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

PubMed

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

2016-06-15

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

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

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

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

DOE PAGES

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae; ...

2017-03-22

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

USGS Publications Warehouse

Chung, Y. Anny; Sinsabaugh, Robert L; Kuske, Cheryl R.; Reed, Sasha C.; Rudgers, Jennifer A.

2017-01-01

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefits of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. The findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.

Soil microbial community responses to altered lignin biosynthesis in Populus tremuloides vary among three distinct soils

Treesearch

Kate L. Bradley; Jessica E. Hancock; Christian P. Giardina; Kurt S. Pregitzer

2007-01-01

The development and use of transgenic plants has steadily increased, but there are still little data about the responses of soil microorganisms to these genetic modifications. We utilized a greenhouse trial approach to evaluate the effects of altered stem lignin in trembling aspen (Populus tremuloides) on soil microbial communities in three soils...

Environmental implications of herbicide resistance: soil biology and ecology

USDA-ARS?s Scientific Manuscript database

Soil microbial community structure and activity are clearly linked to plant communities established in natural and agricultural ecosystems. A limited number of studies confirm that weeds alter their soil environment and select for specific microbial communities in the rhizosphere. Such rhizosphere m...

Species-specific effects of Asian and European earthworms on microbial communities in Mid-Atlantic deciduous forests

USDA-ARS?s Scientific Manuscript database

Earthworm species with different feeding, burrowing, and/or casting behaviors can lead to distinct microbial communities through complex direct and indirect processes. European earthworm invasion into temperate deciduous forests in North America has been shown to alter microbial biomass in the soil ...

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning

USGS Publications Warehouse

Wallenstein, Matthew D.; Hall, Edward K.

2012-01-01

As the earth system changes in response to human activities, a critical objective is to predict how biogeochemical process rates (e.g. nitrification, decomposition) and ecosystem function (e.g. net ecosystem productivity) will change under future conditions. A particular challenge is that the microbial communities that drive many of these processes are capable of adapting to environmental change in ways that alter ecosystem functioning. Despite evidence that microbes can adapt to temperature, precipitation regimes, and redox fluctuations, microbial communities are typically not optimally adapted to their local environment. For example, temperature optima for growth and enzyme activity are often greater than in situ temperatures in their environment. Here we discuss fundamental constraints on microbial adaptation and suggest specific environments where microbial adaptation to climate change (or lack thereof) is most likely to alter ecosystem functioning. Our framework is based on two principal assumptions. First, there are fundamental ecological trade-offs in microbial community traits that occur across environmental gradients (in time and space). These trade-offs result in shifting of microbial function (e.g. ability to take up resources at low temperature) in response to adaptation of another trait (e.g. limiting maintenance respiration at high temperature). Second, the mechanism and level of microbial community adaptation to changing environmental parameters is a function of the potential rate of change in community composition relative to the rate of environmental change. Together, this framework provides a basis for developing testable predictions about how the rate and degree of microbial adaptation to climate change will alter biogeochemical processes in aquatic and terrestrial ecosystems across the planet.

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

PubMed Central

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

2015-01-01

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

Effects of Nutrient Enrichment on Microbial Communities and Carbon Cycling in Wetland Soils

NASA Astrophysics Data System (ADS)

Hartman, W.; Neubauer, S. C.; Richardson, C. J.

2013-12-01

Soil microbial communities are responsible for catalyzing biogeochemical transformations underlying critical wetland functions, including cycling of carbon (C) and nutrients, and emissions of greenhouse gasses (GHG). Alteration of nutrient availability in wetland soils may commonly occur as the result of anthropogenic impacts including runoff from human land uses in uplands, alteration of hydrology, and atmospheric deposition. However, the impacts of altered nutrient availability on microbial communities and carbon cycling in wetland soils are poorly understood. To assess these impacts, soil microbial communities and carbon cycling were determined in replicate experimental nutrient addition plots (control, +N, +P, +NP) across several wetland types, including pocosin peat bogs (NC), freshwater tidal marshes (GA), and tidal salt marshes (SC). Microbial communities were determined by pyrosequencing (Roche 454) extracted soil DNA, targeting both bacteria (16S rDNA) and fungi (LSU) at a depth of ca. 1000 sequences per plot. Wetland carbon cycling was evaluated using static chambers to determine soil GHG fluxes, and plant inclusion chambers were used to determine ecosystem C cycling. Soil bacterial communities responded to nutrient addition treatments in freshwater and tidal marshes, while fungal communities did not respond to treatments in any of our sites. We also compared microbial communities to continuous biogeochemical variables in soil, and found that bacterial community composition was correlated only with the content and availability of soil phosphorus, while fungi responded to phosphorus stoichiometry and soil pH. Surprisingly, we did not find a significant effect of our nutrient addition treatments on most metrics of carbon cycling. However, we did find that several metrics of soil carbon cycling appeared much more related to soil phosphorus than to nitrogen or soil carbon pools. Finally, while overall microbial community composition was weakly correlated with soil carbon cycling, our work did identify a small number of individual taxonomic groups that were more strongly correlated with soil CO2 flux. These results suggest that a small number of microbial groups may potentially serve as keystone taxa (and functional indicators), which simple community fingerprinting approaches may overlook. Our results also demonstrate strong effects of soil phosphorus availability on both microbial communities and soil carbon cycling, even in wetland types traditionally considered to be nitrogen limited.

Simulated nitrogen deposition causes a decline of intra- and extraradical abundance of arbuscular mycorrhizal fungi and changes in microbial community structure in northern hardwood forests

Treesearch

Linda T.A. van Diepen; Erik A. Lilleskov; Kurt S. Pregitzer; R. Michael Miller

2010-01-01

Increased nitrogen (N) deposition caused by human activities has altered ecosystem functioning and biodiversity. To understand the effects of altered N availability, we measured the abundance of arbuscular mycorrhizal fungi (AMF) and the microbial community in northern hardwood forests exposed to long-term (12 years) simulated N deposition (30 kg N ha-1...

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2013-10-01

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

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

PubMed Central

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

2016-01-01

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

STRUCTURE AND FUNCTION OF ANTHROPOGENICALLY ALTERED MICROBIAL COMMUNITIES IN COASTAL WATERS. (R825243)

EPA Science Inventory

Human-based (anthropogenic) nutrient and other pollutant enrichment of the world's coastal waters is causing unprecedented changes in microbial community structure and function. Symptoms of these changes include accelerating eutrophication, the proliferation of harmful microal...

Leaf endophytic fungus interacts with precipitation to alter belowground microbial communities in primary successional dunes

PubMed Central

Bell-Dereske, Lukas; Takacs-Vesbach, Cristina; Kivlin, Stephanie N.; Emery, Sarah M.; Rudgers, Jennifer A.

2017-01-01

Abstract Understanding interactions between above- and belowground components of ecosystems is an important next step in community ecology. These interactions may be fundamental to predicting ecological responses to global change because indirect effects occurring through altered species interactions can outweigh or interact with the direct effects of environmental drivers. In a multiyear field experiment (2010–2015), we tested how experimental addition of a mutualistic leaf endophyte (Epichloë amarillans) associated with American beachgrass (Ammophila breviligulata) interacted with an altered precipitation regime (±30%) to affect the belowground microbial community. Epichloë addition increased host root biomass at the plot scale, but reduced the length of extraradical arbuscular mycorrhizal (AM) fungal hyphae in the soil. Under ambient precipitation alone, the addition of Epichloë increased root biomass per aboveground tiller and reduced the diversity of AM fungi in A. breviligulata roots. Furthermore, with Epichloë added, the diversity of root-associated bacteria declined with higher soil moisture, whereas in its absence, bacterial diversity increased with higher soil moisture. Thus, the aboveground fungal mutualist not only altered the abundance and composition of belowground microbial communities but also affected how belowground communities responded to climate, suggesting that aboveground microbes have potential for cascading influences on community dynamics and ecosystem processes that occur belowground. PMID:28334408

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

NASA Astrophysics Data System (ADS)

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

2002-12-01

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

Nitrogen addition shifts the microbial community in the rhizosphere of Pinus tabuliformis in Northwestern China

PubMed Central

Lv, Fenglian; Xue, Sha; Wang, Guoliang; Zhang, Chao

2017-01-01

Atmospheric nitrogen (N) deposition profoundly alters the soil microbial communities and will thus affect nutrient cycles. The effects of N availability on microbial community, however, are not clear. We used PLFA analysis to evaluate the effects of a gradient of N addition (0, 2.8, 5.6, 11.2, and 22.4 g N m-2 y-1) for three years on the rhizospheric microbial community of Pinus tabuliformis seedlings. The main factors influencing the community were quantified using structural equation modelling and redundancy analysis. At the microbial-community level, N addition increased the total phospholipid fatty acids content by increasing the dissolved organic carbon (DOC) and root biomass. Increases in soil microbial biomass carbon and N, however, was attributed to the increased DOC, N content and decreased pH. At the microbial-groups level, Fungal, arbuscular mycorrhizal fungal (AMF), gram-positive bacterial (GP) abundances and the GP:GN ratio first increased and then decreased with N addition. Nitrogen addition increased the abundances of bacteria, fungi, and actinomycetes mainly by increasing the DOC content and decreasing root biomass. Additionally, the decrease of pH and ammonium N caused by N addition increased the fungal abundances and reduced actinomycete abundances, respectively. Nitrogen addition shifted the rhizospheric microbial community mainly by altering the DOC content and root biomass. The current rate of N deposition (2.5 g N m-2 y-1) benefits plant growth and increases the abundances of fungi, arbuscular mycorrhizal fungi, GP, actinomycetes and the GP:GN ratio. PMID:28234932

Common Hydraulic Fracturing Fluid Additives Alter the Structure and Function of Anaerobic Microbial Communities.

PubMed

Mumford, Adam C; Akob, Denise M; Klinges, J Grace; Cozzarelli, Isabelle M

2018-04-15

The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C 3 H 6 BrNO 4 ). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills. IMPORTANCE Organic components of UOG wastewater can alter microbial communities and biogeochemical processes, which could alter the rates of essential natural attenuation processes. These findings provide new insights into microbial responses following a release of UOG wastewaters and are critical for identifying strategies for the remediation and natural attenuation of impacted environments. This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress.

PubMed

Bharwani, Aadil; Mian, M Firoz; Surette, Michael G; Bienenstock, John; Forsythe, Paul

2017-01-11

Stress-related disorders involve systemic alterations, including disruption of the intestinal microbial community. Given the putative connections between the microbiota, immunity, neural function, and behaviour, we investigated the potential for microbe-induced gut-to-brain signalling to modulate the impact of stress on host behaviour and immunoregulation. Male C57BL/6 mice treated orally over 28 days with either Lactobacillus rhamnosus (JB-1) ™ or vehicle were subjected to chronic social defeat and assessed for alterations in behaviour and immune cell phenotype. 16S rRNA sequencing and mass spectrometry were employed to analyse the faecal microbial community and metabolite profile. Treatment with JB-1 decreased stress-induced anxiety-like behaviour and prevented deficits in social interaction with conspecifics. However, JB-1 did not alter development of aggressor avoidance following social defeat. Microbial treatment attenuated stress-related activation of dendritic cells while increasing IL-10+ regulatory T cells. Furthermore, JB-1 modulated the effect of stress on faecal metabolites with neuroactive and immunomodulatory properties. Exposure to social defeat altered faecal microbial community composition and reduced species richness and diversity, none of which was prevented by JB-1. Stress-related microbiota disruptions persisted in vehicle-treated mice for 3 weeks following stressor cessation. These data demonstrate that despite the complexity of the gut microbiota, exposure to a single microbial strain can protect against certain stress-induced behaviours and systemic immune alterations without preventing dysbiosis. This work supports microbe-based interventions for stress-related disorders.

Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

PubMed Central

Vega Thurber, Rebecca; Burkepile, Deron E.; Correa, Adrienne M. S.; Thurber, Andrew R.; Shantz, Andrew A.; Welsh, Rory; Pritchard, Catharine; Rosales, Stephanie

2012-01-01

With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs. PMID:22957055

Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides.

PubMed

Vega Thurber, Rebecca; Burkepile, Deron E; Correa, Adrienne M S; Thurber, Andrew R; Shantz, Andrew A; Welsh, Rory; Pritchard, Catharine; Rosales, Stephanie

2012-01-01

With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs.

Smoking cessation alters subgingival microbial recolonization.

PubMed

Fullmer, S C; Preshaw, P M; Heasman, P A; Kumar, P S

2009-06-01

Smoking cessation improves the clinical manifestations of periodontitis; however, its effect on the subgingival biofilm, the primary etiological agent of periodontitis, is unclear. The purpose of this study was to investigate, longitudinally, if smoking cessation altered the composition of the subgingival microbial community, by means of a quantitative, cultivation-independent assay for bacterial profiling. Subgingival plaque was collected at baseline, and 3, 6, and 12 months post-treatment from smokers who received root planing and smoking cessation counseling. The plaque was analyzed by terminal restriction fragment length polymorphism (t-RFLP). Microbial profiles differed significantly between smokers and quitters at 6 and 12 months following smoking cessation. The microbial community in smokers was similar to baseline, while quitters demonstrated significantly divergent profiles. Changes in bacterial levels contributed to this shift. These findings reveal a critical role for smoking cessation in altering the subgingival biofilm and suggest a mechanism for improved periodontal health associated with smoking cessation.

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

Treesearch

Aimee T. Classen; Steven T. Overby; Stephen C. Hart; George W. Koch; Thomas G. Whitham

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality of an ecosystem or indirectly by shifting the composition of microbial communities that mediate nutrient processes. We examined the effects of tree susceptibility and resistance to herbivory on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore...

Alteration of soil microbial communities and water quality in restored wetlands

USGS Publications Warehouse

Bossio, D.A.; Fleck, J.A.; Scow, K.M.; Fujii, R.

2006-01-01

Land usage is a strong determinant of soil microbial community composition and activity, which in turn determine organic matter decomposition rates and decomposition products in soils. Microbial communities in permanently flooded wetlands, such as those created by wetland restoration on Sacramento-San Joaquin Delta islands in California, function under restricted aeration conditions that result in increasing anaerobiosis with depth. It was hypothesized that the change from agricultural management to permanently flooded wetland would alter microbial community composition, increase the amount and reactivity of dissolved organic carbon (DOC) compounds in Delta waters; and have a predominant impact on microbial communities as compared with the effects of other environmental factors including soil type and agricultural management. Based on phospholipid fatty acid (PLFA) analysis, active microbial communities of the restored wetlands were changed significantly from those of the agricultural fields, and wetland microbial communities varied widely with soil depth. The relative abundance of monounsaturated fatty acids decreased with increasing soil depth in both wetland and agricultural profiles, whereas branched fatty acids were relatively more abundant at all soil depths in wetlands as compared to agricultural fields. Decomposition conditions were linked to DOC quantity and quality using fatty acid functional groups to conclude that restricted aeration conditions found in the wetlands were strongly related to production of reactive carbon compounds. But current vegetation may have had an equally important role in determining DOC quality in restored wetlands. In a larger scale analysis, that included data from wetland and agricultural sites on Delta islands and data from two previous studies from the Sacramento Valley, an aeration gradient was defined as the predominant determinant of active microbial communities across soil types and land usage. ?? 2005 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Biochar increases plant growth and alters microbial communities via regulating the moisture and temperature of green roof substrates.

PubMed

Chen, Haoming; Ma, Jinyi; Wei, Jiaxing; Gong, Xin; Yu, Xichen; Guo, Hui; Zhao, Yanwen

2018-09-01

Green roofs have increasingly been designed and applied to relieve environmental problems, such as water loss, air pollution as well as heat island effect. Substrate and vegetation are important components of green roofs providing ecosystem services and benefiting the urban development. Biochar made from sewage sludge could be potentially used as the substrate amendment for green roofs, however, the effects of biochar on substrate quality and plant performance in green roofs are still unclear. We evaluated the effects of adding sludge biochar (0, 5, 10, 15 and 20%, v/v) to natural soil planted with three types of plant species (ryegrass, Sedum lineare and cucumber) on soil properties, plant growth and microbial communities in both green roof and ground ecosystems. Our results showed that sludge biochar addition significantly increased substrate moisture, adjusted substrate temperature, altered microbial community structure and increased plant growth. The application rate of 10-15% sludge biochar on the green roof exerted the most significant effects on both microbial and plant biomass by 63.9-89.6% and 54.0-54.2% respectively. Path analysis showed that biochar addition had a strong effect on microbial biomass via changing the soil air-filled porosity, soil moisture and temperature, and promoted plant growth through the positive effects on microbial biomass. These results suggest that the applications of biochar at an appropriate rate can significantly alter plant growth and microbial community structure, and increase the ecological benefits of green roofs via exerting effects on the moisture, temperature and nutrients of roof substrates. Copyright © 2018 Elsevier B.V. All rights reserved.

GEOELECTRICAL EVIDENCE OF MICROBIAL DEGRADATION OF DIESEL CONTAMINATED SEDIMENTS

EPA Science Inventory

The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynami...

Microbial legacies alter decomposition in response to simulated global change

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

Martiny, Jennifer B. H.; Martiny, Adam C.; Weihe, Claudia

Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungalmore » composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities.« less

Microbial legacies alter decomposition in response to simulated global change

DOE PAGES

Martiny, Jennifer B. H.; Martiny, Adam C.; Weihe, Claudia; ...

2016-10-14

Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungalmore » composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities.« less

Response of soil organic carbon fractions, microbial community composition and carbon mineralization to high-input fertilizer practices under an intensive agricultural system

PubMed Central

Wu, Xueping; Gebremikael, Mesfin Tsegaye; Wu, Huijun; Cai, Dianxiong; Wang, Bisheng; Li, Baoguo; Zhang, Jiancheng; Li, Yongshan; Xi, Jilong

2018-01-01

Microbial mechanisms associated with soil organic carbon (SOC) decomposition are poorly understood. We aim to determine the effects of inorganic and organic fertilizers on soil labile carbon (C) pools, microbial community structure and C mineralization rate under an intensive wheat-maize double cropping system in Northern China. Soil samples in 0–10 cm layer were collected from a nine-year field trial involved four treatments: no fertilizer, CK; nitrogen (N) and phosphorus (P) fertilizers, NP; maize straw combined with NP fertilizers, NPS; and manure plus straw and NP fertilizers, NPSM. Soil samples were analyzed to determine labile C pools (including dissolved organic C, DOC; light free organic C, LFOC; and microbial biomass C, MBC), microbial community composition (using phospholipid fatty acid (PLFA) profiles) and SOC mineralization rate (from a 124-day incubation experiment). This study demonstrated that the application of chemical fertilizers (NP) alone did not alter labile C fractions, soil microbial communities and SOC mineralization rate from those observed in the CK treatment. Whereas the use of straw in conjunction with chemical fertilizers (NPS) became an additional labile substrate supply that decreased C limitation, stimulated growth of all PLFA-related microbial communities, and resulted in 53% higher cumulative mineralization of C compared to that of CK. The SOC and its labile fractions explained 78.7% of the variance of microbial community structure. Further addition of manure on the top of straw in the NPSM treatment did not significantly increase microbial community abundances, but it did alter microbial community structure by increasing G+/G- ratio compared to that of NPS. The cumulative mineralization of C was 85% higher under NPSM fertilization compared to that of CK. Particularly, the NPSM treatment increased the mineralization rate of the resistant pool. This has to be carefully taken into account when setting realistic and effective goals for long-term soil C stabilization. PMID:29668702

Response of soil organic carbon fractions, microbial community composition and carbon mineralization to high-input fertilizer practices under an intensive agricultural system.

PubMed

Li, Jing; Wu, Xueping; Gebremikael, Mesfin Tsegaye; Wu, Huijun; Cai, Dianxiong; Wang, Bisheng; Li, Baoguo; Zhang, Jiancheng; Li, Yongshan; Xi, Jilong

2018-01-01

Microbial mechanisms associated with soil organic carbon (SOC) decomposition are poorly understood. We aim to determine the effects of inorganic and organic fertilizers on soil labile carbon (C) pools, microbial community structure and C mineralization rate under an intensive wheat-maize double cropping system in Northern China. Soil samples in 0-10 cm layer were collected from a nine-year field trial involved four treatments: no fertilizer, CK; nitrogen (N) and phosphorus (P) fertilizers, NP; maize straw combined with NP fertilizers, NPS; and manure plus straw and NP fertilizers, NPSM. Soil samples were analyzed to determine labile C pools (including dissolved organic C, DOC; light free organic C, LFOC; and microbial biomass C, MBC), microbial community composition (using phospholipid fatty acid (PLFA) profiles) and SOC mineralization rate (from a 124-day incubation experiment). This study demonstrated that the application of chemical fertilizers (NP) alone did not alter labile C fractions, soil microbial communities and SOC mineralization rate from those observed in the CK treatment. Whereas the use of straw in conjunction with chemical fertilizers (NPS) became an additional labile substrate supply that decreased C limitation, stimulated growth of all PLFA-related microbial communities, and resulted in 53% higher cumulative mineralization of C compared to that of CK. The SOC and its labile fractions explained 78.7% of the variance of microbial community structure. Further addition of manure on the top of straw in the NPSM treatment did not significantly increase microbial community abundances, but it did alter microbial community structure by increasing G+/G- ratio compared to that of NPS. The cumulative mineralization of C was 85% higher under NPSM fertilization compared to that of CK. Particularly, the NPSM treatment increased the mineralization rate of the resistant pool. This has to be carefully taken into account when setting realistic and effective goals for long-term soil C stabilization.

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.

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

Wang, Mengmeng; Liu, Shanshan; Wang, Feng

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

Ecological restoration alters microbial communities in mine tailings profiles

NASA Astrophysics Data System (ADS)

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

2016-04-01

Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

Ecological restoration alters microbial communities in mine tailings profiles.

PubMed

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

2016-04-29

Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

Ecological restoration alters microbial communities in mine tailings profiles

PubMed Central

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

2016-01-01

Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings. PMID:27126064

Intrinsic association between diet and the gut microbiome: current evidence

PubMed Central

Winglee, Kathryn; Fodor, Anthony A

2017-01-01

The gut microbiome performs many crucial functions for the human host, but the molecular mechanisms by which host, microbe and diet interact to mediate health and disease are only starting to be revealed. Here we review the literature on how changes in the diet affect the microbiome. A number of studies have shown that within a geographic region, different diets (such as vegan vs. omnivore) are associated with differences in a modest number of taxa but do not reliably produce radical differences within the gut microbial community. In contrast, studies that look across continents consistently find profoundly different microbial communities between Westernized and traditional populations, although it remains unclear to what extent diet or other differences in lifestyle drive these distinct microbial community structures. Furthermore, studies that place subjects on controlled short term experimental diets have found the resulting alterations to the gut microbial community to generally be small in scope, with changes that do not overcome initial individual differences in microbial community structure. These results emphasize that the human gut microbial community is relatively stable over time. In contrast, short term changes in diet can cause large changes in metabolite profiles, including metabolites processed by the gut microbial community. These results suggest that commensal gut microbes have a great deal of genetic plasticity and can activate different metabolic pathways independent of changes to microbial community composition. Thus, future studies of the how diet impacts host health via the microbiome may wish to focus on functional assays such as transcriptomics and metabolomics, in addition to 16S rRNA and whole-genome metagenome shotgun analyses of DNA. Taken together, the literature is most consistent with a model in which the composition of the adult gut microbial community undergoes modest compositional changes in response to altered diet but can nonetheless respond very rapidly to dietary changes via up- or down-regulation of metabolic pathways that can have profound and immediate consequences for host health. PMID:28690398

Rhizosphere microbial communities of canola and wheat at six paired field sites

USDA-ARS?s Scientific Manuscript database

Plant physical and chemical characteristics are known to alter rhizosphere microbial communities, but the effect of introducing canola (Brassica napus L.) into monoculture wheat (Triticum aestivum L.) rotations is not clear. Results from a field study in eastern Washington showed that winter canola ...

Soil microbial community structure: mechanical disturbance alters soil microbial community

USDA-ARS?s Scientific Manuscript database

Soil microbes are responsible for soil nutrient cycling in both perennial and annual management systems for beef cattle and grain production. In the Southern Plains of Oklahoma, producers plant winter wheat (Triticum aestivum) in rotation with winter canola (Brassica rapa). Producers in the Southern...

Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

NASA Astrophysics Data System (ADS)

di Meo, C. A.; Giovannoni, S.; Fisk, M.

2002-12-01

Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (<20 yrs old) from six different sites along the ridge axis at 9°N, East Pacific Rise were examined for microbial life. Total DNA was extracted from the basalt glass and screened for the presence of both bacteria and archaea using the PCR. Repeated attempts with different primer sets yielded no bacterial genes, whereas archaeal genes were quite abundant. A genetic fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP), was used to compare the archaeal community compositions among the six different basalts. Filtered deep-sea water samples (~15 L) were examined in parallel to identify any overlap between rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the drill hole ~16°C), where petrographic evidence suggested the presence of microbial alteration. Archaeal 16S rRNA genes were amplified, cloned, and twelve clones representing the most abundant groups were sequenced. Eleven out of the twelve clones were 97 to 99% similar to Group I marine Crenarchaeota, while the remaining clone was 95% similar to Euryarchaeota, based on BLAST searches of the GenBank database. Our community-level approach to studying microbes living in volcanic glasses has provided a greater understanding of the microbial communities that potentially alter these materials.

Microbial community controls on decomposition and soil carbon storage

NASA Astrophysics Data System (ADS)

Frey, S. D.

2016-12-01

Soil is one of the most diverse habitats on Earth and one of the least characterized in terms of the identification and ecological roles of soil organisms. Soils also contain the largest repository of organic C in the terrestrial biosphere and the activities of heterotrophic soil organisms are responsible for one of the largest annual fluxes of CO2 to the atmosphere. A fundamental controversy in ecosystem ecology is the degree to which identification of microbial taxa informs our ability to understand and model ecosystem-scale processes, such as soil carbon storage and fluxes. We have evidence that microbial identity does matter, particularly in a global change context where soil microorganisms experience selective pressures to adapt to changing environments. In particular, our work at the Harvard Forest Long-term Ecological Research (LTER) site demonstrates that the microbial community is fundamentally altered by global change stressors (climate warming, nitrogen deposition, biotic invasion) and that microbial taxa exposed to long-term environmental change exhibit an altered capacity to decompose organic matter. This talk will discuss the relative importance of changes in microbial community structure versus microbial physiology for soil organic matter degradation and stabilization.

Microbial responses to southward and northward Cambisol soil transplant

DOE PAGES

Wang, Mengmeng; Liu, Shanshan; Wang, Feng; ...

2015-10-26

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome

PubMed Central

Bokulich, Nicholas A.; Blaser, Martin J.

2015-01-01

Intestinal microbial communities regulate a range of host physiological functions, from energy harvest and glucose homeostasis to immune development and regulation. Suez and colleagues (2014) recently demonstrated that artificial sweeteners alter gut microbial communities, leading to glucose intolerance in both mice and humans. PMID:25440050

MOLECULAR ANALYSIS OF MICROBIAL COMMUNITY STRUCTURES IN PRISTINE AND CONTAMINATED AQUIFERS: FIELD AND LABORATORY MICROCOSM EXPERIMENTS

EPA Science Inventory

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminted (NC) and (ii) examine alterations in micro...

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.

Soil ecosystem functioning under climate change: plant species and community effects

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

Kardol, Paul; Cregger, Melissa; Campany, Courtney E

2010-01-01

Feedbacks of terrestrial ecosystems to climate change depend on soil ecosystem dynamics. Soil ecosystems can directly and indirectly respond to climate change. For example, warming directly alters microbial communities by increasing their activity. Climate change may also alter plant community composition, thus indirectly altering the microbial communities that feed on their inputs. To better understand how climate change may directly and indirectly alter soil ecosystem functioning, we investigated old-field plant community and soil ecosystem responses to single and combined effects of elevated [CO2], warming, and water availability. Specifically, we collected soils at the plot level (plant community soils), and beneathmore » dominant plant species (plant-specific soils). We used microbial enzyme activities and soil nematodes as indicators for soil ecosystem functioning. Our study resulted in two main findings: 1) Overall, while there were some interactions, water, relative to increases in [CO2] and warming, had the largest impact on plant community composition, soil enzyme activities, and soil nematodes. Multiple climate change factors can interact to shape ecosystems, but in this case, those interactions were largely driven by changes in water availability. 2) Indirect effects of climate change, via changes in plant communities, had a significant impact on soil ecosystem functioning and this impact was not obvious when looking at plant community soils. Climate change effects on enzyme activities and soil nematode abundance and community structure strongly differed between plant community soils and plant-specific soils, but also within plant-specific soils. In sum, these results indicate that accurate assessments of climate change impacts on soil ecosystem functioning require incorporating the concurrent changes in plant function and plant community composition. Climate change-induced shifts in plant community composition will likely modify or counteract the direct impact of climate change on soil ecosystem functioning, and hence, these indirect effects should be taken into account when predicting how climate change will alter ecosystem functioning.« less

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.

PubMed

Amaral-Zettler, Linda A; Rocca, Jennifer D; Lamontagne, Michael G; Dennett, Mark R; Gast, Rebecca J

2008-12-15

Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters thatthreaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit rRNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water, and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans, and raw sewage. Correspondence analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as "sentinels" of water quality in the environment.

Contrasting effects of biochar versus manure on soil microbial communities and enzyme activities in an Aridisol.

PubMed

Elzobair, Khalid A; Stromberger, Mary E; Ippolito, James A; Lentz, Rodrick D

2016-01-01

Biochar can increase microbial activity, alter microbial community structure, and increase soil fertility in arid and semi-arid soils, but at relatively high rates that may be impractical for large-scale field studies. This contrasts with organic amendments such as manure, which can be abundant and inexpensive if locally available, and thus can be applied to fields at greater rates than biochar. In a field study comparing biochar and manure, a fast pyrolysis hardwood biochar (22.4 Mg ha(-1)), dairy manure (42 Mg ha(-1) dry wt), a combination of biochar and manure at the aforementioned rates, or no amendment (control) was applied to an Aridisol (n=3) in fall 2008. Plots were annually cropped to corn (Zea maize L.). Surface soils (0-30 cm) were sampled directly under corn plants in late June 2009 and early August 2012, and assayed for microbial community fatty acid methyl ester (FAME) profiles and six extracellular enzyme activities involved in soil C, N, and P cycling. Arbuscular mycorrhizal (AM) fungal colonization was assayed in corn roots in 2012. Biochar had no effect on microbial biomass, community structure, extracellular enzyme activities, or AM fungi root colonization of corn. In the short-term, manure amendment increased microbial biomass, altered microbial community structure, and significantly reduced the relative concentration of the AM fungal biomass in soil. Manure also reduced the percent root colonization of corn by AM fungi in the longer-term. Thus, biochar and manure had contrasting short-term effects on soil microbial communities, perhaps because of the relatively low application rate of biochar. Copyright © 2015 Elsevier Ltd. All rights reserved.

Soil Microbial Responses to Increased Moisture and Organic Resources along a Salinity Gradient in a Polar Desert

PubMed Central

Van Horn, David J.; Okie, Jordan G.; Buelow, Heather N.; Gooseff, Michael N.; Barrett, John E.

2014-01-01

Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region. PMID:24610850

Effects of Land Use Change on C-N cycling: Microbes Matter.

NASA Astrophysics Data System (ADS)

Hofmockel, K.

2012-12-01

Large swaths of the terrestrial landscape have been altered by human actions on Earth's biophysical systems, resulting in the homogenization of Earth's biota, while simultaneously increasing greenhouse gases and reactive nitrogen (N). This is especially poignant in grasslands that have been largely replaced by managed agricultural systems with substantial N inputs, or by unmanaged grasslands that are dominated by exotic species. Impacted ecosystems may be important for global C models, because they comprise a major portion of the global land area, terrestrial NPP and the world's soil C stocks. This research investigates how anthropogenic changes in plant community composition and agricultural management systems influence the composition and function of microbial communities that mediate key aspects of belowground C and N cycling and storage. Data from agroecology and grassland climate change experiments are used to illustrate how microbial responses can have important implications for large scale coupling of C and N cycles. In this study exotic plant species significantly decreased root inputs, causing shifts in microbial community composition, including both specific taxa and functional guilds of bacteria. By contrast, climate change (precipitation manipulation) caused functional responses (increased carbon and phosphorus cycling) that were not detected in the microbial community composition. Mycorrhizal fungi in managed systems were responsive to both root biomass and nitrogen inputs, significantly altering hydrolytic enzyme activity and aggregate turnover. Collectively small-scale processes can alter the ecosystem biogeochemical cycles. Together theses results suggest that linking microbial communities to coupled C-N cycles may have important implications for terrestrial C cycling feedbacks that are an integral part of the anthropocene era.

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

DOE PAGES

Xue, Kai; Xie, Jianping; Zhou, Aifen; ...

2016-05-06

Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on microbial functional gene expressions. Here, we applied functional gene array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA to assess expressed functional genes in active soil microbial communities after nine years of experimental warming in a tallgrass prairie. Our results showed that warming significantly altered the community wide gene expressions. Specifically, expressed genes for degrading more recalcitrant carbon were stimulated by warming, likely linked to the plant community shift toward moremore » C 4 species under warming and to decrease the long-term soil carbon stability. In addition, warming changed expressed genes in labile C degradation and N cycling in different directions (increase and decrease), possibly reflecting the dynamics of labile C and available N pools during sampling. However, the average abundances of expressed genes in phosphorus and sulfur cycling were all increased by warming, implying a stable trend of accelerated P and S processes which might be a mechanism to sustain higher plant growth. Furthermore, the expressed gene composition was closely related to both dynamic (e.g., soil moisture) and stable environmental attributes (e.g., C 4 leaf C or N content), indicating that RNA analyses could also capture certain stable trends in the long-term treatment. Overall, this study revealed the importance of elucidating functional gene expressions of soil microbial community in enhancing our understanding of ecosystem responses to warming.« less

Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert.

PubMed

Van Horn, David J; Okie, Jordan G; Buelow, Heather N; Gooseff, Michael N; Barrett, John E; Takacs-Vesbach, Cristina D

2014-05-01

Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region.

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

PubMed Central

Xue, Kai; Xie, Jianping; Zhou, Aifen; Liu, Feifei; Li, Dejun; Wu, Liyou; Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Luo, Yiqi; Zhou, Jizhong

2016-01-01

Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on microbial functional gene expressions. Here, we applied functional gene array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA to assess expressed functional genes in active soil microbial communities after nine years of experimental warming in a tallgrass prairie. Our results showed that warming significantly altered the community wide gene expressions. Specifically, expressed genes for degrading more recalcitrant carbon were stimulated by warming, likely linked to the plant community shift toward more C4 species under warming and to decrease the long-term soil carbon stability. In addition, warming changed expressed genes in labile C degradation and N cycling in different directions (increase and decrease), possibly reflecting the dynamics of labile C and available N pools during sampling. However, the average abundances of expressed genes in phosphorus and sulfur cycling were all increased by warming, implying a stable trend of accelerated P and S processes which might be a mechanism to sustain higher plant growth. Furthermore, the expressed gene composition was closely related to both dynamic (e.g., soil moisture) and stable environmental attributes (e.g., C4 leaf C or N content), indicating that RNA analyses could also capture certain stable trends in the long-term treatment. Overall, this study revealed the importance of elucidating functional gene expressions of soil microbial community in enhancing our understanding of ecosystem responses to warming. PMID:27199978

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

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

Xue, Kai; Xie, Jianping; Zhou, Aifen

Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on microbial functional gene expressions. Here, we applied functional gene array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA to assess expressed functional genes in active soil microbial communities after nine years of experimental warming in a tallgrass prairie. Our results showed that warming significantly altered the community wide gene expressions. Specifically, expressed genes for degrading more recalcitrant carbon were stimulated by warming, likely linked to the plant community shift toward moremore » C 4 species under warming and to decrease the long-term soil carbon stability. In addition, warming changed expressed genes in labile C degradation and N cycling in different directions (increase and decrease), possibly reflecting the dynamics of labile C and available N pools during sampling. However, the average abundances of expressed genes in phosphorus and sulfur cycling were all increased by warming, implying a stable trend of accelerated P and S processes which might be a mechanism to sustain higher plant growth. Furthermore, the expressed gene composition was closely related to both dynamic (e.g., soil moisture) and stable environmental attributes (e.g., C 4 leaf C or N content), indicating that RNA analyses could also capture certain stable trends in the long-term treatment. Overall, this study revealed the importance of elucidating functional gene expressions of soil microbial community in enhancing our understanding of ecosystem responses to warming.« less

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

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

2006-01-01

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

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

Gulliver, Djuna; Gregory, Kelvin B.; Lowry, Gregorgy V.

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 22 concentration and will create CO 2 concentration gradients that drivemore » changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2 exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2-altered microbial community may impact injectivity, permanence of stored CO 2, and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.« less

Impact of CO 2 on the Evolution of Microbial Communities Exposed to Carbon Storage Conditions, Enhanced Oil Recovery, and CO 2 Leakage

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

Gulliver, Djuna M.; Gregory, Kelvin B.; Lowry, Gregory V.

Geologic carbon storage (GCS) is a crucial part of a proposed mitigation strategy to reduce the anthropogenic carbon dioxide (CO 2) emissions to the atmosphere. During this process, CO 2 is injected as super critical carbon dioxide (SC-CO 2) in confined deep subsurface storage units, such as saline aquifers and depleted oil reservoirs. The deposition of vast amounts of CO 2 in subsurface geologic formations could unintentionally lead to CO 2 leakage into overlying freshwater aquifers. Introduction of CO 2 into these subsurface environments will greatly increase the CO 2 concentration and will create CO 2 concentration gradients that drivemore » changes in the microbial communities present. While it is expected that altered microbial communities will impact the biogeochemistry of the subsurface, there is no information available on how CO 2 gradients will impact these communities. The overarching goal of this project is to understand how CO 2 exposure will impact subsurface microbial communities at temperatures and pressures that are relevant to GCS and CO 2 leakage scenarios. To meet this goal, unfiltered, aqueous samples from a deep saline aquifer, a depleted oil reservoir, and a fresh water aquifer were exposed to varied concentrations of CO 2 at reservoir pressure and temperature. The microbial ecology of the samples was examined using molecular, DNA-based techniques. The results from these studies were also compared across the sites to determine any existing trends. Results reveal that increasing CO 2 leads to decreased DNA concentrations regardless of the site, suggesting that microbial processes will be significantly hindered or absent nearest the CO 2 injection/leakage plume where CO 2 concentrations are highest. At CO 2 exposures expected downgradient from the CO 2 plume, selected microorganisms emerged as dominant in the CO 2 exposed conditions. Results suggest that the altered microbial community was site specific and highly dependent on pH. The site-dependent results suggest a limited ability to predict the emerging dominant species for other CO 2-exposed environments. This study improves the understanding of how a subsurface microbial community may respond to conditions expected from GCS and CO 2 leakage. This is the first step for understanding how a CO 2-altered microbial community may impact injectivity, permanence of stored CO 2, and subsurface water quality. Future work with microbial communities from new subsurface sites would increase the current understanding of this project. Additionally, incorporation of metagenomic methods would increase understanding of potential microbial processes that may be prevalent in CO 2 exposed environments.« less

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities

PubMed Central

Avera, Bethany; Badgley, Brian; Barrett, John E.; Franklin, Josh; Knowlton, Katharine F.; Ray, Partha P.; Smitherman, Crystal

2017-01-01

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function. PMID:28356447

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities.

PubMed

Wepking, Carl; Avera, Bethany; Badgley, Brian; Barrett, John E; Franklin, Josh; Knowlton, Katharine F; Ray, Partha P; Smitherman, Crystal; Strickland, Michael S

2017-03-29

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function. © 2017 The Author(s).

Influence of coral and algal exudates on microbially mediated reef metabolism.

PubMed

Haas, Andreas F; Nelson, Craig E; Rohwer, Forest; Wegley-Kelly, Linda; Quistad, Steven D; Carlson, Craig A; Leichter, James J; Hatay, Mark; Smith, Jennifer E

2013-01-01

Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo'orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.

A survey of alterations in microbial community diversity in marine sediments in response to oil from the Deepwater Horizon spill: Northern Gulf of Mexico shoreline, Texas to Florida

USGS Publications Warehouse

Lisle, John T.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected from the northern Gulf of Mexico (NGOM) coast. These samples had a high probability of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon (DWH) drilling site. The hypothesis for this project was that presence of M-1 oil in coastal sediments would significantly alter the diversity within the microbial communities associated with the impacted sediments. To determine if community-level changes did or did not occur following exposure to M-1 oil, microbial community-diversity fingerprints were generated and compared. Specific sequences within the community's genomic DNA were first amplified using the polymerase chain reaction (PCR) using a primer set that provides possible resolution to the species level. A second nested PCR that was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. These nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Sediment samples with similar fingerprints were grouped and compared to oil-fingerprint data from Rosenbauer and others (2010). The microbial community fingerprints grouped closely when identifying those sites that had been impacted by M-1 oil (N=12) and/or some mixture of M-1 and other oil (N=4), based upon the oil fingerprints. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the NGOM coast. These communities contain microbes capable of degrading oil and related hydrocarbons, making this information relevant to response and recovery of the NGOM from the DWH incident.

Long-Term Nitrogen Amendment Alters the Diversity and Assemblage of Soil Bacterial Communities in Tallgrass Prairie

PubMed Central

Todd, Timothy C.; Blair, John M.; Herman, Michael A.

2013-01-01

Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs) experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion). The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have important implications for both managed and natural grassland ecosystems. PMID:23840782

A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome.

PubMed

Bokulich, Nicholas A; Blaser, Martin J

2014-11-04

Intestinal microbial communities regulate a range of host physiological functions, from energy harvest and glucose homeostasis to immune development and regulation. Suez et al. (2014) recently demonstrated that artificial sweeteners alter gut microbial communities, leading to glucose intolerance in both mice and humans. Copyright © 2014 Elsevier Inc. All rights reserved.

Microbial Community Response to Warming and Correlations to Organic Carbon Degradation in an Arctic Tundra Soil

NASA Astrophysics Data System (ADS)

Yang, Z.; Yang, S.; Zhou, J.; Wullschleger, S. D.; Graham, D. E.; Yang, Y.; Gu, B.

2016-12-01

Climate warming increases microbial activity and thus decomposition of soil organic carbon (SOC) stored in Arctic tundra, but changes in microbial community and its correlations to SOC decomposition are poorly understood. Using a microbial functional gene array (GeoChip 5.0), we examined the microbial functional community structure changes with temperature (-2 and +8 °C) in an anoxic incubation experiment with a high-centered polygon trough soil from Barrow, Alaska. Through a 122-day incubation, we show that functional community structure was significantly altered (P < 0.05) by 8 °C warming, with functional diversity decreasing in response to warming and rapid degradation of the labile soil organic substrates. In contrast, microbial community structure was largely unchanged by -2 °C incubation. In the organic layer soil, gene abundances associated with fermentation, methanogenesis, and iron reduction all decreased significantly (P < 0.05) following the incubation at 8 °C. These observations corroborate strongly with decreased methane and reducing sugar production rates and iron reduction during the incubation. These results demonstrate a rapid and sensitive microbial response to increasing soil temperature, and suggest important roles of microbial communities in moderating SOC degradation and iron cycling in warming Arctic tundra.

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. © 2013 John Wiley & Sons Ltd.

Microbial Community Shifts due to Hydrofracking: Observations from Field-Scale Observations and Laboratory-Scale Incubations

NASA Astrophysics Data System (ADS)

Mouser, P. J.; Ansari, M.; Hartsock, A.; Lui, S.; Lenhart, J.

2012-12-01

The use of fluids containing chemicals and variable water sources during the hydrofracking of unconventional shale is the source of considerable controversy due to perceived risks from altered subsurface biogeochemistry and the potential for contaminating potable water supplies. Rapid shifts in subsurface biogeochemistry are often driven by available macronutrients combined with the abundance and metabolic condition of the subsurface microbiota. While the depth that fracturing occurs in the Marcellus formation is reasonably deep to pose little risk to groundwater supplies, no published studies have systematically characterized the indigenous microbial population and how this community is altered through variable fluid management practices (e.g., chemical composition, source water makeup). In addition, limited information is available on how shallower microbial communities and geochemical conditions might be affected through the accidental release of these fluids to groundwater aquifers. Our measurements indicate field-applied and laboratory-generated fracking fluids contain levels of organic carbon greater than 300 mg/l and nitrogen concentrations greater than 80 mg/l that may differentially stimulate microbial growth in subsurface formations. In contrast to certain inorganic constituents (e.g., chloride) which increase in concentration through the flowback period; dissolved organic carbon levels decrease with time after the fracturing process through multiple attenuation processes (dilution, sorption, microbial utilization). Pyrosequencing data of the 16S rRNA gene indicate a shift from a more diverse source water microbial community to a less diverse community typical of a brine formation as time after fracturing increases. The introduction of varying percentages of a laboratory-generated fracking fluid to microcosm bottles containing groundwater and aquifer media stimulated biogeochemical changes similar to the introduction of landfill leachate, another wastewater containing elevated carbon, nitrogen, and complex organic constituents (e.g., decreased redox conditions, stepwise utilization of available terminal electron acceptors, enriched Fe(II) and sulfide concentrations). These research findings are important for understanding how fluids used during shale energy development may alter in situ microbial communities and provide insight into processes that attenuate the migration of these fluids in shallow aquifers and deep shale formations.

Effects of Bromus tectorum invasion on microbial carbon and nitrogen cycling in two adjacent undisturbed arid grassland communities

USGS Publications Warehouse

Schaeffer, Sean M.; Ziegler, Susan E.; Belnap, Jayne; Evans, R.D.

2012-01-01

Soil nitrogen (N) is an important component in maintaining ecosystem stability, and the introduction of non-native plants can alter N cycling by changing litter quality and quantity, nutrient uptake patterns, and soil food webs. Our goal was to determine the effects of Bromus tectorum (C3) invasion on soil microbial N cycling in adjacent non-invaded and invaded C3 and C4 native arid grasslands. We monitored resin-extractable N, plant and soil δ13C and δ15N, gross rates of inorganic N mineralization and consumption, and the quantity and isotopic composition of microbial phospholipid biomarkers. In invaded C3 communities, labile soil organic N and gross and net rates of soil N transformations increased, indicating an increase in overall microbial N cycling. In invaded C4 communities labile soil N stayed constant, but gross N flux rates increased. The δ13C of phospholipid biomarkers in invaded C4 communities showed that some portion of the soil bacterial population preferentially decomposed invader C3-derived litter over that from the native C4 species. Invasion in C4 grasslands also significantly decreased the proportion of fungal to bacterial phospholipid biomarkers. Different processes are occurring in response to B. tectorum invasion in each of these two native grasslands that: 1) alter the size of soil N pools, and/or 2) the activity of the microbial community. Both processes provide mechanisms for altering long-term N dynamics in these ecosystems and highlight how multiple mechanisms can lead to similar effects on ecosystem function, which may be important for the construction of future biogeochemical process models.

Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut.

PubMed

Yin, Jinbao; Zhang, Xu-Xiang; Wu, Bing; Xian, Qiming

2015-12-01

Antibiotics have been widely used for disease prevention and treatment of the human and animals, and for growth promotion in animal husbandry. Antibiotics can disturb the intestinal microbial community, which play a fundamental role in animals' health. Misuse or overuse of antibiotics can result in increase and spread of microbial antibiotic resistance, threatening human health and ecological safety. In this study, we used Illumina Hiseq sequencing, (1)H nuclear magnetic resonance spectroscopy and metagenomics approaches to investigate intestinal microbial community shift and antibiotic resistance alteration of the mice drinking the water containing tetracycline hydrochloride (TET). Two-week TET administration caused reduction of gut microbial diversity (from 194 to 89 genera), increase in Firmicutes abundance (from 24.9 to 39.8%) and decrease in Bacteroidetes abundance (from 69.8 to 51.2%). Metagenomic analysis showed that TET treatment affected the intestinal microbial functions of carbohydrate, ribosomal, cell wall/membrane/envelope and signal transduction, which is evidenced by the alteration in the metabolites of mouse serum. Meanwhile, in the mouse intestinal microbiota, TET treatment enhanced the abundance of antibiotic resistance genes (ARGs) (from 307.3 to 1492.7 ppm), plasmids (from 425.4 to 3235.1 ppm) and integrons (from 0.8 to 179.6 ppm) in mouse gut. Our results indicated that TET administration can disturb gut microbial community and physiological metabolism of mice, and increase the opportunity of ARGs and mobile genetic elements entering into the environment with feces discharge.

Changes in microbial community structure in the wake of Hurricanes Katrina and Rita

PubMed Central

Amaral-Zettler, Linda A.; Rocca, Jennifer D.; LaMontagne, Michael G.; Dennett, Mark R.; Gast, Rebecca J.

2009-01-01

Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters that threaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit ribosomal RNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans and raw sewage. Correspondence Analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as “sentinels” of water quality in the environment. PMID:19174873

Microbial communities and greenhouse gas emissions associated with the biodegradation of specified risk material in compost

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

Xu, Shanwei; Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1; Reuter, Tim

Highlights: ► Addition of feathers altered bacterial and fungal communities in compost. ► Microbial communities degrading SRM and compost matrix were distinct. ► Addition of feathers may enrich for microbial communities that degrade SRM. ► Inclusion of feather in compost increased both CH{sub 4} and N{sub 2}O emissions from compost. ► Density of methanogens and methanotrophs were weakly associated with CH{sub 4} emissions. - Abstract: Provided that infectious prions (PrP{sup Sc}) are inactivated, composting of specified risk material (SRM) may be a viable alternative to rendering and landfilling. In this study, bacterial and fungal communities as well as greenhouse gasmore » emissions associated with the degradation of SRM were examined in laboratory composters over two 14 day composting cycles. Chicken feathers were mixed into compost to enrich for microbial communities involved in the degradation of keratin and other recalcitrant proteins such as prions. Feathers altered the composition of bacterial and fungal communities primarily during the first cycle. The bacterial genera Saccharomonospora, Thermobifida, Thermoactinomycetaceae, Thiohalospira, Pseudomonas, Actinomadura, and Enterobacter, and the fungal genera Dothideomycetes, Cladosporium, Chaetomium, and Trichaptum were identified as candidates involved in SRM degradation. Feathers increased (P < 0.05) headspace concentrations of CH{sub 4} primarily during the early stages of the first cycle and N{sub 2}O during the second. Although inclusion of feathers in compost increases greenhouse gas emissions, it may promote the establishment of microbial communities that are more adept at degrading SRM and recalcitrant proteins such as keratin and PrP{sup Sc}.« less

Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes.

PubMed

Zhang, Cui-Jing; Delgado-Baquerizo, Manuel; Drake, John E; Reich, Peter B; Tjoelker, Mark G; Tissue, David T; Wang, Jun-Tao; He, Ji-Zheng; Singh, Brajesh K

2018-04-01

Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Stone-isolated carbonatogenic bacteria as inoculants in bioconsolidation treatments for historical limestone.

PubMed

Jroundi, Fadwa; Gómez-Suaga, Patricia; Jimenez-Lopez, Concepción; González-Muñoz, Maria Teresa; Fernandez-Vivas, Maria Antonia

2012-05-15

Stone consolidation treatments that use bacterial biomineralization are mainly based on two strategies: (1) the inoculation of a bacterial culture with proven carbonatogenic ability and/or (2) the application of a culture medium capable of activating those bacteria able to induce the formation of calcium carbonate, from amongst the bacterial community of the stone. While the second strategy has been demonstrated to be effective and, unlike first strategy, it does not introduce any exogenous microorganism into the stone, problems may arise when the bacterial community of the stone is altered, for instance by the use of biocides in the cleaning process. In this study we isolate bacteria that belong to the natural microbial community of the stone and which have proven biomineralization capabilities, with the aim of preparing an inoculum that may be used in stone consolidation treatments wherein the natural community of those stones is altered. With this aim, outdoor experiments were undertaken to activate and isolate bacteria that display high biomineralization capacity from altered calcarenite stone. Most of the bacteria precipitated calcium carbonate in the form of calcite. The selected bacteria were phylogenetically affiliated with members of Actinobacteria, Gamma-proteobacteria and Firmicutes. Furthermore, the capability of these selected carbonatogenic bacteria to consolidate altered calcarenite stone slabs was studied in in vitro experiments, both in the presence and the absence of Myxococcus xanthus, as a potential reinforcement for the bacterial biomineralization. Herein, Acinetobacter species, belonging to the microbial community of the stone, are proposed as powerful carbonatogenic bacteria that, inoculated under appropriate conditions, may be used as inoculum for calcareous stone conservation/consolidation in restoration interventions where the microbial community of the stone is altered. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents.

PubMed

Ochoa-Hueso, Raúl; Collins, Scott L; Delgado-Baquerizo, Manuel; Hamonts, Kelly; Pockman, William T; Sinsabaugh, Robert L; Smith, Melinda D; Knapp, Alan K; Power, Sally A

2018-03-05

The effects of short-term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness, and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought-induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant-microbial interactions and a greater incidence of certain soil-borne diseases. © 2018 John Wiley & Sons Ltd.

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada.

PubMed

Ruuskanen, Matti O; St Pierre, Kyra A; St Louis, Vincent L; Aris-Brosou, Stéphane; Poulain, Alexandre J

2018-01-01

The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.

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

PubMed

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

2017-10-01

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

Implications of altered rainfall and exotic plants on soil microbial communities and carbon biomass

NASA Astrophysics Data System (ADS)

Castro, S.; Lipson, D.; Cleland, E. E.

2016-12-01

Climate and exotic plant disturbances are among the most significant threats to Mediterranean-type ecosystems, compromising their renowned biodiversity and role in the global carbon cycle. Predicted shifts in rainfall patterns have become a particular concern, especially when interactions with other stressors and effects on biogeochemical processes remain poorly understood. To understand the impacts of altered rainfall on belowground dynamics as well as the role of inter- and intra-annual variation and plant community composition, we monitored soil microbial communities under native and exotic plant dominated plots with rainfall manipulation treatments in a semi-arid Mediterranean-type ecosystem. We measured microbial biomass, respiration rates, and community structure across treatments and vegetation types. Soil moisture and dissolved organic carbon were also measured to characterize abiotic soil properties. The soil moisture gradient established by the rainfall treatments had a positive correlation with microbial biomass carbon under native- and exotic-dominated plots but had no effect on respiration rates. A significant reduction in microbial biomass under exotic plants was found in 2013 but not in 2014 and 2015. Substrate-induced respiration values were higher in the exotic-dominated plots during the spring seasons, resulting in a significant interaction between plant community type and season. Bacterial communities showed little variation except in the Proteobacteria phyla, which was lower in exotic plants-dominated plots. Dissolved organic carbon was significantly reduced in exotic-dominated plots by approximately 26% based on average values of all plots throughout. Our results illustrate that rainfall quantity and exotic plants can cause changes in microbial biomass, community composition and respiration rates jeopardizing soil carbon storage. They also reinforce the importance of temporal variability and the need for repeated sampling to correctly interpret environmental changes in semi-arid ecosystems. We conclude that to improve predictions of the implications of global stressors on biogeochemical cycles in semi-arid ecosystems, there is a need to incorporate microbial data with the understanding that it is highly dependent on temporal dynamics and plant community.

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession.

PubMed

Knelman, Joseph E; Graham, Emily B; Prevéy, Janet S; Robeson, Michael S; Kelly, Patrick; Hood, Eran; Schmidt, Steve K

2018-01-01

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

PubMed Central

Knelman, Joseph E.; Graham, Emily B.; Prevéy, Janet S.; Robeson, Michael S.; Kelly, Patrick; Hood, Eran; Schmidt, Steve K.

2018-01-01

Past research demonstrating the importance plant–microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant–microbe interactions with late-successional plants and interspecific plant interactions more generally. PMID:29467741

Reintroduction of locally extinct vertebrates impacts arid soil fungal communities.

PubMed

Clarke, Laurence J; Weyrich, Laura S; Cooper, Alan

2015-06-01

Introduced species have contributed to extinction of native vertebrates in many parts of the world. Changes to vertebrate assemblages are also likely to alter microbial communities through coextinction of some taxa and the introduction of others. Many attempts to restore degraded habitats involve removal of exotic vertebrates (livestock and feral animals) and reintroduction of locally extinct species, but the impact of such reintroductions on microbial communities is largely unknown. We used high-throughput DNA sequencing of the fungal internal transcribed spacer I (ITS1) region to examine whether replacing exotic vertebrates with reintroduced native vertebrates led to changes in soil fungal communities at a reserve in arid central Australia. Soil fungal diversity was significantly different between dune and swale (interdune) habitats. Fungal communities also differed significantly between sites with exotic or reintroduced native vertebrates after controlling for the effect of habitat. Several fungal operational taxonomic units (OTUs) found exclusively inside the reserve were present in scats from reintroduced native vertebrates, providing a direct link between the vertebrate assemblage and soil microbial communities. Our results show that changes to vertebrate assemblages through local extinctions and the invasion of exotic species can alter soil fungal communities. If local extinction of one or several species results in the coextinction of microbial taxa, the full complement of ecological interactions may never be restored. © 2015 John Wiley & Sons Ltd.

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experiments

PubMed Central

Shi, Y.; Zwolinski, M. D.; Schreiber, M. E.; Bahr, J. M.; Sewell, G. W.; Hickey, W. J.

1999-01-01

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly Bacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the Bacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems. PMID:10224013

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

NASA Astrophysics Data System (ADS)

Wood, J. L.; Zhang, C.; Mathews, E. R.; Tang, C.; Franks, A. E.

2016-11-01

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

PubMed Central

Wood, J. L.; Zhang, C.; Mathews, E. R.; Tang, C.; Franks, A. E.

2016-01-01

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization. PMID:27805014

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover.

PubMed

Liang, Yuting; Jiang, Yuji; Wang, Feng; Wen, Chongqing; Deng, Ye; Xue, Kai; Qin, Yujia; Yang, Yunfeng; Wu, Liyou; Zhou, Jizhong; Sun, Bo

2015-12-01

To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time-decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P<0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P<0.001) and highest in the southward transplant (w=0.094, P<0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity.

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau.

PubMed

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Zhou, Huakun; Ganjurjav, Hasbagan; Wang, Xuexia

2016-08-15

Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, <10% variations of microbial diversity was explained by soil properties; and the soil microbial communities among different treatments were similar. The soil microbial community in the cultivated grassland was varied from it in native grasslands. Over 50% variations of soil microbial communities among different treatments were explained by soil nutrients and moisture in each grassland type. Our results suggest that climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau.

PubMed

Meyerhof, Matthew S; Wilson, Jesse M; Dawson, Michael N; Michael Beman, J

2016-12-01

Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

PubMed

Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

2016-05-01

The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples.

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817

Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities.

PubMed

Strickland, Michael S; McCulley, Rebecca L; Nelson, Jim A; Bradford, Mark A

2015-01-01

Inputs of low molecular weight carbon (LMW-C) to soil - primarily via root exudates- are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands) were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ∼3% of the variation observed in function. In comparison, land cover and site explained ∼46 and ∼41% of the variation, respectively. This suggests that exudate composition has little influence on function compared to site/land cover specific factors. Supporting the finding that exudate effects were minor, we found that an absence of LMW-C elicited the greatest difference in function compared to those treatments receiving any LMW-C. Additionally, exudate treatments did not alter microbial community composition and observable differences were instead due to land cover. These results confirm the strong effects of land cover/site legacies on soil microbial communities. In contrast, short-term changes in exudate composition, at meaningful concentrations, may have little impact on microbial function and composition.

Shift in the microbial community composition of surface water and sediment along an urban river.

PubMed

Wang, Lan; Zhang, Jing; Li, Huilin; Yang, Hong; Peng, Chao; Peng, Zhengsong; Lu, Lu

2018-06-15

Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P < 0.05). The bacterial diversity in sediments was significantly higher than their corresponding water samples. Additionally, archaeal communities showed obvious spatial variability in the surface water. The construction of the hydropower station resulted in increased Cyanobacteria abundance in the upstream (32.2%) compared to its downstream (10.3%). Several taxonomic groups of potential fecal indicator bacteria, like Flavobacteria and Bacteroidia, showed an increasing trend in the urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P < 0.01) and NO 3 - (P < 0.05), and metals (Zn, Fe) (P < 0.05) were the most significant drivers determining the microbial community composition in the urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations. Copyright © 2018 Elsevier B.V. All rights reserved.

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm.

PubMed

Xi, Xiuping; Wang, Min; Chen, Yongshan; Yu, Shen; Hong, Youwei; Ma, Jun; Wu, Qian; Lin, Qiaoyin; Xu, Xiangrong

2015-06-15

Residual antibiotics from aquacultural farming may alter microbial community structure in aquatic environments in ways that may adversely or positively impact microbially-mediated ecological functions. This study investigated 26 ponds (26 composited samples) used to produce fish, razor clam and shrimp (farming and drying) and 2 channels (10 samples) in a saltwater aquacultural farm in southern China to characterize microbial community structure (represented by phospholipid fatty acids) in surface sediments (0-10 cm) with long-term exposure to residual antibiotics. 11 out of 14 widely-used antibiotics were quantifiable at μg kg(-1) levels in sediments but their concentrations did not statistically differ among ponds and channels, except norfloxacin in drying shrimp ponds and thiamphenicol in razor clam ponds. Concentrations of protozoan PLFAs were significantly increased in sediments from razor clam ponds while other microbial groups were similar among ponds and channels. Both canonical-correlation and stepwise-multiple-regression analyses on microbial community and residual antibiotics suggested that roxithromycin residuals were significantly related to shifts in microbial community structure in sediments. This study provided field evidence that multiple residual antibiotics at low environmental levels from aquacultural farming do not produce fundamental shifts in microbial community structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Expansion of Phragmites australis alters methane dynamics and methanogen, methanotroph, and sulfate reducing bacteria communities in tidal marsh in Korea

NASA Astrophysics Data System (ADS)

Kim, J.; Lee, J.; Kim, H.; Gauhar, M.; Kang, H.

2016-12-01

Plant invasion is known to change substantially methane dynamics in tidal marshes. However, the exact mechanisms related to methane dynamics change due to plant invasion have not been fully understood. In Suncheon Bay, South Korea, Phragmites australis has invaded the habitat of native species, Suaeda japonica, and becomes dominant vegetation in this area. We measured methane fluxes, soil biogeochemistry, and microbial communities from both vegetation sites throughout a growing season and conducted a chronosequence analysis in order to illustrate the effect of plant invasion on methane dynamics and microbial communities. For analyzing microbial communities, we collected 1m intact soil cores and conducted functional gene-targeted real-time qPCR, T-RFLP, and PLFA. P. australis invasion significantly increased methane emission in a summer season, accompanied by greater dissolved organic carbon and soil water content. Methanogen, methanotroph, and sulfate reducing bacterial communities were gradually changed along with the invasion periods. In particular, abundances ratio of mcrA/pmoA and mcrA/dsrA had a positive correlation with methane emission, which indicates that P. australis invasion reduces methane oxidation by methanotroph, and competitive inhibition between methanogen and sulfate reducing bacteria. In conclusion, P. australis invasion on S. japonica significantly increased methane emission in tidal marsh by altering the microbial communities in a way that C decomposition would be dominated by methanogenesis.

The fate of antibiotic resistance genes and their potential hosts during bio-electrochemical treatment of high-salinity pharmaceutical wastewater.

PubMed

Guo, Ning; Wang, Yunkun; Tong, Tiezheng; Wang, Shuguang

2018-04-15

Pharmaceutical wastewaters containing antibiotics and high salinity can damage traditional biological treatment and result in the proliferation of antibiotic resistance genes (ARGs). Bioelectrochemical system (BES) is a promising approach for treating pharmaceutical wastewater. However, the fate of ARGs in BES and their correlations with microbial communities and horizontal genes transfer are unknown. In this study, we investigated the response of ARGs to bio-electrochemical treatment of chloramphenicol wastewater and their potential hosts under different salinities. Three ARGs encoding efflux pump (cmlA, floR and tetC), one class 1 integron integrase encoding gene (intI1), and sul1 gene (associate with intI1) were analyzed. Correlation analysis between microbial community and ARGs revealed that the abundances of potential hosts of ARGs were strongly affected by salinity, which further determined the alteration in ARGs abundances under different salinities. There were no significant correlations between ARGs and intI1, indicating that horizontal gene transfer was not related to the important changes in ARGs. Moreover, the chloramphenicol removal efficiency was enhanced under a moderate salinity, attributed to the altered microbial community driven by salinity. Therefore, microbial community shift is the major factor for the changes of ARGs and chloramphenicol removal efficiency in BES under different salinities. This study provides new insights on the mechanisms underlying the alteration of ARGs in BES treating high-salinity pharmaceutical wastewater. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Microbial community composition and function beneath temperate trees exposed to elevated atmospheric carbon dioxide and ozone

Treesearch

Rebecca L. Phillips; Donald R. Zak; William E. Holmes; David C. White

2002-01-01

We hypothesized that changes in plant growth resulting from atmospheric CO2 and O3 enrichment would alter the flow of C through soil food webs and that this effect would vary with tree species. To test this idea, we traced the course of C through the soil microbial community using soils from the free-air CO2...

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome

DOE PAGES

Daleo, Pedro; Alberti, Juan; Jumpponen, Ari; ...

2018-04-12

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a nullmore » model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. As a result, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization.« less

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome.

PubMed

Daleo, Pedro; Alberti, Juan; Jumpponen, Ari; Veach, Allison; Ialonardi, Florencia; Iribarne, Oscar; Silliman, Brian

2018-06-01

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a null model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. Furthermore, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization. © 2018 by the Ecological Society of America.

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome

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

Daleo, Pedro; Alberti, Juan; Jumpponen, Ari

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a nullmore » model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. As a result, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization.« less

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

Soil Metabolome and Metabolic Fate: Microbial Insights into Freshwater Tidal Wetland Redox Biogeochemistry

NASA Astrophysics Data System (ADS)

Roy Chowdhury, T.; Bramer, L.; Hoyt, D. W.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.; Bailey, V. L.

2017-12-01

Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands will experience the immediate consequence of climate change as shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the structure and function of the soil microbial populations that in turn will alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of shifting hydrology on the soil microbiome and the role of antecedent moisture condition on redox active microbial processes in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. Our objectives were to characterize changes in the soil microbial community composition in response to soil moisture legacy effects, and to elucidate relationships between community response, geochemical signatures and metabolite profiles in this soil. The 16S rRNA gene sequencing showed significant decreases in bacterial abundance capable of anaerobic metabolism in response to drying, but quickly recovered to the antecedent moisture condition, as observed by redox processes. Metabolomics and biogeochemical process rates generated evidence for moisture-driven redox conditions as principal controls on the community and metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of these pools in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction in compared to methanogenesis. Our results show that anoxic conditions impact microbial communities in both permanently and temporarily saturated conditions and that rapid change in hydrology can increase substrate availability for both aerobic and anaerobic decomposition processes, including methanogenesis.

Do invasive plant species alter soil health?

USDA-ARS?s Scientific Manuscript database

Invasive species may alter soil characteristics or interact with the soil microbial community to yield a competitive advantage. Our objectives were to determine: if invasive plant species alter soil properties important to soil health; and the long-term effects of invasive plant species on soil pro...

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover

PubMed Central

Liang, Yuting; Jiang, Yuji; Wang, Feng; Wen, Chongqing; Deng, Ye; Xue, Kai; Qin, Yujia; Yang, Yunfeng; Wu, Liyou; Zhou, Jizhong; Sun, Bo

2015-01-01

To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time–decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P<0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P<0.001) and highest in the southward transplant (w=0.094, P<0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity. PMID:25989371

Alteration of Rumen Bacteria and Protozoa Through Grazing Regime as a Tool to Enhance the Bioactive Fatty Acid Content of Bovine Milk

PubMed Central

Bainbridge, Melissa L.; Saldinger, Laurel K.; Barlow, John W.; Alvez, Juan P.; Roman, Joe; Kraft, Jana

2018-01-01

Rumen microorganisms are the origin of many bioactive fatty acids (FA) found in ruminant-derived food products. Differences in plant leaf anatomy and chemical composition between cool- and warm-season pastures may alter rumen microorganisms, potentially enhancing the quantity/profile of bioactive FA available for incorporation into milk. The objective of this study was to identify rumen bacteria and protozoa and their cellular FA when cows grazed a warm-season annual, pearl millet (PM), in comparison to a diverse cool-season pasture (CSP). Individual rumen digesta samples were obtained from five Holstein cows in a repeated measures design with 28-day periods. The treatment sequence was PM, CSP, then PM. Microbial DNA was extracted from rumen digesta and sequence reads were produced with Illumina MiSeq. Fatty acids (FA) were identified in rumen bacteria and protozoa using gas-liquid chromatography/mass spectroscopy. Microbial communities shifted in response to grazing regime. Bacteria of the phylum Bacteroidetes were more abundant during PM than CSP (P < 0.05), while protozoa of the genus Eudiplodinium were more abundant during CSP than PM (P < 0.05). Microbial cellular FA profiles differed between treatments. Bacteria and protozoa from cows grazing CSP contained more n-3 FA (P < 0.001) and vaccenic acid (P < 0.01), but lower proportions of branched-chain FA (P < 0.05). Microbial FA correlated with microbial taxa and levels of vaccenic acid, rumenic acid, and α-linolenic acid in milk. In conclusion, grazing regime can potentially be used to alter microbial communities shifting the FA profile of microbial cells, and subsequently, alter the milk FA profile. PMID:29867815

Alteration of Rumen Bacteria and Protozoa Through Grazing Regime as a Tool to Enhance the Bioactive Fatty Acid Content of Bovine Milk.

PubMed

Bainbridge, Melissa L; Saldinger, Laurel K; Barlow, John W; Alvez, Juan P; Roman, Joe; Kraft, Jana

2018-01-01

Rumen microorganisms are the origin of many bioactive fatty acids (FA) found in ruminant-derived food products. Differences in plant leaf anatomy and chemical composition between cool- and warm-season pastures may alter rumen microorganisms, potentially enhancing the quantity/profile of bioactive FA available for incorporation into milk. The objective of this study was to identify rumen bacteria and protozoa and their cellular FA when cows grazed a warm-season annual, pearl millet (PM), in comparison to a diverse cool-season pasture (CSP). Individual rumen digesta samples were obtained from five Holstein cows in a repeated measures design with 28-day periods. The treatment sequence was PM, CSP, then PM. Microbial DNA was extracted from rumen digesta and sequence reads were produced with Illumina MiSeq. Fatty acids (FA) were identified in rumen bacteria and protozoa using gas-liquid chromatography/mass spectroscopy. Microbial communities shifted in response to grazing regime. Bacteria of the phylum Bacteroidetes were more abundant during PM than CSP ( P < 0.05), while protozoa of the genus Eudiplodinium were more abundant during CSP than PM ( P < 0.05). Microbial cellular FA profiles differed between treatments. Bacteria and protozoa from cows grazing CSP contained more n-3 FA ( P < 0.001) and vaccenic acid ( P < 0.01), but lower proportions of branched-chain FA ( P < 0.05). Microbial FA correlated with microbial taxa and levels of vaccenic acid, rumenic acid, and α-linolenic acid in milk. In conclusion, grazing regime can potentially be used to alter microbial communities shifting the FA profile of microbial cells, and subsequently, alter the milk FA profile.

Soil microbial community response to precipitation change in a semi-arid ecosystem

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

Cregger, Melissa; Schadt, Christopher Warren; McDowell, Nathan

2012-01-01

Microbial communities regulate many belowground carbon cycling processes; thus, the impact of climate change on the struc- ture and function of soil microbial communities could, in turn, impact the release or storage of carbon in soils. Here we used a large-scale precipitation manipulation ( 18%, 50%, or ambient) in a pi on-juniper woodland (Pinus edulis-Juniperus mono- sperma) to investigate how changes in precipitation amounts altered soil microbial communities as well as what role seasonal variation in rainfall and plant composition played in the microbial community response. Seasonal variability in precipitation had a larger role in determining the composition of soilmore » microbial communities in 2008 than the direct effect of the experimental precipitation treatments. Bacterial and fungal communities in the dry, relatively moisture-limited premonsoon season were compositionally distinct from communities in the monsoon season, when soil moisture levels and periodicity varied more widely across treatments. Fungal abundance in the drought plots during the dry premonsoon season was particularly low and was 4.7 times greater upon soil wet-up in the monsoon season, suggesting that soil fungi were water limited in the driest plots, which may result in a decrease in fungal degradation of carbon substrates. Additionally, we found that both bacterial and fungal communities beneath pi on pine and juniper were distinct, suggesting that microbial functions beneath these trees are different. We conclude that predicting the response of microbial communities to climate change is highly dependent on seasonal dynam- ics, background climatic variability, and the composition of the associated aboveground community.« less

Molecular analysis of microbial community structures in pristine and contaminated aquifers--Field and laboratory microcosm experiments

USGS Publications Warehouse

Shi, Y.; Zwolinski, M.D.; Schreiber, M.E.; Bahr, J.M.; Sewell, G.W.; Hickey, W.J.

1999-01-01

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experimentsvar callbackToken='531E8ACDB6C8511'; var subCode='asmjournal_sub'; var OAS_sitepage = 'aem.asm.org'; This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantlyBacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of theBacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems.

Carbon and nitrogen inputs affect soil microbial community structure and function

NASA Astrophysics Data System (ADS)

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

2016-12-01

Climate change has been projected to increase energy and nutrient inputs to soils, affecting soil organic matter (SOM) decomposition (priming effect) and microbial communities. However, many important questions remain: how do labile C and/or N inputs affect priming and microbial communities? What is the relationship between them? To address these questions, we applied N (NH4NO3 ; 100 µg N g-1 wk-1), C (13C glucose; 1000 µg C g-1 wk-1), C+N to four different soils for five weeks. We found: 1) N showed no effect, whereas C induced the greatest priming, and C+N had significantly lower priming than C. 2) C and C+N additions increased the relative abundance of actinobacteria, proteobacteria, and firmicutes, but reduced relative abundance of acidobacteria, chloroflexi, verrucomicrobia, planctomycetes, and gemmatimonadetes. 3) Actinobacteria and proteobacteria increased relative abundance over time, but most others decreased over time. 4) substrate additions (N, C, C+N) significantly reduced microbial alpha diversity, which also decreased over time. 5) For beta diversity, C and C+N formed significantly different communities compare to the control and N treatments. Overtime, microbial community structure significantly altered. Four soils have drastically different community structures. These results indicate amounts of substrate C were determinant factors in modulating the rate of SOM decomposition and microbial communities. Variable responses of different microbial communities to labile C and N inputs indicate that complex relationships between priming and microbial functions. In general, we demonstrate that energy inputs can quickly accelerate SOM decomposition whereas extra N input can slow this process, though both had similar microbial community responses.

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

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

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

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

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats

PubMed Central

Mika, Agnieszka; Van Treuren, Will; González, Antonio; Herrera, Jonathan J.; Knight, Rob; Fleshner, Monika

2015-01-01

The mammalian intestine harbors a complex microbial ecosystem that influences many aspects of host physiology. Exposure to specific microbes early in development affects host metabolism, immune function, and behavior across the lifespan. Just as the physiology of the developing organism undergoes a period of plasticity, the developing microbial ecosystem is characterized by instability and may also be more sensitive to change. Early life thus presents a window of opportunity for manipulations that produce adaptive changes in microbial composition. Recent insights have revealed that increasing physical activity can increase the abundance of beneficial microbial species. We therefore investigated whether six weeks of wheel running initiated in the juvenile period (postnatal day 24) would produce more robust and stable changes in microbial communities versus exercise initiated in adulthood (postnatal day 70) in male F344 rats. 16S rRNA gene sequencing was used to characterize the microbial composition of juvenile versus adult runners and their sedentary counterparts across multiple time points during exercise and following exercise cessation. Alpha diversity measures revealed that the microbial communities of young runners were less even and diverse, a community structure that reflects volatility and malleability. Juvenile onset exercise altered several phyla and, notably, increased Bacteroidetes and decreased Firmicutes, a configuration associated with leanness. At the genus level of taxonomy, exercise altered more genera in juveniles than in the adults and produced patterns associated with adaptive metabolic consequences. Given the potential of these changes to contribute to a lean phenotype, we examined body composition in juvenile versus adult runners. Interestingly, exercise produced persistent increases in lean body mass in juvenile but not adult runners. Taken together, these results indicate that the impact of exercise on gut microbiota composition as well as body composition may depend on the developmental stage during which exercise is initiated. PMID:26016739

The skin microbiome: Associations between altered microbial communities and disease.

PubMed

Weyrich, Laura S; Dixit, Shreya; Farrer, Andrew G; Cooper, Alan J; Cooper, Alan J

2015-11-01

A single square centimetre of the human skin can contain up to one billion microorganisms. These diverse communities of bacteria, fungi, mites and viruses can provide protection against disease, but can also exacerbate skin lesions, promote disease and delay wound healing. This review addresses the current knowledge surrounding the healthy skin microbiome and examines how different alterations to the skin microbial communities can contribute to disease. Current methodologies are considered, changes in microbial diversity and colonisation by specific microorganisms are discussed in the context of atopic dermatitis, psoriasis, acne vulgaris and chronic wounds. The recent impact of modern Westernised lifestyles on the human skin microbiome is also examined, as well as the potential benefits and pitfalls of novel therapeutic strategies. Further analysis of the human skin microbiome, and its interactions with the host immune system and other commensal microorganisms, will undoubtedly elucidate molecular mechanisms for disease and reveal gateways for novel therapeutic treatment strategies. © 2015 The Australasian College of Dermatologists.

Deoxygenation alters bacterial diversity and community composition in the ocean's largest oxygen minimum zone.

PubMed

Beman, J Michael; Carolan, Molly T

2013-01-01

Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans' largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

NASA Astrophysics Data System (ADS)

Beman, J. Michael; Carolan, Molly T.

2013-10-01

Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans’ largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-06-03

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

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

The role of macrobiota in structuring microbial communities along rocky shores

DOE PAGES

Pfister, Catherine A.; Gilbert, Jack A.; Gibbons, Sean M.

2014-10-16

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of themore » gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.« less

The role of macrobiota in structuring microbial communities along rocky shores

PubMed Central

Gilbert, Jack A.; Gibbons, Sean M.

2014-01-01

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota. PMID:25337459

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

PubMed

Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

2012-08-01

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

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

PubMed

He, Ruoyang; Yang, Kaijun; Li, Zhijie; Schädler, Martin; Yang, Wanqin; Wu, Fuzhong; Tan, Bo; Zhang, Li; Xu, Zhenfeng

2017-01-01

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

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.

PubMed

Dassen, Sigrid; Cortois, Roeland; Martens, Henk; de Hollander, Mattias; Kowalchuk, George A; van der Putten, Wim H; De Deyn, Gerlinde B

2017-08-01

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Microbiota as Therapeutic Targets.

PubMed

Xavier, Ramnik J

Inflammatory bowel disease (IBD) represents a family of diseases including Crohn's disease and ulcerative colitis. IBD has garnered significant attention in recent years due to successes in 2 areas of basic science: complex human genetics and host-microbe interactions. Advances in understanding the genetics of IBD, mainly driven by genome-wide association studies, have identified more than 160 genetic loci that modulate the risk of disease. Notably, several of these genes have pointed to alterations in host-microbe interactions as being critical factors in pathogenesis. Investigations into the microbial communities of the gastrointestinal tract (or the 'gut microbiome') in IBD have yielded important insights into several aspects of interactions between microbiota and the host immune system, including how alterations to microbial community composition and function have important consequences for immune homeostasis. The anatomy of the gastrointestinal tract plays a role in defining not only intestinal function, but also the microbial ecosystem that lives within the gut. Careful investigations into the composition and function of these microbial communities have suggested that patients with IBD have an imbalance in their gut microbiota, termed dysbiosis. These studies, as well as studies using samples from healthy individuals, have begun to uncover mechanisms of crosstalk between particular microbes (and microbial products) and immunomodulatory pathways, alterations which may drive immune diseases such as IBD. Investigations into the role of the microbiome in IBD have provided important clues to potential pathogenic mechanisms. Harnessing this knowledge to develop therapeutics and identify biomarkers is currently a major translational goal, holding great promise for clinically meaningful progress. © 2016 S. Karger AG, Basel.

Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

USGS Publications Warehouse

Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

2016-01-01

Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.

Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

PubMed Central

Liang, Yuting; Zhao, Huihui; Deng, Ye; Zhou, Jizhong; Li, Guanghe; Sun, Bo

2016-01-01

With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential “keystone” genes, defined as either “hubs” or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions. PMID:26870020

Molecular assessment of the sensitivity of sulfate-reducing microbial communities remediating mine drainage to aerobic stress.

PubMed

Lefèvre, Emilie; Pereyra, Luciana P; Hiibel, Sage R; Perrault, Elizabeth M; De Long, Susan K; Reardon, Kenneth F; Pruden, Amy

2013-09-15

Sulfate-reducing permeable reactive zones (SR-PRZs) are microbially-driven anaerobic systems designed for the removal of heavy metals and sulfate in mine drainage. Environmental perturbations, such as oxygen exposure, may adversely affect system stability and long-term performance. The objective of this study was to examine the effect of two successive aerobic stress events on the performance and microbial community composition of duplicate laboratory-scale lignocellulosic SR-PRZs operated using the following microbial community management strategies: biostimulation with ethanol or carboxymethylcellulose; bioaugmentation with sulfate-reducing or cellulose-degrading enrichments; inoculation with dairy manure only; and no inoculation. A functional gene-based approach employing terminal restriction fragment length polymorphism and quantitative polymerase chain reaction targeting genes of sulfate-reducing (dsrA), cellulose-degrading (cel5, cel48), fermentative (hydA), and methanogenic (mcrA) microbes was applied. In terms of performance (i.e., sulfate removal), biostimulation with ethanol was the only strategy that clearly had an effect (positive) following exposure to oxygen. In terms of microbial community composition, significant shifts were observed over the course of the experiment. Results suggest that exposure to oxygen more strongly influenced microbial community shifts than the different microbial community management strategies. Sensitivity to oxygen exposure varied among different populations and was particularly pronounced for fermentative bacteria. Although the community structure remained altered after exposure, system performance recovered, indicating that SR-PRZ microbial communities were functionally redundant. Results suggest that pre-exposure to oxygen might be a more effective strategy to improve the resilience of SR-PRZ microbial communities relative to bioaugmentation or biostimulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Are Microbial Nanowires Responsible for Geoelectrical Changes at Hydrocarbon Contaminated Sites?

NASA Astrophysics Data System (ADS)

Hager, C.; Atekwana, E. A.; Gorby, Y. A.; Duris, J. W.; Allen, J. P.; Atekwana, E. A.; Ownby, C.; Rossbach, S.

2007-05-01

Significant advances in near-surface geophysics and biogeophysics in particular, have clearly established a link between geoelectrical response and the growth and enzymatic activities of microbes in geologic media. Recent studies from hydrocarbon contaminated sites suggest that the activities of distinct microbial populations, specifically syntrophic, sulfate reducing, and dissimilatory iron reducing microbial populations are a contributing factor to elevated sediment conductivity. However, a fundamental mechanistic understanding of the processes and sources resulting in the measured electrical response remains uncertain. The recent discovery of bacterial nanowires and their electron transport capabilities suggest that if bacterial nanowires permeate the subsurface, they may in part be responsible for the anomalous conductivity response. In this study we investigated the microbial population structure, the presence of nanowires, and microbial-induced alterations of a hydrocarbon contaminated environment and relate them to the sediments' geoelectrical response. Our results show that microbial communities varied substantially along the vertical gradient and at depths where hydrocarbons saturated the sediments, ribosomal intergenic spacer analysis (RISA) revealed signatures of microbial communities adapted to hydrocarbon impact. In contrast, RISA profiles from a background location showed little community variations with depth. While all sites showed evidence of microbial activity, a scanning electron microscope (SEM) study of sediment from the contaminated location showed pervasive development of "nanowire-like structures" with morphologies consistent with nanowires from laboratory experiments. SEM analysis suggests extensive alteration of the sediments by microbial Activity. We conclude that, excess organic carbon (electron donor) but limited electron acceptors in these environments cause microorganisms to produce nanowires to shuttle the electrons as they seek for distant electron acceptors. Hence, electron flow via bacterial nanowires may contribute to the geoelectrical response.

Marine sources influence fog bioaerosol composition in Namibia and Maine

NASA Astrophysics Data System (ADS)

Evans, S. E.; Dueker, E.; Logan, J. R. V.; Weathers, K. C.

2017-12-01

Organic aerosol particles act as condensation nuclei for fogs and clouds (CCN) and are main determinants of fog evolution, chemical processing, and overall aerosol-fog-cloud interactions. Recent work has confirmed the presence of marine bioaerosols, but little is known about their sources, transport, taxonomic diversity or viability. The few studies that have characterized bioaerosols in fog have been limited to culture-based approaches that capture only a fraction of microbial diversity. We characterized fungal and bacterial communities in the fog in two iconic fog systems, the Coast of Maine (USA) and the Namib Desert (Namibia). The biology of fog in both systems was diverse and distinct, by geography, from dry aerosols, and from local sources. The local environment had a dominant influence on fog in both the Namib and Maine; in particular, the biology of fog in Maine, which was collected near the coast, was more similar to microbial communities from the ocean surface. In both systems, differences between pre- and post-fog aerosol communities suggest that fog events can significantly alter microbial aerosol diversity and composition. This insight into the microbial composition of fog indicates that its origin and frequency has the potential to influence the number and diversity of microorganisms that settle in a given environment, and the composition of microbial aerosol communities in ambient or clear conditions. Here we suggest that fog microbes can possess specific traits that enhance nucleation, altering the transport and deposition of marine- and soil-derived organic matter in terrestrial systems.

Response of the soil microbial community and soil nutrient bioavailability to biomass harvesting and reserve tree retention in northern Minnesota aspen-dominated forests

Treesearch

Tera E. Lewandowski; Jodi A. Forrester; David J. Mladenoff; Anthony W. D' Amato; Brian J. Palik

2016-01-01

Intensive forest biomass harvesting, or the removal of harvesting slash (woody debris from tree branches and tops) for use as biofuel, has the potential to negatively affect the soil microbial community (SMC) due to loss of carbon and nutrient inputs from the slash, alteration of the soil microclimate, and increased nutrient leaching. These effects could result in...

Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem

USGS Publications Warehouse

Boot, Claudia M.; Hall, Ed K.; Denef, Karolien; Baron, Jill S.

2016-01-01

Elevated nitrogen (N) deposition due to increased fossil fuel combustion and agricultural practices has altered global carbon (C) cycling. Additions of reactive N to N-limited environments are typically accompanied by increases in plant biomass. Soil C dynamics, however, have shown a range of different responses to the addition of reactive N that seem to be ecosystem dependent. We evaluated the effect of N amendments on biogeochemical characteristics and microbial responses of subalpine forest organic soils in order to develop a mechanistic understanding of how soils are affected by N amendments in subalpine ecosystems. We measured a suite of responses across three years (2011–2013) during two seasons (spring and fall). Following 17 years of N amendments, fertilized soils were more acidic (control mean 5.09, fertilized mean 4.68), and had lower %C (control mean 33.7% C, fertilized mean 29.8% C) and microbial biomass C by 22% relative to control plots. Shifts in biogeochemical properties in fertilized plots were associated with an altered microbial community driven by reduced arbuscular mycorrhizal (control mean 3.2 mol%, fertilized mean 2.5 mol%) and saprotrophic fungal groups (control mean 17.0 mol%, fertilized mean 15.2 mol%), as well as a decrease in N degrading microbial enzyme activity. Our results suggest that decreases in soil C in subalpine forests were in part driven by increased microbial degradation of soil organic matter and reduced inputs to soil organic matter in the form of microbial biomass.

Microbial secondary succession in a chronosequence of chalk grasslands.

PubMed

Kuramae, Eiko E; Gamper, Hannes A; Yergeau, Etienne; Piceno, Yvette M; Brodie, Eoin L; Desantis, Todd Z; Andersen, Gary L; van Veen, Johannes A; Kowalchuk, George A

2010-05-01

Although secondary succession has been studied extensively, we have little knowledge of the succession of soil-borne microbial communities. In this study, we therefore examined the structures of the microbial communities across two separate chronosequences of chalk grasslands in Limburg, the Netherlands, which are at different stages of secondary succession after being abandoned for between 17 and >66 years. Arable fields were also included in the investigation as non-abandoned references. Changes in the soil-borne microbial communities, as determined by phylogenetic microarray and quantitative PCR methodologies, were correlated with the prevailing environmental conditions related to vegetation and soil biochemistry. We observed clear patterns of microbial secondary succession related to soil age, pH and phosphate status, as exemplified by the overrepresentation of Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and alpha-, delta- and epsilon-Proteobacteria at late successional stages. Moreover, effects of secondary succession versus changes in soil pH could be resolved, with pH significantly altering the trajectory of microbial succession.

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

PubMed

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

2018-01-01

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

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

PubMed Central

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

2018-01-01

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

Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake

PubMed Central

Shen, Pu; Murphy, Daniel Vaughan; George, Suman J.; Lapis-Gaza, Hazel; Xu, Minggang

2016-01-01

Agricultural production can be limited by low phosphorus (P) availability, with soil P being constrained by sorption and precipitation reactions making it less available for plant uptake. There are strong links between carbon (C) and nitrogen (N) availability and P cycling within soil P pools, with microorganisms being an integral component of soil P cycling mediating the availability of P to plants. Here we tested a conceptual model that proposes (i) the addition of readily-available organic substrates would increase the size of the microbial biomass thus exhausting the pool of easily-available P and (ii) this would cause the microbial biomass to access P from more recalcitrant pools. In this model it is hypothesised that the size of the microbial population is regulating access to less available P rather than the diversity of organisms contained within this biomass. To test this hypothesis we added mixtures of simple organic compounds that reflect typical root exudates at different C:N ratios to a soil microcosm experiment and assessed changes in soil P pools, microbial biomass and bacterial diversity measures. We report that low C:N ratio (C:N = 12.5:1) artificial root exudates increased the size of the microbial biomass while high C:N ratio (C:N = 50:1) artificial root exudates did not result in a similar increase in microbial biomass. Interestingly, addition of the root exudates did not alter bacterial diversity (measured via univariate diversity indices) but did alter bacterial community structure. Where C, N and P supply was sufficient to support plant growth the increase observed in microbial biomass occurred with a concurrent increase in plant yield. PMID:27893833

Soil microbial biomass and function are altered by 12 years of crop rotation

NASA Astrophysics Data System (ADS)

McDaniel, Marshall D.; Grandy, A. Stuart

2016-11-01

Declines in plant diversity will likely reduce soil microbial biomass, alter microbial functions, and threaten the provisioning of soil ecosystem services. We examined whether increasing temporal plant biodiversity in agroecosystems (by rotating crops) can partially reverse these trends and enhance soil microbial biomass and function. We quantified seasonal patterns in soil microbial biomass, respiration rates, extracellular enzyme activity, and catabolic potential three times over one growing season in a 12-year crop rotation study at the W. K. Kellogg Biological Station LTER. Rotation treatments varied from one to five crops in a 3-year rotation cycle, but all soils were sampled under a corn year. We hypothesized that crop diversity would increase microbial biomass, activity, and catabolic evenness (a measure of functional diversity). Inorganic N, the stoichiometry of microbial biomass and dissolved organic C and N varied seasonally, likely reflecting fluctuations in soil resources during the growing season. Soils from biodiverse cropping systems increased microbial biomass C by 28-112 % and N by 18-58 % compared to low-diversity systems. Rotations increased potential C mineralization by as much as 53 %, and potential N mineralization by 72 %, and both were related to substantially higher hydrolase and lower oxidase enzyme activities. The catabolic potential of the soil microbial community showed no, or slightly lower, catabolic evenness in more diverse rotations. However, the catabolic potential indicated that soil microbial communities were functionally distinct, and microbes from monoculture corn preferentially used simple substrates like carboxylic acids, relative to more diverse cropping systems. By isolating plant biodiversity from differences in fertilization and tillage, our study illustrates that crop biodiversity has overarching effects on soil microbial biomass and function that last throughout the growing season. In simplified agricultural systems, relatively small increases in crop diversity can have large impacts on microbial community size and function, with cover crops appearing to facilitate the largest increases.

Soil microbial community successional patterns during forest ecosystem restoration.

PubMed

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

2011-09-01

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

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

PubMed Central

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

2011-01-01

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

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

PubMed Central

Scholz, Monika; Hutchison, Alan L.; Dinner, Aaron R.; Gilbert, Jack A.; Coleman, Maureen L.

2016-01-01

ABSTRACT Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems. PMID:27999158

Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

NASA Astrophysics Data System (ADS)

Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

2016-09-01

Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

PubMed

He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

2012-02-01

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil.

PubMed

Bagi, Andrea; Riiser, Even Sannes; Molland, Hilde Steine; Star, Bastiaan; Haverkamp, Thomas H A; Sydnes, Magne Olav; Pampanin, Daniela Maria

2018-04-02

The expansion of offshore oil exploration increases the risk of marine species being exposed to oil pollution in currently pristine areas. The adverse effects of oil exposure through toxic properties of polycyclic aromatic hydrocarbons (PAHs) have been well studied in Atlantic cod (Gadus morhua). Nevertheless, the fate of conjugated metabolites in the intestinal tract and their effect on the diversity of intestinal microbial community in fish is less understood. Here, we investigated the intestinal microbial community composition of Atlantic cod after 28 days of exposure to crude oil (concentration range 0.0-0.1 mg/L). Analysis of PAH metabolites in bile samples confirmed that uptake and biotransformation of oil compounds occurred as a result of the exposure. Various evidence for altered microbial communities was found in fish exposed to high (0.1 mg/L) and medium (0.05 mg/L) concentrations of oil when compared to fish exposed to low oil concentration (0.01 mg/L) or no oil (control). First, altered banding patterns were observed on denaturing gradient gel electrophoresis for samples pooled from each treatment group. Secondly, based on 16S rRNA sequences, higher levels of oil exposure were associated with a loss of overall diversity of the gut microbial communities. Furthermore, 8 operational taxonomic units (OTUs) were found to have significantly different relative abundances in samples from fishes exposed to high and medium oil concentrations when compared to samples from the control group and low oil concentration. Among these, only one OTU, a Deferribacterales, had increased relative abundance in samples from fish exposed to high oil concentration. The results presented herein contribute to a better understanding of the effects of oil contamination on the gut microbial community changes in fish and highlight the importance of further studies into the area. Our findings suggest that increased relative abundance of bacteria belonging to the order Deferribacterales may be indicative of exposure to oil at concentrations higher than 0.05 mg/L.

Effects of Non-Indigenous Oysters on Microbial Diversity and Ecosystem Functioning

PubMed Central

Green, Dannielle S.; Boots, Bas; Crowe, Tasman P.

2012-01-01

Invasive ecosystem engineers can physically and chemically alter the receiving environment, thereby affecting biodiversity and ecosystem functioning. The Pacific oyster, Crassostrea gigas, invasive throughout much of the world, can establish dense populations monopolising shorelines and possibly altering ecosystem processes including decomposition and nutrient cycling. The effects of increasing cover of invasive C. gigas on ecosystem processes and associated microbial assemblages in mud-flats were tested experimentally in the field. Pore-water nutrients (NH4 + and total oxidised nitrogen), sediment chlorophyll content, microbial activity, total carbon and nitrogen, and community respiration (CO2 and CH4) were measured to assess changes in ecosystem functioning. Assemblages of bacteria and functionally important microbes, including methanogens, methylotrophs and ammonia-oxidisers were assessed in the oxic and anoxic layers of sediment using terminal restriction length polymorphism of the bacterial 16S rRNA, mxaF, amoA and archaeal mcrA genes respectively. At higher covers (40 and 80%) of oysters there was significantly greater microbial activity, increased chlorophyll content, CO2 (13 fold greater) and CH4 (6 fold greater) emission from the sediment compared to mud-flats without C. gigas. At 10% cover, C. gigas increased the concentration of total oxidised nitrogen and altered the assemblage structure of ammonia-oxidisers and methanogens. Concentrations of pore-water NH4 + were increased by C. gigas regardless of cover. Invasive species can alter ecosystem functioning not only directly, but also indirectly, by affecting microbial communities vital for the maintenance of ecosystem processes, but the nature and magnitude of these effects can be non-linear, depending on invader abundance. PMID:23144762

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

PubMed Central

He, Ruoyang; Yang, Kaijun; Li, Zhijie; Schädler, Martin; Yang, Wanqin; Wu, Fuzhong; Tan, Bo; Zhang, Li

2017-01-01

Forest land-use changes have long been suggested to profoundly affect soil microbial communities. However, how forest type conversion influences soil microbial properties remains unclear in Tibetan boreal forests. The aim of this study was to explore variations of soil microbial profiles in the surface organic layer and subsurface mineral soil among three contrasting forests (natural coniferous forest, NF; secondary birch forest, SF and spruce plantation, PT). Soil microbial biomass, activity and community structure of the two layers were investigated by chloroform fumigation, substrate respiration and phospholipid fatty acid analysis (PLFA), respectively. In the organic layer, both NF and SF exhibited higher soil nutrient levels (carbon, nitrogen and phosphorus), microbial biomass carbon and nitrogen, microbial respiration, PLFA contents as compared to PT. However, the measured parameters in the mineral soils often did not differ following forest type conversion. Irrespective of forest types, the microbial indexes generally were greater in the organic layer than in the mineral soil. PLFAs biomarkers were significantly correlated with soil substrate pools. Taken together, forest land-use change remarkably altered microbial community in the organic layer but often did not affect them in the mineral soil. The microbial responses to forest land-use change depend on soil layer, with organic horizons being more sensitive to forest conversion. PMID:28982191

Grassland to woodland transitions: Dynamic response of microbial community structure and carbon use patterns

NASA Astrophysics Data System (ADS)

Creamer, Courtney A.; Filley, Timothy R.; Boutton, Thomas W.; Rowe, Helen I.

2016-06-01

Woodland encroachment into grasslands is a globally pervasive phenomenon attributed to land use change, fire suppression, and climate change. This vegetation shift impacts ecosystem services such as ground water allocation, carbon (C) and nutrient status of soils, aboveground and belowground biodiversity, and soil structure. We hypothesized that woodland encroachment would alter microbial community structure and function and would be related to patterns in soil C accumulation. To address this hypothesis, we measured the composition and δ13C values of soil microbial phospholipids (PLFAs) along successional chronosequences from C4-dominated grasslands to C3-dominated woodlands (small discrete clusters and larger groves) spanning up to 134 years. Woodland development increased microbial biomass, soil C and nitrogen (N) concentrations, and altered microbial community composition. The relative abundance of gram-negative bacteria (cy19:0) increased linearly with stand age, consistent with decreases in soil pH and/or greater rhizosphere development and corresponding increases in C inputs. δ13C values of all PLFAs decreased with time following woody encroachment, indicating assimilation of woodland C sources. Among the microbial groups, fungi and actinobacteria in woodland soils selectively assimilated grassland C to a greater extent than its contribution to bulk soil. Between the two woodland types, microbes in the groves incorporated relatively more of the relict C4-C than those in the clusters, potentially due to differences in below ground plant C allocation and organo-mineral association. Changes in plant productivity and C accessibility (rather than C chemistry) dictated microbial C utilization in this system in response to shrub encroachment.

Microbial Response to High Temperature Hydrothermal Forcing: AISICS Vent (Lucky Strike, 37°N, MAR) and Prokaryote Community as Example.

NASA Astrophysics Data System (ADS)

Henri, P. A.; Rommevaux, C.; Chavagnac, V.; Degboe, J.; Destrigneville, C.; Boulart, C.; Lesongeur, F.; Castillo, A.; Goodfroy, A.

2015-12-01

To study the hydrothermal forcing on microbial colonization, and impacts on the oceanic crust alteration, an integrated study was led at the Tour Eiffel hydrothermal site (Lucky Strike hydrothermal field, 37°N, MAR). We benefited from an annual survey between 2009 and 2011 of temperatures, along with sampling of focused and diffused fluids for chemical analysis, and chimney sampling and samples from microbial colonization experiments analyzed for prokaryotic composition and rock alteration study. The chemical composition of the fluids show an important increase in the CO2 concentration at the Eiffel Tower site between 2009 and 2010 followed by a decrease between 2010 and 2011. In 2011, several fluid samples show an important depletion in Si, suggesting that some Si was removed by interaction with the stockwork before emission. Our observations, regarding the previous studies of chemical fluid affected by a magmatic event lead us to suppose that a magmatic/tectonic event occurred under the Lucky Strike hydrothermal field between 2009 and 2010. The results of the prokaryotic communities' analysis show that a shift occurred in the dominant microbial metabolisms present in the colonizer retrieved in 2010 and the one retrieved in 2011. Archaeal communities shifted from chemolithoautotropic sulfite/thiosulfate reducers-dominated in 2010 to ammonia oxidizers-dominated in 2011. The bacterial communities also undergo a shift, from a community with diversified metabolisms in 2010 to a community strongly dominated by chemolithoautotrophic sulfide or hydrogen oxidation in 2011. Moreover, in terms of ecological preferendum, the Archaeal communities shifted from thermophilic-dominated to mesophilic-dominated. The present study underline the influence of modifications in gases compositions of hydrothermal fluids subsequently to a degassing of the magma chamber and their impact on the microbial communities living in the vicinity of hydrothermal vents at the Eiffel Tower site.

Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi-arid ecosystems.

PubMed

Nielsen, Uffe N; Ball, Becky A

2015-04-01

Altered precipitation patterns resulting from climate change will have particularly significant consequences in water-limited ecosystems, such as arid to semi-arid ecosystems, where discontinuous inputs of water control biological processes. Given that these ecosystems cover more than a third of Earth's terrestrial surface, it is important to understand how they respond to such alterations. Altered water availability may impact both aboveground and belowground communities and the interactions between these, with potential impacts on ecosystem functioning; however, most studies to date have focused exclusively on vegetation responses to altered precipitation regimes. To synthesize our understanding of potential climate change impacts on dryland ecosystems, we present here a review of current literature that reports the effects of precipitation events and altered precipitation regimes on belowground biota and biogeochemical cycling. Increased precipitation generally increases microbial biomass and fungal:bacterial ratio. Few studies report responses to reduced precipitation but the effects likely counter those of increased precipitation. Altered precipitation regimes have also been found to alter microbial community composition but broader generalizations are difficult to make. Changes in event size and frequency influences invertebrate activity and density with cascading impacts on the soil food web, which will likely impact carbon and nutrient pools. The long-term implications for biogeochemical cycling are inconclusive but several studies suggest that increased aridity may cause decoupling of carbon and nutrient cycling. We propose a new conceptual framework that incorporates hierarchical biotic responses to individual precipitation events more explicitly, including moderation of microbial activity and biomass by invertebrate grazing, and use this framework to make some predictions on impacts of altered precipitation regimes in terms of event size and frequency as well as mean annual precipitation. While our understanding of dryland ecosystems is improving, there is still a great need for longer term in situ manipulations of precipitation regime to test our model. © 2014 John Wiley & Sons Ltd.

Human and Environmental Impacts on River Sediment Microbial Communities

DOE PAGES

Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita; ...

2014-05-19

Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (~65,000 microbial ‘species’ identified) and most novel (93% of OTUsmore » do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.« less

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health

PubMed Central

Huang, Jing; Chen, Zhe; Nie, Yuanjun; Wang, Changbiao

2018-01-01

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality. PMID:29451918

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health.

PubMed

Zhao, Jia; Liu, Jiang; Liang, Hong; Huang, Jing; Chen, Zhe; Nie, Yuanjun; Wang, Changbiao; Wang, Yuguo

2018-01-01

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality.

Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score

PubMed Central

McDole, Tracey; Nulton, James; Barott, Katie L.; Felts, Ben; Hand, Carol; Hatay, Mark; Lee, Hochul; Nadon, Marc O.; Nosrat, Bahador; Salamon, Peter; Bailey, Barbara; Sandin, Stuart A.; Vargas-Angel, Bernardo; Youle, Merry; Zgliczynski, Brian J.; Brainard, Russell E.; Rohwer, Forest

2012-01-01

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing. PMID:22970122

Assessing coral reefs on a Pacific-wide scale using the microbialization score.

PubMed

McDole, Tracey; Nulton, James; Barott, Katie L; Felts, Ben; Hand, Carol; Hatay, Mark; Lee, Hochul; Nadon, Marc O; Nosrat, Bahador; Salamon, Peter; Bailey, Barbara; Sandin, Stuart A; Vargas-Angel, Bernardo; Youle, Merry; Zgliczynski, Brian J; Brainard, Russell E; Rohwer, Forest

2012-01-01

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing.

Characteristics of Faecal Microbiota in Paediatric Crohn's Disease and Their Dynamic Changes During Infliximab Therapy.

PubMed

Wang, Yizhong; Gao, Xuefeng; Ghozlane, Amine; Hu, Hui; Li, Xiaolu; Xiao, Yongmei; Li, Dan; Yu, Guangjun; Zhang, Ting

2018-02-28

Crohn's disease [CD] is known to be associated with gut microbial dysbiosis. Infliximab [IFX] is increasingly used to treat paediatric CD; however, it is not clear how the gut microbiota is modified during IFX treatment. The aim of this study was to characterise the faecal microbiota community composition in paediatric CD patients and to assess its dynamic changes during IFX therapy. A 16S rRNA sequencing approach was applied to determine the compositions of microbial communities in faecal samples. The composition and function of the faecal microbiota were compared between CD patients and healthy controls. Characteristics of faecal microbiome composition in paediatric CD patients before IFX treatment were represented by a lower biodiversity, a gain in Enterococcus, and a significant loss in multiple short-chain fatty acid [SCFA]-producing bacteria, including Anaerostipes, Blautia, Coprococcus, Faecalibacterium, Lachnospira, Odoribacter, Roseburia, Ruminococcus, and Sutterella. Additionally, alterations were observed in metabolic functions of the gut microbial community in CD. IFX treatment increased the biodiversity of gut microbiota and shifted its composition as well as its functional capabilities in the paediatric CD patients toward a healthy status. However, multiple SCFA-producing taxa were not significantly expanded. The sustained response of paediatric CD patients to IFX was associated with abundance of SCFA-producing bacteria. A lower biodiversity with alterations in the composition and function of faecal microbial community, characterising gut microbial dysbiosis, was observed in Chinese paediatric CD patients. IFX diminished the CD-associated gut microbial dysbiosis but was deficient in increasing certain SCFA-producing taxa. Copyright © 2017 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com

Soil ecosystem functioning under climate change: plant species and community effects.

PubMed

Kardol, Paul; Cregger, Melissa A; Campany, Courtney E; Classen, Aimee T

2010-03-01

Feedbacks of terrestrial ecosystems to atmospheric and climate change depend on soil ecosystem dynamics. Soil ecosystems can directly and indirectly respond to climate change. For example, warming directly alters microbial communities by increasing their activity. Climate change may also alter plant community composition, thus indirectly altering the soil communities that depend on their inputs. To better understand how climate change may directly and indirectly alter soil ecosystem functioning, we investigated old-field plant community and soil ecosystem responses to single and combined effects of elevated [CO2], warming, and precipitation in Tennessee (USA). Specifically, we collected soils at the plot level (plant community soils) and beneath dominant plant species (plant-specific soils). We used microbial enzyme activities and soil nematodes as indicators for soil ecosystem functioning. Our study resulted in two main findings: (1) Overall, while there were some interactions, water, relative to increases in [CO2] and warming, had the largest impact on plant community composition, soil enzyme activity, and soil nematodes. Multiple climate-change factors can interact to shape ecosystems, but in our study, those interactions were largely driven by changes in water. (2) Indirect effects of climate change, via changes in plant communities, had a significant impact on soil ecosystem functioning, and this impact was not obvious when looking at plant community soils. Climate-change effects on enzyme activities and soil nematode abundance and community structure strongly differed between plant community soils and plant-specific soils, but also within plant-specific soils. These results indicate that accurate assessments of climate-change impacts on soil ecosystem functioning require incorporating the concurrent changes in plant function and plant community composition. Climate-change-induced shifts in plant community composition will likely modify or counteract the direct impact of atmospheric and climate change on soil ecosystem functioning, and hence, these indirect effects should be taken into account when predicting the manner in which global change will alter ecosystem functioning.

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

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

PubMed

Mandakovic, Dinka; Rojas, Claudia; Maldonado, Jonathan; Latorre, Mauricio; Travisany, Dante; Delage, Erwan; Bihouée, Audrey; Jean, Géraldine; Díaz, Francisca P; Fernández-Gómez, Beatriz; Cabrera, Pablo; Gaete, Alexis; Latorre, Claudio; Gutiérrez, Rodrigo A; Maass, Alejandro; Cambiazo, Verónica; Navarrete, Sergio A; Eveillard, Damien; González, Mauricio

2018-04-12

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.

Historical Contingencies in Microbial Responses to Drought

NASA Astrophysics Data System (ADS)

Hawkes, C.; Waring, B.; Rocca, J.; Kivlin, S.; Giauque, H.; Averill, C.

2014-12-01

Although water is a primary controller of microbial function and we expect climate change to alter water availability in the future, our understanding of how microbial communities respond to a change in moisture and what that means for soil carbon cycling remain poorly understood. In part, this uncertainty arises from a lack of understanding of microbial response mechanisms and how those lead to aggregate soil function. Environmental tracking would be facilitated if microbial communities respond to new climatic conditions via rapid physiological acclimatization, shifts in community composition, or adaptation. In contrast, historical contingencies could be created by dispersal limitation or local adaptation to previous conditions. To address environmental tracking vs. legacies, we examined how soil microbial communities were affected by precipitation at multiple scales and asked whether rainfall was a primary driver of the observed responses. We leveraged a local steep rainfall gradient with field surveys, lab incubations, reciprocal transplants, and rainfall manipulations to approach this problem. Across a steep rainfall gradient, we found that soil microbial communities were strongly associated with historical rainfall, with two-thirds of the variation in community composition explained by mean annual precipitation. In 12-month experimental lab manipulations of soil moisture, soil functional responses were constrained by historical rainfall, with greater activity in soils subjected to their original moisture condition. The constraints of historical rainfall held even after 18 months in reciprocal transplant common gardens along the rainfall gradient and with manipulated dispersal of regional microbial communities. Yet, when water was manipulated at a single site over 4 years, legacies did not develop. Overall, these findings are consistent with long-term rainfall acting as a strong habitat filter and resulting in a legacy of both microbial community composition and physiological capacity that can affect soil carbon cycling. Placing the ecological and evolutionary dynamics of microbial communities in the context of historical and future environmental variation may thus provide us with a framework for improving prediction of ecosystem responses to climate change.

Changes in soil amino composition and microbial N acquisition strategies in response to woody plant invasion of grasslands

USDA-ARS?s Scientific Manuscript database

Changes in land cover have the potential to alter nutrient cycling through changes in carbon input chemistry, microbial community structure, and even soil structure. In the Rio Grande plains region of southern Texas, overgrazing and fire suppression have resulted in progressive encroachment of N-fix...

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

PubMed

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

2015-01-01

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

Root phenotypic differences across a historical gradient of wheat genotypes alter soil rhizosphere communities and their impact on nitrogen cycling

NASA Astrophysics Data System (ADS)

Kallenbach, C.; Junaidi, D.; Fonte, S.; Byrne, P. F.; Wallenstein, M. D.

2017-12-01

Plants and soil microorganisms can exhibit coevolutionary relationships where, for example, in exchange for root carbon, rhizosphere microbes enhance plant fitness through improved plant nutrient availability. Organic agriculture relies heavily on these interactions to enhance crop nitrogen (N) availability. However, modern agriculture and breeding under high mineral N fertilization may have disrupted these interactions through alterations to belowground carbon inputs and associated impacts on the soil microbiome. As sustainability initiatives lead to a restoration of agricultural soil organic matter, modern crop cultivars may still be constrained by crop roots' ability to effectively support microbial-mediated N mineralization. We investigated how differences in root traits across a historical gradient of spring wheat genotypes influence the rhizosphere microbial community and effects on soil N and wheat yield. Five genotypes, representing wild (Wild), pre-Green Revolution (Old), and modern (Modern) wheat, were grown under greenhouse conditions in soils with and without compost to also compare genotype response to difference in native soil microbiomes and organic resource availability. We analyzed rhizosphere soils for microbial community composition, enzyme activities, inorganic N, and microbial biomass. Root length density, surface area, fine root volume and root:shoot ratio were higher in the Wild and Old genotype (Gypsum) compared to the two Modern genotypes (P<0.01). The Wild and Old genotype had a more positive response to compost for root length and diameter, N-cycling enzyme activities, microbial biomass, and soil inorganic N, compared to Modern genotypes. However, under unamended soils, the microbial community and soil N were not affected by genotypes. We also relate how root traits and N cycling across genotypes correspond to microbial community composition. Our preliminary data suggest that the older wheat genotypes and their root traits are more effective at enhancing microbial N mineralization under organically managed soils. Thus, to optimize crop N availability from organic sources, breeding efforts should consider incorporating root traits of older genotypes to better support the beneficial interactions between crop roots and their rhizosphere microbiome.

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract

NASA Astrophysics Data System (ADS)

Li, Dongyao; Chen, Haiqin; Mao, Bingyong; Yang, Qin; Zhao, Jianxin; Gu, Zhennan; Zhang, Hao; Chen, Yong Q.; Chen, Wei

2017-04-01

As a long-standing biomedical model, rats have been frequently used in studies exploring the correlations between gastrointestinal (GI) bacterial biota and diseases. In the present study, luminal and mucosal samples taken along the longitudinal axis of the rat digestive tract were subjected to 16S rRNA gene sequencing-based analysis to determine the baseline microbial composition. Results showed that the community diversity increased from the upper to lower GI segments and that the stratification of microbial communities as well as shift of microbial metabolites were driven by biogeographic location. A greater proportion of lactate-producing bacteria (such as Lactobacillus, Turicibacter and Streptococcus) were found in the stomach and small intestine, while anaerobic Lachnospiraceae and Ruminococcaceae, fermenting carbohydrates and plant aromatic compounds, constituted the bulk of the large-intestinal core microbiota where topologically distinct co-occurrence networks were constructed for the adjacent luminal and mucosal compartments. When comparing the GI microbiota from different hosts, we found that the rat microbial biogeography might represent a new reference, distinct from other murine animals. Our study provides the first comprehensive characterization of the rat GI microbiota landscape for the research community, laying the foundation for better understanding and predicting the disease-related alterations in microbial communities.

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

PubMed

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

2016-01-01

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

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

PubMed

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

2016-11-04

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

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity

DOE PAGES

Liang, Yuting; Wu, Liyou; Clark, Ian M.; ...

2015-04-07

Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receivingmore » nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.« less

Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity

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

Liang, Yuting; Wu, Liyou; Clark, Ian M.

Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receivingmore » nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.« less

Microbial Decomposers Not Constrained by Climate History Along a Mediterranean Climate Gradient

NASA Astrophysics Data System (ADS)

Baker, N. R.; Khalili, B.; Martiny, J. B. H.; Allison, S. D.

2017-12-01

The return of organic carbon to the atmosphere through terrestrial decomposition is mediated through the breakdown of complex organic polymers by extracellular enzymes produced by microbial decomposer communities. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. To address this question, we deployed fine-pore nylon mesh "microbial cage" litterbags containing grassland litter with and without local inoculum across five sites in southern California, spanning a gradient of 10.3-22.8° C in mean annual temperature and 100-400+ mm mean annual precipitation. Litterbags were deployed in October 2014 and collected four times over the course of 14 months. Recovered litter was assayed for mass loss, litter chemistry, microbial biomass, extracellular enzymes (Vmax and Km­), and enzyme temperature sensitivities. We hypothesized that grassland litter would decompose most rapidly in the grassland site, and that access to local microbial communities would enhance litter decomposition rates and microbial activity in the other sites along the gradient. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbes were not restricted in their ability to decompose litter under different climate conditions. Although we observed a strong correlation between bacterial biomass and mass loss across the gradient, litter that was inoculated with local microbial communities lost less mass despite having greater bacterial biomass and potentially accumulating more microbial residues. Our results suggest that microbial community composition may not constrain C-cycling rates under climate change in our system. However, there may be community constraints on decomposition if climate change alters litter chemistry, a mechanism only indirectly addressed by our design.

Bacterial Diversity Across a Turbidite-Stranded Sediment-Water Interface, La Jolla Canyon, CA

NASA Astrophysics Data System (ADS)

Harrison, B. K.; Flood, B.; Myrbo, A.; Bailey, J.

2016-12-01

The emplacement of gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical (e.g., McKay and Pederson, 2014) and biological signatures (e.g., Anschutz et al., 2002) of turbidite deposition, the response of prokaryotes within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and allocthonous material must respond to substantially altered selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine 1) microbial community response to sedimentation 2) preservation and identification of microbial dispersal mechanisms. We collected Illumina MiSeq sequence libraries across an intact marine turbidite boundary at 25cm sediment depth in La Jolla canyon off the coast of California. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, the sedimentary boundary is sharply demarcated at the cm scale by the diversity and abundance of Chloroflexi, Planctomycetes, and Actinobacteria. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the stranded sediment-water interface reflect persistent turbidite-induced changes to the geochemical environment. This work raises the possibility that abrupt sedimentological events may alter the microbial community in a manner that persists with burial.

The microbial community in decaying fallen logs varies with critical period in an alpine forest.

PubMed

Chang, Chenhui; Wu, Fuzhong; Yang, Wanqin; Xu, Zhenfeng; Cao, Rui; He, Wei; Tan, Bo; Justine, Meta Francis

2017-01-01

Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor.

The microbial community in decaying fallen logs varies with critical period in an alpine forest

PubMed Central

Chang, Chenhui; Wu, Fuzhong; Xu, Zhenfeng; Cao, Rui; He, Wei; Tan, Bo; Justine, Meta Francis

2017-01-01

Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor. PMID:28787465

A review on the applications of microbial electrolysis cells in anaerobic digestion.

PubMed

Yu, Zhengsheng; Leng, Xiaoyun; Zhao, Shuai; Ji, Jing; Zhou, Tuoyu; Khan, Aman; Kakde, Apurva; Liu, Pu; Li, Xiangkai

2018-05-01

Anaerobic digestion (AD) has been widely used for biogas or biofuel generation from waste treatment. Because a low production rate and instability of AD occur frequently, various technologies have been applied to improvement of AD. Microbial electrolysis cells (MECs), an emerging technology, can convert organic matter into hydrogen, methane, and other value-added products. Recent studies showed that application of MEC to AD (MEC-AD) can accelerate degradation of a substrate (including recalcitrant compounds) and alter AD microbial community by enriching exoelectrogens and methanogens thus increasing biogas production. With stable microbial communities established, improvement of MEC-AD for methane production was achieved. MEC-AD process can be monitored in real-time by detecting electric signals, which linearly correlate with substrate concentrations. This review attempts to evaluate interactions among the decomposition of substrates, MEC-AD system, and the microbial community. This analysis should provide useful insights into the improvement of methane production and the performance of MEC-AD. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Exotic Legume Tree Species Acacia holosericea Alters Microbial Soil Functionalities and the Structure of the Arbuscular Mycorrhizal Community▿

PubMed Central

Remigi, P.; Faye, A.; Kane, A.; Deruaz, M.; Thioulouse, J.; Cissoko, M.; Prin, Y.; Galiana, A.; Dreyfus, B.; Duponnois, R.

2008-01-01

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. PMID:18203858

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

PubMed Central

Lupatini, Manoeli; Korthals, Gerard W.; de Hollander, Mattias; Janssens, Thierry K. S.; Kuramae, Eiko E.

2017-01-01

Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms. PMID:28101080

Does the aboveground herbivore assemblage influence soil bacterial community composition and richness in subalpine grasslands?

Treesearch

Melanie Hodel; Martin Schütz; Martijn L. Vandegehuchte; Beat Frey; Matthias Albrecht; Matt D. Busse; Anita C. Risch

2014-01-01

Grassland ecosystems support large communities of aboveground herbivores that can alter ecosystem processes. Thus, grazing by herbivores can directly and indirectly affect belowground properties such as the microbial community structure and diversity. Even though multiple species of functionally different herbivores coexist in grassland ecosystems, most studies have...

Mechanisms of microbial destabilization of soil C shifts over decades of warming

NASA Astrophysics Data System (ADS)

DeAngelis, K.; Pold, G.; Chowdhury, P. R.; Schnabel, J.; Grandy, S.; Melillo, J. M.

2017-12-01

Microbes are major actors in regulating the earth's biogeochemical cycles, with temperature-sensitive microbial tradeoffs improving ecosystem biogeochemical models. Meanwhile, the Earth's climate is changing, with decades of warming undercutting the ability of soil to store carbon. Our work explores trends of 26 years of experimental warming in temperate deciduous forest soils, which is associated with cycles of soil carbon degradation punctuated by periods of changes in soil microbial dynamics. Using a combination of biogeochemistry and molecular analytical methods, we explore the hypotheses that substrate availability, community structure, altered temperature sensitivity of microbial turnover-growth efficiency tradeoff, and microbial evolution are responsible for observations of accelerated degradation of soil carbon over time. Amplicon sequencing of microbial communities suggests a small role of changing microbial community composition over decades of warming, but a sustained suppression of fungal biomass is accompanied by increased biomass of Actinobacteria, Actinobacteria, Alphaproteobacteria, Verrucomicrobia and Planctomycetes. Substrate availability plays an important role in microbial dynamics, with depleted labile carbon in the first decade and depleted lignin in the second decade. Increased lignin-degrading enzyme activity supports the suggestion that lignin-like organic matter is an important substrate in chronically warmed soils. Metatranscriptomics data support the suggestion that increased turnover is associated with long-term warming, with metagenomic signals of increased carbohydrate-degrading enzymes in the organic horizon but decreased in the mineral soils. Finally, traits analysis of over 200 cultivated isolates of bacterial species from heated and control soils suggests an expanded ability for degradation of cellulose and hemicellulose but not chitin, supporting the hypothesis that long-term warming is exerting evolutionary pressure on microbial species. Together, these data suggest that after decades of warming both direct kinetic effects and indirect effects of altered substrate availability are affecting microbial ecology and evolution in ways that conspire to destabilize soil organic matter.

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

PubMed

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

2012-07-01

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

Canopy structural alterations to nitrogen functions of the soil microbial community in a Quercus virginiana forest

NASA Astrophysics Data System (ADS)

Moore, L. D.; Van Stan, J. T., II; Rosier, C. L.; Gay, T. E.; Wu, T.

2014-12-01

Forest canopy structure controls the timing, amount and chemical character of precipitation supply to soils through interception and drainage along crown surfaces. Yet, few studies have examined forest canopy structural connections to soil microbial communities (SMCs), and none have measured how this affects SMC N functions. The maritime Quercus virginiana Mill. (southern live oak) forests of St Catherine's Island, GA, USA provide an ideal opportunity to examine canopy structural alterations to SMCs and their functioning, as their throughfall varies substantially across space due to dense Tillandsia usneoides L. (spanish moss) mats bestrewn throughout. To examine the impact of throughfall variability on SMC N functions, we examined points along the canopy coverage continuum: large canopy gaps (0%), bare canopy (50-60%), and canopy of heavy T. usneoides coverage (>=85%). Five sites beneath each of the canopy cover types were monitored for throughfall water/ions and soil leachates chemistry for one storm each month over the growing period (7 months, Mar-2014 to Sep-2014) to compare with soil chemistry and SMC communities sampled every two months throughout that same period (Mar, May, Jul, Sep). DGGE and QPCR analysis of the N functioning genes (NFGs) to characterize the ammonia oxidizing bacterial (AOB-amoA), archaea (AOA-amoA), and ammonification (chiA) communities were used to determine the nitrification and decomposition potential of these microbial communities. PRS™-probes (Western Ag Innovations Inc., Saskatoon, Canada) were then used to determine the availability of NO3-N and NH4+N in the soils over a 6-week period to evaluate whether the differing NFG abundance and community structures resulted in altered N cycling.

Root controls on soil microbial community structure in forest soils.

PubMed

Brant, Justin B; Myrold, David D; Sulzman, Elizabeth W

2006-07-01

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0-10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.

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.

Lake microbial communities are resilient after a whole-ecosystem disturbance

PubMed Central

Shade, Ashley; Read, Jordan S; Youngblut, Nicholas D; Fierer, Noah; Knight, Rob; Kratz, Timothy K; Lottig, Noah R; Roden, Eric E; Stanley, Emily H; Stombaugh, Jesse; Whitaker, Rachel J; Wu, Chin H; McMahon, Katherine D

2012-01-01

Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental microbial communities have capacity to recover after a large disturbance event, we conducted a whole-ecosystem manipulation, during which we imposed an intense disturbance on freshwater microbial communities by artificially mixing a temperate lake during peak summer thermal stratification. We employed environmental sensors and water chemistry analyses to evaluate the physical and chemical responses of the lake, and bar-coded 16S ribosomal RNA gene pyrosequencing and automated ribosomal intergenic spacer analysis (ARISA) to assess the bacterial community responses. The artificial mixing increased mean lake temperature from 14 to 20 °C for seven weeks after mixing ended, and exposed the microorganisms to very different environmental conditions, including increased hypolimnion oxygen and increased epilimnion carbon dioxide concentrations. Though overall ecosystem conditions remained altered (with hypolimnion temperatures elevated from 6 to 20 °C), bacterial communities returned to their pre-manipulation state as some environmental conditions, such as oxygen concentration, recovered. Recovery to pre-disturbance community composition and diversity was observed within 7 (epilimnion) and 11 (hypolimnion) days after mixing. Our results suggest that some microbial communities have capacity to recover after a major disturbance. PMID:22739495

Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest.

PubMed

Mirza, Babur S; Potisap, Chotima; Nüsslein, Klaus; Bohannan, Brendan J M; Rodrigues, Jorge L M

2014-01-01

The Amazon rainforest, the largest equatorial forest in the world, is being cleared for pasture and agricultural use at alarming rates. Tropical deforestation is known to cause alterations in microbial communities at taxonomic and phylogenetic levels, but it is unclear whether microbial functional groups are altered. We asked whether free-living nitrogen-fixing microorganisms (diazotrophs) respond to deforestation in the Amazon rainforest, using analysis of the marker gene nifH. Clone libraries were generated from soil samples collected from a primary forest, a 5-year-old pasture originally converted from primary forest, and a secondary forest established after pasture abandonment. Although diazotroph richness did not significantly change among the three plots, diazotroph community composition was altered with forest-to-pasture conversion, and phylogenetic similarity was higher among pasture communities than among those in forests. There was also 10-fold increase in nifH gene abundance following conversion from primary forest to pasture. Three environmental factors were associated with the observed changes: soil acidity, total N concentration, and C/N ratio. Our results suggest a partial restoration to initial levels of abundance and community structure of diazotrophs following pasture abandonment, with primary and secondary forests sharing similar communities. We postulate that the response of diazotrophs to land use change is a direct consequence of changes in plant communities, particularly the higher N demand of pasture plant communities for supporting aboveground plant growth.

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.

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

DOE PAGES

Mosier, Annika C.; Li, Zhou; Thomas, Brian C.; ...

2014-07-22

Microbial communities that underpin global biogeochemical cycles will likely be influenced by elevated temperature associated with environmental change. In this paper, we test an approach to measure how elevated temperature impacts the physiology of individual microbial groups in a community context, using a model microbial-based ecosystem. The study is the first application of tandem mass tag (TMT)-based proteomics to a microbial community. We accurately, precisely and reproducibly quantified thousands of proteins in biofilms growing at 40, 43 and 46 °C. Elevated temperature led to upregulation of proteins involved in amino-acid metabolism at the level of individual organisms and the entiremore » community. Proteins from related organisms differed in their relative abundance and functional responses to temperature. Elevated temperature repressed carbon fixation proteins from two Leptospirillum genotypes, whereas carbon fixation proteins were significantly upregulated at higher temperature by a third member of this genus. Leptospirillum group III bacteria may have been subject to viral stress at elevated temperature, which could lead to greater carbon turnover in the microbial food web through the release of viral lysate. Finally, overall, these findings highlight the utility of proteomics-enabled community-based physiology studies, and provide a methodological framework for possible extension to additional mixed culture and environmental sample analyses.« less

Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog.

PubMed

Reumer, Max; Harnisz, Monika; Lee, Hyo Jung; Reim, Andreas; Grunert, Oliver; Putkinen, Anuliina; Fritze, Hannu; Bodelier, Paul L E; Ho, Adrian

2018-02-01

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA -based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities. IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects. Copyright © 2018 American Society for Microbiology.

Bisphenol A alters gut microbiome: Comparative metagenomics analysis.

PubMed

Lai, Keng-Po; Chung, Yan-Tung; Li, Rong; Wan, Hin-Ting; Wong, Chris Kong-Chu

2016-11-01

Mounting evidence has shown that an alteration of the gut microbiota is associated with diet, and plays an important role in animal health and metabolic diseases. However, little is known about the influence of environmental contaminants on the gut microbial community. Bisphenol A (BPA), which is widely used for manufacturing plastic products, has recently been classified as an environmental obesogen. Although many studies have demonstrated the metabolic-disrupting effects of BPA on liver and pancreatic functions, the possible effects of this synthetic compound on the metabolic diversity of the intestinal microbiota is unknown. Using 16S rRNA gene sequencing analysis on caecum samples of CD-1 mice, the present study aimed to test the hypothesis that dietary BPA intake may influence the gut microbiota composition and functions, an important attributing factor to development of the metabolic syndrome. A high-fat diet (HFD) and high-sucrose diet (HSD) were included as the positive controls for comparing the changes in the intestinal microbial profiles. Our results demonstrated a significant reduction of species diversity in the gut microbiota of BPA-fed mice. Alpha and beta diversity analyses showed that dietary BPA intake led to a similar gut microbial community structure as that induced by HFD and HSD in mice. In addition, comparative analysis of the microbial communities revealed that both BPA and a HFD favored the growth of Proteobacteria, a microbial marker of dysbiosis. Consistently, growth induction of the family Helicobacteraceae and reduction of the Firmicutes and Clostridia populations were observed in the mice fed BPA or a HFD. Collectively, our study highlighted that the effects of dietary BPA intake on the shift of microbial community structure were similar to those of a HFD and HSD, and revealed microbial markers for the development of diseases associated with an unstable microbiota. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review.

PubMed

Zhu, Xiaomin; Chen, Baoliang; Zhu, Lizhong; Xing, Baoshan

2017-08-01

Biochars have attracted tremendous attention due to their effects on soil improvement; they enhance carbon storage, soil fertility and quality, and contaminant (organic and heavy metal) immobilization and transformation. These effects could be achieved by modifying soil microbial habitats and (or) directly influencing microbial metabolisms, which together induce changes in microbial activity and microbial community structures. This review links microbial responses, including microbial activity, community structures and soil enzyme activities, with changes in soil properties caused by biochars. In particular, we summarized possible mechanisms that are involved in the effects that biochar-microbe interactions have on soil carbon sequestration and pollution remediation. Special attention has been paid to biochar effects on the formation and protection of soil aggregates, biochar adsorption of contaminants, biochar-mediated transformation of soil contaminants by microorganisms, and biochar-facilitated electron transfer between microbial cells and contaminants and soil organic matter. Certain reactive organic compounds and heavy metals in biochar may induce toxicity to soil microorganisms. Adsorption and hydrolysis of signaling molecules by biochar interrupts microbial interspecific communications, potentially altering soil microbial community structures. Further research is urged to verify the proposed mechanisms involved in biochar-microbiota interactions for soil remediation and improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Context dependency and saturating effects of loss of rare soil microbes on plant productivity.

PubMed

Hol, W H Gera; de Boer, Wietse; de Hollander, Mattias; Kuramae, Eiko E; Meisner, Annelein; van der Putten, Wim H

2015-01-01

Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.

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. © 2012 Blackwell Publishing Ltd.

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 nutrient inputs for soil processes. PMID:25938580

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

PubMed

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

2018-01-01

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

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium.

PubMed

Teixeira, Catarina; Almeida, C Marisa R; Nunes da Silva, Marta; Bordalo, Adriano A; Mucha, Ana P

2014-09-15

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. Copyright © 2014 Elsevier B.V. All rights reserved.

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

PubMed Central

Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

PubMed

Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

Microbial diversity of landslide soils assessed by RFLP and SSCP fingerprints.

PubMed

Guida, Marco; Cannavacciuolo, Paolo Losanno; Cesarano, Mara; Borra, Marco; Biffali, Elio; D'Alessandro, Raffaella; De Felice, Bruna

2014-08-01

Landslides are a significant component of natural disasters in most countries around the world. Understanding these destructive phenomena through the analysis of possible correlations between microbial communities and the alteration of the soil responsible for landslides is important in order to reduce their negative consequences. To address this issue, bacterial and fungal communities in soils triggering landslides in Termini-Nerano and Massa Lubrense-Nerano (Naples, Italy) were analysed by genetic profiling techniques. Fingerprints were generated by single-strand conformation polymorphisms (SSCP) and random amplified polymorphic DNA (RAPD). The microbial community in both soil types was enriched in species which could contribute to the degradation process occurring during landslides, forming biofilms and leading to the transformation or the formation of minerals. Indeed, some of the identified bacteria were found to favour the transformation of clay minerals. These findings suggest a possible relationship between bacterial and fungal community-colonising soils and the occurrence of landslides.

Metagenomic Insights of Microbial Feedbacks to Elevated CO2 (Invited)

NASA Astrophysics Data System (ADS)

Zhou, J.; Tu, Q.; Wu, L.; He, Z.; Deng, Y.; Van Nostrand, J. D.

2013-12-01

Understanding the responses of biological communities to elevated CO2 (eCO2) is a central issue in ecology and global change biology, but its impacts on the diversity, composition, structure, function, interactions and dynamics of soil microbial communities remain elusive. In this study, we first examined microbial responses to eCO2 among six FACE sites/ecosystems using a comprehensive functional gene microarray (GeoChip), and then focused on details of metagenome sequencing analysis in one particular site. GeoChip is a comprehensive functional gene array for examining the relationships between microbial community structure and ecosystem functioning and is a very powerful technology for biogeochemical, ecological and environmental studies. The current version of GeoChip (GeoChip 5.0) contains approximately 162,000 probes from 378,000 genes involved in C, N, S and P cycling, organic contaminant degradation, metal resistance, antibiotic resistance, stress responses, metal homeostasis, virulence, pigment production, bacterial phage-mediated lysis, soil beneficial microorganisms, and specific probes for viruses, protists, and fungi. Our experimental results revealed that both ecosystem and CO2 significantly (p < 0.05) affected the functional composition, structure and metabolic potential of soil microbial communities with the ecosystem having much greater influence (~47%) than CO2 (~1.3%) or CO2 and ecosystem (~4.1%). On one hand, microbial responses to eCO2 shared some common patterns among different ecosystems, such as increased abundances for key functional genes involved in nitrogen fixation, carbon fixation and degradation, and denitrification. On the other hand, more ecosystem-specific microbial responses were identified in each individual ecosystem. Such changes in the soil microbial community structure were closely correlated with geographic distance, soil NO3-N, NH4-N and C/N ratio. Further metagenome sequencing analysis of soil microbial communities in one particular site showed eCO2 altered the overall structure of soil microbial communities with ambient CO2 samples retaining a higher functional gene diversity than eCO2 samples. Also the taxonomic diversity of functional genes decreased at eCO2. Random matrix theory (RMT)-based network analysis showed that the identified networks under ambient and elevated CO2 were substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher order organization (meta-modules), topological roles of individual nodes, and network hubs, indicating that elevated CO2 dramatically altered the network interactions among different phylogenetic and functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen content, indicating the potential importance of network interactions in ecosystem functioning. Taken together, this study indicates that eCO2 may decrease the overall functional and taxonomic diversity of soil microbial communities, but such effects appeared to be ecosystem-specific, which makes it more challenging for predicting global or regional terrestrial ecosystems responses to eCO2.

Field and lab conditions alter microbial enzyme and biomass dynamics driving decomposition of the same leaf litter

PubMed Central

Rinkes, Zachary L.; Sinsabaugh, Robert L.; Moorhead, Daryl L.; Grandy, A. Stuart; Weintraub, Michael N.

2013-01-01

Fluctuations in climate and edaphic factors influence field decomposition rates and preclude a complete understanding of how microbial communities respond to plant litter quality. In contrast, laboratory microcosms isolate the intrinsic effects of litter chemistry and microbial community from extrinsic effects of environmental variation. Used together, these paired approaches provide mechanistic insights to decomposition processes. In order to elucidate the microbial mechanisms underlying how environmental conditions alter the trajectory of decay, we characterized microbial biomass, respiration, enzyme activities, and nutrient dynamics during early (<10% mass loss), mid- (10–40% mass loss), and late (>40% mass loss) decay in parallel field and laboratory litter bag incubations for deciduous tree litters with varying recalcitrance (dogwood < maple < maple-oak mixture < oak). In the field, mass loss was minimal (<10%) over the first 50 days (January–February), even for labile litter types, despite above-freezing soil temperatures and adequate moisture during these winter months. In contrast, microcosms displayed high C mineralization rates in the first week. During mid-decay, the labile dogwood and maple litters in the field had higher mass loss per unit enzyme activity than the lab, possibly due to leaching of soluble compounds. Microbial biomass to litter mass (B:C) ratios peaked in the field during late decay, but B:C ratios declined between mid- and late decay in the lab. Thus, microbial biomass did not have a consistent relationship with litter quality between studies. Higher oxidative enzyme activities in oak litters in the field, and higher nitrogen (N) accumulation in the lab microcosms occurred in late decay. We speculate that elevated N suppressed fungal activity and/or biomass in microcosms. Our results suggest that differences in microbial biomass and enzyme dynamics alter the decay trajectory of the same leaf litter under field and lab conditions. PMID:24027563

The effects of wastewater discharge on the microbiological nitrogen cycle of the lake sediments

NASA Astrophysics Data System (ADS)

Saarenheimo, Jatta; Aalto, Sanni L.; Tiirola, Marja

2016-04-01

Anthropogenic wastewater inputs alter the natural dynamics of nitrogen (N) cycle by providing high concentrations of nitrate and organic matter to the sediment microbes. It can also change the microbial community composition and N removal potential but this is currently not that well studied. To study these aspects, we conducted ecosystem-scale experiment in Lake Keurusselkä, Finland. In the experiment, the wastewater discharge to the recipient lake was optimized with sediment filtration, which increased the surface and retention time of the nitrified wastewater with the sediment. In addition to N transformation rates, which showed that optimization enhanced denitrification, we studied the microbial responses at the sediment. Genetic potential of nitrogen transformation processes, such as denitrification, dissimilatory nitrate reduction to ammonium (DNRA) and nitrification were studied by targeting the functional genes (i.e. nirS, nirK, nosZI, nosZII, nrfA, amoAarchaea and amoAbacteria) with quantitative PCR and digital droplet PCR. In addition, changes in the microbial community composition along the wastewater gradient were examined by using next generation sequencing of the 16S rRNA genes. In line with our hypothesis, the relative abundance of denitrifying genes followed the observed denitrification rates, being highest near the nitrate-rich wastewater discharge. Furthermore the microbial community composition in the discharge point differed clearly from the control and downstream sites, having also the highest numbers of rare OTUs. Abundance of nitrifying bacteria was higher than nitrifying archaea near the waste water discharge, whereas the opposite was seen at the control site. The results indicate that wastewater is not only increasing the denitrification rates, but can also alter the structure and genetic potential microbial communities.

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

PubMed

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

2017-08-22

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

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

PubMed Central

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

2017-01-01

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

Composition and physiological profiling of sprout-associated microbial communities

NASA Technical Reports Server (NTRS)

Matos, Anabelle; Garland, Jay L.; Fett, William F.

2002-01-01

The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of inoculation alters the dynamics of community development regardless of the types of organisms involved.

Microbial community composition and trophic role along a marked salinity gradient in Laguna Puilar, Salar de Atacama, Chile.

PubMed

Dorador, Cristina; Fink, Patrick; Hengst, Martha; Icaza, Gonzalo; Villalobos, Alvaro S; Vejar, Drina; Meneses, Daniela; Zadjelovic, Vinko; Burmann, Lisa; Moelzner, Jana; Harrod, Chris

2018-05-09

The geological, hydrological and microbiological features of the Salar de Atacama, the most extensive evaporitic sedimentary basin in the Atacama Desert of northern Chile, have been extensively studied. In contrast, relatively little attention has been paid to the composition and roles of microbial communities in hypersaline lakes which are a unique feature in the Salar. In the present study biochemical, chemical and molecular biological tools were used to determine the composition and roles of microbial communities in water, microbial mats and sediments along a marked salinity gradient in Laguna Puilar which is located in the "Los Flamencos" National Reserve. The bacterial communities at the sampling sites were dominated by members of the phyla Bacteroidetes, Chloroflexi, Cyanobacteria and Proteobacteria. Stable isotope and fatty acid analyses revealed marked variability in the composition of microbial mats at different sampling sites both horizontally (at different sites) and vertically (in the different layers). The Laguna Puilar was shown to be a microbially dominated ecosystem in which more than 60% of the fatty acids at particular sites are of bacterial origin. Our pioneering studies also suggest that the energy budgets of avian consumers (three flamingo species) and dominant invertebrates (amphipods and gastropods) use minerals as a source of energy and nutrients. Overall, the results of this study support the view that the Salar de Atacama is a heterogeneous and fragile ecosystem where small changes in environmental conditions may alter the balance of microbial communities with possible consequences at different trophic levels.

Degraded Land Restoration in Reinstating CH4 Sink

PubMed Central

Singh, Jay Shankar; Gupta, Vijai K.

2016-01-01

Methane (CH4), a potent greenhouse gas, contributes about one third to the global green house gas emissions. CH4-assimilating microbes (mostly methanotrophs) in upland soils play very crucial role in mitigating the CH4 release into the atmosphere. Agricultural, environmental, and climatic shifts can alter CH4 sink profiles of soils, likely through shifts in CH4-assimilating microbial community structure and function. Landuse change, as forest and grassland ecosystems altered to agro-ecosystems, has already attenuated the soil CH4 sink potential, and are expected to be continued in the future. We hypothesized that variations in CH4 uptake rates in soils under different landuse practices could be an indicative of alterations in the abundance and/or type of methanotrophic communities in such soils. However, only a few studies have addressed to number and methanotrophs diversity and their correlation with the CH4 sink potential in soils of rehabilitated/restored lands. We focus on landuse practices that can potentially mitigate CH4 gas emissions, the most prominent of which are improved cropland, grazing land management, use of bio-fertilizers, and restoration of degraded lands. In this perspective paper, it is proposed that restoration of degraded lands can contribute considerably to improved soil CH4 sink strength by retrieving/conserving abundance and assortment of efficient methanotrophic communities. We believe that this report can assist in identifying future experimental directions to the relationships between landuse changes, methane-assimilating microbial communities and soil CH4 sinks. The exploitation of microbial communities other than methanotrophs can contribute significantly to the global CH4 sink potential and can add value in mitigating the CH4 problems. PMID:27379053

Degraded Land Restoration in Reinstating CH4 Sink.

PubMed

Singh, Jay Shankar; Gupta, Vijai K

2016-01-01

Methane (CH4), a potent greenhouse gas, contributes about one third to the global green house gas emissions. CH4-assimilating microbes (mostly methanotrophs) in upland soils play very crucial role in mitigating the CH4 release into the atmosphere. Agricultural, environmental, and climatic shifts can alter CH4 sink profiles of soils, likely through shifts in CH4-assimilating microbial community structure and function. Landuse change, as forest and grassland ecosystems altered to agro-ecosystems, has already attenuated the soil CH4 sink potential, and are expected to be continued in the future. We hypothesized that variations in CH4 uptake rates in soils under different landuse practices could be an indicative of alterations in the abundance and/or type of methanotrophic communities in such soils. However, only a few studies have addressed to number and methanotrophs diversity and their correlation with the CH4 sink potential in soils of rehabilitated/restored lands. We focus on landuse practices that can potentially mitigate CH4 gas emissions, the most prominent of which are improved cropland, grazing land management, use of bio-fertilizers, and restoration of degraded lands. In this perspective paper, it is proposed that restoration of degraded lands can contribute considerably to improved soil CH4 sink strength by retrieving/conserving abundance and assortment of efficient methanotrophic communities. We believe that this report can assist in identifying future experimental directions to the relationships between landuse changes, methane-assimilating microbial communities and soil CH4 sinks. The exploitation of microbial communities other than methanotrophs can contribute significantly to the global CH4 sink potential and can add value in mitigating the CH4 problems.

Gut microbiota of liver transplantation recipients.

PubMed

Sun, Li-Ying; Yang, Yun-Sheng; Qu, Wei; Zhu, Zhi-Jun; Wei, Lin; Ye, Zhi-Sheng; Zhang, Jian-Rui; Sun, Xiao-Ye; Zeng, Zhi-Gui

2017-06-19

The characteristics of intestinal microbial communities may be affected by changes in the pathophysiology of patients with end-stage liver disease. Here, we focused on the characteristics of intestinal fecal microbial communities in post-liver transplantation (LT) patients in comparison with those in the same individuals pre-LT and in healthy individuals. The fecal microbial communities were analyzed via MiSeq-PE250 sequencing of the V4 region of 16S ribosomal RNA and were then compared between groups. We found that the gut microbiota of patients with severe liver disease who were awaiting LT was significantly different from that of healthy controls, as represented by the first principal component (p = 0.0066). Additionally, the second principal component represented a significant difference in the gut microbiota of patients between pre-LT and post-LT surgery (p = 0.03125). After LT, there was a significant decrease in the abundance of certain microbial species, such as Actinobacillus, Escherichia, and Shigella, and a significant increase in the abundance of other microbial species, such as Micromonosporaceae, Desulfobacterales, the Sarcina genus of Eubacteriaceae, and Akkermansia. Based on KEGG profiles, 15 functional modules were enriched and 21 functional modules were less represented in the post-LT samples compared with the pre-LT samples. Our study demonstrates that fecal microbial communities were significantly altered by LT.

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.

Microbial succession and stimulation following a test well injection simulating CO2 leakage into shallow Newark Basin aquifers

NASA Astrophysics Data System (ADS)

Dueker, M.; Clauson, K.; Yang, Q.; Umemoto, K.; Seltzer, A. M.; Zakharova, N. V.; Matter, J. M.; Stute, M.; Takahashi, T.; Goldberg, D.; O'Mullan, G. D.

2012-12-01

Despite growing appreciation for the importance of microbes in altering geochemical reactions in the subsurface, the microbial response to geological carbon sequestration injections and the role of microbes in altering metal mobilization following leakage scenarios in shallow aquifers remain poorly constrained. A Newark Basin test well was utilized in field experiments to investigate patterns of microbial succession following injection of CO2 saturated water into isolated aquifer intervals. Additionally, laboratory mesocosm experiments, including microbially-active and inactive (autoclave sterilized) treatments, were used to constrain the microbial role in mineral dissolution, trace metal release, and gas production (e.g. hydrogen and methane). Hydrogen production was detected in both sterilized and unsterilized laboratory mesocosm treatments, indicating abiotic hydrogen production may occur following CO2 leakage, and methane production was detected in unsterilized, microbially active mesocosms. In field experiments, a decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), the production of hydrogen gas, and increased bacterial cell concentrations. 16S ribosomal RNA clone libraries, from samples collected before and after the test well injection, were compared in an attempt to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injection, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia, Acidobacteria and other microbes associated with iron reducing and syntrophic metabolism. The concurrence of increased microbial cell concentration, and rapid microbial community succession, with increased concentrations of hydrogen gas suggests that abiotically produced hydrogen may serve as an ecologically-relevant energy source stimulating changes in aquifer microbial communities immediately following CO2 leakage.

Alternative Protein Sources in the Diet Modulate Microbiota and Functionality in the Distal Intestine of Atlantic Salmon (Salmo salar)

PubMed Central

Jaramillo-Torres, Alexander; Kortner, Trond M.; Merrifield, Daniel L.; Tinsley, John; Bakke, Anne Marie; Krogdahl, Åshild

2016-01-01

ABSTRACT The present study aimed to investigate whether alternative dietary protein sources modulate the microbial communities in the distal intestine (DI) of Atlantic salmon, and whether alterations in microbiota profiles are reflected in modifications in host intestinal function and health status. A 48-day feeding trial was conducted, in which groups of fish received one of five diets: a reference diet in which fishmeal (diet FM) was the only protein source and four experimental diets with commercially relevant compositions containing alternative ingredients as partial replacements of fishmeal, i.e., poultry meal (diet PM), a mix of soybean meal and wheat gluten (diet SBMWG), a mix of soy protein concentrate and poultry meal (diet SPCPM), and guar meal and wheat gluten (diet GMWG). Samples were taken of DI digesta and mucosa for microbial profiling using high-throughput sequencing and from DI whole tissue for immunohistochemistry and expression profiling of marker genes for gut health. Regardless of diet, there were significant differences between the microbial populations in the digesta and the mucosa in the salmon DI. Microbial richness was higher in the digesta than the mucosa. The digesta-associated bacterial communities were more affected by the diet than the mucosa-associated microbiota. Interestingly, both legume-based diets (SBMWG and GMWG) presented high relative abundance of lactic acid bacteria in addition to alteration in the expression of a salmon gene related to cell proliferation (pcna). It was, however, not possible to ascertain the cause-effect relationship between changes in bacterial communities and the host's intestinal responses to the diets. IMPORTANCE The intestine of cultivated Atlantic salmon shows symptoms of compromised function, which are most likely caused by imbalances related to the use of new feed ingredients. Intestinal microbiota profiling may become in the future a valuable endpoint measurement in order to assess fish intestinal health status and effects of diet. The present study aimed to gain information about whether alternative dietary protein sources modulate the microbial communities in the Atlantic salmon intestine and whether alterations in microbiota profiles are reflected in alterations in host intestinal function and health status. We demonstrate here that there are substantial differences between the intestinal digesta and mucosa in the presence and abundance of bacteria. The digesta-associated microbiota showed clear dependence on the diet composition, whereas mucosa-associated microbiota appeared to be less affected by diet composition. Most important, the study identified bacterial groups associated with diet-induced gut dysfunction that may be utilized as microbial markers of gut health status in fish. PMID:27986728

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

NASA Astrophysics Data System (ADS)

Wang, Haitao; Marshall, Christopher W.; Cheng, Minying; Xu, Huijuan; Li, Hu; Yang, Xiaoru; Zheng, Tianling

2017-03-01

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Microbial community changes as a possible factor controlling carbon sequestration in subsoil

NASA Astrophysics Data System (ADS)

Strücker, Juliane; Jörgensen, Rainer Georg

2015-04-01

In order to gain more knowledge regarding the microbial community and their influence on carbon sequestration in subsoil two depth profiles with different soil organic carbon (SOC) concentrations were sampled. The SOC concentrations developed naturally due to deposition and erosion. This experiment offers the opportunity to investigate to which extend natural SOC availability or other subsoil specific conditions influence the composition and the functional diversity of the microbial community and in return if there is any evidence how the microbial community composition affects carbon sequestration under these conditions. Soil samples were taken at four different depths on two neighbouring arable sites; one Kolluvisol with high SOC concentrations (8-12 g/kg) throughout the profile and one Luvisol with low SOC concentrations (3-4 g/kg) below 30 cm depth. The multi substrate induced respiration (MSIR) method was used to identify shifts in the functional diversity of the microbial community along the depth profiles. Amino sugars Muramic Acid and Glucosamine were measured as indicators for bacterial and fungal residues and ergosterol was determined as marker for saprotrophic fungi. The results of the discriminant analysis of the respiration values obtained from the 17 substrates used in the MSIR show that the substrate use in subsoil is different from the substrate use in topsoil. The amino sugar analysis and the ratio of ergosterol to microbial biomass C indicate that the fungal dominance of the microbial community decreases with depth. The results from this study support previous findings, which also observed decreasing fungal dominance with depth. Furthermore the MSIR approach shows clearly that not only the composition of the microbial community but also their substrate use changes with depth. Thus, a different microbial community with altered substrate requirements could be an important reason for enhanced carbon sequestration in subsoil. The fact that the MSIR was also able to differentiate between the two sites proves the assumption that resources are an important factor controlling the functional diversity of the microbial community, as abiotic factors are very similar for the two profiles, but the sites show a different depth gradient for SOC.

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.

Flooding forested groundwater recharge areas modifies microbial communities from top soil to groundwater table.

PubMed

Schütz, Kirsten; Nagel, Peter; Vetter, Walter; Kandeler, Ellen; Ruess, Liliane

2009-01-01

Subsurface microorganisms are crucial for contaminant degradation and maintenance of groundwater quality. This study investigates the microbial biomass and community composition [by phospholipid fatty acids (PLFAs)], as well as physical and chemical soil characteristics at woodland flooding sites of an artificial groundwater recharge system used for drinking water production. Vertical soil profiles to c. 4 m at two watered and one nonwatered site were analyzed. The microbial biomass was equal in watered and nonwatered sites, and considerable fractions (25-42%) were located in 40-340 cm depth. The microbial community structure differed significantly between watered and nonwatered sites, predominantly below 100 cm depth. Proportions of the bacterial PLFAs 16:1omega5, 16:1omega7, cy17:0 and 18:1omega9t, and the long-chained PLFAs 22:1omega9 and 24:1omega9 were more prominent at the watered sites, whereas branched, saturated PLFAs (iso/anteiso) dominated at the nonwatered site. PLFA community indices indicated stress response (trans/cis ratio), higher nutrient availability (unsaturation index) and changes in membrane fluidity (iso/anteiso ratio) due to flooding. In conclusion, water recharge processes led to nutrient input and altered environmental conditions, which resulted in a highly active and adapted microbial community residing in the vadose zone that effectively degraded organic compounds.

Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe.

PubMed

Zhang, Ximei; Johnston, Eric R; Li, Linghao; Konstantinidis, Konstantinos T; Han, Xingguo

2017-04-01

Identifying soil microbial feedbacks to increasing temperatures and moisture alterations is critical for predicting how terrestrial ecosystems will respond to climate change. We performed a 5-year field experiment manipulating warming, watering and their combination in a semiarid temperate steppe in northern China. Warming stimulated the abundance of genes responsible for degrading recalcitrant soil organic matter (SOM) and reduced SOM content by 13%. Watering, and warming plus watering also increased the abundance of recalcitrant SOM catabolism pathways, but concurrently promoted plant growth and increased labile SOM content, which somewhat offset SOM loss. The treatments also increased microbial biomass, community complexity and metabolic potential for nitrogen and sulfur assimilation. Both microbial and plant community composition shifted with the treatment conditions, and the sample-to-sample compositional variations of the two communities (pairwise β-diversity distances) were significantly correlated. In particular, microbial community composition was substantially correlated with the dominant plant species (~0.54 Spearman correlation coefficient), much more than with measured soil indices, affirming a tight coupling between both biological communities. Collectively, our study revealed the direction and underlying mechanisms of microbial feedbacks to warming and suggested that semiarid regions of northern steppes could act as a net carbon source under increased temperatures, unless precipitation increases concurrently.

Effects of uranium concentration on microbial community structure and functional potential.

PubMed

Sutcliffe, Brodie; Chariton, Anthony A; Harford, Andrew J; Hose, Grant C; Greenfield, Paul; Elbourne, Liam D H; Oytam, Yalchin; Stephenson, Sarah; Midgley, David J; Paulsen, Ian T

2017-08-01

Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg -1 ), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg -1 sediment and above. At uranium concentrations of ≥ 1500 mg U kg -1 , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Long-term impact of hydrological regime on structure and functions of microbial communities in riverine wetland sediments.

PubMed

Foulquier, Arnaud; Volat, Bernadette; Neyra, Marc; Bornette, Gudrun; Montuelle, Bernard

2013-08-01

In a context of global change, alterations in the water cycle may impact the structure and function of terrestrial and aquatic ecosystems. Wetlands are particularly at risk because hydrological regime has a major influence on microbially mediated biogeochemical processes in sediments. While the influence of water availability on wetland biogeochemical processes has been comprehensively studied, the influence of hydrological regime on microbial community structure has been overlooked. We tested for the effect of hydrological regime on the structure and functions of microbial communities by comparing sediments collected at multiple sites in the Ain département (Eastern France). Each site consisted of two plots, one permanently and one seasonally inundated. At the time of sampling, all plots were continuously inundated for more than 6 months but still harboured distinct bacterial communities. This change in community structure was not associated with marked modifications in the rates of microbial activities involved in the C and N cycles. These results suggest that the observed structural change could be related to bacterial taxa responding to the environmental variations associated with different hydrological regimes, but not strongly associated with the biogeochemical processes monitored here. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison

PubMed Central

Febria, Catherine M.; Hosen, Jacob D.; Crump, Byron C.; Palmer, Margaret A.; Williams, D. Dudley

2015-01-01

Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure and predict the timing, intensity and frequency of wet-dry events. Unsurprisingly, published datasets on microbial community structure and function are limited in scope and temporal resolution and vary widely in the molecular methods applied. We compared environmental and microbial community datasets for permanent and temporary tributaries of two different North American headwater stream systems: Speed River (Ontario, Canada) and Parkers Creek (Maryland, USA). We explored whether taxonomic diversity and community composition were altered as a result of flow permanence and compared community composition amongst streams using different 16S microbial community methods (i.e., T-RFLP and Illumina MiSeq). Contrary to our hypotheses, and irrespective of method, community composition did not respond strongly to drying. In both systems, community composition was related to site rather than drying condition. Additional network analysis on the Parkers Creek dataset indicated a shift in the central microbial relationships between temporary and permanent streams. In the permanent stream at Parkers Creek, associations of methanotrophic taxa were most dominant, whereas associations with taxa from the order Nitrospirales were more dominant in the temporary stream, particularly during dry conditions. We compared these results with existing published studies from around the world and found a wide range in community responses to drying. We conclude by proposing three hypotheses that may address contradictory results and, when tested across systems, may expand understanding of the responses of microbial communities in temporary streams to natural and human-induced fluctuations in flow-status and permanence. PMID:26089816

The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry.

PubMed

Liu, Shanshan; Wang, Feng; Xue, Kai; Sun, Bo; Zhang, Yuguang; He, Zhili; Van Nostrand, Joy D; Zhou, Jizhong; Yang, Yunfeng

2015-03-01

Soil transplant into warmer regions has been shown to alter soil microbiology. In contrast, little is known about the effects of soil transplant into colder regions, albeit that climate cooling has solicited attention in recent years. To address this question, we transplanted bare fallow soil over large transects from southern China (subtropical climate zone) to central (warm temperate climate zone) and northern China (cold temperate climate zone). After an adaptation period of 4 years, soil nitrogen components, microbial biomass and community structures were altered. However, the effects of soil transplant on microbial communities were dampened by maize cropping, unveiling a negative interaction between cropping and transplant. Further statistical analyses with Canonical correspondence analysis and Mantel tests unveiled annual average temperature, relative humidity, aboveground biomass, soil pH and NH4 (+) -N content as environmental attributes closely correlated with microbial functional structures. In addition, average abundances of amoA-AOA (ammonia-oxidizing archaea) and amoA-AOB (ammonia-oxidizing bacteria) genes were significantly (P < 0.05) correlated with soil nitrification capacity, hence both AOA and AOB contributed to the soil functional process of nitrification. These results suggested that the soil nitrogen cycle was intimately linked with microbial community structure, and both were subjected to disturbance by soil transplant to colder regions and plant cropping. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

PubMed

Haberman, Yael; Tickle, Timothy L; Dexheimer, Phillip J; Kim, Mi-Ok; Tang, Dora; Karns, Rebekah; Baldassano, Robert N; Noe, Joshua D; Rosh, Joel; Markowitz, James; Heyman, Melvin B; Griffiths, Anne M; Crandall, Wallace V; Mack, David R; Baker, Susan S; Huttenhower, Curtis; Keljo, David J; Hyams, Jeffrey S; Kugathasan, Subra; Walters, Thomas D; Aronow, Bruce; Xavier, Ramnik J; Gevers, Dirk; Denson, Lee A

2014-08-01

Interactions between the host and gut microbial community likely contribute to Crohn disease (CD) pathogenesis; however, direct evidence for these interactions at the onset of disease is lacking. Here, we characterized the global pattern of ileal gene expression and the ileal microbial community in 359 treatment-naive pediatric patients with CD, patients with ulcerative colitis (UC), and control individuals. We identified core gene expression profiles and microbial communities in the affected CD ilea that are preserved in the unaffected ilea of patients with colon-only CD but not present in those with UC or control individuals; therefore, this signature is specific to CD and independent of clinical inflammation. An abnormal increase of antimicrobial dual oxidase (DUOX2) expression was detected in association with an expansion of Proteobacteria in both UC and CD, while expression of lipoprotein APOA1 gene was downregulated and associated with CD-specific alterations in Firmicutes. The increased DUOX2 and decreased APOA1 gene expression signature favored oxidative stress and Th1 polarization and was maximally altered in patients with more severe mucosal injury. A regression model that included APOA1 gene expression and microbial abundance more accurately predicted month 6 steroid-free remission than a model using clinical factors alone. These CD-specific host and microbe profiles identify the ileum as the primary inductive site for all forms of CD and may direct prognostic and therapeutic approaches.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms.

PubMed

Jung, Jaejoon; Philippot, Laurent; Park, Woojun

2016-03-14

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

PubMed Central

Jung, Jaejoon; Philippot, Laurent; Park, Woojun

2016-01-01

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship. PMID:26972977

A review of the environmental implications of in situ remediation by nanoscale zero valent iron (nZVI): Behavior, transport and impacts on microbial communities.

PubMed

Lefevre, Emilie; Bossa, Nathan; Wiesner, Mark R; Gunsch, Claudia K

2016-09-15

The increasing use of strategies incorporating nanoscale zero valent iron (nZVI) for soil and groundwater in situ remediation is raising some concerns regarding the potential adverse effects nZVI could have on indigenous microbial communities and ecosystem functioning. This review provides an overview of the current literature pertaining to the impacts of nZVI applications on microbial communities. Toxicity studies suggest that cell membrane disruption and oxidative stress through the generation of Fe(2+) and reactive oxygen species by nZVI are the main mechanisms contributing to nZVI cytotoxicity. In addition, nZVI has been shown to substantially alter the taxonomic and functional composition of indigenous microbial communities. However, because the physico-chemical conditions encountered in situ highly modulate nZVI toxicity, a better understanding of the environmental factors affecting nZVI toxicity and transport in the environment is of primary importance in evaluating the ecological consequences that could result from a more extensive use of nZVI. Copyright © 2016 Elsevier B.V. All rights reserved.

Response of Free-Living Nitrogen-Fixing Microorganisms to Land Use Change in the Amazon Rainforest

PubMed Central

Mirza, Babur S.; Potisap, Chotima; Nüsslein, Klaus; Bohannan, Brendan J. M.

2014-01-01

The Amazon rainforest, the largest equatorial forest in the world, is being cleared for pasture and agricultural use at alarming rates. Tropical deforestation is known to cause alterations in microbial communities at taxonomic and phylogenetic levels, but it is unclear whether microbial functional groups are altered. We asked whether free-living nitrogen-fixing microorganisms (diazotrophs) respond to deforestation in the Amazon rainforest, using analysis of the marker gene nifH. Clone libraries were generated from soil samples collected from a primary forest, a 5-year-old pasture originally converted from primary forest, and a secondary forest established after pasture abandonment. Although diazotroph richness did not significantly change among the three plots, diazotroph community composition was altered with forest-to-pasture conversion, and phylogenetic similarity was higher among pasture communities than among those in forests. There was also 10-fold increase in nifH gene abundance following conversion from primary forest to pasture. Three environmental factors were associated with the observed changes: soil acidity, total N concentration, and C/N ratio. Our results suggest a partial restoration to initial levels of abundance and community structure of diazotrophs following pasture abandonment, with primary and secondary forests sharing similar communities. We postulate that the response of diazotrophs to land use change is a direct consequence of changes in plant communities, particularly the higher N demand of pasture plant communities for supporting aboveground plant growth. PMID:24162570

Interactive effects of multiple climate change factors on ammonia oxidizers and denitrifiers in a temperate steppe.

PubMed

Zhang, Cui-Jing; Shen, Ju-Pei; Sun, Yi-Fei; Wang, Jun-Tao; Zhang, Li-Mei; Yang, Zhong-Ling; Han, Hong-Yan; Wan, Shi-Qiang; He, Ji-Zheng

2017-04-01

Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques, were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition. Only the abundance of ammonia-oxidizing bacteria significantly increased by nitrogen addition and decreased by watering. The interactions of watering × warming on the bacterial amoA community and warming × nitrogen addition on the nosZ community were found. Redundancy analysis indicated that the ammonia-oxidizing archaeal community was affected by total N and total carbon, while the community of bacterial amoA and nosZ were significantly affected by soil pH. According to a structural equation modeling analysis, climate change influenced net primary production indirectly by altering microbial abundance and activities. These results indicated that microbial responses to the combination of chronic global change tend to be smaller than expected from single-factor global change manipulations. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest.

PubMed

Du, Can; Geng, Zengchao; Wang, Qiang; Zhang, Tongtong; He, Wenxiang; Hou, Lin; Wang, Yueling

2017-09-01

Microbial communities in subsurface soil are specialized for their environment, which is distinct from that of the surface communities. However, little is known about the microbial communities (bacteria and fungi) that exist in the deeper soil horizons. Vertical changes in microbial alpha-diversity (Chao1 and Shannon indices) and community composition were investigated at four soil depths (0-10, 10-20, 20-40, and 40-60 cm) in a natural secondary forest of Betula albosinensis by high-throughput sequencing of the 16S and internal transcribed spacer rDNA regions. The numbers of operational taxonomic units (OTUs), and the Chao1 and Shannon indices decreased in the deeper soil layers. Each soil layer contained both mutual and specific OTUs. In the 40-60 cm soil layer, 175 and 235 specific bacterial and fungal OTUs were identified, respectively. Acidobacteria was the most dominant bacterial group in all four soil layers, but reached its maximum at 40-60 cm (62.88%). In particular, the 40-60 cm soil layer typically showed the highest abundance of the fungal genus Inocybe (47.46%). The Chao1 and Shannon indices were significantly correlated with the soil organic carbon content. Redundancy analysis indicated that the bacterial communities were closely correlated with soil organic carbon content (P = 0.001). Collectively, these results indicate that soil nutrients alter the microbial diversity and relative abundance and affect the microbial composition.

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

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

Graham, Emily B.; Stegen, James C.

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

DOE PAGES

Graham, Emily B.; Stegen, James C.

2017-11-01

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores.

PubMed

Kohl, Kevin D; Dearing, M D

2012-09-01

For decades, ecologists have hypothesised that exposure to plant secondary compounds (PSCs) modifies herbivore-associated microbial community composition. This notion has not been critically evaluated in wild mammalian herbivores on evolutionary timescales. We investigated responses of the microbial communities of two woodrat species (Neotoma bryanti and N. lepida). For each species, we compared experienced populations that independently converged to feed on the same toxic plant (creosote bush, Larrea tridentata) to naïve populations with no exposure to creosote toxins. The addition of dietary PSCs significantly altered gut microbial community structure, and the response was dependent on previous experience. Microbial diversity and relative abundances of several dominant phyla increased in experienced woodrats in response to PSCs; however, opposite effects were observed in naïve woodrats. These differential responses were convergent in experienced populations of both species. We hypothesise that adaptation of the foregut microbiota to creosote PSCs in experienced woodrats drives this differential response. © 2012 Blackwell Publishing Ltd/CNRS.

Rhizosphere Microbial Community Structure in Relation to Root Location and Plant Iron Nutritional Status

PubMed Central

Yang, Ching-Hong; Crowley, David E.

2000-01-01

Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status. PMID:10618246

Nitrogen amendments have predictable effects on soil microbial communities and processes

NASA Astrophysics Data System (ADS)

Ramirez, K. S.; Craine, J. M.; Fierer, N.

2011-12-01

Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) through anthropogenic activities. While there has been much effort devoted to quantifying aboveground impacts of anthropogenic N effects, less work has focused on identifying belowground impacts. Bacteria play critical roles in ecosystem processes and identifying how anthropogenic N impacts bacterial communities may elucidate how critical microbially-mediated ecosystem functions are altered by N additions. In order to connect changes in soil processes to changes in the microbial community, we need to first determine if the changes are consistent across different soil types and ecosystems. We assessed the patterns of N effects across a variety of ecosystems in two ways. First, utilizing long-term experimental N gradients at Cedar Creek LTER, MN and Kellogg Biological Station LTER, MI, we examined the response of microbial communities to anthropogenic N additions. Using high-throughput pyrosequencing techniques we quantified changes in soil microbial communities across the nitrogen gradients. We observed strong directional shifts in community composition at both sites; N fertilization consistently impacted both the phylogenetic and taxonomic structure of soil bacterial community structure in a predictable manner regardless of ecosystem type. For example, at both sites Acidobacteria experienced significant declines as nitrogen increased, while other groups such as Actinobacteria and Bacteroidetes increased in relative abundance. Our results suggest that bacterial communities across these N fertility gradients are structured by either nitrogen and/or soil carbon availability, rather than by shifts in the plant community or soil pH indirectly associated with the elevated nitrogen inputs. Still, this field-work does not incorporate changes in soil processes (e.g. soil respiration) or microbial activity (e.g. microbial biomass and extracellular enzyme activity), or separate N from C effects. To address these factors, we performed a lab experiment, amending 30 soils collected from across North America with inorganic N. From this year-long incubation we obtained soil respiration, microbial biomass, bacterial community and extracellular enzyme activity measurements. Across all soil types we consistently observed a significant decrease in both soil respiration, approximately 10%, and microbial biomass, approximately 35%. Using high-throughput pyrosequencing we identified seven bacterial groups that responded significantly to the N additions, including those observed in our field survey. Together, this work suggests that increases in soil N shifts the functional capabilities of the microbial community and highlights possibly mechanisms behind the observed changes.

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

PubMed

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

2017-11-01

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

Plant, Microbiome, and Biogeochemistry: Quantifying moss-associated N fixation in Alaska

NASA Astrophysics Data System (ADS)

Stuart, J.; Mack, M. C.; Holland Moritz, H.; Fierer, N.; McDaniels, S.; Lewis, L.

2017-12-01

The future carbon (C) sequestration potential of the Arctic and boreal zones, currently the largest terrestrial C sink globally, is linked to nitrogen (N) cycling and N availability vis-a-vis C accumulation and plant species composition. Pristine environments in Alaska have low anthropogenic N deposition (<1 kg N ha-1 yr-1), and the main source of new N to these ecosystems is through previously overlooked N-fixation from microbial communities on mosses. Despite the importance of moss associated N-fixation, the relationship between moss species, microbial communities, and fixation rates remains ambiguous. In the summer of 2016, the fixation rates of 20 moss species from sites around both Fairbanks and Toolik Lake were quantified using 15N2 incubations. Subsequently, the microbial community and moss genome of the samples were also analyzed by collaborators. The most striking result is that all sampled moss genera fixed N, including well-studied feather mosses such as Hylocomium splendens and Pleurozium schreberi as well as less common but ecologically relevant mosses such as Aulacomnium spp., Dicranum spp., Ptilium crista-castrensis, and Tomentypnum nitens. Across all samples, preliminary fixation rates ranged from 0.004-19.994 µg N g-1 moss d-1. Depending upon percent cover, moss-associated N fixation is the largest input of new N to the ecosystem. Given this, linking variation in N-fixation rates to microbial and moss community structures can be helpful in predicting future trends of C and N cycling in northern latitudes. Vegetation changes, alterations in downstream biogeochemical N processes, and anthropogenic N deposition could all interact with or alter moss associated N-fixation, thereby changing ecosystem N inputs. Further elucidation of the species level signal in N-fixation rates and microbial community will augment our knowledge of N cycling in northern latitudes, both current and future.

Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils

PubMed Central

Billings, Andrew F.; Blanchard, Jeff L.; Burkhardt, Daniel B.; Frey, Serita D.; Melillo, Jerry M.; Schnabel, Julia; van Diepen, Linda T. A.

2016-01-01

ABSTRACT As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world. IMPORTANCE The massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change. PMID:27590813

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil

DOE PAGES

Khdhiri, Mondher; Piché-Choquette, Sarah; Tremblay, Julien; ...

2017-03-31

The enrichment of H 2-oxidizing bacteria (HOB) by H 2 generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. In this paper, we report that the energy potential of H 2, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H 2more » mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H 2 exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H 2 while enhancing community level carbon substrate utilization potential and lowering CH 4 uptake activity in soil. We found that H 2 triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H 2 exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. Finally, we argue that further examination of direct and indirect effects of H 2 on soil microbial communities will lead to a better understanding of the H 2 fertilization effect and soil biogeochemical processes.« less

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil

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

Khdhiri, Mondher; Piché-Choquette, Sarah; Tremblay, Julien

The enrichment of H 2-oxidizing bacteria (HOB) by H 2 generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. In this paper, we report that the energy potential of H 2, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H 2more » mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H 2 exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H 2 while enhancing community level carbon substrate utilization potential and lowering CH 4 uptake activity in soil. We found that H 2 triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H 2 exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. Finally, we argue that further examination of direct and indirect effects of H 2 on soil microbial communities will lead to a better understanding of the H 2 fertilization effect and soil biogeochemical processes.« less

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

PubMed Central

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

2018-01-01

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

Structural and functional alterations in the colonic microbiome of the rat in a model of stress induced irritable bowel syndrome

PubMed Central

Fourie, Nicolaas H.; Wang, Dan; Abey, Sarah K.; Creekmore, Amy L.; Hong, Shuangsong; Martin, Christiana G.; Wiley, John W.

2017-01-01

ABSTRACT Stress is known to perturb the microbiome and exacerbate irritable bowel syndrome (IBS) associated symptoms. Characterizing structural and functional changes in the microbiome is necessary to understand how alterations affect the biomolecular environment of the gut in IBS. Repeated water avoidance (WA) stress was used to induce IBS-like symptoms in rats. The colon-mucosa associated microbiome was characterized in 13 stressed and control animals by 16S sequencing. In silico analysis of the functional domains of microbial communities was done by inferring metagenomic profiles from 16S data. Microbial communities and functional profiles were compared between conditions. WA animals exhibited higher α-diversity and moderate divergence in community structure (β-diversity) compared with controls. Specific clades and taxa were consistently and significantly modified in the WA animals. The WA microbiome was particularly enriched in Proteobacteria and depleted in several beneficial taxa. A decreased capacity in metabolic domains, including energy- and lipid-metabolism, and an increased capacity for fatty acid and sulfur metabolism was inferred for the WA microbiome. The stressed condition favored the proliferation of a greater diversity of microbes that appear to be functionally similar, resulting in a functionally poorer microbiome with implications for epithelial health. Taxa, with known beneficial effects, were found to be depleted, which supports their relevance as therapeutic agents to restore microbial health. Microbial sulfur metabolism may form a key component of visceral nerve sensitization pathways and is therefore of interest as a target metabolic domain in microbial ecological restoration. PMID:28059627

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

PubMed Central

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

2015-01-01

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

Biofouling of reverse osmosis membranes: effects of cleaning on biofilm microbial communities, membrane performance, and adherence of extracellular polymeric substances.

PubMed

Al Ashhab, Ashraf; Sweity, Amer; Bayramoglu, Bihter; Herzberg, Moshe; Gillor, Osnat

2017-05-01

Laboratory-scale reverse osmosis (RO) flat-sheet systems were used with two parallel flow cells, one treated with cleaning agents and a control (ie undisturbed). The cleaning efforts increased the affinity of extracellular polymeric substances (EPS) to the RO membrane and altered the biofilm surface structure. Analysis of the membrane biofilm community composition revealed the dominance of Proteobacteria. However, within the phylum Proteobacteria, γ-Proteobacteria dominated the cleaned membrane biofilm, while β-Proteobacteria dominated the control biofilm. The composition of the fungal phyla was also altered by cleaning, with enhancement of Ascomycota and suppression of Basidiomycota. The results suggest that repeated cleaning cycles select for microbial groups that strongly attach to the RO membrane surface by producing rigid and adhesive EPS that hampers membrane performance.

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

PubMed Central

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

2014-01-01

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

Why fruit rots: theoretical support for Janzen's theory of microbe-macrobe competition.

PubMed

Ruxton, Graeme D; Wilkinson, David M; Schaefer, H Martin; Sherratt, Thomas N

2014-05-07

We present a formal model of Janzen's influential theory that competition for resources between microbes and vertebrates causes microbes to be selected to make these resources unpalatable to vertebrates. That is, fruit rots, seeds mould and meat spoils, in part, because microbes gain a selective advantage if they can alter the properties of these resources to avoid losing the resources to vertebrate consumers. A previous model had failed to find circumstances in which such a costly spoilage trait could flourish; here, we present a simple analytic model of a general situation where costly microbial spoilage is selected and persists. We argue that the key difference between the two models lies in their treatments of microbial dispersal. If microbial dispersal is sufficiently spatially constrained that different resource items can have differing microbial communities, then spoilage will be selected; however, if microbial dispersal has a strong homogenizing effect on the microbial community then spoilage will not be selected. We suspect that both regimes will exist in the natural world, and suggest how future empirical studies could explore the influence of microbial dispersal on spoilage.

Environmental Control on Microbial Turnover of Leaf Carbon in Streams – Ecological Function of Phototrophic-Heterotrophic Interactions

PubMed Central

Fabian, Jenny; Zlatanović, Sanja; Mutz, Michael; Grossart, Hans-Peter; van Geldern, Robert; Ulrich, Andreas; Gleixner, Gerd; Premke, Katrin

2018-01-01

In aquatic ecosystems, light availability can significantly influence microbial turnover of terrestrial organic matter through associated metabolic interactions between phototrophic and heterotrophic communities. However, particularly in streams, microbial functions vary significantly with the structure of the streambed, that is the distribution and spatial arrangement of sediment grains in the streambed. It is therefore essential to elucidate how environmental factors synergistically define the microbial turnover of terrestrial organic matter in order to better understand the ecological role of photo-heterotrophic interactions in stream ecosystem processes. In outdoor experimental streams, we examined how the structure of streambeds modifies the influence of light availability on microbial turnover of leaf carbon (C). Furthermore, we investigated whether the studied relationships of microbial leaf C turnover to environmental conditions are affected by flow intermittency commonly occurring in streams. We applied leaves enriched with a 13C-stable isotope tracer and combined quantitative and isotope analyses. We thereby elucidated whether treatment induced changes in C turnover were associated with altered use of leaf C within the microbial food web. Moreover, isotope analyses were combined with measurements of microbial community composition to determine whether changes in community function were associated with a change in community composition. In this study, we present evidence, that environmental factors interactively determine how phototrophs and heterotrophs contribute to leaf C turnover. Light availability promoted the utilization of leaf C within the microbial food web, which was likely associated with a promoted availability of highly bioavailable metabolites of phototrophic origin. However, our results additionally confirm that the structure of the streambed modifies light-related changes in microbial C turnover. From our observations, we conclude that the streambed structure influences the strength of photo-heterotrophic interactions by defining the spatial availability of algal metabolites in the streambed and the composition of microbial communities. Collectively, our multifactorial approach provides valuable insights into environmental controls on the functioning of stream ecosystems.

Alteration of microbial community structure affects diesel biodegradation in an Arctic soil.

PubMed

Bell, Terrence H; Yergeau, Etienne; F Juck, Dave; G Whyte, Lyle; W Greer, Charles

2013-07-01

A wide range of microbial taxa are active in hydrocarbon-contaminated Arctic soils, and many are capable of hydrocarbon metabolism. The most effective hydrocarbon degraders may not naturally dominate following contamination events, so shifts in microbial abundance could potentially increase hydrocarbon biodegradation. In this study, we contaminated an Arctic soil with diesel and used gentamicin and vancomycin to inhibit distinct portions of the microbial community. We measured diesel loss using gas chromatography, bacterial and fungal abundance with qPCR, and assessed bacterial diversity and community composition through Ion Torrent sequencing of 16S rRNA gene amplicons. The combined addition of both antibiotics increased diesel biodegradation significantly relative to the no-antibiotic treatment, despite reduced bacterial and fungal abundance; however, this effect was not observed when nutrients were also added. All treatments produced unique bacterial communities, and both Xanthomonadaceae and Micrococcineae were dominant in the dual antibiotic treatment. The bacterial communities resulting from dual gentamicin and vancomycin addition were similar both with and without nutrients, although nutrient addition produced a much larger fungal population, which may partly explain the differences in biodegradation between these two treatments. These results suggest that the most efficient hydrocarbon-degrading community may not always be promoted naturally in contaminated soils. © Her Majesty the Queen in Right of Canada 2013.

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

PubMed

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

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities

USGS Publications Warehouse

Mumford, Adam C.; Akob, Denise M.; Klinges, J. Grace; Cozzarelli, Isabelle M.

2018-01-01

The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C3H6BrNO4). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills.

A Seafloor Microbial Biome Hosted within Incipient Ferromanganese Crusts

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

Templeton, Alexis S.; Knowles, A. S.; Eldridge, D. L.

2009-11-15

Unsedimented volcanic rocks exposed on the seafloor at ridge systems and Seamounts host complex, abundant and diverse microbial communities that are relatively cosmopolitan in distribution (Lysnes, Thorseth et al. 2004; Mason, Stingl et al. 2007; Santelli, Orcutt et al. 2008). The most commonly held hypothesis is that the energy released by the hydration, dissolution and oxidative alteration of volcanic glasses in seawater drives the formation of an ocean crust biosphere (Thorseth, Furnes et al. 1992; Fisk, Giovannoni et al. 1998; Furnes and Staudigel 1999). The combined thermodynamically favorable weathering reactions could theoretically support anywhere from 105 to 109 cells/gram ofmore » rock depending upon the metabolisms utilized and cellular growth rates and turnover (Bach and Edwards 2003; Santelli, Orcutt et al. 2008). Yet microbially-mediated basalt alteration and energy conservation has not been directly demonstrated on the seafloor. By using synchrotron-based x-ray microprobe mapping, x-ray absorption spectroscopy and high-resolution scanning and transmission electron microscopy observations of young volcanic glasses recovered from the outer flanks of Loihi Seamount, we intended to identify the initial rates and mechanisms of microbial basalt colonization and bioalteration. Instead, here we show that microbial biofilms are intimately associated with ferromanganese crusts precipitating onto basalt surfaces from cold seawater. Thus we hypothesize that microbial communities colonizing seafloor rocks are established and sustained by external inputs of potential energy sources, such as dissolved and particulate Fe(II), Mn(II) and organic matter, rather than rock dissolution.« less

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

PubMed

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

2014-03-04

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

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment

PubMed Central

Kinsela, Andrew S.; Bligh, Mark W.; Harrison, Jennifer J.; Payne, Timothy E.

2017-01-01

ABSTRACT During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. PMID:28667104

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment.

PubMed

Vázquez-Campos, Xabier; Kinsela, Andrew S; Bligh, Mark W; Harrison, Jennifer J; Payne, Timothy E; Waite, T David

2017-09-01

During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. Copyright © 2017 Vázquez-Campos et al.

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

Legacy effects overwhelm the short-term effects of exotic plant invasion and restoration on soil microbial community structure, enzyme activities, and nitrogen cycling.

PubMed

Elgersma, Kenneth J; Ehrenfeld, Joan G; Yu, Shen; Vor, Torsten

2011-11-01

Plant invasions can have substantial consequences for the soil ecosystem, altering microbial community structure and nutrient cycling. However, relatively little is known about what drives these changes, making it difficult to predict the effects of future invasions. In addition, because most studies compare soils from uninvaded areas to long-established dense invasions, little is known about the temporal dependence of invasion impacts. We experimentally manipulated forest understory vegetation in replicated sites dominated either by exotic Japanese barberry (Berberis thunbergii), native Viburnums, or native Vacciniums, so that each vegetation type was present in each site-type. We compared the short-term effect of vegetation changes to the lingering legacy effects of the previous vegetation type by measuring soil microbial community structure (phospholipid fatty acids) and function (extracellular enzymes and nitrogen mineralization). We also replaced the aboveground litter in half of each plot with an inert substitute to determine if changes in the soil microbial community were driven by aboveground or belowground plant inputs. We found that after 2 years, the microbial community structure and function was largely determined by the legacy effect of the previous vegetation type, and was not affected by the current vegetation. Aboveground litter removal had only weak effects, suggesting that changes in the soil microbial community and nutrient cycling were driven largely by belowground processes. These results suggest that changes in the soil following either invasion or restoration do not occur quickly, but rather exhibit long-lasting legacy effects from previous belowground plant inputs.

Coastal urbanisation affects microbial communities on a dominant marine holobiont.

PubMed

Marzinelli, Ezequiel M; Qiu, Zhiguang; Dafforn, Katherine A; Johnston, Emma L; Steinberg, Peter D; Mayer-Pinto, Mariana

2018-01-01

Host-associated microbial communities play a fundamental role in the life of eukaryotic hosts. It is increasingly argued that hosts and their microbiota must be studied together as 'holobionts' to better understand the effects of environmental stressors on host functioning. Disruptions of host-microbiota interactions by environmental stressors can negatively affect host performance and survival. Substantial ecological impacts are likely when the affected hosts are habitat-forming species (e.g., trees, kelps) that underpin local biodiversity. In marine systems, coastal urbanisation via the addition of artificial structures is a major source of stress to habitat formers, but its effect on their associated microbial communities is unknown. We characterised kelp-associated microbial communities in two of the most common and abundant artificial structures in Sydney Harbour-pier-pilings and seawalls-and in neighbouring natural rocky reefs. The kelp Ecklonia radiata is the dominant habitat-forming species along 8000 km of the temperate Australian coast. Kelp-associated microbial communities on pilings differed significantly from those on seawalls and natural rocky reefs, possibly due to differences in abiotic (e.g., shade) and biotic (e.g., grazing) factors between habitats. Many bacteria that were more abundant on kelp on pilings belonged to taxa often associated with macroalgal diseases, including tissue bleaching in Ecklonia . There were, however, no differences in kelp photosynthetic capacity between habitats. The observed differences in microbial communities may have negative effects on the host by promoting fouling by macroorganisms or by causing and spreading disease over time. This study demonstrates that urbanisation can alter the microbiota of key habitat-forming species with potential ecological consequences.

A Mechanistic Study of Plant and Microbial Controls over R* for Nitrogen in an Annual Grassland

PubMed Central

Levine, Jonathan M.; HilleRisLambers, Janneke

2014-01-01

Differences in species' abilities to capture resources can drive competitive hierarchies, successional dynamics, community diversity, and invasions. To investigate mechanisms of resource competition within a nitrogen (N) limited California grassland community, we established a manipulative experiment using an R* framework. R* theory holds that better competitors within a N limited community should better depress available N in monoculture plots and obtain higher abundance in mixture plots. We asked whether (1) plant uptake or (2) plant species influences on microbial dynamics were the primary drivers of available soil N levels in this system where N structures plant communities. To disentangle the relative roles of plant uptake and microbially-mediated processes in resource competition, we quantified soil N dynamics as well as N pools in plant and microbial biomass in monoculture plots of 11 native or exotic annual grassland plants over one growing season. We found a negative correlation between plant N content and soil dissolved inorganic nitrogen (DIN, our measure of R*), suggesting that plant uptake drives R*. In contrast, we found no relationship between microbial biomass N or potential net N mineralization and DIN. We conclude that while plant-microbial interactions may have altered the overall quantity of N that plants take up, the relationship between species' abundance and available N in monoculture was largely driven by plant N uptake in this first year of growth. PMID:25170943

Changes in bacterial community after application of three different herbicides.

PubMed

Moretto, Jéssica Aparecida Silva; Altarugio, Lucas Miguel; Andrade, Pedro Avelino; Fachin, Ana Lúcia; Andreote, Fernando Dini; Stehling, Eliana Guedes

2017-07-06

The native soil microbiota is very important to maintain the quality of that environment, but with the intensive use of agrochemicals, changes in microbial biomass and formation of large quantities of toxic waste were observed in soil, groundwater and surface water. Thereby, the goal of this study was to evaluate if the selective pressure exerted by the presence of the herbicides atrazine, diuron and 2,4-D changes the bacterial community structure of an agricultural soil, using denaturing gradient gel electrophoresis technique. According to PERMANOVA analysis, a greater effect of the herbicide persistence time in the soil, the effect of the herbicide class and the effect of interaction between these two factors (persistence time and herbicide class) were observed. In conclusion, the results showed that the selective pressure exerted by the presence of these herbicides altered the composition of the local microbiota, being atrazine and diuron that most significantly affected the bacterial community in soil, and the herbicide 2,4-D was the one that less altered the microbial community and that bacterial community was reestablished first. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tropical Land Use Conversion Effects on Soil Microbial Community Structure and Function: Emerging Patterns and Knowledge Gaps

NASA Astrophysics Data System (ADS)

Seeley, M.; Marin-Spiotta, E.

2016-12-01

Modifications in vegetation due to land use conversions (LUC) between primary forests, pasture, cropping systems, tree plantations, and secondary forests drive shifts in soil microbial communities. These microbial community alterations affect carbon sequestration, nutrient cycling, aboveground biomass, and numerous other soil processes. Despite their importance, little is known about soil microbial organisms' response to LUC, especially in tropical regions where LUC rates are greatest. This project identifies current trends and uncertainties in tropical soil microbiology by comparing 56 published studies on LUC in tropical regions. This review indicates that microbial biomass and functional groups shifted in response to LUC, supporting demonstrated trends in changing soil carbon stocks due to LUC. Microbial biomass was greatest in primary forests when compared to secondary forests and in all forests when compared to both cropping systems and tree plantations. No trend existed when comparing pasture systems and forests, likely due to variations in pasture fertilizer use. Cropping system soils had greater gram positive and less gram negative bacteria than forest soils, potentially resulting in greater respiration of older carbon stocks in agricultural soils. Bacteria dominated primary forests while fungal populations were greatest in secondary forests. To characterize changes in microbial communities resulting from land use change, research must reflect the biophysical variation across the tropics. A chi-squared test revealed that the literature sites represented mean annual temperature variation across the tropics (p-value=0.66).

Arctic gypsum endoliths: a biogeochemical characterization of a viable and active microbial community

NASA Astrophysics Data System (ADS)

Ziolkowski, L. A.; Mykytczuk, N. C. S.; Omelon, C. R.; Johnson, H.; Whyte, L. G.; Slater, G. F.

2013-11-01

Extreme environmental conditions such as those found in the polar regions on Earth are thought to test the limits of life. Microorganisms living in these environments often seek protection from environmental stresses such as high UV exposure, desiccation and rapid temperature fluctuations, with one protective habitat found within rocks. Such endolithic microbial communities, which often consist of bacteria, fungi, algae and lichens, are small-scale ecosystems comprised of both producers and consumers. However, the harsh environmental conditions experienced by polar endolithic communities are thought to limit microbial diversity and therefore the rate at which they cycle carbon. In this study, we characterized the microbial community diversity, turnover rate and microbe-mineral interactions of a gypsum-based endolithic community in the polar desert of the Canadian high Arctic. 16S/18S/23S rRNA pyrotag sequencing demonstrated the presence of a diverse community of phototrophic and heterotrophic bacteria, archaea, algae and fungi. Stable carbon isotope analysis of the viable microbial membranes, as phospholipid fatty acids and glycolipid fatty acids, confirmed the diversity observed by molecular techniques and indicated that present-day atmospheric carbon is assimilated into the microbial community biomass. Uptake of radiocarbon from atmospheric nuclear weapons testing during the 1960s into microbial lipids was used as a pulse label to determine that the microbial community turns over carbon on the order of 10 yr, equivalent to 4.4 g C m-2 yr-1 gross primary productivity. Scanning electron microscopy (SEM) micrographs indicated that mechanical weathering of gypsum by freeze-thaw cycles leads to increased porosity, which ultimately increases the habitability of the rock. In addition, while bacteria were adhered to these mineral surfaces, chemical analysis by micro-X-ray fluorescence (μ-XRF) spectroscopy suggests little evidence for microbial alteration of minerals, which contrasts with other endolithic habitats. While it is possible that these communities turn over carbon quickly and leave little evidence of microbe-mineral interaction, an alternative hypothesis is that the soluble and friable nature of gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas

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

Mohan, Arvind Murali; Hartsock, Angela; Hammack, Richard W

2013-12-01

Hydraulic fracturing for natural gas extraction from shale produces waste brine known as flowback that is impounded at the surface prior to reuse and/or disposal. During impoundment, microbial activity can alter the fate of metals including radionuclides, give rise to odorous compounds, and result in biocorrosion that complicates water and waste management and increases production costs. Here, we describe the microbial ecology at multiple depths of three flowback impoundments from the Marcellus shale that were managed differently. 16S rRNA gene clone libraries revealed that bacterial communities in the untreated and biocide-amended impoundments were depth dependent, diverse, and most similar tomore » species within the taxa [gamma]-proteobacteria, [alpha]-proteobacteria, δ-proteobacteria, Clostridia, Synergistetes, Thermotogae, Spirochetes, and Bacteroidetes. The bacterial community in the pretreated and aerated impoundment was uniform with depth, less diverse, and most similar to known iodide-oxidizing bacteria in the [alpha]-proteobacteria. Archaea were identified only in the untreated and biocide-amended impoundments and were affiliated to the Methanomicrobia class. This is the first study of microbial communities in flowback water impoundments from hydraulic fracturing. The findings expand our knowledge of microbial diversity of an emergent and unexplored environment and may guide the management of flowback impoundments.« less

The prebiotics 3′Sialyllactose and 6′Sialyllactose diminish stressor-induced anxiety-like behavior and colonic microbiota alterations: evidence for effects on the gut-brain axis

PubMed Central

Tarr, Andrew J.; Galley, Jeffrey D.; Fisher, Sydney; Chichlowski, Maciej; Berg, Brian M.; Bailey, Michael T.

2015-01-01

There are extensive bidirectional interactions between the gut microbiota and the central nervous system (CNS), and studies demonstrate that stressor exposure significantly alters gut microbiota community structure. We tested whether oligosaccharides naturally found in high levels in human milk, which have been reported to impact brain development and enhance the growth of beneficial commensal microbes, would prevent stressor-induced alterations in gut microbial community composition and attenuate stressor-induced anxiety-like behavior. Mice were fed standard laboratory diet, or laboratory diet containing the human milk oligosaccharides 3′Sialyllactose (3′SL) or 6′Sialyllactose (6′SL) for two weeks prior to being exposed to either a social disruption stressor or a non-stressed control condition. Stressor exposure significantly changed the structure of the colonic mucosa-associated microbiota in control mice, as indicated by changes in beta diversity. The stressor resulted in anxiety-like behavior in both the light/dark preference and open field tests in control mice. This effect was associated with a reduction in immature neurons in the dentate gyrus as indicated by doublecortin (DCX) immunostaining. These effects were not evident in mice fed milk oligosaccharides; stressor exposure did not significantly change microbial community structure in mice fed 3′SL or 6′SL. In addition, 3′SL and 6′SL helped maintain normal behavior on tests of anxiety-like behavior and normal numbers of DCX+ immature neurons. These studies indicate that milk oligosaccharides support normal microbial communities and behavioral responses during stressor exposure, potentially through effects on the gut microbiota-brain axis. PMID:26144888

An investigation into the effects of silver nanoparticles on natural microbial communities in two freshwater sediments.

PubMed

Bao, Shaopan; Wang, Han; Zhang, Weicheng; Xie, Zhicai; Fang, Tao

2016-12-01

The expanding production and usage of commercial silver nanoparticles (AgNPs) will inevitably increase their environmental release, with sediments as a substantial sink. However, little knowledge is available about the potential impacts of AgNPs on freshwater sediment microbial communities, as well as the interactions between microbial communities and biogeochemical factors in AgNPs polluted sediment. To address these issues, two different sediments: a eutrophic freshwater sediment and an oligotrophic freshwater sediment, were exposed to 1 mg/g of either AgNO 3 , uncoated AgNPs (35-nm and 75-nm), or polyvinylpyrrolidone coated AgNPs (PVP-AgNPs) (30-50 nm) for 45 days. High-throughput sequencing of 16S ribosomal ribonucleic acid (16S rRNA) genes using the Illumina MiSeq platform was conducted to evaluate the effects of Ag addition on bacterial community composition. Moreover, sediment microbial biomass and activity were assessed by counting cultivable bacterial number and determining enzyme activities. During the 45-day exposure, compared with no amendment control, some treatments had resulted in significant changes and alterations of sediment biomass or bacterial enzyme activities shortly. While the microbial components at phylum level were rarely affected by AgNPs addition, and as confirmed by the statistical analysis with two-factor analysis of similarities (ANOSIM), there were no significant differences on bacterial community structure across the amended treatments. Redundancy analysis further demonstrated that chemical parameters acid-volatile sulfide (AVS) and simultaneously extracted silver (SE-Ag) in sediment significantly structured the overall bacterial community in sediments spiked with various silver species. In summary, these findings suggested that the ecotoxicity of AgNPs may be attenuated by the transformation under complex environmental conditions and the self-adaption of sediment microbial communities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Contrasting the Genetic Patterns of Microbial Communities in Soda Lakes with and without Cyanobacterial Bloom

PubMed Central

Andreote, Ana P. D.; Dini-Andreote, Francisco; Rigonato, Janaina; Machineski, Gabriela Silva; Souza, Bruno C. E.; Barbiero, Laurent; Rezende-Filho, Ary T.; Fiore, Marli F.

2018-01-01

Soda lakes have high levels of sodium carbonates and are characterized by salinity and elevated pH. These ecosystems are found across Africa, Europe, Asia, Australia, North, Central, and South America. Particularly in Brazil, the Pantanal region has a series of hundreds of shallow soda lakes (ca. 600) potentially colonized by a diverse haloalkaliphilic microbial community. Biological information of these systems is still elusive, in particular data on the description of the main taxa involved in the biogeochemical cycling of life-important elements. Here, we used metagenomic sequencing to contrast the composition and functional patterns of the microbial communities of two distinct soda lakes from the sub-region Nhecolândia, state of Mato Grosso do Sul, Brazil. These two lakes differ by permanent cyanobacterial blooms (Salina Verde, green-water lake) and by no record of cyanobacterial blooms (Salina Preta, black-water lake). The dominant bacterial species in the Salina Verde bloom was Anabaenopsis elenkinii. This cyanobacterium altered local abiotic parameters such as pH, turbidity, and dissolved oxygen and consequently the overall structure of the microbial community. In Salina Preta, the microbial community had a more structured taxonomic profile. Therefore, the distribution of metabolic functions in Salina Preta community encompassed a large number of taxa, whereas, in Salina Verde, the functional potential was restrained across a specific set of taxa. Distinct signatures in the abundance of genes associated with the cycling of carbon, nitrogen, and sulfur were found. Interestingly, genes linked to arsenic resistance metabolism were present at higher abundance in Salina Verde and they were associated with the cyanobacterial bloom. Collectively, this study advances fundamental knowledge on the composition and genetic potential of microbial communities inhabiting tropical soda lakes. PMID:29520256

Contrasting the Genetic Patterns of Microbial Communities in Soda Lakes with and without Cyanobacterial Bloom.

PubMed

Andreote, Ana P D; Dini-Andreote, Francisco; Rigonato, Janaina; Machineski, Gabriela Silva; Souza, Bruno C E; Barbiero, Laurent; Rezende-Filho, Ary T; Fiore, Marli F

2018-01-01

Soda lakes have high levels of sodium carbonates and are characterized by salinity and elevated pH. These ecosystems are found across Africa, Europe, Asia, Australia, North, Central, and South America. Particularly in Brazil, the Pantanal region has a series of hundreds of shallow soda lakes (ca. 600) potentially colonized by a diverse haloalkaliphilic microbial community. Biological information of these systems is still elusive, in particular data on the description of the main taxa involved in the biogeochemical cycling of life-important elements. Here, we used metagenomic sequencing to contrast the composition and functional patterns of the microbial communities of two distinct soda lakes from the sub-region Nhecolândia, state of Mato Grosso do Sul, Brazil. These two lakes differ by permanent cyanobacterial blooms (Salina Verde, green-water lake) and by no record of cyanobacterial blooms (Salina Preta, black-water lake). The dominant bacterial species in the Salina Verde bloom was Anabaenopsis elenkinii . This cyanobacterium altered local abiotic parameters such as pH, turbidity, and dissolved oxygen and consequently the overall structure of the microbial community. In Salina Preta, the microbial community had a more structured taxonomic profile. Therefore, the distribution of metabolic functions in Salina Preta community encompassed a large number of taxa, whereas, in Salina Verde, the functional potential was restrained across a specific set of taxa. Distinct signatures in the abundance of genes associated with the cycling of carbon, nitrogen, and sulfur were found. Interestingly, genes linked to arsenic resistance metabolism were present at higher abundance in Salina Verde and they were associated with the cyanobacterial bloom. Collectively, this study advances fundamental knowledge on the composition and genetic potential of microbial communities inhabiting tropical soda lakes.

Warming enhances old organic carbon decomposition through altering functional microbial communities

DOE PAGES

Cheng, Lei; Zhang, Naifang; Yuan, Mengting; ...

2017-04-21

Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) as the atmosphere and changes in soil C stocks may have a major impact on future atmospheric carbon dioxide concentrations and climate. Over the past two decades, much research has been devoted to examining the influence of warming on SOM decomposition in topsoil. Most SOM, however, is old and stored in subsoil. The fate of subsoil SOM under future warming remains highly uncertain. Here, by combining a long-term field warming experiment and a meta-analysis study, we showed that warming significantly increased SOM decomposition in subsoil. We alsomore » showed that a decade of warming promoted decomposition of subsoil SOM with turnover times of decades to millennia in a tall grass prairie and this effect was largely associated with shifts in the functional gene structure of microbial communities. By coupling stable isotope probing with metagenomics, we found that microbial communities in warmed soils possessed a higher relative abundance of key functional genes involved in the degradation of organic materials with varying recalcitrance than those in control soils. These findings suggest warming may considerably alter the stability of the vast pool of old SOM in subsoil, contributing to the long-term positive feedback between the C cycle and climate.« less

Warming enhances old organic carbon decomposition through altering functional microbial communities

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

Cheng, Lei; Zhang, Naifang; Yuan, Mengting

Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) as the atmosphere and changes in soil C stocks may have a major impact on future atmospheric carbon dioxide concentrations and climate. Over the past two decades, much research has been devoted to examining the influence of warming on SOM decomposition in topsoil. Most SOM, however, is old and stored in subsoil. The fate of subsoil SOM under future warming remains highly uncertain. Here, by combining a long-term field warming experiment and a meta-analysis study, we showed that warming significantly increased SOM decomposition in subsoil. We alsomore » showed that a decade of warming promoted decomposition of subsoil SOM with turnover times of decades to millennia in a tall grass prairie and this effect was largely associated with shifts in the functional gene structure of microbial communities. By coupling stable isotope probing with metagenomics, we found that microbial communities in warmed soils possessed a higher relative abundance of key functional genes involved in the degradation of organic materials with varying recalcitrance than those in control soils. These findings suggest warming may considerably alter the stability of the vast pool of old SOM in subsoil, contributing to the long-term positive feedback between the C cycle and climate.« less

Warming enhances old organic carbon decomposition through altering functional microbial communities

PubMed Central

Cheng, Lei; Zhang, Naifang; Yuan, Mengting; Xiao, Jing; Qin, Yujia; Deng, Ye; Tu, Qichao; Xue, Kai; Van Nostrand, Joy D; Wu, Liyou; He, Zhili; Zhou, Xuhui; Leigh, Mary Beth; Konstantinidis, Konstantinos T; Schuur, Edward AG; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong

2017-01-01

Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) as the atmosphere and changes in soil C stocks may have a major impact on future atmospheric carbon dioxide concentrations and climate. Over the past two decades, much research has been devoted to examining the influence of warming on SOM decomposition in topsoil. Most SOM, however, is old and stored in subsoil. The fate of subsoil SOM under future warming remains highly uncertain. Here, by combining a long-term field warming experiment and a meta-analysis study, we showed that warming significantly increased SOM decomposition in subsoil. We also showed that a decade of warming promoted decomposition of subsoil SOM with turnover times of decades to millennia in a tall grass prairie and this effect was largely associated with shifts in the functional gene structure of microbial communities. By coupling stable isotope probing with metagenomics, we found that microbial communities in warmed soils possessed a higher relative abundance of key functional genes involved in the degradation of organic materials with varying recalcitrance than those in control soils. These findings suggest warming may considerably alter the stability of the vast pool of old SOM in subsoil, contributing to the long-term positive feedback between the C cycle and climate. PMID:28430189

Warming enhances old organic carbon decomposition through altering functional microbial communities.

PubMed

Cheng, Lei; Zhang, Naifang; Yuan, Mengting; Xiao, Jing; Qin, Yujia; Deng, Ye; Tu, Qichao; Xue, Kai; Van Nostrand, Joy D; Wu, Liyou; He, Zhili; Zhou, Xuhui; Leigh, Mary Beth; Konstantinidis, Konstantinos T; Schuur, Edward Ag; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong

2017-08-01

Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) as the atmosphere and changes in soil C stocks may have a major impact on future atmospheric carbon dioxide concentrations and climate. Over the past two decades, much research has been devoted to examining the influence of warming on SOM decomposition in topsoil. Most SOM, however, is old and stored in subsoil. The fate of subsoil SOM under future warming remains highly uncertain. Here, by combining a long-term field warming experiment and a meta-analysis study, we showed that warming significantly increased SOM decomposition in subsoil. We also showed that a decade of warming promoted decomposition of subsoil SOM with turnover times of decades to millennia in a tall grass prairie and this effect was largely associated with shifts in the functional gene structure of microbial communities. By coupling stable isotope probing with metagenomics, we found that microbial communities in warmed soils possessed a higher relative abundance of key functional genes involved in the degradation of organic materials with varying recalcitrance than those in control soils. These findings suggest warming may considerably alter the stability of the vast pool of old SOM in subsoil, contributing to the long-term positive feedback between the C cycle and climate.

Microbial deterioration of artistic tiles from the façade of the Grande Albergo Ausonia & Hungaria (Venice, Italy).

PubMed

Giacomucci, Lucia; Bertoncello, Renzo; Salvadori, Ornella; Martini, Ilaria; Favaro, Monica; Villa, Federica; Sorlini, Claudia; Cappitelli, Francesca

2011-08-01

The Grande Albergo Ausonia & Hungaria (Venice Lido, Italy) has an Art Nouveau polychrome ceramic coating on its façade, which was restored in 2007. Soon after the conservation treatment, many tiles of the façade decoration showed coloured alterations putatively attributed to the presence of microbial communities. To confirm the presence of the biological deposit and the stratigraphy of the Hungaria tiles, stereomicroscope, optical and environmental scanning electron microscope observations were made. The characterisation of the microbial community was performed using a PCR-DGGE approach. This study reported the first use of a culture-independent approach to identify the total community present in biodeteriorated artistic tiles. The case study examined here reveals that the coloured alterations on the tiles were mainly due to the presence of cryptoendolithic cyanobacteria. In addition, we proved that the microflora present on the tiles was generally greatly influenced by the environment of the Hungaria hotel. We found several microorganisms related to the alkaline environment, which is in the range of the tile pH, and related to the aquatic environment, the presence of the acrylic resin Paraloid B72® used during the 2007 treatment and the pollutants of the Venice lagoon.

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

PubMed Central

Twing, Katrina I.; Brazelton, William J.; Kubo, Michael D. Y.; Hyer, Alex J.; Cardace, Dawn; Hoehler, Tori M.; McCollom, Tom M.; Schrenk, Matthew O.

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments. PMID:28298908

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.

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

PubMed

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

PubMed Central

Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; Konopka, Allan E.; Nelson, William C.; Arntzen, Evan V.; Chrisler, William B.; Chu, Rosalie K.; Danczak, Robert E.; Fansler, Sarah J.; Kennedy, David W.; Resch, Charles T.; Tfaily, Malak

2016-01-01

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater–surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater–surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds. PMID:27052662

Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.

PubMed

Stegen, James C; Fredrickson, James K; Wilkins, Michael J; Konopka, Allan E; Nelson, William C; Arntzen, Evan V; Chrisler, William B; Chu, Rosalie K; Danczak, Robert E; Fansler, Sarah J; Kennedy, David W; Resch, Charles T; Tfaily, Malak

2016-04-07

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater-surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater-surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds.

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

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

Lu, Z.; Deng, Y.; Nostrand, J.D. Van

2011-06-15

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in U.S. history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared to outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep-sea. Various other microbial functional genes relevant to carbon, nitrogen, phosphorus, sulfurmore » and iron cycling, metal resistance, and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could play a significant role in biodegradation of oil spills in deep-sea environments.« less

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

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

PubMed

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

2016-07-01

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

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Tools and perspectives for a unified approach to understanding microbial ecology in the critical zone

NASA Astrophysics Data System (ADS)

Gallery, R. E.; Aronson, E. L.; Fairbanks, D.; Murphy, M. A.; Rich, V. I.; Hart, S. C.

2015-12-01

Microbial communities that control nutrient transformation and storage in ecosystems are themselves influenced by landscape topography and vegetative cover. Globally, disturbances such as fires and insect outbreaks are increasing in frequency and severity with enormous impacts on global carbon cycling. The resiliency of soil microbial communities to these heterogeneous disturbances determines rates of nutrient transformations as well as ecosystem structure and recovery. Natural and anthropogenic disturbances are a common thread throughout Critical Zone Observatories and ecosystems in general. Using the 2013 Thompson Ridge Fire in the Jemez River Basin CZO as a case study, we examine the effect of a wildfire disturbance regime on successional changes in soil microbiota and ecosystem fluxes across a landscape with high topographic variation. We find that, layered over the topographic controls of hotspots of biogeochemical activity, fire alters organic substrate quality, microbial biomass, community structure, and activity. For example, fire increases soil pH, which is commonly found as an explanatory variable describing bacterial community structure. Soil microbes excrete exoenzymes to decompose polymers and acquire nutrients, and these activities can indicate changing microbial function or soil quality. In these mixed conifer forests, we find shifts from carbon to nitrogen-dominated exoenzyme activities in burned forests with alkaline soils, suggesting shifts of microbial taxa and function that correspond with recovering soil microbial biomass. More generally we ask - what combination of tools and perspectives is needed to fully understand soil microbial ecology and biogeochemistry of the critical zone? Results from an NSF Science Across Virtual Institutes (SAVI) CZO Network Biogeochemistry Workshop highlight the importance of incorporating a standard suite of microbial activity and community assays along with soil biogeochemical and flux measurements to enable comparisons across the broader CZO network. These characterizations would provide regional microbial function and biodiversity data in a standardized framework that can be used to enable more effective management and valuation of critical zone services and inform projections under global change scenarios.

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

PubMed Central

Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

2018-01-01

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Alternative Protein Sources in the Diet Modulate Microbiota and Functionality in the Distal Intestine of Atlantic Salmon (Salmo salar).

PubMed

Gajardo, Karina; Jaramillo-Torres, Alexander; Kortner, Trond M; Merrifield, Daniel L; Tinsley, John; Bakke, Anne Marie; Krogdahl, Åshild

2017-03-01

The present study aimed to investigate whether alternative dietary protein sources modulate the microbial communities in the distal intestine (DI) of Atlantic salmon, and whether alterations in microbiota profiles are reflected in modifications in host intestinal function and health status. A 48-day feeding trial was conducted, in which groups of fish received one of five diets: a reference diet in which fishmeal (diet FM) was the only protein source and four experimental diets with commercially relevant compositions containing alternative ingredients as partial replacements of fishmeal, i.e., poultry meal (diet PM), a mix of soybean meal and wheat gluten (diet SBMWG), a mix of soy protein concentrate and poultry meal (diet SPCPM), and guar meal and wheat gluten (diet GMWG). Samples were taken of DI digesta and mucosa for microbial profiling using high-throughput sequencing and from DI whole tissue for immunohistochemistry and expression profiling of marker genes for gut health. Regardless of diet, there were significant differences between the microbial populations in the digesta and the mucosa in the salmon DI. Microbial richness was higher in the digesta than the mucosa. The digesta-associated bacterial communities were more affected by the diet than the mucosa-associated microbiota. Interestingly, both legume-based diets (SBMWG and GMWG) presented high relative abundance of lactic acid bacteria in addition to alteration in the expression of a salmon gene related to cell proliferation ( pcna ). It was, however, not possible to ascertain the cause-effect relationship between changes in bacterial communities and the host's intestinal responses to the diets. IMPORTANCE The intestine of cultivated Atlantic salmon shows symptoms of compromised function, which are most likely caused by imbalances related to the use of new feed ingredients. Intestinal microbiota profiling may become in the future a valuable endpoint measurement in order to assess fish intestinal health status and effects of diet. The present study aimed to gain information about whether alternative dietary protein sources modulate the microbial communities in the Atlantic salmon intestine and whether alterations in microbiota profiles are reflected in alterations in host intestinal function and health status. We demonstrate here that there are substantial differences between the intestinal digesta and mucosa in the presence and abundance of bacteria. The digesta-associated microbiota showed clear dependence on the diet composition, whereas mucosa-associated microbiota appeared to be less affected by diet composition. Most important, the study identified bacterial groups associated with diet-induced gut dysfunction that may be utilized as microbial markers of gut health status in fish. Copyright © 2017 Gajardo et al.

Dynamic Autoinoculation and the Microbial Ecology of a deep Water Hydrocarbon Irruption

DTIC Science & Technology

2012-12-11

gas hydrate) likely altered plume com- position near the source, leavrngintruswrscknimatedbythemost soluble compounds, such as gases (2-4, 9, 10, 12...well. These results may reconcile disparate observations of the physical dynamics and microbial community structure of the deep plume . Model...feeds bacterial metabolism and cellular growth. We focused entirely on the deep plume horizon spanning 1,000-1,300 m water depth, applying

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China.

PubMed

Xun, Weibing; Zhao, Jun; Xue, Chao; Zhang, Guishan; Ran, Wei; Wang, Boren; Shen, Qirong; Zhang, Ruifu

2016-06-01

Different fertilization managements of red soil, a kind of Ferralic Cambisol, strongly affected the soil properties and associated microbial communities. The association of the soil microbial community and functionality with long-term fertilization management in the unique low-productivity red soil ecosystem is important for both soil microbial ecology and agricultural production. Here, 454 pyrosequencing analysis of 16S recombinant ribonucleic acid genes and GeoChip4-NimbleGen-based functional gene analysis were used to study the soil bacterial community composition and functional genes involved in soil organic carbon degradation. Long-term nitrogen-containing chemical fertilization-induced soil acidification and fertility decline and significantly altered the soil bacterial community, whereas long-term organic fertilization and fallow management improved the soil quality and maintained the bacterial diversity. Short-term quicklime remediation of the acidified soils did not change the bacterial communities. Organic fertilization and fallow management supported eutrophic ecosystems, in which copiotrophic taxa increased in relative abundance and have a higher intensity of labile-C-degrading genes. However, long-term nitrogen-containing chemical fertilization treatments supported oligotrophic ecosystems, in which oligotrophic taxa increased in relative abundance and have a higher intensity of recalcitrant-C-degrading genes but a lower intensity of labile-C-degrading genes. Quicklime application increased the relative abundance of copiotrophic taxa and crop production, although these effects were utterly inadequate. This study provides insights into the interaction of soil bacterial communities, soil functionality and long-term fertilization management in the red soil ecosystem; these insights are important for improving the fertility of unique low-productivity red soil. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Soil fungal abundance and diversity: another victim of the invasive plant Centaurea maculosa.

PubMed

Broz, Amanda K; Manter, Daniel K; Vivanco, Jorge M

2007-12-01

Interactions between plants and soil microbes are important determinants of both above- and belowground community composition, and ultimately ecosystem function. As exotic plants continue to invade and modify native plant communities, there has been increasing interest in determining the influence of exotic invasives on native soil microbial communities. Here, using highly sensitive molecular techniques, we examine fungal abundance and diversity in the soil surrounding a particularly aggressive invasive plant species in North America, Centaurea maculosa Lam. In mixed stands, we show that this invasive weed can alter the native fungal community composition within its own rhizosphere and that of neighboring native plants. At higher densities, the effect of C. maculosa on native soil fungal communities was even greater. Our results demonstrate that this invasive weed can have significant effects not only on visible aboveground biodiversity but also on the native soil microbial community that extends beyond its rhizosphere.

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

Deng, Ye; Zhang, Ping; Qin, Yujia

When trying to discern network interactions among different species/populations in microbial communities interests have been evoked in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. We modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the networkmore » interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140–269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. In particular, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.« less

Microbial stress-response physiology and its implications for ecosystem function.

PubMed

Schimel, Joshua; Balser, Teri C; Wallenstein, Matthew

2007-06-01

Microorganisms have a variety of evolutionary adaptations and physiological acclimation mechanisms that allow them to survive and remain active in the face of environmental stress. Physiological responses to stress have costs at the organismal level that can result in altered ecosystem-level C, energy, and nutrient flows. These large-scale impacts result from direct effects on active microbes' physiology and by controlling the composition of the active microbial community. We first consider some general aspects of how microbes experience environmental stresses and how they respond to them. We then discuss the impacts of two important ecosystem-level stressors, drought and freezing, on microbial physiology and community composition. Even when microbial community response to stress is limited, the physiological costs imposed on soil microbes are large enough that they may cause large shifts in the allocation and fate of C and N. For example, for microbes to synthesize the osmolytes they need to survive a single drought episode they may consume up to 5% of total annual net primary production in grassland ecosystems, while acclimating to freezing conditions switches Arctic tundra soils from immobilizing N during the growing season to mineralizing it during the winter. We suggest that more effectively integrating microbial ecology into ecosystem ecology will require a more complete integration of microbial physiological ecology, population biology, and process ecology.

Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle.

PubMed

Silveira, Cynthia B; Gregoracci, Gustavo B; Coutinho, Felipe H; Silva, Genivaldo G Z; Haggerty, John M; de Oliveira, Louisi S; Cabral, Anderson S; Rezende, Carlos E; Thompson, Cristiane C; Francini-Filho, Ronaldo B; Edwards, Robert A; Dinsdale, Elizabeth A; Thompson, Fabiano L

2017-01-01

Corals display circadian physiological cycles, changing from autotrophy during the day to heterotrophy during the night. Such physiological transition offers distinct environments to the microbial community associated with corals: an oxygen-rich environment during daylight hours and an oxygen-depleted environment during the night. Most studies of coral reef microbes have been performed on samples taken during the day, representing a bias in the understanding of the composition and function of these communities. We hypothesized that coral circadian physiology alters the composition and function of microbial communities in reef boundary layers. Here, we analyzed microbial communities associated with the momentum boundary layer (MBL) of the Brazilian endemic reef coral Mussismilia braziliensis during a diurnal cycle, and compared them to the water column. We determined microbial abundance and nutrient concentration in samples taken within a few centimeters of the coral's surface every 6 h for 48 h, and sequenced microbial metagenomes from a subset of the samples. We found that dominant taxa and functions in the coral MBL community were stable over the time scale of our sampling, with no significant shifts between night and day samples. Interestingly, the two water column metagenomes sampled 1 m above the corals were also very similar to the MBL metagenomes. When all samples were analyzed together, nutrient concentration significantly explained 40% of the taxonomic dissimilarity among dominant genera in the community. Functional profiles were highly homogenous and not significantly predicted by any environmental variables measured. Our data indicated that water flow may overrule the effects of coral physiology in the MBL bacterial community, at the scale of centimeters, and suggested that sampling resolution at the scale of millimeters may be necessary to address diurnal variation in community composition.

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

DOE PAGES

Penton, Christopher R.; St. Louis, Derek; Pham, Amanda; ...

2015-07-21

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

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

Penton, Christopher R.; St. Louis, Derek; Pham, Amanda

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

PubMed Central

Turner, Stephanie; Mikutta, Robert; Meyer-Stüve, Sandra; Guggenberger, Georg; Schaarschmidt, Frank; Lazar, Cassandre S.; Dohrmann, Reiner; Schippers, Axel

2017-01-01

Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR) and community composition (pyrosequencing) as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand). Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate), O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR) and community patterns (T-RFLP) were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to subsoil conditions, especially in nutrient-depleted old soils. PMID:28579976

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.

PubMed

King, Andrew J; Preheim, Sarah P; Bailey, Kathryn L; Robeson, Michael S; Roy Chowdhury, Taniya; Crable, Bryan R; Hurt, Richard A; Mehlhorn, Tonia; Lowe, Kenneth A; Phelps, Tommy J; Palumbo, Anthony V; Brandt, Craig C; Brown, Steven D; Podar, Mircea; Zhang, Ping; Lancaster, W Andrew; Poole, Farris; Watson, David B; W Fields, Matthew; Chandonia, John-Marc; Alm, Eric J; Zhou, Jizhong; Adams, Michael W W; Hazen, Terry C; Arkin, Adam P; Elias, Dwayne A

2017-03-07

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

DOE PAGES

King, Andrew J.; Preheim, Sarah P.; Bailey, Kathryn L.; ...

2017-01-23

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in-situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads) and biogeochemical parameters monitored by quantifying 53 metals, 12 organic acids, 14 anions and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community, and responded to DO. This also directly influenced the pH and so the biotic impacts ofmore » DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.« less

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

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

King, Andrew J.; Preheim, Sarah P.; Bailey, Kathryn L.

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in-situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads) and biogeochemical parameters monitored by quantifying 53 metals, 12 organic acids, 14 anions and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community, and responded to DO. This also directly influenced the pH and so the biotic impacts ofmore » DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.« less

Trichoderma Biofertilizer Links to Altered Soil Chemistry, Altered Microbial Communities, and Improved Grassland Biomass.

PubMed

Zhang, Fengge; Huo, Yunqian; Cobb, Adam B; Luo, Gongwen; Zhou, Jiqiong; Yang, Gaowen; Wilson, Gail W T; Zhang, Yingjun

2018-01-01

In grasslands, forage and livestock production results in soil nutrient deficits as grasslands typically receive no nutrient inputs, leading to a loss of grassland biomass. The application of mature compost has been shown to effectively increase grassland nutrient availability. However, research on fertilization regime influence and potential microbial ecological regulation mechanisms are rarely conducted in grassland soil. We conducted a two-year experiment in meadow steppe grasslands, focusing on above- and belowground consequences of organic or Trichoderma biofertilizer applications and potential soil microbial ecological mechanisms underlying soil chemistry and microbial community responses. Grassland biomass significantly ( p = 0.019) increased following amendment with 9,000 kg ha -1 of Trichoderma biofertilizer (composted cattle manure + inoculum) compared with other assessed organic or biofertilizer rates, except for BOF3000 (fertilized with 3,000 kg ha -1 biofertilizer). This rate of Trichoderma biofertilizer treatment increased soil antifungal compounds that may suppress pathogenic fungi, potentially partially responsible for improved grassland biomass. Nonmetric multidimensional scaling (NMDS) revealed soil chemistry and fungal communities were all separated by different fertilization regime. Trichoderma biofertilizer (9,000 kg ha -1 ) increased relative abundances of Archaeorhizomyces and Trichoderma while decreasing Ophiosphaerella . Trichoderma can improve grassland biomass, while Ophiosphaerella has the opposite effect as it may secrete metabolites causing grass necrosis. Correlations between soil properties and microbial genera showed plant-available phosphorus may influence grassland biomass by increasing Archaeorhizomyces and Trichoderma while reducing Ophiosphaerella . According to our structural equation modeling (SEM), Trichoderma abundance was the primary contributor to aboveground grassland biomass. Our results suggest Trichoderma biofertilizer could be an important tool for management of soils and ultimately grassland plant biomass.

Trichoderma Biofertilizer Links to Altered Soil Chemistry, Altered Microbial Communities, and Improved Grassland Biomass

PubMed Central

Zhang, Fengge; Huo, Yunqian; Cobb, Adam B.; Luo, Gongwen; Zhou, Jiqiong; Yang, Gaowen; Wilson, Gail W. T.; Zhang, Yingjun

2018-01-01

In grasslands, forage and livestock production results in soil nutrient deficits as grasslands typically receive no nutrient inputs, leading to a loss of grassland biomass. The application of mature compost has been shown to effectively increase grassland nutrient availability. However, research on fertilization regime influence and potential microbial ecological regulation mechanisms are rarely conducted in grassland soil. We conducted a two-year experiment in meadow steppe grasslands, focusing on above- and belowground consequences of organic or Trichoderma biofertilizer applications and potential soil microbial ecological mechanisms underlying soil chemistry and microbial community responses. Grassland biomass significantly (p = 0.019) increased following amendment with 9,000 kg ha−1 of Trichoderma biofertilizer (composted cattle manure + inoculum) compared with other assessed organic or biofertilizer rates, except for BOF3000 (fertilized with 3,000 kg ha−1 biofertilizer). This rate of Trichoderma biofertilizer treatment increased soil antifungal compounds that may suppress pathogenic fungi, potentially partially responsible for improved grassland biomass. Nonmetric multidimensional scaling (NMDS) revealed soil chemistry and fungal communities were all separated by different fertilization regime. Trichoderma biofertilizer (9,000 kg ha−1) increased relative abundances of Archaeorhizomyces and Trichoderma while decreasing Ophiosphaerella. Trichoderma can improve grassland biomass, while Ophiosphaerella has the opposite effect as it may secrete metabolites causing grass necrosis. Correlations between soil properties and microbial genera showed plant-available phosphorus may influence grassland biomass by increasing Archaeorhizomyces and Trichoderma while reducing Ophiosphaerella. According to our structural equation modeling (SEM), Trichoderma abundance was the primary contributor to aboveground grassland biomass. Our results suggest Trichoderma biofertilizer could be an important tool for management of soils and ultimately grassland plant biomass. PMID:29760689

Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin

PubMed Central

Callac, Nolwenn; Rommevaux-Jestin, Céline; Rouxel, Olivier; Lesongeur, Françoise; Liorzou, Céline; Bollinger, Claire; Ferrant, Antony; Godfroy, Anne

2013-01-01

Oceanic basalts host diverse microbial communities with various metabolisms involved in C, N, S, and Fe biogeochemical cycles which may contribute to mineral and glass alteration processes at, and below the seafloor. In order to study the microbial colonization on basaltic glasses and their potential biotic/abiotic weathering products, two colonization modules called AISICS (“Autonomous in situ Instrumented Colonization System”) were deployed in hydrothermal deep-sea sediments at the Guaymas Basin for 8 days and 22 days. Each AISICS module contained 18 colonizers (including sterile controls) filled with basaltic glasses of contrasting composition. Chemical analyses of ambient fluids sampled through the colonizers showed a greater contribution of hydrothermal fluids (maximum temperature 57.6°C) for the module deployed during the longer time period. For each colonizer, the phylogenetic diversity and metabolic function of bacterial and archaeal communities were explored using a molecular approach by cloning and sequencing. Results showed large microbial diversity in all colonizers. The bacterial distribution was primarily linked to the deployment duration, as well as the depth for the short deployment time module. Some 16s rRNA sequences formed a new cluster of Epsilonproteobacteria. Within the Archaea the retrieved diversity could not be linked to either duration, depth or substrata. However, mcrA gene sequences belonging to the ANME-1 mcrA-guaymas cluster were found sometimes associated with their putative sulfate-reducers syntrophs depending on the colonizers. Although no specific glass alteration texture was identified, nano-crystals of barite and pyrite were observed in close association with organic matter, suggesting a possible biological mediation. This study gives new insights into the colonization steps of volcanic rock substrates and the capability of microbial communities to exploit new environmental conditions. PMID:23986754

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

PubMed

Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

2016-09-01

There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events. © 2016 John Wiley & Sons Ltd.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Identifying the role of plant-microbial interactions in driving Arctic carbon cycle changes using a 13C isotope tracer

NASA Astrophysics Data System (ADS)

Hough, M.; Tfaily, M. M.; Blazewicz, S.; Dorrepaal, E.; Crill, P. M.; Rich, V. I.; Saleska, S. R.

2017-12-01

Thawing arctic permafrost (which contains 30-50% of global soil carbon) is expected to drive substantial alterations to carbon (C) cycling that will accelerate climate change. As permafrost thaws, old C may decompose more rapidly and be released as methane (CH4) and carbon dioxide (CO2), but thawing soil can also increase plant productivity as perennial shrub communities transition to faster growing annual wetland plants. The effect of plant community changes on the C cycle is not yet well understood. It could mitigate C loss if C input rates are high enough, or it could increase contributions to CH4 emission (a more potent greenhouse gas than CO2) if it decomposes anaerobically. To investigate the influence of fresh plant litter inputs on peat organic material, microbial communities, and greenhouse gas emissions we traced 13C-enriched plant material from Eriophorum and Sphagnum plants added to arctic peat decomposition incubations into each of these components. High resolution FT-ICR mass spectrometry showed changes in the types of enriched compounds over time indicative of microbial processing. Density fractionation of microbial DNA showed enrichment of the microbial community indicating uptake of 13C-enriched compounds from the plant litter. CO2 and CH4 fluxes were highly 13C enriched and showed three distinct phases of flux after litter addition which were not seen in incubations with no litter added. Together, these lines of evidence indicate that fresh litter inputs may play an important role in structuring microbial decomposition. Future work will explore this influence through closer examination of organic matter and microbial community changes during decomposition.

Anthropogenic protection alters the microbiome in intertidal mangrove wetlands in Hainan Island.

PubMed

Yun, Juanli; Deng, Yongcui; Zhang, Hongxun

2017-08-01

Intertidal mangrove wetlands are of great economic and ecological importance. The regular influence of tides has led to the microbial communities in these wetlands differing significantly from those in other habitats. In this study, we investigated the microbiomes of the two largest mangrove wetlands in Hainan Island, China, which have different levels of anthropogenic protection. Soil samples were collected from the root zone of 13 mangrove species. The microbial composition, including key functional groups, was assessed using Illumina sequencing. Bioinformatics analysis showed that there was a significant difference in the microbiomes between the protected Bamen Bay and the unprotected Dongzhai Bay. The overall microbiome was assigned into 78 phyla and Proteobacteria was the most abundant phylum at both sites. In the protected wetland, there were fewer marine-related microbial communities, such as sulfate-reducing bacteria, and more terrestrial-related communities, such as Verrucomicrobia methanotrophs. We also observed distinct microbial compositions among the different mangrove species at the protected site. Our data suggest that the different microbiomes of the two mangrove wetlands are the result of a complex interaction of the different environmental variables at the two sites.

Global changes alter soil fungal communities and alter rates of organic matter decomposition

NASA Astrophysics Data System (ADS)

Moore, J.; Frey, S. D.

2016-12-01

Global changes - such as warming, more frequent and severe droughts, increasing atmospheric CO2, and increasing nitrogen (N) deposition rates - are altering ecosystem processes. The balance between soil carbon (C) accumulation and decomposition is determined in large part by the activity and biomass of detrital organisms, namely soil fungi, and yet their sensitivity to global changes remains unresolved. We present results from a meta-analysis of 200+ studies spanning manipulative and observational field experiments to quantify fungal responses to global change and expected consequences for ecosystem C dynamics. Warming altered the functional soil microbial community by reducing the ratio of fungi to bacteria (f:b) total fungal biomass. Additionally, warming reduced lignolytic enzyme activity generally by one-third. Simulated N deposition affected f:b differently than warming, but the effect on fungal biomass and activity was similar. The effect of N-enrichment on f:b was contingent upon ecosystem type; f:b increased in alpine meadows and heathlands but decreased in temperate forests following N-enrichment. Across ecosystems, fungal biomass marginally declined by 8% in N-enriched soils. In general, N-enrichment reduced fungal lignolytic enzyme activity, which could explain why soil C accumulates in some ecosystems following warming and N-enrichment. Several global change experiments have reported the surprising result that soil C builds up following increases in temperature and N deposition rates. While site-specific studies have examined the role of soil fungi in ecosystem responses to global change, we present the first meta-analysis documenting general patterns of global change impacts on soil fungal communities, biomass, and activity. In sum, we provide evidence that soil microbial community shifts and activity plays a large part in ecosystem responses to global changes, and have the potential to alter the magnitude of the C-climate feedback.

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

PubMed

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

2011-01-01

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

Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation.

PubMed

Lee, Keehoon; Pletcher, Steven D; Lynch, Susan V; Goldberg, Andrew N; Cope, Emily K

2018-01-01

Recent studies leveraging next-generation sequencing and functional approaches to understand the human microbiota have demonstrated the presence of diverse, niche-specific microbial communities at nearly every mucosal surface. These microbes contribute to the development and function of physiologic and immunological features that are key to host health status. Not surprisingly, several chronic inflammatory diseases have been attributed to dysbiosis of microbiota composition or function, including chronic rhinosinusitis (CRS). CRS is a heterogeneous disease characterized by inflammation of the sinonasal cavity and mucosal microbiota dysbiosis. Inflammatory phenotypes and bacterial community compositions vary considerably across individuals with CRS, complicating current studies that seek to address causality of a dysbiotic microbiome as a driver or initiator of persistent sinonasal inflammation. Murine models have provided some experimental evidence that alterations in local microbial communities and microbially-produced metabolites influence health status. In this perspective, we will discuss the clinical implications of distinct microbial compositions and community-level functions in CRS and how mucosal microbiota relate to the diverse inflammatory endotypes that are frequently observed. We will also describe specific microbial interactions that can deterministically shape the pattern of co-colonizers and the resulting metabolic products that drive or exacerbate host inflammation. These findings are discussed in the context of CRS-associated inflammation and in other chronic inflammatory diseases that share features observed in CRS. An improved understanding of CRS patient stratification offers the opportunity to personalize therapeutic regimens and to design novel treatments aimed at manipulation of the disease-associated microbiota to restore sinus health.

Heterotrophic Soil Respiration in Warming Experiments: Using Microbial Indicators to Partition Contributions from Labile and Recalcitrant Soil Organic Carbon. Final Report

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

Bradford, M A; Melillo, J M; Reynolds, J F

2010-06-10

The central objective of the proposed work was to develop a genomic approach (nucleic acid-based) that elucidates the mechanistic basis for the observed impacts of experimental soil warming on forest soil respiration. The need to understand the mechanistic basis arises from the importance of such information for developing effective adaptation strategies for dealing with projected climate change. Specifically, robust predictions of future climate will permit the tailoring of the most effective adaptation efforts. And one of the greatest uncertainties in current global climate models is whether there will be a net loss of carbon from soils to the atmosphere asmore » climate warms. Given that soils contain approximately 2.5 times as much carbon as the atmosphere, a net loss could lead to runaway climate warming. Indeed, most ecosystem models predict that climate warming will stimulate microbial decomposition of soil carbon, producing such a positive feedback to rising global temperatures. Yet the IPCC highlights the uncertainty regarding this projected feedback. The uncertainty arises because although warming-experiments document an initial increase in the loss of carbon from soils, the increase in respiration is short-lived, declining to control levels in a few years. This attenuation could result from changes in microbial physiology with temperature. We explored possible microbial responses to warming using experiments and modeling. Our work advances our understanding of how soil microbial communities and their activities are structured, generating insight into how soil carbon might respond to warming. We show the importance of resource partitioning in structuring microbial communities. Specifically, we quantified the relative abundance of fungal taxa that proliferated following the addition of organic substrates to soil. We added glycine, sucrose, cellulose, lignin, or tannin-protein to soils in conjunction with 3-bromo-deoxyuridine (BrdU), a nucleotide analog. Active microbes absorb BrdU from the soil solution; if they multiply in response to substrate additions, they incorporate the BrdU into their DNA. After allowing soils to incubate, we extracted BrdU-labeled DNA and sequenced the ITS regions of fungal rDNA. Fungal taxa that proliferated following substrate addition were likely using the substrate as a resource for growth. We found that the structure of active fungal communities varied significantly among substrates. The active fungal community under glycine was significantly different from those under other conditions, while the active communities under sucrose and cellulose were marginally different from each other and the control. These results indicate that the overall community structure of active fungi was altered by the addition of glycine, sucrose, and cellulose and implies that some fungal taxa respond to changes in resource availability. The community composition of active fungi is also altered by experimental warming. We found that glycine-users tended to increase under warming, while lignin-, tannin/protein-, and sucrose-users declined. The latter group of substrates requires extracellular enzymes for use, but glycine does not. It is possible that warming selects for fungal species that target, in particular, labile substrates. Linking these changes in microbial communities and resource partitioning to soil carbon dynamics, we find that substrate mineralization rates are, in general, significantly lower in soils exposed to long-term warming. This suggests that microbial use of organic substrates is impaired by warming. Yet effects are dependent on substrate identity. There are fundamental differences in the metabolic capabilities of the communities in the control and warmed soils. These differences might relate to the changes in microbial community composition, which appeared to be associated with groups specialized on different resources. We also find that functional responses indicate temperature acclimation of the microbial community. There are distinct seasonal patterns and to long-term soil warming, with higher-temperature optima for soils exposed to warmer temperatures. To relate these changes within the microbial community to potential positive feedbacks between climate warming and soil respiration, we develop a microbial-enzyme model to simulate the responses of soil carbon to warming. We find that declines in microbial biomass and degradative enzymes can explain the observed attenuation of soil-carbon emissions in response to warming. Specifically, reduced carbon-use efficiency limits the biomass of microbial decomposers and mitigates loss of soil carbon. However, microbial adaptation or a change in microbial communities could lead to an upward adjustment of the efficiency of carbon use, counteracting the decline in microbial biomass and accelerating soil-carbon loss. We conclude that the soil-carbon response to climate warming depends on the efficiency of soil microbes in using carbon.« less

Rapid determination of soil quality and earthworm impacts on soil microbial communities using fluorescence-based respirometry

NASA Astrophysics Data System (ADS)

Prendergast-Miller, Miranda T.; Thurston, Josh; Taylor, Joe; Helgason, Thorunn; Ashauer, Roman; Hodson, Mark E.

2017-04-01

We applied a fluorescence-based respirometry method currently devised for aquatic ecotoxicology studies to rapidly measure soil microbial oxygen consumption as a function of soil quality. In this study, soil was collected from an arable wheat field and the field margin. These two soil habitats are known to differ in their soil quality due to differences in their use and management as well as plant, microbial and earthworm community. The earthworm Lumbricus terrestris was incubated in arable or margin soil for three weeks. After this initial phase, a transfer experiment was then conducted to test the hypothesis that earthworm 'migration' alters soil microbial community function and diversity. In this transfer experiment, earthworms incubated in margin soil were transferred to arable soil. The converse transfer (i.e. earthworms incubated in arable soil) was also conducted. Soils of each type with no earthworms were also incubated as controls. After a further four week incubation, the impact of earthworm migration on the soil microbial community was tested by measuring oxygen consumption. Replicated soil slurry subsamples were aliquoted into individual respirometer wells (600 μl volume) on a glass 24-well microplate (Loligo Systems, Denmark) fitted with non-invasive, reusable oxygen sensor spots. The sealed microplate was then attached to an oxygen fluorescence sensor (SDR SensorDish Reader, PreSens, Germany). Oxygen consumption was measured in real-time over a 2 hr period following standard operating procedures. Soil microbial activity was measured with and without an added carbon source (glucose or cellulose, 50 mg C L-1). Using this system, we were able to differentiate between soil type, earthworm treatment and C source. Earthworm-driven impacts on soil microbial oxygen consumption were also supported by changes in soil microbial community structure and diversity revealed using DNA-based sequencing techniques. This method provides a simple and rapid system for measuring soil quality and has the potential for use in a variety of scenarios investigating impacts on soil microbial function.

Effects of Recurring Droughts on Extracellular Enzyme Activity in Mountain Grassland

NASA Astrophysics Data System (ADS)

Fuchslueger, L.; Bahn, M.; Kienzl, S.; Hofhansl, F.; Schnecker, J.; Richter, A.

2015-12-01

Water availability is a key factor for biogeochemical processes and determines microbial activity and functioning, and thereby organic matter decomposition in soils by affecting the osmotic potential, soil pore connectivity, substrate diffusion and nutrient availability. Low water availability during drought periods therefore directly affects microbial activity. Recurring drought periods likely induce shifts in microbial structure that might be reflected in altered responses of microbial turnover of organic matter by extracellular enzymes. To study this we measured a set of potential extracellular enzyme activity rates (cellobiohydrolase CBH; leucine-amino-peptidase LAP; phosphatase PHOS; phenoloxidase POX), in grassland soils that were exposed to extreme experimental droughts during the growing seasons of up to five subsequent years. During the first drought period after eight weeks of rain exclusion all measured potential enzyme activities were significantly decreased. In parallel, soil extractable organic carbon and nitrogen concentrations increased and microbial community structure, determined by phospholipid fatty acid analysis, changed. In soils that were exposed to two and three drought periods only PHOS decreased. After four years of drought again CBH, PHOS and POX decreased, while LAP was unaffected; after five years of drought PHOS and POX decreased and CBH and LAP remained stable. Thus, our results suggest that recurring extreme drought events can cause different responses of extracellular enzyme activities and that the responses change over time. We will discuss whether and to what degree these changes were related to shifts in microbial community composition. However, independent of whether a solitary or a recurrent drought was imposed, in cases when enzyme activity rates were altered during drought, they quickly recovered after rewetting. Overall, our data suggest that microbial functioning in mountain grassland is sensitive to drought, but highly resilient even after five years of drought.

Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers.

PubMed

Amalfitano, Stefano; Fazi, Stefano; Zoppini, Annamaria; Barra Caracciolo, Anna; Grenni, Paola; Puddu, Alberto

2008-02-01

In the semiarid Mediterranean regions, water scarcity represents a common physiological stress for microbial communities residing in river sediments. However, the effect of drying has not yet adequately been evaluated when analyzing riverine microbiological processes. The bacterial community structure (abundance, biomass, composition) and functioning (carbon production, live cell percentage) were assessed during experimental desiccation in microcosms with sediments from different Mediterranean temporary rivers (Tagliamento, Krathis, Mulargia, Pardiela). Our results showed that the overall responses to drying of the bacterial community were independent from sediment origin and strictly related to water content. During desiccation, a prompt decline (up to 100%) of the initial bacterial carbon production was followed by a slower decrease in abundance and biomass, with an overall reduction of 74% and 78%, respectively. By the end of the experiment, live cells were still abundant but depressed in their main metabolic functions, thus resulting in a drastic increase in the community turnover time. Only 14% of the initial live cell biomass was available in dry sediments to immediately start the reactivation of the aquatic microbial food web after the arrival of new water. Community composition analysis showed a relative increase in alpha- and beta-Proteobacteria, when passing from wet to dry conditions. Our results suggest that the occurrence of drought events could affect carbon cycling through the freshwater microbial compartment, by temporarily limiting microbial mineralization and altering bacterial community structure.

Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments.

PubMed

Laverock, Bonnie; Smith, Cindy J; Tait, Karen; Osborn, A Mark; Widdicombe, Steve; Gilbert, Jack A

2010-12-01

Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction fragment length polymorphism analysis was used to investigate variation in the structure of bacterial communities in sediment bioturbated by the burrowing shrimp Upogebia deltaura or Callianassa subterranea. Analyses of 229 sediment samples revealed significant differences between bacterial communities inhabiting shrimp burrows and those inhabiting ambient surface and subsurface sediments. Bacterial communities in burrows from both shrimp species were more similar to those in surface-ambient than subsurface-ambient sediment (R=0.258, P<0.001). The presence of shrimp was also associated with changes in bacterial community structure in surrounding surface sediment, when compared with sediments uninhabited by shrimp. Bacterial community structure varied with burrow depth, and also between individual burrows, suggesting that the shrimp's burrow construction, irrigation and maintenance behaviour affect the distribution of bacteria within shrimp burrows. Subsequent sequence analysis of bacterial 16S rRNA genes from surface sediments revealed differences in the relative abundance of bacterial taxa between shrimp-inhabited and uninhabited sediments; shrimp-inhabited sediment contained a higher proportion of proteobacterial sequences, including in particular a twofold increase in Gammaproteobacteria. Chao1 and ACE diversity estimates showed that taxon richness within surface bacterial communities in shrimp-inhabited sediment was at least threefold higher than that in uninhabited sediment. This study shows that bioturbation can result in significant structural and compositional changes in sediment bacterial communities, increasing bacterial diversity in surface sediments and resulting in distinct bacterial communities even at depth within the burrow. In an area of high macrofaunal abundance, this could lead to alterations in the microbial transformations of important nutrients at the sediment-water interface.

Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate.

PubMed

Barnard, Romain L; Osborne, Catherine A; Firestone, Mary K

2015-03-17

A large soil CO2 pulse is associated with rewetting soils after the dry summer period under a Mediterranean-type climate, significantly contributing to grasslands' annual carbon budget. Rapid reactivation of soil heterotrophs and a pulse of available carbon are both required to fuel the CO2 pulse. Understanding of the effects of altered summer precipitation on the metabolic state of indigenous microorganisms may be important in predicting changes in carbon cycling. Here, we investigated the effects of extending winter rainfall into the normally dry summer period on soil microbial response to a controlled rewetting event, by following the present (DNA-based) and potentially active (rRNA-based) soil bacterial and fungal communities in intact soil cores (from a California annual grassland) previously subjected to three different precipitation patterns over 4 months (full summer dry season, extended wet season and absent dry season). Phylogenetic marker genes for bacteria and fungi were sequenced before and after rewetting, and the abundance of these genes and transcripts was measured. After having experienced markedly different antecedent water conditions, the potentially active bacterial communities showed a consistent wet-up response. We found a significant positive relation between the extent of change in the structure of the potentially active bacterial community and the magnitude of the CO2 pulse upon rewetting dry soils. We suggest that the duration of severe dry summer conditions characteristic of the Mediterranean climate is important in conditioning the response potential of the soil microbial community to wet-up as well as in framing the magnitude of the associated CO2 pulse.

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem.

PubMed

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

2017-01-01

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

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes

PubMed Central

Santos-Medellín, Christian; Edwards, Joseph; Liechty, Zachary; Nguyen, Bao

2017-01-01

ABSTRACT Plant roots support complex microbial communities that can influence plant growth, nutrition, and health. While extensive characterizations of the composition and spatial compartmentalization of these communities have been performed in different plant species, there is relatively little known about the impact of abiotic stresses on the root microbiota. Here, we have used rice as a model to explore the responses of root microbiomes to drought stress. Using four distinct genotypes, grown in soils from three different fields, we tracked the drought-induced changes in microbial composition in the rhizosphere (the soil immediately surrounding the root), the endosphere (the root interior), and unplanted soils. Drought significantly altered the overall bacterial and fungal compositions of all three communities, with the endosphere and rhizosphere compartments showing the greatest divergence from well-watered controls. The overall response of the bacterial microbiota to drought stress was taxonomically consistent across soils and cultivars and was primarily driven by an enrichment of multiple Actinobacteria and Chloroflexi, as well as a depletion of several Acidobacteria and Deltaproteobacteria. While there was some overlap in the changes observed in the rhizosphere and endosphere communities, several drought-responsive taxa were compartment specific, a pattern likely arising from preexisting compositional differences, as well as plant-mediated processes affecting individual compartments. These results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in restructuring of root microbial communities and suggest the possibility that constituents of the altered plant microbiota might contribute to plant survival under extreme environmental conditions. PMID:28720730

Using Plant Phylogenetic Relatedness as a Predictor for Plants' Control on Soil Microbial Communities and Nitrogen Cycling

NASA Astrophysics Data System (ADS)

Potter, T.; Bowman, W. D.

2016-12-01

Despite the known importance of soil microbes and their influence on soil processes, a mechanistic understanding is still needed to predict how plants and soil microbes interact at scales that are relevant to community and ecosystem-scale processes. Closely related plant species have similar traits aboveground, but we don't know whether this is also true for belowground traits that affect soil microbial community structure and function. Determining how tightly plant phylogeny and plant functional traits are linked to soil microbial communities is a useful approach for discovering plant-microbe associations that are generalizable across plant species (a limitation of studies that employ a single or few plant species). Using this approach, we conducted a greenhouse study with seven congeneric grasses (genus Poa) and their native soils to examine whether plants' influences on microbial community structure were consistent with plant phylogenetic relatedness and/or plant functional traits. Seeds of each Poa species were planted in native soil (from the seed source population) as well as a homogenized soil from all seven populations. Additionally, a nitrogen treatment was added to address how an environmental change (such as nitrogen deposition) alters plant-microbe associations. Rhizosphere community composition of bacteria and fungi was obtained via marker gene sequencing to compare community composition across plant species. Patterns in plant-microbe associations across plant species reveal plant control on nutrient cycling via plant species' influence on microbial community structure. These results determine if we are ready to generalize about plant-microbe interactions at the genus level, an important stepping-stone to applying knowledge of plant-microbe interactions to larger ecological scales.

The microbial perspective of organic matter turnover and nutrient cycling in tropical soils

NASA Astrophysics Data System (ADS)

Rasche, Frank

2017-04-01

A primary goal of low-input small-holder farming systems in the tropics is the appropriate management of organic matter (OM) turnover and nutrient cycling via adapted agricultural practices. These emphasize the promotion of soil organic matter (SOM) turnover and carbon (C) sequestration, nutrient use efficiency and soil microbial activity. Since soil microbial communities are acknowledged as key players in the terrestrial C and nutrient (e.g., nitrogen (N), phosphorus (P)) cycles, they may respond sensitively to agricultural management with shifts in their community structure as well as functional traits (i.e., decomposition, mineralization). This may be in particular evident for tropical, agricultural soils which show an accelerated microbial decomposition activity induced by favourable climatic and unique physico-chemical soil conditions. While modern molecular techniques advanced primarily the understanding about the microbiome and their functional traits interacting closely with SOM dynamics in temperate soils, tropical soils under agricultural use have been still neglected to a great extent. The majority of available studies revealed mainly descriptive data on the structural composition of microbial communities rather than questioning if detected structural alterations of the soil microbiome influenced key processes in N and P cycling which actually maintain ecosystem functioning and soil productivity. This talk highlights latest efforts in deploying molecular techniques to study the compositional status of soil microbial decomposer communities and their functional attributes in response to land use change and OM management in tropical agro-ecosystems.

N2O and N2 emissions from contrasting soil environments - interactive effects of soil nitrogen, hydrology and microbial communities

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Elberling, Bo; Ribbons, Relena; Hedo, Javier; José Fernández Alonso, Maria; Krych, Lukasz; Sandris Nielsen, Dennis; Kitzler, Barbara

2016-04-01

Reactive nitrogen (N) in the environment has doubled relative to the natural global N cycle with consequences for biogeochemical cycling of soil N. Also, climate change is expected to alter precipitation patterns and increase soil temperatures which in Arctic environments may accelerate permafrost thawing. The combination of changes in the soil N cycle and hydrological regimes may alter microbial transformations of soil N with unknown impacts on N2O and N2 emissions from temperate and Arctic soils. We present the first results of soil N2O and N2 emissions, chemistry and microbial communities over soil hydrological gradients (upslope, intermediate and wet) across a global N deposition gradient. The global gradient covered an N-limited high Arctic tundra (Zackenberg-ZA), a pacific temperate rain forest (Vancouver Island-VI) and an N saturated forest in Austria (Klausenleopoldsdorf-KL). The N2O and N2 emissions were measured from intact cores at field moisture in a He-atmosphere system. Extractable NH4+ and NO3-, organic and microbial C and N and potential enzyme-activities were determined on soil samples. Soil genomic DNA was subjected to MiSeq-based tag-encoded 16S rRNA and ITS gene amplicon sequencing for the bacterial and fungal community structure. Similar soil moisture levels were observed for the upslope, intermediate and wet locations at ZA, VI and KL, respectively. Extractable NO3- was highest at the N rich KL and lowest at ZA and showed no trend with soil moisture similar to NH4+. At ZA and VI soil NH4+ was higher than NO3- indicating a tighter N cycling. N2O emissions increased with soil moisture at all sites. The N2O emissions for the wet locations ranked similarly to NO3- with the largest response to soil moisture at KL. N2 emissions were remarkably similar across the sites and increased with soil wetness. Microbial C and N also increased with soil moisture and were overall lowest at the N rich KL site. The potential activity of protease enzyme was site dependent indicating different capacities for N turnover of the microbial community. These findings indicate a positive feedback between increased soil N and wetter soils that promotes N2O relative to N2. These interactions may be site specific due to differential functional diversity of the soil microbial community. Future characterization of the community structure will shed light on the link between the role of microbial groups related to soil N cycling pathways and the resultant partitioning of N2O and N2 emissions in these contrasting environments.

Microbial limitation in a changing world: A stoichiometric approach for predicting microbial resource limitation and fluxes

NASA Astrophysics Data System (ADS)

Midgley, M.; Phillips, R.

2014-12-01

Microbes mediate fluxes of carbon (C), nitrogen (N), and phosphorus (P) in soils depending on ratios of available C, N, and P relative to microbial demand. Hence, characterizing microbial C and nutrient limitation in soils is critical for predicting how ecosystems will respond to human alterations of climate and nutrient availability. Here, we take a stoichiometric approach to assessing microbial C, N, and P limitation by using threshold element ratios (TERs). TERs enable shifting resource limitation to be assessed by matching C, N and P ratios from microbial biomass, extracellular enzyme activities, and soil nutrient concentrations. We assessed microbial nutrient limitation in temperate forests dominated by trees that associate with one of two mycorrhizal symbionts: arbsucular mycorrhizal (AM) or ectomycorrhizal (ECM) fungi. We found that both ECM and AM microbial communities were co-limited by C and N, supporting conventional wisdom that microbes are C-limited and temperate forests are N-limited. However, AM microbial communities were relatively more C-limited than ECM communities (P=0.001). In response to chronic field N fertilization, both AM and ECM communities became relatively more P-limited (P=0.011), but they remained N- and C-limited overall. Thus, realistic levels of N deposition may not dampen microbial N limitation. Reflecting differences in relative limitation, N mineralization rates were higher in AM soils than in ECM soils (P=0.004) while C mineralization rates were higher in ECM soils than in AM soils (P=0.023). There were no significant differences in P flux between AM and ECM soils or detectable mineralization responses to N addition, indicating that mineralization rates are closely tied to C and nutrient limitation. Overall, we found that 1) microbial resource limitation can be detected without resource addition; and 2) TERs and ratios of labile resources are viable tools for predicting mineralization responses to resource additions.

Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle.

PubMed

Zhou, Mi; Peng, Yong-Jia; Chen, Yanhong; Klinger, Christen M; Oba, Masahito; Liu, Jian-Xin; Guan, Le Luo

2018-03-27

Understanding the host impact on its symbiotic microbiota is important in redirecting the rumen microbiota and thus improving animal performance. The current study aimed to understand how rumen microbiota were altered and re-established after being emptied and receiving content from donor, thus to understand the impact of such process on rumen microbial fermentation and to explore the microbial phylotypes with higher manipulation potentials. Individual animal had strong effect on the re-establishment of the bacterial community according to the observed profiles detected by both fingerprinting and pyrosequencing. Most of the bacterial profile recovery patterns and extents at genus level varied among steers; and each identified bacterial genus responded to transfaunation differently within each host. Coriobacteriaceae, Coprococcus, and Lactobacillus were found to be the most responsive and tunable genera by exchanging rumen content. Besides, the association of 18 bacterial phylotypes with host fermentation parameters suggest that these phylotypes should also be considered as the regulating targets in improving host feed efficiency. In addition, the archaeal community had different re-establishment patterns for each host as determined by fingerprint profiling: it was altered after receiving non-native microbiome in some animals, while it resumed its original status after the adaptation period in the other ones. The highly individualized microbial re-establishment process suggested the importance of considering host genetics, microbial functional genomics, and host fermentation/performance assessment when developing effective and selective microbial manipulation methods for improving animal feed efficiency.

Alteration of Microbial Communities Colonizing Leaf Litter in a Temperate Woodland Stream by Growth of Trees under Conditions of Elevated Atmospheric CO2 ▿

PubMed Central

Kelly, John J.; Bansal, Amit; Winkelman, Jonathan; Janus, Lori R.; Hell, Shannon; Wencel, Marie; Belt, Patricia; Kuehn, Kevin A.; Rier, Steven T.; Tuchman, Nancy C.

2010-01-01

Elevated atmospheric CO2 can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO2 would result in changes in the size and composition of microbial communities colonizing leaves in a woodland stream. Three tree species, Populus tremuloides, Salix alba, and Acer saccharum, were grown under ambient (360 ppm) or elevated (720 ppm) CO2, and their leaves were incubated in a woodland stream. Elevated-CO2 treatment resulted in significant increases in the phenolic and tannin contents and C/N ratios of leaves. Microbial effects, which occurred only for P. tremuloides leaves, included decreased fungal biomass and decreased bacterial counts. Analysis of fungal and bacterial communities on P. tremuloides leaves via terminal restriction fragment length polymorphism (T-RFLP) and clone library sequencing revealed that fungal community composition was mostly unchanged by the elevated-CO2 treatment, whereas bacterial communities showed a significant shift in composition and a significant increase in diversity. Specific changes in bacterial communities included increased numbers of alphaproteobacterial and cytophaga-flavobacter-bacteroides (CFB) group sequences and decreased numbers of betaproteobacterial and firmicutes sequences, as well as a pronounced decrease in overall Gram-positive bacterial sequences. PMID:20543045

Alteration of microbial communities colonizing leaf litter in a temperate woodland stream by growth of trees under conditions of elevated atmospheric CO2.

PubMed

Kelly, John J; Bansal, Amit; Winkelman, Jonathan; Janus, Lori R; Hell, Shannon; Wencel, Marie; Belt, Patricia; Kuehn, Kevin A; Rier, Steven T; Tuchman, Nancy C

2010-08-01

Elevated atmospheric CO(2) can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO(2) would result in changes in the size and composition of microbial communities colonizing leaves in a woodland stream. Three tree species, Populus tremuloides, Salix alba, and Acer saccharum, were grown under ambient (360 ppm) or elevated (720 ppm) CO(2), and their leaves were incubated in a woodland stream. Elevated-CO(2) treatment resulted in significant increases in the phenolic and tannin contents and C/N ratios of leaves. Microbial effects, which occurred only for P. tremuloides leaves, included decreased fungal biomass and decreased bacterial counts. Analysis of fungal and bacterial communities on P. tremuloides leaves via terminal restriction fragment length polymorphism (T-RFLP) and clone library sequencing revealed that fungal community composition was mostly unchanged by the elevated-CO(2) treatment, whereas bacterial communities showed a significant shift in composition and a significant increase in diversity. Specific changes in bacterial communities included increased numbers of alphaproteobacterial and cytophaga-flavobacter-bacteroides (CFB) group sequences and decreased numbers of betaproteobacterial and firmicutes sequences, as well as a pronounced decrease in overall gram-positive bacterial sequences.

Temporal assessment of microbial communities in soils of two contrasting mangroves.

PubMed

Rigonato, Janaina; Kent, Angela D; Gumiere, Thiago; Branco, Luiz Henrique Zanini; Andreote, Fernando Dini; Fiore, Marli Fátima

Variations in microbial communities promoted by alterations in environmental conditions are reflected in similarities/differences both at taxonomic and functional levels. Here we used a natural gradient within mangroves from seashore to upland, to contrast the natural variability in bacteria, cyanobacteria and diazotroph assemblages in a pristine area compared to an oil polluted area along a timespan of three years, based on ARISA (bacteria and cyanobacteria) and nifH T-RFLP (diazotrophs) fingerprinting. The data presented herein indicated that changes in all the communities evaluated were mainly driven by the temporal effect in the contaminated area, while local effects were dominant on the pristine mangrove. A positive correlation of community structure between diazotrophs and cyanobacteria was observed, suggesting the functional importance of this phylum as nitrogen fixers in mangroves soils. Different ecological patterns explained the microbial behavior in the pristine and polluted mangroves. Stochastic models in the pristine mangrove indicate that there is not a specific environmental factor that determines the bacterial distribution, while cyanobacteria and diazotrophs better fitted in deterministic model in the same area. For the contaminated mangrove site, deterministic models better represented the variations in the communities, suggesting that the presence of oil might change the microbial ecological structures over time. Mangroves represent a unique environment threatened by global change, and this study contributed to the knowledge of the microbial distribution in such areas and its response on persistent contamination historic events. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

DOE PAGES

Moore, Jessica A. M.; Jiang, Jiang; Patterson, Courtney M.; ...

2015-10-20

Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant-microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are presentmore » in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free-living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil insitu in a temperate mixed deciduous forest. We added 13C-labelled substrate to trace metabolized carbon in respiration and measured carbon-degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13C-labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free-living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady-state model simulations suggested that root presence increased mineral-associated and particulate organic carbon pools, while mycorrhizal fungal presence had a greater influence on particulate than mineral-associated organic carbon pools.Synthesis. Our results suggest that the activity of enzymes involved in organic matter decomposition was contingent upon root-mycorrhizal-microbial interactions. Using our experimental data in a decomposition simulation model, we show that root-mycorrhizal-microbial interactions may have longer-term legacy effects on soil carbon sequestration. Lastly, our study suggests that roots stimulate microbial activity in the short term, but contribute to soil carbon storage over longer periods of time.« less

Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

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

Moore, Jessica A. M.; Jiang, Jiang; Patterson, Courtney M.

Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant-microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are presentmore » in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free-living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil insitu in a temperate mixed deciduous forest. We added 13C-labelled substrate to trace metabolized carbon in respiration and measured carbon-degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13C-labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free-living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady-state model simulations suggested that root presence increased mineral-associated and particulate organic carbon pools, while mycorrhizal fungal presence had a greater influence on particulate than mineral-associated organic carbon pools.Synthesis. Our results suggest that the activity of enzymes involved in organic matter decomposition was contingent upon root-mycorrhizal-microbial interactions. Using our experimental data in a decomposition simulation model, we show that root-mycorrhizal-microbial interactions may have longer-term legacy effects on soil carbon sequestration. Lastly, our study suggests that roots stimulate microbial activity in the short term, but contribute to soil carbon storage over longer periods of time.« less

Oxidative Weathering and Microbial Diversity of an Inactive Seafloor Hydrothermal Sulfide Chimney

PubMed Central

Li, Jiangtao; Cui, Jiamei; Yang, Qunhui; Cui, Guojie; Wei, Bingbing; Wu, Zijun; Wang, Yong; Zhou, Huaiyang

2017-01-01

When its hydrothermal supply ceases, hydrothermal sulfide chimneys become inactive and commonly experience oxidative weathering on the seafloor. However, little is known about the oxidative weathering of inactive sulfide chimneys, nor about associated microbial community structures and their succession during this weathering process. In this work, an inactive sulfide chimney and a young chimney in the early sulfate stage of formation were collected from the Main Endeavor Field of the Juan de Fuca Ridge. To assess oxidative weathering, the ultrastructures of secondary alteration products accumulating on the chimney surface were examined and the presence of possible Fe-oxidizing bacteria (FeOB) was investigated. The results of ultrastructure observation revealed that FeOB-associated ultrastructures with indicative morphologies were abundantly present. Iron oxidizers primarily consisted of members closely related to Gallionella spp. and Mariprofundus spp., indicating Fe-oxidizing species likely promote the oxidative weathering of inactive sulfide chimneys. Abiotic accumulation of Fe-rich substances further indicates that oxidative weathering is a complex, dynamic process, alternately controlled by FeOB and by abiotic oxidization. Although hydrothermal fluid flow had ceased, inactive chimneys still accommodate an abundant and diverse microbiome whose microbial composition and metabolic potential dramatically differ from their counterparts at active vents. Bacterial lineages within current inactive chimney are dominated by members of α-, δ-, and γ-Proteobacteria and they are deduced to be closely involved in a diverse set of geochemical processes including iron oxidation, nitrogen fixation, ammonia oxidation and denitrification. At last, by examining microbial communities within hydrothermal chimneys at different formation stages, a general microbial community succession can be deduced from early formation stages of a sulfate chimney to actively mature sulfide structures, and then to the final inactive altered sulfide chimney. Our findings provide valuable insights into the microbe-involved oxidative weathering process and into microbial succession occurring at inactive hydrothermal sulfide chimney after high-temperature hydrothermal fluids have ceased venting. PMID:28785251

Afforestation alters community structure of soil fungi.

PubMed

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

2010-07-01

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

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin.

PubMed

Roesch, Luiz Fernando Wurdig; Silveira, Rita C; Corso, Andréa L; Dobbler, Priscila Thiago; Mai, Volker; Rojas, Bruna S; Laureano, Álvaro M; Procianoy, Renato S

2017-01-01

Administering intravenous antibiotics during labor to women at risk for transmitting Group B Streptococcus (GBS) can prevent infections in newborns. However, the impact of intrapartum antibiotic prophylaxis on mothers' microbial community composition is largely unknown. We compared vaginal microbial composition in pregnant women experiencing preterm birth at ≤ 32 weeks gestation that received intrapartum antibiotic prophylaxis with that in controls. Microbiota in vaginal swabs collected shortly before delivery from GBS positive women that received penicillin intravenously during labor or after premature rupture of membranes was compared to controls. Microbiota was analyzed by 16S rRNA sequencing using the PGM Ion Torrent to determine the effects of penicillin use during hospitalization and GBS status on its composition. Penicillin administration was associated with an altered vaginal microbial community composition characterized by increased microbial diversity. Lactobacillus sp. contributed only 13.1% of the total community in the women that received penicillin compared to 88.1% in the controls. Streptococcus sp. were present in higher abundance in GBS positive woman compared to controls, with 60% of the total vaginal microbiota in severe cases identified as Streptococcus sp. Vaginal communities of healthy pregnant women were dominated by Lactobacillus sp. and contained low diversity, while Group B Streptococcus positive women receiving intrapartum antibiotic prophylaxis had a modified vaginal microbiota composition with low abundance of Lactobacillus but higher microbial diversity.

Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas.

PubMed

Murali Mohan, Arvind; Hartsock, Angela; Hammack, Richard W; Vidic, Radisav D; Gregory, Kelvin B

2013-12-01

Hydraulic fracturing for natural gas extraction from shale produces waste brine known as flowback that is impounded at the surface prior to reuse and/or disposal. During impoundment, microbial activity can alter the fate of metals including radionuclides, give rise to odorous compounds, and result in biocorrosion that complicates water and waste management and increases production costs. Here, we describe the microbial ecology at multiple depths of three flowback impoundments from the Marcellus shale that were managed differently. 16S rRNA gene clone libraries revealed that bacterial communities in the untreated and biocide-amended impoundments were depth dependent, diverse, and most similar to species within the taxa γ-proteobacteria, α-proteobacteria, δ-proteobacteria, Clostridia, Synergistetes, Thermotogae, Spirochetes, and Bacteroidetes. The bacterial community in the pretreated and aerated impoundment was uniform with depth, less diverse, and most similar to known iodide-oxidizing bacteria in the α-proteobacteria. Archaea were identified only in the untreated and biocide-amended impoundments and were affiliated to the Methanomicrobia class. This is the first study of microbial communities in flowback water impoundments from hydraulic fracturing. The findings expand our knowledge of microbial diversity of an emergent and unexplored environment and may guide the management of flowback impoundments. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Microbial Community Response to Carbon Substrate Amendment in Mercury Impacted Sediments: Implications on Microbial Methylation of Mercury.

NASA Astrophysics Data System (ADS)

Elias, D. A.; Somenahally, A. C.; Moberly, J. G.; Hurt, R. A., Jr.; Brown, S. D.; Podar, M.; Palumbo, A. V.; Gilmour, C. C.

2015-12-01

Methylmercury (MeHg) is a neurotoxic and bio-accumulative product of the microbial methylation of inorganic mercury (Hg(II)). Methylating organisms are now known to exist in almost all anaerobic niches including fermentation, Fe(III)- and sulfate- reduction as well as methanogenesis. The study objective was to determine the effect of different carbon sources on the microbial community and methylating populations in particular along a Hg contaminated creek. Sediment cores from upstream and downstream at the Hg contaminated East Fork Poplar Creek (EFPC), Oak Ridge TN, and a background site were sectioned by depth, and Hg-methylation potential (HgMP) assays were performed using stable isotope spikes. Sediments from the lowest depth possessed the highest in-situ activity. Replicate samples were amended with different carbon substrates (cellulose, acetate, propionate, lactate, ethanol and methanol), spiked with stable isotopes for HgMP assays and incubated for 24hrs. Sequencing of the 16S rRNA gene was performed to determine alterations in Bacterial and Archaeal population dynamics. Additionally, bioinformatics and our new qualitative and quantitative hgcAB primers were utilized to determine microbial community structure alterations and correlate organism and gene abundance with altered MeHg generation. HgMP was significantly reduced in cellulose amended sediments while acetate and propionate slightly decreased HgMP in both sites. Methanol, ethanol and lactate increased the HgMP in EFPC downstream while cellulose amendment significantly decreased the Proteobacteria, and the Firmicutes increased but none are currently known to produce MeHg. Geobacter bemidjiensis in particular significantly decreased in cellulose amended sediments in all three sites from being predominant in-situ. This suggests that in EFPC downstream and background sites, the prevalent Hg-methyaltors might be Deltaprotebacteria, since upstream, cellulose amendment did not reduce HgMP even though relative composition of Deltaproteobacteria decreased significantly. Hence the phylogenetic distribution of Hg-methylating bacteria upstream may be much broader. Most Archaea belonged to either Euryarchaeota or Crenarchaeota, but there were no consistent trends with specific groups among the treatments.

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients.

PubMed

Jacobs, Jonathan P; Goudarzi, Maryam; Singh, Namita; Tong, Maomeng; McHardy, Ian H; Ruegger, Paul; Asadourian, Miro; Moon, Bo-Hyun; Ayson, Allyson; Borneman, James; McGovern, Dermot P B; Fornace, Albert J; Braun, Jonathan; Dubinsky, Marla

2016-11-01

Microbes may increase susceptibility to inflammatory bowel disease (IBD) by producing bioactive metabolites that affect immune activity and epithelial function. We undertook a family based study to identify microbial and metabolic features of IBD that may represent a predisease risk state when found in healthy first-degree relatives. Twenty-one families with pediatric IBD were recruited, comprising 26 Crohn's disease patients in clinical remission, 10 ulcerative colitis patients in clinical remission, and 54 healthy siblings/parents. Fecal samples were collected for 16S ribosomal RNA gene sequencing, untargeted liquid chromatography-mass spectrometry metabolomics, and calprotectin measurement. Individuals were grouped into microbial and metabolomics states using Dirichlet multinomial models. Multivariate models were used to identify microbes and metabolites associated with these states. Individuals were classified into 2 microbial community types. One was associated with IBD but irrespective of disease status, had lower microbial diversity, and characteristic shifts in microbial composition including increased Enterobacteriaceae, consistent with dysbiosis. This microbial community type was associated similarly with IBD and reduced microbial diversity in an independent pediatric cohort. Individuals also clustered bioinformatically into 2 subsets with shared fecal metabolomics signatures. One metabotype was associated with IBD and was characterized by increased bile acids, taurine, and tryptophan. The IBD-associated microbial and metabolomics states were highly correlated, suggesting that they represented an integrated ecosystem. Healthy relatives with the IBD-associated microbial community type had an increased incidence of elevated fecal calprotectin. Healthy first-degree relatives can have dysbiosis associated with an altered intestinal metabolome that may signify a predisease microbial susceptibility state or subclinical inflammation. Longitudinal prospective studies are required to determine whether these individuals have a clinically significant increased risk for developing IBD.

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

PubMed

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

2017-03-01

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

Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils.

PubMed

Pold, Grace; Billings, Andrew F; Blanchard, Jeff L; Burkhardt, Daniel B; Frey, Serita D; Melillo, Jerry M; Schnabel, Julia; van Diepen, Linda T A; DeAngelis, Kristen M

2016-11-15

As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world. The massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change. Copyright © 2016 Pold et al.

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

PubMed Central

Turnbaugh, Peter J.; Ridaura, Vanessa K.; Faith, Jeremiah J.; Rey, Federico E.; Knight, Rob; Gordon, Jeffrey I.

2010-01-01

Diet and nutritional status are among the most important, modifiable determinants of human health. The nutritional value of food is influenced in part by a person’s gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelationships between diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent, metagenomic analysis of the temporal, spatial and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized, and reproduced much of the bacterial diversity of the donor’s microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a high-fat/high-sugar “Western” diet shifted the structure of the microbiota within a single day, changed the representation of metabolic pathways in the microbiome, and altered microbiome gene expression. Reciprocal transplants involving various combinations of donor and recipient diets revealed that colonization history influences the initial structure of the microbial community, but that these effects can be rapidly altered by diet. Humanized mice fed the Western diet have increased adiposity; this trait is transmissible via microbiota transplantation. Humanized gnotobiotic mice will be useful for conducting proof-of-principle “clinical trials” that test the effects of environmental and genetic factors on the gut microbiota and host physiology. PMID:20368178

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish

PubMed Central

Barton, Carrie L.; Proffitt, Sarah; Tanguay, Robert L.; Sharpton, Thomas J.

2016-01-01

Growing evidence indicates that disrupting the microbial community that comprises the intestinal tract, known as the gut microbiome, can contribute to the development or severity of disease. As a result, it is important to discern the agents responsible for microbiome disruption. While animals are frequently exposed to a diverse array of environmental chemicals, little is known about their effects on gut microbiome stability and structure. Here, we demonstrate how zebrafish can be used to glean insight into the effects of environmental chemical exposure on the structure and ecological dynamics of the gut microbiome. Specifically, we exposed forty-five adult zebrafish to triclosan-laden food for four or seven days or a control diet, and analyzed their microbial communities using 16S rRNA amplicon sequencing. Triclosan exposure was associated with rapid shifts in microbiome structure and diversity. We find evidence that several operational taxonomic units (OTUs) associated with the family Enterobacteriaceae appear to be susceptible to triclosan exposure, while OTUs associated with the genus Pseudomonas appeared to be more resilient and resistant to exposure. We also found that triclosan exposure is associated with topological alterations to microbial interaction networks and results in an overall increase in the number of negative interactions per microbe in these networks. Together these data indicate that triclosan exposure results in altered composition and ecological dynamics of microbial communities in the gut. Our work demonstrates that because zebrafish afford rapid and inexpensive interrogation of a large number of individuals, it is a useful experimental system for the discovery of the gut microbiome’s interaction with environmental chemicals. PMID:27191725

Stress during pregnancy alters temporal and spatial dynamics of the maternal and offspring microbiome in a sex-specific manner

PubMed Central

Jašarević, Eldin; Howard, Christopher D.; Misic, Ana M.; Beiting, Daniel P.; Bale, Tracy L.

2017-01-01

The microbiome is a regulator of host immunity, metabolism, neurodevelopment, and behavior. During early life, bacterial communities within maternal gut and vaginal compartments can have an impact on directing these processes. Maternal stress experience during pregnancy may impact offspring development by altering the temporal and spatial dynamics of the maternal microbiome during pregnancy. To examine the hypothesis that maternal stress disrupts gut and vaginal microbial dynamics during critical prenatal and postnatal windows, we used high-resolution 16S rRNA marker gene sequencing to examine outcomes in our mouse model of early prenatal stress. Consistent with predictions, maternal fecal communities shift across pregnancy, a process that is disrupted by stress. Vaginal bacterial community structure and composition exhibit lasting disruption following stress exposure. Comparison of maternal and offspring microbiota revealed that similarities in bacterial community composition was predicted by a complex interaction between maternal body niche and offspring age and sex. Importantly, early prenatal stress influenced offspring bacterial community assembly in a temporal and sex-specific manner. Taken together, our results demonstrate that early prenatal stress may influence offspring development through converging modifications to gut microbial composition during pregnancy and transmission of dysbiotic vaginal microbiome at birth. PMID:28266645

Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition.

PubMed

Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

2017-11-01

The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.

454 pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas.

PubMed

Li, Yuanyuan; Chen, Longqian; Wen, Hongyu; Zhou, Tianjian; Zhang, Ting; Gao, Xiali

2014-03-28

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coalmining reclamation areas was suggested.

Characterization of bacterial and archaeal communities in air-cathode microbial fuel cells, open circuit and sealed-off reactors.

PubMed

Shehab, Noura; Li, Dong; Amy, Gary L; Logan, Bruce E; Saikaly, Pascal E

2013-11-01

A large percentage of organic fuel consumed in a microbial fuel cell (MFC) is lost as a result of oxygen transfer through the cathode. In order to understand how this oxygen transfer affects the microbial community structure, reactors were operated in duplicate using three configurations: closed circuit (CC; with current generation), open circuit (OC; no current generation), and sealed off cathodes (SO; no current, with a solid plate placed across the cathode). Most (98 %) of the chemical oxygen demand (COD) was removed during power production in the CC reactor (maximum of 640 ± 10 mW/m(2)), with a low percent of substrate converted to current (coulombic efficiency of 26.5 ± 2.1 %). Sealing the cathode reduced COD removal to 7 %, but with an open cathode, there was nearly as much COD removal by the OC reactor (94.5 %) as the CC reactor. Oxygen transfer into the reactor substantially affected the composition of the microbial communities. Based on analysis of the biofilms using 16S rRNA gene pyrosequencing, microbes most similar to Geobacter were predominant on the anodes in the CC MFC (72 % of sequences), but the most abundant bacteria were Azoarcus (42 to 47 %) in the OC reactor, and Dechloromonas (17 %) in the SO reactor. Hydrogenotrophic methanogens were most predominant, with sequences most similar to Methanobacterium in the CC and SO reactor, and Methanocorpusculum in the OC reactors. These results show that oxygen leakage through the cathode substantially alters the bacterial anode communities, and that hydrogenotrophic methanogens predominate despite high concentrations of acetate. The predominant methanogens in the CC reactor most closely resembled those in the SO reactor, demonstrating that oxygen leakage alters methanogenic as well as general bacterial communities.

Conversion of rainforest into agroforestry and monoculture plantation in China: Consequences for soil phosphorus forms and microbial community.

PubMed

Wang, Jinchuang; Ren, Changqi; Cheng, Hanting; Zou, Yukun; Bughio, Mansoor Ahmed; Li, Qinfen

2017-10-01

Microbial communities and their associated enzyme activities affect quantity and quality of phosphorus (P) in soils. Land use change is likely to alter microbial community structure and feedback on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to land use and shifts in the amount and quality of soil phosphorus (P). We investigated effects of the conversion of rainforests into rubber agroforests (AF), young rubber (YR), and mature rubber (MR) plantations on soil P fractions (i.e., labile P, moderately labile P, occluded P, Ca P, and residual P) in Hainan Island, Southern China. Microbial community composition and microbial enzyme were assayed to assess microbial community response to forest conversion. In addition, we also identified soil P fractions that were closely related to soil microbial and chemical properties in these forests. Conversion of forest to pure rubber plantations and agroforestry system caused a negative response in soil microorganisms and activity. The bacteria phospholipid fatty acid (PLFAs) levels in young rubber, mature rubber and rubber agroforests decreased after forest conversion, while the fungal PLFAs levels did not change. Arbuscular mycorrhizal fungi (AMF) (16:1w5c) had the highest value of 0.246μmol(gOC) -1 in natural forest, followed by rubber agroforests, mature rubber and young rubber. Level of soil acid phosphatase activity declined soon (5 years) after forest conversion compared to natural forest, but it improved in mature rubber and agroforestry system. Labile P, moderately labile P, occluded P and residual P were highest in young rubber stands, while moderately labile, occluded and residual P were lowest in rubber agroforestry system. Soil P fractions such as labile P, moderately labile P, and Ca P were the most important contributors to the variation in soil microbial community composition. We also found that soil P factions differ significantly among the four transformation systems. Soil labile P faction and its potential sources (moderately labile P, occluded P, and residual P) were positively correlated with NO 3 - , but negatively correlated with AMF, suggesting that these properties play key roles in P transformation. Our study indicated that land use had an impact on microbial community composition and functions, which consequently influenced soil phosphorus availability and cycling. Copyright © 2017 Elsevier B.V. All rights reserved.

Warming alters community size structure and ecosystem functioning

PubMed Central

Dossena, Matteo; Yvon-Durocher, Gabriel; Grey, Jonathan; Montoya, José M.; Perkins, Daniel M.; Trimmer, Mark; Woodward, Guy

2012-01-01

Global warming can affect all levels of biological complexity, though we currently understand least about its potential impact on communities and ecosystems. At the ecosystem level, warming has the capacity to alter the structure of communities and the rates of key ecosystem processes they mediate. Here we assessed the effects of a 4°C rise in temperature on the size structure and taxonomic composition of benthic communities in aquatic mesocosms, and the rates of detrital decomposition they mediated. Warming had no effect on biodiversity, but altered community size structure in two ways. In spring, warmer systems exhibited steeper size spectra driven by declines in total community biomass and the proportion of large organisms. By contrast, in autumn, warmer systems had shallower size spectra driven by elevated total community biomass and a greater proportion of large organisms. Community-level shifts were mirrored by changes in decomposition rates. Temperature-corrected microbial and macrofaunal decomposition rates reflected the shifts in community structure and were strongly correlated with biomass across mesocosms. Our study demonstrates that the 4°C rise in temperature expected by the end of the century has the potential to alter the structure and functioning of aquatic ecosystems profoundly, as well as the intimate linkages between these levels of ecological organization. PMID:22496185

A Review of the Environmental Implications of in situ Remediation by Nanoscale Zero Valent Iron (nZVI): Behavior, Transport and Impacts on Microbial Communities

PubMed Central

Lefevre, Emilie; Bossa, Nathan; Wiesner, Mark R.; Gunsch, Claudia K.

2016-01-01

The increasing use of strategies incorporating nanoscale zero valent iron (nZVI) for soil and groundwater in situ remediation is raising some concerns regarding the potential adverse effects nZVI could have on indigenous microbial communities and ecosystem functioning. This review provides an overview of the current literature pertaining to the impacts of nZVI applications on microbial communities. Toxicity studies suggest that cell membrane disruption and oxidative stress through the generation of Fe2+ and reactive oxygen species by nZVI are the main mechanisms contributing to nZVI cytotoxicity. In addition, nZVI has been shown to substantially alter the taxonomic and functional composition of indigenous communities. However, because the physico-chemical conditions encountered in situ highly modulate nZVI toxicity, a better understanding of the environmental factors affecting nZVI toxicity and transport in the environment is of primary importance in evaluating the ecological consequences that could result from a more extensive use of nZVI. PMID:26897610

Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest.

PubMed

Vivanco, Lucía; Rascovan, Nicolás; Austin, Amy T

2018-01-01

Plant-microbial interactions in the litter layer represent one of the most relevant interactions for biogeochemical cycling as litter decomposition is a key first step in carbon and nitrogen turnover. However, our understanding of these interactions in the litter layer remains elusive. In an old-growth mixed Nothofagus forest in Patagonia, we studied the effects of single tree species identity and the mixture of three tree species on the fungal and bacterial composition in the litter layer. We also evaluated the effects of nitrogen (N) addition on these plant-microbial interactions. In addition, we compared the magnitude of stimulation of litter decomposition due to home field advantage (HFA, decomposition occurs more rapidly when litter is placed beneath the plant species from which it had been derived than beneath a different plant species) and N addition that we previously demonstrated in this same forest, and used microbial information to interpret these results. Tree species identity had a strong and significant effect on the composition of fungal communities but not on the bacterial community of the litter layer. The microbial composition of the litter layer under the tree species mixture show an averaged contribution of each single tree species. N addition did not erase the plant species footprint on the fungal community, and neither altered the bacterial community. N addition stimulated litter decomposition as much as HFA for certain tree species, but the mechanisms behind N and HFA stimulation may have differed. Our results suggest that stimulation of decomposition from N addition might have occurred due to increased microbial activity without large changes in microbial community composition, while HFA may have resulted principally from plant species' effects on the litter fungal community. Together, our results suggest that plant-microbial interactions can be an unconsidered driver of litter decomposition in temperate forests.

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

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

Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to documentmore » the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.« less

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

DOE PAGES

Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; ...

2016-10-24

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to documentmore » the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.« less

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

PubMed Central

Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; Sharon, Itai; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Singh, Andrea; Wilkins, Michael J.; Karaoz, Ulas; Brodie, Eoin L.; Williams, Kenneth H.; Hubbard, Susan S.; Banfield, Jillian F.

2016-01-01

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles. PMID:27774985

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

NASA Astrophysics Data System (ADS)

Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; Sharon, Itai; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Singh, Andrea; Wilkins, Michael J.; Karaoz, Ulas; Brodie, Eoin L.; Williams, Kenneth H.; Hubbard, Susan S.; Banfield, Jillian F.

2016-10-01

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.

Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex.

PubMed

Daae, F L; Økland, I; Dahle, H; Jørgensen, S L; Thorseth, I H; Pedersen, R B

2013-07-01

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions. © 2013 John Wiley & Sons Ltd.

Peatland Microbial Communities and Decomposition Processes in the James Bay Lowlands, Canada

PubMed Central

Preston, Michael D.; Smemo, Kurt A.; McLaughlin, James W.; Basiliko, Nathan

2012-01-01

Northern peatlands are a large repository of atmospheric carbon due to an imbalance between primary production by plants and microbial decomposition. The James Bay Lowlands (JBL) of northern Ontario are a large peatland-complex but remain relatively unstudied. Climate change models predict the region will experience warmer and drier conditions, potentially altering plant community composition, and shifting the region from a long-term carbon sink to a source. We collected a peat core from two geographically separated (ca. 200 km) ombrotrophic peatlands (Victor and Kinoje Bogs) and one minerotrophic peatland (Victor Fen) located near Victor Bog within the JBL. We characterized (i) archaeal, bacterial, and fungal community structure with terminal restriction fragment length polymorphism of ribosomal DNA, (ii) estimated microbial activity using community level physiological profiling and extracellular enzymes activities, and (iii) the aeration and temperature dependence of carbon mineralization at three depths (0–10, 50–60, and 100–110 cm) from each site. Similar dominant microbial taxa were observed at all three peatlands despite differences in nutrient content and substrate quality. In contrast, we observed differences in basal respiration, enzyme activity, and the magnitude of substrate utilization, which were all generally higher at Victor Fen and similar between the two bogs. However, there was no preferential mineralization of carbon substrates between the bogs and fens. Microbial community composition did not correlate with measures of microbial activity but pH was a strong predictor of activity across all sites and depths. Increased peat temperature and aeration stimulated CO2 production but this did not correlate with a change in enzyme activities. Potential microbial activity in the JBL appears to be influenced by the quality of the peat substrate and the presence of microbial inhibitors, which suggests the existing peat substrate will have a large influence on future JBL carbon dynamics. PMID:22393328

Will anticipated future climatic conditions affect belowground C utilization? - Insights into the role of microbial functional groups in a temperate heath/grassland.

NASA Astrophysics Data System (ADS)

Reinsch, Sabine; Michelsen, Anders; Sárossy, Zsuzsa; Egsgaard, Helge; Kappel Schmidt, Inger; Jakobsen, Iver; Ambus, Per

2013-04-01

The global terrestrial soil organic matter stock is the biggest terrestrial carbon pool (1500 Pg C) of which about 4 % is turned over annually. Thus, terrestrial ecosystems have the potential to accelerate or diminish atmospheric climate change effects via belowground carbon processes. We investigated the effect of elevated CO2 (510 ppm), prolonged spring/summer droughts and increased temperature (1 ˚C) on belowground carbon allocation and on the recovery of carbon by the soil microbial community. An in-situ 13C-carbon pulse-labeling experiment was carried out in a temperate heath/grassland (Denmark) in May 2011. Recently assimilated 13C-carbon was traced into roots, soil and microbial biomass 1, 2 and 8 days after pulse-labeling. The importance of the microbial community in C utilization was investigated using 13C enrichment patterns in microbial functional groups on the basis of phospholipid fatty acids (PLFAs) in roots. Gram-negative and gram-positive bacteria were distinguished from the decomposer groups of actinomycetes (belonging to the group of gram-positive bacteria) and saprophytic fungi. Mycorrhizal fungi specific PLFAs were not detected probably due to limited sample size in combination with restricted sensitivity of the used GC-c-IRMS setup. Climate treatments did not affect 13C allocation into roots, soil and microbial biomass carbon and also the total microbial biomass size stayed unchanged as frequently observed. However, climate treatments changed the composition of the microbial community: elevated CO2 significantly reduced the abundance of gram-negative bacteria (17:0cy) but did not affect the abundance of decomposers. Drought favored the bacterial community whereas increased temperatures showed reduced abundance of gram-negative bacteria (19:0cy) and changed the actinomycetes community (10Me16:0, 10Me18:0). However, not only the microbial community composition was affected by the applied climatic conditions, but also the activity of microbial functional groups in their utilization of recently assimilated carbon. Particularly the negative effect of the future treatment combination (CO2×T×D) on actinomycetes activity was surprising. By means of activity patterns of gram-negative bacteria, we observed the fastest carbon turnover rate under elevated CO2, and the slowest under extended drought conditions. A changed soil microbial community in combination with altered activities of different microbial functional groups leads to the conclusion that carbon allocation belowground was different under ambient and future climatic conditions and indicated reduced utilization of soil organic matter in the future due to a change of actinomycetes abundance and activity.

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses.

PubMed

Ge, Zhongming; Sheh, Alexander; Feng, Yan; Muthupalani, Sureshkumar; Ge, Lili; Wang, Chuanwu; Kurnick, Susanna; Mannion, Anthony; Whary, Mark T; Fox, James G

2018-05-22

C57BL/6 (B6) mice from Taconic Sciences (Tac) and the Jackson Laboratory (Jax) were infected with H. pylori PMSS1 (Hp) for 16 week; there was no significant difference in the gastric histologic activity index between Hp infected Tac and Jax B6. However, the degree of gastric mucous metaplasia and Th1-associated IgG2c levels in response to Hp infection were increased in Tac mice over Jax mice, whereas the colonization levels of gastric Hp were higher by 8-fold in Jax B6 compared with Tac B6. Additionally, mRNA expression of gastric Il-1β, Il-17A and RegIIIγ were significantly lower in the infected Tac compared to the infected Jax mice. There were significant differences in the microbial community structures in stomach, colon, and feces between Jax and Tac B6 females. Differences in gastric microbial communities between Jax and Tac B6 females are predicted to affect the metagenome. Moreover, Hp infection perturbed the microbial community structures in the stomach, colon and feces of Jax mice, but only altered the colonic microbial composition of Tac mice. Our data indicate that the GI microbiome of Tac B6 mice is compositionally distinct from Jax B6 mice, which likely resulted in different pathological, immunological, and microbial responses to Hp infection.

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. © 2013 John Wiley & Sons Ltd.

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

PubMed

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

2017-08-01

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

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 change on soil, these results challenge the assumption that different soil microbial communities will be ‘functionally equivalent’ as climate change progresses, and they emphasize the need for better ecological metrics of soil microbial communities to help predict C cycle responses to climate change in tropical biomes. PMID:25520527

Veterinary antibiotic effects on atrazine degradation and soil microorganisms

USDA-ARS?s Scientific Manuscript database

Veterinary antibiotics (VAs) in manure applied to agricultural lands may change agrichemical degradation by altering soil microbial community structure or function. The objectives of this study were to investigate the influence of two VAs, sulfamethazine (SMZ) and oxytetracycline (OTC), on atrazine ...

Nitrogen management for first-year corn after alfalfa

USDA-ARS?s Scientific Manuscript database

Rotating alfalfa with corn can increase corn yield potential due to improved soil physical properties that enhance water infiltration and root extension, altered soil microbial communities, and reduced pest pressure. In addition, fertilizer nitrogen (N) requirements are commonly reduced by about 100...

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

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

Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.

Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositionalmore » difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.« less

Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities.

PubMed

Ordoñez, Yuli Marcela; Fernandez, Belen Rocio; Lara, Lidia Susana; Rodriguez, Alia; Uribe-Vélez, Daniel; Sanders, Ian R

2016-01-01

Arbuscular mycorrhizal fungi (AMF) and phosphate solubilizing Pseudomonas bacteria (PSB) could potentially interact synergistically because PSB solubilize phosphate into a form that AMF can absorb and transport to the plant. However, very little is known about the interactions between these two groups of microorganisms and how they influence the growth of each other. We tested whether different strains of bacteria, that have the capacity to solubilize phosphate, are able to grow along AMF hyphae and differentially influence the growth of AMF both outside the roots of carrot in in vitro conditions and inside the roots of potato in the presence of a microbial community. We found strong effects of AMF on the growth of the different bacterial strains. Different bacterial strains also had very strong effects on the growth of AMF extraradical hyphae outside the roots of carrot and on colonization of potato roots by AMF. The differential effects on colonization occurred in the presence of a microbial community. Our results show that these two important groups of rhizosphere microorganisms indeed interact with each other. Such interactions could potentially lead to synergistic effects between the two groups but this could depend on whether the bacteria truly solubilize phosphate in the rhizosphere in the presence of microbial communities.

Functional effects of the bacterial insecticide Bacillus thuringiensis var. kurstaki on aquatic microbial communities.

PubMed

Kreutzweiser, D P; Gringorten, J L; Thomas, D R; Butcher, J T

1996-04-01

Epilithic microbial communities were colonized on leaf disks and exposed to commercial preparations of Bacillus thuringiensis var. kurstaki (Btk) in aquatic microcosms. Responses in terms of microbial respiration, bacterial cell density, protozoan density, and microbial decomposition activity were measured. Test concentrations for treatments with Dipel 64AF and Dipel 8AF in microcosms were the expected environmental concentration (EEC) of 20 IU/ml, 100x the EEC, and 1000x the EEC. Bacterial cell density in the biofilm of leaf disks was significantly increased at concentrations as low as the EEC. There were no concomitant alterations in protozoan density. Microbial respiration was significantly increased, and decomposition activity was significantly decreased, but only at the artificially high concentration of 1000x the EEC. This effect was attributed to the spore-crystal component rather than formulation ingredients. Microbial decomposition of leaf material was also determined in outdoor stream channels treated at concentrations ranging from the EEC to 100x the EEC. Although there tended to be reduced decomposition activity in treated channels, there were no significant differences in mass loss of leaf material between treated and control channels. Various regression, classification, and ordination procedures were applied to the experimental data, and none indicated significant treatment effects. These results from laboratory and controlled field experiments indicate that contamination of watercourses with Btk is unlikely to result in significant adverse effects on microbial community function in terms of detrital decomposition.

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil.

PubMed

Resende, Juliana Alves; Godon, Jean-Jacques; Bonnafous, Anaïs; Arcuri, Pedro Braga; Silva, Vânia Lúcia; Otenio, Marcelo Henrique; Diniz, Cláudio Galuppo

2016-04-01

Anaerobic digestion is an alternative method for the treatment of animal manure and wastewater. The anaerobic bioconversion of biomass requires a multi-step biological process, including microorganisms with distinct roles. The diversity and composition of microbial structure in pilot-scale anaerobic digestion operating at ambient temperature in Brazil were studied. Influence of the seasonal and temporal patterns on bacterial and archaeal communities were assessed by studying the variations in density, dynamic and diversity and structure. The average daily biogas produced in the summer and winter months was 18.7 and 16 L day(-1), respectively, and there was no difference in the average methane yield. Quantitative PCR analysis revealed that no differences in abundances and dynamics were found for bacterial communities and the total number of Archaea in different seasons. Analysis of bacterial clone libraries revealed a predominance of Firmicutes (54.5 %/summer and 46.7 %/winter) and Bacteroidetes (31.4 %/summer and 44.4 %/winter). Within the Archaea, the phylum Euryarchaeota was predominant in both digesters. Phylogenetic distribution showed changes in percentage between the phyla identified, but no alterations were recorded in the quality and amount of produced methane or community dynamics. The results may suggest that redundancy of microbial groups may have occurred, pointing to a more complex microbial community in the ecosystem related to this ambient temperature system.

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

PubMed

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

2017-09-01

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

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

PubMed

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

2013-01-01

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

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach

PubMed Central

Crespo-Medina, Melitza; Twing, Katrina I.; Kubo, Michael D. Y.; Hoehler, Tori M.; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O.

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems. PMID:25452748

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach.

PubMed

Crespo-Medina, Melitza; Twing, Katrina I; Kubo, Michael D Y; Hoehler, Tori M; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite-hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil.

PubMed

Khdhiri, Mondher; Piché-Choquette, Sarah; Tremblay, Julien; Tringe, Susannah G; Constant, Philippe

2017-06-01

The enrichment of H 2 -oxidizing bacteria (HOB) by H 2 generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H 2 , when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H 2 mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H 2 exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H 2 while enhancing community level carbon substrate utilization potential and lowering CH 4 uptake activity in soil. We found that H 2 triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H 2 exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H 2 on soil microbial communities will lead to a better understanding of the H 2 fertilization effect and soil biogeochemical processes. IMPORTANCE An innovative dynamic microcosm chamber system was used to demonstrate that H 2 diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH 4 oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H 2 rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB. Copyright © 2017 American Society for Microbiology.

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead

USGS Publications Warehouse

Blunt, Susanna M.; Sackett, Joshua D.; Rosen, Michael R.; Benotti, Mark J.; Trenholm, Rebecca A.; Vanderford, Brett J.; Hedlund, Brian P.; Moser, Duane P.

2018-01-01

The role of microbial communities in the degradation of trace organic contaminants in the environment is little understood. In this study, the biotransformation potential of 27 pharmaceuticals and endocrine-disrupting compounds was examined in parallel with a characterization of the native microbial community in water samples from four sites variously impacted by urban run-off and wastewater discharge in Lake Mead, Nevada and Arizona, USA. Samples included relatively pristine Colorado River water at the upper end of the lake, nearly pure tertiary-treated municipal wastewater entering via the Las Vegas Wash, and waters of mixed influence (Las Vegas Bay and Boulder Basin), which represented a gradient of treated wastewater effluent impact. Microbial diversity analysis based on 16S rRNA gene censuses revealed the community at this site to be distinct from the less urban-impacted locations, although all sites were similar in overall diversity and richness. Similarly, Biolog EcoPlate assays demonstrated that the microbial community at Las Vegas Wash was the most metabolically versatile and active. Organic contaminants added as a mixture to laboratory microcosms were more rapidly and completely degraded in the most wastewater-impacted sites (Las Vegas Wash and Las Vegas Bay), with the majority exhibiting shorter half-lives than at the other sites or in a bacteriostatic control. Although the reasons for enhanced degradation capacity in the wastewater-impacted sites remain to be established, these data are consistent with the acclimatization of native microorganisms (either through changes in community structure or metabolic regulation) to effluent-derived trace contaminants. This study suggests that in urban, wastewater-impacted watersheds, prior exposure to organic contaminants fundamentally alters the structure and function of microbial communities, which in turn translates into greater potential for the natural attenuation of these compounds compared to more pristine sites.

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead.

PubMed

Blunt, Susanna M; Sackett, Joshua D; Rosen, Michael R; Benotti, Mark J; Trenholm, Rebecca A; Vanderford, Brett J; Hedlund, Brian P; Moser, Duane P

2018-05-01

The role of microbial communities in the degradation of trace organic contaminants in the environment is little understood. In this study, the biotransformation potential of 27 pharmaceuticals and endocrine-disrupting compounds was examined in parallel with a characterization of the native microbial community in water samples from four sites variously impacted by urban run-off and wastewater discharge in Lake Mead, Nevada and Arizona, USA. Samples included relatively pristine Colorado River water at the upper end of the lake, nearly pure tertiary-treated municipal wastewater entering via the Las Vegas Wash, and waters of mixed influence (Las Vegas Bay and Boulder Basin), which represented a gradient of treated wastewater effluent impact. Microbial diversity analysis based on 16S rRNA gene censuses revealed the community at this site to be distinct from the less urban-impacted locations, although all sites were similar in overall diversity and richness. Similarly, Biolog EcoPlate assays demonstrated that the microbial community at Las Vegas Wash was the most metabolically versatile and active. Organic contaminants added as a mixture to laboratory microcosms were more rapidly and completely degraded in the most wastewater-impacted sites (Las Vegas Wash and Las Vegas Bay), with the majority exhibiting shorter half-lives than at the other sites or in a bacteriostatic control. Although the reasons for enhanced degradation capacity in the wastewater-impacted sites remain to be established, these data are consistent with the acclimatization of native microorganisms (either through changes in community structure or metabolic regulation) to effluent-derived trace contaminants. This study suggests that in urban, wastewater-impacted watersheds, prior exposure to organic contaminants fundamentally alters the structure and function of microbial communities, which in turn translates into greater potential for the natural attenuation of these compounds compared to more pristine sites. Copyright © 2017. Published by Elsevier B.V.

Response of soil bacterial community to repeated applications of carbendazim.

PubMed

Wang, Xiuguo; Song, Min; Wang, Yiqi; Gao, Chunming; Zhang, Qun; Chu, Xiaoqiang; Fang, Hua; Yu, Yunlong

2012-01-01

The effect of repeated carbendazim applications on functional diversity of culturable microorganisms and bacterial community composition was studied under field conditions. The functional diversity of soil culturable microbial community (Shannon index, H') reduced significantly (P<0.05) after the first introduction of carbendazim at levels of 0.94, 1.88 and 4.70 kg active ingredient (a.i.)ha(-1) and then recovered to that in the control with subsequent applications. An evident (P<0.01) difference in the bacterial community composition was observed after the second carbendazim application by Temperature Gradient Gel Electrophoresis (TGGE) analysis of 16S rRNA genes amplified from treated and control soils, which remained after the third and fourth treatments. Our results indicated that repeated carbendazim applications have a transient harmful effect on functional diversity of soil culturable microbial community and result in an alteration in bacterial community composition largely due to one species within the γ-proteobacterium. Copyright © 2011 Elsevier Inc. All rights reserved.

Irrigation and weed control alter soil microbiology and nutrient availability in North Carolina Sandhill peach orchards.

PubMed

Zhang, Yi; Wang, Liangju; Yuan, Yongge; Xu, Jing; Tu, Cong; Fisk, Connie; Zhang, Weijian; Chen, Xin; Ritchie, David; Hu, Shuijin

2018-02-15

Orchard management practices such as weed control and irrigation are primarily aimed at maximizing fruit yields and economic profits. However, the impact of these practices on soil fertility and soil microbiology is often overlooked. We conducted a two-factor experimental manipulation of weed control by herbicide and trickle irrigation in a nutrient-poor peach (Prunus persica L. cv. Contender) orchard near Jackson Springs, North Carolina. After three and eight years of treatments, an array of soil fertility parameters were examined, including soil pH, soil N, P and cation nutrients, microbial biomass and respiration, N mineralization, and presence of arbuscular mycorrhizal fungi (AMF). Three general trends emerged: 1) irrigation significantly increased soil microbial biomass and activity, 2) infection rate of mycorrhizal fungi within roots were significantly higher under irrigation than non-irrigation treatments, but no significant difference in the AMF community composition was detected among treatments, 3) weed control through herbicides reduced soil organic matter, microbial biomass and activity, and mineral nutrients, but had no significant impacts on root mycorrhizal infection and AMF communities. Weed-control treatments directly decreased availability of soil nutrients in year 8, especially soil extractable inorganic N. Weed control also appears to have altered the soil nutrients via changes in soil microbes and altered net N mineralization via changes in soil microbial biomass and activity. These results indicate that long-term weed control using herbicides reduces soil fertility through reducing organic C inputs, nutrient retention and soil microbes. Together, these findings highlight the need for alternative practices such as winter legume cover cropping that maintain and/or enhance organic inputs to sustain the soil fertility. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction

PubMed Central

Liang, Yuting; Van Nostrand, Joy D.; N′Guessan, Lucie A.; Peacock, Aaron D.; Deng, Ye; Long, Philip E.; Resch, C. Tom; Wu, Liyou; He, Zhili; Li, Guanghe; Hazen, Terry C.; Lovley, Derek R.

2012-01-01

To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation. PMID:22327592

Arbuscular Mycorrhizal Fungal Hyphae Alter Soil Bacterial Community and Enhance Polychlorinated Biphenyls Dissipation

PubMed Central

Qin, Hua; Brookes, Philip C.; Xu, Jianming

2016-01-01

We investigated the role of arbuscular mycorrhizal fungal (AMF) hyphae in alternation of soil microbial community and Aroclor 1242 dissipation. A two-compartment rhizobox system with double nylon meshes in the central was employed to exclude the influence of Cucurbita pepo L. root exudates on hyphal compartment soil. To assess the quantitative effect of AMF hyphae on soil microbial community, we separated the hyphal compartment soil into four horizontal layers from the central mesh to outer wall (e.g., L1–L4). Soil total PCBs dissipation rates ranged from 35.67% of L4 layer to 57.39% of L1 layer in AMF inoculated treatment, which were significant higher than the 17.31% of the control (P < 0.05). The dissipation rates of tri-, tetrachlorinated biphenyls as well as the total PCBs were significantly correlated with soil hyphal length (P < 0.01). Real-time quantitative PCR results indicated that the Rhodococcus-like bphC gene was 2–3 orders of magnitude more than that of Pseudomonas-like bphC gene, and was found responded positively to AMF. Phylogenetic analyses of the 16S rDNA sequenced by the Illumina Miseq sequencing platform indicated that AMF hyphae altered bacterial community compositions. The phylum Betaproteobacteria and Actinobacteria were dominated in the soil, while Burkholderiales and Actinomycetales were dominated at the order level. Taxa from the Comamonadaceae responded positively to AMF and trichlorinated biphenyl dissipation, while taxa from the Oxalobacteraceae and Streptomycetaceae responded negatively to AMF and PCB congener dissipation. Our results suggested that the AMF hyphal exudates as well as the hyphae per se did have quantitative effects on shaping soil microbial community, and could modify the PCBs dissipation processes consequently. PMID:27379068

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils.

PubMed

Walker, Jennifer K M; Egger, Keith N; Henry, Gregory H R

2008-09-01

Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.

Microbial community responses to 17 years of altered precipitation are seasonally dependent and coupled to co-varying effects of water content on vegetation and soil C

USGS Publications Warehouse

Sorensen, Patrick O.; Germino, Matthew J.; Feris, Kevin P.

2013-01-01

Precipitation amount and seasonal timing determine the duration and distribution of water available for plant and microbial activity in the cold desert sagebrush steppe. In this study, we sought to determine if a sustained shift in the amount and timing of precipitation would affect soil microbial diversity, community composition, and soil carbon (C) storage. Field plots were irrigated (+200 mm) during the dormant or growing-season for 17 years. Microbial community responses were assessed over the course of a year at two depths (15–20 cm, 95–100 cm) by terminal restriction fragment length polymorphism (T-RFLP), along with co-occurring changes in plant cover and edaphic properties. Bacterial richness, Shannon Weaver diversity, and composition in shallow soils (15–20 cm) as well as evenness in deep soils (95–100 cm) differed across irrigation treatments during July. Irrigation timing affected fungal community diversity and community composition during the dormant season and most strongly in deep soils (95–100 cm). Dormant-season irrigation increased the ratio of shrubs to forbs and reduced soil C in shallow soils by 16% relative to ambient conditions. It is unclear whether or not soil C will continue to decline with continued treatment application or if microbial adaptation could mitigate sustained soil C losses. Future changes in precipitation timing will affect soil microbes in a seasonally dependent manner and be coupled to co-varying effects of water content on vegetation and soil C.

Perfluoroalkyl Acids Shift Microbial Community Structure Across Experimental Scales

NASA Astrophysics Data System (ADS)

Weathers, T. S.; Sharp, J.

2016-12-01

Perfluoroalkyl acids (PFAAs) are contaminants of emerging concern that have increasingly been found in groundwater and drinking water systems. Previously, we demonstrated that PFAAs significantly alter the abundance of specific microbial clades in batch reductive dechlorinating systems, resulting in decreased chlorinated solvent attenuation capabilities. To further understand the impacts of PFAA exposure on subsurface microbial processes and PFAA transport, we investigated changes in microbial community structure as a function of PFAA presence in flow-through columns simulating aquifer transport. Phylogenetic analysis using high throughput, next generation sequencing performed after exposure to 250 pore volumes of source zone concentrations of PFAAs (10 mg/L each of 11 analytes including PFOS and PFOA) resulted in patterns that mirrored those observed in batch systems, demonstrating a conservation of community dynamics across experimental scales. Of the nine clades observed in both batch and flow-through systems, six were similarly impacted as a function of PFAA exposure, regardless of the experimental differences in transport and redox state. Specifically, the presence of PFAAs enhanced the relative abundance of Archaea, Bacteroidetes (phylum), and the family Veillonellaceae in both systems. Repressed clades include the genus Sedimentibacter, Ruminococcaceae (family), and the Anaerolineales, which contains Dehalococcoides, a genus known for its ability to fully dechlorinate TCE. As PFAAs are often co-located with TCE and BTEX, changes in microbial community structure can result in hindered bioremediation of these co-contaminants. Consideration of community shifts and corresponding changes in behavior, such as repressed reductive dechlorination or increased biofilm formation, will aid in the development of conceptual site models that account for co-contaminant bioremediation potential and PFAA transport.

Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities.

PubMed

Guo, Yanqing; Chen, Xiaotian; Wu, Yuanyuan; Zhang, Lu; Cheng, Jimin; Wei, Gehong; Lin, Yanbing

2018-04-18

Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems. Copyright © 2018. Published by Elsevier B.V.

Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs.

PubMed

Newell-Fugate, Annie E; Lenz, Katherine; Skenandore, Cassandra; Nowak, Romana A; White, Bryan A; Braundmeier-Fleming, Andrea

2017-01-01

Forty percent of American women are obese and at risk for type II diabetes, impaired immune function, and altered microbiome diversity, thus impacting overall health. We investigated whether obesity induced by an excess calorie, high fat diet containing hydrogenated fats, fructose, and coconut oil (HFD) altered glucose homeostasis, peripheral immunity, and urogenital microbial dynamics. We hypothesized that HFD would cause hyperglycemia, increase peripheral inflammation, and alter urogenital microbiota to favor bacterial taxonomy associated with inflammation. We utilized female Ossabaw mini-pigs to model a 'thrifty' metabolic phenotype associated with increased white adipose tissue mass. Pigs were fed HFD (~4570 kcal/pig/day) or lean (~2000 kcal/pig/day) diet for a total of 9 estrous cycles (~6 months). To determine the effect of cycle stage on cytokines and the microbiome, animals had samples collected during cycles 7 and 9 on certain days of the cycle: D1, 4, 8, 12, 16, 18. Vaginal swabs or cervical flushes assessed urogenital microbiota. Systemic fatty acids, insulin, glucose, and cytokines were analyzed. Pig weights and morphometric measurements were taken weekly. Obese pigs had increased body weight, length, heart and belly girth but similar glucose concentrations. Obese pigs had decreased cytokine levels (IL-1β, TNF-α, IL-4, IL-10), arachidonic acid and plasma insulin, but increased levels of vaccenic acid. Obese pigs had greater urogenital bacterial diversity, including several taxa known for anti-inflammatory properties. Overall, induction of obesity did not induce inflammation but shifted the microbial communities within the urogenital tract to an anti-inflammatory phenotype. We postulate that the coconut oil in the HFD oil may have supported normal glucose homeostasis and modulated the immune response, possibly through regulation of microbial community dynamics and fatty acid metabolism. This animal model holds promise for the study of how different types of obesity and high fat diets may affect metabolism, immune phenotype, and microbial dynamics.

Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs

PubMed Central

Skenandore, Cassandra; Nowak, Romana A.; White, Bryan A.; Braundmeier-Fleming, Andrea

2017-01-01

Forty percent of American women are obese and at risk for type II diabetes, impaired immune function, and altered microbiome diversity, thus impacting overall health. We investigated whether obesity induced by an excess calorie, high fat diet containing hydrogenated fats, fructose, and coconut oil (HFD) altered glucose homeostasis, peripheral immunity, and urogenital microbial dynamics. We hypothesized that HFD would cause hyperglycemia, increase peripheral inflammation, and alter urogenital microbiota to favor bacterial taxonomy associated with inflammation. We utilized female Ossabaw mini-pigs to model a ‘thrifty’ metabolic phenotype associated with increased white adipose tissue mass. Pigs were fed HFD (~4570 kcal/pig/day) or lean (~2000 kcal/pig/day) diet for a total of 9 estrous cycles (~6 months). To determine the effect of cycle stage on cytokines and the microbiome, animals had samples collected during cycles 7 and 9 on certain days of the cycle: D1, 4, 8, 12, 16, 18. Vaginal swabs or cervical flushes assessed urogenital microbiota. Systemic fatty acids, insulin, glucose, and cytokines were analyzed. Pig weights and morphometric measurements were taken weekly. Obese pigs had increased body weight, length, heart and belly girth but similar glucose concentrations. Obese pigs had decreased cytokine levels (IL-1β, TNF-α, IL-4, IL-10), arachidonic acid and plasma insulin, but increased levels of vaccenic acid. Obese pigs had greater urogenital bacterial diversity, including several taxa known for anti-inflammatory properties. Overall, induction of obesity did not induce inflammation but shifted the microbial communities within the urogenital tract to an anti-inflammatory phenotype. We postulate that the coconut oil in the HFD oil may have supported normal glucose homeostasis and modulated the immune response, possibly through regulation of microbial community dynamics and fatty acid metabolism. This animal model holds promise for the study of how different types of obesity and high fat diets may affect metabolism, immune phenotype, and microbial dynamics. PMID:28704429

Effects of dissolved CO2 on Shallow Freshwater Microbial Communities simulating a CO2 Leakage Scenario

NASA Astrophysics Data System (ADS)

Gulliver, D. M.; Lowry, G. V.; Gregory, K.

2013-12-01

Geological carbon sequestration is likely to be part of a comprehensive strategy to minimize the atmospheric release of greenhouse gasses, establishing a concern of sequestered CO2 leakage into overlying potable aquifers. Leaking CO2 may affect existing biogeochemical processes and therefore water quality. There is a critical need to understand the evolution of CO2 exposed microbial communities that influence the biogeochemistry in these freshwater aquifers. The evolution of microbial ecology for different CO2 exposure concentrations was investigated using fluid-slurry samples obtained from a shallow freshwater aquifer (55 m depth, 0.5 MPa, 22 °C, Escatawpa, MS). The microbial community of well samples upstream and downstream of CO2 injection was characterized. In addition, batch vessel experiments were conducted with the upstream aquifer samples exposed to varying pCO2 from 0% to 100% under reservoir temperature and pressure for up to 56 days. The microbial community of the in situ experiment and the batch reactor experiment were analyzed with 16S rRNA clone libraries and qPCR. In both the in situ experiment and the batch reactor experiment, DNA concentration did not correlate with CO2 exposure. Both the in situ experiment and the batch reactors displayed a changing microbial community with increased CO2 exposure. The well water isolate, Curvibacter, appeared to be the most tolerant genus to high CO2 concentrations in the in situ experiments and to mid-CO2 concentrations in the batch reactors. In batch reactors with pCO2 concentrations higher than experienced in situ (pCO2 = 0.5 MPa), Pseudomonas appeared to be the most tolerant genus. Findings provide insight into a dynamic biogeochemical system that will alter with CO2 exposure. Adapted microbial populations will eventually give rise to the community that will impact the metal mobility and water quality. Knowledge of the surviving microbial populations will enable improved models for predicting the fate of CO2 following leakage and lead to better strategies for ensuring the quality of potable aquifer water.

[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.

Profile Changes in the Soil Microbial Community When Desert Becomes Oasis

PubMed Central

Li, Chen-hua; Tang, Li-song; Jia, Zhong-jun; Li, Yan

2015-01-01

The conversion of virgin desert into oasis farmland creates two contrasting types of land-cover. During oasis formation with irrigation and fertilizer application, however, the changes in the soil microbial population, which play critical roles in the ecosystem, remain poorly understood. We applied high-throughput pyrosequencing to investigate bacterial and archaeal communities throughout the profile (0–3 m) in an experimental field, where irrigation and fertilization began in 1990 and cropped with winter wheat since then. To assess the effects of cultivation, the following treatments were compared with the virgin desert: CK (no fertilizer), PK, NK, NP, NPK, NPKR, and NPKM (R: straw residue; M: manure fertilizer). Irrigation had a greater impact on the overall microbial community than fertilizer application. The greatest impact occurred in topsoil (0–0.2 m), e.g., Cyanobacteria (25% total abundance) were most abundant in desert soil, while Actinobacteria (26%) were most abundant in oasis soil. The proportions of extremophilic and photosynthetic groups (e.g., Deinococcus-Thermus and Cyanobacteria) decreased, while the proportions of R-strategy (e.g., Gammaproteobacteria including Xanthomonadales), nitrifying (e.g., Nitrospirae), and anaerobic bacteria (e.g., Anaerolineae) increased throughout the oasis profile. Archaea occurred only in oasis soil. The impact of fertilizer application was mainly reflected in the non-dominant communities or finer taxonomic divisions. Oasis formation led to a dramatic shift in microbial community and enhanced soil enzyme activities. The rapidly increased soil moisture and decreased salt caused by irrigation were responsible for this shift. Furthermore, difference in fertilization and crop growth altered the organic carbon contents in the soil, which resulted in differences of microbial communities within oasis. PMID:26426279

Estimation of microbial metabolism and co-occurrence patterns in fracture groundwaters of deep crystalline bedrock at Olkiluoto, Finland

NASA Astrophysics Data System (ADS)

Bomberg, M.; Lamminmäki, T.; Itävaara, M.

2015-08-01

The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is great but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. The great sequencing depth revealed that up to 95 and 99 % of the bacterial and archaeal communities, respectively, were composed of only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3 and 6 fold more bacterial and archaeal taxa. Several clusters of co-occurring rare taxa were identified, which correlated significantly with physicochemical parameters, such as salinity, concentration of inorganic or organic carbon, sulphur, pH and depth. The metabolic properties of the microbial communities were predicted using PICRUSt. The rough prediction showed that the metabolic pathways included commonly fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier conditions on Earth, but could also be induced again if changes in their living conditions occur. In this study only the rare taxa correlated with any physicochemical parameters. Thus these microorganisms can respond to environmental change caused by physical or biological factors that may lead to alterations in the diversity and function of the microbial communities in crystalline bedrock environments.

Vaginal microbiota of women with frequent vulvovaginal candidiasis.

PubMed

Zhou, Xia; Westman, Rachel; Hickey, Roxana; Hansmann, Melanie A; Kennedy, Colleen; Osborn, Thomas W; Forney, Larry J

2009-09-01

Vulvovaginal candidiasis (VVC) is an insidious infection that afflicts a large proportion of women of all ages, and 5 to 8% of affected women experience recurrent VVC (RVVC). The aim of this study was to explore the possible importance of vaginal bacterial communities in reducing the risk of RVVC. The species composition and diversity of microbial communities were evaluated for 42 women with and without frequent VVC based on profiles of terminal restriction fragment polymorphisms of 16S rRNA genes and phylogenetic analysis of cloned 16S rRNA gene sequences from the numerically dominant microbial populations. The data showed that there were no significant differences between the vaginal microbial communities of women in the two groups (likelihood score, 5.948; bootstrap P value, 0.26). Moreover, no novel bacteria were found in the communities of women with frequent VVC. The vaginal communities of most women in both groups (38/42; 90%) were dominated by species of Lactobacillus. The results of this study failed to provide evidence for the existence of altered or unusual vaginal bacterial communities in women who have frequent VVC compared to women who do not have frequent VVC. The findings suggest that commensal vaginal bacterial species may not be able to prevent VVC.

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin

PubMed Central

Roesch, Luiz Fernando Wurdig; Silveira, Rita C.; Corso, Andréa L.; Dobbler, Priscila Thiago; Mai, Volker; Rojas, Bruna S.; Laureano, Álvaro M.; Procianoy, Renato S.

2017-01-01

Background Administering intravenous antibiotics during labor to women at risk for transmitting Group B Streptococcus (GBS) can prevent infections in newborns. However, the impact of intrapartum antibiotic prophylaxis on mothers’ microbial community composition is largely unknown. We compared vaginal microbial composition in pregnant women experiencing preterm birth at ≤ 32 weeks gestation that received intrapartum antibiotic prophylaxis with that in controls. Methods Microbiota in vaginal swabs collected shortly before delivery from GBS positive women that received penicillin intravenously during labor or after premature rupture of membranes was compared to controls. Microbiota was analyzed by 16S rRNA sequencing using the PGM Ion Torrent to determine the effects of penicillin use during hospitalization and GBS status on its composition. Results Penicillin administration was associated with an altered vaginal microbial community composition characterized by increased microbial diversity. Lactobacillus sp. contributed only 13.1% of the total community in the women that received penicillin compared to 88.1% in the controls. Streptococcus sp. were present in higher abundance in GBS positive woman compared to controls, with 60% of the total vaginal microbiota in severe cases identified as Streptococcus sp. Conclusions Vaginal communities of healthy pregnant women were dominated by Lactobacillus sp. and contained low diversity, while Group B Streptococcus positive women receiving intrapartum antibiotic prophylaxis had a modified vaginal microbiota composition with low abundance of Lactobacillus but higher microbial diversity. PMID:28178310

Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

PubMed Central

Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

2015-01-01

Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

Effects of redox fluctuations on microbial community ecology post-wildfire in a high elevation mixed-conifer catchment in northern New Mexico.

NASA Astrophysics Data System (ADS)

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

2015-12-01

Wildfires are increasing in size and severity across the western United States with impacts on regional biogeochemical cycling. The resiliency of resident soil microbial communities determines rates of nutrient transformations as well as forest structure and recovery. Redox conditions in soil determine metabolic activities of microorganisms, which first consume oxygen and a succession of alternative terminal electron acceptors to support growth and metabolism using a variety of carbon sources. Controls on redox zonation are largely unknown in dominantly oxic soils, and microbial community adaptation and response to fluctuations in redox potential in a sub-alpine forested post-disturbance catchment has not been studied. Previous work has shown that fluctuating or rising water tables result in redox-dynamic sites, which can be 'hot spots' of biogeochemical activity depending on landscape position. Fire-induced tree mortality results in altered hydrologic flow paths and decreased evapotranspiration, leading to potential for intensified hot spot activity. We are testing such coupling of microbial activity with fluctuations in redox status using field measurements and laboratory incubation experiments. The 2013 Thompson Ridge Fire in the Jemez River Basin (NM) Critical Zone Observatory provides a highly-contextualized opportunity to examine how disturbance regime affects changes in soil microbial community dynamics and fluctuations in reduction-oxidation potential (as quantified by continuous CZO measurements of O2, CO2 and Eh as a function of soil depth and landscape location). We hypothesize that areas of depositional convergence in the catchment, which have been shown to exhibit more reducing conditions, will host microbial communities that are better adapted to fluctuating redox conditions and exhibit a greater diversity in functional capabilities. In these mixed conifer forests we find shifts in redox potential status in relation to depth and topography where more reducing conditions typically occur in convergent zones and at depth. These results highlight the significance of fluctuating oxygen-depleted zones in aerobic soils on microbial community activity and structure, linking community response to larger scale ecosystem processes.

Microbial functional diversity alters the structure and sensitivity of oxygen deficient zones

NASA Astrophysics Data System (ADS)

Penn, Justin; Weber, Thomas; Deutsch, Curtis

2016-09-01

Oxygen deficient zones (ODZs) below the ocean surface regulate marine productivity by removing bioavailable nitrogen (N). A complex microbial community mediates N loss, but the interplay of its diverse metabolisms is poorly understood. We present an ecosystem model of the North Pacific ODZ that reproduces observed chemical distributions yet predicts different ODZ structure, rates, and climatic sensitivity compared to traditional geochemical models. An emergent lower O2 limit for aerobic nitrification lies below the upper O2 threshold for anaerobic denitrification, creating a zone of microbial coexistence that causes a larger ODZ but slower total rates of N loss. The O2-dependent competition for the intermediate nitrite produces gradients in its oxidation versus reduction, anammox versus heterotrophic denitrification, and the net ecological stoichiometry of N loss. The latter effect implies that an externally driven ODZ expansion should favor communities that more efficiently remove N, increasing the sensitivity of the N cycle to climate change.

Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.

PubMed

Soliman, Taha; Reimer, James D; Yang, Sung-Yin; Villar-Briones, Alejandro; Roy, Michael C; Jenke-Kodama, Holger

2017-01-01

Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan "Kaichu-Doro" Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores ( n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m) than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60-80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA) of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs) revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae) were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.

Anaerobic soil disinfestation and Brassica seed meal amendment alter soil microbiology and system resistance

USDA-ARS?s Scientific Manuscript database

Brassica seed meal amendments and anaerobic soil disinfestation control a spectrum of soil-borne plant pathogens via a diversity of mechanisms. Transformations in microbial community structure and function in certain instances were determinants of disease control and enhanced plant performance. Fo...

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

The potential for retreating alpine glaciers to alter alpine ecosystems in the Colorado Front Range

NASA Astrophysics Data System (ADS)

Hall, E.; Baron, J.

2013-12-01

Glaciers are retreating at an unprecedented rate. In mid-latitude alpine ecosystems the presence of glaciers and rock glaciers govern rates and ecology of alpine and sub-alpine ecosystems. Changes in the thermal environment due to the loss of isothermal habitat and inputs from glacier melt chemistry are altering alpine ecosystems in unpredictable ways. In particular, glacier may be a source of nitrogen that is altering alpine ecosystem dynamics. Loch Vale Watershed (LVWS) located within Rocky Mountain National Park. LVWS contains a surface glacier (Andrew's glacier) and a rock glacier (Taylor's glacier) at the headwater of each of the two drainages within the watershed. We collected precipitation from a National Atmospheric Deposition Site and surface water from multiple alpine lakes and streams during a particularly high and low snow year in the Colorado Front Range. We also sampled stream and lake sediments at each site to analyze the associated microbial community. Concentrations of nitrate and ammonium, relative abundance of amoA (the gene responsible for a key step in the microbial nitrification pathway), and the dual isotope signal to nitrate all point to snow melt as a key deliverer of nitrogen to ecosystems along the Colorado Front Range. However, late summer surface water chemistry is isotopically similar to the chemistry of glacial ice. This suggests that retreating glacier may be an additional source of N to alpine ecosystems and have the potential to alter microbial community composition, biogeochemical rate processes, and ecosystem function. These dynamics are most likely not unique to the Colorado Front Range and should be globally distributed as glaciers continue to retreat in high altitude ecosystems around the world.

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3.

PubMed

Wang, Peng; Marsh, Ellen L; Ainsworth, Elizabeth A; Leakey, Andrew D B; Sheflin, Amy M; Schachtman, Daniel P

2017-11-03

Rising atmospheric concentrations of CO 2 and O 3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO 2 and O 3 (eCO 2 and eO 3 ) the endosphere, rhizosphere and soil were sampled from soybeans under eCO 2 and maize under eO 3 . The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO 2 , associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO 3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO 2 and O 3 .

Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China

PubMed Central

Xie, Haiyang; Li, Ang; Lu, Haifeng; Xu, Shaoyan; Zhou, Lin; Zhang, Hua; Cui, Guangying; Chen, Xinhua; Liu, Yuanxing; Wu, Liming; Qin, Nan; Sun, Ranran; Wang, Wei; Li, Lanjuan; Wang, Weilin; Zheng, Shusen

2017-01-01

Pancreatic carcinoma (PC) is a lethal cancer. Gut microbiota is associated with some risk factors of PC, e.g. obesity and types II diabetes. However, the specific gut microbial profile in clinical PC in China has never been reported. This prospective study collected 85 PC and 57 matched healthy controls (HC) to analyze microbial characteristics by MiSeq sequencing. The results showed that gut microbial diversity was decreased in PC with an unique microbial profile, which partly attributed to its decrease of alpha diversity. Microbial alterations in PC featured by the increase of certain pathogens and lipopolysaccharides-producing bacteria, and the decrease of probiotics and butyrate-producing bacteria. Microbial community in obstruction cases was separated from the un-obstructed cases. Streptococcus was associated with the bile. Furthermore, 23 microbial functions e.g. Leucine and LPS biosynthesis were enriched, while 13 functions were reduced in PC. Importantly, based on 40 genera associated with PC, microbial markers achieves a high classification power with AUC of 0.842. In conclusion, gut microbial profile was unique in PC, providing a microbial marker for non-invasive PC diagnosis. PMID:29221120

Species-Specific Viromes in the Ancestral Holobiont Hydra

PubMed Central

Anton-Erxleben, Friederike; Lim, Yan Wei; Schmieder, Robert; Fraune, Sebastian; Franzenburg, Sören; Insua, Santiago; Machado, GloriaMay; Haynes, Matthew; Little, Mark; Kimble, Robert; Rosenstiel, Philip; Rohwer, Forest L.; Bosch, Thomas C. G.

2014-01-01

Recent evidence showing host specificity of colonizing bacteria supports the view that multicellular organisms are holobionts comprised of the macroscopic host in synergistic interdependence with a heterogeneous and host-specific microbial community. Whereas host-bacteria interactions have been extensively investigated, comparatively little is known about host-virus interactions and viral contribution to the holobiont. We sought to determine the viral communities associating with different Hydra species, whether these viral communities were altered with environmental stress, and whether these viruses affect the Hydra-associated holobiont. Here we show that each species of Hydra harbors a diverse host-associated virome. Primary viral families associated with Hydra are Myoviridae, Siphoviridae, Inoviridae, and Herpesviridae. Most Hydra-associated viruses are bacteriophages, a reflection of their involvement in the holobiont. Changes in environmental conditions alter the associated virome, increase viral diversity, and affect the metabolism of the holobiont. The specificity and dynamics of the virome point to potential viral involvement in regulating microbial associations in the Hydra holobiont. While viruses are generally regarded as pathogenic agents, our study suggests an evolutionary conserved ability of viruses to function as holobiont regulators and, therefore, constitutes an emerging paradigm shift in host-microbe interactions. PMID:25343582

Species-specific viromes in the ancestral holobiont Hydra.

PubMed

Grasis, Juris A; Lachnit, Tim; Anton-Erxleben, Friederike; Lim, Yan Wei; Schmieder, Robert; Fraune, Sebastian; Franzenburg, Sören; Insua, Santiago; Machado, GloriaMay; Haynes, Matthew; Little, Mark; Kimble, Robert; Rosenstiel, Philip; Rohwer, Forest L; Bosch, Thomas C G

2014-01-01

Recent evidence showing host specificity of colonizing bacteria supports the view that multicellular organisms are holobionts comprised of the macroscopic host in synergistic interdependence with a heterogeneous and host-specific microbial community. Whereas host-bacteria interactions have been extensively investigated, comparatively little is known about host-virus interactions and viral contribution to the holobiont. We sought to determine the viral communities associating with different Hydra species, whether these viral communities were altered with environmental stress, and whether these viruses affect the Hydra-associated holobiont. Here we show that each species of Hydra harbors a diverse host-associated virome. Primary viral families associated with Hydra are Myoviridae, Siphoviridae, Inoviridae, and Herpesviridae. Most Hydra-associated viruses are bacteriophages, a reflection of their involvement in the holobiont. Changes in environmental conditions alter the associated virome, increase viral diversity, and affect the metabolism of the holobiont. The specificity and dynamics of the virome point to potential viral involvement in regulating microbial associations in the Hydra holobiont. While viruses are generally regarded as pathogenic agents, our study suggests an evolutionary conserved ability of viruses to function as holobiont regulators and, therefore, constitutes an emerging paradigm shift in host-microbe interactions.

Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea

PubMed Central

Trajanoski, Slave; Lackner, Stefan; Stocker, Gernot; Hinterleitner, Thomas; Gülly, Christian; Högenauer, Christoph

2013-01-01

Background & Aims Diseases of the human gastrointestinal (GI) tract are often accompanied by diarrhea with profound alterations in the GI microbiota termed dysbiosis. Whether dysbiosis is due to the disease itself or to the accompanying diarrhea remains elusive. With this study we characterized the net effects of osmotic diarrhea on the composition of the GI microbiota in the absence of disease. Methods We induced osmotic diarrhea in four healthy adults by oral administration of polyethylene glycol 4000 (PEG). Stool as well as mucosa specimens were collected before, during and after diarrhea and 16S rDNA-based microbial community profiling was used to assess the microbial community structure. Results Stool and mucosal microbiotas were strikingly different, with Firmicutes dominating the mucosa and Bacteroidetes the stools. Osmotic diarrhea decreased phylotype richness and showed a strong tendency to equalize the otherwise individualized microbiotas on the mucosa. Moreover, diarrhea led to significant relative shifts in the phyla Bacteroidetes and Firmicutes and to a relative increase in the abundance of Proteobacteria on the mucosa, a phenomenon also noted in several inflammatory and diarrheal GI diseases. Conclusions Changes in microbial community structure induced by osmotic diarrhea are profound and show similarities to changes observed in other GI diseases including IBD. These effects so must be considered when specimens from diarrheal diseases (i.e. obtained by stratification of samples according to diarrheal status) or conditions wherein bowel preparations like PEG (i.e. specimens obtained during endoscopy) are used. PMID:23409050

Effectiveness of beneficial plant-microbe interactions under hypobaric and hypoxic conditions in an advanced life support system

NASA Astrophysics Data System (ADS)

MacIntyre, Olathe; Stasiak, Michael; Cottenie, Karl; Trevors, Jack; Dixon, Mike

An assembled microbial community in the hydroponics solution of an advanced life support system may improve plant performance and productivity in three ways: (1) exclusion of plant pathogens from the initial community, (2) resistance to infection, and (3) plant-growth promotion. However, the plant production area is likely to have a hypobaric (low pressure) and hypoxic (low oxygen) atmosphere to reduce structural mass and atmosphere leakage, and these conditions may alter plant-microbe interactions. Plant performance and productivity of radish (Raphanus sativus L. cv. Cherry Bomb II) grown under hypobaric and hypoxic conditions were investigated at the University of Guelph's Controlled Environment Systems Research Facility. Changes in the microbial communities that routinely colonized the re-circulated nutrient solution, roots, and leaves of radishes in these experiments were quantified in terms of similarity in community composition, abundance of bacteria, and community diversity before and after exposure to hypobaric and hypoxic conditions relative to communities maintained at ambient growth conditions. The microbial succession was affected by extreme hypoxia (2 kPa oxygen partial pressure) while hypobaria as low as 10 kPa total pressure had little effect on microbial ecology. There were no correlations found between the physiological profile of these unintentional microbial communities and radish growth. The effects of hypobaric and hypoxic conditions on specific plant-microbe interactions need to be determined before beneficial gnotobiotic communities can be developed for use in space. The bacterial strains Tal 629 of Bradyrhizobium japonicum and WCS417 of Pseudomonas fluorescens, and the plant pathogen Fusarium oxysporum f. sp. raphani will be used in future experiments. B. japonicum Tal 629 promotes radish growth in hydroponics systems and P. fluorescens WCS417 induces systemic resistance to fusarium wilt (F. oxysporum f. sp. raphani) in radish under ambient conditions. Techniques used to investigate the interactions between radish and these microbes under hypobaric and hypoxic conditions will be discussed.

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor

PubMed Central

Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2017-01-01

Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ13C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106–198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field. PMID:27754478

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor.

PubMed

Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-Ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2017-02-01

Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ 13 C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106-198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field.

Changes in Rumen Microbial Community Composition during Adaption to an In Vitro System and the Impact of Different Forages

PubMed Central

Lengowski, Melanie B.; Zuber, Karin H. R.; Witzig, Maren; Möhring, Jens; Boguhn, Jeannette; Rodehutscord, Markus

2016-01-01

This study examined ruminal microbial community composition alterations during initial adaption to and following incubation in a rumen simulation system (Rusitec) using grass or corn silage as substrates. Samples were collected from fermenter liquids at 0, 2, 4, 12, 24, and 48 h and from feed residues at 0, 24, and 48 h after initiation of incubation (period 1) and on day 13 (period 2). Microbial DNA was extracted and real-time qPCR was used to quantify differences in the abundance of protozoa, methanogens, total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminobacter amylophilus, Prevotella bryantii, Selenomonas ruminantium, and Clostridium aminophilum. We found that forage source and sampling time significantly influenced the ruminal microbial community. The gene copy numbers of most microbial species (except C. aminophilum) decreased in period 1; however, adaption continued through period 2 for several species. The addition of fresh substrate in period 2 led to increasing copy numbers of all microbial species during the first 2–4 h in the fermenter liquid except protozoa, which showed a postprandial decrease. Corn silage enhanced the growth of R. amylophilus and F. succinogenes, and grass silage enhanced R. albus, P. bryantii, and C. aminophilum. No effect of forage source was detected on total bacteria, protozoa, S. ruminantium, or methanogens or on total gas production, although grass silage enhanced methane production. This study showed that the Rusitec provides a stable system after an adaption phase that should last longer than 48 h, and that the forage source influenced several microbial species. PMID:26928330

Carbon turnover in topsoil and subsoil: The microbial response to root litter additions and different environmental conditions in a reciprocal soil translocation experiment

NASA Astrophysics Data System (ADS)

Preusser, Sebastian; Poll, Christian; Marhan, Sven; Kandeler, Ellen

2017-04-01

At the global scale, soil organic carbon (SOC) represents the largest active terrestrial organic carbon (OC) pool. Carbon dynamics in subsoil, however, vary from those in topsoil with much lower C concentrations in subsoil than in topsoil horizons, although more than 50 % of SOC is stored in subsoils below 30 cm soil depth. In addition, microorganisms in subsoil are less abundant, more heterogeneously distributed and the microbial communities have a lower diversity than those in topsoil. Especially in deeper soil, the impact of changes in habitat conditions on microorganisms involved in carbon cycling are largely unexplored and consequently the understanding of microbial functioning is limited. A reciprocal translocation experiment allowed us to investigate the complex interaction effects of altered environmental and substrate conditions on microbial decomposer communities in both topsoil and subsoil habitats under in situ conditions. We conducted this experiment with topsoil (5 cm soil depth) and subsoil (110 cm) samples of an acid and sandy Dystric Cambisol from a European beech (Fagus sylvatica L.) forest in Lower Saxony, Germany. In total 144 samples were buried into three depths (5 cm, 45 cm and 110 cm) and 13C-labelled root litter was added to expose the samples to different environmental conditions and to increase the substrate availability, respectively. Samples were taken in three month intervals up to a maximum exposure time of one year to follow the temporal development over the experimental period. Analyses included 13Cmic and 13C PLFA measurements to investigate the response of microbial abundance, community structure and 13C-root decomposition activity under the different treatments. Environmental conditions in the respective soil depths such as soil temperature and water content were recorded throughout the experimental period. All microbial groups (gram+ and gram- bacteria, fungi) showed highest relative 13C incorporation in 110 cm depth and samples with root addition had generally higher microbial abundances than those with no root addition. Here, especially fungi benefited from the additional carbon source with highly increased abundances in all incorporation depths. Also the altered environmental conditions in the different incorporation depths significantly influenced the different microbial groups. The steepest decrease with depth was detected in fungal abundance, while bacteria were less affected and increased in relative abundance in soil samples incorporated into subsoil layers. The highest seasonal variability in microbial abundance, however, was determined in 5 cm incorporation depth demonstrating the higher amplitude in micro-climatic and micro-environmental conditions in this near-surface soil habitat. In summary, this experiment demonstrated that carbon quality and quantity are the main factors restricting fungal abundance in deeper soil layers, while bacterial decomposer communities are adapted to a wider range of habitat conditions.

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment.

PubMed

Angell, John H; Peng, Xuefeng; Ji, Qixing; Craick, Ian; Jayakumar, Amal; Kearns, Patrick J; Ward, Bess B; Bowen, Jennifer L

2018-01-01

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes ( amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

Paleobiological Perspectives on Early Microbial Evolution

PubMed Central

Knoll, Andrew H.

2015-01-01

Microfossils, stromatolites, and chemical biosignatures indicate that Earth became a biological planet more than 3.5 billion years ago, making most of life's history microbial. Proterozoic rocks preserve a rich record of cyanobacteria, including derived forms that differentiate multiple cell types. Stromatolites, in turn, show that microbial communities covered the seafloor from tidal flats to the base of the photic zone. The Archean record is more challenging to interpret, particularly on the question of cyanobacterial antiquity, which remains to be resolved. In the late Neoproterozoic Era, increasing oxygen and radiating eukaryotes altered the biosphere, with planktonic algae gaining ecological prominence in the water column, whereas seaweeds and, eventually, animals spread across shallow seafloors. From a microbial perspective, however, animals, algae, and, later, plants simply provided new opportunities for diversification, and, to this day, microbial metabolisms remain the only essential components of biogeochemical cycles. PMID:26134315

Sample storage conditions significantly influence faecal microbiome profiles

PubMed Central

Choo, Jocelyn M; Leong, Lex EX; Rogers, Geraint B

2015-01-01

Sequencing-based studies of the human faecal microbiota are increasingly common. Appropriate storage of sample material is essential to avoid the introduction of post-collection bias in microbial community composition. Rapid freezing to −80 °C is commonly considered to be best-practice. However, this is not feasible in many studies, particularly those involving sample collection in participants’ homes. We determined the extent to which a range of stabilisation and storage strategies maintained the composition of faecal microbial community structure relative to freezing to −80 °C. Refrigeration at 4 °C, storage at ambient temperature, and the use of several common preservative buffers (RNAlater, OMNIgene.GUT, Tris-EDTA) were assessed relative to freezing. Following 72 hours of storage, faecal microbial composition was assessed by 16 S rRNA amplicon sequencing. Refrigeration was associated with no significant alteration in faecal microbiota diversity or composition. However, samples stored using other conditions showed substantial divergence compared to −80 °C control samples. Aside from refrigeration, the use of OMNIgene.GUT resulted in the least alteration, while the greatest change was seen in samples stored in Tris-EDTA buffer. The commercially available OMNIgene.GUT kit may provide an important alternative where refrigeration and cold chain transportation is not available. PMID:26572876

Sample storage conditions significantly influence faecal microbiome profiles.

PubMed

Choo, Jocelyn M; Leong, Lex E X; Rogers, Geraint B

2015-11-17

Sequencing-based studies of the human faecal microbiota are increasingly common. Appropriate storage of sample material is essential to avoid the introduction of post-collection bias in microbial community composition. Rapid freezing to -80 °C is commonly considered to be best-practice. However, this is not feasible in many studies, particularly those involving sample collection in participants' homes. We determined the extent to which a range of stabilisation and storage strategies maintained the composition of faecal microbial community structure relative to freezing to -80 °C. Refrigeration at 4 °C, storage at ambient temperature, and the use of several common preservative buffers (RNAlater, OMNIgene.GUT, Tris-EDTA) were assessed relative to freezing. Following 72 hours of storage, faecal microbial composition was assessed by 16 S rRNA amplicon sequencing. Refrigeration was associated with no significant alteration in faecal microbiota diversity or composition. However, samples stored using other conditions showed substantial divergence compared to -80 °C control samples. Aside from refrigeration, the use of OMNIgene.GUT resulted in the least alteration, while the greatest change was seen in samples stored in Tris-EDTA buffer. The commercially available OMNIgene.GUT kit may provide an important alternative where refrigeration and cold chain transportation is not available.

Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57.

PubMed

Schofield, B J; Lachner, N; Le, O T; McNeill, D M; Dart, P; Ouwerkerk, D; Hugenholtz, P; Klieve, A V

2018-03-01

The probiotic Bacillus amyloliquefaciens H57 increased weight gain, increased nitrogen retention and increased feed intake in ruminants when administered to the diet. This study aims to develop a better understanding of this probiotic effect by analysing changes in the rumen prokaryotic community. Sequencing the 16S rRNA gene PCR amplicons of the rumen microbiome, revealed that ewes fed H57 had a significantly different rumen microbial community structure to Control sheep. In contrast, dairy calves showed no significant differences in rumen community structure between treatment groups. In both instances, H57 was below detection in the rumen community profile and was only present at low relative abundance as determined by qPCR. The altered rumen microbial community in sheep likely contributes to increased weight gain through more efficient digestion of plant material. As no change occurred in the rumen community of dairy calves it is suggested that increased weight gain may be due to changes in community function rather than structure. The low relative abundance of H57 as determined by qPCR, suggests that weight gain was not directly mediated by the probiotic, but rather by influencing animal behaviour (feed consumption) and/or altering the native rumen community structure or function. This study provides a novel look at the rumen prokaryotic community in both sheep and dairy calves when fed H57. These findings improve our understanding for the potential rumen community involvement in H57-enabled weight gain. The study reveals that the probiotic B. amyloliquefaciens H57 is capable of benefiting ruminants without colonizing the rumen, suggesting an indirect mechanism of action. © 2018 The Society for Applied Microbiology.

Organo-mineral complexation alters carbon and nitrogen cycling in stream microbial assemblages

NASA Astrophysics Data System (ADS)

Hunter, William Ross; Wanek, Wolfgang; Prommer, Judith; Mooshammer, Maria; Battin, Tom

2014-05-01

Inland waters are of global biogeochemical importance receiving carbon inputs of ~ 4.8 Pg C y-1. Of this 12 % is buried, 18 % transported to the oceans, and 70 % supports aquatic secondary production. However, the mechanisms that determine the fate of organic matter (OM) in these systems are poorly defined. One important aspect is the formation of organo-mineral complexes in aquatic systems and their potential as a route for OM transport and burial vs. microbial utilization as organic carbon (C) and nitrogen (N) sources. Organo-mineral particles form by sorption of dissolved OM to freshly eroded mineral surfaces and may contribute to ecosystem-scale particulate OM fluxes. We tested the availability of mineral-sorbed OM as a C & N source for streamwater microbial assemblages and streambed biofilms. Organo-mineral particles were constructed in vitro by sorption of 13C:15N-labelled amino acids to hydrated kaolin particles, and microbial degradation of these particles compared with equivalent doses of 13C:15N-labelled free amino acids. Experiments were conducted in 120 ml mesocosms over 7 days using biofilms and streamwater sampled from the Oberer Seebach stream (Austria), tracing assimilation and mineralization of 13C and 15N labels from mineral-sorbed and dissolved amino acids. Here we present data on the effects of organo-mineral sorption upon amino acid mineralization and its C:N stoichiometry. Organo-mineral sorption had a significant effect upon microbial activity, restricting C and N mineralization by both the biofilm and streamwater treatments. Distinct differences in community response were observed, with both dissolved and mineral-stabilized amino acids playing an enhanced role in the metabolism of the streamwater microbial community. Mineral-sorption of amino acids differentially affected C & N mineralization and reduced the C:N ratio of the dissolved amino acid pool. The present study demonstrates that organo-mineral complexes restrict microbial degradation of OM and may, consequently, alter the carbon and nitrogen cycling dynamics within aquatic ecosystems.

Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots.

PubMed

Bressan, Mélanie; Roncato, Marie-Anne; Bellvert, Floriant; Comte, Gilles; Haichar, Feth Zahar; Achouak, Wafa; Berge, Odile

2009-11-01

A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched (13)CO(2) atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.

Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability.

PubMed

Rothman, Jason A; Carroll, Mark J; Meikle, William G; Anderson, Kirk E; McFrederick, Quinn S

2018-02-03

Honey bees (Apis mellifera) provide vital pollination services for a variety of agricultural crops around the world and are known to host a consistent core bacterial microbiome. This symbiotic microbial community is essential to many facets of bee health, including likely nutrient acquisition, disease prevention and optimal physiological function. Being that the bee microbiome is likely involved in the digestion of nutrients, we either provided or excluded honey bee colonies from supplemental floral forage before being used for almond pollination. We then used 16S rRNA gene sequencing to examine the effects of forage treatment on the bees' microbial gut communities over four months. In agreement with previous studies, we found that the honey bee gut microbiota is quite stable over time. Similarly, we compared the gut communities of bees from separate colonies and sisters sampled from within the same hive over four months. Surprisingly, we found that the gut microbial communities of individual sisters from the same colony can exhibit as much variation as bees from different colonies. Supplemental floral forage had a subtle effect on the composition of the microbiome during the month of March only, with strains of Gilliamella apicola, Lactobacillus, and Bartonella being less proportionally abundant in bees exposed to forage in the winter. Collectively, our findings show that there is unexpected longitudinal variation within the gut microbial communities of sister honey bees and that supplemental floral forage can subtly alter the microbiome of managed honey bees.

Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation.

PubMed

Deng, Ye; Zhang, Ping; Qin, Yujia; Tu, Qichao; Yang, Yunfeng; He, Zhili; Schadt, Christopher Warren; Zhou, Jizhong

2016-01-01

Discerning network interactions among different species/populations in microbial communities has evoked substantial interests in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. Here, we modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140-269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. Particularly, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system

DOE PAGES

Deng, Ye; Zhang, Ping; Qin, Yujia; ...

2015-08-11

When trying to discern network interactions among different species/populations in microbial communities interests have been evoked in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. We modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the networkmore » interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140–269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. In particular, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.« less

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.

A Metagenomic Survey of Limestone Hill in Taiwan

NASA Astrophysics Data System (ADS)

Hsu, Y. W.; Li, K. Y.; Chen, Y. W.; Huang, T. Y.; Chen, W. J.; Shih, Y. J.; Chen, J. S.; Fan, C. W.; Hsu, B. M.

2016-12-01

The limestone of Narro-Sky in Tainliao, Taiwan is of Pleistocene reef limestones interbedded in clastic layers that covered the Takangshan anticlines. Understanding how microbial relative abundance was changed in response to changes of environmental factors may contribute to better comprehension of roles that microorganisms play in altering the landscape structures. In this study, microorganisms growing on the wall of limestone, in the water dripping from the limestone wall and of soil underneath the wall were collected from different locations where the environmental factors such as daytime illumination, humidity, or pH are different. Next generation sequencing (NGS) was carried out to examine the compositions and richness of microbial community. The metagenomics were clustered into operational taxonomic units (OTUs) to analyze relative abundance, diversities and principal coordinates analysis (PCoA). Our results showed the soil sample has the highest alpha diversity while water sample has the lowest. Four major phyla, which are Proteobacteria, Acidobacteria, Actinobacteria, and Cyanobacteria, account for 80 % of total microbial biomass in all groups. Cyanobacteria were found most abundantly in limestone wall instead of water or soil of weathering limestone. The PCoA dimensional patterns of each phylum showed a trace of microbial community dynamic changes, which might be affected by environmental factors. This study provides the insights to understand how environmental factors worked together with microbial community to shape landscape structures.

The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection

PubMed Central

Jani, Andrea J.; Briggs, Cheryl J.

2014-01-01

Symbiotic microbial communities may interact with infectious pathogens sharing a common host. The microbiome may limit pathogen infection or, conversely, an invading pathogen can disturb the microbiome. Documentation of such relationships during naturally occurring disease outbreaks is rare, and identifying causal links from field observations is difficult. This study documented the effects of an amphibian skin pathogen of global conservation concern [the chytrid fungus Batrachochytrium dendrobatidis (Bd)] on the skin-associated bacterial microbiome of the endangered frog, Rana sierrae, using a combination of population surveys and laboratory experiments. We examined covariation of pathogen infection and bacterial microbiome composition in wild frogs, demonstrating a strong and consistent correlation between Bd infection load and bacterial community composition in multiple R. sierrae populations. Despite the correlation between Bd infection load and bacterial community composition, we observed 100% mortality of postmetamorphic frogs during a Bd epizootic, suggesting that the relationship between Bd and bacterial communities was not linked to variation in resistance to mortal disease and that Bd infection altered bacterial communities. In a controlled experiment, Bd infection significantly altered the R. sierrae microbiome, demonstrating a causal relationship. The response of microbial communities to Bd infection was remarkably consistent: Several bacterial taxa showed the same response to Bd infection across multiple field populations and the laboratory experiment, indicating a somewhat predictable interaction between Bd and the microbiome. The laboratory experiment demonstrates that Bd infection causes changes to amphibian skin bacterial communities, whereas the laboratory and field results together strongly support Bd disturbance as a driver of bacterial community change during natural disease dynamics. PMID:25385615

Benthic microbial abundance and activities in an intensively trawled ecosystem (Thermaikos Gulf, Aegean Sea)

NASA Astrophysics Data System (ADS)

Polymenakou, Paraskevi N.; Pusceddu, Antonio; Tselepides, Anastasios; Polychronaki, Thalia; Giannakourou, Antonia; Fiordelmondo, Carla; Hatziyanni, Eleni; Danovaro, Roberto

2005-12-01

Abundance of benthic bacteria, heterotrophic nanoflagellates and ciliates, extracellular enzymatic activities, bacterial C production, C mineralisation and sediment community oxygen consumption rates were measured in the Thermaikos Gulf (Northeastern Mediterranean), before (September 2001), and during intense trawling activities (October 2001 and February 2002). The biochemical composition of sedimentary organic matter has revealed that bottom trawling had an effect on the trophic state of Thermaikos Gulf. Changes on the benthic microbial food web were also recorded, during the three sampling seasons. Even though trawling-induced sediment resuspension did not alter significantly the abundance of the microbial components, with the exception of the most impacted station, it determined changes regarding their relative importance. Thus, the ratios of bacterium to nanoflagellates and ciliate to nanoflagellates abundance increased in the trawled stations, causing a sudden increase in bacterial C production, in comparison to the non-trawled station. Four months later, the effects of trawling on the microbial food web were less evident, masked possibly by the drastic decrease in the water temperature. The results of the present work suggest that bottom trawling induces alteration of the sedimentological variables and can be considered as a factor affecting the function of the microbial food web in marine coastal ecosystems. These alterations cause faster mobilisation of organic C buried in the sediment and increase nutrient concentrations and availability in the system, thus inducing an effect that could lead to coastal eutrophication.

Elevated enzyme activities in soils under the invasive nitrogen-fixing tree Falcataria moluccana

Treesearch

Steven D. Allison; Caroline Nielsen; R. Flint Hughes

2006-01-01

Like other N-fixing invasive species in Hawaii, Falcataria moluccana dramatically alters forest structure, litterfall quality and quantity, and nutrient dynamics. We hypothesized that these biogeochemical changes would also affect the soil microbial community and the extracellular enzymes responsible for carbon and nutrient mineralization. Across...

Comparison of tillage treatments on greenhouse gas fluxes in winter wheat

USDA-ARS?s Scientific Manuscript database

Tillage is commonly used to control weeds and prepare fields for planting. Repeated tillage can result in soil drying, sudden bursts of mineralized carbon and nitrogen from soil organic matter, and alterations in soil microbial communities. The effects of tillage on winter wheat cropping systems an...

Effects of trifluralin on the soil microbial community and functional groups involved in nitrogen cycling.

PubMed

Du, Pengqiang; Wu, Xiaohu; Xu, Jun; Dong, Fengshou; Liu, Xingang; Zheng, Yongquan

2018-04-10

Large amounts of trifluralin are applied each year for weed control; however, its effects on soil microbial communities and functions are unknown. Two agricultural soils, one silty loam and one silty clay were spiked with TFL (0, 0.84, 8.4, and 84 mg kg -1 ) and studied the effects using a laboratory microcosm approach. The half-lives were 44.19-61.83 d in all cases. Bacterial abundance increased 1.12-5.56 times by TFL, but the diversity decreased. From the next-generation sequencing results, TFL altered the bacterial community structure, which initially diverged from the control community structure, then recovered, and then diverged again. Linear discriminant analysis effect size indicated that Sphingomonas and Xanthomonadaceae were the predominant species on day 7 and 15 in TFL treatments. N 2 -fixing bacteria were initially increased, then decreased, and then recovered, and it was positively correlated with NH 4 + -N content. Compared with the control, ammonia-oxidizing bacteria were decreased by 25.51-92.63%, ammonia-oxidizing archaea were decreased by 17.12-85.21% (except day 7), and the NO 3 - -N concentration was also inhibited. In contrast to bacteria, fungal abundance was inhibited without any observable effects on fungal diversity or community structure. These results suggest that TFL impacts soil bacterial community and alters functional microorganisms involved in soil N processing. Copyright © 2018 Elsevier B.V. All rights reserved.

Ocean acidification reduces induction of coral settlement by crustose coralline algae.

PubMed

Webster, Nicole S; Uthicke, Sven; Botté, Emanuelle S; Flores, Florita; Negri, Andrew P

2013-01-01

Crustose coralline algae (CCA) are a critical component of coral reefs as they accrete carbonate for reef structure and act as settlement substrata for many invertebrates including corals. CCA host a diversity of microorganisms that can also play a role in coral settlement and metamorphosis processes. Although the sensitivity of CCA to ocean acidification (OA) is well established, the response of their associated microbial communities to reduced pH and increased CO2 was previously not known. Here we investigate the sensitivity of CCA-associated microbial biofilms to OA and determine whether or not OA adversely affects the ability of CCA to induce coral larval metamorphosis. We experimentally exposed the CCA Hydrolithon onkodes to four pH/pCO2 conditions consistent with current IPCC predictions for the next few centuries (pH: 8.1, 7.9, 7.7, 7.5, pCO2 : 464, 822, 1187, 1638 μatm). Settlement and metamorphosis of coral larvae was reduced on CCA pre-exposed to pH 7.7 (pCO2  = 1187 μatm) and below over a 6-week period. Additional experiments demonstrated that low pH treatments did not directly affect the ability of larvae to settle, but instead most likely altered the biochemistry of the CCA or its microbial associates. Detailed microbial community analysis of the CCA revealed diverse bacterial assemblages that altered significantly between pH 8.1 (pCO2  = 464 μatm) and pH 7.9 (pCO2  = 822 μatm) with this trend continuing at lower pH/higher pCO2 treatments. The shift in microbial community composition primarily comprised changes in the abundance of the dominant microbes between the different pH treatments and the appearance of new (but rare) microbes at pH 7.5. Microbial shifts and the concomitant reduced ability of CCA to induce coral settlement under OA conditions projected to occur by 2100 is a significant concern for the development, maintenance and recovery of reefs globally. © 2012 Blackwell Publishing Ltd.

In situ carbon turnover dynamics and the role of soil microorganisms therein: a climate warming study in an Alpine ecosystem.

PubMed

Djukic, Ika; Zehetner, Franz; Watzinger, Andrea; Horacek, Micha; Gerzabek, Martin H

2013-01-01

Litter decomposition represents one of the largest fluxes in the global terrestrial carbon cycle. The aim of this study was to improve our understanding of the factors governing decomposition in alpine ecosystems and how their responses to changing environmental conditions change over time. Our study area stretches over an elevation gradient of 1000 m on the Hochschwab massif in the Northern Limestone Alps of Austria. We used high-to-low elevation soil translocation to simulate the combined effects of changing climatic conditions, shifting vegetation zones, and altered snow cover regimes. In original and translocated soils, we conducted in situ decomposition experiments with maize litter and studied carbon turnover dynamics as well as temporal response patterns of the pathways of carbon during microbial decomposition over a 2-year incubation period. A simulated mean annual soil warming (through down-slope translocation) of 1.5 and 2.7 °C, respectively, resulted in a significantly accelerated turnover of added maize carbon. Changes in substrate quantity and quality in the course of the decomposition appeared to have less influence on the microbial community composition and its substrate utilization than the prevailing environmental/site conditions, to which the microbial community adapted quickly upon change. In general, microbial community composition and function significantly affected substrate decomposition rates only in the later stage of decomposition when the differentiation in substrate use among the microbial groups became more evident. Our study demonstrated that rising temperatures in alpine ecosystems may accelerate decomposition of litter carbon and also lead to a rapid adaptation of the microbial communities to the new environmental conditions. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Microbial community functional structure in response to micro-aerobic conditions in sulfate-reducing sulfur-producing bioreactor.

PubMed

Yu, Hao; Chen, Chuan; Ma, Jincai; Xu, Xijun; Fan, Ronggui; Wang, Aijie

2014-05-01

Limited oxygen supply to anaerobic wastewater treatment systems had been demonstrated as an effective strategy to improve elemental sulfur (S(0)) recovery, coupling sulfate reduction and sulfide oxidation. However, little is known about the impact of dissolved oxygen (DO) on the microbial functional structures in these systems. We used a high throughput tool (GeoChip) to evaluate the microbial community structures in a biological desulfurization reactor under micro-aerobic conditions (DO: 0.02-0.33 mg/L). The results indicated that the microbial community functional compositions and structures were dramatically altered with elevated DO levels. The abundances of dsrA/B genes involved in sulfate reduction processes significantly decreased (p < 0.05, LSD test) at relatively high DO concentration (DO: 0.33 mg/L). The abundances of sox and fccA/B genes involved in sulfur/sulfide oxidation processes significantly increased (p < 0.05, LSD test) in low DO concentration conditions (DO: 0.09 mg/L) and then gradually decreased with continuously elevated DO levels. Their abundances coincided with the change of sulfate removal efficiencies and elemental sulfur (S(0)) conversion efficiencies in the bioreactor. In addition, the abundance of carbon degradation genes increased with the raising of DO levels, showing that the heterotrophic microorganisms (e.g., fermentative microorganisms) were thriving under micro-aerobic condition. This study provides new insights into the impacts of micro-aerobic conditions on the microbial functional structure of sulfate-reducing sulfur-producing bioreactors, and revealed the potential linkage between functional microbial communities and reactor performance. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Effect of high loading on substrate utilization kinetics and microbial community structure in super fast submerged membrane bioreactor.

PubMed

Sözen, S; Çokgör, E U; Başaran, S Teksoy; Aysel, M; Akarsubaşı, A; Ergal, I; Kurt, H; Pala-Ozkok, I; Orhon, D

2014-05-01

The study investigated the effect of high substrate loading on substrate utilization kinetics, and changes inflicted on the composition of the microbial community in a superfast submerged membrane bioreactor. Submerged MBR was sequentially fed with a substrate mixture and acetate; its performance was monitored at steady-state, at extremely low sludge age values of 2.0, 1.0 and 0.5d, all adjusted to a single hydraulic retention time of 8.0 h. Each MBR run was repeated when substrate feeding was increased from 200 mg COD/L to 1000 mg COD/L. Substrate utilization kinetics was altered to significantly lower levels when the MBR was adjusted to higher substrate loadings. Molecular analysis of the biomass revealed that variable process kinetics could be correlated with parallel changes in the composition of the microbial community, mainly by a replacement mechanism, where newer species, better adapted to the new growth conditions, substituted others that are washed out from the system. Copyright © 2014 Elsevier Ltd. All rights reserved.

Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease

PubMed Central

Casey, Jordan M.; Ainsworth, Tracy D.; Choat, J. Howard; Connolly, Sean R.

2014-01-01

Microbial community structure on coral reefs is strongly influenced by coral–algae interactions; however, the extent to which this influence is mediated by fishes is unknown. By excluding fleshy macroalgae, cultivating palatable filamentous algae and engaging in frequent aggression to protect resources, territorial damselfish (f. Pomacentridae), such as Stegastes, mediate macro-benthic dynamics on coral reefs and may significantly influence microbial communities. To elucidate how Stegastes apicalis and Stegastes nigricans may alter benthic microbial assemblages and coral health, we determined the benthic community composition (epilithic algal matrix and prokaryotes) and coral disease prevalence inside and outside of damselfish territories in the Great Barrier Reef, Australia. 16S rDNA sequencing revealed distinct bacterial communities associated with turf algae and a two to three times greater relative abundance of phylotypes with high sequence similarity to potential coral pathogens inside Stegastes's territories. These potentially pathogenic phylotypes (totalling 30.04% of the community) were found to have high sequence similarity to those amplified from black band disease (BBD) and disease affected corals worldwide. Disease surveys further revealed a significantly higher occurrence of BBD inside S. nigricans's territories. These findings demonstrate the first link between fish behaviour, reservoirs of potential coral disease pathogens and the prevalence of coral disease. PMID:24966320

Arbuscular mycorrhizal assemblages in native plant roots change in the presence of invasive exotic grasses

USGS Publications Warehouse

Hawkes, C.V.; Belnap, J.; D'Antonio, C.; Firestone, M.K.

2006-01-01

Plant invasions have the potential to significantly alter soil microbial communities, given their often considerable aboveground effects. We examined how plant invasions altered the arbuscular mycorrhizal fungi of native plant roots in a grassland site in California and one in Utah. In the California site, we used experimentally created plant communities composed of exotic (Avena barbata, Bromus hordeaceus) and native (Nassella pulchra, Lupinus bicolor) monocultures and mixtures. In the Utah semi-arid grassland, we took advantage of invasion by Bromus tectorum into long-term plots dominated by either of two native grasses, Hilaria jamesii or Stipa hymenoides. Arbuscular mycorrhizal fungi colonizing roots were characterized with PCR amplification of the ITS region, cloning, and sequencing. We saw a significant effect of the presence of exotic grasses on the diversity of mycorrhizal fungi colonizing native plant roots. In the three native grasses, richness of mycorrhizal fungi decreased; in the native forb at the California site, the number of fungal RFLP patterns increased in the presence of exotics. The exotic grasses also caused the composition of the mycorrhizal community in native roots to shift dramatically both in California, with turnover of Glomus spp., and Utah, with replacement of Glomus spp. by apparently non-mycorrhizal fungi. Invading plants may be able to influence the network of mycorrhizal fungi in soil that is available to natives through either earlier root activity or differential carbon provision compared to natives. Alteration of the soil microbial community by plant invasion can provide a mechanism for both successful invasion and the resulting effects of invaders on the ecosystem. ?? Springer 2006.

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, which is important in the case of the long-term use of this compound. PMID:28337188

Alternations of Structure and Functional Activity of Below Ground Microbial Communities at Elevated Atmospheric Carbon Dioxide

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

He, Zhili; Xu, Meiying; Deng, Ye

2010-05-17

The global atmospheric concentration of CO2 has increased by more than 30percent since the industrial revolution. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been well studied, its influences on belowground microbial communities are poorly understood and controversial. In this study, we showed a significant change in the structure and functional potential of soil microbial communities at eCO2 in a grassland ecosystem, the BioCON (Biodiversity, CO2 and Nitrogen) experimental site (http://www.biocon.umn.edu/) using a comprehensive functional gene array, GeoChip 3.0, which contains about 28,0000 probes and covers approximately 57,000 gene variants from 292 functionalmore » gene families involved in carbon, nitrogen, phosphorus and sulfur cycles as well as other functional processes. GeoChip data indicated that the functional structure of microbial communities was markedly different between ambient CO2 (aCO2) and eCO2 by detrended correspondence analysis (DCA) of all 5001 detected functional gene probes although no significant differences were detected in the overall microbial diversity. A further analysis of 1503 detected functional genes involved in C, N, P, and S cycles showed that a considerable portion (39percent) of them were only detected under either aCO2 (14percent) or eCO2 (25percent), indicating that the functional characteristics of the microbial community were significantly altered by eCO2. Also, for those shared genes (61percent) detected, some significantly (p<0.05) changed their abundance at eCO2. Especially, genes involved in labile C degradation, such as amyA, egl, and ara for starch, cellulose, and hemicelluloses, respectively, C fixation (e.g., rbcL, pcc/acc), N fixation (nifH), and phosphorus utilization (ppx) were significantly increased under eCO2, while those involved in decomposing recalcitrant C, such as glx, lip, and mnp for lignin degradation remained unchanged. This study provides insights into our understanding of belowground microbial communities and their feedbacks to terrestrial ecosystems at eCO2.« less

Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots

PubMed Central

Martin, Belinda C.; Gleeson, Deirdre; Statton, John; Siebers, Andre R.; Grierson, Pauline; Ryan, Megan H.; Kendrick, Gary A.

2018-01-01

Seagrass roots host a diverse microbiome that is critical for plant growth and health. Composition of microbial communities can be regulated in part by root exudates, but the specifics of these interactions in seagrass rhizospheres are still largely unknown. As light availability controls primary productivity, reduced light may impact root exudation and consequently the composition of the root microbiome. Hence, we analyzed the influence of light availability on root exudation and community structure of the root microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms for 2 weeks; control (100% surface irradiance (SI), medium (40% SI), low (20% SI) and fluctuating light (10 days 20% and 4 days 100%). 16S rDNA amplicon sequencing revealed that microbial diversity, composition and predicted function were strongly influenced by the presence of seagrass roots, such that root microbiomes were unique to each seagrass species. Reduced light availability altered seagrass root exudation, as characterized using fluorescence spectroscopy, and altered the composition of seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment – a critical, but often overlooked space. PMID:29375529

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

PubMed

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

2018-06-01

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

New insights into the effects of support matrix on the removal of organic micro-pollutants and the microbial community in constructed wetlands.

PubMed

Zhang, Liang; Lyu, Tao; Ramírez Vargas, Carlos Andrés; Arias, Carlos A; Carvalho, Pedro N; Brix, Hans

2018-09-01

Constructed wetlands (CWs) are an eco-friendly and cost-effective technology to remove organic micro-pollutants (OMPs) from wastewater. The support matrix is an important component in CWs as it has a primary role in the growth and development of plants and microbes. However, the roles of the support matrix in CWs in removing OMPs have not been systematically studied. Therefore, in this study, six common materials (sand, zeolite, blast iron slag, petcoke, polonite and crushed autoclaved aerated concrete (CAAC)) as support matrixes were firstly investigated by batch tests to explore their adsorption capacities to selected OMPs (ibuprofen, iohexol, tebuconazole and imazalil). Results showed that the adsorption capacities of the materials were low (at the level of μg/g) compared to well-known sorbents (at the level of mg/g), such as activated carbon and carbon nanotubes. Columns packed with the six materials, respectively, were then built up to study the effects of different materials on microbial community. In the medium-term study (66 days), the removal of four OMPs in all the columns increased by 2-58% from day 25 to day 66, and was mainly attributed to microbial degradation. Furthermore, Community-level physiological profiling (CLPP) analysis indicates that material presence shaped the microbial community metabolic function not only in the interstitial water but also in the biofilm. Overall, all the findings demonstrate that although the adsorption capacities of the common materials are low, they may be a driver to improve the removal of OMPs by altering microbial community function in CWs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

PubMed

Yan, Zaisheng; He, Yuhong; Cai, Haiyuan; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Krumholz, Lee R; Jiang, He-Long

2017-08-01

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

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

PubMed

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

2014-03-06

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

Biodegradation of organic matter and anodic microbial communities analysis in sediment microbial fuel cells with/without Fe(III) oxide addition.

PubMed

Xu, Xun; Zhao, Qingliang; Wu, Mingsong; Ding, Jing; Zhang, Weixian

2017-02-01

To enhance the biodegradation of organic matter in sediment microbial fuel cell (SMFC), Fe(III) oxide, as an alternative electron acceptor, was added into the sediment. Results showed that the SMFC with Fe(III) oxide addition obtained higher removal efficiencies for organics than the SMFC without Fe(III) oxide addition and open circuit bioreactor, and produced a maximum power density (P max ) of 87.85mW/m 2 with a corresponding maximum voltage (V max ) of 0.664V. The alteration of UV-254 and specific ultraviolet absorbance (SUVA) also demonstrated the organic matter in sediments can be effectively removed. High-throughput sequencing of anodic microbial communities indicated that bacteria from the genus Geobacter were predominantly detected (21.23%) in the biofilm formed on the anode of SMFCs, while Pseudomonas was the most predominant genus (18.12%) in the presence of Fe(III) oxide. Additionally, compared with the open circuit bioreactor, more electrogenic bacteria attached to the biofilm of anode in SMFCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biochar alters the resistance and resilience to drought in a tropical soil

NASA Astrophysics Data System (ADS)

Liang, Chenfei; Zhu, Xiaolin; Fu, Shenglei; Méndez, Ana; Gascó, Gabriel; Paz-Ferreiro, Jorge

2014-05-01

Soil microbes play a key role in nutrient cycling and carbon sequestration. Global change can alter soil microbial population composition and behavior. Biochar addition has been explored in the last years as a way to mitigate global warming. However, responses of microbial communities to biochar addition in particular in relation to abiotic disturbances are seldom documented. An example of these disturbances, which is predicted to be exacerbated with global warming, is regional drought. It has been known that fungal-based food webs are more resistant to drought than their bacterial counterparts. Our study found that biochar addition can increase the resistance of both the bacterial and fungal networks to drought. Contrary to expected, this result was not related to a change in the dominance of fungal or bacteria. In general, soil amended with biochar was characterized by a faster recovery of soil microbial properties to its basal values. Biochar addition to the soil also suppressed the Birch effect, a result that has not been previously reported.

Diet rapidly and reproducibly alters the human gut microbiome

PubMed Central

David, Lawrence A.; Maurice, Corinne F.; Carmody, Rachel N.; Gootenberg, David B.; Button, Julie E.; Wolfe, Benjamin E.; Ling, Alisha V.; Devlin, A. Sloan; Varma, Yug; Fischbach, Michael A.; Biddinger, Sudha B.; Dutton, Rachel J.; Turnbaugh, Peter J.

2013-01-01

Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut1–5, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. PMID:24336217

Assessing the potential for rhizoremediation of PCB contaminated soils in northern regions using native species

PubMed Central

Slater, Heather; Gouin, Todd; Leigh, Mary Beth

2011-01-01

Rhizosphere bioremediation of polychlorinated biphenyls (PCBs) offers a potentially inexpensive approach to remediating contaminated soils that is particularly attractive in remote regions including the Arctic. We assessed the abilities of two tree species native to Alaska, Salix alaxensis (felt-leaf willow) and Picea glauca (white spruce), to promote microbial biodegradation of PCBs via the release of phytochemicals upon fine root death. Crushed fine roots, biphenyl (PCB analogue) or salicylate (willow secondary compound) were added to microcosms containing soil spiked with PCBs and resultant PCB disappearance, soil toxicity and microbial community changes were examined. After 180 d, soil treated with willow root crushates showed a significantly greater PCB loss than untreated soils for some PCB congeners, including the toxic congeners, PCB 77, 105 and 169, and showed a similar PCB loss pattern (in both extent of degradation and congeners degraded) to biphenyl-treated microcosms. Neither P. glauca (white spruce) roots nor salicylate enhanced PCB loss, indicating that biostimulation is plant species specific and was not mediated by salicylate. Soil toxicity assessed using the Microtox bioassay indicated that the willow treatment resulted in a less toxic soil environment. Molecular microbial community analyses indicated that biphenyl and salicylate promoted shifts in microbial community structure and composition that differed distinctly from each other and from the crushed root treatments. The biphenyl utilizing bacterium, Cupriavidus spp. was isolated from the soil. The findings suggest that S. alaxensis may be an effective plant for rhizoremediation by altering microbial community structure, enhancing the loss of some PCB congeners and reducing the toxicity of the soil environment. PMID:21596420

The use of high throughput DNA sequence analysis to assess the endophytic microbiome of date palm roots grown under different levels of salt stress.

PubMed

Yaish, Mahmoud W; Al-Harrasi, Ibtisam; Alansari, Aliya S; Al-Yahyai, Rashid; Glick, Bernard R

2016-09-01

Date palms are able to grow under diverse abiotic stress conditions including in saline soils, where microbial communities may be help in the plant's salinity tolerance. These communities able to produce specific growth promoting substances can enhance date palm growth in a saline environment. However, these communities are poorly defined. In the work reported here, the date palm endophytic bacterial and fungal communities were identified using the pyrosequencing method, and the microbial differential abundance in the root upon exposure to salinity stress was estimated. Approximately 150,061 reads were produced from the analysis of six ribosomal DNA libraries, which were prepared from endophytic microorganisms colonizing date palm root tissues. DNA sequence analysis of these libraries predicted the presence of a variety of bacterial and fungal endophytic species, some known and others unknown. The microbial community compositions of 30% and 8% of the bacterial and fungal species, respectively, were significantly (p ≤ 0.05) altered in response to salinity stress. Differential enrichment analysis showed that microbe diversity indicated by the Chao, Shannon and Simpson indices were slightly reduced, however, the overall microbial community structures were not significantly affected as a consequence of salinity. This may reflect a buffering effect by the host plant on the internal environments that these communities are colonizing. Some of the endophytes identified in this study were strains that were previously isolated from saline and marine environments. This suggests possible interactions with the plant that are favorable to salinity tolerance in date palm. [Int Microbiol 19(3):143-155 (2016)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

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

PubMed

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

2006-12-01

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

Interaction of Gut Microbiota with Bile Acid Metabolism and its Influence on Disease States

PubMed Central

Staley, Christopher; Weingarden, Alexa R.

2016-01-01

Primary bile acids serve important roles in cholesterol metabolism, lipid digestion, host-microbe interactions, and regulatory pathways in the human host. While most bile acids are reabsorbed and recycled via enterohepatic cycling, ~5% serve as substrates for bacterial biotransformation in the colon. Enzymes involved in various transformations have been characterized from cultured gut bacteria and reveal taxa-specific distribution. More recently, bioinformatic approaches have revealed greater diversity in isoforms of these enzymes, and the microbial species in which they are found. Thus, the functional roles played by the bile acid-transforming gut microbiota and the distribution of resulting secondary bile acids, in the bile acid pool, may be profoundly affected by microbial community structure and function. Bile acids and the composition of the bile acid pool have historically been hypothesized to be associated with several disease states, including recurrent Clostridium difficile infection, inflammatory bowel diseases, metabolic syndrome, and several cancers. Recently, however, emphasis has been placed on how microbial communities in the dysbiotic gut may alter the bile acid pool to potentially cause or mitigate disease onset. This review highlights the current understanding of the interactions between the gut microbial community, bile acid biotransformation, and disease states, and addresses future directions to better understand these complex associations. PMID:27888332

Phage or foe: an insight into the impact of viral predation on microbial communities.

PubMed

Fernández, Lucía; Rodríguez, Ana; García, Pilar

2018-05-01

Since their discovery, bacteriophages have been traditionally regarded as the natural enemies of bacteria. However, recent advances in molecular biology techniques, especially data from "omics" analyses, have revealed that the interplay between bacterial viruses and their hosts is far more intricate than initially thought. On the one hand, we have become more aware of the impact of viral predation on the composition and genetic makeup of microbial communities thanks to genomic and metagenomic approaches. Moreover, data obtained from transcriptomic, proteomic, and metabolomic studies have shown that responses to phage predation are complex and diverse, varying greatly depending on the bacterial host, phage, and multiplicity of infection. Interestingly, phage exposure may alter different phenotypes, including virulence and biofilm formation. The complexity of the interactions between microbes and their viral predators is also evidenced by the link between quorum-sensing signaling pathways and bacteriophage resistance. Overall, new data increasingly suggests that both temperate and virulent phages have a positive effect on the evolution and adaptation of microbial populations. From this perspective, further research is still necessary to fully understand the interactions between phage and host under conditions that allow co-existence of both populations, reflecting more accurately the dynamics in natural microbial communities.

Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments

PubMed Central

2016-01-01

Sediments within the Okinawa back-arc basin overlay a subsurface hydrothermal network, creating intense temperature gradients with sediment depth and potential limits for microbial diversity. We investigated taxonomic changes across 45 m of recovered core with a temperature gradient of 3°C/m from the dynamic Iheya North Hydrothermal System. The interval transitions sharply from low-temperature marine mud to hydrothermally altered clay at 10 meters below seafloor (mbsf). Here, we present taxonomic results from an analysis of the 16S rRNA gene that support a conceptual model in which common marine subsurface taxa persist into the subsurface, while high temperature adapted archaeal taxa show localized peaks in abundances in the hydrothermal clay horizons. Specifically, the bacterial phylum Chloroflexi accounts for a major proportion of the total microbial community within the upper 10 mbsf, whereas high temperature archaea (Terrestrial Hot Spring Crenarchaeotic Group and methanotrophic archaea) appear in varying local abundances in deeper, hydrothermal clay horizons with higher in situ temperatures (up to 55°C, 15 mbsf). In addition, geochemical evidence suggests that methanotrophy may be occurring in various horizons. There is also relict DNA (i.e., DNA preserved after cell death) that persists in horizons where the conditions suitable for microbial communities have ceased. PMID:28096736

Fungal and bacterial community succession differs for three wood types during decay in a forest soil.

PubMed

Prewitt, Lynn; Kang, Youngmin; Kakumanu, Madhavi L; Williams, Mark

2014-08-01

Wood decomposition by soil microorganisms is vital to carbon and nutrient cycles of forested ecosystems. Different wood types decompose at different rates; however, it is not known if there are differences in microbial community succession associated with the decay of different wood types. In this study, the microbial community associated with the decay of pine (decay-susceptible wood), western red cedar (decay resistant) and ACQ-treated pine (Ammoniacal Copper Quaternary, preservative-treated pine for decay resistance) in forest soil was characterized using DNA sequencing, phospholipid fatty acid (PLFA) analysis, and microbial activity over a 26-month period. Bray-Curtis ordination using an internal transcribed spacer (ITS) sequence and PLFA data indicated that fungal communities changed during succession and that wood type altered the pattern of succession. Nondecay fungi decreased over the 26 months of succession; however, by 18 months of decay, there was a major shift in the fungal communities. By this time, Trametes elegans dominated cedar and Phlebia radiata dominated pine and ACQ-treated pine. The description of PLFA associated with ACQ-treated pine resembled cedar more than pine; however, both PLFA and ITS descriptions indicated that fungal communities associated with ACQ-treated pine were less dynamic, perhaps a result of the inhibition by the ACQ preservative, compared with pine and cedar. Overall, fungal community composition and succession were associated with wood type. Further research into the differences in community composition will help to discern their functional importance to wood decay.

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.

PubMed

Zhang, Zhimin; Li, Dapeng

2018-05-31

Adoption of thermal processing of the diet drives human evolution and gut microbiota diversity changes in a dietary habit-dependent manner. However, whether thermal processing of food triggers gut microbial variation remains unknown. Herein, we compared the microbiota of non-thermally processed and thermally processed food (NF and TF) and investigated gut microbiota associated with NF and TF in catfish Silurus meridionalis and C57BL/6 mice to assess effects of thermal processing of food on gut microbiota and to further identify the differences in host responses. We found no differences in overall microbial composition and structure in the pairwise NF and TF, but identified differential microbial communities between food and gut. Both fish and mice fed TF had significantly lower gut microbial diversity than those fed NF. Moreover, thermal processing of food triggered the changes in their microbial communities. Comparative host studies further indicated host species determined gut microbial assemblies, even if fed with the same food. Fusobacteria was the most abundant phylum in the fish, and Bacteroidetes and Firmicutes dominated in the mice. Besides the consistent reduction of Bacteroidetes and the balanced Protebacteria, the response of other dominated gut microbiota in the fish and mice to TF was taxonomically opposite at the phylum level, and those further found at the genus level. Our results reveal that thermal processing of food strongly contributes to the reduction of gut microbial diversity and differentially drives microbial alterations in a host-dependent manner, suggesting specific adaptations of host-gut microbiota in vertebrates responding to thermal processing of food. These findings open a window of opportunity to understand the decline in gut microbial diversity and the community variation in human evolution and provide new insights into the host-specific microbial assemblages associated with the use of processing techniques in food preparation in humans and domesticated animals.

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

O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less

An integrative view of microbiome-host interactions in inflammatory bowel diseases

PubMed Central

Wlodarska, Marta; Kostic, Aleksandar D.; Xavier, Ramnik J.

2015-01-01

Summary The intestinal microbiota, which is composed of bacteria, viruses, and micro-eukaryotes, acts as an accessory organ system with distinct functions along the intestinal tract that are critical for health. This review focuses on how the microbiota drives intestinal disease through alterations in microbial community architecture, disruption of the mucosal barrier, modulation of innate and adaptive immunity, and dysfunction of the enteric nervous system. Inflammatory bowel disease is used as a model system to understand these microbial-driven pathologies, but the knowledge gained in this space is extended to less well studied intestinal diseases that may also have an important microbial component, including environmental enteropathy and chronic colitis-associated colorectal cancer. PMID:25974300

PAH effects on meio- and microbial benthic communities strongly depend on bioavailability.

PubMed

Lindgren, J Fredrik; Hassellöv, Ida-Maja; Dahllöf, Ingela

2014-01-01

The effects of anthropogenic pollutants in dissimilar habitats can vary depending on differences in bioavailability. The factors determining bioavailability are not yet fully understood. This study was performed to evaluate whether analysis of total PAH concentrations in sediments is a satisfactory measurement to indicate environmental effects or if bioavailability is needed to be taken into account. We have here performed a 60-day experiment, where nominal PAH concentrations of 1,300 μg/kg sediment were added to three different marine sediments. Meiofaunal and microbial communities were analyzed for alterations in community response at 30 and 60 days. Results showed that bioavailability of PAHs varied between the three different sediments. Nonetheless, the petroleum addition gave rise to significant negative effects on all three sediments at both time points. The two direct measurements of toxicity on the microbial community, potential nitrification and denitrification, displayed a lower effect of the PAH addition in the muddy sediment at both time points, compared to the other two sediment types. No effects were seen in the analysis of meiofaunal community structure. Measurements of PAH bioavailability in the three sediment types concurred with the results from the microbial community, revealing a lower bioavailability in the muddy sediment compared to the other two sediment types, 34% compared to sandy and 18% compared to organic at day 0. At day 60 it was 61% lower compared to sandy and 20% lower compared to organic. The negative effects of the PAH addition on the microbial nitrogen cycle were in six out of eight cases best correlated to the amount of alkylated bioavailable PAH in the sediments, and thus microbial nitrogen cycle is a possible good indicator for assessing PAH-induced stress. The results presented here have implications for risk analysis studies of petroleum-contaminated marine sediments; consequently, sediment characteristics and its effects on bioavailability are important to include. In addition, these results add to the understanding that bioavailability measurements of PAHs are a more correct assessment compared to measurements of total PAH concentrations, and need to be included when estimating effects of PAHs in marine benthic communities. Copyright © 2013 Elsevier B.V. All rights reserved.

The mycobiome of the human urinary tract: potential roles for fungi in urology

PubMed Central

Underhill, David M.

2017-01-01

The mycobiome, defined as the fungal microbiota within a host environment, is an important but understudied component of the human microbial ecosystem. New culture-independent approaches to determine microbial diversity, such as next-generation sequencing methods, have discovered specific, characteristic, commensal fungal populations present in different body sites. These studies have also identified diverse patterns in fungal communities associated with various diseases. While alterations in urinary bacterial communities have been noted in disease states, a comprehensive description of the urinary mycobiome has been lacking. Early evidence suggests the urinary mycobiome is a diverse community with high intraindividual variability. In other disease systems, the mycobiome is thought to interact with other biomes and the host to play a role in organ homeostasis and pathology; further study will be needed to elucidate the role fungi play in bladder health and disease. PMID:28217696

Temporal Stability of the Human Skin Microbiome.

PubMed

Oh, Julia; Byrd, Allyson L; Park, Morgan; Kong, Heidi H; Segre, Julia A

2016-05-05

Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states. Copyright © 2016 Elsevier Inc. All rights reserved.

Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes.

PubMed

Semenkovich, Nicholas P; Planer, Joseph D; Ahern, Philip P; Griffin, Nicholas W; Lin, Charles Y; Gordon, Jeffrey I

2016-12-20

The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to define chromatin accessibility in predicted enhancer regions of intestinal αβ + and γδ + intraepithelial lymphocytes purified from germ-free mice, their conventionally raised (CONV-R) counterparts, and mice reared germ free and then colonized with CONV-R gut microbiota at the end of the suckling-weaning transition. Characterizing genes adjacent to traditional enhancers and super-enhancers revealed signaling networks, metabolic pathways, and enhancer-associated transcription factors affected by the microbiota. Our results support the notion that epigenetic modifications help define microbial community-affiliated functional features of host immune cell lineages.

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

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

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

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 burnedmore » 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.« less

Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives

PubMed Central

Yamaguchi, Nobuyasu; Roberts, Michael; Castro, Sarah; Oubre, Cherie; Makimura, Koichi; Leys, Natalie; Grohmann, Elisabeth; Sugita, Takashi; Ichijo, Tomoaki; Nasu, Masao

2014-01-01

Previous space research conducted during short-term flight experiments and long-term environmental monitoring on board orbiting space stations suggests that the relationship between humans and microbes is altered in the crewed habitat in space. Both human physiology and microbial communities adapt to spaceflight. Microbial monitoring is critical to crew safety in long-duration space habitation and the sustained operation of life support systems on space transit vehicles, space stations, and surface habitats. To address this critical need, space agencies including NASA (National Aeronautics and Space Administration), ESA (European Space Agency), and JAXA (Japan Aerospace Exploration Agency) are working together to develop and implement specific measures to monitor, control, and counteract biological contamination in closed-environment systems. In this review, the current status of microbial monitoring conducted in the International Space Station (ISS) as well as the results of recent microbial spaceflight experiments have been summarized and future perspectives are discussed. PMID:25130885

The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly

PubMed Central

Pepe-Ranney, Charles; Hall, Edward K.

2015-01-01

The influence of resource availability on planktonic and biofilm microbial community membership is poorly understood. Heterotrophic bacteria derive some to all of their organic carbon (C) from photoautotrophs while simultaneously competing with photoautotrophs for inorganic nutrients such as phosphorus (P) or nitrogen (N). Therefore, C inputs have the potential to shift the competitive balance of aquatic microbial communities by increasing the resource space available to heterotrophs (more C) while decreasing the resource space available to photoautotrophs (less mineral nutrients due to increased competition from heterotrophs). To test how resource dynamics affect membership of planktonic communities and assembly of biofilm communities we amended a series of flow-through mesocosms with C to alter the availability of C among treatments. Each mesocosm was fed with unfiltered seawater and incubated with sterilized microscope slides as surfaces for biofilm formation. The highest C treatment had the highest planktonic heterotroph abundance, lowest planktonic photoautotroph abundance, and highest biofilm biomass. We surveyed bacterial 16S rRNA genes and plastid 23S rRNA genes to characterize biofilm and planktonic community membership and structure. Regardless of resource additions, biofilm communities had higher alpha diversity than planktonic communities in all mesocosms. Heterotrophic plankton communities were distinct from heterotrophic biofilm communities in all but the highest C treatment where heterotrophic plankton and biofilm communities resembled each other after 17 days. Unlike the heterotrophs, photoautotrophic plankton communities were different than photoautotrophic biofilm communities in composition in all treatments including the highest C treatment. Our results suggest that although resource amendments affect community membership and structure, microbial lifestyle (biofilm vs. planktonic) has a stronger influence on community composition. PMID:26236289

Enhancement of maize growth and alteration of the rhizosphere microbial community by phosphate-solubilizing fungus Aspergillus aculeatus P93

USDA-ARS?s Scientific Manuscript database

Over-application of phosphatic fertilizers has adversely impacted agricultural sustainability and the environment in China and other regions of the world resulting in the need for alternative strategies, such as the use of phosphate-solubilizing microbes. Aspergillus aculeatus P93, isolated from th...

Herbivore species identity and composition affect soil enzymatic activity through altered plant composition in a coastal tallgrass prairie

USDA-ARS?s Scientific Manuscript database

Although single species of herbivores are known to affect soil microbial communities, the effects of herbivore species identity and functional composition on soil microbes is unknown. We tested the effects of single species of orthopterans and multiple species combinations on soil enzymatic activity...

Microbial decomposition is highly sensitive to leaf litter emersion in a permanent temperate stream.

PubMed

Mora-Gómez, Juanita; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Romaní, Anna M

2018-04-15

Drought frequency and intensity in some temperate regions are forecasted to increase under the ongoing global change, which might expose permanent streams to intermittence and have severe repercussions on stream communities and ecosystem processes. In this study, we investigated the effect of drought duration on microbial decomposition of Populus nigra leaf litter in a temperate permanent stream (Oliveira, NW Portugal). Specifically, we measured the response of the structural (assemblage composition, bacterial and fungal biomass) and functional (leaf litter decomposition, extracellular enzyme activities (EEA), and fungal sporulation) parameters of fungal and bacterial communities on leaf litter exposed to emersion during different time periods (7, 14 and 21d). Emersion time affected microbial assemblages and litter decomposition, but the response differed among variables. Leaf decomposition rates and the activity of β-glucosidase, cellobiohydrolase and phosphatase were gradually reduced with increasing emersion time, while β-xylosidase reduction was similar when emersion last for 7 or more days, and the phenol oxidase reduction was similar at 14 and 21days of leaf emersion. Microbial biomass and fungal sporulation were reduced after 21days of emersion. The structure of microbial assemblages was affected by the duration of the emersion period. The shifts in fungal assemblages were correlated with a decreased microbial capacity to degrade lignin and hemicellulose in leaf litter exposed to emersion. Additionally, some resilience was observed in leaf litter mass loss, bacterial biomass, some enzyme activities and structure of fungal assemblages. Our study shows that drought can strongly alter structural and functional aspects of microbial decomposers. Therefore, the exposure of leaf litter to increasing emersion periods in temperate streams is expected to affect decomposer communities and overall decomposition of plant material by decelerating carbon cycling in streams. Copyright © 2017 Elsevier B.V. All rights reserved.

Shifts in the Physiology and Stoichiometric Needs of Soil Microbial Communities from Subarctic Soils in Response to Warming: Icelandic Geothermal Gradients as a Model.

NASA Astrophysics Data System (ADS)

Marañón-Jiménez, S.; Soong, J.; Leblans, N. I. W.; Sigurdsson, B. D.; Peñuelas, J.; Richter, A.; Asensio, D.; Fransen, E.; Janssens, I. A.

2017-12-01

Large amounts of CO2 can be released to the atmosphere from a faster mineralization of soil organic matter at warmer temperatures, thus inducing climate change feedbacks. Specifically, soils at high northern latitudes store more than half of the global surface soil carbon and are particularly vulnerable to temperature-driven C losses, since they warm more rapidly. Alterations to the temperature sensitivity, physiological functioning and stoichiometric constrains of soil microorganisms in response to rising temperatures can play a key role in these soil carbon (C) losses. We present results of several incubation experiments using soils from geothermal soil temperature gradients in Iceland that have undergone a range of warming intensities for seven years, encompassing the full range of IPCC warming scenarios for the northern region. Soil microbes from warmed soils did not show changes in their temperature sensitivity at the physiological level. On the contrary, seven years of chronic soil warming provoked a permanent increase of microbial metabolic quotients (i.e., respiration per unit of biomass), and a subsequent reduction in the C retained in biomass as substrate became limiting. After the initial depletion of labile soil C, increasing energy demands for metabolic maintenance and resource acquisition at higher temperatures may have triggered permanent functional changes or community shifts towards increasing respiratory costs of soil decomposers. Pointing to this, microbial communities showed a strong C limitation even at ambient soil temperatures, obscuring any metabolic response to nitrogen and phosphorous additions. The tight C:N stoichiometric constrains of soil microbial communities and the strong C limitation for microbial biomass may lead to a reduced capacity of microbial N retention, explaining the equivalent soil C and N losses found in response to soil warming. These results highlight the need to incorporate potential changes in microbial physiological functioning and stoichiometric needs into models, in order to accurately predict future changes in soil C stocks in response to global warming.

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

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

PubMed

Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue

2018-02-01

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

Cognitive Impairment by Antibiotic-Induced Gut Dysbiosis: Analysis of Gut Microbiota-Brain Communication

PubMed Central

Fröhlich, Esther E.; Farzi, Aitak; Mayerhofer, Raphaela; Reichmann, Florian; Jačan, Angela; Wagner, Bernhard; Zinser, Erwin; Bordag, Natalie; Magnes, Christoph; Fröhlich, Eleonore; Kashofer, Karl; Gorkiewicz, Gregor; Holzer, Peter

2016-01-01

Emerging evidence indicates that disruption of the gut microbial community (dysbiosis) impairs mental health. Germ-free mice and antibiotic-induced gut dysbiosis are two approaches to establish causality in gut microbiota-brain relationships. However, both models have limitations, as germ-free mice display alterations in blood-brain barrier and brain ultrastructure and antibiotics may act directly on the brain. We hypothesized that the concerns related to antibiotic-induced gut dysbiosis can only adequately be addressed if the effect of intragastric treatment of adult mice with multiple antibiotics on (i) gut microbial community, (ii) metabolite profile in the colon, (iii) circulating metabolites, (iv) expression of neuronal signaling molecules in distinct brain areas and (v) cognitive behavior is systematically investigated. Of the antibiotics used (ampicillin, bacitracin, meropenem, neomycin, vancomycin), ampicillin had some oral bioavailability but did not enter the brain. 16S rDNA sequencing confirmed antibiotic-induced microbial community disruption, and metabolomics revealed that gut dysbiosis was associated with depletion of bacteria-derived metabolites in the colon and alterations of lipid species and converted microbe-derived molecules in the plasma. Importantly, novel object recognition, but not spatial, memory was impaired in antibiotic-treated mice. This cognitive deficit was associated with brain region-specific changes in the expression of cognition-relevant signaling molecules, notably brain-derived neurotrophic factor, N-methyl-D-aspartate receptor subunit 2B, serotonin transporter and neuropeptide Y system. We conclude that circulating metabolites and the cerebral neuropeptide Y system play an important role in the cognitive impairment and dysregulation of cerebral signaling molecules due to antibiotic-induced gut dysbiosis. PMID:26923630

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

PubMed Central

Rasche, Frank; Knapp, Daniela; Kaiser, Christina; Koranda, Marianne; Kitzler, Barbara; Zechmeister-Boltenstern, Sophie; Richter, Andreas; Sessitsch, Angela

2011-01-01

It was hypothesized that seasonality and resource availability altered through tree girdling were major determinants of the phylogenetic composition of the archaeal and bacterial community in a temperate beech forest soil. During a 2-year field experiment, involving girdling of beech trees to intercept the transfer of easily available carbon (C) from the canopy to roots, members of the dominant phylogenetic microbial phyla residing in top soils under girdled versus untreated control trees were monitored at bimonthly intervals through 16S rRNA gene-based terminal restriction fragment length polymorphism profiling and quantitative PCR analysis. Effects on nitrifying and denitrifying groups were assessed by measuring the abundances of nirS and nosZ genes as well as bacterial and archaeal amoA genes. Seasonal dynamics displayed by key phylogenetic and nitrogen (N) cycling functional groups were found to be tightly coupled with seasonal alterations in labile C and N pools as well as with variation in soil temperature and soil moisture. In particular, archaea and acidobacteria were highly responsive to soil nutritional and soil climatic changes associated with seasonality, indicating their high metabolic versatility and capability to adapt to environmental changes. For these phyla, significant interrelations with soil chemical and microbial process data were found suggesting their potential, but poorly described contribution to nitrification or denitrification in temperate forest soils. In conclusion, our extensive approach allowed us to get novel insights into effects of seasonality and resource availability on the microbial community, in particular on hitherto poorly studied bacterial phyla and functional groups. PMID:20882059

Dynamics of Cathode-Associated Microbial Communities and Metabolite Profiles in a Glycerol-Fed Bioelectrochemical System

PubMed Central

Dennis, Paul G.; Harnisch, Falk; Yeoh, Yun Kit; Tyson, Gene W.

2013-01-01

Electrical current can be used to supply reducing power to microbial metabolism. This phenomenon is typically studied in pure cultures with added redox mediators to transfer charge. Here, we investigate the development of a current-fed mixed microbial community fermenting glycerol at the cathode of a bioelectrochemical system in the absence of added mediators and identify correlations between microbial diversity and the respective product outcomes. Within 1 week of inoculation, a Citrobacter population represented 95 to 99% of the community and the metabolite profiles were dominated by 1,3-propanediol and ethanol. Over time, the Citrobacter population decreased in abundance while that of a Pectinatus population and the formation of propionate increased. After 6 weeks, several Clostridium populations and the production of valerate increased, which suggests that chain elongation was being performed. Current supply was stopped after 9 weeks and was associated with a decrease in glycerol degradation and alcohol formation. This decrease was reversed by resuming current supply; however, when hydrogen gas was bubbled through the reactor during open-circuit operation (open-circuit potential) as an alternative source of reducing power, glycerol degradation and metabolite production were unaffected. Cyclic voltammetry revealed that the community appeared to catalyze the hydrogen evolution reaction, leading to a +400-mV shift in its onset potential. Our results clearly demonstrate that current supply can alter fermentation profiles; however, further work is needed to determine the mechanisms behind this effect. In addition, operational conditions must be refined to gain greater control over community composition and metabolic outcomes. PMID:23603684

Phylogenetic and Metagenomic Analyses of Substrate-Dependent Bacterial Temporal Dynamics in Microbial Fuel Cells

PubMed Central

Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

2014-01-01

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate. PMID:25202990

Phylogenetic and metagenomic analyses of substrate-dependent bacterial temporal dynamics in microbial fuel cells.

PubMed

Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

2014-01-01

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate.

Extracellular Enzyme Activity Profile in a Chemically Enhanced Water Accommodated Fraction of Surrogate Oil: Toward Understanding Microbial Activities After the Deepwater Horizon Oil Spill

PubMed Central

Kamalanathan, Manoj; Xu, Chen; Schwehr, Kathy; Bretherton, Laura; Beaver, Morgan; Doyle, Shawn M.; Genzer, Jennifer; Hillhouse, Jessica; Sylvan, Jason B.; Santschi, Peter; Quigg, Antonietta

2018-01-01

Extracellular enzymes and extracellular polymeric substances (EPS) play a key role in overall microbial activity, growth and survival in the ocean. EPS, being amphiphilic in nature, can act as biological surfactant in an oil spill situation. Extracellular enzymes help microbes to digest and utilize fractions of organic matter, including EPS, which can stimulate growth and enhance microbial activity. These natural processes might have been altered during the 2010 Deepwater Horizon oil spill due to the presence of hydrocarbon and dispersant. This study aims to investigate the role of bacterial extracellular enzymes during exposure to hydrocarbons and dispersant. Mesocosm studies were conducted using a water accommodated fraction of oil mixed with the chemical dispersant, Corexit (CEWAF) in seawater collected from two different locations in the Gulf of Mexico and corresponding controls (no additions). Activities of five extracellular enzymes typically found in the EPS secreted by the microbial community – α- and β-glucosidase, lipase, alkaline phosphatase, leucine amino-peptidase – were measured using fluorogenic substrates in three different layers of the mesocosm tanks (surface, water column and bottom). Enhanced EPS production and extracellular enzyme activities were observed in the CEWAF treatment compared to the Control. Higher bacterial and micro-aggregate counts were also observed in the CEWAF treatment compared to Controls. Bacterial genera in the order Alteromonadaceae were the most abundant bacterial 16S rRNA amplicons recovered. Genomes of Alteromonadaceae commonly have alkaline phosphatase and leucine aminopeptidase, therefore they may contribute significantly to the measured enzyme activities. Only Alteromonadaceae and Pseudomonadaceae among bacteria detected here have higher percentage of genes for lipase. Piscirickettsiaceae was abundant; genomes from this order commonly have genes for leucine aminopeptidase. Overall, this study provides insights into the alteration to the microbial processes such as EPS and extracellular enzyme production, and to the microbial community, when exposed to the mixture of oil and dispersant. PMID:29740422

Effect of oxygen minimum zone formation on communities of marine protists

PubMed Central

Orsi, William; Song, Young C; Hallam, Steven; Edgcomb, Virginia

2012-01-01

Changes in ocean temperature and circulation patterns compounded by human activities are leading to oxygen minimum zone (OMZ) expansion with concomitant alteration in nutrient and climate active trace gas cycling. Here, we report the response of microbial eukaryote populations to seasonal changes in water column oxygen-deficiency using Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island British Columbia, as a model ecosystem. We combine small subunit ribosomal RNA gene sequencing approaches with multivariate statistical methods to reveal shifts in operational taxonomic units during successive stages of seasonal stratification and renewal. A meta-analysis is used to identify common and unique patterns of community composition between Saanich Inlet and the anoxic/sulfidic Cariaco Basin (Venezuela) and Framvaren Fjord (Norway) to show shared and unique responses of microbial eukaryotes to oxygen and sulfide in these three environments. Our analyses also reveal temporal fluctuations in rare populations of microbial eukaryotes, particularly anaerobic ciliates, that may be of significant importance to the biogeochemical cycling of methane in OMZs. PMID:22402396

Pyrogenic Carbon as a Nonlinear Driver in the Carbon and Nitrogen Cycles

NASA Astrophysics Data System (ADS)

Masiello, C. A.; Silberg, J. J.; Cheng, H. Y.; Gao, X.; Del Valle, I.

2016-12-01

Our first conceptual models of pyrogenic carbon's effects on the carbon cycle treated this material as a form of organic matter whose environmental residence time was long enough to render it inert, and PyC was modeled as an unreactive mass that moved through C cycle reservoirs essentially unmodified. This concept saw modifications with the recognition that some fractions of PyC were labile. For example, the reactive sugars and lignin monomers cleaved off the lignocellulose matrix by heating have lifetimes on the order of hours to weeks. However, the now-common multiple component model of PyC does not satisfactorily explain many nonlinearities that have been observed when it is added to soils. These nonlinearities include the positive and negative "priming" effects sometimes triggered, where the presence of PyC in some matrices can trigger shifts in the overall microbial community metabolism, as well as alteration of microbial community structure, shifts in the behavior of belowground and aboveground plant parasites, and shifted rates of greenhouse gas emissions that are not well-correlated to shifts in soil hydrologic processes. To understand the effects of PyC on the global C and N cycles, we will need a better understanding of the mechanisms behind PyC-driven C and N cycle nonlinearities. This talk will examine potential mechanisms driving the nonlinearities observed in soil systems following the introduction of PyC. Potential mechanisms discussed will include PyC effects on soil microbial communication and PyC effects on microbial electron transfer. Cell-cell communication through the secretion and detection of small molecules is used by soil microbes to manage many biogeochemically relevant processes including production of biofilms, production of extracellular enzymes, and management of methanogenesis and denitrification. PyC disrupts microbial cell-cell communication differentially, altering some species' ability to communicate more than others. Electron transfer between microbes is a central part of many environmental syntrophies, including those responsible for methanogenesis, and has been shown to be altered by the presence of PyC. Both these processes may underlie observed ecosystem-scale shifts following PyC amendment to soils.

Structure of a microbial community in soil after prolonged addition of low levels of simulated acid rain

PubMed

Pennanen; Fritze; Vanhala; Kiikkila; Neuvonen; Baath

1998-06-01

Humus samples were collected 12 growing seasons after the start of a simulated acid rain experiment situated in the subarctic environment. The acid rain was simulated with H2SO4, a combination of H2SO4 and HNO3, and HNO3 at two levels of moderate acidic loads close to the natural anthropogenic pollution levels of southern Scandinavia. The higher levels of acid applications resulted in acidification, as defined by humus chemistry. The concentrations of base cations decreased, while the concentrations of exchangeable H+, Al, and Fe increased. Humus pH decreased from 3.83 to 3.65. Basal respiration decreased with decreasing humus pH, and total microbial biomass, measured by substrate-induced respiration and total amount of phospholipid fatty acids (PLFA), decreased slightly. An altered PLFA pattern indicated a change in the microbial community structure at the higher levels of acid applications. In general, branched fatty acids, typical of gram-positive bacteria, increased in the acid plots. PLFA analysis performed on the bacterial community growing on agar plates also showed that the relative amount of PLFA specific for gram-positive bacteria increased due to the acidification. The changed bacterial community was adapted to the more acidic environment in the acid-treated plots, even though bacterial growth rates, estimated by thymidine and leucine incorporation, decreased with pH. Fungal activity (measured as acetate incorporation into ergosterol) was not affected. This result indicates that bacteria were more affected than fungi by the acidification. The capacity of the bacterial community to utilize 95 different carbon sources was variable and only showed weak correlations to pH. Differences in the toxicities of H2SO4 and HNO3 for the microbial community were not found.

Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition

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

Luo, Wensui; Zhou, Jizhong; Wu, Weimin

2007-01-01

A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 mM or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonatemore » (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and geoundwater geochemistry alter microbial communities responsible for U(VI) reduction.« less

CO2 leakage alters biogeochemical and ecological functions of submarine sands

PubMed Central

Molari, Massimiliano; Guilini, Katja; Lott, Christian; Weber, Miriam; de Beer, Dirk; Meyer, Stefanie; Ramette, Alban; Wegener, Gunter; Wenzhöfer, Frank; Martin, Daniel; Cibic, Tamara; De Vittor, Cinzia; Vanreusel, Ann; Boetius, Antje

2018-01-01

Subseabed CO2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO2 impact studies. For this, we compared ecological functions of naturally CO2-vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO2 fluxes (up to 4 to 7 mol CO2 m−2 hour−1) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (−80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (−90%). The observed ecological effects of CO2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO2. PMID:29441359

CO2 leakage alters biogeochemical and ecological functions of submarine sands.

PubMed

Molari, Massimiliano; Guilini, Katja; Lott, Christian; Weber, Miriam; de Beer, Dirk; Meyer, Stefanie; Ramette, Alban; Wegener, Gunter; Wenzhöfer, Frank; Martin, Daniel; Cibic, Tamara; De Vittor, Cinzia; Vanreusel, Ann; Boetius, Antje

2018-02-01

Subseabed CO 2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO 2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO 2 impact studies. For this, we compared ecological functions of naturally CO 2 -vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO 2 fluxes (up to 4 to 7 mol CO 2 m -2 hour -1 ) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (-80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (-90%). The observed ecological effects of CO 2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO 2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO 2 .

Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient.

PubMed

Collins, Courtney G; Stajich, Jason E; Weber, Sören E; Pombubpa, Nuttapon; Diez, Jeffrey M

2018-04-19

Global climate and land use change are altering plant and soil microbial communities worldwide, particularly in arctic and alpine biomes where warming is accelerated. The widespread expansion of woody shrubs into historically herbaceous alpine plant zones is likely to interact with climate to affect soil microbial community structure and function; however, our understanding of alpine soil ecology remains limited. This study aimed to (i) determine whether the diversity and community composition of soil fungi vary across elevation gradients and to (ii) assess the impact of woody shrub expansion on these patterns. In the White Mountains of California, sagebrush (Artemisia rothrockii) shrubs have been expanding upwards into alpine areas since 1960. In this study, we combined observational field data with a manipulative shrub removal experiment along an elevation transect of alpine shrub expansion. We utilized next-generation sequencing of the ITS1 region for fungi and joint distribution modelling to tease apart effects of the environment and intracommunity interactions on soil fungi. We found that soil fungal diversity declines and community composition changes with increasing elevation. Both abiotic factors (primarily soil moisture and soil organic C) and woody sagebrush range expansion had significant effects on these patterns. However, fungal diversity and relative abundance had high spatial variation, overwhelming the predictive power of vegetation type, elevation and abiotic soil conditions at the landscape scale. Finally, we observed positive and negative associations among fungal taxa which may be important in structuring community responses to global change. © 2018 John Wiley & Sons Ltd.

Elevated temperature alters carbon cycling in a model microbial community

NASA Astrophysics Data System (ADS)

Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

2013-12-01

Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other microbial activities. When scaled to more complex ecosystems and integrated into Earth System Models, this approach could significantly improve predictions of global carbon-climate feedbacks. Experiments such as these are a critical first step designed at understanding climate change impacts in order to better predict ecosystem adaptations, assess the viability of mitigation strategies, and inform relevant policy decisions.

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 leads to higher contents of mineral N and net nitrification rates. In turn, the increasing N availability may stimulate plant growth and hence, induce a positive feedback between treeline advances and soil nitrogen cycling through soil microbial communities.

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

USGS Publications Warehouse

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

2006-01-01

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function. ?? 2006 Springer Science+Business Media, Inc.

HORSE SPECIES SYMPOSIUM: Canine intestinal microbiology and metagenomics: From phylogeny to function.

PubMed

Guard, B C; Suchodolski, J S

2016-06-01

Recent molecular studies have revealed a complex microbiota in the dog intestine. Convincing evidence has been reported linking changes in microbial communities to acute and chronic gastrointestinal inflammation, especially in canine inflammatory bowel disease (IBD). The most common microbial changes observed in intestinal inflammation are decreases in the bacterial phyla Firmicutes (i.e., Lachnospiraceae, Ruminococcaceae, and ) and Bacteroidetes, with concurrent increases in Proteobacteria (i.e., ). Due to the important role of microbial-derived metabolites for host health, it is important to elucidate the metabolic consequences of gastrointestinal dysbiosis and physiological pathways implicated in specific disease phenotypes. Metagenomic studies have used shotgun sequencing of DNA as well as phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to characterize functional changes in the bacterial metagenome in gastrointestinal disease. Furthermore, wide-scale and untargeted measurements of metabolic products derived by the host and the microbiota in intestinal samples allow a better understanding of the functional alterations that occur in gastrointestinal disease. For example, changes in bile acid metabolism and tryptophan catabolism recently have been reported in humans and dogs. Also, metabolites associated with the pentose phosphate pathway were significantly altered in chronic gastrointestinal inflammation and indicate the presence of oxidative stress in dogs with IBD. This review focuses on the advancements made in canine metagenomics and metabolomics and their implications in understanding gastrointestinal disease as well as the development of better treatment approaches.

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

PubMed Central

Singh, Baneshwar; Minick, Kevan J.; Strickland, Michael S.; Wickings, Kyle G.; Crippen, Tawni L.; Tarone, Aaron M.; Benbow, M. Eric; Sufrin, Ness; Tomberlin, Jeffery K.; Pechal, Jennifer L.

2018-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences. PMID:29354106

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function.

PubMed

Singh, Baneshwar; Minick, Kevan J; Strickland, Michael S; Wickings, Kyle G; Crippen, Tawni L; Tarone, Aaron M; Benbow, M Eric; Sufrin, Ness; Tomberlin, Jeffery K; Pechal, Jennifer L

2017-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3-732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences.

Bioremediation using Novosphingobium strain DY4 for 2,4-dichlorophenoxyacetic acid-contaminated soil and impact on microbial community structure.

PubMed

Dai, Yu; Li, Ningning; Zhao, Qun; Xie, Shuguang

2015-04-01

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is commonly used for weed control. The ubiquity of 2,4-D has gained increasing environmental concerns. Biodegradation is an attractive way to clean up 2,4-D in contaminated soil. However, information on the bioaugmentation trial for remediating contaminated soil is still very limited. The impact of bioaugmentation using 2,4-D-degraders on soil microbial community remains unknown. The present study investigated the bioremediation potential of a novel degrader (strain DY4) for heavily 2,4-D-polluted soil and its bioaugmentation impact on microbial community structure. The strain DY4 was classified as a Novosphingobium species within class Alphaproteobacteria and harbored 2,4-D-degrading TfdAα gene. More than 50 and 95 % of the herbicide could be dissipated in bioaugmented soil (amended with 200 mg/kg 2,4-D) respectively in 3-4 and 5-7 days after inoculation of Novosphingobium strain DY4. A significant growth of the strain DY4 was observed in bioaugmented soil with the biodegradation of 2,4-D. Moreover, herbicide application significantly altered soil bacterial community structure but bioaumentation using the strain DY4 showed a relatively weak impact.

Long-term variation in above and belowground plant inputs alters soil organic matter biogeochemistry at the molecular-level

NASA Astrophysics Data System (ADS)

Simpson, M. J.; Pisani, O.; Lin, L.; Lun, O.; Simpson, A.; Lajtha, K.; Nadelhoffer, K. J.

2015-12-01

The long-term fate of soil carbon reserves with global environmental change remains uncertain. Shifts in moisture, altered nutrient cycles, species composition, or rising temperatures may alter the proportions of above and belowground biomass entering soil. However, it is unclear how long-term changes in plant inputs may alter the composition of soil organic matter (SOM) and soil carbon storage. Advanced molecular techniques were used to assess SOM composition in mineral soil horizons (0-10 cm) after 20 years of Detrital Input and Removal Treatment (DIRT) at the Harvard Forest. SOM biomarkers (solvent extraction, base hydrolysis and cupric (II) oxide oxidation) and both solid-state and solution-state nuclear magnetic resonance (NMR) spectroscopy were used to identify changes in SOM composition and stage of degradation. Microbial activity and community composition were assessed using phospholipid fatty acid (PLFA) analysis. Doubling aboveground litter inputs decreased soil carbon content, increased the degradation of labile SOM and enhanced the sequestration of aliphatic compounds in soil. The exclusion of belowground inputs (No roots and No inputs) resulted in a decrease in root-derived components and enhanced the degradation of leaf-derived aliphatic structures (cutin). Cutin-derived SOM has been hypothesized to be recalcitrant but our results show that even this complex biopolymer is susceptible to degradation when inputs entering soil are altered. The PLFA data indicate that changes in soil microbial community structure favored the accelerated processing of specific SOM components with littler manipulation. These results collectively reveal that the quantity and quality of plant litter inputs alters the molecular-level composition of SOM and in some cases, enhances the degradation of recalcitrant SOM. Our study also suggests that increased litterfall is unlikely to enhance soil carbon storage over the long-term in temperate forests.

Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts.

PubMed

Maier, Stefanie; Tamm, Alexandra; Wu, Dianming; Caesar, Jennifer; Grube, Martin; Weber, Bettina

2018-04-01

Biological soil crusts (biocrusts) cover about 12% of the Earth's land masses, thereby providing ecosystem services and affecting biogeochemical fluxes on a global scale. They comprise photoautotrophic cyanobacteria, algae, lichens and mosses, which grow together with heterotrophic microorganisms, forming a model system to study facilitative interactions and assembly principles in natural communities. Biocrusts can be classified into cyanobacteria-, lichen-, and bryophyte-dominated types, which reflect stages of ecological succession. In this study, we examined whether these categories include a shift in heterotrophic communities and whether this may be linked to altered physiological properties. We analyzed the microbial community composition by means of qPCR and high-throughput amplicon sequencing and utilized flux measurements to investigate their physiological properties. Our results revealed that once 16S and 18S rRNA gene copy numbers increase, fungi become more predominant and alpha diversity increases with progressing succession. Bacterial communities differed significantly between biocrust types with a shift from more generalized to specialized organisms along succession. CO 2 gas exchange measurements revealed large respiration rates of late successional crusts being significantly higher than those of initial biocrusts, and different successional stages showed distinct NO and HONO emission patterns. Thus, our study suggests that the photoautotrophic organisms facilitate specific microbial communities, which themselves strongly influence the overall physiological properties of biocrusts and hence local to global nutrient cycles.

Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease.

PubMed

Casey, Jordan M; Ainsworth, Tracy D; Choat, J Howard; Connolly, Sean R

2014-08-07

Microbial community structure on coral reefs is strongly influenced by coral-algae interactions; however, the extent to which this influence is mediated by fishes is unknown. By excluding fleshy macroalgae, cultivating palatable filamentous algae and engaging in frequent aggression to protect resources, territorial damselfish (f. Pomacentridae), such as Stegastes, mediate macro-benthic dynamics on coral reefs and may significantly influence microbial communities. To elucidate how Stegastes apicalis and Stegastes nigricans may alter benthic microbial assemblages and coral health, we determined the benthic community composition (epilithic algal matrix and prokaryotes) and coral disease prevalence inside and outside of damselfish territories in the Great Barrier Reef, Australia. 16S rDNA sequencing revealed distinct bacterial communities associated with turf algae and a two to three times greater relative abundance of phylotypes with high sequence similarity to potential coral pathogens inside Stegastes's territories. These potentially pathogenic phylotypes (totalling 30.04% of the community) were found to have high sequence similarity to those amplified from black band disease (BBD) and disease affected corals worldwide. Disease surveys further revealed a significantly higher occurrence of BBD inside S. nigricans's territories. These findings demonstrate the first link between fish behaviour, reservoirs of potential coral disease pathogens and the prevalence of coral disease. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

DOE PAGES

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.; ...

2016-12-03

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. In order to assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling.more » Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.« less

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

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

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. In order to assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling.more » Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.« less

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

NASA Astrophysics Data System (ADS)

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.; Stegen, James C.; Hobson, Chad; Wilkins, Michael J.

2016-12-01

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. To assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.

Bioaugmentation of Hydrogenispora ethanolica LX-B affects hydrogen production through altering indigenous bacterial community structure.

PubMed

Yang, Zhiman; Guo, Rongbo; Shi, Xiaoshuang; He, Shuai; Wang, Lin; Dai, Meng; Qiu, Yanling; Dang, Xiaoxiao

2016-07-01

Bioaugmentation can facilitate hydrogen production from complex organic substrates, but it still is unknown how indigenous microbial communities respond to the added bacteria. Here, using a Hydrogenispora ethanolica LX-B (named as LX-B) bioaugmentation experiments, the distribution of metabolites and the responses of indigenous bacterial communities were investigated via batch cultivation (BC) and repeated batch cultivation (RBC). In BC the LX-B/sludge ratio of 0.12 achieved substantial high hydrogen yield, which was over twice that of control. In RBC one-time bioaugmentation and repeated batch bioaugmentation of LX-B resulted in the hydrogen yield that was average 1.2-fold and 0.8-fold higher than that in control, respectively. This improved hydrogen production performance mainly benefited from a shift in composition of the indigenous bacterial community caused by LX-B bioaugmentation. The findings represented an important step in understanding the relationship between bioaugmentation, a shift in bacterial communities, and altered bioreactor performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessing the potential for rhizoremediation of PCB contaminated soils in northern regions using native tree species.

PubMed

Slater, Heather; Gouin, Todd; Leigh, Mary Beth

2011-06-01

Rhizosphere bioremediation of polychlorinated biphenyls (PCBs) offers a potentially inexpensive approach to remediating contaminated soils that is particularly attractive in remote regions including the Arctic. We assessed the abilities of two tree species native to Alaska, Salix alaxensis (felt-leaf willow) and Picea glauca (white spruce), to promote microbial biodegradation of PCBs via the release of phytochemicals upon fine root death. Crushed fine roots, biphenyl (PCB analogue) or salicylate (willow secondary compound) were added to microcosms containing soil spiked with PCBs and resultant PCB disappearance, soil toxicity and microbial community changes were examined. After 180d, soil treated with willow root crushates showed a significantly greater PCB loss than untreated soils for some PCB congeners, including the toxic congeners, PCB 77, 105 and 169, and showed a similar PCB loss pattern (in both extent of degradation and congeners degraded) to biphenyl-treated microcosms. Neither P. glauca (white spruce) roots nor salicylate enhanced PCB loss, indicating that biostimulation is plant species specific and was not mediated by salicylate. Soil toxicity assessed using the Microtox bioassay indicated that the willow treatment resulted in a less toxic soil environment. Molecular microbial community analyses indicated that biphenyl and salicylate promoted shifts in microbial community structure and composition that differed distinctly from each other and from the crushed root treatments. The biphenyl utilizing bacterium, Cupriavidus spp. was isolated from the soil. The findings suggest that S. alaxensis may be an effective plant for rhizoremediation by altering microbial community structure, enhancing the loss of some PCB congeners and reducing the toxicity of the soil environment. Copyright © 2011 Elsevier Ltd. All rights reserved.

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

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

Knelman, Joseph E.; Graham, Emily B.; Prevéy, Janet S.

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and successional trajectories in plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study we sought to examine how emblematic shifts from early-successional Alnus sinuata (alder) to late successional Picea sitchensis (spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield tomore » delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early-successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate drives shifts in the relative abundance of major taxa of bacteria in alder-influenced soils, including declines in those that are enriched by alder. We found these effects to be spruce-specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Our results show that spruce leachate addition more strongly structures bacterial communities than alders (less dispersion in bacterial community beta diversity). Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.« less