria, Firmicutes, Actinobacteria and Chloroflexi). FAV2 sequences were distributed in the same phyla with the exception of Chloroflexi that was represented below 1%. Results indicate a high abundance of thermo-acidophilic chemolithotrophs in site FAV1 dominated by Acidithiobacillus ferrooxidans (25%), Nitrosococcus halophilus (10%), Alicyclobacillus spp. (7%) and the rare species Ktedonobacter racemifer (11%). The bacterial community at FAV2 soil is dominated by

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

    Science.gov (United States)

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

    2014-01-01

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

  12. An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

    Science.gov (United States)

    Yang, Hongwu; Li, Juan; Xiao, Yunhua; Gu, Yabing; Liu, Hongwei; Liang, Yili; Liu, Xueduan; Hu, Jin; Meng, Delong; Yin, Huaqun

    2017-01-01

    The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health. PMID:29163453

  13. Testing the effect of a microbial-based soil amendment on aggregate stability and erodibility

    DEFF Research Database (Denmark)

    Malozo, Mponda; Iversen, Bo Vangsø; Heckrath, Goswin Johann

    to the rainfall-runoff experiment where the microbial-based product had a clear effect on soil erodibility. In relation to measurement of aggregate stability as well as clay dispersion, the picture was less clear. Especially for the sandy Tanzania soil with a low content of organic matter, a clear effect was seen...... aggregate stability and erodibility. Two commercial products, gypsum and a microbial-based solution were used for the experiment and were tested on two Danish sandy loamy soils as well on a sandy soil from Tanzania. The carrier of the microbial-based product, a glycerol solution, was tested as well....... In the laboratory, soils were treated with the soil amendments in a two-step procedure at controlled water contents following aerobic incubation in closed containers. Water-aggregate stability and clay dispersion were measured on soil aggregates less than 8 mm in diameter. Aggregate stability was measured...

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

    Science.gov (United States)

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

    2017-12-01

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

  15. Influence of black carbon addition on phenanthrene dissipation and microbial community structure in soil

    International Nuclear Information System (INIS)

    Wang Ping; Wang Haizhen; Wu Laosheng; Di Hongjie; He Yan; Xu Jianming

    2012-01-01

    Biodegradation processes and changes in microbial community structure were investigated in black carbon (BC) amended soils in a laboratory experiment using two soils (black soil and red soil). We applied different percentages of charcoal as BC (0%, 0.5% and 1% by weight) with 100 mg kg −1 of phenanthrene. Soil samples were collected at different incubation times (0, 7, 15, 30, 60, 120 d). The amendment with BC caused a marked decrease in the dissipation (ascribed to mainly degradation and/or sequestration) of phenanthrene residues from soil. Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil, 0.5% BC amendments were higher. There were significant changes in the PLFA pattern in phenanthrene-spiked soils with time but BC had little effect on the microbial community structure of phenanthrene-spiked soils, as indicated by principal component analysis (PCA) of the PLFA signatures. - Highlights: ► Extracted phenanthrene increased substantially as the BC amount increased. ► Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil. ► BC caused a marked decrease in the dissipation of phenanthrene from soil. ► PLFA pattern in phenanthrene-spiked soils with time had significant changes. - BC amendments on phenanthrene extraction were different for two soils and time was a more effective factor in microbial community changes.

  16. Mechanisms of microbial destabilization of soil C shifts over decades of warming

    Science.gov (United States)

    DeAngelis, K.; Pold, G.; Chowdhury, P. R.; Schnabel, J.; Grandy, S.; Melillo, J. M.

    2017-12-01

    Microbes are major actors in regulating the earth's biogeochemical cycles, with temperature-sensitive microbial tradeoffs improving ecosystem biogeochemical models. Meanwhile, the Earth's climate is changing, with decades of warming undercutting the ability of soil to store carbon. Our work explores trends of 26 years of experimental warming in temperate deciduous forest soils, which is associated with cycles of soil carbon degradation punctuated by periods of changes in soil microbial dynamics. Using a combination of biogeochemistry and molecular analytical methods, we explore the hypotheses that substrate availability, community structure, altered temperature sensitivity of microbial turnover-growth efficiency tradeoff, and microbial evolution are responsible for observations of accelerated degradation of soil carbon over time. Amplicon sequencing of microbial communities suggests a small role of changing microbial community composition over decades of warming, but a sustained suppression of fungal biomass is accompanied by increased biomass of Actinobacteria, Actinobacteria, Alphaproteobacteria, Verrucomicrobia and Planctomycetes. Substrate availability plays an important role in microbial dynamics, with depleted labile carbon in the first decade and depleted lignin in the second decade. Increased lignin-degrading enzyme activity supports the suggestion that lignin-like organic matter is an important substrate in chronically warmed soils. Metatranscriptomics data support the suggestion that increased turnover is associated with long-term warming, with metagenomic signals of increased carbohydrate-degrading enzymes in the organic horizon but decreased in the mineral soils. Finally, traits analysis of over 200 cultivated isolates of bacterial species from heated and control soils suggests an expanded ability for degradation of cellulose and hemicellulose but not chitin, supporting the hypothesis that long-term warming is exerting evolutionary pressure on microbial

  17. Changes in Mineralization Activity of Microbial Communities Depending on Physico-Chemical Properties of Soils and Cadmium Contamination

    Directory of Open Access Journals (Sweden)

    A.R. Gilmullina

    2016-09-01

    Full Text Available The effects of glucose and cadmium addition, as well as their combination on the CO2 efflux from soils, which differed by the total organic carbon content and texture, were studied. Glucose (10 g/kg addition induced an increase in the CO2 efflux from soil and a decrease in the content of dissolved organic carbon. The intensity of this effect reduced in samples with the low total organic carbon content. Cadmium (300 mg/kg addition alone did not affect the studied parameters. In case of combined addition of glucose and cadmium, the mineralization activity of microbial community was mainly determined by glucose amendment.

  18. Soil microbial C:N ratio is a robust indicator of soil productivity for paddy fields

    Science.gov (United States)

    Li, Yong; Wu, Jinshui; Shen, Jianlin; Liu, Shoulong; Wang, Cong; Chen, Dan; Huang, Tieping; Zhang, Jiabao

    2016-10-01

    Maintaining good soil productivity in rice paddies is important for global food security. Numerous methods have been developed to evaluate paddy soil productivity (PSP), most based on soil physiochemical properties and relatively few on biological indices. Here, we used a long-term dataset from experiments on paddy fields at eight county sites and a short-term dataset from a single field experiment in southern China, and aimed at quantifying relationships between PSP and the ratios of carbon (C) to nutrients (N and P) in soil microbial biomass (SMB). In the long-term dataset, SMB variables generally showed stronger correlations with the relative PSP (rPSP) compared to soil chemical properties. Both correlation and variation partitioning analyses suggested that SMB N, P and C:N ratio were good predictors of rPSP. In the short-term dataset, we found a significant, negative correlation of annual rice yield with SMB C:N (r = -0.99), confirming SMB C:N as a robust indicator for PSP. In treatments of the short-term experiment, soil amendment with biochar lowered SMB C:N and improved PSP, while incorporation of rice straw increased SMB C:N and reduced PSP. We conclude that SMB C:N ratio does not only indicate PSP but also helps to identify management practices that improve PSP.

  19. The impact of genetically modified crops on soil microbial communities.

    Science.gov (United States)

    Giovannetti, Manuela; Sbrana, Cristiana; Turrini, Alessandra

    2005-01-01

    Genetically modified (GM) plants represent a potential benefit for environmentally friendly agriculture and human health. Though, poor knowledge is available on potential hazards posed by unintended modifications occurring during genetic manipulation. The increasing amount of reports on ecological risks and benefits of GM plants stresses the need for experimental works aimed at evaluating the impact of GM crops on natural and agro-ecosystems. Major environmental risks associated with GM crops include their potential impact on non-target soil microorganisms playing a fundamental role in crop residues degradation and in biogeochemical cycles. Recent works assessed the effects of GM crops on soil microbial communities on the basis of case-by-case studies, using multimodal experimental approaches involving different target and non-target organisms. Experimental evidences discussed in this review confirm that a precautionary approach should be adopted, by taking into account the risks associated with the unpredictability of transformation events, of their pleiotropic effects and of the fate of transgenes in natural and agro-ecosystems, weighing benefits against costs.

  20. RESPONSE OF SOIL MICROBIAL BIOMASS AND COMMUNITY COMPOSITION TO CHRONIC NITROGEN ADDITIONS AT HARVARD FOREST

    Science.gov (United States)

    Soil microbial communities may respond to anthropogenic increases in ecosystem nitrogen (N) availability, and their response may ultimately feedback on ecosystem carbon and N dynamics. We examined the long-term effects of chronic N additions on soil microbes by measuring soil mi...

  1. Effects of Microbial and Phosphate Amendments on the Bioavailability of Lead (Pb) in Shooting Range Soil

    Energy Technology Data Exchange (ETDEWEB)

    Brigmon, Robin; Wilson, Christina; Knox, Anna; Seaman, John; Smith, Garriet

    2005-06-16

    , or U and contains about 27% total phosphate, most of which is available. FA and NCA are two types of rock phosphates that release small amounts of phosphate over time. Total phosphate is around 30% with only 1-2% phosphate available (Knox et al. 2005). In this study, we describe the influence of combining the two microbial and three phosphate amendments on reducing lead bioavailability in shooting range soil.

  2. Microbial utilization of low molecular weight organics in soil depends on the substances properties

    Science.gov (United States)

    Gunina, Anna

    2016-04-01

    LMWOS T1 /2 in SOM with C oxidation state, number of C atoms or number of -COOH groups in LMWOS demonstrates that intercellular metabolic pathways are more important. Mineralization of LMWOS amounted for 20-90% of total applied amount. Maximum mineralization was found for carboxylic acids and minimum for sugars, whereas 14C incorporation into cytosol and SOM pools followed the opposite trend. There were close positive correlation between the portion of mineralized C and substance oxidation state, but negative with the amount of C incorporated into the cytosol and SOM pools. This shows that substance properties affect the final partitioning of LMWOS-C between mineralized and utilized pools. Thus, initial uptake of LMWOS from soil solution and final partitioning of LMWOS-C between the mineralized and microbially utilized pools are related to their chemical properties. In contrast, LMWOS mineralization dynamics is regulated by intercellular metabolization pathways.

  3. The large-scale process of microbial carbonate precipitation for nickel remediation from an industrial soil.

    Science.gov (United States)

    Zhu, Xuejiao; Li, Weila; Zhan, Lu; Huang, Minsheng; Zhang, Qiuzhuo; Achal, Varenyam

    2016-12-01

    Microbial carbonate precipitation is known as an efficient process for the remediation of heavy metals from contaminated soils. In the present study, a urease positive bacterial isolate, identified as Bacillus cereus NS4 through 16S rDNA sequencing, was utilized on a large scale to remove nickel from industrial soil contaminated by the battery industry. The soil was highly contaminated with an initial total nickel concentration of approximately 900 mg kg -1 . The soluble-exchangeable fraction was reduced to 38 mg kg -1 after treatment. The primary objective of metal stabilization was achieved by reducing the bioavailability through immobilizing the nickel in the urease-driven carbonate precipitation. The nickel removal in the soils contributed to the transformation of nickel from mobile species into stable biominerals identified as calcite, vaterite, aragonite and nickelous carbonate when analyzed under XRD. It was proven that during precipitation of calcite, Ni 2+ with an ion radius close to Ca 2+ was incorporated into the CaCO 3 crystal. The biominerals were also characterized by using SEM-EDS to observe the crystal shape and Raman-FTIR spectroscopy to predict responsible bonding during bioremediation with respect to Ni immobilization. The electronic structure and chemical-state information of the detected elements during MICP bioremediation process was studied by XPS. This is the first study in which microbial carbonate precipitation was used for the large-scale remediation of metal-contaminated industrial soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Microbial community changes in heathland soil communities along a geographical gradient: Interaction with climate change manipulations

    DEFF Research Database (Denmark)

    Sowerby, A.; Emmett, B.; Beier, C.

    2005-01-01

    . Microbial extra-cellular enzyme production is linked to microbial activity as well as soil physico-chemical properties, making soil enzymes one of the more reactive components of terrestrial ecosystems and potentially excellent indicators of soil microbial functional status and diversity. Across all sites...... and over all the substrates, organic matter content was exponentially, inversely related to enzyme activity. Although the increase in temperature produced by the CLIMOOR roofs was small (on average 0.9 degrees C), this was sufficient to increase enzyme activity in all sites (on average by 45...

  5. Heavy Metal Phytoremediation: Microbial Indicators of Soil Health for the Assessment of Remediation Efficiency

    Science.gov (United States)

    Epelde, Lur; Ma Becerril, José; Alkorta, Itziar; Garbisu, Carlos

    Phytoremediation is an effective, non-intrusive, inexpensive, aesthetically pleasing, socially accepted, promising phytotechnology for the remediation of polluted soils. The objective of any soil remediation process must be not only to remove the contaminant(s) from the soil but, most importantly, to restore the continued capacity of the soil to perform or function according to its potential (i.e., to recover soil health). Hence, indicators of soil health are needed to properly assess the efficiency of a phytoremediation process. Biological indicators of soil health, especially those related to the size, activity and diversity of the soil microbial communities, are becoming increasingly used, due to their sensitivity and capacity to provide information that integrates many environmental factors. In particular, microbial indicators of soil health are valid tools to evaluate the success of metal phytoremediation procedures such as phytoextraction and phytostabilization processes.

  6. Composted Cattle Manure Increases Microbial Activity and Soil Fertility More Than Composted Swine Manure in a Submerged Rice Paddy

    Directory of Open Access Journals (Sweden)

    Suvendu Das

    2017-09-01

    Full Text Available Livestock waste composts with minimum inorganic fertilizer as a soil amendment in low-input intensive farming are a feasible agricultural practice to improve soil fertility and productivity and to mitigate soil degradation. The key benefits of the practice rely on the activities of soil microorganisms. However, the role of different livestock composts [composted cattle manure (CCM vs. composted swine manure (CSM] on soil microbes, their activities and the overall impact on soil fertility and productivity in a flooded paddy remains elusive. This study compares the effectiveness of CCM and CSM amendment on bacterial communities, activities, nutrient availability, and crop yield in a flooded rice cropping system. We used deep 16S amplicon sequencing and soil enzyme activities to decipher bacterial communities and activities, respectively. Both CCM and CSM amendment significantly increased soil pH, nutrient availability (C, N, and P, microbial biomass, soil enzyme activities indicative for C and N cycles, aboveground plant biomass and grain yield. And the increase in above-mentioned parameters was more prominent in the CCM treatment compared to the CSM treatment. The CCM amendment increased species richness and stimulated copiotrophic microbial groups (Alphaproteobacteria, Betaproteobacteria, and Firmicutes which are often involved in degradation of complex organic compounds. Moreover, some dominant species (e.g., Azospirillum zeae, Azospirillum halopraeferens, Azospirillum rugosum, Clostridium alkalicellulosi, Clostridium caenicola, Clostridium termitidis, Clostridium cellulolyticum, Magnetospirillum magnetotacticum, Pleomorphomonas oryzae, Variovorax boronicumulans, Pseudomonas xanthomarina, Pseudomonas stutzeri, and Bacillus niacini which have key roles in plant growth promotion and/or lignocellulose degradation were enhanced under CCM treatment compared to CSM treatment. Multivariate analysis revealed that soil pH and available carbon (C and

  7. Soil microbial activity under conventional and organic production of bean and maize

    Directory of Open Access Journals (Sweden)

    Marinković Jelena B.

    2016-01-01

    Full Text Available The objective of this study was to compare the effects of conventional and organic production system on microbial activity in the soil cultivated with bean and maize crops. The trial in Đurđevo was set up according to the conventional farming system, while organic farming system was used in Futog. Two maize hybrids and two bean cultivars were used in the trial. Soil samples were collected in two periods during 2014 (before sowing, at flowering stage of bean crops, and at 9-11 leaf stage of maize at two depths, at both locations. The following microbiological parameters were tested: the total number of micro­organisms, number of ammonifiers, Azotobacter sp., free nitrogen fixing bacteria, fungi, actinomycetes, and activity of dehydrogenase enzyme. The results showed that the total number of microorganisms, number of free N-fixers and dehydrogenase activity were higher within organic production, while Azotobacter sp. was more abundant in conventional production. Variations in the number of ammonifiers, fungi and actinomycetes in relation to the type of production were not obtained. Significant differences in microbial activity were also obtained between period and depths of sampling.

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

    Science.gov (United States)

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

    2017-12-01

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

  9. Total organic carbon in aggregates as a soil recovery indicator

    Science.gov (United States)

    Luciene Maltoni, Katia; Rodrigues Cassiolato, Ana Maria; Amorim Faria, Glaucia; Dubbin, William

    2015-04-01

    The soil aggregation promotes physical protection of organic matter, preservation of which is crucial to improve soil structure, fertility and ensure the agro-ecosystems sustainability. The no-tillage cultivation system has been considered as one of the strategies to increase total soil organic carbono (TOC) contents and soil aggregation, both are closely related and influenced by soil management systems. The aim of this study was to evaluate the distribution of soil aggregates and the total organic carbon inside aggregates, with regard to soil recovery, under 3 different soil management systems, i.e. 10 and 20 years of no-tillage cultivation as compared with soil under natural vegetation (Cerrado). Undisturbed soils (0-5; 5-10; and 10-20 cm depth) were collected from Brazil, Central Region. The soils, Oxisols from Cerrado, were collected from a field under Natural Vegetation-Cerrado (NV), and from fields that were under conventional tillage since 1970s, and 10 and 20 years ago were changed to no-tillage cultivation system (NT-10; NT-20 respectively). The undisturbed samples were sieved (4mm) and the aggregates retained were further fractionated by wet sieving through five sieves (2000, 1000, 500, 250, and 50 μm) with the aggregates distribution expressed as percentage retained by each sieve. The TOC was determined, for each aggregate size, by combustion (Thermo-Finnigan). A predominance of aggregates >2000 μm was observed under NV treatment (92, 91, 82 %), NT-10 (64, 73, 61 %), and NT-20 (71, 79, 63 %) for all three depths (0-5; 5-10; 10-20 cm). In addition greater quantities of aggregates in sizes 1000, 500, 250 and 50 μm under NT-10 and NT-20 treatments, explain the lower aggregate stability under these treatments compared to the soil under NV. The organic C concentration for NV in aggregates >2000 μm was 24,4; 14,2; 8,7 mg/g for each depth (0-5; 5-10; 10-20 cm, respectively), higher than in aggregates sized 250-50 μm (7,2; 5,5; 4,4 mg/g) for all depths

  10. Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

    Directory of Open Access Journals (Sweden)

    Stephanie Turner

    2017-05-01

    Full Text Available Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR and community composition (pyrosequencing as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand. Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate, O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR and community patterns (T-RFLP were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to

  11. Enhancement and inhibition of microbial activity in hydrocarbon- contaminated arctic soils: Implications for nutrient-amended bioremediation

    Science.gov (United States)

    Braddock, J.F.; Ruth, M.L.; Catterall, P.H.; Walworth, J.L.; McCarthy, K.A.

    1997-01-01

    Bioremediation is being used or proposed as a treatment option at many hydrocarbon-contaminated sites. One such site is a former bulk-fuel storage facility near Barrow, AK, where contamination persists after approximately 380 m3 of JP-5 was spilled in 1970. The soil at the site is primarily coarse sand with low organic carbon (soil from this site in laboratory microcosms and in mesocosms incubated for 6 weeks in the field. Nitrogen was the major limiting nutrient in this system, but microbial populations and activity were maximally enhanced by additions of both nitrogen and phosphorus. When nutrients were added to soil in the field at three levels of N:P (100:45, 200:90, and 300:135 mg/kg soil), the greatest stimulation in microbial activity occurred at the lowest, rather than the highest, level of nutrient addition. The total soil-water potentials ranged from -2 to -15 bar with increasing levels of fertilizer. Semivolatile hydrocarbon concentrations declined significantly only in the soils treated at the low fertilizer level. These results indicate that an understanding of nutrient effects at a specific site is essential for successful bioremediation.Bioremediation is being used or proposed as a treatment option at many hydrocarbon-contaminated sites. One such site is a former bulk-fuel storage facility near Barrow, AK, where contamination persists after approximately 380 m3 of JP-5 was spilled in 1970. The soil at the site is primarily coarse sand with low organic carbon (soil from this site in laboratory microcosms and in mesocosms incubated for 6 weeks in the field. Nitrogen was the major limiting nutrient in this system, but microbial populations and activity were maximally enhanced by additions of both nitrogen and phosphorus. When nutrients were added to soil in the field at three levels of N:P (100:45, 200:90, and 300:135 mg/kg soil), the greatest stimulation in microbial activity occurred at the lowest, rather than the highest, level of nutrient addition

  12. Microbial community assembly patterns under incipient conditions in a basaltic soil system

    Science.gov (United States)

    Sengupta, A.; Stegen, J.; Alves Meira Neto, A.; Wang, Y.; Chorover, J.; Troch, P. A. A.; Maier, R. M.

    2017-12-01

    In sub-surface environments, the biotic components are critically linked to the abiotic processes. However, there is limited understanding of community establishment, functional associations, and community assembly processes of such microbes in sub-surface environments. This study presents the first analysis of microbial signatures in an incipient terrestrial basalt soil system conducted under controlled conditions. A sub-meter scale sampling of a soil mesocosm revealed the contrasting distribution patterns of simple soil parameters such as bulk density and electrical conductivity. Phylogenetic analysis of 16S rRNA gene indicated the presence of a total 40 bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and highest abundance of Proteobacteria throughout the system. Community diversity patterns were inferred to be dependent on depth profile and average water content in the system. Predicted functional gene analysis suggested mixotrophy lifestyles with both autotrophic and heterotrophic metabolisms, likelihood of a unique salt tolerant methanogenic pathway with links to novel Euryarchea, signatures of an incomplete nitrogen cycle, and predicted enzymes of extracellular iron (II) to iron (III) conversion followed by intracellular uptake, transport and regulation. Null modeling revealed microbial community assembly was predominantly governed by variable selection, but the influence of the variable selection did not show systematic spatial structure. The presence of significant heterogeneity in predicted functions and ecologically deterministic shifts in community composition in a homogeneous incipient basalt highlights the complexity exhibited by microorganisms even in the simplest of environmental systems. This presents an opportunity to further develop our understanding of how microbial communities establish, evolve, impact, and respond in sub-surface environments.

  13. Forest wildfire increases soil microbial biomass C:N:P stoichiometry in long-term effects

    Science.gov (United States)

    Zhou, Xuan

    2017-04-01

    Boreal forest fire strongly influences carbon (C) stock in permafrost soil by thawing permafrost table which accelerated microbe decomposition process. We studied soil microbial biomass stoichiometry in a gradient of four (3 yr, 25 yr, 46 yr and more than 100 yr) ages since fire in Canada boreal forest. Soil microbial biomass (MB) in long-term after fire is significantly higher than in short-term. MB C and nitrogen (N) were mainly dominated by corresponding soil element concentration and inorganic P, while MB phosphorus (P) changes were fully explained by soil N. Fire ages and soil temperature positively increased MB N and P, indicating the negative impact by fire. Microbial C:N:P gradually increased with fire ages from 15:2:1 to 76:6:1 and then drop down to 17:2:1 in the oldest fire ages. The degree of homeostasis of microbial C, N and P are close to 1 indicates non-homoeostasis within microbial elements, while it of C:N:P is close to 8 shows a strong homeostasis within element ratios and proved microbial stoichiometric ratio is not driven by soil element ratios. In conclusion, i) microbial biomass elements highly depends on soil nutrient supply rather than fire ages; ii) wildfire decreased microbial stoichiometry immediate after fire but increased with years after fire (YF) which at least 3 times higher than > 100 fire ages; iii) microbial biomass C, N and P deviated from strict homeostasis but C:N:P ratio reflects stronger homeostasis.

  14. Modification of soil microbial activity and several hydrolases in a forest soil artificially contaminated with copper

    Science.gov (United States)

    Bellas, Rosa; Leirós, Mā Carmen; Gil-Sotres, Fernando; Trasar-Cepeda, Carmen

    2010-05-01

    Soils have long been exposed to the adverse effects of human activities, which negatively affect soil biological activity. As a result of their functions and ubiquitous presence microorganisms can serve as environmental indicators of soil pollution. Some features of soil microorganisms, such as the microbial biomass size, respiration rate, and enzyme activity are often used as bioindicators of the ecotoxicity of heavy metals. Although copper is essential for microorganisms, excessive concentrations have a negative influence on processes mediated by microorganisms. In this study we measured the response of some microbial indicators to Cu pollution in a forest soil, with the aim of evaluating their potential for predicting Cu contamination. Samples of an Ah horizon from a forest soil under oakwood vegetation (Quercus robur L.) were contaminated in the laboratory with copper added at different doses (0, 120, 360, 1080 and 3240 mg kg-1) as CuCl2×2H2O. The soil samples were kept for 7 days at 25 °C and at a moisture content corresponding to the water holding capacity, and thereafter were analysed for carbon and nitrogen mineralization capacity, microbial biomass C, seed germination and root elongation tests, and for urease, phosphomonoesterase, catalase and ß-glucosidase activities. In addition, carbon mineralization kinetics were studied, by plotting the log of residual C against incubation time, and the metabolic coefficient, qCO2, was estimated. Both organic carbon and nitrogen mineralization were lower in polluted samples, with the greatest decrease observed in the sample contaminated with 1080 mg kg-1. In all samples carbon mineralization followed first order kinetics; the C mineralization constant was lower in contaminated than in uncontaminated samples and, in general, decreased with increasing doses of copper. Moreover, it appears that copper contamination not only reduced the N mineralization capacity, but also modified the N mineralization process, since in

  15. Sub-soil microbial activity under rotational cotton crops in Australia

    Science.gov (United States)

    Polain, Katherine; Knox, Oliver; Wilson, Brian; Pereg, Lily

    2016-04-01

    Soil microbial communities contribute significantly to soil organic matter formation, stabilisation and destabilisation, through nutrient cycling and biodegradation. The majority of soil microbial research examines the processes occurring in the top 0 cm to 30 cm of the soil, where organic nutrients are easily accessible. In soils such as Vertosols, the high clay content causes swelling and cracking. When soil cracking is coupled with rain or an irrigation event, a flush of organic nutrients can move down the soil profile, becoming available for subsoil microbial community use and potentially making a significant contribution to nutrient cycling and biodegradation in soils. At present, the mechanisms and rates of soil nutrient turnover (such as carbon and nitrogen) at depth under cotton rotations are mostly speculative and the process-response relationships remain unclear, although they are undoubtedly underpinned by microbial activity. Our research aims to determine the contribution and role of soil microbiota to the accumulation, cycling and mineralisation of carbon and nitrogen through the whole root profile under continuous cotton (Gossypium hirsutum) and cotton-maize rotations in regional New South Wales, Australia. Through seasonal work, we have established both baseline and potential microbial activity rates from 0 cm to 100 cm down the Vertosol profile, using respiration and colourimetric methods. Further whole soil profile analyses will include determination of microbial biomass and isotopic carbon signatures using phospholipid fatty acid (PLFA) methodology, identification of microbial communities (sequencing) and novel experiments to investigate potential rates of nitrogen mineralisation and quantification of associated genes. Our preliminary observations and the hypotheses tested in this three-year study will be presented.

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

    Science.gov (United States)

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

    2014-03-01

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

  17. [Effects of bio-crust on soil microbial biomass and enzyme activities in copper mine tailings].

    Science.gov (United States)

    Chen, Zheng; Yang, Gui-de; Sun, Qing-ye

    2009-09-01

    Bio-crust is the initial stage of natural primary succession in copper mine tailings. With the Yangshanchong and Tongguanshan copper mine tailings in Tongling City of Anhui Province as test objects, this paper studied the soil microbial biomass C and N and the activities of dehydrogenase, catalase, alkaline phosphatase, and urease under different types of bio-crust. The bio-crusts improved the soil microbial biomass and enzyme activities in the upper layer of the tailings markedly. Algal crust had the best effect in improving soil microbial biomass C and N, followed by moss-algal crust, and moss crust. Soil microflora also varied with the type of bio-crust. No'significant difference was observed in the soil enzyme activities under the three types of bio-crust. Soil alkaline phosphatase activity was significantly positively correlated with soil microbial biomass and dehydrogenase and urease activities, but negatively correlated with soil pH. In addition, moss rhizoid could markedly enhance the soil microbial biomass and enzyme activities in moss crust rhizoid.

  18. Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

    Science.gov (United States)

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

    2011-01-01

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

  19. Potential impact of soil microbial heterogeneity on the persistence of hydrocarbons in contaminated subsurface soils.

    Science.gov (United States)

    Aleer, Sam; Adetutu, Eric M; Weber, John; Ball, Andrew S; Juhasz, Albert L

    2014-04-01

    In situ bioremediation is potentially a cost effective treatment strategy for subsurface soils contaminated with petroleum hydrocarbons, however, limited information is available regarding the impact of soil spatial heterogeneity on bioremediation efficacy. In this study, we assessed issues associated with hydrocarbon biodegradation and soil spatial heterogeneity (samples designated as FTF 1, 5 and 8) from a site in which in situ bioremediation was proposed for hydrocarbon removal. Test pit activities showed similarities in FTF soil profiles with elevated hydrocarbon concentrations detected in all soils at 2 m below ground surface. However, PCR-DGGE-based cluster analysis showed that the bacterial community in FTF 5 (at 2 m) was substantially different (53% dissimilar) and 2-3 fold more diverse than communities in FTF 1 and 8 (with 80% similarity). When hydrocarbon degrading potential was assessed, differences were observed in the extent of (14)C-benzene mineralisation under aerobic conditions with FTF 5 exhibiting the highest hydrocarbon removal potential compared to FTF 1 and 8. Further analysis indicated that the FTF 5 microbial community was substantially different from other FTF samples and dominated by putative hydrocarbon degraders belonging to Pseudomonads, Xanthomonads and Enterobacteria. However, hydrocarbon removal in FTF 5 under anaerobic conditions with nitrate and sulphate electron acceptors was limited suggesting that aerobic conditions were crucial for hydrocarbon removal. This study highlights the importance of assessing available microbial capacity prior to bioremediation and shows that the site's spatial heterogeneity can adversely affect the success of in situ bioremediation unless area-specific optimizations are performed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Assessment of microbial activity and biomass in different soils exposed to nicosulfuron

    Directory of Open Access Journals (Sweden)

    Ljiljana Šantrić

    2014-09-01

    Full Text Available The effects of the herbicide nicosulfuron on the abundance of cellulolytic and proteolytic microorganisms, activity of β-glucosidase and protease enzymes, and microbial phosphorus biomass were examined. A laboratory bioassay was set up on two types of agricultural soils differing in physicochemical properties. The following concentrations were tested: 0.3, 0.6, 3.0 and 30.0 mg a.i./kg of soil. Samples were collected 3, 7, 14, 30 and 45 days after treatment with nicosulfuron. The results showed that nicosulfuron significantly reduced the abundance of cellulolytic microorganisms in both soils, as well as microbial biomass phosphorus in sandy loam soil. The herbicide was found to stimulate β-glucosidase and protease activity in both types of soil and microbial biomass phosphorus in loamy soil. Proteolytic microorganisms remained unaffected by nicosulfuron.

  1. The effects of different uranium concentrations on soil microbial populations and enzymatic activities

    International Nuclear Information System (INIS)

    Bagherifam, S.; Lakziyan, A.; Ahmadi, S. J.; Fotovvat, A.; Rahimi, M. F.

    2010-01-01

    Uranium is an ubiquitous constituent of natural environment with an average concentration of 4 mg/kg in earth crust. However, in local areas it may exceed the normal concentration due to human activities resulting in radionuclide contamination in groundwater and surface soil. The effect of six levels of uranium concentration (0, 50, 100,250. 500 and 1000 mg kg -1 ) on soil phosphatase activities and microbial populations were studied in a completely randomized design as a factorial experiment with three replications. The results showed a significant decrease in phosphatase activity. The result of the experiment suggests that soil microbial populations (bacteria, funji and actinomycetes) decrease by increasing the uranium levels in the soil. Therefore, assessment of soil enzymatic activities and microbial populations can be helpful as a useful index for a better management of uranium and radioactive contaminated soils.

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

    Science.gov (United States)

    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 rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

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

    Science.gov (United States)

    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.

  4. Soil carbon content and relative abundance of high affinity H2-oxidizing bacteria predict atmospheric H2 soil uptake activity better than soil microbial community composition

    NARCIS (Netherlands)

    Khdhiri, Mondher; Hesse, Laura; Popa, Maria Elena; Quiza, Liliana; Lalonde, Isabelle; Meredith, Laura K.; Röckmann, Thomas; Constant, Philippe

    2015-01-01

    Soil-atmosphere exchange of H2 is controlled by gas diffusion and the microbial production and oxidation activities in soil. Among these parameters, the H2 oxidation activity catalyzed by soil microorganisms harboring high affinity hydrogenase is the most difficult variable to parameterize because

  5. Soil Microbial and Faunal Community Responses to Bt-Maize and Insecticide in Two Soils

    DEFF Research Database (Denmark)

    Griffiths, B. S.; Caul, S.; Thompson, J.

    2006-01-01

    The effects of maize (Zea mays L.), genetically modified to express the Cry1Ab protein (Bt), and an insecticide on soil microbial and faunal communities were assessed in a glasshouse experiment. Soil for the experiment was taken from field sites where the same maize cultivars were grown to allow...

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

    Science.gov (United States)

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

    2016-12-15

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

  7. Impacts of Activated Carbon Amendment on Hg Methylation, Demethylation and Microbial Activity in Marsh Soils

    Science.gov (United States)

    Gilmour, C. C.; Ghosh, U.; Santillan, E. F. U.; Soren, A.; Bell, J. T.; Butera, D.; McBurney, A. W.; Brown, S.; Henry, E.; Vlassopoulos, D.

    2015-12-01

    In-situ sorbent amendments are a low-impact approach for remediation of contaminants in sediments, particular in habitats like wetlands that provide important ecosystem services. Laboratory microcosm trials (Gilmour et al. 2013) and early field trials show that activated carbon (AC) can effectively increase partitioning of both inorganic Hg and methylmercury to the solid phase. Sediment-water partitioning can serve as a proxy for Hg and MeHg bioavailability in soils. One consideration in using AC in remediation is its potential impact on organisms. For mercury, a critical consideration is the potential impact on net MeHg accumulation and bioavailability. In this study, we specifically evaluated the impact of AC on rates of methylmercury production and degradation, and on overall microbial activity, in 4 different Hg-contaminated salt marsh soils. The study was done over 28 days in anaerobic, sulfate-reducing slurries. A double label of enriched mercury isotopes (Me199Hg and inorganic 201Hg) was used to separately follow de novo Me201Hg production and Me199Hg degradation. AC amendments decreased both methylation and demethylation rate constants relative to un-amended controls, but the impact on demethylation was stronger. The addition of 5% (dry weight) regenerated AC to soil slurries drove demethylation rate constants to nearly zero; i.e. MeHg sorption to AC almost totally blocked its degradation. The net impact was increased solid phase MeHg concentrations in some of the soil slurries with the highest methylation rate constants. However, the net impact of AC amendments was to increase MeHg (and inorganic Hg) partitioning to the soil phase and decrease concentrations in the aqueous phase. AC significantly decreased aqueous phase inorganic Hg and MeHg concentrations after 28 days. Overall, the efficacy of AC in reducing aqueous MeHg was highest in the soils with the highest MeHg concentrations. The AC addition did not significantly impact microbial activity, as

  8. Slow pyrolyzed biochars from crop residues for soil metal(loid) immobilization and microbial community abundance in contaminated agricultural soils.

    Science.gov (United States)

    Igalavithana, Avanthi Deshani; Park, Jinje; Ryu, Changkook; Lee, Young Han; Hashimoto, Yohey; Huang, Longbin; Kwon, Eilhann E; Ok, Yong Sik; Lee, Sang Soo

    2017-06-01

    This study evaluated the feasibility of using biochars produced from three types of crop residues for immobilizing Pb and As and their effects on the abundance of microbial community in contaminated lowland paddy (P-soil) and upland (U-soil) agricultural soils. Biochars were produced from umbrella tree [Maesopsis eminii] wood bark [WB], cocopeat [CP], and palm kernel shell [PKS] at 500 °C by slow pyrolysis at a heating rate of 10 °C min -1 . Soils were incubated with 5% (w w -1 ) biochars at 25 °C and 70% water holding capacity for 45 d. The biochar effects on metal immobilization were evaluated by sequential extraction of the treated soil, and the microbial community was determined by microbial fatty acid profiles and dehydrogenase activity. The addition of WB caused the largest decrease in Pb in the exchangeable fraction (P-soil: 77.7%, U-soil: 91.5%), followed by CP (P-soil: 67.1%, U-soil: 81.1%) and PKS (P-soil: 9.1%, U-soil: 20.0%) compared to that by the control. In contrast, the additions of WB and CP increased the exchangeable As in U-soil by 84.6% and 14.8%, respectively. Alkalinity and high phosphorous content of biochars might be attributed to the Pb immobilization and As mobilization, respectively. The silicon content in biochars is also an influencing factor in increasing the As mobility. However, no considerable effects of biochars on the microbial community abundance and dehydrogenase activity were found in both soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Microbial enzyme activities of peatland soils in south central Alaska lowlands

    Science.gov (United States)

    Microbial enzyme activities related to carbon and nutrient acquisition were measured on Alaskan peatland soils as indicators of nutrient limitation and biochemical sustainability. Peat decomposition is mediated by microorganisms and enzymes that in turn are limited by various ph...

  10. Evaluation of microbial diversity of different soil layers at a contaminated diesel site

    CSIR Research Space (South Africa)

    Maila, MP

    2005-01-01

    Full Text Available with high TPH removal. Analysis of the microbial diversity in the different soil layers using functional diversity (community-level physiological profile, via Biolog) and genetic diversity using polymerase chain reaction-denaturing gradient gel...

  11. Biodegradation of ciprofloxacin in water and soil and its effects on the microbial communities

    International Nuclear Information System (INIS)

    Girardi, Cristobal; Greve, Josephine; Lamshöft, Marc; Fetzer, Ingo; Miltner, Anja; Schäffer, Andreas; Kästner, Matthias

    2011-01-01

    Highlights: ► Mineralisation of toxic pollutants can be higher in soil than in water. ► Ciprofloxacin affects the microbial communities and activities in soil. ► Toxicity of ciprofloxacin is reduced in soil due to sorption processes. ► Despite the buffering capacity of soil, ciprofloxacin remains active. ► Ciprofloxacin resistance can develop in soils contaminated with this antibiotic. - Abstract: While antibiotics are frequently found in the environment, their biodegradability and ecotoxicological effects are not well understood. Ciprofloxacin inhibits active and growing microorganisms and therefore can represent an important risk for the environment, especially for soil microbial ecology and microbial ecosystem services. We investigated the biodegradation of 14 C-ciprofloxacin in water and soil following OECD tests (301B, 307) to compare its fate in both systems. Ciprofloxacin is recalcitrant to biodegradation and transformation in the aqueous system. However, some mineralisation was observed in soil. The lower bioavailability of ciprofloxacin seems to reduce the compound's toxicity against microorganisms and allows its biodegradation. Moreover, ciprofloxacin strongly inhibits the microbial activities in both systems. Higher inhibition was observed in water than in soil and although its antimicrobial potency is reduced by sorption and aging in soil, ciprofloxacin remains biologically active over time. Therefore sorption does not completely eliminate the effects of this compound.

  12. Effects of Biochar Blends on Microbial Community Composition in Two Coastal Plain Soils

    Directory of Open Access Journals (Sweden)

    Thomas F. Ducey

    2015-11-01

    Full Text Available The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure. These impacts are modulated not only by the biochar composition, but also on the soil’s physicochemical characteristics. This indicates that soil characteristics must be considered prior to biochar amendment. A significant portion of the soils of the southeastern coastal plain are severely degraded and, therefore, candidates for biochar amendment to strengthen soil fertility. In this study we focused on two common soil series in the southeastern coastal plain, utilizing feedstocks endemic to the area. We chose feedstocks in four ratios (100% pine chip; 80:20 mixture of pine chip to poultry litter; 50:50 mixture of pine chip to poultry litter; 100% poultry litter prior to pyrolysis and soil amendment as a biochar product. Soil was analyzed for bioavailable nutrients via Mehlich-1 extractions, as well as microbial community composition using phospholipid fatty acid analysis (PLFA. Our results demonstrated significant shifts in microbial community composition in response to biochar amendment, the effects of which were greatest with 100% poultry litter biochar. Strong relationships between PLFAs and several Mehlich-1 extractable nutrients (Al, Cu, Fe, and P were observed.

  13. Biodegradation of ciprofloxacin in water and soil and its effects on the microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Girardi, Cristobal, E-mail: cristobal.girardi-lavin@ufz.de [UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstrasse 15, 04318 Leipzig (Germany); Greve, Josephine [Minnesota State University, Mankato, MN 56001 8400 (United States); Lamshoeft, Marc [Institute of Environmental Research (INFU), TU Dortmund University, Otto-Hahn-Str. 6, NRW 44221 Dortmund (Germany); Fetzer, Ingo [UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstrasse 15, 04318 Leipzig (Germany); Miltner, Anja [UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstrasse 15, 04318 Leipzig (Germany); Schaeffer, Andreas [Department of Environmental Biology and Chemodynamics, Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074 Aachen (Germany); Kaestner, Matthias [UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstrasse 15, 04318 Leipzig (Germany)

    2011-12-30

    Highlights: Black-Right-Pointing-Pointer Mineralisation of toxic pollutants can be higher in soil than in water. Black-Right-Pointing-Pointer Ciprofloxacin affects the microbial communities and activities in soil. Black-Right-Pointing-Pointer Toxicity of ciprofloxacin is reduced in soil due to sorption processes. Black-Right-Pointing-Pointer Despite the buffering capacity of soil, ciprofloxacin remains active. Black-Right-Pointing-Pointer Ciprofloxacin resistance can develop in soils contaminated with this antibiotic. - Abstract: While antibiotics are frequently found in the environment, their biodegradability and ecotoxicological effects are not well understood. Ciprofloxacin inhibits active and growing microorganisms and therefore can represent an important risk for the environment, especially for soil microbial ecology and microbial ecosystem services. We investigated the biodegradation of {sup 14}C-ciprofloxacin in water and soil following OECD tests (301B, 307) to compare its fate in both systems. Ciprofloxacin is recalcitrant to biodegradation and transformation in the aqueous system. However, some mineralisation was observed in soil. The lower bioavailability of ciprofloxacin seems to reduce the compound's toxicity against microorganisms and allows its biodegradation. Moreover, ciprofloxacin strongly inhibits the microbial activities in both systems. Higher inhibition was observed in water than in soil and although its antimicrobial potency is reduced by sorption and aging in soil, ciprofloxacin remains biologically active over time. Therefore sorption does not completely eliminate the effects of this compound.

  14. Soil microbial diversity, site conditions, shelter forest land, saline water drip-irrigation, drift desert.

    Science.gov (United States)

    Jin, Zhengzhong; Lei, Jiaqiang; Li, Shengyu; Xu, Xinwen

    2013-10-01

    Soil microbes in forest land are crucial to soil development in extreme areas. In this study, methods of conventional culture, PLFA and PCR-DGGE were utilized to analyze soil microbial quantity, fatty acids and microbial DNA segments of soils subjected to different site conditions in the Tarim Desert Highway forest land. The main results were as follows: the soil microbial amount, diversity indexes of fatty acid and DNA segment differed significantly among sites with different conditions (F 84%), followed by actinomycetes and then fungi (<0.05%). Vertical differences in the soil microbial diversity were insignificant at 0-35 cm. Correlation analysis indicated that the forest trees grew better as the soil microbial diversity index increased. Therefore, construction of the Tarim Desert Highway shelter-forest promoted soil biological development; however, for enhancing sand control efficiency and promoting sand development, we should consider the effects of site condition in the construction and regeneration of shelter-forest ecological projects. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

    Science.gov (United States)

    Fierer, Noah; Leff, Jonathan W; Adams, Byron J; Nielsen, Uffe N; Bates, Scott Thomas; Lauber, Christian L; Owens, Sarah; Gilbert, Jack A; Wall, Diana H; Caporaso, J Gregory

    2012-12-26

    For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

  16. Monitoring Soil Microbial Activities in Different Cropping Systems Using Combined Methods

    Institute of Scientific and Technical Information of China (English)

    YUAN Zhimin; LIU Haijun; HAN Jun; SUN Jingjing; WU Xiaoying; YAO Jun

    2017-01-01

    Cropping activities may affect soil microbial activities and biomass,which would affect C and N cycling in soil and thus the crop yields and quality.In the present study,a combination of microcalorimetric,enzyme activity (sucrase,urease,catalase,and fluorescein diacetate hydrolysis),and real-time polymerase chain reaction (RT-PCR) analyses was used to investigate microbial status of farmland soils,collected from 5 different sites in Huazhong Agriculture University,China.Our results showed that among the 5 sites,both positive and negative impacts of cropping activities on soil microbial activity were observed.Enzyme activity analysis showed that cropping activities reduced soil sucrase and urease activities,which would influence the C and N cycles in soil.Much more attentions should be given to microbial status affected by cropping activities in future.According to the correlation analysis,fluorescein diacetate hydrolysis showed a significantly (P < 0.05) negative correlation with the time to reach the maximum power output (R =--0.898),but a significantly (P < 0.05) positive correlation with bacterial gene copy number (R =0.817).Soil catalase activity also showed a significantly (P < 0.05) positive correlation with bacterial gene copy number (R =0.965).Using combined methods would provide virtual information of soil microbial status.

  17. Soil Microbial Functional and Fungal Diversity as Influenced by Municipal Sewage Sludge Accumulation

    OpenAIRE

    Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy; Jezierska-Tys, Stefania; Nwaichi, Eucharia Oluchi

    2014-01-01

    Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS) and from a sewage sludge landfill that was 3 m from a SS landfill (SS3) were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Avera...

  18. Application of Sodium Silicate Enhances Cucumber Resistance to Fusarium Wilt and Alters Soil Microbial Communities

    Directory of Open Access Journals (Sweden)

    Xingang Zhou

    2018-05-01

    Full Text Available Exogenous silicates can enhance plant resistance to pathogens and change soil microbial communities. However, the relationship between changes in soil microbial communities and enhanced plant resistance remains unclear. Here, effects of exogenous sodium silicate on cucumber (Cucumis sativus L. seedling resistance to Fusarium wilt caused by the soil-borne pathogen Fusarium oxysporum f.sp. cucumerinum Owen (FOC were investigated by drenching soil with 2 mM sodium silicate. Soil bacterial and fungal community abundances and compositions were estimated by real-time PCR and high-throughput amplicon sequencing; then, feedback effects of changes in soil biota on cucumber seedling resistance to FOC were assessed. Moreover, effects of sodium silicate on the growth of FOC and Streptomyces DHV3-2, an antagonistic bacterium to FOC, were investigated both in vitro and in the soil environment. Results showed that exogenous sodium silicate enhanced cucumber seedling growth and resistance to FOC. In bare soil, sodium silicate increased bacterial and fungal community abundances and diversities. In cucumber-cultivated soil, sodium silicate increased bacterial community abundances, but decreased fungal community abundances and diversities. Sodium silicate also changed soil bacterial and fungal communality compositions, and especially, decreased the relative abundances of microbial taxa containing plant pathogens but increased these with plant-beneficial potentials. Moreover, sodium silicate increased the abundance of Streptomyces DHV3-2 in soil. Soil biota from cucumber-cultivated soil treated with sodium silicate decreased cucumber seedling Fusarium wilt disease index, and enhanced cucumber seedling growth and defense-related enzyme activities in roots. Sodium silicate at pH 9.85 inhibited FOC abundance in vitro, but did not affect FOC abundance in soil. Overall, our results suggested that, in cucumber-cultivated soil, sodium silicate increased cucumber seedling

  19. Impact of long-term Diesel Contamination on Soil Microbial Community Structure

    NARCIS (Netherlands)

    Sutton, N.B.; Maphosa, F.; Morillo, J.A.; Abu Al-Soud, W.; Langenhoff, A.A.M.; Grotenhuis, J.T.C.; Rijnaarts, H.H.M.; Smidt, H.

    2013-01-01

    Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical

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

    Science.gov (United States)

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

    2011-01-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of...

  1. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  2. Forest soil microbial communities: Using metagenomic approaches to survey permanent plots

    Science.gov (United States)

    Amy L. Ross-Davis; Jane E. Stewart; John W. Hanna; John D. Shaw; Andrew T. Hudak; Theresa B. Jain; Robert J. Denner; Russell T. Graham; Deborah S. Page-Dumroese; Joanne M. Tirocke; Mee-Sook Kim; Ned B. Klopfenstein

    2014-01-01

    Forest soil ecosystems include some of the most complex microbial communities on Earth (Fierer et al. 2012). These assemblages of archaea, bacteria, fungi, and protists play essential roles in biogeochemical cycles (van der Heijden et al. 2008) and account for considerable terrestrial biomass (Nielsen et al. 2011). Yet, determining the microbial composition of forest...

  3. The effect of soil habitat connectivity on microbial interactions, community structure and diversity: a microcosm-based approach

    NARCIS (Netherlands)

    Wolf, A.B.

    2014-01-01

    Soils contain tremendous microbial phylogenetic and functional diversity. Recent advances in the application of molecular methods into microbial ecology have provided a new appreciation of the extent of soil-borne microbial diversity, but our understanding of the forces that shape and maintain this

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

    Directory of Open Access Journals (Sweden)

    P. Kotas

    2018-03-01

    Full Text Available 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.

  5. Soil mi