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Sample records for affected soil microbial

  1. Soil microbial diversity and soil functioning affect competition among grasses in experimental microcosms.

    PubMed

    Bonkowski, Michael; Roy, Jacques

    2005-03-01

    A gradient of microbial diversity in soil was established by inoculating pasteurized soil with microbial populations of different complexity, which were obtained by a combination of soil fumigation and filtering techniques. Four different soil diversity treatments were planted with six different grass species either in monoculture or in polyculture to test how changes of general microbial functions, such as catabolic diversity and nutrient recycling efficiency would affect the performance of the plant communities. Relatively harsh soil treatments were necessary to elicit visible effects on major soil processes such as decomposition and nitrogen cycling due to the high redundancy and resilience of soil microbial communities. The strongest effects of soil diversity manipulations on plant growth occurred in polycultures where interspecific competition between plants was high. In polycultures, soil diversity reduction led to a gradual, linear decline in biomass production of one subordinate grass species (Bromus hordeaceus), which was compensated by increased growth of two intermediate competitors (Aegilops geniculata, B. madritensis). This negative covariance in growth of competing grass species smoothed the effects of soil diversity manipulations at the plant community level. As a result, total shoot biomass production remained constant. Apparently the effects of soil diversity manipulations were buffered because functional redundancy at both, the microbial and the plant community level complemented each other. The results further suggests that small trade-offs in plant fitness due to general functional shifts at the microbial level can be significant for the outcome of competition in plant communities and thus diversity at much larger scales.

  2. Microbial Carbon Cycling in Permafrost-Affected Soils

    SciTech Connect

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

    2011-01-01

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

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

    PubMed

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

    2016-06-15

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales.

    PubMed

    Zeglin, L H; Bottomley, P J; Jumpponen, A; Rice, C W; Arango, M; Lindsley, A; McGowan, A; Mfombep, P; Myrold, D D

    2013-10-01

    Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting "Ambient" and "Altered" (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential = -0.01 and -0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracellular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 +/- 0.03 > 0.46 +/- 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (beta-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal:bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet

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

    PubMed

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

    2014-05-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed Central

    Tate, Robert L.

    1979-01-01

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

  9. Soil contamination with olive mill wastes negatively affects microbial communities, invertebrates and plants.

    PubMed

    Hentati, Olfa; Oliveira, Vanessa; Sena, Clara; Bouji, Mohamed Seddik Mahmoud; Wali, Ahmed; Ksibi, Mohamed

    2016-10-01

    The aim of the present study was to evaluate the ecotoxicological effects of olive mill waste (OMW) on soil habitat function. To this end, soil samples from OMW evaporating ponds (S1-S5) located at Agareb (Sfax, Tunisia) and a reference soil (R) were collected. The effects of OMW on the springtails Folsomia candida (F.c.), the earthworm species Eisenia fetida (E.f.), Enchytraeus crypticus (E.c.) reproduction and on the soil living microbial communities were investigated. E.f. reproduction and tomato growth assays were performed in the reference soil amended with 0.43 to 7.60 % (wOMW/wref-soil) mass ratios of dried OMW. Changes in microbial function diversity were explored using sole-carbon-source utilization profiles (BiologEcoPlates(®)). E.f. absolutely avoided (100 %) the most polluted soil (S4) while the F.c. moderately avoided (37.5 ± 7.5 %) the same soil. E.c. reproduction in S4 was significantly lower than in S1, S2, S3 and S5, and was the highest in R soil. Estimated effect concentration EC50 for juveniles' production by E.f., and for tomato fresh weight and chlorophyll content were 0.138, 0.6 and 1.13 %, respectively. Community level physiological profiles (CLPPs) were remarkably different in R and S4 and a higher similarity was observed between soils S1, S2, S3 and S5. Principal component analysis (PCA) revealed that differences between soil microbial functional diversity were mainly due to high polyphenol concentrations, while the salinity negatively affected E.c. reproduction in OMW contaminated soils. These results clearly reflect the high toxicity of dried OMW when added to agricultural soils, causing severe threats to terrestrial ecosystem functions and services provided by invertebrates and microbial communities.

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

    PubMed

    Lancaster, Sarah H; Haney, Richard L; Senseman, Scott A; Hons, Frank M; Chandler, James M

    2006-09-20

    Adoption of glyphosate-based weed control systems has led to increased use of the herbicide with continued use of additional pesticides. Combinations of pesticides may affect soil microbial activity differently than pesticides applied alone. Research was conducted to evaluate the influence of glyphosate-based cotton pest management systems on soil microbial activity. Soil was treated with commercial formulations of trifluralin, aldicarb, and mefenoxam + pentachloronitrobenzene (PCNB) with or without glyphosate (applied as Roundup WeatherMax). The soil microbial activity was measured by quantifying C and N mineralization. Soil microbial biomass was determined using the chloroform fumigation-incubation method. Soils treated with glyphosate alone exhibited greater cumulative C mineralization 30 days after treatment than all other treatments, which were similar to the untreated control. The addition of Roundup WeatherMax reduced C mineralization in soils treated with fluometuron, aldicarb, or mefenoxam + PCNB formulations. These results indicate that glyphosate-based herbicides alter the soil microbial response to other pesticides.

  11. Winter climate change affects growing-season soil microbial biomass and activity in northern hardwood forests.

    PubMed

    Durán, Jorge; Morse, Jennifer L; Groffman, Peter M; Campbell, John L; Christenson, Lynn M; Driscoll, Charles T; Fahey, Timothy J; Fisk, Melany C; Mitchell, Myron J; Templer, Pamela H

    2014-11-01

    Understanding the responses of terrestrial ecosystems to global change remains a major challenge of ecological research. We exploited a natural elevation gradient in a northern hardwood forest to determine how reductions in snow accumulation, expected with climate change, directly affect dynamics of soil winter frost, and indirectly soil microbial biomass and activity during the growing season. Soils from lower elevation plots, which accumulated less snow and experienced more soil temperature variability during the winter (and likely more freeze/thaw events), had less extractable inorganic nitrogen (N), lower rates of microbial N production via potential net N mineralization and nitrification, and higher potential microbial respiration during the growing season. Potential nitrate production rates during the growing season were particularly sensitive to changes in winter snow pack accumulation and winter soil temperature variability, especially in spring. Effects of elevation and winter conditions on N transformation rates differed from those on potential microbial respiration, suggesting that N-related processes might respond differently to winter climate change in northern hardwood forests than C-related processes.

  12. Land-use and soil depth affect resource and microbial stoichiometry in a tropical mountain rainforest region of southern Ecuador.

    PubMed

    Tischer, Alexander; Potthast, Karin; Hamer, Ute

    2014-05-01

    Global change phenomena, such as forest disturbance and land-use change, significantly affect elemental balances as well as the structure and function of terrestrial ecosystems. However, the importance of shifts in soil nutrient stoichiometry for the regulation of belowground biota and soil food webs have not been intensively studied for tropical ecosystems. In the present account, we examine the effects of land-use change and soil depth on soil and microbial stoichiometry along a land-use sequence (natural forest, pastures of different ages, secondary succession) in the tropical mountain rainforest region of southern Ecuador. Furthermore, we analyzed (PLFA-method) whether shifts in the microbial community structure were related to alterations in soil and microbial stoichiometry. Soil and microbial stoichiometry were affected by both land-use change and soil depth. After forest disturbance, significant decreases of soil C:N:P ratios at the pastures were followed by increases during secondary succession. Microbial C:N ratios varied slightly in response to land-use change, whereas no fixed microbial C:P and N:P ratios were observed. Shifts in microbial community composition were associated with soil and microbial stoichiometry. Strong positive relationships between PLFA-markers 18:2n6,9c (saprotrophic fungi) and 20:4 (animals) and negative associations between 20:4 and microbial N:P point to land-use change affecting the structure of soil food webs. Significant deviations from global soil and microbial C:N:P ratios indicated a major force of land-use change to alter stoichiometric relationships and to structure biological systems. Our results support the idea that soil biotic communities are stoichiometrically flexible in order to adapt to alterations in resource stoichiometry.

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed

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

    2016-10-01

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

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

    PubMed

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

    2013-07-01

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

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

    PubMed

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

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

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

    PubMed Central

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. Salinity affects microbial activity and soil organic matter content in tidal wetlands.

    PubMed

    Morrissey, Ember M; Gillespie, Jaimie L; Morina, Joseph C; Franklin, Rima B

    2014-04-01

    Climate change-associated sea level rise is expected to cause saltwater intrusion into many historically freshwater ecosystems. Of particular concern are tidal freshwater wetlands, which perform several important ecological functions including carbon sequestration. To predict the impact of saltwater intrusion in these environments, we must first gain a better understanding of how salinity regulates decomposition in natural systems. This study sampled eight tidal wetlands ranging from freshwater to oligohaline (0-2 ppt) in four rivers near the Chesapeake Bay (Virginia). To help isolate salinity effects, sites were selected to be highly similar in terms of plant community composition and tidal influence. Overall, salinity was found to be strongly negatively correlated with soil organic matter content (OM%) and C : N, but unrelated to the other studied environmental parameters (pH, redox, and above- and below-ground plant biomass). Partial correlation analysis, controlling for these environmental covariates, supported direct effects of salinity on the activity of carbon-degrading extracellular enzymes (β-1, 4-glucosidase, 1, 4-β-cellobiosidase, β-D-xylosidase, and phenol oxidase) as well as alkaline phosphatase, using a per unit OM basis. As enzyme activity is the putative rate-limiting step in decomposition, enhanced activity due to salinity increases could dramatically affect soil OM accumulation. Salinity was also found to be positively related to bacterial abundance (qPCR of the 16S rRNA gene) and tightly linked with community composition (T-RFLP). Furthermore, strong relationships were found between bacterial abundance and/or composition with the activity of specific enzymes (1, 4-β-cellobiosidase, arylsulfatase, alkaline phosphatase, and phenol oxidase) suggesting salinity's impact on decomposition could be due, at least in part, to its effect on the bacterial community. Together, these results indicate that salinity increases microbial decomposition rates

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

    PubMed

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

    2015-02-01

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

  4. Microbial biomass and carbon mineralization in agricultural soils as affected by pesticide addition.

    PubMed

    Kumar, Anjani; Nayak, A K; Shukla, Arvind K; Panda, B B; Raja, R; Shahid, Mohammad; Tripathi, Rahul; Mohanty, Sangita; Rath, P C

    2012-04-01

    A laboratory study was conducted with four pesticides, viz. a fungicide (carbendazim), two insecticides (chlorpyrifos and cartap hydrochloride) and an herbicide (pretilachlor) applied to a sandy clay loam soil at a field rate to determine their effect on microbial biomass carbon (MBC) and carbon mineralization (C(min)). The MBC content of soil increased with time up to 30 days in cartap hydrochloride as well as chlorpyrifos treated soil. Thereafter, it decreased and reached close to the initial level by 90th day. However, in carbendazim treated soil, the MBC showed a decreasing trend up to 45 days and subsequently increased up to 90 days. In pretilachlor treated soil, MBC increased through the first 15 days, and thereafter decreased to the initial level. Application of carbendazim, chlorpyrifos and cartap hydrochloride decreased C(min) for the first 30 days and then increased afterwards, while pretilachlor treated soil showed an increasing trend.

  5. Factors affecting the microbial degradation of phenanthrene in soil. (Reannouncement with new availability information)

    SciTech Connect

    Manilal, V.B.; Alexander, M.

    1991-12-31

    Because phenanthrene was mineralized more slowly in soils than in liquid media, a study was conducted to determine the environmental factors that may account for the slow biodegradation in soil. Mineralization was enhanced by additions of phosphate but not potassium, and it was reduced by additions of nitrate. Aeration or amending the soil with glucose affected the rate of mineralization, although not markedly. Phenanthrene was sorbed to soil constituents, the extent of sorption being directly related to the percentage of organic matter in the soil. Soluble phenanthrene was not detected after addition of the compound to a muck soil. The rate of mineralization was slow in the organic soil and higher in mineral soils with lower percentages of organic matter. We suggest that sorption by soil organic matter slows the biodegradation of polycyclic aromatic hydrocarbons that are otherwise readily metabolized.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  8. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

    PubMed Central

    Simonin, Marie; Richaume, Agnès; Guyonnet, Julien P.; Dubost, Audrey; Martins, Jean M. F.; Pommier, Thomas

    2016-01-01

    Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg−1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function. PMID:27659196

  9. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

    NASA Astrophysics Data System (ADS)

    Simonin, Marie; Richaume, Agnès; Guyonnet, Julien P.; Dubost, Audrey; Martins, Jean M. F.; Pommier, Thomas

    2016-09-01

    Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg‑1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function.

  10. Does the preferential microbial colonisation of ferromagnesian minerals affect mineral weathering in soil?

    PubMed

    Wilson, Michael J; Certini, Giacomo; Campbell, Colin D; Anderson, Ian C; Hillier, Stephen

    2008-09-01

    Fungal activity is thought to play a direct and effective role in the breakdown and dissolution of primary minerals and in the synthesis of clay minerals in soil environments, with important consequences for plant growth and ecosystem functioning. We have studied primary mineral weathering in volcanic soils developed on trachydacite in southern Tuscany using a combination of qualitative and quantitative mineralogical and microbiological techniques. Specifically, we characterized the weathering and microbiological colonization of the magnetically separated ferromagnesian minerals (biotite and orthopyroxene) and non-ferromagnesian constituents (K-feldspar and volcanic glass) of the coarse sand fraction (250-1,000 microm). Our results show that in the basal horizons of the soils, the ferromagnesian minerals are much more intensively colonized by microorganisms than K-feldspar and glass, but that the composition of the microbial communities living on the two mineral fractions is similar. Moreover, X-ray diffraction, optical and scanning electron microscope observations show that although the ferromagnesian minerals are preferentially associated with an embryonic form of the clay mineral halloysite, they are still relatively fresh. We interpret our results as indicating that in this instance microbial activity, and particularly fungal activity, has not been an effective agent of mineral weathering, that the association with clay minerals is indirect, and that fungal weathering of primary minerals may not be as important a source of plant nutrients as previously claimed.

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

    PubMed

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

    2016-01-15

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

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

    PubMed

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

    2016-04-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  14. The soil microbial community composition and soil microbial carbon uptake are more affected by soil type than by different vegetation types (C3 and C4 plants) and seasonal changes

    NASA Astrophysics Data System (ADS)

    Griselle Mellado Vazquez, Perla; Lange, Markus; Gleixner, Gerd

    2016-04-01

    This study investigates the influence of different vegetation types (C3 and C4 plants), soil type and seasonal changes on the soil microbial biomass, soil microbial community composition and soil microbial carbon (C) uptake. We collected soil samples in winter (non-growing season) and summer (growing season) in 2012 from an experimental site cropping C3 and C4 plants for 6 years on two different soil types (sandy and clayey). The amount of phospholipid fatty acids (PLFAs) and their compound-specific δ13C values were used to determined microbial biomass and the flow of C from plants to soil microorganisms, respectively. Higher microbial biomass was found in the growing season. The microbial community composition was mainly explained by soil type. Higher amounts of SOC were driving the predominance of G+ bacteria, actinobacteria and cyclic G- bacteria in sandy soils, whereas root biomass was significantly related to the increased proportions of G- bacteria in clayey soils. Plant-derived C in G- bacteria increased significantly in clayey soils in the growing season. This increase was positively and significantly driven by root biomass. Moreover, changes in plant-derived C among microbial groups pointed to specific capabilities of different microbial groups to decompose distinct sources of C. We concluded that soil texture and favorable growth conditions driven by rhizosphere interactions are the most important factors controlling the soil microbial community. Our results demonstrate that a change of C3 plants vs. C4 plants has only a minor effect on the soil microbial community. Thus, such experiments are well suited to investigate soil organic matter dynamics as they allow to trace the C flow from plants into the soil microbial community without changing the community abundance and composition.

  15. Top-down control of carbon sequestration: grazing affects microbial structure and function in salt marsh soils.

    PubMed

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

    2017-03-20

    Tidal wetlands have been increasingly recognized as long-term carbon sinks in recent years. Work on carbon sequestration and decomposition processes in tidal wetlands focused so far mainly on effects of global-change factors such as sea-level rise and increasing temperatures. However, little is known about effects of land use, such as livestock grazing, on organic matter decomposition and ultimately carbon sequestration. The present work aims at understanding the mechanisms by which large herbivores can affect organic matter decomposition in tidal wetlands. This was achieved by studying both direct animal-microbe interactions and indirect animal-plant-microbe interactions in grazed and ungrazed areas of two long-term experimental field sites at the German North Sea coast. We assessed bacterial and fungal gene abundance using quantitative PCR, as well as the activity of microbial exo-enzymes by conducting fluorometric assays. We demonstrate that grazing can have a profound impact on the microbial community structure of tidal wetland soils, by consistently increasing the fungi-to-bacteria ratio by 38-42%, and therefore potentially exerts important control over carbon turnover and sequestration. The observed shift in the microbial community was primarily driven by organic matter source, with higher contributions of recalcitrant autochthonous (terrestrial) vs. easily degradable allochthonous (marine) sources in grazed areas favoring relative fungal abundance. We propose a novel and indirect form of animal-plant-microbe interaction: top-down control of aboveground vegetation structure determines the capacity of allochthonous organic matter trapping during flooding and thus the structure of the microbial community. Furthermore, our data provide the first evidence that grazing slows down microbial exo-enzyme activity and thus decomposition through changes in soil redox chemistry. Activities of enzymes involved in C cycling were reduced by 28-40%, while activities of

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  17. Pyrene biodegradation in an industrial soil exposed to simulated rhizodeposition: how does it affect functional microbial abundance?

    PubMed

    Meng, Liang; Zhu, Yong-Guan

    2011-02-15

    Rhizodeposition is an important biogeochemical process for the phytoremediation of contaminated substrates. This study investigated the effects of various rhizodeposition components from celery (Apium graveolens) on pyrene biodegradation and microbial abundance in a long-term contaminated soil. Batch microcosms simulating in situ contaminated soil were amended with lipophilic extract, water-soluble extract, or debris from celery root to mimic plant rhizodeposition within 70 days. Soil was intermittently analyzed for pyrene concentration and target gene abundance estimated by real-time PCR. Lipophilic extract was the major simulated rhizodeposit enhancing pyrene biodegradation, while water-soluble extract stimulated microbial growth most efficiently. The relative abundance of total polycyclic aromatic hydrocarbon (PAH) degraders was enhanced by lipophilic extract but inhibited by the other two rhizodeposits, indicating that these components exerted different selective pressures on PAH degrader community. Moreover, PAH catabolic pathway may involve in the pollutant detoxification and fatty acid metabolism by microorganisms, which were also affected by rhizodeposition. These results provide insights into plant-microbe interactions responsible for PAH biodegradation and offer opportunities to facilitate PAH phytoremediation in industrial sites.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  20. [Soil microbial ecological process and microbial functional gene diversity].

    PubMed

    Zhang, Jing; Zhang, Huiwen; Li, Xinyu; Su, Zhencheng; Zhang, Chenggang

    2006-06-01

    Soil microbes in terrestrial ecosystem carry out a series of important ecological functions, such as geo-chemical cycling of elements, degradation of pollutants, and buffering to the acute changes of environment, etc. Soil microbial ecological function has a close relation with soil function, and the changes in the structure and composition of soil microbial populations can directly affect the realization of soil function. Through their produced enzymes, soil microbes take part in a series of metabolic activities, and the functional genes of coded enzymes are the functional markers of microbes. In recent ten years, molecular ecology focusing on the functional gene diversity has been developed rapidly, which gives us a new cut-in point to understand soil microbial ecological function from the point of functional gene. This paper reviewed the research advances in the functional gene diversity correlated to soil microbial ecological function, with the perspectives in this field discussed.

  1. Biochar addition impacts soil microbial community in tropical soils

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    De Philippis, Roberto

    2015-04-01

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

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

    EPA Science Inventory

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

  5. ETBE (ethyl tert butyl ether) and TAME (tert amyl methyl ether) affect microbial community structure and function in soils.

    PubMed

    Bartling, Johanna; Esperschütz, Jürgen; Wilke, Berndt-Michael; Schloter, Michael

    2011-03-15

    Ethyl tert butyl ether (ETBE) and tert amyl methyl ether (TAME) are oxygenates used in gasoline in order to reduce emissions from vehicles. The present study investigated their impact on a soil microflora that never was exposed to any contamination before. Therefore, soil was artificially contaminated and incubated over 6 weeks. Substrate induced respiration (SIR) measurements and phospholipid fatty acid (PLFA) analysis indicated shifts in both, microbial function and structure during incubation. The results showed an activation of microbial respiration in the presence of ETBE and TAME, suggesting biodegradation by the microflora. Furthermore, PLFA concentrations decreased in the presence of ETBE and TAME and Gram-positive bacteria became more dominant in the microbial community.

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

    PubMed

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

    2014-04-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

    Morrison, D.E.; Alexander, M.

    1997-08-01

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

  10. Do Chernobyl-like contaminations with (137)Cs and (90)Sr affect the microbial community, the fungal biomass and the composition of soil organic matter in soil?

    PubMed

    Niedrée, Bastian; Berns, Anne E; Vereecken, Harry; Burauel, Peter

    2013-04-01

    (137)Cs and (90)Sr are the main radionuclides responsible for contamination of agricultural soils due to core melts in nuclear power plants such as Chernobyl or Fukushima. The present study focused on effects of Chernobyl-like contaminations on the bacterial and fungal community structure, the fungal biomass and the formation of soil organic matter in native and in sterilized and reinoculated soils. 2% wheat straw [m/m] was applied to a typical agricultural soil, artificially contaminated with (137)Cs and (90)Sr, and it was then incubated in microcosms for three months at 20 °C and 50% of the water-holding capacity. The development of the microbial communities was monitored with 16S and 18S rDNA denaturing gradient gel electrophoresis (DGGE). The quantification of the ergosterol content was used as a proxy for changes in the fungal biomass. Changes in the soil organic matter were determined using the (13)C cross polarization/magic angle spinning nuclear magnet resonance technique ((13)C-CP/MAS NMR). Slight but significant population shifts in the DGGE gel patterns could be related to the applied radionuclides. However, radiation-induced impacts could not be seen in either the chemical composition of the soil organic matter or in the development of the fungal biomass. Impacts caused by sterilization and reinoculation prevailed in the microcosms of the present study. Contaminations with (137)Cs or (90)Sr up to 50-fold that of the hotspots occurring in Chernobyl led to minor changes in soil microbial functions suggesting a strong resilience of natural soils with respect to radioactive contamination.

  11. Factors affecting soil cohesion

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  12. Microbial effect on soil hydraulic properties

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  15. Post fumigation recovery of soil microbial community structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  16. Microbial hotspots and hot moments in soil

    NASA Astrophysics Data System (ADS)

    Kuzyakov, Yakov; Blagodatskaya, Evgenia

    2015-04-01

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

  17. Microbial Contribution to Organic Carbon Sequestration in Mineral Soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  19. Inter-specific competition, but not different soil microbial communities, affects N chemical forms uptake by competing graminoids of upland grasslands.

    PubMed

    Medina-Roldán, Eduardo; Bardgett, Richard D

    2012-01-01

    Evidence that plants differ in their ability to take up both organic (ON) and inorganic (IN) forms of nitrogen (N) has increased ecologists' interest on resource-based plant competition. However, whether plant uptake of IN and ON responds to differences in soil microbial community composition and/or functioning has not yet been explored, despite soil microbes playing a key role in N cycling. Here, we report results from a competition experiment testing the hypothesis that soil microbial communities differing in metabolic activity as a result of long-term differences to grazing exposure could modify N uptake of Eriophorum vaginatum L. and Nardus stricta L. These graminoids co-occur on nutrient-poor, mountain grasslands where E. vaginatum decreases and N. stricta increases in response to long-term grazing. We inoculated sterilised soil with soil microbial communities from continuously grazed and ungrazed grasslands and planted soils with both E. vaginatum and N. stricta, and then tracked uptake of isotopically labelled NH(4) (+) (IN) and glycine (ON) into plant tissues. The metabolically different microbial communities had no effect on N uptake by either of the graminoids, which might suggest functional equivalence of soil microbes in their impacts on plant N uptake. Consistent with its dominance in soils with greater concentrations of ON relative to IN in the soluble N pool, Eriophorum vaginatum took up more glycine than N. stricta. Nardus stricta reduced the glycine proportion taken up by E. vaginatum, thus increasing niche overlap in N usage between these species. Local abundances of these species in mountain grasslands are principally controlled by grazing and soil moisture, although our results suggest that changes in the relative availability of ON to IN can also play a role. Our results also suggest that coexistence of these species in mountain grasslands is likely based on non-equilibrium mechanisms such as disturbance and/or soil heterogeneity.

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

    PubMed

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

    2011-07-01

    Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO(2) (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. Soil microbial communities as affected by organic fertilizer and sunn hemp as a cover crop in organic sweet pepper production in Puerto Rico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Organic production in Puerto Rico is at an early stage and research is needed to validate the sustainability of different management practices. This research initiated evaluation of selected soil properties including the microbial communities to evaluate the effects of Tropic sunn (Crotalaria juncea...

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2015-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Kallenbach, Cynthia M.; Grandy, A. Stuart

    2014-05-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

    USGS Publications Warehouse

    Waldrop, M.P.; Firestone, M.K.

    2006-01-01

    Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling

  8. Tillage system affects microbiological properties of soil

    NASA Astrophysics Data System (ADS)

    Delgado, A.; de Santiago, A.; Avilés, M.; Perea, F.

    2012-04-01

    Soil tillage significantly affects organic carbon accumulation, microbial biomass, and subsequently enzymatic activity in surface soil. Microbial activity in soil is a crucial parameter contributing to soil functioning, and thus a basic quality factor for soil. Since enzymes remain soil after excretion by living or disintegrating cells, shifts in their activities reflect long-term fluctuations in microbial biomass. In order to study the effects of no-till on biochemical and microbiological properties in comparison to conventional tillage in a representative soil from South Spain, an experiment was conducted since 1982 on the experimental farm of the Institute of Agriculture and Fisheries Research of Andalusia (IFAPA) in Carmona, SW Spain (37o24'07''N, 5o35'10''W). The soil at the experimental site was a very fine, montomorillonitic, thermic Chromic Haploxerert (Soil Survey Staff, 2010). A randomized complete block design involving three replications and the following two tillage treatments was performed: (i) Conventional tillage, which involved mouldboard plowing to a depth of 50 cm in the summer (once every three years), followed by field cultivation to a depth of 15 cm before sowing; crop residues being burnt, (ii) No tillage, which involved controlling weeds before sowing by spraying glyphosate and sowing directly into the crop residue from the previous year by using a planter with double-disk openers. For all tillage treatments, the crop rotation (annual crops) consisted of winter wheat, sunflower, and legumes (pea, chickpea, or faba bean, depending on the year), which were grown under rainfed conditions. Enzymatic activities (ß-glucosidase, dehydrogenase, aryl-sulphatase, acid phosphatase, and urease), soil microbial biomass by total viable cells number by acridine orange direct count, the density of cultivable groups of bacteria and fungi by dilution plating on semi-selective media, the physiological profiles of the microbial communities by BiologR, and the

  9. [Effects of land use pattern on soil microbial biomass carbon in Xishuangbanna].

    PubMed

    Fang, Li-na; Yang, Xiao-dong; Du, Jie

    2011-04-01

    In January 2006 - September 2007, a controlled litter-removal and root-cutting experiment was conducted to study the effects of different land use patterns (secondary forest or rubber plantation) on soil microbial biomass carbon in Xishuangbanna, China. After the secondary forest converted into rubber plantation, soil nutrient contents and plant carbon input decreased obviously, and soil microbial biomass carbon had a significant decrease. These two forest types had a higher soil microbial biomass carbon in rainy season than in dry season. In secondary forest, soil microbial biomass carbon was significantly positively correlated with soil temperature; while in rubber plantation, the microbial biomass carbon was positively correlated with soil moisture. In secondary forest, soil microbial biomass carbon was controlled by the nutrient inputs from plant roots, but less affected by litter amount. Also in secondary forest, soil microbial biomass carbon was significantly positively correlated with fine-root biomass and its C and N inputs. In rubber plantation, both the fine-root biomass and its C and N inputs and the litter amount had lesser effects on soil microbial biomass carbon. These results suggested that planting rubber induced the decreases of soil nutrient contents and pH value, and, added with serious artificial disturbances, reduced the soil microbial biomass carbon and changed its controlling factors, which in turn would affect other soil ecological processes.

  10. Soil warming alters microbial substrate use in alpine soils.

    PubMed

    Streit, Kathrin; Hagedorn, Frank; Hiltbrunner, David; Portmann, Magdalena; Saurer, Matthias; Buchmann, Nina; Wild, Birgit; Richter, Andreas; Wipf, Sonja; Siegwolf, Rolf T W

    2014-04-01

    Will warming lead to an increased use of older soil organic carbon (SOC) by microbial communities, thereby inducing C losses from C-rich alpine soils? We studied soil microbial community composition, activity, and substrate use after 3 and 4 years of soil warming (+4 °C, 2007-2010) at the alpine treeline in Switzerland. The warming experiment was nested in a free air CO2 enrichment experiment using depleted (13)CO2 (δ(13)C = -30‰, 2001-2009). We traced this depleted (13)C label in phospholipid fatty acids (PLFA) of the organic layer (0-5 cm soil depth) and in C mineralized from root-free soils to distinguish substrate ages used by soil microorganisms: fixed before 2001 ('old'), from 2001 to 2009 ('new') or in 2010 ('recent'). Warming induced a sustained stimulation of soil respiration (+38%) without decline in mineralizable SOC. PLFA concentrations did not reveal changes in microbial community composition due to soil warming, but soil microbial metabolic activity was stimulated (+66%). Warming decreased the amount of new and recent C in the fungal biomarker 18:2ω6,9 and the amount of new C mineralized from root-free soils, implying a shift in microbial substrate use toward a greater use of old SOC. This shift in substrate use could indicate an imbalance between C inputs and outputs, which could eventually decrease SOC storage in this alpine ecosystem.

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

    PubMed

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

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Spohn, Marie; Chodak, Marcin

    2015-04-01

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

  13. Substrate and nutrient limitation regulating microbial growth in soil

    NASA Astrophysics Data System (ADS)

    Bååth, Erland

    2015-04-01

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

  14. Desert gerbils affect bacterial composition of soil.

    PubMed

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

    2013-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  17. Soil and plant effects on microbial community structure.

    PubMed

    Buyer, Jeffrey S; Roberts, Daniel P; Russek-Cohen, Estelle

    2002-11-01

    We investigated the effects of two different plant species (corn and soybean) and three different soil types on microbial community structure in the rhizosphere. Our working hypothesis was that the rhizosphere effect would be strongest on fast-growing aerobic heterotrophs, while there would be little or no rhizosphere effect on oligotrophic and other slow-growing microorganisms. Culturable bacteria and fungi had larger population densities in the rhizosphere than in bulk soil. Communities were characterized by soil fatty acid analysis and by substrate utilization assays for bacteria and fungi. Fatty acid analysis revealed a very strong soil effect but little plant effect on the microbial community, indicating that the overall microbial community structure was not affected by the rhizosphere. There was a strong rhizosphere effect detected by the substrate utilization assay for fast-growing aerobic heterotrophic bacterial community structure, with soil controls and rhizosphere samples clearly distinguished from each other. There was a much weaker rhizosphere effect on fungal communities than on bacterial communities as measured by the substrate utilization assays. At this coarse level of community analysis, the rhizosphere microbial community was impacted most by soil effects, and the rhizosphere only affected a small portion of the total bacteria.

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

    PubMed

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

    2015-04-07

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

  19. Soil microbial community of abandoned sand fields.

    PubMed

    Elhottová, D; Szili-Kovács, T; Tríska, J

    2002-01-01

    Microbiological evaluation of sandy grassland soils from two different stages of secondary succession on abandoned fields (4 and 8 years old fallow) was carried out as a part of research focused on restoration of semi-natural vegetation communities in Kiskunság National Park in Hungary. There was an apparent total N and organic C enrichment, stimulation of microbial growth and microbial community structure change on fields abandoned by agricultural practice (small family farm) in comparison with native undisturbed grassland. A successional trend of the microbial community was found after 4 and 8 years of fallow-lying soil. It consisted in a shift of r-survival strategy to more efficient C economy, in a decrease of specific respiration and metabolic activity, forced accumulation of storage bacterial compounds and increased fungal distribution. The composition of microbial phospholipid fatty acids mixture of soils abandoned at various times was significantly different.

  20. Belowground environmental effects of transgenic crops: a soil microbial perspective.

    PubMed

    Turrini, Alessandra; Sbrana, Cristiana; Giovannetti, Manuela

    2015-04-01

    Experimental studies investigated the effects of transgenic crops on the structure, function and diversity of soil and rhizosphere microbial communities playing key roles in belowground environments. Here we review available data on direct, indirect and pleiotropic effects of engineered plants on soil microbiota, considering both the technology and the genetic construct utilized. Plants modified to express phytopathogen/phytoparasite resistance, or traits beneficial to food industries and consumers, differentially affected soil microorganisms depending on transformation events, experimental conditions and taxa analyzed. Future studies should address the development of harmonized methodologies by taking into account the complex interactions governing soil life.

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

    NASA Astrophysics Data System (ADS)

    Wang, G.; Or, D.

    2012-04-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2016-01-15

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

  5. Soil microbial response to waste potassium silicate drilling fluid.

    PubMed

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

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2013-11-01

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

  9. Effect of roundup ultra on microbial activity and biomass from selected soils.

    PubMed

    Haney, R L; Senseman, S A; Hons, F M

    2002-01-01

    Herbicides applied to soils potentially affect soil microbial activity. The quantity and frequency of Roundup Ultra [RU; N-(phosphonomethyl)glycine; Monsanto, St. Louis, MO] applications have escalated with the advent of Roundup-tolerant crops. The objective of this study was to determine the effect of Roundup Ultra on soil microbial biomass and activity across a range of soils varying in fertility. The isoproplyamine salt of glyphosate was applied in the form of RU at a rate of 234 mg active ingredient kg(-1) soil based on an assumed 2-mm glyphosate-soil interaction depth. Roundup Ultra significantly stimulated soil microbial activity as measured by C and N mineralization, as well as soil microbial biomass. Cumulative C mineralization as well as mineralization rate increased above background levels for all soils tested with addition of RU. There were strong linear relationships between C and N mineralized, as well as between soil microbial C and N (r2 = 0.96 and 0.95, respectively). The slopes of the relationships with RU addition approximated three. Since the isopropylamine salt of glyphosate has a C to N ratio of 3:1, the data strongly suggest that RU was the direct cause of the enhanced microbial activity. An increase in the C mineralization rate occurred the first day following RU addition and continued for 14 d. Roundup Ultra appeared to be rapidly degraded by soil microbes regardless of soil type or organic matter content, even at high application rates, without adversely affecting microbial activity.

  10. Non-microbial methane emissions from soils

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  11. [Effects of different straw recycling and tillage methods on soil respiration and microbial activity].

    PubMed

    Li, Xiao-sha; Wu, Ning; Liu, Ling; Feng, Yu-peng; Xu, Xu; Han, Hui-fang; Ning, Tang-yuan; Li, Zeng-jia

    2015-06-01

    To explore the effects of different tillage methods and straw recycling on soil respiration and microbial activity in summer maize field during the winter wheat and summer maize double cropping system, substrate induced respiration method and CO2 release method were used to determine soil microbial biomass carbon, microbial activity, soil respiration, and microbial respiratory quotient. The experiment included 3 tillage methods during the winter wheat growing season, i.e., no-tillage, subsoiling and conventional tillage. Each tillage method was companied with 2 straw management patterns, i.e., straw recycling and no straw. The results indicated that the conservation tillage methods and straw recycling mainly affected 0-10 cm soil layer. Straw recycling could significantly improve the microbial biomass carbon and microbial activity, while decrease microbial respiratory quotient. Straw recycling could improve the soil respiration at both seedling stage and anthesis, however, it could reduce the soil respiration at filling stage, wax ripeness, and harvest stage. Under the same straw application, compared with conventional tillage, the soil respiration and microbial respiratory quotient in both subsoiling and no-tillage were reduced, while the microbial biomass carbon and microbial activity were increased. During the summer maize growing season, soil microbial biomass carbon and microbial activity were increased in straw returning with conservation tillage, while the respiratory quotient was reduced. In 0-10 cm soil layer, compared with conventional tillage, straw recycling with subsoiling and no-tillage significantly increased soil microbial biomass carbon by 95.8% and 74.3%, and increased soil microbial activity by 97.1% and 74.2%, respectively.

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

    SciTech Connect

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

    1993-12-01

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

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

    PubMed

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

    2014-05-01

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

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

    PubMed

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

    2012-11-15

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

  15. [Effect of long-term fertilization on microbial community functional diversity in black soil].

    PubMed

    Liu, Jing-xin; Chi, Feng-qin; Xu, Xiu-hong; Kuang, En-jun; Zhang, Jiu-ming; Su, Qing-rui; Zhou, Bao-ku

    2015-10-01

    In order to study the effects of long-term different fertilization on microbial community functional diversity in arable black. soil, we examined microbial metabolic activities in two soil la- yers (0-20 cm, 20-40 cm) under four treatments (CK, NPK, M, MNPK) from a 35-year continuous fertilization field at the Ministry of Agriculture Key Field Observation Station of Harbin Black Soil Ecology Environment using Biolog-ECO method. The results showed that: in the 0-20 cm soil layer, combined application of organic and inorganic fertilizer(MNPK) increased the rate of soil microbial carbon source utilization and community metabolism richness, diversity and dominance; In the 20-40 cm layer, these indices of the MNPK treatment was lower than that of the NPK treat- ment; while NPK treatment decreased soil microbial community metabolism evenness in both layers. Six groups of carbon sources used by soil microbes of all the treatments were different between the two soil layers, and the difference was significant among all treatments in each soil layer (P < 0.05) , while the variations among treatments were different in the two soil layers. Canonical correspondence analysis (CCA) showed that soil microbial community metabolic function of all the treatments was different between the two soil layers, and there was difference among all treatments in each soil layer, while the influences of soil nutrients on soil microbial community metabolic function of all treatments were similar in each soil layer. It was concluded that long-term different fertilization affected soil microbial community functional diversity in both tillage soil layer and down soil layers, and chemical fertilization alone had a larger influence on the microbial community functional diversity in the 20-40 cm layer.

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

    PubMed

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

    2015-01-01

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

  17. Microbial assemblages in soil microbial succession after glacial retreat in Svalbard (high arctic).

    PubMed

    Kastovská, Klára; Elster, Josef; Stibal, Marek; Santrůcková, Hana

    2005-10-01

    Microbial community composition (cyanobacteria and eukaryotic microalgae abundance and diversity, bacterial abundance, and soil respiration) was studied in subglacial and periglacial habitats on five glaciers near Ny-Alesund, Svalbard (79 degrees N). Soil microbial communities from nonvegetated sites (subglacial, recently deglaciated, and cryoconite sediments) and sites with plant cover (deglaciated some hundreds of years ago) were analyzed. Physicochemical analyses (pH, texture, water content, organic matter, total C and N content) were also performed on the samples. In total, 57 taxa of 23 genera of cyanobacteriaand algae were identified. Algae from the class Chlorophyceae (25 species) and cyanobacteria (23 species) were richest in biodiversity. The numbers of identified species in single habitat types were 23 in subglacial, 39 inbarren, 22 in cryoconite, and 24 in vegetated soils. The highest cyanobacterial and algal biovolume and cell numbers, respectively, were present in cryoconite (13x10(4) microm3 mg-1 soil and 508 cells per mg of soil), followed by barren (5.7x10(4) and 188), vegetated (2.6x10(4) and 120), and subglacial (0.1x10(4) and 5) soils. Cyanobacteria prevailed in all soil samples. Algae (mainly green algae) were present only as accessory organisms. The density of bacteria showed a slightly different trend to that of the cyanobacterial and algal assemblages. The highest number of bacteria was present in vegetated (mean: 13,722x10(8) cells per mg of soil dry wt.), followed by cryoconite (3802x10(8)), barren (654x10(8)), and subglacial (78x10(8)) soils. Response of cyanobacteria and algae to physical parameters showed that soil texture and water content are important for biomass development. In addition, it is shown that nitrogen and water content are the main factors affecting bacterial abundance and overall soil respiration. Redundancy analysis (RDA) with forward selection was used to create a model explaining variability in cyanobacterial, algal

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity.

    PubMed

    Carini, Paul; Marsden, Patrick J; Leff, Jonathan W; Morgan, Emily E; Strickland, Michael S; Fierer, Noah

    2016-12-19

    Extracellular DNA from dead microorganisms can persist in soil for weeks to years(1-3). Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide(4). We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this 'relic DNA' remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions.

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

    PubMed

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

    2015-02-01

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

  1. Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

    SciTech Connect

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

    2010-05-17

    Increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity are three main environmental changes occurring on a global scale. The BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve started in 1997, to better understand how these changes would affect soil systems. To understand how increasing nitrogen deposition affects the microbial community diversity, heterogeneity, and functional structure impact soil microbial communities, 12 samples were collected from the BioCON plots in which nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition and 12 samples from without added fertilizer. DNA from the 24 samples was extracted using a freeze-grind protocol, amplified, labeled with a fluorescent dye, and then hybridized to GeoChip, a functional gene array containing probes for genes involved in N, S and C cycling, metal resistance and organic contaminant degradation. Detrended correspondence analysis (DCA) of all genes detected was performed to analyze microbial community patterns. The first two axes accounted for 23.5percent of the total variation. The samples fell into two major groups: fertilized and non-fertilized, suggesting that nitrogenous fertilizer had a significant impact on soil microbial community structure and diversity. The functional gene numbers detected in fertilized samples was less that detected in non-fertilizer samples. Functional genes involving in the N cycling were mainly discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  3. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

    PubMed

    Su, Jian-Qiang; Ding, Long-Jun; Xue, Kai; Yao, Huai-Ying; Quensen, John; Bai, Shi-Jie; Wei, Wen-Xue; Wu, Jin-Shui; Zhou, Jizhong; Tiedje, James M; Zhu, Yong-Guan

    2015-01-01

    The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  6. Crabgrass (Digitaria sanguinalis) allelochemicals that interfere with crop growth and the soil microbial community.

    PubMed

    Zhou, Bin; Kong, Chui-Hua; Li, Yong-Hua; Wang, Peng; Xu, Xiao-Hua

    2013-06-05

    Three chemicals, veratric acid, maltol, and (−)-loliolide, were isolated from crabgrass and their structures were identified by spectroscopic analysis. The chemicals were detected in crabgrass root exudates and rhizosphere soils, and their concentrations ranged from 0.16 to 8.10 μg/g. At an approximate concentration determined in crabgrass root exudates, all chemicals significantly inhibited the growth of wheat, maize, and soybean and reduced soil microbial biomass carbon. Phospholipid fatty acid profiling showed that veratric acid, maltol, and (−)-loliolide affected the signature lipid biomarkers of soil bacteria, actinobacteria, and fungi, resulting in changes in soil microbial community structures. There were significant relationships between crop growth and soil microbes under the chemicals' application. Chemical-specific changes in the soil microbial community generated negative feedback on crop growth. The results suggest that veratric acid, maltol, and (−)-loliolide released from crabgrass may act as allelochemicals interfering with crop growth and the soil microbial community.

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

    PubMed

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  9. Substrate-induced changes in microbial community-level physiological profiles and their application to discriminate soil microbial communities.

    PubMed

    Chen, Jian; Xie, Huijun; Zhuang, Xuliangli; Zhuang, Guoqiang; Bai, Zhihui; Zhang, Hongxun

    2008-01-01

    The addition of simple substrates could affect the microbial respiration in soils. This substrate-induced respiration is widely used to estimate the soil microbial biomass, but little attention has been paid to its influence on the changes of community-level physiological profiles. In this study, the process of microbial communities responding to the added substrate using sole-carbon-source utilization (BIOLOG) was investigated. BIOLOG is biased toward fast-growing bacteria; this advantage was taken to detect the prompt response of the active microbial communities to the added substrate. Four soil samples from agricultural fields adjacent to heavy metal mines were amended with L-arginine, citric acid, or D-glucose. Substrate amendments could, generally, not only increase the metabolic activity of the microbial communities, but also change the metabolic diverse patterns compared with no-substrate control. By tracking the process, it was found that the variance between substrate-induced treatment and control fluctuated greatly during the incubation course, and the influences of these three substrates were different. In addition, the application of these induced changes to discriminate soil microbial communities was tested. The distance among all samples was greatly increased, which further showed the functional variance among microbial communities in soils. This can be very useful in the discrimination of microbial communities even with high similarity.

  10. Environmental Controls of Microbial Resource Partitioning in Soils

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2017-01-01

    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. PMID:28198425

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

    PubMed Central

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

    2015-01-01

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

  15. The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

    PubMed Central

    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. PMID:27798702

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

    PubMed

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

    2009-08-01

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

  17. Microbial Mechanisms Enhancing Soil C Storage

    SciTech Connect

    Zak, Donald

    2015-09-24

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

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

    NASA Astrophysics Data System (ADS)

    Urbanek, Emilia; Qassem, Khalid

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  20. Soil amendments yield persisting changes in the microbial communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed Central

    Kim, Minsu; Or, Dani

    2016-01-01

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

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

    PubMed

    Kim, Minsu; Or, Dani

    2016-01-01

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

  3. Functional activity of soil microbial communities in post-fire pine stands of Tolyatti, Samara oblast

    NASA Astrophysics Data System (ADS)

    Maksimova, E. Yu.; Kudinova, A. G.; Abakumov, E. V.

    2017-02-01

    The state of microbial communities in gray-humus soils (Eutric Fluvic Arenosols (Ochric)) of pine stands in the city of Tolyatti after forest fires of 2010 is analyzed. It is shown that fires exert negative effects on the structure and metabolic activity of microbial communities in the postpyrogenic soils. The content of the carbon of microbial biomass and the intensity of microbial respiration in the upper organic horizons of the post-fire plots decrease by 6.5 and 3.4 times, respectively, in comparison with those in the soils of background plots. However, the fire has not affected the studied microbiological parameters of the soils at the depths of more than 10 cm. The maximum content of the carbon of microbial biomass carbon and the maximum intensity of microbial respiration have been found in the subsurface AY2 and AC horizons two-three years the fire. An increase in the microbial metabolic quotient (the ratio of soil respiration to microbial biomass) attests to the disturbance of the ecophysiological state of soil microbial communities after the pyrogenic impact.

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

    2014-09-15

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

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

    EPA Science Inventory

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  8. Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests.

    PubMed

    Flores-Rentería, Dulce; Curiel Yuste, Jorge; Rincón, Ana; Brearley, Francis Q; García-Gil, Juan Carlos; Valladares, Fernando

    2015-05-01

    Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

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

    SciTech Connect

    Francis, A. J.; Dodge, C. J.

    2015-12-01

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

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

    DOE PAGES

    Francis, A. J.; Dodge, C. J.

    2015-12-01

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

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

    PubMed

    Francis, A J; Dodge, C J

    2015-12-01

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

  12. [Microbial response mechanism for drying and rewetting effect on soil respiration in grassland ecosystem: a review].

    PubMed

    He, Yun-Long; Qi, Yu-Chun; Dong, Yun-She; Peng, Qin; Sun, Liang-Jie; Jia, Jun-Qiang; Guo, Shu-Fang; Yan, Zhong-Qing

    2014-11-01

    As one of the most important and wide distribution community type among terrestrial ecosystems, grassland ecosystem plays a critical role in the global carbon cycles and climate regulation. China has extremely rich grassland resources, which have a huge carbon sequestration potential and are an important part of the global carbon cycle. Drying and rewetting is a common natural phenomenon in soil, which might accelerate soil carbon mineralization process, increase soil respiration and exert profound influence on microbial activity and community structure. Under the background of the global change, the changes in rainfall capacity, strength and frequency would inevitably affect soil drying and wetting cycles, and thus change the microbial activity and community structure as well as soil respiration, and then exert important influence on global carbon budget. In this paper, related references in recent ten years were reviewed. The source of soil released, the trend of soil respiration over time and the relationship between soil respiration and microbial biomass, microbial activity and microbial community structure during the processes of dry-rewetting cycle were analyzed and summarized, in order to better understand the microbial response mechanism for drying and rewetting effecting on soil respiration in grassland ecosystem, and provide a certain theoretical basis for more accurate evaluation and prediction of future global carbon balance of terrestrial ecosystems and climate change.

  13. Capturing the Spatial Variability of Microbial Communties within Agricultural Soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding patterns in spatial variability of soil microbial communities can provide important insights into the mechanisms that control ecosystem function. The level of replication required to adequately characterize the variability of soil communities across both small and large geographic and ...

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

    NASA Astrophysics Data System (ADS)

    Elhottová, Dana; Jirout, Jiří; Pižl, Václav

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed Central

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

    2015-01-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities. PMID:26195343

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  19. Successive DNA extractions improve characterization of soil microbial communities

    PubMed Central

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

    2017-01-01

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

  20. Soil microbial properties under different vegetation types on Mountain Han.

    PubMed

    Wang, Miao; Qu, Laiye; Ma, Keming; Yuan, Xiu

    2013-06-01

    This study investigated the influence of broadleaf and conifer vegetation on soil microbial communities in a distinct vertical distribution belt in Northeast China. Soil samples were taken at 0-5, 5-10 and 10-20 cm depths from four vegetation types at different altitudes, which were characterized by poplar (Populus davidiana) (1250-1300 m), poplar (P. davidiana) mixed with birch (Betula platyphylla) (1370-1550 m), birch (B. platyphylla) (1550-1720 m), and larch (Larix principis-rupprechtii) (1840-1890 m). Microbial biomass and community structure were determined using the fumigation-extraction method and phospholipid fatty acid (PLFA) analysis, and soil fungal community level physiological profiles (CLPP) were characterized using Biolog FF Microplates. It was found that soil properties, especially soil organic carbon and water content, contributed significantly to the variations in soil microbes. With increasing soil depth, the soil microbial biomass, fungal biomass, and fungal catabolic ability diminished; however, the ratio of fungi to bacteria increased. The fungal ratio was higher under larch forests compared to that under poplar, birch, and their mixed forests, although the soil microbial biomass was lower. The direct contribution of vegetation types to the soil microbial community variation was 12%. If the indirect contribution through soil organic carbon was included, variations in the vegetation type had substantial influences on soil microbial composition and diversity.

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

    SciTech Connect

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

    2011-03-01

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

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

    PubMed

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

    2011-03-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. Interactive effects of nitrogen and phosphorus on soil microbial communities in a tropical forest.

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. Temperature and Microbial Activity Effects on Soil Carbon Stabilization

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  10. Microbial responses to southward and northward Cambisol soil transplant.

    PubMed

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

    2015-12-01

    Soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity at both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO3 ¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO3 ¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.

  11. Flooding Effects on Soil Microbial Communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Astrophysics Data System (ADS)

    Qin, K.; Peay, K.

    2015-12-01

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

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

    PubMed Central

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

    2012-01-01

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

  14. Potential microbial contamination during sampling of permafrost soil assessed by tracers

    PubMed Central

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

    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 biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. PMID:28230151

  15. Potential microbial contamination during sampling of permafrost soil assessed by tracers

    NASA Astrophysics Data System (ADS)

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

    2017-02-01

    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 biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

  16. Potential microbial contamination during sampling of permafrost soil assessed by tracers.

    PubMed

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S

    2017-02-23

    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 biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  18. Effects of manure compost application on soil microbial community diversity and soil microenvironments in a temperate cropland in China.

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2016-02-04

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions.

    PubMed

    Jassey, Vincent E J; Chiapusio, Geneviève; Binet, Philippe; Buttler, Alexandre; Laggoun-Défarge, Fatima; Delarue, Frédéric; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Francez, André-Jean; Gilbert, Daniel

    2013-03-01

    Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands.

  4. Soil C and N models that integrate microbial diversity.

    PubMed

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

    Industrial agriculture is yearly responsible for the loss of 55-100 Pg of historical soil carbon and 9.9 Tg of reactive nitrogen worldwide. Therefore, management practices should be adapted to preserve ecological processes and reduce inputs and environmental impacts. In particular, the management of soil organic matter (SOM) is a key factor influencing C and N cycles. Soil microorganisms play a central role in SOM dynamics. For instance, microbial diversity may explain up to 77 % of carbon mineralisation activities. However, soil microbial diversity is actually rarely taken into account in models of C and N dynamics. Here, we review the influence of microbial diversity on C and N dynamics, and the integration of microbial diversity in soil C and N models. We found that a gain of microbial richness and evenness enhances soil C and N dynamics on the average, though the improvement of C and N dynamics depends on the composition of microbial community. We reviewed 50 models integrating soil microbial diversity. More than 90 % of models integrate microbial diversity with discrete compartments representing conceptual functional groups (64 %) or identified taxonomic groups interacting in a food web (28 %). Half of the models have not been tested against an empirical dataset while the other half mainly consider fixed parameters. This is due to the difficulty to link taxonomic and functional diversity.

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

    NASA Astrophysics Data System (ADS)

    Schaefer, D.; Qiao, N.

    2011-12-01

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

  6. Microbial-based inoculants impact nitrous oxide emissions from an incubated soil medium containing urea fertilizers.

    PubMed

    Calvo, Pamela; Watts, Dexter B; Ames, Robert N; Kloepper, Joseph W; Torbert, H Allen

    2013-01-01

    There is currently much interest in developing crop management practices that will decrease NO emissions from agricultural soils. Many different approaches are being investigated, but to date, no studies have been published on how microbial inoculants affect NO emissions. This study was conducted to test the hypothesis that microbial-based inoculants known to promote root growth and nutrient uptake can reduce NO emissions in the presence of N fertilizers under controlled conditions. Carbon dioxide and CH fluxes were also measured to evaluate microbial respiration and determine the aerobic and anaerobic conditions of the incubated soil. The microbial-based treatments investigated were SoilBuilder (SB), a metabolite extract of SoilBuilder (SBF), and a mixture of four strains of plant growth-promoting spp. Experiments included two different N fertilizer treatments, urea and urea-NHNO 32% N (UAN), and an unfertilized control. Emissions of NO and CO were determined from soil incubations and analyzed with gas chromatography. After 29 d of incubation, cumulative NO emissions were reduced 80% by SB and 44% by SBF in soils fertilized with UAN. Treatment with spp. significantly reduced NO production on Days 1 and 2 of the incubation in soils fertilized with UAN. In the unfertilized treatment, cumulative emissions of NO were significantly reduced 92% by SBF. Microbial-based treatments did not reduce NO emissions associated with urea application. Microbial-based treatments increased CO emissions from soils fertilized with UAN, suggesting a possible increase in microbial activity. Overall, the results demonstrated that microbial-based inoculants can reduce NO emissions associated with N fertilizer application, and this response varies with the type of microbial-based inoculant and fertilizer.

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

    PubMed

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

    2015-09-15

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

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

    EPA Science Inventory

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

  9. [Soil microbial activity variation after land use changes in savannah, Llanos Orientales, Venezuela].

    PubMed

    Gómez, Yrma; Paolini, Jorge

    2011-03-01

    In West plains of Venezuela, the traditional land use of the Trachypogon savannah, has been the extensive grazing. The pressure over these savannahs to obtain a major animal productivity has stimulated the introduction of exotic forage plants, such as Brachiaria brizantha and Andropogon gayanus. In spite that great savannah extensions have been subject to this land use change, information about the effect that pastures and grazing activity have on microbial activity in these soils is scarce. So the objective of this study was to determine the impact that the extensive grazing and cover substitution have on microbial activity. The soil sampling was carried out during the dry and rainy seasons. The employed parameters to determine changes in soil microbial activity were the substrate induced respiration (SIR), basal respiration (BR), the dehydrogenase activity (DHS), the fluorescein diacetate hydrolysis (FDA) and the arginene ammonification (AA). The similarity of the structural soil characteristics studied allows us to infer, that the differences in the microbiological parameters are determined by climatic conditions and soil management. The results show that there is a low microbial activity in these soils. The rainy season caused an increase in all the microbiological parameters determined. B. brizantha made a greater contribution to soil carbon and promoted a greater heterotrophic activity. The extensive grazing and the low stocking rate in the West plain savannas did not affect the microbial activity in these soils.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    SciTech Connect

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

    2015-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Voroney, Paul; Paul, Eldor

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    SciTech Connect

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Maksimova, Ekaterina

    2015-04-01

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

  16. Relationships between bacterial diversity, microbial biomass, and litter quality in soils under different plant covers in northern Rio de Janeiro State, Brazil.

    PubMed

    Ndaw, S M; Gama-Rodrigues, A C; Gama-Rodrigues, E F; Sales, K R N; Rosado, A S

    2009-09-01

    Microbial populations are primarily responsible for the decomposition of organic residues, the nutrients cycle, and the flow of energy inside of soil. The present study was undertaken to link soil microbiological and soil biochemical parameters with soil- and litter-quality conditions in the surface layer from 5 sites differing in plant cover, in stand age, and in land-use history. The aim was to see how strongly these differences affect the soil microbial attributes and to identify how microbiological processes and structures can be influenced by soil and litter quality. Soil and litter samples were collected from 5 sites according to different land use: preserved forest, nonpreserved forest, secondary forest, pasture, and eucalyptus plantation. Soil and litter microbial biomass and activity were analysed and DNA was extracted from soil. The DNA concentrations and soil microbial C and N correlated positively and significantly, suggesting that these are decisive nutrients for microbial growth and time required for microbial biomass renewal. The litter microbial biomass represented a source of C and N higher than soil microbial biomass and can be an important layer to contribute to tropical soil with low C and N availability. The litter quality influenced the litter and soil microbial biomass and activity and the soil bacterial diversity. The chemical and nutritional quality of the litter influenced the structure and microbial community composition in the eucalyptus plantation.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  19. Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain).

    PubMed

    Bárcenas-Moreno, Gema; García-Orenes, Fuensanta; Mataix-Solera, Jorge; Mataix-Beneyto, Jorge

    2016-12-15

    Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study.

  20. Exploring Microbial Iron Oxidation in Wetland Soils

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    SciTech Connect

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

    1995-12-01

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

  3. Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest

    USGS Publications Warehouse

    Waldrop, M.P.; Harden, J.W.

    2008-01-01

    Boreal forests contain significant quantities of soil carbon that may be oxidized to CO2 given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short-term effects of wildfire to the long-term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both 13C lignin decomposition and microbial respiration

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

    PubMed

    Waring, Bonnie G; Hawkes, Christine V

    2015-05-01

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

  5. Short term changes of microbial processes in Icelandic soils to increasing temperatures

    NASA Astrophysics Data System (ADS)

    Guicharnaud, R.; Arnalds, O.; Paton, G. I.

    2010-02-01

    Temperature change is acknowledged to have a significant effect on soil biological processes and the corresponding sequestration of carbon and cycling of nutrients. Soils at high latitudes are likely to be particularly impacted by increases in temperature. Icelandic soils experience unusually frequent freeze and thaw cycles compare to other Arctic regions, which are increasing due to a warming climate. As a consequence these soils are frequently affected by short term temperature fluctuations. In this study, the short term response of a range of soil microbial parameters (respiration, nutrient availability, microbial biomass carbon, arylphosphatase and dehydrogenase activity) to temperature changes was measured in sub-arctic soils collected from across Iceland. Sample sites reflected two soil temperature regimes (cryic and frigid) and two land uses (pasture and arable). The soils were sampled from the field frozen, equilibrated at -20 °C and then incubated for two weeks at -10 °C, -2 °C, +2 °C and +10 °. Respiration and enzymatic activity were temperature dependent. The soil temperature regime affected the soil microbial biomass carbon sensitivity to temperatures. When soils where sampled from the cryic temperature regime a decreasing soil microbial biomass was detected when temperatures rose above the freezing point. Frigid soils, sampled from milder climatic conditions, where unaffected by difference in temperatures. Nitrogen mineralisation did not change with temperature. At -10 °C, dissolved organic carbon accounted for 88% of the fraction of labile carbon which was significantly greater than that recorded at +10 °C when dissolved organic carbon accounted for as low as 42% of the labile carbon fraction.

  6. Ohmic resistance affects microbial community and ...

    EPA Pesticide Factsheets

    Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial community and electrochemical kinetic parameters for biofilms on individual anodes in a multi-anode MXC to better comprehend anode fundamentals. Microbial community analysis using 16S rRNA illumine sequencing showed that Geobactor genus, one of the most kinetically efficient anode-respiring bacteria (ARB), was abundant (87%) only on the biofilm anode closest to a reference electrode in which current density was the highest among four anodes. In comparison, Geobacter populations were less than 11% for other three anodes more distant from the reference electrode, generating small current density. Half-saturation anode potential (EKA) was the lowest at -0.251 to -0.242 V (vs. standard hydrogen electrode) for the closest anode, while EKA was as high as -0.134 V for the farthest anode. Our study clearly proves that ohmic resistance changes anode potential which mainly causes different biofilm communities on individual anodes and consequently influences anode kinetics. This study explored the use of multiple anodes in microelectrochemical cells and the microbial community on these anodes, as a function of the efficiency in producing hydrogen peroxide.

  7. Carbon nanotubes as plant growth regulators: effects on tomato growth, reproductive system, and soil microbial community.

    PubMed

    Khodakovskaya, Mariya V; Kim, Bong-Soo; Kim, Jong Nam; Alimohammadi, Mohammad; Dervishi, Enkeleda; Mustafa, Thikra; Cernigla, Carl E

    2013-01-14

    Multi-walled carbon nanotubes (CNTs) can affect plant phenotype and the composition of soil microbiota. Tomato plants grown in soil supplemented with CNTs produce two times more flowers and fruit compared to plants grown in control soil. The effect of carbon nanotubes on microbial community of CNT-treated soil is determined by denaturing gradient gel electrophoresis and pyrosequencing analysis. Phylogenetic analysis indicates that Proteobacteria and Bacteroidetes are the most dominant groups in the microbial community of soil. The relative abundances of Bacteroidetes and Firmicutes are found to increase, whereas Proteobacteria and Verrucomicorbia decrease with increasing concentration of CNTs. The results of comparing diversity indices and species level phylotypes (OTUs) between samples showed that there is not a significant affect on bacterial diversity.

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

    USGS Publications Warehouse

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

    2013-01-01

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

  9. [Genetic diversity of microbial communities in tea orchard soil].

    PubMed

    Xue, Dong; Yao, Huai-Ying; Huang, Chang-Yong

    2007-04-01

    In this paper, the total microbial DNA was extracted from the soils in 8-, 50- and 90 years old tea orchards, adjacent wasteland, and 90 years old forestland in Meijiawu tea area of Hangzhou. The 16S rDNA V3 fragment was amplified by PCR, and the polymorphism of this fragment was analyzed by DGGE. The results indicated that both the tea orchard age and the land use type had significant effects on soil microbial genetic diversity. There was a significant difference (P < 0.05) in the microbial genetic diversity index among wasteland, tea orchards and forestland, which was decreased in the order of wasteland > tea orchard > forestland. For the tea orchards of different ages, the soil microbial genetic diversity index, microbial biomass C, and basal respiration were significantly higher in 50 years old than in 8 and 90 years old tea orchards.

  10. Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China.

    PubMed

    Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

    2017-03-28

    Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration.

  11. Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

    PubMed Central

    Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

    2017-01-01

    Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration. PMID:28349918

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Siczek, A.; Frąc, M.

    2012-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  15. Different degrees of plant invasion significantly affect the richness of the soil fungal community.

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

    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 < 0.01) linear regression function, which suggested that invertase was a good indicator of the magnitude of soil microbial respiration.

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

    PubMed

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

    2012-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. Nutrient Limitation of Microbial Mediated Decomposition and Arctic Soil Chronology

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    Soils of northern permafrost regions currently contain twice as much carbon as the entire Earth's atmosphere. Traditionally, environmental constraints have limited microbial activity resulting in restricted decomposition of soil organic matter in these systems and accumulation of massive amounts of soil organic carbon (SOC), however climate change is reducing the constraints of decomposition in arctic permafrost regions. Carbon cycling in nutrient poor, arctic ecosystems is tightly coupled to other biogeochemical cycles. Several studies have suggested strong nitrogen limitations of primary productivity and potentially warm-season microbial activity in these nutrient deficient soils. Nitrogen is required for microbial extracellular enzyme production which drives the decomposition of soil organic matter (SOM). Nitrogen limited arctic soils may also experience limitation via labile carbon availability despite the SOM rich environment due to low extracellular enzyme production. Few studies have directly addressed nutrient induced microbial limitation in SOC rich arctic tundra soils, and even less is known about the potential for nutrient co-limitation. Additionally, through the process of becoming deglaciated, sites within close proximity to one another may have experienced drastic differences in their effective soil ages due to the varied length of their active histories. Many soil properties and nutrient deficiencies are directly related to soil age, however this chronology has not previously been a focus of research on nutrient limitation of arctic soil microbial activity. Understanding of nutrient limitations, as well as potential co-limitation, on arctic soil microbial activity has important implications for carbon cycling and the ultimate fate of the current arctic SOC reservoir. Analyses of nutrient limitation on soils of a single site are not adequate for fully understanding the controls on soil microbial activity across a vast land mass with large variation in

  3. Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization

    PubMed Central

    Zhao, Mengxin; Wu, Linwei; Gao, Qun; Wang, Feng; Wen, Chongqing; Wang, Mengmeng; Liang, Yuting; Zhou, Jizhong

    2016-01-01

    ABSTRACT Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty

  4. Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization.

    PubMed

    Zhao, Mengxin; Sun, Bo; Wu, Linwei; Gao, Qun; Wang, Feng; Wen, Chongqing; Wang, Mengmeng; Liang, Yuting; Hale, Lauren; Zhou, Jizhong; Yang, Yunfeng

    2016-01-01

    Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    PubMed

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

    2014-04-01

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

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

    PubMed

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

    2016-04-01

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

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

    PubMed Central

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

    2014-01-01

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

  12. Impact of fungicide mancozeb at different application rates on soil microbial populations, soil biological processes, and enzyme activities in soil.

    PubMed

    Walia, Abhishek; Mehta, Preeti; Guleria, Shiwani; Chauhan, Anjali; Shirkot, C K

    2014-01-01

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

  13. Responses of microbial activity and decomposer organisms to contamination in microcosms containing coniferous forest soil.

    PubMed

    Salminen, J; Liiri, M; Haimi, J

    2002-09-01

    Soil respiration from microcosms contaminated with pentachlorophenol, 2-ethanolhexanoate, creosote, CuSO4, and benomyl was measured in order to evaluate usefulness of soil microcosms and microbial respiration rate monitoring as a toxicity test in soils with high organic matter content. Coniferous forest soil and its organisms were used as test objects. In addition, how a short-term low temperature period including frost affects respiration dynamics in stressed soils was studied, i.e., whether contaminants reduce resistance of the community to other (also natural) stresses. In addition, at the end of the experiment, effects of contaminants on faunal and microbial community structures were analyzed. Soil respiration measurements from the microcosms appeared to be a sensitive parameter for testing community-level effects of chemicals in the soil with high organic matter content. An 84-day exposure had acute effects, long-term effects, delaying effects, and total recovery of community respiration. Direct negative and indirect positive effects of chemical contamination on the community of soil organisms were found. Responses to contamination of soil respiration rate and structure of the soil community were parallel. Addition of pentachlorophenol, 2-ethanolhexane, and Cu into the soil reduced frost resistance of the decomposer community. It was concluded that soil respiration monitoring of artificially contaminated soil microcosms seems to be a useful tool for testing community-level toxic effects of chemicals.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  16. Modification of soil microbial activity and several hydrolases in a forest soil artificially contaminated with copper

    NASA Astrophysics Data System (ADS)

    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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed Central

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

    2016-01-01

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

  19. [Characteristics of soil microbial biomass and community composition in three types of plantations in southern subtropical area of China].

    PubMed

    Wang, Wei-Xia; Shi, Zuo-Min; Luo, Da; Liu, Shi-Rong; Lu, Li-Hua

    2013-07-01

    By using fumigation-extraction method and phospholipid fatty acids (PLFAs) analysis, this paper studied the characteristics of soil microbial biomass and community composition in the Erythrophleum fordii, Castanopsis hystrix, and Pinus massoniana plantations in south subtropical China. The soil microbial biomass, total PLFAs, bacterial PLFAs, and fungal PLFAs in the plantations were significantly affected by the plantation type and season, and the soil microbial biomass, total PLFAs, and individual PLFA signatures were higher in dry season than in rainy season. The C. hystrix plantation had the highest soil microbial biomass carbon and total PLFAs, while the E. fordii plantation had the highest soil microbial biomass nitrogen. There was a significant positive correlation between the soil pH and arbuscular mycorrhizal fungal (AMF) PLFA (16:1omega5c). The soil total PLFAs, gram-positive bacterial PLFAs, saprophytic fungal PLFA (18:2omega6,9c), and the ratio of gram-positive to gram-negative bacterial PLFAs were significantly positively correlated with soil organic carbon, total nitrogen, and total phosphorus, suggesting that the soil organic carbon, total nitrogen, and total phosphorus contents were the most important nutrient factors affecting the numbers and types of the soil microorganisms. In addition, the ectomycorrhizae fungal PLFA (18:1omega9c) and AMF PLFA were significantly correlated with the soil C/N ratio.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    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.

  3. Soil microbial response to tetracycline in two different soils amended with cow manure.

    PubMed

    Chessa, Luigi; Pusino, Alba; Garau, Giovanni; Mangia, Nicoletta Pasqualina; Pinna, Maria Vittoria

    2016-03-01

    High amounts of antibiotics are introduced in the soil environment by manure amendment, which is the most important spreading route in soil, with a potential ecotoxicological impact on the environment. The objectives of this study were (a) to assess the tetracycline (Tc) bioavailability in a clay and in a sandy soil, and (b) to evaluate the effects of the Tc and cow manure on the structure and function of soil microbial communities. Clay and sandy soils were spiked with Tc at the concentrations of 100 and 500 mg Tc kg(-1) soil, and were amended or not with cow manure. The clay soil showed greater Tc sorption capacity and bioavailable Tc was between 0.157 and 4.602 mg kg(-1) soil. Tc dose and time-dependent effects on soil microbial communities were investigated by fluorescein diacetate activity, phospholipid fatty acids analysis, as well as by Biolog community level physiological profile and microbial counts at 2, 7 and 60 days after Tc and/or manure addition. The added Tc caused detrimental effect on the microbial activity and structure, particularly in the short term at the highest concentrations. However, the Tc effect was transient' it decreased after 7 days and totally disappeared within 60 days. Cow manure shifted the bacterial structure in both soils, increased the microbial activity in clay soil and contributed to recover the microbial structure in Tc-spiked manure treatments.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  7. Sheep-urine-induced changes in soil microbial community structure.

    PubMed

    Nunan, Naoise; Singh, Brajesh; Reid, Eileen; Ord, Brian; Papert, Artemis; Squires, Julie; Prosser, Jim I; Wheatley, Ron E; McNicol, Jim; Millard, Peter

    2006-05-01

    Soil microbial communities play an important role in nutrient cycling and nutrient availability, especially in unimproved soils. In grazed pastures, sheep urine causes local changes in nutrient concentration which may be a source of heterogeneity in microbial community structure. In the present study, we investigated the effects of synthetic urine on soil microbial community structure, using physiological (community level physiological profiling, CLPP), biochemical (phospholipid fatty acid analysis, PLFA) and molecular (denaturing gradient gel electrophoresis, DGGE) fingerprinting methods. PLFA data suggested that synthetic urine treatment had no significant effect on total microbial (total PLFA), total bacterial or fungal biomass; however, significant changes in microbial community structure were observed with both PLFA and DGGE data. PLFA data suggested that synthetic urine induced a shift towards communities with higher concentrations of branched fatty acids. DGGE banding patterns derived from control and treated soils differed, due to a higher proportion of DNA sequences migrating only to the upper regions of the gel in synthetic urine-treated samples. The shifts in community structure measured by PLFA and DGGE were significantly correlated with one another, suggesting that both datasets reflected the same changes in microbial communities. Synthetic urine treatment preferentially stimulated the use of rhizosphere-C in sole-carbon-source utilisation profiles. The changes caused by synthetic urine addition accounted for only 10-15% of the total variability in community structure, suggesting that overall microbial community structure was reasonably stable and that changes were confined to a small proportion of the communities.

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

  9. Soil invertebrate fauna affect N2 O emissions from soil.

    PubMed

    Kuiper, Imke; de Deyn, Gerlinde B; Thakur, Madhav P; van Groenigen, Jan Willem

    2013-09-01

    Nitrous oxide (N2 O) emissions from soils contribute significantly to global warming. Mitigation of N2 O emissions is severely hampered by a lack of understanding of its main controls. Fluxes can only partly be predicted from soil abiotic factors and microbial analyses - a possible role for soil fauna has until now largely been overlooked. We studied the effect of six groups of soil invertebrate fauna and tested the hypothesis that all of them increase N2 O emissions, although to different extents. We conducted three microcosm experiments with sandy soil and hay residue. Faunal groups included in our experiments were as follows: fungal-feeding nematodes, mites, springtails, potworms, earthworms and isopods. In experiment I, involving all six faunal groups, N2 O emissions declined with earthworms and potworms from 78.4 (control) to 37.0 (earthworms) or 53.5 (potworms) mg N2 O-N m(-2) . In experiment II, with a higher soil-to-hay ratio and mites, springtails and potworms as faunal treatments, N2 O emissions increased with potworms from 51.9 (control) to 123.5 mg N2 O-N m(-2) . Experiment III studied the effect of potworm density; we found that higher densities of potworms accelerated the peak of the N2 O emissions by 5 days (P < 0.001), but the cumulative N2 O emissions remained unaffected. We propose that increased soil aeration by the soil fauna reduced N2 O emissions in experiment I, whereas in experiment II N2 O emissions were driven by increased nitrogen and carbon availability. In experiment III, higher densities of potworms accelerated nitrogen and carbon availability and N2 O emissions, but did not increase them. Overall, our data show that soil fauna can suppress, increase, delay or accelerate N2 O emissions from soil and should therefore be an integral part of future N2 O studies.

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

    PubMed

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

    2016-04-05

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

  11. Rhizosphere effect of Scirpus triqueter on soil microbial structure during phytoremediation of diesel-contaminated wetland.

    PubMed

    Wei, Jing; Liu, Xiaoyan; Zhang, Xinying; Chen, Xueping; Liu, Shanshan; Chen, Lisha

    2014-01-01

    Though phytoremediation has been widely used to restore various contaminated sites, it is still unclear how soil microbial communities respond microecologically to plants and pollutants during the process. In this paper, batch microcosms imitating in situ phytoremediation of petroleum-contaminated wetland by Scirpus triqueter were set up to monitor the influence of plant rhizosphere effect on soil microbes. Palmitic acid, one of the main root exudates of S. triqueter, was added to strengthen rhizosphere effect. Abundances of certain microbial subgroups were quantified by phospholipid fatty acid profiles. Results showed that diesel removal extents were significantly higher in the rhizosphere (57.6 +/-4.2-65.5 +/- 6.9%) than those in bulk soil (27.8 +/-6.5-36.3 +/- 3.2%). In addition, abundances of saturated, monounsaturated, and polyunsaturated fatty acids were significantly higher (P < 0.05) in planted soil than those in the bulk soil. When it was less than 15,000 mg diesel kg soil-1, increasing diesel concentration led to higher abundances of fungi, Gram-positive and Gram-negative bacteria. The addition of palmitic acid amplified the rhizosphere effect on soil microbial populations and diesel removal. Principal component analysis revealed that plant rhizosphere effect was the dominant factor affecting microbial structure. These results provided new insights into plant-microbe-pollutant coactions responsible for diesel degradation, and they were valuable to facilitate phytoremediation of diesel contamination in wetland habitats.

  12. Microbially-mediated fate of {sup 14}C-pyrene in soil organic matter

    SciTech Connect

    Guthroe, E.A.; Pfaender, F.K.

    1995-12-31

    Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental contaminants that result from both natural and anthropogenic combustion processes. Several microbial processes are known to influence the fate of PAH in soil. Their effect on PAH structure and mobility can affect the potential health risk exposure to humans and indigenous organisms in soil. Microbial metabolism of PAHs can result in the accumulation of more polar by-products or the formation of by-products that may be further metabolized or mineralized by other microorganisms. A third possible fate is the incorporation of PAHs into soil organic matter via various sorption/binding processes. Experiments were conducted to determine the extent of {sup 14}C-pyrene associations with soil organic matter (SOM) in adapted and non-adapted soils. Changes in microbial respiration (CO{sub 2} efflux), {sup 14}C volatile organics, {sup 14}C water soluble metabolites and {sup 14}C SOM were measured in aerated soil systems treated individually with 100 mg/kg [4,5,9,10-{sup 14}C] pyrene over time. Mass balances were generated based on V products in water extracts, CO{sub 2} efflux. SOM, {sup 14}C-volatiles, and residual soil. The {sup 14}C products in SOM were further fractionated into humic acids (HA), fulvic acids (FA), and humin. The presence of an adapted, microbial community enhances {sup 14}C-pyrene mineralization and increases the {sup 14}C product accumulation in water extracts and fulvic acids (FA).

  13. Measurements of microbial community activities in individual soil macroaggregates

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  15. Development of soil microbial communities during tallgrass prairie restoration

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  16. Distribution of chromium contamination and microbial activity in soil aggregates.

    PubMed

    Tokunaga, Tetsu K; Wan, Jiamin; Hazen, Terry C; Schwartz, Egbert; Firestone, Mary K; Sutton, Stephen R; Newville, Matthew; Olson, Keith R; Lanzirotti, Antonio; Rao, William

    2003-01-01

    Biogeochemical transformations of redox-sensitive chemicals in soils can be strongly transport-controlled and localized. This was tested through experiments on chromium diffusion and reduction in soil aggregates that were exposed to chromate solutions. Reduction of soluble Cr(VI) to insoluble Cr(II) occurred only within the surface layer of aggregates with higher available organic carbon and higher microbial respiration. Sharply terminated Cr diffusion fronts develop when the reduction rate increases rapidly with depth. The final state of such aggregates consists of a Cr-contaminated exterior, and an uncontaminated core, each having different microbial community compositions and activity. Microbial activity was significantly higher in the more reducing soils, while total microbial biomass was similar in all of the soils. The small fraction of Cr(VI) remaining unreduced resides along external surfaces of aggregates, leaving it potentially available to future transport down the soil profile. Using the Thiele modulus, Cr(VI) reduction in soil aggregates is shown to be diffusion rate- and reaction rate-limited in anaerobic and aerobic aggregates, respectively. Thus, spatially resolved chemical and microbiological measurements are necessary within anaerobic soil aggregates to characterize and predict the fate of Cr contamination. Typical methods of soil sampling and analyses that average over redox gradients within aggregates can erase important biogeochemical spatial relations necessary for understanding these environments.

  17. Integrating microbial diversity in soil carbon dynamic models parameters

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  18. Effects of inorganic and organic amendment on soil chemical properties, enzyme activities, microbial community and soil quality in yellow clayey soil.

    PubMed

    Liu, Zhanjun; Rong, Qinlei; Zhou, Wei; Liang, Guoqing

    2017-01-01

    Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive rice growing seasons to investigate the effect of applying chemical fertilizer (NPK), NPK plus green manure (NPKG), NPK plus pig manure (NPKM), and NPK plus straw (NPKS) on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC), activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI) and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72) was comparable to that of the NPK (0.77), NPKG (0.81) and NPKS (0.79) treatments but significantly lower compared with NPKM (0.85). The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil.

  19. Effects of inorganic and organic amendment on soil chemical properties, enzyme activities, microbial community and soil quality in yellow clayey soil

    PubMed Central

    Liu, Zhanjun; Rong, Qinlei; Zhou, Wei; Liang, Guoqing

    2017-01-01

    Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive rice growing seasons to investigate the effect of applying chemical fertilizer (NPK), NPK plus green manure (NPKG), NPK plus pig manure (NPKM), and NPK plus straw (NPKS) on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC), activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI) and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72) was comparable to that of the NPK (0.77), NPKG (0.81) and NPKS (0.79) treatments but significantly lower compared with NPKM (0.85). The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil. PMID:28263999

  20. The influence of soil heavy metals pollution on soil microbial biomass, enzyme activity, and community composition near a copper smelter.

    PubMed

    Wang, YuanPeng; Shi, JiYan; Wang, Hui; Lin, Qi; Chen, XinCai; Chen, YingXu

    2007-05-01

    The environmental risk of heavy metal pollution is pronounced in soils adjacent to large industrial complexes. It is important to investigate the functioning of soil microorganisms in ecosystems exposed to long-term contamination by heavy metals. We studied the potential effects of heavy metals on microbial biomass, activity, and community composition in soil near a copper smelter in China. The results showed that microbial biomass C was negatively affected by the elevated metal levels and was closely correlated with heavy metal stress. Enzyme activity was greatly depressed by conditions in the heavy metal-contaminated sites. Good correlation was observed between enzyme activity and the distance from the smelter. Elevated metal loadings resulted in changes in the activity of the soil microbe, as indicated by changes in their metabolic profiles from correlation analysis. Significant decrease of soil phosphatase activities was found in the soils 200 m away from the smelter. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis demonstrated that heavy metals pollution had a significant impact on bacterial and actinomycetic community structure. There were negative correlations between soil microbial biomass, phosphatase activity, and NH(4)NO(3) extractable heavy metals. The soil microorganism activity and community composition could be predicted significantly using the availability of Cu and Zn. By combining different monitoring approaches from different viewpoints, the set of methods applied in this study were sensitive to site differences and contributed to a better understanding of heavy metals effects on the structure, size and activity of microbial communities in soils. The data presented demonstrate the role of heavy metals pollution in understanding the heavy metal toxicity to soil microorganism near a copper smelter in China.

  1. Temperature sensitivity of microbial respiration, nitrogen mineralization, and potential soil enzyme activities in organic alpine soils

    NASA Astrophysics Data System (ADS)

    Koch, Oliver; Tscherko, Dagmar; Kandeler, Ellen

    2007-12-01

    Investigations focusing on the temperature sensitivity of microbial activity and nutrient turnover in soils improve our understanding of potential effects of global warming. This study investigates the temperature sensitivity of C mineralization, N mineralization, and potential enzyme activities involved in the C and N cycle (tyrosine amino-peptidase, leucine amino-peptidase, ß-glucosidase, ß-xylosidase, N-acetyl-ß-glucosaminidase). Four different study sites in the Austrian alpine zone were selected, and soils were sampled in three seasons (summer, autumn, and winter). A simple first-order exponential equation was used to calculate constant Q10 values for the C and N mineralization over the investigated temperature range (0-30°C). The Q10 values of the C mineralization (average 2.0) for all study sites were significantly higher than for the N mineralization (average 1.7). The Q10 values of both activities were significantly negatively related to a soil organic matter quality index calculated by the ratios of respiration to the organic soil carbon and mineralized N to the total soil nitrogen. The chemical soil properties or microbial biomass did not affect the Q10 values of C and N mineralization. Moreover, the Q10 values showed no distinct pattern according to sampling date, indicating that the substrate quality and other factors are more important. Using a flexible model function, the analysis of relative temperature sensitivity (RTS) showed that the temperature sensitivity of activities increased with decreasing temperature. The C and N mineralization and potential amino-peptidase activities (tyrosine and leucine) showed an almost constant temperature dependence over 0-30°C. In contrast, ß-glucosidase, ß-xylosidase, and N-acetyl-ß-glucosaminidase showed a distinctive increase in temperature sensitivity with decreasing temperature. Low temperature at the winter sampling date caused a greater increase in the RTS of all microbial activities than for the

  2. Stability of soil microbial structure and activity depends on microbial diversity.

    PubMed

    Tardy, Vincent; Mathieu, Olivier; Lévêque, Jean; Terrat, Sébastien; Chabbi, Abad; Lemanceau, Philippe; Ranjard, Lionel; Maron, Pierre-Alain

    2014-04-01

    Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.

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

    NASA Astrophysics Data System (ADS)

    Tate, Robert, III; Mikita, Robyn

    2010-05-01

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

  4. Microbial ecology and biogeochemistry of continental Antarctic soils

    PubMed Central

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

    2014-01-01

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

  5. Impact of Metal Pollution and Thlaspi caerulescens Growth on Soil Microbial Communities▿

    PubMed Central

    Epelde, Lur; Becerril, José M.; Kowalchuk, George A.; Deng, Ye; Zhou, Jizhong; Garbisu, Carlos

    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 to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts of Zn and/or Cd pollution and Thlaspi caerulescens growth on key soil microbial properties: basal respiration; substrate-induced respiration (SIR); bacterial community structure as assessed by PCR-denaturing gradient gel electrophoresis (DGGE); community sizes of total bacteria, ammonia-oxidizing bacteria, and chitin-degrading bacteria as assessed by quantitative PCR (Q-PCR); and functional gene distributions as determined by functional gene arrays (GeoChip). T. caerulescens proved to be suitable for Zn and Cd phytoextraction: shoots accumulated up to 8,211 and 1,763 mg kg−1 (dry weight [DW]) of Zn and Cd, respectively. In general, Zn pollution led to decreased levels of basal respiration and ammonia-oxidizing bacteria, while T. caerulescens growth increased the values of substrate-induced respiration (SIR) and total bacteria. In soils polluted with 1,000 mg Zn kg−1 and 250 mg Cd kg−1 (DW), soil bacterial community profiles and the distribution of microbial functional genes were most affected by the presence of metals. Metal-polluted and planted soils had the highest percentage of unique genes detected via the GeoChip (35%). It was possible to track microbial responses to planting with T. caerulescens and to gain insight into the effects of metal pollution on soilborne microbial communities. PMID:20935131

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

    PubMed Central

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

    2008-01-01

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

  7. Soil microbial and nutrient responses to 7 years of seasonally altered precipitation in a Chihuahuan Desert grassland.

    PubMed

    Bell, Colin W; Tissue, David T; Loik, Michael E; Wallenstein, Matthew D; Acosta-Martinez, Veronica; Erickson, Richard A; Zak, John C

    2014-05-01

    Soil microbial communities in Chihuahuan Desert grasslands generally experience highly variable spatiotemporal rainfall patterns. Changes in precipitation regimes can affect belowground ecosystem processes such as decomposition and nutrient cycling by altering soil microbial community structure and function. The objective of this study was to determine if increased seasonal precipitation frequency and magnitude over a 7-year period would generate a persistent shift in microbial community characteristics and soil nutrient availability. We supplemented natural rainfall with large events (one/winter and three/summer) to simulate increased precipitation based on climate model predictions for this region. We observed a 2-year delay in microbial responses to supplemental precipitation treatments. In years 3-5, higher microbial biomass, arbuscular mycorrhizae abundance, and soil enzyme C and P acquisition activities were observed in the supplemental water plots even during extended drought periods. In years 5-7, available soil P was consistently lower in the watered plots compared to control plots. Shifts in soil P corresponded to higher fungal abundances, microbial C utilization activity, and soil pH. This study demonstrated that 25% shifts in seasonal rainfall can significantly influence soil microbial and nutrient properties, which in turn may have long-term effects on nutrient cycling and plant P uptake in this desert grassland.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  9. Soil microbial activities in Mediterranean environment as desertification indicators along a pluviometric gradient.

    NASA Astrophysics Data System (ADS)

    Novosadova, I.; Zahora, J.; Ruiz Sinoga, J. D.

    2009-04-01

    In the Mediterranean areas of Southern Spain, unsuitable agricultural practices with adverse environmental conditions (López Bermúdez and Albaladejo, 1990), have led to a permanent degradation and loss of soil fertility. This includes deterioration of the natural plant cover, which protects against erosion by contributing organic matter, the main prerequisite of ecosystem sustainability (Grace et al., 1994). Physico-chemical, microbiological and biochemical soil properties are very responsive and provide immediate and precise information on small changes occurring in soil (Dick and Tabatabai, 1993). There is increasing evidence that such parameters are also sensitive indicators of ecology stress suffered by a soil and its recovery, since microbial activity has a direct influence on the stability and fertility of ecosystems (Smith and Papendick, 1993). One method for recovering degraded soils of such semiarid regions, with their low organic matter content, is to enhance primary productivity and carbon sequestration without any additional nitrogen fertilization and preferably without incorporation of leguminous plants (Martinez Mena et al., 2008). Carbon rich materials can sustain microbial activity and growth, thus enhancing biogeochemical nutrient cycles (Pascual et al., 1997). The present study is focused in the role of physico-chemical and microbial soil properties in Mediterranean environment, in terms of in situ and ex situ microbial transformation of soil carbon and nitrogen, in order to characterise the key soil microbial activities which could strongly affect carbon and nitrogen turnover in soil and hereby soil fertility and soil organic matter "quality". These microbial activities could at unsuitable agricultural practices with adverse environmental conditions induce unfavourable hydrologycal tempo-spatial response. The final results shown modifications in the soil properties studied with the increasing of the aridity. Such changes suppose the soil

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

    PubMed

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

    2016-02-01

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

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

    DOE PAGES

    Deng, Ye; He, Zhili; Xiong, Jinbo; ...

    2015-10-23

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

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

    SciTech Connect

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

    2015-10-23

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

  13. Plant lignin content altered by soil microbial community.

    PubMed

    Bennett, Alison E; Grussu, Dominic; Kam, Jason; Caul, Sandra; Halpin, Claire

    2015-04-01

    Questions have been raised in various fields of research about the consequences of plants with modified lignin production. As a result of their roles in nutrient cycling and plant diversity, plant-soil interactions should be a major focus of ecological studies on lignin-modified plants. However, most studies have been decomposition studies conducted in a single soil or in sterile soil. Thus, we understand little about plant-soil interactions in living lignin-modified plants. In lignin mutants of three different barley (Hordeum vulgare) cultivars and their corresponding wild-types associated with three different soil microbial communities, we asked: do plant-soil microbiome interactions influence the lignin content of plants?; does a mutation in lignin production alter the outcome of plant-soil microbiome interactions?; does the outcome of plant-soil microbiome interactions depend on host genotype or the presence of a mutation altering lignin production? In roots, the soil community explained 6% of the variation in lignin content, but, in shoots, the soil community explained 21% of the variation in lignin content and was the only factor influencing lignin content. Neither genotype nor mutations in lignin production explained associations with fungi. Lignin content changes in response to a plant's soil microbial community, and may be a defensive response to particular components of the soil community.

  14. Microbial Decomposition of Extracellular DNA in Clay Soils

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

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

    NASA Astrophysics Data System (ADS)

    Mykhailova, Larysa; Fischer, Thomas; Iurchenko, Valentina

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Bamminger, Chris; Poll, Christian; Marhan, Sven

    2014-05-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

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

    2015-12-01

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

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

    SciTech Connect

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

    2014-09-17

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed Central

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

    2016-01-01

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

  9. Microbial response to repeated treatments of manure containing sulfadiazine and chlortetracycline in soil.

    PubMed

    Fang, Hua; Han, Yu L; Yin, Yuan M; Jin, Xiang X; Wang, Shao Y; Tang, Fei F; Cai, Lin; Yu, Yun L

    2014-01-01

    Substantive addition of antibiotic-contaminated manure to agricultural soil may lead to "persistent" residues of antibiotics and may affect soil health. Therefore, this study examines the effects of repeated manure treatments containing sulfadiazine (SDZ) and chlortetracycline (CTC) residues, both individually and combined, on the functional diversity and structure of soil microbial communities in the soils under laboratory conditions. The average well color development (AWCD), Simpson diversity index (1/D, dominant populations), Shannon-Wiener diversity index (H', richness), and McIntosh diversity index (U, evenness) in the antibiotics-treated soils decreased in the first 60-day treatment and then gradually recovered or even exceeded the initial level in the unamended soils with increasing treatment frequency. A total of 11 specific bands in temperature gradient gel electrophoresis (TGGE) profiles were observed and sequence analyzed for five repeated treatments, and most of them belonged to the phyla Firmicutes, Actinobacteria, and Proteobacteria. These results indicate that repeated treatments of manure containing SDZ and CTC residues can alter soil microbial community structure, although they have a temporary suppression effect on soil microbial functional diversity.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  11. Potential impact of soil microbial heterogeneity on the persistence of hydrocarbons in contaminated subsurface soils.

    PubMed

    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.

  12. Soil microbial community response to hexavalent chromium in planted and unplanted soil.

    PubMed

    Ipsilantis, Ioannis; Coyne, Mark S

    2007-01-01

    Theories suggest that rapid microbial growth rates lead to quicker development of metal resistance. We tested these theories by adding hexavalent chromium [Cr(VI)] to soil, sowing Indian mustard (Brassica juncea), and comparing rhizosphere and bulk soil microbial community responses. Four weeks after the initial Cr(VI) application we measured Cr concentration, microbial biomass by fumigation extraction and soil extract ATP, tolerance to Cr and growth rates with tritiated thymidine incorporation, and performed community substrate use analysis with BIOLOG GN plates. Exchangeable Cr(VI) levels were very low, and therefore we assumed the Cr(VI) impact was transient. Microbial biomass was reduced by Cr(VI) addition. Microbial tolerance to Cr(VI) tended to be higher in the Cr-treated rhizosphere soil relative to the non-treated systems, while microorganisms in the Cr-treated bulk soil were less sensitive to Cr(VI) than microorganisms in the non-treated bulk soil. Microbial diversity as measured by population evenness increased with Cr(VI) addition based on a Gini coefficient derived from BIOLOG substrate use patterns. Principal component analysis revealed separation between Cr(VI) treatments, and between rhizosphere and bulk soil treatments. We hypothesize that because of Cr(VI) addition there was indirect selection for fast-growing organisms, alleviation of competition among microbial communities, and increase in Cr tolerance in the rhizosphere due to the faster turnover rates in that environment.

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Rath, Kristin; Rousk, Johannes

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-05-12

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

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

  19. Microbial community succession in an unvegetated, recently deglaciated soil.

    PubMed

    Nemergut, Diana R; Anderson, Suzanne P; Cleveland, Cory C; Martin, Andrew P; Miller, Amy E; Seimon, Anton; Schmidt, Steven K

    2007-01-01

    Primary succession is a fundamental process in macroecosystems; however, if and how soil development influences microbial community structure is poorly understood. Thus, we investigated changes in the bacterial community along a chronosequence of three unvegetated, early successional soils ( approximately 20-year age gradient) from a receding glacier in southeastern Peru using molecular phylogenetic techniques. We found that evenness, phylogenetic diversity, and the number of phylotypes were lowest in the youngest soils, increased in the intermediate aged soils, and plateaued in the oldest soils. This increase in diversity was commensurate with an increase in the number of sequences related to common soil bacteria in the older soils, including members of the divisions Acidobacteria, Bacteroidetes, and Verrucomicrobia. Sequences related to the Comamonadaceae clade of the Betaproteobacteria were dominant in the youngest soil, decreased in abundance in the intermediate age soil, and were not detected in the oldest soil. These sequences are closely related to culturable heterotrophs from rock and ice environments, suggesting that they originated from organisms living within or below the glacier. Sequences related to a variety of nitrogen (N)-fixing clades within the Cyanobacteria were abundant along the chronosequence, comprising 6-40% of phylotypes along the age gradient. Although there was no obvious change in the overall abundance of cyanobacterial sequences along the chronosequence, there was a dramatic shift in the abundance of specific cyanobacterial phylotypes, with the intermediate aged soils containing the greatest diversity of these sequences. Most soil biogeochemical characteristics showed little change along this approximately 20-year soil age gradient; however, soil N pools significantly increased with soil age, perhaps as a result of the activity of the N-fixing Cyanobacteria. Our results suggest that, like macrobial communities, soil microbial

  20. Microbial carbon turnover in the plant-rhizosphere-soil continuum

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    PubMed

    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.

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

    PubMed

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

    2015-06-02

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

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

    PubMed

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

    2008-08-15

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

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

    SciTech Connect

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

    2009-11-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed Central

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

    2016-01-01

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

  7. Soil microbial responses to elevated CO₂ and O₃ in a nitrogen-aggrading agroecosystem.

    PubMed

    Cheng, Lei; Booker, Fitzgerald L; Burkey, Kent O; Tu, Cong; Shew, H David; Rufty, Thomas W; Fiscus, Edwin L; Deforest, Jared L; Hu, Shuijin

    2011-01-01

    Climate change factors such as elevated atmospheric carbon dioxide (CO₂) and ozone (O₃) can exert significant impacts on soil microbes and the ecosystem level processes they mediate. However, the underlying mechanisms by which soil microbes respond to these environmental changes remain poorly understood. The prevailing hypothesis, which states that CO₂- or O₃-induced changes in carbon (C) availability dominate microbial responses, is primarily based on results from nitrogen (N)-limiting forests and grasslands. It remains largely unexplored how soil microbes respond to elevated CO₂ and O₃ in N-rich or N-aggrading systems, which severely hinders our ability to predict the long-term soil C dynamics in agroecosystems. Using a long-term field study conducted in a no-till wheat-soybean rotation system with open-top chambers, we showed that elevated CO₂ but not O₃ had a potent influence on soil microbes. Elevated CO₂(1.5×ambient) significantly increased, while O₃ (1.4×ambient) reduced, aboveground (and presumably belowground) plant residue C and N inputs to soil. However, only elevated CO₂ significantly affected soil microbial biomass, activities (namely heterotrophic respiration) and community composition. The enhancement of microbial biomass and activities by elevated CO₂ largely occurred in the third and fourth years of the experiment and coincided with increased soil N availability, likely due to CO₂-stimulation of symbiotic N₂ fixation in soybean. Fungal biomass and the fungi∶bacteria ratio decreased under both ambient and elevated CO₂ by the third year and also coincided with increased soil N availability; but they were significantly higher under elevated than ambient CO₂. These results suggest that more attention should be directed towards assessing the impact of N availability on microbial activities and decomposition in projections of soil organic C balance in N-rich systems under future CO₂ scenarios.

  8. Effects of Picoxystrobin and 4-n-Nonylphenol on Soil Microbial Community Structure and Respiration Activity

    PubMed Central

    Stenrød, Marianne; Klemsdal, Sonja S.; Norli, Hans Ragnar; Eklo, Ole Martin

    2013-01-01

    There is widespread use of chemical amendments to meet the demands for increased productivity in agriculture. Potentially toxic compounds, single or in mixtures, are added to the soil medium on a regular basis, while the ecotoxicological risk assessment procedures mainly follow a chemical by chemical approach. Picoxystrobin is a fungicide that has caused concern due to studies showing potentially detrimental effects to soil fauna (earthworms), while negative effects on soil microbial activities (nitrification, respiration) are shown to be transient. Potential mixture situations with nonylphenol, a chemical frequently occurring as a contaminant in sewage sludge used for land application, infer a need to explore whether these chemicals in mixture could alter the potential effects of picoxystrobin on the soil microflora. The main objective of this study was to assess the effects of picoxystrobin and nonylphenol, as single chemicals and mixtures, on soil microbial community structure and respiration activity in an agricultural sandy loam. Effects of the chemicals were assessed through measurements of soil microbial respiration activity and soil bacterial and fungal community structure fingerprints, together with a degradation study of the chemicals, through a 70 d incubation period. Picoxystrobin caused a decrease in the respiration activity, while 4-n-nonylphenol caused an increase in respiration activity concurring with a rapid degradation of the substance. Community structure fingerprints were also affected, but these results could not be directly interpreted in terms of positive or negative effects, and were indicated to be transient. Treatment with the chemicals in mixture caused less evident changes and indicated antagonistic effects between the chemicals in soil. In conclusion, the results imply that the application of the fungicide picoxystrobin and nonylphenol from sewage sludge application to agricultural soil in environmentally relevant concentrations, as

  9. Effects of picoxystrobin and 4-n-nonylphenol on soil microbial community structure and respiration activity.

    PubMed

    Stenrød, Marianne; Klemsdal, Sonja S; Norli, Hans Ragnar; Eklo, Ole Martin

    2013-01-01

    There is widespread use of chemical amendments to meet the demands for increased productivity in agriculture. Potentially toxic compounds, single or in mixtures, are added to the soil medium on a regular basis, while the ecotoxicological risk assessment procedures mainly follow a chemical by chemical approach. Picoxystrobin is a fungicide that has caused concern due to studies showing potentially detrimental effects to soil fauna (earthworms), while negative effects on soil microbial activities (nitrification, respiration) are shown to be transient. Potential mixture situations with nonylphenol, a chemical frequently occurring as a contaminant in sewage sludge used for land application, infer a need to explore whether these chemicals in mixture could alter the potential effects of picoxystrobin on the soil microflora. The main objective of this study was to assess the effects of picoxystrobin and nonylphenol, as single chemicals and mixtures, on soil microbial community structure and respiration activity in an agricultural sandy loam. Effects of the chemicals were assessed through measurements of soil microbial respiration activity and soil bacterial and fungal community structure fingerprints, together with a degradation study of the chemicals, through a 70 d incubation period. Picoxystrobin caused a decrease in the respiration activity, while 4-n-nonylphenol caused an increase in respiration activity concurring with a rapid degradation of the substance. Community structure fingerprints were also affected, but these results could not be directly interpreted in terms of positive or negative effects, and were indicated to be transient. Treatment with the chemicals in mixture caused less evident changes and indicated antagonistic effects between the chemicals in soil. In conclusion, the results imply that the application of the fungicide picoxystrobin and nonylphenol from sewage sludge application to agricultural soil in environmentally relevant concentrations, as

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    SciTech Connect

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  13. Measurements of Microbial Community Activities in Individual Soil Macroaggregates

    SciTech Connect

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

    2012-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Wilton, E.; Flanagan, L. B.

    2014-12-01

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

  15. Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial diversity of agricultural soils is well documented, but information on leafy green producing soils is limited. Our goal was to assess bacterial composition and diversity in leafy green producing soils using pyrosequencing, and to identify factors affecting bacterial community structures. C...

  16. Kraft mill residues effects on Monterey pine growth and soil microbial activity.

    PubMed

    Jordan, Miguel; Sánchez, Miguel Angel; Padilla, Leandro; Céspedes, Ricardo; Osses, Miguel; González, Bernardo

    2002-01-01

    The production of bleached Kraft pulp generates inorganic and organic residues that are usually deposited on the soil surface or land-filled. Studies conducted to address the impact of these wastes on the environment are scarce. In this work, Monterey pine (Pinus radiata D. Don), an important tree for pulping, was evaluated for germination and development under greenhouse conditions in forest soils exposed to solid residues of the cellulose industry using the Kraft process. Soils exposed to 10 to 60% ashes, 10 to 70% fly ashes, or 10 to 30% dregs allowed substantial seed germination and seedling growth. In contrast, soils exposed to low proportions of brown rejects, grits, or a mixture of all these residues were detrimental for germination, plant growth, or both. The strongest negative effect (no germination) was observed with as low as 10% grits. The changes in pH and/or water content caused by solid wastes did not correlate with detrimental effects observed in various soil-residue combinations. No significant changes in the microbial community of soils exposed to these solid residues were observed by determination of culturable counts, or by terminal-restriction fragment length polymorphism analysis of the microbial community DNA. The presence of organic residues did not affect the ability of the soil microbial community to remove typical pulp bleaching chloroaromatics. However, inorganic wastes strongly decreased the removal of such compounds.

  17. Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

    PubMed Central

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

    2012-01-01

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

  18. [Effects of colistin sulfate residue on soil microbial community structure].

    PubMed

    Ma, Yi; Peng, Jin-Ju; Chen, Jin-Jun; Fan, Ting-Li; Sun, Yong-Xue

    2014-06-01

    By using fumigation extraction and phospholipid fatty acid (PLFA) methods, the change of characteristics of soil microbial community structure caused by residue of colistin sulfate (CS) was studied. The results showed that the CS (w(cs) > or = 5 mg x kg(-1)) had a significant effect on the microbial biomass carbon (MBC) and it was dose-dependent where MBC decreased with the increase of CS concentration in soil. The MBC in soil decreased by 52. 1% when the CS concentration reached 50 mg x kg(-1). The total PLFA of soil in each CS treatment was significantly decreased during the sampling period compared with the control group and showed a dose-dependent relationship. The soil microbial community structure and diversity in the low CS group (w(cs) = 0.5 mg x kg(-1)) were not significantly different from the control group on 7th and 49th day. However, they were significantly different on 21st and 35th day especially in the high CS group (w(cs) = 50 mg x kg(-1)). It was concluded that CS could change the structure of soil microorganisms and varied with time which might be caused by the chemical conversion and degradation of CS in soil.

  19. Explicitly representing soil microbial processes in Earth system models: Soil microbes in earth system models

    SciTech Connect

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

    2015-10-01

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

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

    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.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

    Terence L. Marsh

    2004-05-26

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

  6. Enhanced biodegradation of hydrocarbons in soil by microbial biosurfactant, sophorolipid.

    PubMed

    Kang, Seok-Whan; Kim, Young-Bum; Shin, Jae-Dong; Kim, Eun-Ki

    2010-03-01

    Effectiveness of a microbial biosurfactant, sophorolipid, was evaluated in washing and biodegradation of model hydrocarbons and crude oil in soil. Thirty percent of 2-methylnaphthalene was effectively washed and solubilized with 10 g/L of sophorolipid with similar or higher efficiency than that of commercial surfactants. Addition of sophorolipid in soil increased biodegradation of model compounds: 2-methylnaphthalene (95% degradation in 2 days), hexadecane (97%, 6 days), and pristane (85%, 6 days). Also, effective biodegradation method of crude oil in soil was observed by the addition of sophorolipid, resulting in 80% biodegradation of saturates and 72% aromatics in 8 weeks. These results showed the potentials of the microbial biosurfactant, sophorolipid, as an effective surfactant for soil washing and as an in situ biodegradation enhancer.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2007-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  12. Microbial inoculants and their impact on soil microbial communities: a review.

    PubMed

    Trabelsi, Darine; Mhamdi, Ridha

    2013-01-01

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

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

    PubMed Central

    2013-01-01

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

  14. The exotic legume tree species Acacia holosericea alters microbial soil functionalities and the structure of the arbuscular mycorrhizal community.

    PubMed

    Remigi, P; Faye, A; Kane, A; Deruaz, M; Thioulouse, J; Cissoko, M; Prin, Y; Galiana, A; Dreyfus, B; Duponnois, R

    2008-03-01

    The response of microbial functional diversity as well as its resistance to stress or disturbances caused by the introduction of an exotic tree species, Acacia holosericea, ectomycorrhized or not with Pisolithus albus, was examined. The results show that this ectomycorrhizal fungus promotes drastically the growth of this fast-growing tree species in field conditions after 7 years of plantation. Compared to the crop soil surrounding the A. holosericea plantation, this exotic tree species, associated or not with the ectomycorrhizal symbiont, induced strong modifications in soil microbial functionalities (assessed by measuring the patterns of in situ catabolic potential of microbial communities) and reduced soil resistance in response to increasing stress or disturbance (salinity, temperature, and freeze-thaw and wet-dry cycles). In addition, A. holosericea strongly modified the structure of arbuscular mycorrhizal fungus communities. These results show clearly that exotic plants may be responsible for important changes in soil microbiota affecting the structure and functions of microbial communities.

  15. Comparative Toxicities of Salts on Microbial Processes in Soil

    PubMed Central

    Maheshwari, Arpita; Bengtson, Per; Rousk, Johannes

    2016-01-01

    Soil salinization is a growing threat to global agriculture and carbon sequestration, but to date it remains unclear how microbial processes will respond. We studied the acute response to salt exposure of a range of anabolic and catabolic microbial processes, including bacterial (leucine incorporation) and fungal (acetate incorporation into ergosterol) growth rates, respiration, and gross N mineralization and nitrification rates. To distinguish effects of specific ions from those of overall ionic strength, we compared the addition of four salts frequently associated with soil salinization (NaCl, KCl, Na2SO4, and K2SO4) to a nonsaline soil. To compare the tolerance of different microbial processes to salt and to interrelate the toxicity of different salts, concentration-response relationships were established. Growth-based measurements revealed that fungi were more resistant to salt exposure than bacteria. Effects by salt on C and N mineralization were indistinguishable, and in contrast to previous studies, nitrification was not found to be more sensitive to salt exposure than other microbial processes. The ion-specific toxicity of certain salts could be observed only for respiration, which was less inhibited by salts containing SO42− than Cl− salts, in contrast to the microbial growth assessments. This suggested that the inhibition of microbial growth was explained solely by total ionic strength, while ion-specific toxicity also should be considered for effects on microbial decomposition. This difference resulted in an apparent reduction of microbial growth efficiency in response to exposure to SO42− salts but not to Cl− salts; no evidence was found to distinguish K+ and Na+ salts. PMID:26801570

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  17. USE OF FATTY ACID STABLE CARBON ISOTOPE RATIO TO INDICATE MICROBIAL CARBON SOURCE IN TROPICAL SOILS

    EPA Science Inventory


    We use measurements of the concentration and stable carbon isotope ratio of individual microbial phospholipid fatty acids (PLFAs) in soils as indicators of live microbial biomass levels, broad microbial community structure, and microbial carbon source. For studies of soil o...

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

    PubMed

    Yan, Xun; Luo, Xuegang; Zhao, Min

    2016-01-01

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

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

    PubMed

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

    2016-04-01

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

  20. Responses of soil microbial communities to experimental warming in alpine grasslands on the qinghai-tibet plateau.

    PubMed

    Zhang, Bin; Chen, Shengyun; He, Xingyuan; Liu, Wenjie; Zhao, Qian; Zhao, Lin; Tian, Chunjie

    2014-01-01

    Global surface temperature is predicted to increase by at least 1.5°C by the end of this century. However, the response of soil microbial communities to global warming is still poorly understood, especially in high-elevation grasslands. We therefore conducted an experiment on three types of alpine grasslands on the Qinghai-Tibet Plateau to study the effect of experimental warming on abundance and composition of soil microbial communities at 0-10 and 10-20 cm depths. Plots were passively warmed for 3 years using open-top chambers and compared to adjacent control plots at ambient temperature. Soil microbial communities were assessed using phospholipid fatty acid (PLFA) analysis. We found that 3 years of experimental warming consistently and significantly increased microbial biomass at the 0-10 cm soil depth of alpine swamp meadow (ASM) and alpine steppe (AS) grasslands, and at both the 0-10 and 10-20 cm soil depths of alpine meadow (AM) grasslands, due primarily to the changes in soil temperature, moisture, and plant coverage. Soil microbial community composition was also significantly affected by warming at the 0-10 cm soil depth of ASM and AM and at the 10-20 cm soil depth of AM. Warming significantly decreased the ratio of fungi to bacteria and thus induced a community shift towards bacteria at the 0-10 cm soil depth of ASM and AM. While the ratio of arbuscular mycorrhizal fungi to saprotrophic fungi (AMF/SF) was significantly decreased by warming at the 0-10 cm soil depth of ASM, it was increased at the 0-10 cm soil depth of AM. These results indicate that warming had a strong influence on soil microbial communities in the studied high-elevation grasslands and that the effect was dependent on grassland type.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  2. [Microbial metabolism in typical flooded paddy soils ].

    PubMed

    Cai, Yuanfeng; Wu, Yucheng; Wang, Shuwei; Yan, Xiaoyuan; Zhu, Yongguan; Jia, Zhongjun

    2014-09-04

    [OBJECTIVE] The object of this study is to reveal the composition of active microorganism and their metabolic activities in flooded paddy soils with long-term fertilization ( Mineral nitrogen, phosphorus, and potassium, NPK) and without fertilizer (Control check, CK) by environmental transcriptomics. [METHODS] Flooded soil microcosms were incubated in the laboratory for two weeks, then total RNA were extracted from the soil for transcriptome sequencing. Resulting fastq files were uploaded to the Metagenomics Analysis Server (MG-RAST) for taxonomic analysis, gene annotation and function classification. [RESULTS] Transcripts from diverse active microorganism, including bacteria ( > 95% ) , archaea, eukaryotes and viruses, were detected in both flooded paddy soils of CK and NPK treatments. Most of the transcripts (active genes) of bacteria and archaea were derived from Proteobacteria (more than 50% of total bacterial transcripts) and Thaumarchaaeota (about 70% of total archaeal transcripts ) respectively in both treatments. Transcriptional activity of Acidobacteria in NPK treatment paddy soil was significantly higher than that in CK treatment paddy soil. As for other phyla of bacteria and archaea, there were no significant differences of transcriptional activity of them between CK and NPK treatment paddy soils. The highest expressed gene in both CK and NPK treatment paddy soils is ABC transporter encoding gene which related to the transmembrane transport of substances. Based on gene function category of COG (Clusters of Orthologous Genes), Subsystem and KEGG (Kyoto Encyclopedia of Genes and Genomes) database, we found that the main metabolic activities of microorganisms in both CK and NPK treatment paddy soils were related to energy production and conversion, carbohydrate metabolism, protein metabolism and amino acid metabolism, and the dominant KEGG pathways were oxidative phosphorylation and aminoacyl-tRNA biosynthesis. [ CONCLUSION] Composition of active

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

    NASA Astrophysics Data System (ADS)

    Daly, Amanda; Grandy, A. Stuart

    2016-04-01

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

  4. Microbial community structure and activity in arsenic-, chromium- and copper-contaminated soils.

    PubMed

    Turpeinen, Riina; Kairesalo, Timo; Häggblom, Max M

    2004-01-01

    Microbial community structure, potential microbial activity and As resistance were affected by arsenic (As), chromium (Cr) and copper (Cu) contamination in soils of abandoned wood impregnating plants. Contaminated soils differed in the concentrations of soil acid-soluble and total water-soluble As, Cr and Cu, and in the concentration of bioavailable As analyzed with a bacterial sensor. Phospholipid fatty acid (PLFA) and 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) profiles indicated that exposure to high metal contamination or subsequent effects of this exposure permanently changed microbial community structure. The total number of colony forming units (CFU) was not affected by metal contamination and the As(V)-resistant bacterial ratio to total heterotrophic plate counts was high (0.5-1.1) and relatively independent of the concentration of As. In contrast, the proportion of As(III)-resistant bacteria was dependent on the concentration of As in the soils and a significant positive relationship was found between the bioavailability of As and the proportion of As(III)-resistant bacteria. Dominant As-resistant isolates from contaminated soils were identified by their fatty acid methyl ester (FAME) profiles as Acinetobacter, Edwardsiella, Enterobacter, Pseudomonas, Salmonella and Serratia species. No differences were noted in glucose mineralization among contaminated and control soil samples within sites. Based on [(14)C]glucose mineralization the community was able to compensate for the reduced diversity. According to t-RFLP results, this was not due to a reversion towards the unexposed community, but mainly due to the appearance of new dominating species. This study, combining complementary culture-dependent and -independent methods, suggests that microbes are able to respond to soil metal contamination and maintain metabolic activity apparently through changes in microbial community structure and selection for resistance.

  5. Non-microbial methane formation in oxic soils

    NASA Astrophysics Data System (ADS)

    Jugold, A.; Althoff, F.; Hurkuck, M.; Greule, M.; Lenhart, K.; Lelieveld, J.; Keppler, F.

    2012-12-01

    Methane plays an important role as a radiatively and chemically active gas in our atmosphere. Until recently, sources of atmospheric methane in the biosphere have been attributed to strictly anaerobic microbial processes during degradation of organic matter. However, a large fraction of methane produced in the anoxic soil layers does not reach the atmosphere due to methanotrophic consumption in the overlaying oxic soil. Although methane fluxes from aerobic soils have been observed, an alternative source other than methanogenesis has not been identified thus far. Here we provide evidence for non-microbial methane formation in soils under oxic conditions. We found that soils release methane upon heating and other environmental factors like ultraviolet irradiation, and drying-rewetting cycles. We suggest that chemical formation of methane during degradation of soil organic matter may represent the missing soil source that is needed to fully understand the methane cycle in aerobic soils. Although the emission fluxes are relatively low when compared to those from wetlands, they may be important in warm and wet regions subjected to ultraviolet radiation. We suggest that this methane source is highly sensitive to global change.

  6. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

    Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2015-01-01

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

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

    PubMed

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

    2015-12-01

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

  11. Measures of Microbial Biomass for Soil Carbon Decomposition Models

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  12. Soil Mineralogy and Substrate Quality Effects on Microbial Priming

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  13. Soil microbial diversity patterns of a lowland spring environment.

    PubMed

    Vasileiadis, Sotirios; Puglisi, Edoardo; Arena, Maria; Cappa, Fabrizio; van Veen, Johannes A; Cocconcelli, Pier S; Trevisan, Marco

    2013-11-01

    The Po river plain lowland springs represent unique paradigms of managed environments. Their current locations used to be swamps that were drained 6-7 centuries ago, and they have been in constant use ever since. Our aims were to identify the effects of land use on the microbial communities of these soils, look for associated diversity drivers, and assess the applicability of ecology theories with respect to identified patterns. We screened the microbial diversity across a land use transect via high-throughput sequencing of partial 16S rrRNA gene amplicons. Land use had a major effect on soil properties and microbial community structures. Total organic carbon and pH were major diversity drivers for Bacteria, and pH was important for Archaea. We identified the potential contribution of soil amendments to the indigenous microbial communities, and also gained insights into potential roles of taxa in the organic carbon turnover. Verrucomicrobia coincided with the higher values of the recalcitrant organic carbon. Actinobacteria and Acidobacteria correlated with the more labile organic carbon. Finally, the higher diversity found in the soils less enzymatically active and relatively poorer in nutrients, may be explained to an extent by niche-based theories such as the resource heterogeneity hypothesis and Connell's intermediate disturbance hypothesis.

  14. Changes in Soil Microbial Community Structure with Flooding

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  15. High-Resolution Dynamics of Microbial Communities during Dissimilatory Selenate Reduction in Anoxic Soil.

    PubMed

    Navarro, Ronald R; Aoyagi, Tomo; Kimura, Makoto; Itoh, Hideomi; Sato, Yuya; Kikuchi, Yoshitomo; Ogata, Atsushi; Hori, Tomoyuki

    2015-07-07

    Selenate is one of the most common toxic metal compounds in contaminated soils. Its redox status can be changed by microbial activity, thus affecting its water solubility and soil mobility. However, current knowledge of microbial dynamics has been limited by the low sensitivity of past isolation and identification protocols. Here, high-throughput Illumina sequencing of 16S rRNA genes was applied to monitor the shift of the microorganisms in an anoxic contaminated soil after Se(VI) and acetate amendment. An autoclaved soil with both chemicals and a live soil with acetate alone were used as controls. Preliminary chemical analysis clearly showed the occurrence of biological selenate reduction coupled with acetate oxidation. Principal coordinate analysis and diversity indices of Illumina-derived sequence data showed dynamic succession and diversification of the microbial community in response to selenate reduction. High-resolution phylogenetic analysis revealed that the relative frequency of an operational taxonomic unit (OTU) from the genus Dechloromonas increased remarkably from 0.2% to 36% as a result of Se(VI) addition. Multiple OTUs representing less abundant microorganisms from the Rhodocyclaceae and Comamonadaceae families had significant increases as well. This study demonstrated that these microorganisms are concertedly involved in selenate reduction of the employed contaminated soil under anoxic conditions.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-12-02

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

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

    NASA Astrophysics Data System (ADS)

    Djukic, Ika; Moiseev, Pavel; Hagedorn, Frank

    2016-04-01

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

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

    PubMed

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

    2014-08-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kazemi, S.; Lanoil, B. D.

    2014-12-01

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

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

    PubMed

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

    2014-06-03

    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.

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

    PubMed

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

    2015-06-02

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

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

    NASA Astrophysics Data System (ADS)

    Stark, J.

    2015-12-01

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

  7. Effects of temperature on microbial C metabolism in peat and mineral soil

    NASA Astrophysics Data System (ADS)

    Hagerty, S.; Dijkstra, P.; Miller, E.; Schwartz, E.; KOCH, G. W.; Hungate, B. A.

    2013-12-01

    Microbial metabolism, the main mechanism responsible for soil CO2 emissions, plays an important role in the global C cycle. Increased temperature generally stimulates decomposition and respiration, indicative of increased microbial C metabolism and possibly greater energy demand by microbes for growth and maintenance. Changes in microbial metabolism with temperature may manifest differently in microbial communities from soils with different C availability because it is generally expected that when more organic C is present, carbon use efficiency (CUE) will be lower and more CO2 will be released per unit C assimilated by microbes than when less C substrate is available. In this study we examined the effect of temperature on C processing in peat and mineral soil from the Marcel Experimental Forest in Minnesota. Samples were incubated for 7 days at 5, 10, 15, and 20°C. We used position-specific 13C-labeled tracers to model C flux through the central C metabolic network (i.e. glycolysis, pentose phosphate pathway, and the citric acid cycle) and to asses the CUE of microbial communities. We also measured total CO2 production and microbial biomass, and we calculated the metabolic quotient (qCO2), which is the rate of CO2, respired per unit of microbial biomass. We found that temperature and soil type did not affect CUE and patterns of C flow through the central C metabolic network. Increased temperature stimulated respiration and decreased qCO2 in peat more than the mineral soil. These results suggest temperature affects rate of C cycling, but does not alter the relative demand for energy production and biosynthesis per unit substrate-C. This implies, in contrast to expectations that at higher temperatures more substrate will be used to offset greater demand for maintenance energy, warmer temperatures will not alter the balance of growth and maintenance energy by soil microbes. Moreover, substrate availability did not result in ';wasteful' C use, but increased C cycling

  8. Non-microbial methane formation in oxic soils

    NASA Astrophysics Data System (ADS)

    Jugold, A.; Althoff, F.; Hurkuck, M.; Greule, M.; Lelieveld, J.; Keppler, F.

    2012-09-01

    Methane plays an important role as a radiatively and chemically active gas in our atmosphere. Until recently, sources of atmospheric methane in the biosphere have been attributed to strictly anaerobic microbial processes during degradation of organic matter. However, a large fraction of methane produced in the anoxic soil layers does not reach the atmosphere due to methanotrophic consumption in the overlaying oxic soil. Although methane fluxes from aerobic soils have been observed an alternative source other than methanogenesis has not been identified thus far. Here we provide evidence for non-microbial methane formation in soils under oxic conditions. We found that soils release methane upon heating and other environmental factors like ultraviolet irradiation, and drying-rewetting cycles. We suggest that chemical formation of methane during degradation of soil organic matter may represent the missing soil source that is needed to fully understand the complete methane cycle within the pedosphere. Although the emission fluxes are relatively low when compared to those from wetlands, they may be important in warm and wet regions subjected to ultraviolet radiation. We suggest that this methane source is highly sensitive to global change.

  9. Coarse Woody Debris Increases Microbial Community Functional Diversity but not Enzyme Activities in Reclaimed Oil Sands Soils.

    PubMed

    Kwak, Jin-Hyeob; Chang, Scott X; Naeth, M Anne; Schaaf, Wolfgang

    2015-01-01

    Forest floor mineral soil mix (FMM) and peat mineral soil mix (PMM) are cover soils commonly used for upland reclamation post open-pit oil sands mining in northern Alberta, Canada. Coarse woody debris (CWD) can be used to regulate soil temperature and water content, to increase organic matter content, and to create microsites for the establishment of microorganisms and vegetation in upland reclamation. We studied the effects of CWD on soil microbial community level physiological profile (CLPP) and soil enzyme activities in FMM and PMM in a reclaimed landscape in the oil sands. This experiment was conducted with a 2 (FMM vs PMM) × 2 (near CWD vs away from CWD) factorial design with 6 replications. The study plots were established with Populus tremuloides (trembling aspen) CWD placed on each plot between November 2007 and February 2008. Soil samples were collected within 5 cm from CWD and more than 100 cm away from CWD in July, August and September 2013 and 2014. Microbial biomass was greater (p<0.05) in FMM than in PMM, in July, and August 2013 and July 2014, and greater (p<0.05) near CWD than away from CWD in FMM in July and August samplings. Soil microbial CLPP differed between FMM and PMM (p<0.01) according to a principal component analysis and CWD changed microbial CLPP in FMM (p<0.05) but not in PMM. Coarse woody debris increased microbial community functional diversity (average well color development in Biolog Ecoplates) in both cover soils (p<0.05) in August and September 2014. Carbon degrading soil enzyme activities were greater in FMM than in PMM (p<0.05) regardless of distance from CWD but were not affected by CWD. Greater microbial biomass and enzyme activities in FMM than in PMM will increase organic matter decomposition and nutrient cycling, improving plant growth. Enhanced microbial community functional diversity by CWD application in upland reclamation has implications for accelerating upland reclamation after oil sands mining.

  10. Nitrogen starvation affects bacterial adhesion to soil

    PubMed Central

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

    2008-01-01

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

  11. Soil N dynamics related to soil C and microbial changes during long-term incubation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowledge of the pools and fluxes of C and N soil components is required to interpret ecosystem functioning and improve biogeochemical models. Two former grassland soils, where wheat or corn are currently growing, were studied by kinetic analysis of microbial biomass C and N changes, C and N minera...

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  15. Soil resources area affects herbivore health.

    PubMed

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

    2011-06-01

    Soil productivity effects nutritive quality of food plants, growth of humans and animals, and reproductive health of domestic animals. Game-range surveys sometimes poorly explained variations in wildlife populations, but classification of survey data by major soil types improved effectiveness. Our study evaluates possible health effects of lower condition and reproductive rates for wild populations of Odocoileus virginianus Zimmerman (white-tailed deer) in some physiographic regions of Mississippi. We analyzed condition and reproductive data for 2400 female deer from the Mississippi Department of Wildlife, Fisheries, and Parks herd health evaluations from 1991-1998. We evaluated age, body mass (Mass), kidney mass, kidney fat mass, number of corpora lutea (CL) and fetuses, as well as fetal ages. Region affected kidney fat index (KFI), which is a body condition index, and numbers of fetuses of adults (P≤0.001). Region affected numbers of CL of adults (P≤0.002). Mass and conception date (CD) were affected (P≤0.001) by region which interacted significantly with age for Mass (P≤0.001) and CD (P<0.04). Soil region appears to be a major factor influencing physical characteristics of female deer.

  16. [Soil microbial diversity in typical Karst peak-cluster depression under effects of different de-farming patterns].

    PubMed

    He, Xun-Yang; Su, Yi-Rong; Liang, Yue-Ming; Yang, Shan; Wang, Ke-Lin

    2010-02-01

    By using denaturing gradient gel electrophoresis (DGGE) and Biolog_Eco micro-plate technique, this paper studied the soil microbial genetic taxonomic and bacterial metabolic functional diversities under four de-farming patterns, i. e., natural restoration (NT, dominant plant species Neyraudia reynaudiana and Miscanthus floridulus), economic plantation (CM, Cajanus cajan and Castanea mollissima), zero-tillage (PI, Pennisetum purpureum and Zenia insign), and conventional tillage (MB, maize-soybean intercropping), in a typical Karst peak-cluster depression. All test de-farming patterns had significant effects on the soil microbial community structure and bacterial metabolic pattern. The community structure of soil fungi was more affected by the de-farming patterns than that of soil bacteria, while the later was more affected by seasonal variation. After 6-7 years of de-farming, soil bacterial taxonomic Shannon diversity indices had no significant differences under the four de-farming patterns, while soil fungal taxonomic Shannon diversity indices were significantly higher under CM and PI than under NT and MB. The soil bacterial metabolic functional diversity under PI was obviously lower than those under other de-farming patterns. Therefore, soil fungal genetic and bacterial metabolic diversities were more sensitive to de-farming patterns than soil bacterial genetic diversity did. Among the four de-farming patterns, economic plantation had the superiority in maintaining soil microbial genetic and bacterial metabolic functional diversities, being a better de-farming pattern.

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

    EPA Science Inventory

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  19. Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe.

    PubMed

    Cline, Lauren C; Zak, Donald R; Upchurch, Rima A; Freedman, Zachary B; Peschel, Anna R

    2017-02-01

    Foraging intensity of large herbivores may exert an indirect top-down ecological force on soil microbial communities via changes in plant litter inputs. We investigated the responses of the soil microbial community to elk (Cervus elaphus) winter range occupancy across a long-term foraging exclusion experiment in the sagebrush steppe of the North American Rocky Mountains, combining phylogenetic analysis of fungi and bacteria with shotgun metagenomics and extracellular enzyme assays. Winter foraging intensity was associated with reduced bacterial richness and increasingly distinct bacterial communities. Although fungal communities did not respond linearly to foraging intensity, a greater β-diversity response to winter foraging exclusion was observed. Furthermore, winter foraging exclusion increased soil cellulolytic and hemicellulolytic enzyme potential and higher foraging intensity reduced chitinolytic gene abundance. Thus, future changes in winter range occupancy may shape biogeochemical processes via shifts in microbial communities and subsequent changes to their physiological capacities to cycle soil C and N.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  1. Effect of antimony on the microbial growth and the activities of soil enzymes.

    PubMed

    An, Youn-Joo; Kim, Minjin

    2009-02-01

    The effects of antimony (Sb) on microbial growth inhibition and activities of soil enzymes were investigated in the present study. Test bacterial species were Escherichia coli, Bacillus subtilis and Streptococcus aureus. Among the microorganisms tested, S. aureus was the most sensitive. The 50% effects on the inhibition of specific growth rate of E. coli, B. subtilis, and, S. aureus were 555, 18.4, and 15.8 mg Sb L(-1), respectively. A silt loam soil was amended with antimony and incubated in a controlled condition. Microbial activities of dehydrogenase, acid phosphatase (P cycle), arylsulfatase (S cycle), beta-glucosidase (C cycle), urease (N cycle), and fluorescein diacetate hydrolase in soil were measured. Activities of urease and dehydrogenase were related with antimony and can be an early indication of antimony contamination. The maximum increase in soil urease activity by antimony was up to 168% after 3d compared with the control. The activities of other four enzymes (acid phosphatase, fluorescein diacetate hydrolase, arylsulfatase and ss-glucosidase) were less affected by antimony. This study suggested that antimony affects nitrogen cycle in soil by changing urease activity under the neutral pH, however, soil enzyme activities may not be a good protocol due to their complex response patterns to antimony pollution.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

    Yu, Shen; Ehrenfeld, Joan G.

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. Imidacloprid induces changes in the structure, genetic diversity and catabolic activity of soil microbial communities.

    PubMed

    Cycoń, Mariusz; Markowicz, Anna; Borymski, Sławomir; Wójcik, Marcin; Piotrowska-Seget, Zofia

    2013-12-15

    This is the first report describing the effect of imidacloprid applied at field rate (FR, 1 mg/kg of soil) and 10 times the FR (10*FR, 10 mg/kg of soil) on the structural, genetic and physiological diversity of soil bacterial community as determined by the phospholipid fatty acid (PLFA), the denaturing gradient gel electrophoresis (DGGE), and the community level physiological profile (CLPP) approaches. PLFA profiles showed that imidacloprid significantly shifted the microbial community structure and decreased the biomass of the total, bacterial and fungal PLFAs, however, this effect was transient at the FR dosage. The alterations in DGGE patterns caused by imidacloprid application, confirmed considerable changes in the overall richness and diversity of dominant bacteria. Although, as a result of imidacloprid application, the metabolic activity of microbial communities was generally lower, the richness and functional biodiversity of the soil microbial community were not negatively affected. In general, the analysis of the variance indicated that the measured parameters were significantly affected by treatment and the incubation time, however, the incubation time effect explained most of the observed variance. Imidacloprid degradation and the appearance of some new bands in DGGE profiles suggest the evolution of bacteria capable of degrading imidacloprid among indigenous microflora.

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed Central

    Lazzaro, Anna; Hilfiker, Daniela; Zeyer, Josef

    2015-01-01

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

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

    PubMed

    Lazzaro, Anna; Hilfiker, Daniela; Zeyer, Josef

    2015-01-01

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

  10. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils.

    PubMed

    de Castro, Alinne Pereira; Sartori da Silva, Maria Regina Silveira; Quirino, Betania Ferraz; da Cunha Bustamante, Mercedes Maria; Krüger, Ricardo Henrique

    2016-01-01

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

  11. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

    PubMed Central

    Pereira de Castro, Alinne; Sartori da Silva, Maria Regina Silveira; Quirino, Betania Ferraz; da Cunha Bustamante, Mercedes Maria; Krüger, Ricardo Henrique

    2016-01-01

    The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture. PMID:26849674

  12. Carbon fiber enhanced bioelectricity generation in soil microbial fuel cells.

    PubMed

    Li, Xiaojing; Wang, Xin; Zhao, Qian; Wan, Lili; Li, Yongtao; Zhou, Qixing

    2016-11-15

    The soil microbial fuel cell (MFC) is a promising biotechnology for the bioelectricity recovery as well as the remediation of organics contaminated soil. However, the electricity production and the remediation efficiency of soil MFC are seriously limited by the tremendous internal resistance of soil. Conductive carbon fiber was mixed with petroleum hydrocarbons contaminated soil and significantly enhanced the performance of soil MFC. The maximum current density, the maximum power density and the accumulated charge output of MFC mixed carbon fiber (MC) were 10, 22 and 16 times as high as those of closed circuit control due to the carbon fiber productively assisted the anode to collect the electron. The internal resistance of MC reduced by 58%, 83% of which owed to the charge transfer resistance, resulting in a high efficiency of electron transfer from soil to anode. The degradation rates of total petroleum hydrocarbons enhanced by 100% and 329% compared to closed and opened circuit controls without the carbon fiber respectively. The effective range of remediation and the bioelectricity recovery was extended from 6 to 20cm with the same area of air-cathode. The mixed carbon fiber apparently enhanced the bioelectricity generation and the remediation efficiency of soil MFC by means of promoting the electron transfer rate from soil to anode. The use of conductively functional materials (e.g. carbon fiber) is very meaningful for the remediation and bioelectricity recovery in the bioelectrochemical remediation.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  14. Microbial Community Structure and Function of Soil Following Ecosystem Conversion from Native Forests to Teak Plantation Forests

    PubMed Central

    de Gannes, Vidya; Bekele, Isaac; Dipchansingh, Denny; Wuddivira, Mark N.; De Cairies, Sunshine; Boman, Mattias; Hickey, William J.

    2016-01-01

    Soil microbial communities can form links between forest trees and functioning of forest soils, yet the impacts of converting diverse native forests to monoculture plantations on soil microbial communities are limited. This study tested the hypothesis that conversion from a diverse native to monoculture ecosystem would be paralleled by a reduction in the diversity of the soil microbial communities. Soils from Teak (Tectona grandis) plantations and adjacent native forest were examined at two locations in Trinidad. Microbial community structure was determined via Illumina sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) regions, and by phospholipid fatty acid (PLFA) analysis. Functional characteristics of microbial communities were assessed by extracellular enzyme activity (EEA). Conversion to Teak plantation had no effect on species richness or evenness of bacterial or fungal communities, and no significant effect on EEA. However, multivariate analyses (nested and two-way crossed analysis of similarity) revealed significant effects (p < 0.05) of forest type (Teak vs. native) upon the composition of the microbial communities as reflected in all three assays of community structure. Univariate analysis of variance identified two bacterial phyla that were significantly more abundant in the native forest soils than in Teak soils (Cyanobacteria, p = 0.0180; Nitrospirae, p = 0.0100) and two more abundant in Teak soils than in native forest (candidate phyla TM7, p = 0.0004; WS6, p = 0.044). Abundance of an unidentified class of arbuscular mycorrhizal fungi (AMF) was significantly greater in Teak soils, notable because Teak is colonized by AMF rather than by ectomycorrihzal fungi that are symbionts of the native forest tree species. In conclusion, microbial diversity indices were not affected in the conversion of native forest to teak plantation, but examination of specific bacterial taxa showed that there were significant differences in

  15. Soil biological activity as affected by tillage intensity

    NASA Astrophysics Data System (ADS)

    Gajda, A.; Przewłoka, B.

    2012-02-01

    The effect of tillage intensity on changes of microbiological activity and content of particulate organic matter in soil under winter wheat duirng 3 years was studied. Microbial response related to the tillage-induced changes in soil determined on the content of biomass C and N, the rate of CO2 evolution, B/F ratio, the activity of dehydrogenases, acid and alkaline phosphatases, soil C/N ratio and microbial biomass C/N ratio confirmed the high sensitivity of soil microbial populations to the tillage system applied. After three year studies, the direct sowing system enhanced the increase of labile fraction of organic matter content in soil. There were no significant changes in the labile fraction quantity observed in soil under conventional tillage. Similar response related to the tillage intensity was observed in particulate organic matter quantities expressed as a percentage of total organic matter in soil. A high correlation coefficients calculated between contents of soil microbial biomass C and N, particulate organic matter and potentially mineralizable N, and the obtained yields of winter wheat grown on experimental fields indicated on a high importance of biological quality of status of soil for agricultural crop production.

  16. Influence of Herbicide Triasulfuron on Soil Microbial Community in an Unamended Soil and a Soil Amended with Organic Residues

    PubMed Central

    Pose-Juan, Eva; Igual, José M.; Sánchez-Martín, María J.; Rodríguez-Cruz, M. S.

    2017-01-01

    The effect of organic amendments and pesticides on a soil microbial community has garnered considerable interest due to the involvement of microorganisms in numerous soil conservation and maintenance reactions. The aim of this work was to assess the influence on a soil microbial community of the simultaneous application of the herbicide triasulfuron at three doses (2, 10, and 50 mg kg-1), with an organic amendment [sewage sludge (SS) or green compost (GC)]. Dissipation kinetics, soil microbial biomass, dehydrogenase activity (DHA) and respiration, and the profile of phospholipid fatty acids (PLFAs) extracted from the soil, were determined in unamended (S) soil and amended (S+SS and S+GC) ones. Triasulfuron dissipation followed the single first-order kinetics model. Half-life (DT50) values were higher in the amended soils than in the unamended one for the 10 and 50 mg kg-1 doses. The dissipation rates were lower in the S+GC soil for the three herbicide doses applied. In general, soil biomass, DHA and respiration values increased in SS- and GC-amended soils compared to the unamended one. DHA values decreased (S and S+SS) or increased (S+GC) with the incubation time of soil with herbicide at the different doses applied. Respiration values increased with the herbicide doses applied and decreased with the incubation time, although maximum values were obtained for soils treated with the highest dose after 70 days of incubation. PLFA analysis indicated different effects of triasulfuron on the soil microbial community structure depending on the organic amendments. While the increasing triasulfuron doses resulted in deeper alterations in the S soil, the time after triasulfuron application was the most important variation in the S+SS and S+GC soils. The overall results indicate that the soil amendment has an effect on herbicide dissipation rate and the soil microbial community. Initially, a high dose of triasulfuron had detrimental effects on the soil microbial community

  17. Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach

    PubMed Central

    Gourmelon, Véronique; Maggia, Laurent; Powell, Jeff R.; Gigante, Sarah; Hortal, Sara; Gueunier, Claire; Letellier, Kelly; Carriconde, Fabian

    2016-01-01

    Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions

  18. Short-term effects of combined iprodione and vermicompost applications on soil microbial community structure.

    PubMed

    Verdenelli, Romina A; Lamarque, Alicia L; Meriles, José M

    2012-01-01

    the breakdown of iprodione in soils. Furthermore, elevated dosages of iprodione may potentially affect the microbial community structure and diversity of the soil, which may lead to the deterioration of soil quality and fertility.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  20. The PAMPA datasets: a metagenomic survey of microbial communities in Argentinean pampean soils

    PubMed Central

    2013-01-01

    Background Soil is among the most diverse and complex environments in the world. Soil microorganisms play an essential role in biogeochemical cycles and affect plant growth and crop production. However, our knowledge of the relationship between species-assemblies and soil ecosystem processes is still very limited. The aim of this study was to generate a comprehensive metagenomic survey to evaluate the effect of high-input agricultural practices on soil microbial communities. Results We collected soil samples from three different areas in the Argentinean Pampean region under three different types of land uses and two soil sources (bulk and rhizospheric). We extracted total DNA from all samples and also synthetized cDNA from rhizospheric samples. Using 454-FLX technology, we generated 112 16S ribosomal DNA and 14 16S ribosomal RNA amplicon libraries totaling 1.3 M reads and 36 shotgun metagenome libraries totaling 17.8 million reads (7.7 GB). Our preliminary results suggested that water availability could be the primary driver that defined microbial assemblages over land use and soil source. However, when water was not a limiting resource (annual precipitation >800 mm) land use was a primary driver. Conclusion This was the first metagenomic study of soil conducted in Argentina and our datasets are among the few large soil datasets publicly available. The detailed analysis of these data will provide a step forward in our understanding of how soil microbiomes respond to high-input agricultural systems, and they will serve as a useful comparison with other soil metagenomic studies worldwide. PMID:24450949

  1. Non-target impact of fungicide tetraconazole on microbial communities in soils with different agricultural management.

    PubMed

    Sułowicz, Sławomir; Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2016-08-01

    Effect of the fungicide tetraconazole on microbial community in silt loam soils from orchard with long history of triazole application and from grassland with no known history of fungicide usage was investigated. Triazole tetraconazole that had never been used on these soils before was applied at the field rate and at tenfold the FR. Response of microbial communities to tetraconazole was investigated during 28-day laboratory experiment by determination of changes in their biomass and structure (phospholipid fatty acids method-PLFA), activity (fluorescein diacetate hydrolysis-FDA) as well as changes in genetic (DGGE) and functional (Biolog) diversity. Obtained results indicated that the response of soil microorganisms to tetraconazole depended on the management of the soils. DGGE patterns revealed that both dosages of fungicide affected the structure of bacterial community and the impact on genetic diversity and richness was more prominent in orchard soil. Values of stress indices-the saturated/monounsaturated PLFAs ratio and the cyclo/monounsaturated precursors ratio, were almost twice as high and the Gram-negative/Gram-positive ratio was significantly lower in the orchard soil compared with the grassland soil. Results of principal component analysis of PLFA and Biolog profiles revealed significant impact of tetraconazole in orchard soil on day 28, whereas changes in these profiles obtained for grassland soil were insignificant or transient. Obtained results indicated that orchards soil seems to be more vulnerable to tetraconazole application compared to grassland soil. History of pesticide application and agricultural management should be taken into account in assessing of environmental impact of studied pesticides.

  2. Microbial contents of soil from fire pits

    NASA Astrophysics Data System (ADS)

    Moon, K.; Esparza, V.; de Sandre, J.; Cheney, S.; Anderson, A.; White, M. A.

    2006-12-01

    Forest fires generate polycylic aromatic hydrocarbons (PAHs) that can lead to carcinogenic compounds, which are potential health risks. PAHs can be degraded to water and carbon dioxide by certain soil microbes. Thus, during participation in a NASA-funded summer research experience at Utah State University, our high school student team sampled soils from a month-old fire pit in which plant materials had been burnt. We detected in soil samples, from surface, 10 and 20 cm depths, microbes that would grow on a defined minimal medium source. Other microbes were cultured from the roots of plants that had established at the fire pit. A diversity of microbes was present in all samples based on visible differences in cell shape and color. It was surprising that the surface ash, although exposed to sunlight over the month interval, had culturable colonies. Many of these culturable bacteria were pigmented perhaps as a protection against UV radiation from the sun. We searched for genes in the microbes that encoded enzymes called dioxygenases that in other bacteria are involved in degradation of PAHs. This test involved using polymerase chain reactions to detect the genes. PCR products were found in two of the fifteen isolates tested although their sizes differed from the control gene product from a PAH-degrading mycobacterium isolate. These results suggest that the soils did contain microbes with the possib