Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

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

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Media Ion Composition Controls Regulatory and Virulence Response of Salmonella in Spaceflight

PubMed Central

Wilson, James W.; Ott, C. Mark; Quick, Laura; Davis, Richard; zu Bentrup, Kerstin Höner; Crabbé, Aurélie; Richter, Emily; Sarker, Shameema; Barrila, Jennifer; Porwollik, Steffen; Cheng, Pui; McClelland, Michael; Tsaprailis, George; Radabaugh, Timothy; Hunt, Andrea; Shah, Miti; Nelman-Gonzalez, Mayra; Hing, Steve; Parra, Macarena; Dumars, Paula; Norwood, Kelly; Bober, Ramona; Devich, Jennifer; Ruggles, Ashleigh; CdeBaca, Autumn; Narayan, Satro; Benjamin, Joseph; Goulart, Carla; Rupert, Mark; Catella, Luke; Schurr, Michael J.; Buchanan, Kent; Morici, Lisa; McCracken, James; Porter, Marc D.; Pierson, Duane L.; Smith, Scott M.; Mergeay, Max; Leys, Natalie; Stefanyshyn-Piper, Heidemarie M.; Gorie, Dominic; Nickerson, Cheryl A.

2008-01-01

The spaceflight environment is relevant to conditions encountered by pathogens during the course of infection and induces novel changes in microbial pathogenesis not observed using conventional methods. It is unclear how microbial cells sense spaceflight-associated changes to their growth environment and orchestrate corresponding changes in molecular and physiological phenotypes relevant to the infection process. Here we report that spaceflight-induced increases in Salmonella virulence are regulated by media ion composition, and that phosphate ion is sufficient to alter related pathogenesis responses in a spaceflight analogue model. Using whole genome microarray and proteomic analyses from two independent Space Shuttle missions, we identified evolutionarily conserved molecular pathways in Salmonella that respond to spaceflight under all media compositions tested. Identification of conserved regulatory paradigms opens new avenues to control microbial responses during the infection process and holds promise to provide an improved understanding of human health and disease on Earth. PMID:19079590

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.

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.

Environmental Stress-mediated EPS Production Shape Microbial Activity on Various Hydrated Rough Surfaces

NASA Astrophysics Data System (ADS)

Wang, G.; Liu, L.; Chen, G.

2016-12-01

The complex environmental physical and chemical processes and interplay with the associating biological responses are keys to understanding the environmental microbiology ensconced in environmental remediation, water quality control, food safety, nutrient cycling, and etc., yet remain poorly understood. Using experimental micromodels, we study how environmental conditions (e.g., hydration fluctuation, nutrient limitation, pH variation, etc.) affect microbial extracellular polymeric substances (EPS) production and their configuration within various hydrated surfaces, and impacts on microbial motility, surface attachment, aggregation, and other bioremediation activities. To elucidate the potential mechanisms underlying the complex bio-physicochemical processes, we developed an individual-based and spatio-temporally resolved modeling platform that explicitly considers microscale aqueous-phase configuration and nutrient transport/diffusion and associated biophysical processes affecting individual microbial cell life history. We quantitatively explore the effects of the above microscale environmental processes on bio-physicochemical interactions affecting microbial growth, motility, surface attachment and aggregation, and shaping population interactions and functions. Simulation scenarios of microbial induced pollutant (e.g., roxarsone) biotransformation on various hydrated rough surfaces will also be present.

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, an...

Using Integrated Environmental Modeling to Automate a Process-Based Quantitative Microbial Risk Assessment (presentation)

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and...

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

NASA Astrophysics Data System (ADS)

Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel; David, Maude M.; McFarland, Jack; Blazewicz, Steven J.; Harden, Jennifer; Turetsky, Merritt R.; McGuire, A. David; Shah, Manesh B.; Verberkmoes, Nathan C.; Lee, Lang Ho; Mavrommatis, Kostas; Jansson, Janet K.

2015-05-01

Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular `omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.

PubMed

Hultman, Jenni; Waldrop, Mark P; Mackelprang, Rachel; David, Maude M; McFarland, Jack; Blazewicz, Steven J; Harden, Jennifer; Turetsky, Merritt R; McGuire, A David; Shah, Manesh B; VerBerkmoes, Nathan C; Lee, Lang Ho; Mavrommatis, Kostas; Jansson, Janet K

2015-05-14

Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular 'omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

Representing life in the Earth system with soil microbial functional traits in the MIMICS model

NASA Astrophysics Data System (ADS)

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

2015-02-01

Projecting biogeochemical responses to global environmental change requires multi-scaled perspectives that consider organismal diversity, ecosystem processes and global fluxes. However, microbes, the drivers of soil organic matter decomposition and stabilization, remain notably absent from models used to project carbon cycle-climate feedbacks. We used a microbial trait-based soil carbon (C) model, with two physiologically distinct microbial communities to improve current estimates of soil C storage and their likely response to perturbations. Drawing from the application of functional traits used to model other ecosystems, we incorporate copiotrophic and oligotrophic microbial functional groups in the MIcrobial-MIneral Carbon Stabilization (MIMICS) model, which incorporates oligotrophic and copiotrophic functional groups, akin to "gleaner" vs. "opportunist" plankton in the ocean, or r vs. K strategists in plant and animals communities. Here we compare MIMICS to a conventional soil C model, DAYCENT, in cross-site comparisons of nitrogen (N) enrichment effects on soil C dynamics. MIMICS more accurately simulates C responses to N enrichment; moreover, it raises important hypotheses involving the roles of substrate availability, community-level enzyme induction, and microbial physiological responses in explaining various soil biogeochemical responses to N enrichment. In global-scale analyses, we show that current projections from Earth system models likely overestimate the strength of the land C sink in response to increasing C inputs with elevated carbon dioxide (CO2). Our findings illustrate that tradeoffs between theory and utility can be overcome to develop soil biogeochemistry models that evaluate and advance our theoretical understanding of microbial dynamics and soil biogeochemical responses to environmental change.

Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses

PubMed Central

Azarbad, Hamed; van Gestel, Cornelis A. M.; Niklińska, Maria; Laskowski, Ryszard; Röling, Wilfred F. M.; van Straalen, Nico M.

2016-01-01

Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the “costs” of adaptation to metals affect the responses of metal-tolerant communities to other stress factors (“stress-on-stress”). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors. PMID:27314330

Metagenomics-Enabled Understanding of Soil Microbial Feedbacks to Climate Warming

NASA Astrophysics Data System (ADS)

Zhou, J.; Wu, L.; Zhili, H.; Kostas, K.; Luo, Y.; Schuur, E. A. G.; Cole, J. R.; Tiedje, J. M.

2014-12-01

Understanding the response of biological communities to climate warming is a central issue in ecology and global change biology, but it is poorly understood microbial communities. To advance system-level predictive understanding of the feedbacks of belowground microbial communities to multiple climate change factors and their impacts on soil carbon (C) and nitrogen (N) cycling processes, we have used integrated metagenomic technologies (e.g., target gene and shotgun metagenome sequencing, GeoChip, and isotope) to analyze soil microbial communities from experimental warming sites in Alaska (AK) and Oklahoma (OK), and long-term laboratory incubation. Rapid feedbacks of microbial communities to warming were observed in the AK site. Consistent with the changes in soil temperature, moisture and ecosystem respiration, microbial functional community structure was shifted after only 1.5-year warming, indicating rapid responses and high sensitivity of this permafrost ecosystem to climate warming. Also, warming stimulated not only functional genes involved in aerobic respiration of both labile and recalcitrant C, contributing to an observed 24% increase in 2010 growing season and 56% increase of decomposition of a standard substrate, but also functional genes for anaerobic processes (e.g., denitrification, sulfate reduction, methanogenesis). Further comparisons by shotgun sequencing showed significant differences of microbial community structure between AK and OK sites. The OK site was enriched in genes annotated for cellulose degradation, CO2 production, denitrification, sporulation, heat shock response, and cellular surface structures (e.g., trans-membrane transporters for glucosides), while the AK warmed plots were enriched in metabolic pathways related to labile C decomposition. Together, our results demonstrate the vulnerability of permafrost ecosystem C to climate warming and the importance of microbial feedbacks in mediating such vulnerability.

Biophysical processes supporting the diversity of microbial life in soil

PubMed Central

Tecon, Robin

2017-01-01

Abstract Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure—the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning. PMID:28961933

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

USDA-ARS?s Scientific Manuscript database

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and human health effect...

Insights into Feast-Famine polyhydroxyalkanoate (PHA)-producer selection: Microbial community succession, relationships with system function and underlying driving forces.

PubMed

Huang, Long; Chen, Zhiqiang; Wen, Qinxue; Zhao, Lizhi; Lee, Duu-Jong; Yang, Lian; Wang, Yao

2017-12-18

The Feast-Famine (FF) process has been frequently used to select polyhydroxyalkanoate (PHA)-accumulating mixed cultures (MCs), but there has been little insight into the ecophysiology of the microbial community during the selection process. In three FF systems with well-defined conditions, synchronized variations in higher-order properties of MCs and complicate microbial community succession mainly including enrichment and elimination of non-top competitors and unexpected turnover of top competitors, were observed. Quantification of PHA-accumulating function genes (phaC) revealed that the top competitors maintained the PHA synthesis by playing consecutive roles when the highly dynamic turnover occurred. Due to its specific physiological characteristics during the PHA-accumulating process, Thauera strain OTU 7 was found to be responsible for the fluctuating SVI, which threatened the robustness of the FF system. This trait was also responsible for its later competitive exclusion by the other PHA-producer, Paracoccus strain OTU 1. Deterministic processes dominated the entire FF system, resulting in the inevitable microbial community succession in the acclimation phase and maintenance of the stable PHA-accumulating function in the maturation phase. However, neutral processes, likely caused by predation from bacterial phages, also occurred, which led to the unpredictable temporal dynamics of the top competitors. Copyright © 2017. Published by Elsevier Ltd.

Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils

PubMed Central

Álvarez-Yela, Astrid Catalina; Gómez-Cano, Fabio; Zambrano, María Mercedes; Husserl, Johana; Danies, Giovanna; Restrepo, Silvia; González-Barrios, Andrés Fernando

2017-01-01

Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community. PMID:28767679

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

PubMed Central

Zeglin, Lydia H.

2015-01-01

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors. PMID:26042102

Microbial biogeography: putting microorganisms on the map.

PubMed

Martiny, Jennifer B Hughes; Bohannan, Brendan J M; Brown, James H; Colwell, Robert K; Fuhrman, Jed A; Green, Jessica L; Horner-Devine, M Claire; Kane, Matthew; Krumins, Jennifer Adams; Kuske, Cheryl R; Morin, Peter J; Naeem, Shahid; Ovreås, Lise; Reysenbach, Anna-Louise; Smith, Val H; Staley, James T

2006-02-01

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Assessment of microbial products in the biosorption process of Cu(II) onto aerobic granular sludge: Extracellular polymeric substances contribution and soluble microbial products release.

PubMed

Huang, Linxian; Li, Meilin; Si, Guangchao; Wei, Jinglin; Ngo, Huu Hao; Guo, Wenshan; Xu, Weiying; Du, Bin; Wei, Qin; Wei, Dong

2018-05-18

In the present study, the responses of microbial products in the biosorption process of Cu(II) onto aerobic granular sludge were evaluated by using batch and spectroscopic approaches. Batch experimental data showed that extracellular polymeric substances (EPSs) contributed to Cu(II) removal from an aqueous solution, especially when treating low metal concentrations, whereas soluble microbial products (SMPs) were released under the metal stress during biosorption process. A three-dimensional excitation-emission matrix (3D-EEM) identified four main fluorescence peaks in the EPS, i.e., tryptophan protein-like, aromatic protein-like, humic-like and fulvic acid-like substances, and their fluorescence intensities decreased gradually in the presence of Cu(II) during the sorption process. Particularly, tryptophan protein-like substances quenched the Cu(II) binding to a much higher extent through a static quenching process with less than one class of binding sites. According to the synchronous fluorescence spectra, the whole fluorescence intensity of released SMP samples expressed an increased trend with different degrees along with contact time. Two-dimensional correlation spectroscopy (2D-COS) suggested that the fulvic-like fluorescence fraction might be more susceptible to metal exposure than other fractions. The result of molecular weight distribution demonstrated that the SMPs released from the biosorption process differed significantly according to contact time. The result obtained could provide new insights into the responses of microbial products from aerobic granular sludge with heavy metal treatment. Copyright © 2018. Published by Elsevier Inc.

Environmentally Responsible Microbiological Production of Energetic Ingredients

DTIC Science & Technology

2007-11-01

effort was to develop an environmentally benign and economical microbial process for nitro-energetics production . The specific targets of this method...microbial production of nitro-based EM. As the processes and compounds of choice, RDX/HMX (nitramine) generation was selected. Microorganisms capable of...Current synthetic methods for the production of RDX and HMX utilize hexamine as the precursor. Hexamine is an industrial chemical available on a large

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Chain response of microbial loop to the decay of a diatom bloom in the East China Sea

NASA Astrophysics Data System (ADS)

Wu, Linnan; Lin, Shiquan; Huang, Lingfeng; Lu, Jiachang; Chen, Wenzhao; Guo, Weidong; Zhang, Wuchang; Xiao, Tian; Sun, Jun

2016-02-01

Algal bloom has been regarded as one of the key causes for the summer hypoxia phenomena in the bottom water adjacent to the Yangtze River estuary in the East China Sea. Although a series of biological processes within microbial loop are involved in the development of oxygen depletion during the bloom decay, little has been known about the dynamics of microorganisms in response to the decaying process of the bloom through trophic interaction context. Here, we report some preliminary results of our observations about the response of microbial loop to the bloom decay, based on the onboard incubation experiments for 10 days during a diatom bloom near the Yangtze River estuary in August, 2011. Light and dark incubations were conducted to simulate the bloom decay inside and below the euphotic layer, respectively. In the first stage of bloom decay (Day 0 to Day 4), rapid response was found in heterotrophic bacteria (HB) and ciliate growth, which was in accordance with the decrease of total Chl a, indicating a "bottom-up" control at the early stage of bloom decay. However, the increase of heterotrophic nanoflagellates (HNF) abundance was rather inconspicuous, suggesting predation pressure on HNF from ciliate or other predator at this stage. In the second stage (Day 4 to Day 8), HB and ciliate decreased rapidly with the increase of HNF, revealing the release of HNF form ciliate predation, which suggested a "top-down" control. In the last stage of our experiment (Day 8 to Day 10), the trophic interactions were more complex, but it also implied a "top-down" control within the microbial loop. Meanwhile, virus had been monitored in the whole process of our incubations. It was found that virus lysed microalgae at the first stage, and lysed HB at the second stage. In addition, the bacterial mortality was principally caused by HNF grazing in the light-sufficient incubations and by viral lysis in the light-insufficient incubations. Our results suggest tight trophic interactions within the microbial loop in the decaying process of the algal bloom, which may assist our understanding of the role of microbial loop in hypoxia formation in coastal waters.

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

Representing life in the Earth system with soil microbial functional traits in the MIMICS model

NASA Astrophysics Data System (ADS)

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

2015-06-01

Projecting biogeochemical responses to global environmental change requires multi-scaled perspectives that consider organismal diversity, ecosystem processes, and global fluxes. However, microbes, the drivers of soil organic matter decomposition and stabilization, remain notably absent from models used to project carbon (C) cycle-climate feedbacks. We used a microbial trait-based soil C model with two physiologically distinct microbial communities, and evaluate how this model represents soil C storage and response to perturbations. Drawing from the application of functional traits used to model other ecosystems, we incorporate copiotrophic and oligotrophic microbial functional groups in the MIcrobial-MIneral Carbon Stabilization (MIMICS) model; these functional groups are akin to "gleaner" vs. "opportunist" plankton in the ocean, or r- vs. K-strategists in plant and animal communities. Here we compare MIMICS to a conventional soil C model, DAYCENT (the daily time-step version of the CENTURY model), in cross-site comparisons of nitrogen (N) enrichment effects on soil C dynamics. MIMICS more accurately simulates C responses to N enrichment; moreover, it raises important hypotheses involving the roles of substrate availability, community-level enzyme induction, and microbial physiological responses in explaining various soil biogeochemical responses to N enrichment. In global-scale analyses, we show that MIMICS projects much slower rates of soil C accumulation than a conventional soil biogeochemistry in response to increasing C inputs with elevated carbon dioxide (CO2) - a finding that would reduce the size of the land C sink estimated by the Earth system. Our findings illustrate that tradeoffs between theory and utility can be overcome to develop soil biogeochemistry models that evaluate and advance our theoretical understanding of microbial dynamics and soil biogeochemical responses to environmental change.

Microbial processes in the Kanda Bay, a meromictic water body artifically separated from the White Sea.

PubMed

Savvichev, A S; Demidenko, N A; Krasnova, E D; Kalmatskaya, O V; Kharcheva, A N; Ivanov, M V

2017-05-01

Sings of meromixis are found by means of microbiological and biogeochemical investigations in the southernn part of the Kanda Bay, an artificial water body separated front the White Sea with a railway dam. The concentration of oxygen in the bottom layer attained 1.9 mmol/L, intensity of the process of microbial sulfate reduction, 3.0 μmol of sulfur/(L day). The concentration of dissolved methane, 3.7 μmol/L. Isotopic composition of carbon in methane (δ 13 C (CH 4 ) =-79.2‰) indicates to its microbial genesis. At present, Kanda Bay is a sole in Russia man-made marine water body for which there are data on the rate of microbial processes responsible for formation of bottom water layer containing hydrogen sulfide and methane.

Microbial food safety - modeling and applications

USDA-ARS?s Scientific Manuscript database

Microbial food safety is a key issue for the food processing industry, and enhancing food safety is everyone’s responsibility from food producers to consumers. Financial losses to the economy due to foodborne illness are in the billions of dollars, annually. Foodborne illness can be caused by patho...

Microbial interactions in building of communities

PubMed Central

Wright, Christopher J.; Burns, Logan H.; Jack, Alison A.; Back, Catherine R.; Dutton, Lindsay C.; Nobbs, Angela H.; Lamont, Richard J.; Jenkinson, Howard F.

2012-01-01

SUMMARY Establishment of a community is considered to be essential for microbial growth and survival in the human oral cavity. Biofilm communities have increased resilience to physical forces, antimicrobial agents, and nutritional variations. Specific cell-to-cell adherence processes, mediated by adhesin-receptor pairings on respective microbial surfaces, are able to direct community development. These interactions co-localize species in mutually beneficial relationships, such as streptococci, veillonellae, Porphyromonas gingivalis and Candida albicans. In transition from the planktonic mode of growth to a biofilm community, microorganisms undergo major transcriptional and proteomic changes. These occur in response to sensing of diffusible signals, such as autoinducer molecules, and to contact with host tissues or other microbial cells. Underpinning many of these processes are intracellular phosphorylation events that regulate a large number of microbial interactions relevant to community formation and development. PMID:23253299

Monitoring the microbial community during solid-state acetic acid fermentation of Zhenjiang aromatic vinegar.

PubMed

Xu, Wei; Huang, Zhiyong; Zhang, Xiaojun; Li, Qi; Lu, Zhenming; Shi, Jinsong; Xu, Zhenghong; Ma, Yanhe

2011-09-01

Zhenjiang aromatic vinegar is one of the most famous Chinese traditional vinegars. In this study, change of the microbial community during its fermentation process was investigated. DGGE results showed that microbial community was comparatively stable, and the diversity has a disciplinary series of changes during the fermentation process. It was suggested that domestication of microbes and unique cycle-inoculation style used in the fermentation of Zhenjiang aromatic vinegar were responsible for comparatively stable of the microbial community. Furthermore, two clone libraries were constructed. The results showed that bacteria presented in the fermentation belonged to genus Lactobacillus, Acetobacter, Gluconacetobacter, Staphylococcus, Enterobacter, Pseudomonas, Flavobacterium and Sinorhizobium, while the fungi were genus Saccharomyces. DGGE combined with clone library analysis was an effective and credible technique for analyzing the microbial community during the fermentation process of Zhenjiang aromatic vinegar. Real-time PCR results suggested that the biomass showed a "system microbes self-domestication" process in the first 5 days, then reached a higher level at the 7th day before gradually decreasing until the fermentation ended at the 20th day. This is the first report to study the changes of microbial community during fermentation process of Chinese traditional solid-state fermentation of vinegar. Copyright © 2011 Elsevier Ltd. All rights reserved.

Soil Microbial Properties and Plant Growth Responses to Carbon and Water Addition in a Temperate Steppe: The Importance of Nutrient Availability

PubMed Central

Guo, Chengyuan; Wang, Renzhong; Xiao, Chunwang

2012-01-01

Background Global climatic change is generally expected to stimulate net primary production, and consequently increase soil carbon (C) input. The enhanced C input together with potentially increased precipitation may affect soil microbial processes and plant growth. Methodology/Principal Findings To examine the effects of C and water additions on soil microbial properties and plant growth, we conducted an experiment lasting two years in a temperate steppe of northeastern China. We found that soil C and water additions significantly affected microbial properties and stimulated plant growth. Carbon addition significantly increased soil microbial biomass and activity but had a limited effect on microbial community structure. Water addition significantly increased soil microbial activity in the first year but the response to water decreased in the second year. The water-induced changes of microbial activity could be ascribed to decreased soil nitrogen (N) availability and to the shift in soil microbial community structure. However, no water effect on soil microbial activity was visible under C addition during the two years, likely because C addition alleviated nutrient limitation of soil microbes. In addition, C and water additions interacted to affect plant functional group composition. Water addition significantly increased the ratio of grass to forb biomass in C addition plots but showed only minor effects under ambient C levels. Our results suggest that soil microbial activity and plant growth are limited by nutrient (C and N) and water availability, and highlight the importance of nutrient availability in modulating the responses of soil microbes and plants to potentially increased precipitation in the temperate steppe. Conclusions/Significance Increased soil C input and precipitation would show significant effects on soil microbial properties and plant growth in the temperate steppe. These findings will improve our understanding of the responses of soil microbes and plants to the indirect and direct climate change effects. PMID:22496905

Sensing of dangerous DNA.

PubMed

Gasser, Stephan; Zhang, Wendy Y L; Tan, Nikki Yi Jie; Tripathi, Shubhita; Suter, Manuel A; Chew, Zhi Huan; Khatoo, Muznah; Ngeow, Joanne; Cheung, Florence S G

2017-07-01

The presence of damaged and microbial DNA can pose a threat to the survival of organisms. Cells express various sensors that recognize specific aspects of such potentially dangerous DNA. Recognition of damaged or microbial DNA by sensors induces cellular processes that are important for DNA repair and inflammation. Here, we review recent evidence that the cellular response to DNA damage and microbial DNA are tightly intertwined. We also discuss insights into the parameters that enable DNA sensors to distinguish damaged and microbial DNA from DNA present in healthy cells. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Filling the gap: using non-invasive geophysical methods to monitor the processes leading to enhanced carbon turnover induced by periodic water table fluctuations

NASA Astrophysics Data System (ADS)

Mellage, A.; Pronk, G.; Atekwana, E. A.; Furman, A.; Rezanezhad, F.; Van Cappellen, P.

2017-12-01

Subsurface transition environments such as the capillary fringe are characterized by steep gradients in redox conditions. Spatial and temporal variations in electron acceptor and donor availability - driven by hydrological changes - may enhance carbon turnover, in some cases resulting in pulses of CO2-respiration. Filling the mechanistic knowledge gap between the hydrological driver and its biogeochemical effects hinges on our ability to monitor microbial activity and key geochemical markers at a high spatial and temporal resolution. However, direct access to subsurface biogeochemical processes is logistically difficult, invasive and usually expensive. In-line, non-invasive geophysical techniques - Spectral Induced Polarization (SIP) and Electrodic Potential (EP), specifically - offer a comparatively inexpensive alternative and can provide data with high spatial and temporal resolution. The challenge lies in linking electrical responses to specific changes in biogeochemical processes. We conducted SIP and EP measurements on a soil column experiment where an artificial soil mixture was subjected to monthly drainage and imbibition cycles. SIP responses showed a clear dependence on redox zonation and microbial abundance. Temporally variable responses exhibited no direct moisture dependence suggesting that the measured responses recorded changes in microbial activity and coincided with the depth interval over which enhanced carbon turnover was observed. EP measurements detected the onset of sulfate mineralization and mapped its depth zonation. SIP and EP signals thus detected enhanced microbial activity within the water table fluctuation zone as well as the timing of the development of specific reactive processes. These findings can be used to relate measured electrical signals to specific reaction pathways and help inform reactive transport models, increasing their predictive capabilities.

Lipids as paleomarkers to constrain the marine nitrogen cycle

PubMed Central

Rush, Darci

2017-01-01

Summary Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past. PMID:28142226

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.

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.

Inactivation of conserved genes induces microbial aversion, drug detoxification, and innate immunity in C.elegans

PubMed Central

Melo, Justine A.; Ruvkun, Gary

2012-01-01

Summary The nematode C. elegans consumes benign bacteria such as E. coli and is repelled by pathogens and toxins. Here we show that RNAi and toxin-mediated disruption of core cellular activities, including translation, respiration, and protein turnover, stimulates behavioral avoidance of attractive E. coli. RNAi of such essential processes also induces expression of detoxification and innate immune response genes in the absence of toxins or pathogens. Disruption of core processes in non-neuronal tissues can stimulate aversion behavior, revealing a neuroendocrine axis of control. Microbial avoidance requires serotonergic and Jnk kinase signaling. We propose that surveillance pathways oversee critical cellular activities to detect pathogens, many of which deploy toxins and virulence factors to disrupt these same host pathways. Variation in cellular surveillance and endocrine pathways controlling behavior, detoxification and immunity selected by past toxin or microbial interactions could underlie aberrant responses to foods, medicines, and microbes. PMID:22500807

Responses of redwood soil microbial community structure and N transformations to climate change

Treesearch

Damon C. Bradbury; Mary K. Firestone

2012-01-01

Soil microorganisms perform critical ecosystem functions, including decomposition, nitrogen (N) mineralization and nitrification. Soil temperature and water availability can be critical determinants of the rates of these processes as well as microbial community composition and structure. This research examined how changes in climate affect bacterial and fungal...

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes.

PubMed

Wang, Cheng; Dong, Da; Strong, P J; Zhu, Weijing; Ma, Zhuang; Qin, Yong; Wu, Weixiang

2017-08-16

Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting. Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure and underwent an initial increase and then a decrease in abundance. By contrast, hosts for tetracycline resistance genes (tetM-tetW-tetO-tetS) exhibited a constant decline through time. The transcriptional patterns of a core resistome over the course of composting were identified, and microbial phylogeny was the key determinant in defining the varied transcriptional response of resistome to this dynamic biological process. This research demonstrated the benefits of composting for manure treatment. It reduced the risk of emerging environmental contaminants such as tetracyclines, tetracycline resistance genes, and clinically relevant pathogens carrying ARGs, as well as RNA viruses and bacteriophages.

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.

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.

Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation

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

Williams, Kenneth H.; Kemna, Andreas; Wilkins, Michael J.

2009-08-05

Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1more » Hz) andwasdependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous phase response were enriched in Fe(II), dissolved sulfide, and cell-associated FeS nanoparticles. The accumulation of mineral precipitates and electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the anomalous IP response and revealing the usefulness of multifrequency IP measurements for monitoring mineralogical and geochemical changes accompanying stimulated subsurface bioremediation.« less

Recovery of microbial communities and carbon cycling processes following drought manipulation in southern California

NASA Astrophysics Data System (ADS)

Allison, S. D.; Martiny, J. B. H.; Martiny, A.; Berlemont, R.; Treseder, K. K.; Goulden, M.; Brodie, E.

2016-12-01

Predicting the functioning of microbial communities under changing environmental conditions remains a key challenge in Earth system science. Metagenomics and other high-throughput molecular approaches can help address this challenge by revealing the functional potential of microbial communities. We coupled metagenomics with models and experimental manipulations to address microbial responses to drought in a California grassland ecosystem along with the consequences for carbon cycling. We developed an approach for extracting trait information from metagenomic data and asked: 1) What is the phylogenetic structure of drought response traits? 2) What is the relationship between these traits and those involved in carbohydrate degradation? 3) How do both classes of traits vary seasonally and with precipitation manipulation? 4) How resilient are these traits in the face of perturbation? We found that drought response traits are phylogenetically conserved at an equivalent of 5-8% ribosomal RNA gene sequence dissimilarity. Experimental drought treatment selected for the genetic potential to degrade starch, xylan, and mixed polysaccharides, suggesting a link between drought response and carbon cycling traits. In addition, microbial communities exposed to experimental drought showed a reduced potential to degrade plant biomass. Particularly among bacteria, seasonal drought had a larger impact on microbial composition, abundance, and carbohydrate-degrading genes compared to experimental drought. Bacterial communities were also more resilient to drought perturbation than fungal communities, which showed legacies of drought perturbation for up to three years. Altogether, these findings imply that microbial communities exhibit trait diversity that facilitates resilience but with substantial time lags and consequences for carbon turnover. This information is being used to inform new trait-based models that address the challenge of predicting microbial functioning under precipitation change.

Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil.

PubMed

Militon, Cécile; Boucher, Delphine; Vachelard, Cédric; Perchet, Geoffrey; Barra, Vincent; Troquet, Julien; Peyretaillade, Eric; Peyret, Pierre

2010-12-01

The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium. FEMS Microbiology Ecology © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original French government works.

Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem

PubMed Central

He, Zhili; Xiong, Jinbo; Kent, Angela D; Deng, Ye; Xue, Kai; Wang, Gejiao; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2014-01-01

The concentrations of atmospheric carbon dioxide (CO2) and tropospheric ozone (O3) have been rising due to human activities. However, little is known about how such increases influence soil microbial communities. We hypothesized that elevated CO2 (eCO2) and elevated O3 (eO3) would significantly affect the functional composition, structure and metabolic potential of soil microbial communities, and that various functional groups would respond to such atmospheric changes differentially. To test these hypotheses, we analyzed 96 soil samples from a soybean free-air CO2 enrichment (SoyFACE) experimental site using a comprehensive functional gene microarray (GeoChip 3.0). The results showed the overall functional composition and structure of soil microbial communities shifted under eCO2, eO3 or eCO2+eO3. Key functional genes involved in carbon fixation and degradation, nitrogen fixation, denitrification and methane metabolism were stimulated under eCO2, whereas those involved in N fixation, denitrification and N mineralization were suppressed under eO3, resulting in the fact that the abundance of some eO3-supressed genes was promoted to ambient, or eCO2-induced levels by the interaction of eCO2+eO3. Such effects appeared distinct for each treatment and significantly correlated with soil properties and soybean yield. Overall, our analysis suggests possible mechanisms of microbial responses to global atmospheric change factors through the stimulation of C and N cycling by eCO2, the inhibition of N functional processes by eO3 and the interaction by eCO2 and eO3. This study provides new insights into our understanding of microbial functional processes in response to global atmospheric change in soybean agro-ecosystems. PMID:24108327

Response of microbial activities and diversity to PAHs contamination at coal tar contaminated land

NASA Astrophysics Data System (ADS)

Zhao, Xiaohui; Sun, Yujiao; Ding, Aizhong; Zhang, Dan; Zhang, Dayi

2015-04-01

Coal tar is one of the most hazardous and concerned organic pollutants and the main hazards are polycyclic aromatic hydrocarbons (PAHs). The indigenous microorganisms in soils are capable to degrade PAHs, with essential roles in biochemical process for PAHs natural attenuation. This study investigated 48 soil samples (from 8 depths of 6 boreholes) in Beijing coking and chemistry plant (China) and revealed the correlation between PAHs contamination, soil enzyme activities and microbial community structure, by 16S rRNA denaturing gradient gel electrophoresis (DGGE). At the site, the key contaminants were identified as naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene and anthracene, and the total PAHs concentration ranged from 0.1 to 923.9 mg/kg dry soil. The total PAHs contamination level was positively correlated (p<0.05) with the bacteria count (0.9×107-14.2×107 CFU/mL), catalase activities (0.554-6.230 mL 0.02 M KMnO4/g•h) and dehydrogenase activities (1.9-30.4 TF μg/g•h soil), showing the significant response of microbial population and degrading functions to the organic contamination in soils. The PAHs contamination stimulated the PAHs degrading microbes and promoted their biochemical roles in situ. The positive relationship between bacteria count and dehydrogenase activities (p<0.05) suggested the dominancy of PAHs degrading bacteria in the microbial community. More interestingly, the microbial community deterioration was uncovered via the decline of microbial biodiversity (richness from 16S rRNA DGGE) against total PAHs concentration (p<0.05). Our research described the spatial profiles of PAHs contamination and soil microbial functions at the PAHs heavily contaminated sites, offering deeper understanding on the roles of indigenous microbial community in natural attenuation process.

Lipids as paleomarkers to constrain the marine nitrogen cycle.

PubMed

Rush, Darci; Sinninghe Damsté, Jaap S

2017-06-01

Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction-oxidation transformations of bio-available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio-available nitrogen species. As most microorganisms are soft-bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically-important cycle, and provides examples of biomarker applications in the geological past. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

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.

Risk of Adverse Health Effects Due to Host-Microorganism Interactions

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Oubre, Cherie; Wallace, Sarah; Mehta, Satish; Pierson, Duane

2016-01-01

Numerous spaceflight experiments have been conducted to investigate alterations in microbial responses resulting from culture during spaceflight and spaceflight-analogs. However, recent studies investigating spaceflight-associated alterations in microbial virulence have initiated the review and production of evidence to better understand the impact these alterations would have on the incidence of infectious disease during a spaceflight exploration mission. The preponderance of evidence indicates that alterations in microbial gene expression and phenotype (including virulence) are occurring; however, the clinical implications of such changes are still unclear. Greater knowledge is required including a better understanding of the mechanism behind unique spaceflight-associated microbial responses to determine how this environmental stimulus impacts various microorganisms, their diversity and concentration in the spacecraft and crew microbiome, their impact on the vehicle and crew, and their resistance to current mitigation and antibiotic regimens. This knowledge will enable us to determine requirements, guidelines, and processes for design and monitoring of the next generation vehicles.

Environmental Regulation of Microbial Community Structure

NASA Technical Reports Server (NTRS)

Bebout, Leslie; DesMarais, D.; Heyenga, G.; Nelson, F.; DeVincenzi, D. (Technical Monitor)

2002-01-01

Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.

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

Wieder, William R.; Allison, Steven D.; Davidson, Eric A.

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

Disifin (sodium tosylchloramide) and Toll-like receptors (TLRs): evolving importance in health and diseases.

PubMed

Ofodile, Okom Nkili F C

2007-12-01

Disifin has emerged as a unique and very effective agent used in disinfection of wounds, disinfection of surfaces, materials and water, and other substances contaminated with almost every type of pathogenic microorganism ranging from viruses, bacteria, fungi and yeast, and, very possibly, protozoan parasites, as well. The major active component of Disifin is tosylchloramide sodium (chloramine T). However, the mechanism by which Disifin suppresses the activities of pathogenic microbial agents remains enigmatic. The molecular mechanisms, and the receptors and the signal transducing pathways responsible for the biological effects of Disifin are largely unknown. Despite considerable advances, enormous investigative efforts and large resources invested in the research on infectious diseases, microbial infection still remains a public health problem in many parts of the world. The exact nature of the pathogenic agents responsible for many infectious diseases, and the nature of the receptors mediating the associated inflammatory events are incompletely understood. Recent advances in understanding the molecular basis for mammalian host immune responses to microbial invasion suggest that the first line of defense against microbes is the recognition of pathogen-associated molecular patterns (PAMPs) by a family of transmembrane pattern-recognizing and signal transducing receptor proteins called Toll-like receptors (TLRs). The TLR family plays an instructive role in innate immune responses against microbial pathogens, as well as the subsequent induction of adaptive immune responses. TLRs mediate recognition and inflammatory responses to a wide range of microbial products and are crucial for effective host defense by eradication of the invading pathogens. Now, recent updates demonstrated the ability of Disifin-derived products, Disifin-Animal and Disifin-Pressant to effectively suppress the progression and activities of Chikungunya fever and that of avian influenza A virus [A/cardialis/Germany/72, H7N1: the agent of a highly pathogenic avian influenza (HPAI)] infection, respectively. Overall, the above findings led me to suggest that Disifin and TLRs may mechanistically overlap in the processes of executing their functions against pathogenic microbial organisms. Thus, elucidating and better understanding of the molecular underpinnings responsible for the biochemical effects of Disifin-products, and the nature and mode of the interaction(s) of Disifin with TLRs in the process of exerting their biological effects may open a novel dimension in the research of infectious diseases, which may provide novel therapeutic targets for the prevention and treatment of a wide range of infectious diseases.

Different Mechanisms of Soil Microbial Response to Global Change Result in Different Outcomes in the MIMICS-CN Model

NASA Astrophysics Data System (ADS)

Kyker-Snowman, E.; Wieder, W. R.; Grandy, S.

2017-12-01

Microbial-explicit models of soil carbon (C) and nitrogen (N) cycling have improved upon simulations of C and N stocks and flows at site-to-global scales relative to traditional first-order linear models. However, the response of microbial-explicit soil models to global change factors depends upon which parameters and processes in a model are altered by those factors. We used the MIcrobial-MIneral Carbon Stabilization Model with coupled N cycling (MIMICS-CN) to compare modeled responses to changes in temperature and plant inputs at two previously-modeled sites (Harvard Forest and Kellogg Biological Station). We spun the model up to equilibrium, applied each perturbation, and evaluated 15 years of post-perturbation C and N pools and fluxes. To model the effect of increasing temperatures, we independently examined the impact of decreasing microbial C use efficiency (CUE), increasing the rate of microbial turnover, and increasing Michaelis-Menten kinetic rates of litter decomposition, plus several combinations of the three. For plant inputs, we ran simulations with stepwise increases in metabolic litter, structural litter, whole litter (structural and metabolic), or labile soil C. The cumulative change in soil C or N varied in both sign and magnitude across simulations. For example, increasing kinetic rates of litter decomposition resulted in net releases of both C and N from soil pools, while decreasing CUE produced short-term increases in respiration but long-term accumulation of C in litter pools and shifts in soil C:N as microbial demand for C increased and biomass declined. Given that soil N cycling constrains the response of plant productivity to global change and that soils generate a large amount of uncertainty in current earth system models, microbial-explicit models are a critical opportunity to advance the modeled representation of soils. However, microbial-explicit models must be improved by experiments to isolate the physiological and stoichiometric parameters of soil microbes that shift under global change.

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

The Microbiome Structure of Oklahoma Cropland and Prairie Soils and its Response to Seasonal Forcing and Management Practices

NASA Astrophysics Data System (ADS)

Cornell, C. R.; Peterson, B.; Zhou, J.; Xiao, X.; Wawrik, B.

2017-12-01

Greenhouse gases (GHG) emissions from soils are primarily the consequence of microbial processes. Agricultural management of soils is known to affect the structure of microbial communities, and it is likely that dominant GHG emitting microbial activities are impacted via requisite practices. To gain better insight into the impact of seasonal forcing and management practices on the microbiome structure in Oklahoma agricultural soils, a seasonal study was conducted. Over a year period, samples were collected bi-weekly during wet months, and monthly during dry months from two grassland and two managed agricultural sites in El Reno, Oklahoma. Microbial community structure was determined in quadruplicate for each site and time point via 16S rRNA gene sequencing. Measures of soil water content, subsoil nitrate, ammonium, organic matter, total nitrogen, and biomass were also taken for each time point. Data analysis revealed several important trends, indicating greater microbial diversity in native grassland and distinct microbial community changes in response to management practices. The native grassland soils also contained greater microbial biomass than managed soils and both varied in response to rainfall events. Native grassland soils harbor more diverse microbial communities, with the diversity and biomass decreasing along a gradient of agricultural management intensity. These data indicate that microbial community structure in El Reno soils occurs along a continuum in which native grasslands and highly managed agricultural soils (tilling and manure application) form end members. Integration with measurements from eddy flux towers into modelling efforts using the DeNitrification-DeComposition (DNDC) model is currently being explored to improve predictions of GHG emissions from grassland soils.

Disentangling the drivers of soil organic matter decay as temperature changes by integrating reductionist systems with soil data

NASA Astrophysics Data System (ADS)

Billings, Sharon; Ballantyne, Ford, IV; Min, Kyungjin; Lehmeier, Christoph; Ziegler, Susan

2014-05-01

Accurately predicting decomposition rates of soil organic matter (SOM) as temperature increases is critical for projecting future atmospheric [CO2]. SOM decay is catalyzed by exo-enzymes (EEs) produced by microorganisms and secreted into the soil. Microbes take up liberated resources for metabolic processes and release diverse compounds, including CO2. Historically, investigations of the influence of temperature on heterotrophic CO2 release have focused on CO2 response, including its isotopic composition; recent studies also assess EE activity and microbial community composition. However, it is difficult to generalize from such studies how temperature will influence SOM decay and CO2 release because the responses of EEs, microbial resource demand, biomass production rates, and respiration rates are not parsed. Quantifying the individual temperature responses of all of these processes in unaltered soil is not tractable. However, we can use experimentally simplified systems to quantify fundamental biochemical and physiological responses to temperature and compare these results to those from environmental samples. For example, we can quantify the degree to which EE kinetics in isolation induce changes in availability of microbially assimilable resources as temperature changes and calculate associated changes in relative availability of assimilable carbon and nitrogen (C:N flow ratio), in isolation from altered microbial resource demand or uptake. We also can assess EE activity and CO2 release at different temperatures in diverse soils, integrating temperature responses of EE kinetics and microbial communities. Discrepancies in the temperature responses between real soils and isolated enzyme-substrate reactions can reveal how adaptive responses of microbial communities influence the temperature responses of soil heterotrophic CO2 release. We have shown in purified reactions that C:N flow ratios increase with temperature at pH 4.5, but decline between pH 6.5 and 8.5. If soil microbes exhibited no change in resource demand or C allocation with altered C:N flow ratios and if relative C availability was tightly coupled to respiration, we would expect variation in C:N flow ratios predicted by purified solutions to be expressed in analogous, relative patterns of C mineralization. However, the positive response of heterotrophic CO2 release to similar temperature increases in five strongly acidic forest soils (three boreal, one cool temperate, and one warm temperate) was much smaller than in a neutral-pH grassland or an alkaline desert, the opposite of what we might predict if C:N flow ratio was the only driver of respiratory responses to temperature. We also observe distinct d13C of CO2 respired from pure cultures in which substrate composition and availability are strictly controlled as temperature changes, reflecting fundamental shifts in C flux through metabolic pathways. These changes in d13C-CO2 with warming are greater than those observed in soils. Combined, these CO2 and d13C-CO2 data suggest that soil microbial adaptation to temperature is a meaningful driver of heterotrophic respiratory responses to temperature. We highlight the utility of reductionist experimental systems for characterizing fundamental SOM decay rates and changes in microbial C metabolism at different temperatures, and integrating them with analogous data derived from soils to quantify the role of microbial adaptation as a driver of SOM decay.

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

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

Myrold, David D.; Bottomely, Peter J.; Jumpponen, Ari

2014-09-17

Soils process and store large amounts of C; however, considerable uncertainty still exists about the details of that influence microbial partitioning of C into soil C pools, and what are the main influential forces that control the fraction of the C input that is stabilized. The soil microbial community is genotypically and phenotypically diverse. Despite our ability to predict the kinds of regional environmental changes that will accompany global climate change, it is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C depositedmore » into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts genotypically and physiologically to changes in soil moisture brought about by shifts in precipitation. Our overarching goal is to harness the power of multiple meta-omics tools to gain greater understanding of the functioning of whole-soil microbial communities and their role in C cycling. We will do this by meeting the following three objectives: 1. Further develop and optimize a combination of meta-omics approaches to study how environmental factors affect microbially-mediated C cycling processes. 2. Determine the impacts of long-term changes in precipitation timing on microbial C cycling using an existing long-term field manipulation of a tallgrass prairie soil. 3. Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes. We took advantage of our state-of-the-art expertise in community “omics” to better understand the functioning soil C cycling within the Great Prairie ecosystem, including our ongoing Konza Prairie soil metagenome flagship project at JGI and the unique rainfall manipulation plots (RaMPs) established at this site more than a decade ago. We employed a systems biology approach, considering the complex soil microbial community as a functioning system and using state-of-the-art metatranscriptomic, metaproteomic, and metabolomic approaches. These omics tools were refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments were designed to specifically identify microbial community members and processes that are instrumental players in processing of C in the prairie soils and how these processes are impacted by wetting and drying events. This project addresses a key ecosystem in the United States that current climate models predict will be subjected to dramatic changes in rainfall patterns as a result of global warming. Currently Mollisols, such as those of the tallgrass prairie, are thought to sequester more C than is released into the atmosphere, but it is not known what changes in rainfall patterns will have on future C fluxes. Through an analysis of the molecular response of the soil microbial community to shifts in precipitation cycles that are accompanied by phenologically driven changes in quality of plant C rhizodeposits, we gained deeper insight into how the metabolism of microbes has adapted to different precipitation regimes and the impact of this adaption on the fate of C deposited into soil. In doing so, we addressed key questions about the microbial cycling of C in soils that have been identified by the DOE.« less

Historical climate controls soil respiration responses to current soil moisture.

PubMed

Hawkes, Christine V; Waring, Bonnie G; Rocca, Jennifer D; Kivlin, Stephanie N

2017-06-13

Ecosystem carbon losses from soil microbial respiration are a key component of global carbon cycling, resulting in the transfer of 40-70 Pg carbon from soil to the atmosphere each year. Because these microbial processes can feed back to climate change, understanding respiration responses to environmental factors is necessary for improved projections. We focus on respiration responses to soil moisture, which remain unresolved in ecosystem models. A common assumption of large-scale models is that soil microorganisms respond to moisture in the same way, regardless of location or climate. Here, we show that soil respiration is constrained by historical climate. We find that historical rainfall controls both the moisture dependence and sensitivity of respiration. Moisture sensitivity, defined as the slope of respiration vs. moisture, increased fourfold across a 480-mm rainfall gradient, resulting in twofold greater carbon loss on average in historically wetter soils compared with historically drier soils. The respiration-moisture relationship was resistant to environmental change in field common gardens and field rainfall manipulations, supporting a persistent effect of historical climate on microbial respiration. Based on these results, predicting future carbon cycling with climate change will require an understanding of the spatial variation and temporal lags in microbial responses created by historical rainfall.

Microbial production of organic acids in aquitard sediments and its role in aquifer geochemistry

USGS Publications Warehouse

McMahon, P.B.; Chapelle, F.H.

1991-01-01

MICROBIAL activity in aquifers plays an important part in the chemical evolution of ground water1-5. The most important terminal electron-accepting microbial processes in deeply buried anaerobic aquifers are iron reduction, sulphate reduction and methanogenesis5-8, each of which requires simple organic compounds or hydrogen (H2) as electron donors. Until now, the source of these compounds was unknown because the concentrations of dissolved organic carbon and sedimentary organic carbon in aquifers are extremely low9-11. Here we show that rates of microbial fermentation exceed rates of respiration in organic-rich aquitards (low-permeability sediments stratigraphically adjacent to higher-permeability aquifer sediments), resulting in a net accumulation of simple organic acids in pore waters. In aquifers, however, respiration outpaces fermentation, resulting in a net consumption of organic acids. The concentration gradient that develops in response to these two processes drives a net diffusive flux of organic acids from aquitards to aquifers. Diffusion calculations demonstrate that rates of organic acid transport are sufficient to account for observed rates of microbial respiration in aquifers. This overall process effectively links the large pool of sedimentary organic carbon in aquitards to microbial respiration in aquifers, and is a principal mechanism driving groundwater chemistry changes in aquifers.

Functional microbial community response to nutrient pulses by artificial groundwater recharge practice in surface soils and subsoils.

PubMed

Schütz, Kirsten; Kandeler, Ellen; Nagel, Peter; Scheu, Stefan; Ruess, Liliane

2010-06-01

Subsurface microorganisms are essential constituents of the soil purification processes associated with groundwater quality. In particular, soil enzyme activity determines the biodegradation of organic compounds passing through the soil profile. Transects from surface soil to a depth of 3.5 m were investigated for microbial and chemical soil characteristics at two groundwater recharge sites and one control site. The functional diversity of the microbial community was analyzed via the activity of eight enzymes. Acid phosphomonoesterase was dominant across sites and depths, followed by L-leucine aminopeptidase and beta-glucosidase. Structural [e.g. phospholipid fatty acid (PLFA) pattern] and functional microbial diversities were linked to each other at the nonwatered site, whereas amendment with nutrients (DOC, NO(3)(-)) by flooding uncoupled this relationship. Microbial biomass did not differ between sites, whereas microbial respiration was the highest at the watered sites. Hence, excess nutrients available due to artificial groundwater recharge could not compensate for the limitation by others (e.g. phosphorus as assigned by acid phosphomonoesterase activity). Instead, at a similar microbial biomass, waste respiration via overflow metabolism occurred. In summary, ample supply of carbon by flooding led to a separation of decomposition and microbial growth, which may play an important role in regulating purification processes during groundwater recharge.

Seasonal variation in functional properties of microbial communities in beech forest soil

PubMed Central

Koranda, Marianne; Kaiser, Christina; Fuchslueger, Lucia; Kitzler, Barbara; Sessitsch, Angela; Zechmeister-Boltenstern, Sophie; Richter, Andreas

2013-01-01

Substrate quality and the availability of nutrients are major factors controlling microbial decomposition processes in soils. Seasonal alteration in resource availability, which is driven by plants via belowground C allocation, nutrient uptake and litter fall, also exerts effects on soil microbial community composition. Here we investigate if seasonal and experimentally induced changes in microbial community composition lead to alterations in functional properties of microbial communities and thus microbial processes. Beech forest soils characterized by three distinct microbial communities (winter and summer community, and summer community from a tree girdling plot, in which belowground carbon allocation was interrupted) were incubated with different 13C-labeled substrates with or without inorganic N supply and analyzed for substrate use and various microbial processes. Our results clearly demonstrate that the three investigated microbial communities differed in their functional response to addition of various substrates. The winter communities revealed a higher capacity for degradation of complex C substrates (cellulose, plant cell walls) than the summer communities, indicated by enhanced cellulase activities and reduced mineralization of soil organic matter. In contrast, utilization of labile C sources (glucose) was lower in winter than in summer, demonstrating that summer and winter community were adapted to the availability of different substrates. The saprotrophic community established in girdled plots exhibited a significantly higher utilization of complex C substrates than the more plant root associated community in control plots if additional nitrogen was provided. In this study we were able to demonstrate experimentally that variation in resource availability as well as seasonality in temperate forest soils cause a seasonal variation in functional properties of soil microorganisms, which is due to shifts in community structure and physiological adaptations of microbial communities to altered resource supply. PMID:23645937

Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.

PubMed

Pajares, Silvia; Bonilla-Rosso, German; Travisano, Michael; Eguiarte, Luis E; Souza, Valeria

2012-08-01

Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment.

Origin of microbial biomineralization and magnetotaxis during the Archean.

PubMed

Lin, Wei; Paterson, Greig A; Zhu, Qiyun; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A; Zhu, Rixiang; Kirschvink, Joseph L; Pan, Yongxin

2017-02-28

Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth's dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

Response of a salt marsh microbial community to metal contamination

NASA Astrophysics Data System (ADS)

Mucha, Ana P.; Teixeira, Catarina; Reis, Izabela; Magalhães, Catarina; Bordalo, Adriano A.; Almeida, C. Marisa R.

2013-09-01

Salt marshes are important sinks for contaminants, namely metals that tend to accumulate around plant roots and could eventually be taken up in a process known as phytoremediation. On the other hand, microbial communities display important roles in the salt marsh ecosystems, such as recycling of nutrients and/or degradation of organic contaminants. Thus, plants can benefit from the microbial activity in the phytoremediation process. Nevertheless, above certain levels, metals are known to be toxic to microorganisms, fact that can eventually compromise their ecological functions. In this vein, the aim of present study was to investigate, in the laboratory, the effect of selected metals (Cd, Cu and Pb) on the microbial communities associated to the roots of two salt marsh plants. Sediments colonized by Juncus maritimus and Phragmites australis were collected in the River Lima estuary (NW Portugal), and spiked with each of the metals at three different Effects Range-Median (ERM) concentrations (1, 10×, 50×), being ERM the sediment quality guideline that indicates the concentration above which adverse biological effects may frequently occur. Spiked sediments were incubated with a nutritive saline solution, being left in the dark under constant agitation for 7 days. The results showed that, despite the initial sediments colonized by J. maritimus and P. australis displayed significant (p < 0.05) differences in terms of microbial community structure (evaluated by ARISA), they presented similar microbial abundances (estimated by DAPI). Also, in terms of microbial abundance, both sediments showed a similar response to metal addition, with a decrease in number of cells only observed for the higher addition of Cu. Nevertheless, both Cu and Pb, at intermediate metals levels promote a shift in the microbial community structure, with possibly effect on the ecological function of these microbial communities in salt marshes. These changes may affect plants phytoremediation potential and further work on this subject is in need.

Developing and using artificial soils to analyze soil microbial processes

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Deep subsurface microbial processes

USGS Publications Warehouse

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of other habitats, the study of deep subsurface microbiology is still in its infancy.

Investigating the long-term legacy of drought and warming on the soil microbial community across five European shrubland ecosystems.

PubMed

Rousk, Johannes; Smith, Andrew R; Jones, Davey L

2013-12-01

We investigated how the legacy of warming and summer drought affected microbial communities in five different replicated long-term (>10 years) field experiments across Europe (EU-FP7 INCREASE infrastructure). To focus explicitly on legacy effects (i.e., indirect rather than direct effects of the environmental factors), we measured microbial variables under the same moisture and temperature in a brief screening, and following a pre-incubation at stable conditions. Specifically, we investigated the size and composition of the soil microbial community (PLFA) alongside measurements of bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth rates, previously shown to be highly responsive to changes in environmental factors, and microbial respiration. We found no legacy effects on the microbial community size, composition, growth rates, or basal respiration rates at the effect sizes used in our experimental setup (0.6 °C, about 30% precipitation reduction). Our findings support previous reports from single short-term ecosystem studies thereby providing a clear evidence base to allow long-term, broad-scale generalizations to be made. The implication of our study is that warming and summer drought will not result in legacy effects on the microbial community and their processes within the effect sizes here studied. While legacy effects on microbial processes during perturbation cycles, such as drying-rewetting, and on tolerance to drought and warming remain to be studied, our results suggest that any effects on overall ecosystem processes will be rather limited. Thus, the legacies of warming and drought should not be prioritized factors to consider when modeling contemporary rates of biogeochemical processes in soil. © 2013 John Wiley & Sons Ltd.

The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment.

PubMed

Bastida, F; Jehmlich, N; Lima, K; Morris, B E L; Richnow, H H; Hernández, T; von Bergen, M; García, C

2016-03-01

The linkage between phylogenetic and functional processes may provide profound insights into the effects of hydrocarbon contamination and biodegradation processes in high-diversity environments. Here, the impacts of petroleum contamination and the bioremediation potential of compost amendment, as enhancer of the microbial activity in semiarid soils, were evaluated in a model experiment. The analysis of phospholipid fatty-acids (PLFAs) and metaproteomics allowed the study of biomass, phylogenetic and physiological responses of the microbial community in polluted semiarid soils. Petroleum pollution induced an increase of proteobacterial proteins during the contamination, while the relative abundance of Rhizobiales lowered in comparison to the non-contaminated soil. Despite only 0.55% of the metaproteome of the compost-treated soil was involved in biodegradation processes, the addition of compost promoted the removal of polycyclic aromatic hydrocarbons (PAHs) and alkanes up to 88% after 50 days. However, natural biodegradation of hydrocarbons was not significant in soils without compost. Compost-assisted bioremediation was mainly driven by Sphingomonadales and uncultured bacteria that showed an increased abundance of catabolic enzymes such as catechol 2,3-dioxygenases, cis-dihydrodiol dehydrogenase and 2-hydroxymuconic semialdehyde. For the first time, metaproteomics revealed the functional and phylogenetic relationships of petroleum contamination in soil and the microbial key players involved in the compost-assisted bioremediation. Copyright © 2015 Elsevier B.V. All rights reserved.

Biochemical capacitance of Geobacter sulfurreducens biofilms.

PubMed

Bueno, Paulo R; Schrott, Germán D; Bonanni, Pablo S; Simison, Silvia N; Busalmen, Juan P

2015-08-10

An electrical model able to decouple the electron pathway from microbial cell machinery impedance terms is introduced. In this context, capacitance characteristics of the biofilm are clearly resolved. In other words, the model allows separating, according to the advantage of frequency and spectroscopic response approach, the different terms controlling the performance of the microbial biofilm respiratory process and thus the directly related electricity production process. The model can be accurately fitted to voltammetry measurements obtained under steady-state conditions and also to biofilm discharge amperometric measurements. The implications of biological aspects of the electrochemical or redox capacitance are discussed theoretically in the context of current knowledge with regard to structure and physiological activity of microbial Geobacter biofilms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Assessing stress responses to atmospheric cold plasma exposure using Escherichia coli knock-out mutants.

PubMed

Han, L; Boehm, D; Patil, S; Cullen, P J; Bourke, P

2016-08-01

This study investigated the effect of atmospheric cold plasma (ACP) exposure-induced stress on microbial inactivation patterns and the regulation of genes involved in the microbial stress response in conjunction with key processing parameters of exposure time and post-treatment storage time. Cell suspensions of Escherichia coli BW 25113 and its isogenic knock-out mutants in rpoS, soxR, soxS, oxyR and dnaK genes were treated with high-voltage ACP in a sealed package for 1, 3 and 5 min followed by 0-, 1- and 24-h post-treatment storage. Reactive oxygen species (ROS) densities and colony formation were determined. ΔrpoS strain showed higher microbial reduction and greater cell permeability than other mutants, while ΔoxyR only showed this effect after 5 min of treatment. With increased post-treatment storage time, ΔsoxS and ΔsoxR had increased sensitivity and resistance respectively. ΔdnaK cell suspensions had much higher ROS than other strains and showed increased sensitivity with 24 h post-treatment storage. RpoS and oxyR genes have both short-term and long-term regulatory effects under plasma stress. However, knocking out dnaK gene had an immediate response on ROS scavenging and long-term repairing mechanisms. ΔsoxR and ΔsoxS had different responses to ACP treatment with the increase in post-treatment time in relation to clearance of reactive species implying the different characteristics and functions as subunits. By comparing the response of mutants under ACP exposure to key processing parameters, the mechanism of microbial inactivation was partly revealed with respect to cellular regulation and repairing genes. © 2016 The Society for Applied Microbiology.

Stoichiometry constrains microbial response to root exudation - insights from a model and a field experiment in a temperate forest

NASA Astrophysics Data System (ADS)

Drake, J. E.; Darby, B. A.; Giasson, M.-A.; Kramer, M. A.; Phillips, R. P.; Finzi, A. C.

2012-06-01

Healthy plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exo-enzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The causal role of exudation, however, is difficult to isolate with in-situ observations, given the complex nature of the rhizosphere environment. We investigated the potential effects of root exudation on microbial and exo-enzyme activity using a theoretical model of decomposition and a field experiment, with a specific focus on the stoichiometric constraint of nitrogen (N) availability. The field experiment isolated the effect of exudation by pumping solutions of exudate mimics through microlysimeter "root simulators" into intact forest soils over two 50-day periods. Using a combined model-experiment approach, we tested two hypotheses: (1) exudation alone is sufficient to stimulate microbial and exo-enzyme activity in rhizosphere soils, and (2) microbial response to C-exudates (carbohydrates and organic acids) is constrained by N-limitation. Experimental delivery of exudate mimics containing C and N significantly increased microbial respiration, microbial biomass, and the activity of exo-enzymes that decompose labile components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exo-enzymes that degrade recalcitrant SOM (e.g., polyphenols, lignin). However, delivery of C-only exudates had no effect on microbial biomass or overall exo-enzyme activity, and only increased microbial respiration. The theoretical decomposition model produced complementary results; the modeled microbial response to C-only exudates was constrained by limited N supply to support the synthesis of N-rich microbial biomass and exo-enzymes, while exuding C and N together elicited an increase in modeled microbial biomass, exo-enzyme activity, and decomposition. Thus, hypothesis (2) was supported, while hypothesis (1) was only supported when C and N compounds were exuded together. This study supports a cause-and-effect relationship between root exudation and enhanced microbial activity, and suggests that exudate stoichiometry is an important and underappreciated driver of microbial activity in rhizosphere soils.

Microbial hotspots and hot moments in soil

NASA Astrophysics Data System (ADS)

Kuzyakov, Yakov; Blagodatskaya, Evgenia

2015-04-01

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

Microbial diversity and community structure across environmental gradients in an seawater intruded shallow confined aquifer

NASA Astrophysics Data System (ADS)

Zhang, X.; Hu, B.

2017-12-01

Seawater intrusion has been an important topic in coastal hydrogeology and making previously freshwater ecosystems saline. Plant and animal responses to variation in the freshwater-saline interface have been well studied in the coastal zone. However, little is known about the biogeography or stability of microbial community response to seawater intrusion. The objective of this study is to characterize and compare bacterial and archaea community diversity and composition in 15 groundwater samples with varied salinity using high-throughput-sequencing of 16S ribosomal RNA genes. The dominant taxonomic group identified in all samples are proteobacteria for bacteria and crenarchaeota for archaea. The other main bacterial groups are varied in samples with different salinities including bacteroidetes, firmicutes and several unidentified taxonomys. A combination of environmental factors seems to influence the microbial community composition where organic carbon is a primary factor shaping microbial communities. Correlation analysis between the relative abundance of bacterial taxa and geochemical parameters uggested that rare taxa may contribute to biogeochemical processes taking place at the mixing zone of freshewater and saltwater. Our results help to understand how the physical and chemical factors shape the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes and the efficacy of new remediation efforts.

Do microbial processes regulate the stability of a coral atoll's enclosed pelagic ecosystem?

EPA Science Inventory

Complex marine ecosystems contain multiple feedback cycles that can cause unexpected responses to perturbations. To better predict these responses, complicated models are increasingly being developed to enable the study of feedback cycles. However, the sparseness of ecological da...

Tracking composition of microbial communities for simultaneous nitrification and denitrification in polyurethane foam.

PubMed

Chen, Yuan; Wang, Li; Ma, Fang; Yang, Ji-xian; Qiu, Shan

2014-01-01

The process of simultaneous nitrification and denitrification (SND) of immobilized microorganisms in polyurethane form is discussed. The effect of different positions within the polyurethane carrier on microbial community response for the SND process is investigated by a combination of denaturing gradient gel electrophoresis profiles of the 16S rRNA gene V3 region and scanning electron microscopy. Results show that polyurethane, which consists of a unique porous structure, is an ideal platform for biofilm stratification of aerobe, anaerobe and facultative microorganisms in regard to the SND process. The community structure diversity response to different positions was distinct. The distributions of various functional microbes, detected from the surface aerobic stratification to the interior anaerobic stratification of polyurethane, were mainly nitrifying and denitrifying bacteria. Meanwhile aerobic denitrifying bacteria such as Paracoccus sp., Agrobacterium rubi and Ochrobactrum sp. were also adhered to the interior and surface of polyurethane. The SND process occurring on polyurethane foam was carried out by two independent processes: nitrogen removal and aerobic denitrification.

(A)biotic processes control soil carbon dynamics: quantitative assessment of model complexity, stability and response to perturbations for improving ESMs

NASA Astrophysics Data System (ADS)

Georgiou, K.; Abramoff, R. Z.; Harte, J.; Riley, W. J.; Torn, M. S.

2016-12-01

As global temperatures and atmospheric CO2 concentrations continue to increase, soil microbial activity and decomposition of soil organic matter (SOM) are expected to follow suit, potentially limiting soil carbon storage. Traditional global- and ecosystem-scale models simulate SOM decomposition using linear kinetics, which are inherently unable to reproduce carbon-concentration feedbacks, such as priming of native SOM at elevated CO2 concentrations. Recent studies using nonlinear microbial models of SOM decomposition seek to capture these interactions, and several groups are currently integrating these microbial models into Earth System Models (ESMs). However, despite their widespread ability to exhibit nonlinear responses, these models vary tremendously in complexity and, consequently, dynamics. In this study, we explore, both analytically and numerically, the emergent oscillatory behavior and insensitivity of SOM stocks to carbon inputs that have been deemed `unrealistic' in recent microbial models. We discuss the sources of instability in four models of varying complexity, by sequentially reducing complexity of a detailed model that includes microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We also present an alternative representation of microbial turnover that limits population sizes and, thus, reduces oscillations. We compare these models to several long-term carbon input manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that traditional linear and nonlinear models cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures, and that modifying microbial turnover results in more realistic predictions. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in ESMs.

Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Commercial Antimicrobials Using a Next Generation Sequencing Approach

PubMed Central

Ae Kim, Sun; Hong Park, Si; In Lee, Sang; Owens, Casey M.; Ricke, Steven C.

2017-01-01

The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence. Microbiome sequencing was utilized to identify microbial population changes over processing and antimicrobial treatments. Only the PAA treatment exhibited significant reduction of APC at the post chilling step while both Amplon and PAA yielded detectable Campylobacter reductions at all steps. Based on microbiome sequencing, Firmicutes were the predominant bacterial group at the phyla level with over 50% frequency in all steps while the relative abundance of Proteobacteria decreased as processing progressed. Overall microbiota between rinsate and APC plate microbial populations revealed generally similar patterns at the phyla level but they were different at the genus level. Both antimicrobials appeared to be effective on reducing problematic bacteria and microbiome can be utilized to identify optimal indicator microorganisms for enhancing product quality. PMID:28230180

Inactivation of Salmonella spp. in ground chicken using High Pressure Processing

USDA-ARS?s Scientific Manuscript database

High pressure processing (HPP) is a safe and effective process for improving the microbial safety and shelf-life of foods. Salmonella is a common contaminant in poultry meat and is frequently responsible for foodborne illness associated with contaminated poultry meat. In this study the inactivation...

New directions in coral reef microbial ecology.

PubMed

Garren, Melissa; Azam, Farooq

2012-04-01

Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem.

PubMed

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-03-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem

PubMed Central

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-01-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models. PMID:26925871

Colloidal Nanomolybdenum Influence upon the Antioxidative Reaction of Chickpea Plants ( Cicer arietinum L.)

NASA Astrophysics Data System (ADS)

Taran, Nataliya; Batsmanova, Ludmila; Kosyk, Oksana; Smirnov, Oleksandr; Kovalenko, Mariia; Honchar, Liubov; Okanenko, Alexander

2016-10-01

The use of colloidal solutions of metals as micronutrients enhances plant resistance to unfavorable environmental conditions and ensures high yields of food crops. The purpose of the study was a comparative evaluation of presowing treatment with nanomolybdenum and microbiological preparation impact upon the development of adaptive responses in chickpea plants. Oxidative processes did not develop in all variants of the experiment but in variants treated with microbial preparation, and joint action of microbial and nanopreparations even declined, as evidenced by the reduction of thiobarbituric acid reactive substances in photosynthetic tissues by 15 %. The activity of superoxide dismutase increased (by 15 %) in variant "nanomolybdenum" and joint action "microbial + nanomolybdenum," but it decreased by 20 % in variants with microbial preparation treatment. The same dependence was observed in changes of catalase activity. Antioxidant status factor, which takes into account the ratio of antioxidant to pro-oxidant, was the highest in variants with joint action of microbial preparation and nanomolybdenum (0.7), the lowest in variants with microbial treatment only (0.1). Thus, the results show that the action of nanoparticles of molybdenum activated antioxidant enzymes and decreased oxidative processes, thus promoting adaptation of plants.

[Effects of plateau zokor disturbance and restoration years on soil nutrients and microbial functional diversity in alpine meadow].

PubMed

Hu, Lei; Ade, Lu-ji; Zi, Hong-biao; Wang, Chang-ting

2015-09-01

To explore the dynamic process of restoration succession in degraded alpine meadow that had been disturbed by plateau zokors in the eastern Tibetan Plateau, we examined soil nutrients and microbial functional diversity using conventional laboratory analysis and the Biolog-ECO microplate method. Our study showed that: 1) The zokors disturbance significantly reduced soil organic matter, total nitrogen, available nitrogen and phosphorus contents, but had no significant effects on soil total phosphorus and potassium contents; 2) Soil microbial carbon utilization efficiency, values of Shannon, Pielou and McIntosh indexes increased with alpine meadow restoration years; 3) Principal component analysis (PCA) showed that carbohydrates and amino acids were the main carbon sources for maintaining soil microbial community; 4) Redundancy analysis ( RDA) indicated that soil pH, soil organic matter, total nitrogen, available nitrogen, and total potassium were the main factors influencing the metabolic rate of soil microbial community and microbial functional diversity. In summary, variations in soil microbial functional diversity at different recovery stages reflected the microbial response to aboveground vegetation, soil microbial composition and soil nutrients.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

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

Graham, Emily B.; Crump, Alex R.; Resch, Charles T.

Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptualmore » model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.« less

Manganese biomining: A review.

PubMed

Das, A P; Sukla, L B; Pradhan, N; Nayak, S

2011-08-01

Biomining comprises of processing and extraction of metal from their ores and concentrates using microbial techniques. Currently this is used by the mining industry to extract copper, uranium and gold from low grade ores but not for low grade manganese ore in industrial scale. The study of microbial genomes, metabolites and regulatory pathways provide novel insights to the metabolism of bioleaching microorganisms and their synergistic action during bioleaching operations. This will promote understanding of the universal regulatory responses that the biomining microbial community uses to adapt to their changing environment leading to high metal recovery. Possibility exists of findings ways to imitate the entire process during industrial manganese biomining endeavor. This paper reviews the current status of manganese biomining research operations around the world, identifies factors that drive the selection of biomining as a processing technology, describes challenges in exploiting these innovations, and concludes with a discussion of Mn biomining's future. Copyright © 2011 Elsevier Ltd. All rights reserved.

In situ studies of microbial inactivation during high pressure processing

NASA Astrophysics Data System (ADS)

Maldonado, Jose Antonio; Schaffner, Donald W.; Cuitiño, Alberto M.; Karwe, Mukund V.

2016-01-01

High pressure processing (HPP) has been shown to reduce microbial concentration in foods. The mechanisms of microbial inactivation by HPP have been associated with damage to cell membranes. The real-time response of bacteria to HPP was measured to elucidate the mechanisms of inactivation, which can aid in designing more effective processes. Different pressure cycling conditions were used to expose Enterobacter aerogenes cells to HPP. Propidium iodide (PI) was used as a probe, which fluoresces after penetrating cells with damaged membranes and binding with nucleic acids. A HPP vessel with sapphire windows was used for measuring fluorescence in situ. Membrane damage was detected during pressurization and hold time, but not during depressurization. The drop in fluorescence was larger than expected after pressure cycles at higher pressure and longer times. This indicated possible reversible disassociation of ribosomes resulting in additional binding of PI to exposed RNA under pressure and its release after depressurization.

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

PubMed Central

Holden, Sandra R.; Treseder, Kathleen K.

2013-01-01

Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm) and biotic (insect, pathogen) disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7, 19.1, and 41.7% reductions in microbial biomass, respectively). In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics. PMID:23801985

Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples

NASA Astrophysics Data System (ADS)

Edgcomb, V. P.; Taylor, C.; Pachiadaki, M. G.; Honjo, S.; Engstrom, I.; Yakimov, M.

2016-07-01

Obtaining an accurate picture of microbial processes occurring in situ is essential for our understanding of marine biogeochemical cycles of global importance. Water samples are typically collected at depth and returned to the sea surface for processing and downstream experiments. Metatranscriptome analysis is one powerful approach for investigating metabolic activities of microorganisms in their habitat and which can be informative for determining responses of microbiota to disturbances such as the Deepwater Horizon oil spill. For studies of microbial processes occurring in the deep sea, however, sample handling, pressure, and other changes during sample recovery can subject microorganisms to physiological changes that alter the expression profile of labile messenger RNA. Here we report a comparison of gene expression profiles for whole microbial communities in a bathypelagic water column sample collected in the Eastern Mediterranean Sea using Niskin bottle sample collection and a new water column sampler for studies of marine microbial ecology, the Microbial Sampler - In Situ Incubation Device (MS-SID). For some taxa, gene expression profiles from samples collected and preserved in situ were significantly different from potentially more stressful Niskin sampling and preservation on deck. Some categories of transcribed genes also appear to be affected by sample handling more than others. This suggests that for future studies of marine microbial ecology, particularly targeting deep sea samples, an in situ sample collection and preservation approach should be considered.

Silage review: Using molecular approaches to define the microbial ecology of silage.

PubMed

McAllister, T A; Dunière, L; Drouin, P; Xu, S; Wang, Y; Munns, K; Zaheer, R

2018-05-01

Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media. Evidence suggested that many of the members of these microbial populations were viable but unculturable, resulting in classical studies underestimating the true microbial diversity associated with ensiling. Polymerase chain reaction-based techniques, including length heterogeneity PCR, terminal RFLP, denaturing gradient gel electrophoresis, and automated ribosomal intergenic spacer analysis, were the first molecular methods used to study silage microbial communities. Further advancements in whole comparative genomic, metagenomic, and metatranscriptomic sequencing have or are in the process of superseding these methods, enabling microbial communities during ensiling to be defined with a degree of detail that is impossible using classical microbiology. These methods have identified new microbial species in silage, as well as characterized shifts in microbial communities with forage type and composition, ensiling method, and in response to aerobic exposure. Strain- and species-specific primers have been used to track the persistence and contribution of silage inoculants to the ensiling process and the role of specific species of yeast and fungi in silage spoilage. Sampling and the methods used to isolate genetic materials for further molecular analysis can have a profound effect on results. Primer selection for PCR amplification and the presence of inhibitors can also lead to biases in the interpretation of sequence data. Bioinformatic analyses are reliant on the integrity and presence of sequence data within established databases and can be subject to low taxonomic resolution. Despite these limitations, advancements in molecular biology are poised to revolutionize our current understanding of the microbial ecology of silage. Published by FASS Inc. and Elsevier Inc. on behalf of the American Dairy Science Association®. All rights reserved.

Deriving site-specific soil clean-up values for metals and metalloids: Rationale for including protection of soil microbial processes

PubMed Central

Kuperman, Roman G; Siciliano, Steven D; Römbke, Jörg; Oorts, Koen

2014-01-01

Although it is widely recognized that microorganisms are essential for sustaining soil fertility, structure, nutrient cycling, groundwater purification, and other soil functions, soil microbial toxicity data were excluded from the derivation of Ecological Soil Screening Levels (Eco-SSL) in the United States. Among the reasons for such exclusion were claims that microbial toxicity tests were too difficult to interpret because of the high variability of microbial responses, uncertainty regarding the relevance of the various endpoints, and functional redundancy. Since the release of the first draft of the Eco-SSL Guidance document by the US Environmental Protection Agency in 2003, soil microbial toxicity testing and its use in ecological risk assessments have substantially improved. A wide range of standardized and nonstandardized methods became available for testing chemical toxicity to microbial functions in soil. Regulatory frameworks in the European Union and Australia have successfully incorporated microbial toxicity data into the derivation of soil threshold concentrations for ecological risk assessments. This article provides the 3-part rationale for including soil microbial processes in the development of soil clean-up values (SCVs): 1) presenting a brief overview of relevant test methods for assessing microbial functions in soil, 2) examining data sets for Cu, Ni, Zn, and Mo that incorporated soil microbial toxicity data into regulatory frameworks, and 3) offering recommendations on how to integrate the best available science into the method development for deriving site-specific SCVs that account for bioavailability of metals and metalloids in soil. Although the primary focus of this article is on the development of the approach for deriving SCVs for metals and metalloids in the United States, the recommendations provided in this article may also be applicable in other jurisdictions that aim at developing ecological soil threshold values for protection of microbial processes in contaminated soils. PMID:24376192

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

PubMed

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

2014-11-01

Understanding the responses of terrestrial ecosystems to global change remains a major challenge of ecological research. We exploited a natural elevation gradient in a northern hardwood forest to determine how reductions in snow accumulation, expected with climate change, directly affect dynamics of soil winter frost, and indirectly soil microbial biomass and activity during the growing season. Soils from lower elevation plots, which accumulated less snow and experienced more soil temperature variability during the winter (and likely more freeze/thaw events), had less extractable inorganic nitrogen (N), lower rates of microbial N production via potential net N mineralization and nitrification, and higher potential microbial respiration during the growing season. Potential nitrate production rates during the growing season were particularly sensitive to changes in winter snow pack accumulation and winter soil temperature variability, especially in spring. Effects of elevation and winter conditions on N transformation rates differed from those on potential microbial respiration, suggesting that N-related processes might respond differently to winter climate change in northern hardwood forests than C-related processes. © 2014 John Wiley & Sons Ltd.

Beyond the standard plate count: genomic views into microbial food ecology

USDA-ARS?s Scientific Manuscript database

Food spoilage is a complex process that involves multiple species with specific niches and metabolic processes; bacterial culturing techniques are the traditional methods for identifying the microbes responsible. These culture-dependent methods may be considered selective, targeting the isolation of...

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

Allison, Steven D.

The role of specific micro-organisms in the carbon cycle, and their responses to environmental change, are unknown in most ecosystems. This knowledge gap limits scientists’ ability to predict how important ecosystem processes, like soil carbon storage and loss, will change with climate and other environmental factors. The investigators addressed this knowledge gap by transplanting microbial communities from different environments into new environments and measuring the response of community composition and carbon cycling over time. Using state-of-the-art sequencing techniques, computational tools, and nanotechnology, the investigators showed that microbial communities on decomposing plant material shift dramatically with natural and experimentally-imposed drought. Microbialmore » communities also shifted in response to added nitrogen, but the effects were smaller. These changes had implications for carbon cycling, with lower rates of carbon loss under drought conditions, and changes in the efficiency of decomposition with nitrogen addition. Even when transplanted into the same conditions, microbial communities from different environments remained distinct in composition and functioning for up to one year. Changes in functioning were related to differences in enzyme gene content across different microbial groups. Computational approaches developed for this project allowed the conclusions to be tested more broadly in other ecosystems, and new computer models will facilitate the prediction of microbial traits and functioning across environments. The data and models resulting from this project benefit the public by improving the ability to predict how microbial communities and carbon cycling functions respond to climate change, nutrient enrichment, and other large-scale environmental changes.« less

Historical climate controls soil respiration responses to current soil moisture

PubMed Central

Waring, Bonnie G.; Rocca, Jennifer D.; Kivlin, Stephanie N.

2017-01-01

Ecosystem carbon losses from soil microbial respiration are a key component of global carbon cycling, resulting in the transfer of 40–70 Pg carbon from soil to the atmosphere each year. Because these microbial processes can feed back to climate change, understanding respiration responses to environmental factors is necessary for improved projections. We focus on respiration responses to soil moisture, which remain unresolved in ecosystem models. A common assumption of large-scale models is that soil microorganisms respond to moisture in the same way, regardless of location or climate. Here, we show that soil respiration is constrained by historical climate. We find that historical rainfall controls both the moisture dependence and sensitivity of respiration. Moisture sensitivity, defined as the slope of respiration vs. moisture, increased fourfold across a 480-mm rainfall gradient, resulting in twofold greater carbon loss on average in historically wetter soils compared with historically drier soils. The respiration–moisture relationship was resistant to environmental change in field common gardens and field rainfall manipulations, supporting a persistent effect of historical climate on microbial respiration. Based on these results, predicting future carbon cycling with climate change will require an understanding of the spatial variation and temporal lags in microbial responses created by historical rainfall. PMID:28559315

Optimization of microbial detoxification for an aquatic mercury-contaminated environment.

PubMed

Figueiredo, Neusa L; Canário, João; Serralheiro, Maria Luísa; Carvalho, Cristina

2017-01-01

Mercury (Hg) reduction performed by microorganisms is well recognized as a biological means for remediation of contaminated environment. Recently, studies demonstrated that Hg-resistant microorganisms of Tagus Estuary are involved in metal reduction processes. In the present study, aerobic microbial community isolated from a highly Hg-contaminated area of Tagus Estuary was used to determine the optimization of the reduction process in conditions such as the contaminated ecosystem. Factorial design methodology was employed to examine the influence of glucose, sulfate, iron, and chloride on Hg reduction. In the presence of several concentrations of these elements, microbial community reduced Hg in a range of 37-61% of the initial 0.1 mg/ml Hg 2+ levels. The response prediction through central composite design showed that the increase of sulfate concentration led to an optimal response in Hg reduction by microbial community, while the rise in chloride levels markedly decreased metal reduction. Iron may exert antagonistic effects depending upon the media composition. These results are useful in understanding the persistence of Hg contamination in Tagus Estuary after inactivation of critical industrial units, as well as data might also be beneficial for development of new bioremediation strategies either in Tagus Estuary and/or in other Hg-contaminated aquatic environments.

Functional ecology of an Antarctic Dry Valley

PubMed Central

Chan, Yuki; Van Nostrand, Joy D.; Zhou, Jizhong; Pointing, Stephen B.

2013-01-01

The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution. PMID:23671121

Functional ecology of an Antarctic Dry Valley.

PubMed

Chan, Yuki; Van Nostrand, Joy D; Zhou, Jizhong; Pointing, Stephen B; Farrell, Roberta L

2013-05-28

The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution.

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.

The transcriptional response of microbial communities in thawing Alaskan permafrost soils.

PubMed

Coolen, Marco J L; Orsi, William D

2015-01-01

Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw.

The transcriptional response of microbial communities in thawing Alaskan permafrost soils

PubMed Central

Coolen, Marco J. L.; Orsi, William D.

2015-01-01

Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw. PMID:25852660

Final Technical Report to DOE for the Award DE-SC0004601

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

Zhou, Jizhong

Understanding the responses, adaptations and feedback mechanisms of biological communities to climate change is critical to project future state of earth and climate systems. Although significant amount of knowledge is available on the feedback responses of aboveground communities to climate change, little is known about the responses of belowground microbial communities due to the challenges in analyzing soil microbial community structure. Thus the goal overall goal of this study is to provide system-level, predictive mechanistic understanding of the temperature sensitivity of soil carbon (C) decomposition to climate warming by using cutting-edge integrated metagenomic technologies. Towards this goal, the following fourmore » objectives will be pursued: (i) To determine phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems; (ii) To delineate the responses of microbial community structure, functions and activities to climate change in the temperate grassland and tundra ecosystems; (iii) To determine the temperature sensitivity of microbial respiration in soils with different mixtures of labile versus recalcitrant C, and the underlying microbiological basis for temperature sensitivity of these pools; and (iv) To synthesize all experimental data for revealing microbial control of ecosystem carbon processes in responses to climate change. We have achieved our goals for all four proposed objectives. First, we determined the phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems. For this objective, we have developed a novel phasing amplicon sequencing (PAS) approach for MiSeq sequencing of amplicons. This approach has been used for sequencing various phylogenetic and functional genes related to ecosystem functioning. A comprehensive functional gene array (e.g., GeoChip 5.0) has also been developed and used for soil microbial community analysis in this study. In addition, shot-gun metagenome sequencing along with the above approaches have been used to understand the phylogenetic and functional diversity, composition, and structure of soil microbial communities in both temperature grassland and tundra ecosystems. Second, we determined the response of soil microbial communities to climate warming in both temperate grassland and tundra ecosystems using various methods. Our major findings are: (i) Microorganisms are very rapid to respond to climate warming in the tundra ecosystem, AK, which is vulnerable, too. (ii) Climate warming also significantly shifted the metabolic diversity, composition and structure of microbial communities, and key metabolic pathways related to carbon turnover, such as cellulose degradation (~13%) and CO2 production (~10%), and to nitrogen cycling, including denitrification (~12%) were enriched by warming. (iii) Warming also altered the expression patterns of microbial functional genes important to ecosystem functioning and stability through GeoChip and metatranscriptomic analysis of soil microbial communities at the OK site. Third, we analyzed temperature sensitivity of C decomposition to climate warming for both AK and OK soils through laboratory incubations. Key results include: (i) Alaska tundra soils showed that after one year of incubation, CT in the top 15 cm could be as high as 25% and 15% of the initial soil C content at 25°C and 15°C incubations, respectively. (ii) analysis of 456 incubated soil samples with 16S rRNA gene, ITS and GeoChip hybridization showed that warming shifted the phylogenretic and functional diversity, composition, structure and metabolic potential of soil microbial communities, and at different stages of incubation, key populations and functional genes significantly changed along with soil substrate changes. Functional gene diversity and functional genes for degrading labile C components decrease along incubation when labile C components are exhausting, but the genes related to degrading recalcitrant C increase. These molecular data will be directly used for modeling. Fourth, we have developed novel approaches to integrate and model experimental data to understand microbial control of ecosystem C processes in response to climate change. We compared different methods to calculate Q10 for estimating temperature sensitivity, and new approaches for Q10 calculation and molecular ecological network analysis were also developed. Using those newly developed approaches, our result indicated that Q10s increased with the recalcitrance of C pools, suggesting that longer incubation studies are needed in order to assess the temperature sensitivity of slower C pools, especially at low temperature regimes. This project has been very productive, resulting in 42 papers published or in press, 4 submitted, and 13 in preparation.« less

Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

PubMed Central

Guo, Xue; Zhou, Xishu; Hale, Lauren; Yuan, Mengting; Feng, Jiajie; Ning, Daliang; Shi, Zhou; Qin, Yujia; Liu, Feifei; Wu, Liyou; He, Zhili; Van Nostrand, Joy D.; Liu, Xueduan; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong

2018-01-01

Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010–2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices. PMID:29904372

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

PubMed

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

2017-08-01

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

Investigation of extractive microbial transformation in nonionic surfactant micelle aqueous solution using response surface methodology.

PubMed

Xue, Yingying; Qian, Chen; Wang, Zhilong; Xu, Jian-He; Yang, Rude; Qi, Hanshi

2010-01-01

Extractive microbial transformation of L-phenylacetylcarbinol (L-PAC) in nonionic surfactant Triton X-100 micelle aqueous solution was investigated by response surface methodology. Based on the Box-Behnken design, a mathematical model was developed for the predication of mutual interactions between benzaldehyde, Triton X-100, and glucose on L-PAC production. It indicated that the negative or positive effect of nonionic surfactant strongly depended on the substrate concentration. The model predicted that the optimal concentration of benzaldehyde, Triton X-100, and glucose was 1.2 ml, 15 g, and 2.76 g per 100 ml, respectively. Under the optimal condition, the maximum L-PAC production was 27.6 mM, which was verified by a time course of extractive microbial transformation. A discrete fed-batch process for verification of cell activity was also presented.

Detergent assisted lipid extraction from wet yeast biomass for biodiesel: A response surface methodology approach.

PubMed

Yellapu, Sravan Kumar; Bezawada, Jyothi; Kaur, Rajwinder; Kuttiraja, Mathiazhakan; Tyagi, Rajeshwar D

2016-10-01

The lipid extraction from the microbial biomass is a tedious and high cost dependent process. In the present study, detergent assisted lipids extraction from the culture of the yeast Yarrowia lipolytica SKY-7 was carried out. Response surface methodology (RSM) was used to investigate the effect of three principle parameters (N-LS concentration, time and temperature) on microbial lipid extraction efficiency % (w/w). The results obtained by statistical analysis showed that the quadratic model fits in all cases. Maximum lipid recovery of 95.3±0.3% w/w was obtained at the optimum level of process variables [N-LS concentration 24.42mg (equal to 48mgN-LS/g dry biomass), treatment time 8.8min and reaction temperature 30.2°C]. Whereas the conventional chloroform and methanol extraction to achieve total lipid recovery required 12h at 60°C. The study confirmed that oleaginous yeast biomass treatment with N-lauroyl sarcosine would be a promising approach for industrial scale microbial lipid recovery. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Towards a predictive understanding of belowground process responses to climate change: have we moved any closer?

Treesearch

Elise Pendall; Lindsey Rustad; Josh Schimel

2008-01-01

Belowground processes, including root production and exudation, microbial activity and community dynamics, and biogeochemical cycling interact to help regulate climate change. Feedbacks associated with these processes, such as warming-enhanced decomposition rates, give rise to major uncertainties in predictions of future climate. Uncertainties associated with these...

[Improving industrial microbial stress resistance by metabolic engineering: a review].

PubMed

Fu, Ruiyan; Li, Yin

2010-09-01

Metabolic engineering is a technologic platform for industrial strain improvement and aims not only at modifying microbial metabolic fluxes, but also improving the physiological performance of industrial microbes. Microbes will meet multiple stresses in industrial processes. Consequently, elicited gene responses might result in a decrease in overall cell fitness and the efficiency of biotransformation. Thus, it is crucial to develop robust and productive microbial strains that can be integrated into industrial-scale bioprocesses. In this review, we focus on the progress of these novel methods and strategies for engineering stress-tolerance phenotypes referring to rational metabolic engineering and inverse metabolic engineering in recent years. In addition, we also address problems existing in this area and future research needs of microbial physiological functionality engineering.

Pan-Arctic patterns of planktonic heterotrophic microbial abundance and processes: Controlling factors and potential impacts of warming

NASA Astrophysics Data System (ADS)

Maranger, Roxane; Vaqué, Dolors; Nguyen, Dan; Hébert, Marie-Pier; Lara, Elena

2015-12-01

The Arctic Ocean is rapidly changing where increasing water temperatures and rapid loss of summer sea-ice will likely influence the structure and functioning of the entire ecosystem. The aim of this study was to synthesize the current state of knowledge on microbial abundances and processes from a regional Pan-Arctic perspective, characterize regulating factors and attempt to predict how patterns may change under a warming scenario. Here we identify some generalized patterns of different microbial variables between the Pacific-fed and the Atlantic-fed sectors of the Arctic Ocean. Bacterial production (BP), abundance and grazing rates by protists (GT) were all higher in the Atlantic-fed region. Bacterial loss by viral lyses (VL) was proportionally more important in the Pacific-fed sector, suggesting a reduced C transfer efficiency within the microbial loop of that region. Using a cross-comparative approach and all available data to build Arrhenius plots, we found a differential response to warming temperatures among various microbial processes. BP and GT responded similarly and more strongly to increases in temperature than VL did, suggesting a shift in the overall influence of viral mortality under a warming scenario. However, together with temperature, resource-related factors also exerted an influence in regulating these rates. We identified large information gaps for more classically studied microbial variable from several Arctic seas. Furthermore, there is limited information on less conventional pathways such as grazing by mixotrophic species, which may be playing a significant role in Arctic microbial trophodynamics. Although generalized patterns could be elucidated, more information is needed to predict and understand how a changing Arctic will alter microbial C pathways and major biogeochemical cycles on regional and seasonal scales.

Data-Driven Microbial Modeling for Soil Carbon Decomposition and Stabilization

NASA Astrophysics Data System (ADS)

Luo, Yiqi; Chen, Ji; Chen, Yizhao; Feng, Wenting

2017-04-01

Microorganisms have long been known to catalyze almost all the soil organic carbon (SOC) transformation processes (e.g., decomposition, stabilization, and mineralization). Representing microbial processes in Earth system models (ESMs) has the potential to improve projections of SOC dynamics. We have recently examined (1) relationships of microbial functions with environmental factors and (2) microbial regulations of decomposition and other key soil processes. According to three lines of evidence, we have developed a data-driven enzyme (DENZY) model to simulate soil microbial decomposition and stabilization. First, our meta-analysis of 64 published field studies showed that field experimental warming significantly increased soil microbial communities abundance, which is negatively correlated with the mean annual temperature. The negative correlation indicates that warming had stronger effects in colder than warmer regions. Second, we found that the SOC decomposition, especially the transfer between labile SOC and protected SOC, is nonlinearly regulated by soil texture parameters, such as sand and silt contents. Third, we conducted a global analysis of the C-degrading enzyme activities, soil respiration, and SOC content under N addition. Our results show that N addition has contrasting effects on cellulase (hydrolytic C-degrading enzymes) and ligninase (oxidative C-degrading enzymes) activities. N-enhanced cellulase activity contributes to the minor stimulation of soil respiration whereas N-induced repression on ligninase activity drives soil C sequestration. Our analysis links the microbial extracellular C-degrading enzymes to the SOC dynamics at ecosystem scales across scores of experimental sites around the world. It offers direct evidence that N-induced changes in microbial community and physiology play fundamental roles in controlling the soil C cycle. Built upon those three lines of empirical evidence, the DENZY model includes two enzyme pools and explicitly characterizes two classes of extracellular enzyme activities: one that degrades organic molecules containing both C and N (e.g., chitin or protein) and another that degrades only C (e.g., cellulose). The DENZY model assumes that the microbes allocate resources to different enzyme pools so as to exactly satisfy microbial CN ratio stoichiometry in response to changes in climate conditions and soil attributes. The DENZY model can simulate differential effects of nitrogen fertilization on the two groups of enzymes and thus soil respiration and SOC dynamics. We will select field experimental sites to test the DENZY model. With increasing amounts of available observations and data synthesis, this DENZY model will be better parameterized and have a potential to reveal how responses of microbial enzymes to environmental changes regulate soil carbon decomposition and stabilization.

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.

The implications of microbial and substrate limitation for the fates of carbon in different organic soil horizon types of boreal forest ecosystems: a mechanistically based model analysis

USGS Publications Warehouse

He, Y.; Zhuang, Q.; Harden, Jennifer W.; McGuire, A. David; Fan, Z.; Liu, Y.; Wickland, Kimberly P.

2014-01-01

The large amount of soil carbon in boreal forest ecosystems has the potential to influence the climate system if released in large quantities in response to warming. Thus, there is a need to better understand and represent the environmental sensitivity of soil carbon decomposition. Most soil carbon decomposition models rely on empirical relationships omitting key biogeochemical mechanisms and their response to climate change is highly uncertain. In this study, we developed a multi-layer microbial explicit soil decomposition model framework for boreal forest ecosystems. A thorough sensitivity analysis was conducted to identify dominating biogeochemical processes and to highlight structural limitations. Our results indicate that substrate availability (limited by soil water diffusion and substrate quality) is likely to be a major constraint on soil decomposition in the fibrous horizon (40–60% of soil organic carbon (SOC) pool size variation), while energy limited microbial activity in the amorphous horizon exerts a predominant control on soil decomposition (>70% of SOC pool size variation). Elevated temperature alleviated the energy constraint of microbial activity most notably in amorphous soils, whereas moisture only exhibited a marginal effect on dissolved substrate supply and microbial activity. Our study highlights the different decomposition properties and underlying mechanisms of soil dynamics between fibrous and amorphous soil horizons. Soil decomposition models should consider explicitly representing different boreal soil horizons and soil–microbial interactions to better characterize biogeochemical processes in boreal forest ecosystems. A more comprehensive representation of critical biogeochemical mechanisms of soil moisture effects may be required to improve the performance of the soil model we analyzed in this study.

Effects of phosphorus and nitrogen additions on tropical soil microbial activity in the context of experimental warming

NASA Astrophysics Data System (ADS)

Foley, M.; Nottingham, A.; Turner, B. L.

2017-12-01

Soil warming is generally predicted to increase microbial mineralization rates and accelerate soil C losses which could establish a positive feedback to climatic warming. Tropical rain forests account for a third of global soil C, yet the responseto of tropical soil C a warming climate remains poorly understood. Despite predictions of soil C losses, decomposition of soil organic matter (SOM) in tropical soils may be constrained by several factors including microbial nutrient deficiencies. We performed an incubation experiment in conjunction with an in-situ soil warming experiment in a lowland tropical forest on Barro Colorado Island, Panama, to measure microbial response to two key nutrient additions in shallow (0-10cm) and deep (50-100 cm) soils. We compared the response of lowland tropical soils to montane tropical soils, predicting that lowland soils would display the strongest response to phosphorus additions. Soils were treated with either carbon alone (C), nitrogen (CN), phosphorus (CP) or nitrogen and phosphorus combined (CNP). Carbon dioxide (CO2) production was measured by NaOH capture and titrimetric analysis for 10 days. Cumulative CO2 production in montane soils increased significantly with all additions, suggesting these soils are characterized by a general microbial nutrient deficiency. The cumulative amount of C respired in deep soils from the lowland site increased significantly with CP and CNP additions, suggesting that microbial processes in deep lowland tropical soils are phosphorus-limited. These results support the current understanding that lowland tropical forests are growing on highly weathered, phosphorus-deplete soils, and provide novel insight that deep tropical SOM may be stabilized by a lack of biologically-available phosphorus. Further, this data suggests tropical soil C losses under elevated temperature may be limited by a strong microbial phosphorus deficiency.

Spatial and temporal dynamics of microbial communities in a human-perturbed estuary of China

NASA Astrophysics Data System (ADS)

Hu, A.; Yu, C. P.; Hou, L.

2015-12-01

Estuaries are responsible for the transport and transformation of nutrients and organic matters from the continent to the adjacent coastal zone, and therefore play critical roles in global biogeochemical cycles. They are under increasing stress from human activities, especially in China, yet we still know little about the responses of microbial communities that mediate biogeochemical processes. Here, we investigated planktonic and benthic microbial communities in the human-perturbed Jiulong River estuary (JRE), southern China by using Illumina 16S ribosomal RNA amplicon sequencing. The results of taxonomic assignments indicated that Beta- (23.32%), Alpha- (22.21%), Gammaproteobacteria (14.83%), Actinobacteria (8.67%), and Flavobacteria (7.56%) were the five most abundant classes in estuarine surface waters, while benthic microbial communities were dominated by Gamma- (20.09%), Delta- (14.68%), Beta- (9.82%), Alphaproteobacteria (7.63%), and Anaerolineae (7.25%). The results of Adnois and ANOSIM tests confirmed that the compositions of microbial communities from waters and sediments of the JRE were significantly different from each other, and then salinity may be the primary factor controlling spatial distributions of planktonic and benthic microbial communities in this estuary. At the temporal scale, planktonic communities showed a more clear variation pattern. Remarkably, the ratios of Thaumarchaeota (putative ammonia-oxidizing archaea) to Nitrosomonadales (ammonia-oxidizing bacteria) either in water or sediments of the JRE increased from freshwater to marine end, suggesting that bacterial and archaeal nitrifiers occupy low-salinity and high-salinity niches, respectively. The nutrient concentrations and salinity might be the most important factors which are responsible for this niche diversification. Overall, this study shed light on our understanding of the biogeographic patterns and its ecological drivers of estuarine microbial communities.

Plant diversity does not buffer drought effects on early-stage litter mass loss rates and microbial properties.

PubMed

Vogel, Anja; Eisenhauer, Nico; Weigelt, Alexandra; Scherer-Lorenzen, Michael

2013-09-01

Human activities are decreasing biodiversity and changing the climate worldwide. Both global change drivers have been shown to affect ecosystem functioning, but they may also act in concert in a non-additive way. We studied early-stage litter mass loss rates and soil microbial properties (basal respiration and microbial biomass) during the summer season in response to plant species richness and summer drought in a large grassland biodiversity experiment, the Jena Experiment, Germany. In line with our expectations, decreasing plant diversity and summer drought decreased litter mass loss rates and soil microbial properties. In contrast to our hypotheses, however, this was only true for mass loss of standard litter (wheat straw) used in all plots, and not for plant community-specific litter mass loss. We found no interactive effects between global change drivers, that is, drought reduced litter mass loss rates and soil microbial properties irrespective of plant diversity. High mass loss rates of plant community-specific litter and low responsiveness to drought relative to the standard litter indicate that soil microbial communities were adapted to decomposing community-specific plant litter material including lower susceptibility to dry conditions during summer months. Moreover, higher microbial enzymatic diversity at high plant diversity may have caused elevated mass loss of standard litter. Our results indicate that plant diversity loss and summer drought independently impede soil processes. However, soil decomposer communities may be highly adapted to decomposing plant community-specific litter material, even in situations of environmental stress. Results of standard litter mass loss moreover suggest that decomposer communities under diverse plant communities are able to cope with a greater variety of plant inputs possibly making them less responsive to biotic changes. © 2013 John Wiley & Sons Ltd.

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.

Predicting effects of climate change on the composition and function of soil microbial communities

NASA Astrophysics Data System (ADS)

Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

2008-12-01

Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences of these predictable changes in community composition were measured with functional arrays that detect genes involved in the metabolism of carbon, nitrogen and other elements. The response of soil microbial communities to altered precipitation can be predicted from the distribution of microbial taxa across moisture gradients.

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 Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

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

Methe, Barbara; Lipton, Mary; Mahadevan, Krishna

Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives ofmore » this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling development. The model as created is capable of predicting the response of the community structure in changing environments such as anoxic/oxic conditions or limitations by carbon or nutrients. The ability to more accurately model these responses is critical to understanding carbon and energy flows in an ecosystem is critical towards improving our ability to make predictions that can be used to design more efficient remediation and management strategies, and better understand the implications of environmental perturbations on these ecosystems.« less

Towards a paradigm shift in the modeling of soil organic carbon decomposition for earth system models

NASA Astrophysics Data System (ADS)

He, Yujie

Soils are the largest terrestrial carbon pools and contain approximately 2200 Pg of carbon. Thus, the dynamics of soil carbon plays an important role in the global carbon cycle and climate system. Earth System Models are used to project future interactions between terrestrial ecosystem carbon dynamics and climate. However, these models often predict a wide range of soil carbon responses and their formulations have lagged behind recent soil science advances, omitting key biogeochemical mechanisms. In contrast, recent mechanistically-based biogeochemical models that explicitly account for microbial biomass pools and enzyme kinetics that catalyze soil carbon decomposition produce notably different results and provide a closer match to recent observations. However, a systematic evaluation of the advantages and disadvantages of the microbial models and how they differ from empirical, first-order formulations in soil decomposition models for soil organic carbon is still needed. This dissertation consists of a series of model sensitivity and uncertainty analyses and identifies dominant decomposition processes in determining soil organic carbon dynamics. Poorly constrained processes or parameters that require more experimental data integration are also identified. This dissertation also demonstrates the critical role of microbial life-history traits (e.g. microbial dormancy) in the modeling of microbial activity in soil organic matter decomposition models. Finally, this study surveys and synthesizes a number of recently published microbial models and provides suggestions for future microbial model developments.

Microbial carbon pump and its significance for carbon sequestration in soils

NASA Astrophysics Data System (ADS)

Liang, Chao

2017-04-01

Studies of the decomposition, transformation and stabilization of soil organic carbon have dramatically increased in recent years due to growing interest in studying the global carbon cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic carbon reservoir in soils depends upon microbial involvement because soil carbon dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microbe-mediated processes lead to soil carbon stabilization. Here, two pathways, ex vivo modification and in vivo turnover, were defined to jointly explain soil carbon dynamics driven by microbial catabolism and/or anabolism. Accordingly, a conceptual framework consisting of the raised concept of the soil "microbial carbon pump" (MCP) was demonstrated to describe how microbes act as an active player in soil carbon storage. The hypothesis is that the long-term microbial assimilation process may facilitate the formation of a set of organic compounds that are stabilized (whether via protection by physical interactions or a reduction in activation energy due to chemical composition), ultimately leading to the sequestration of microbial-derived carbon in soils. The need for increased efforts was proposed to seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil carbon dynamics to the responses of the terrestrial carbon cycle under global change.

Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

PubMed Central

Maphosa, Farai; Lieten, Shakti H.; Dinkla, Inez; Stams, Alfons J.; Smidt, Hauke; Fennell, Donna E.

2012-01-01

Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants. PMID:23060869

Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment

PubMed Central

Graves, Christopher J.; Makrides, Elizabeth J.; Schmidt, Victor T.; Giblin, Anne E.; Cardon, Zoe G.

2016-01-01

ABSTRACT Environmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities. IMPORTANCE In this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance. PMID:26944843

Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment.

PubMed

Graves, Christopher J; Makrides, Elizabeth J; Schmidt, Victor T; Giblin, Anne E; Cardon, Zoe G; Rand, David M

2016-05-01

Environmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities. In this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance. Copyright © 2016 Graves et al.

Distinct respiratory responses of soils to complex organic substrate are governed predominantly by soil architecture and its microbial community.

PubMed

Fraser, F C; Todman, L C; Corstanje, R; Deeks, L K; Harris, J A; Pawlett, M; Whitmore, A P; Ritz, K

2016-12-01

Factors governing the turnover of organic matter (OM) added to soils, including substrate quality, climate, environment and biology, are well known, but their relative importance has been difficult to ascertain due to the interconnected nature of the soil system. This has made their inclusion in mechanistic models of OM turnover or nutrient cycling difficult despite the potential power of these models to unravel complex interactions. Using high temporal-resolution respirometery (6 min measurement intervals), we monitored the respiratory response of 67 soils sampled from across England and Wales over a 5 day period following the addition of a complex organic substrate (green barley powder). Four respiratory response archetypes were observed, characterised by different rates of respiration as well as different time-dependent patterns. We also found that it was possible to predict, with 95% accuracy, which type of respiratory behaviour a soil would exhibit based on certain physical and chemical soil properties combined with the size and phenotypic structure of the microbial community. Bulk density, microbial biomass carbon, water holding capacity and microbial community phenotype were identified as the four most important factors in predicting the soils' respiratory responses using a Bayesian belief network. These results show that the size and constitution of the microbial community are as important as physico-chemical properties of a soil in governing the respiratory response to OM addition. Such a combination suggests that the 'architecture' of the soil, i.e. the integration of the spatial organisation of the environment and the interactions between the communities living and functioning within the pore networks, is fundamentally important in regulating such processes.

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

PubMed Central

Khachane, Amit; Dungait, Jennifer A. J.; Fraser, Fiona; Hopkins, David W.; Wookey, Philip A.; Singh, Brajesh K.; Freitag, Thomas E.; Hartley, Iain P.; Prosser, James I.

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited. PMID:27798702

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

PubMed

Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

Microbially mediated transformations of phosphorus in the sea: new views of an old cycle.

PubMed

Karl, David M

2014-01-01

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

PubMed

Ebrahimi, Ali; Or, Dani

2016-09-01

Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

Probing soil C metabolism in response to temperature: results from experiments and modeling

NASA Astrophysics Data System (ADS)

Dijkstra, P.; Dalder, J.; Blankinship, J.; Selmants, P. C.; Schwartz, E.; Koch, G. W.; Hart, S.; Hungate, B. A.

2010-12-01

C use efficiency (CUE) is one of the least understood aspects of soil C cycling, has a very large effect on soil respiration and C sequestration, and decreases with elevated temperature. CUE is directly related to substrate partitioning over energy production and biosynthesis. The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We have developed a new stable isotope approach using position-specific 13C-labeled metabolic tracers to measure these fundamental metabolic processes in intact soil communities (1). We use this new approach, combined with models of soil metabolic flux patterns, to analyze the response of microbial energy production, biosynthesis, and CUE to temperature. The method consists of adding small but precise amounts of position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through various metabolic pathways. A simplified metabolic model consisting of 23 reactions is iteratively solved using results of the metabolic tracer experiments and information on microbial precursor demand under different temperatures. This new method enables direct study of fundamental aspects of microbial energy production, C use efficiency, and soil organic matter formation in response to temperature. (1) Dijkstra P, Blankinship JC, Selmants PC, Hart SC, Koch GW, Schwarz E and Hungate BA. Probing metabolic flux patterns of soil microbial communities using parallel position-specific tracer labeling. Soil Biology and Biochemistry (accepted)

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

PubMed Central

De Filippis, Francesca; Genovese, Alessandro; Ferranti, Pasquale; Gilbert, Jack A.; Ercolini, Danilo

2016-01-01

Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipid catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. The results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality. PMID:26911915

Photochemical and microbial alterations of DOM spectroscopic properties in the estuarine system Ria de Aveiro.

PubMed

Santos, L; Santos, E B H; Dias, J M; Cunha, A; Almeida, A

2014-08-01

The influence of photochemical transformations of chromophoric dissolved organic matter (CDOM) on microbial communities was evaluated in the estuarine system Ria de Aveiro. Two sites, representative of the marine and brackish water zones of the estuary, were surveyed regularly in order to determine seasonal and vertical profiles of variation of CDOM properties. Optical parameters of CDOM indicative of aromaticity and molecular weight were used to establish CDOM sources, and microbial abundance and activity was characterized. Additionally, microcosm experiments were performed in order to simulate photochemical reactions of CDOM and to evaluate microbial responses to light-induced changes in CDOM composition. The CDOM of the two estuarine zones showed different spectral characteristics, with significantly higher values of the specific ultra-violet absorbance at 254 nm (SUVA254) (5.5 times) and of the absorption coefficient at 350 nm (a350) (12 times) and lower SR (S275-295/S350-400) ratio at brackish water compared with the marine zone, reflecting the different amounts and prevailing sources of organic matter, as well as distinct riverine and oceanic influences. At the marine zone, the abundance of bacteria and the activity of Leu-AMPase correlated with a350 and a254, suggesting a microbial contribution to the HMW CDOM pool. The irradiation of DOM resulted in a decrease of the values of a254 and a350 and an increase of the slope S275-295 and of the ratios E2 : E3 (a250/a365) and SR, which in turn increase its bioavailability. However, the extent of photoinduced transformations and microbial responses was dependent on the initial optical characteristics of CDOM. In Ria de Aveiro both photochemical and microbial processes yielded optical changes in CDOM and the overall results of these combined processes determine the fate of CDOM in the estuarine system and have an influence on local productivity and in adjacent coastal areas.

Role of soil microbial processes in integrated pest management

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

Francis, A.J.

1987-01-01

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

Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene.

PubMed

Babin, Doreen; Ding, Guo-Chun; Pronk, Geertje Johanna; Heister, Katja; Kögel-Knabner, Ingrid; Smalla, Kornelia

2013-10-01

Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

NASA Astrophysics Data System (ADS)

Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

2015-10-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

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

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).

Salt marsh sediment bacteria: their distribution and response to external nutrient inputs.

PubMed

Bowen, Jennifer L; Crump, Byron C; Deegan, Linda A; Hobbie, John E

2009-08-01

A primary focus among microbial ecologists in recent years has been to understand controls on the distribution of microorganisms in various habitats. Much less attention has been paid to the way that environmental disturbance interacts with processes that regulate bacterial community composition. We determined how human disturbance affected the distribution and community structure of salt marsh sediment bacteria by using denaturing gradient gel electrophoresis of 16S rRNA in five different habitats in each of four salt marshes located in northeastern Massachusetts, USA. Two of the four marsh creeks were experimentally enriched 15 x above background by the addition of nitrogen and phosphorus fertilizers for two or more growing seasons. Our results indicate that extrinsic factors acting at broad scales do not influence the distribution of salt marsh sediment bacteria. Intrinsic factors, controlled by local-scale environmental heterogeneity, do play a role in structuring these sediment microbial communities, although nutrient enrichment did not have a consequential effect on the microbial community in most marsh habitats. Only in one habitat, a region of the marsh creek wall that is heavily colonized by filamentous algae, did we see any effect of fertilization on the microbial community structure. When similar habitats were compared among marshes, there was considerable convergence in the microbial community composition during the growing season. Environmental factors that correlated best with microbial community composition varied with habitat, suggesting that habitat-specific intrinsic forces are primarily responsible for maintaining microbial diversity in salt marsh sediments.

Regulation of Hydrolytic Enzyme Activity in Aquatic Microbial Communities Hosted by Carnivorous Pitcher Plants.

PubMed

Young, Erica B; Sielicki, Jessica; Grothjan, Jacob J

2018-04-20

Carnivorous pitcher plants Sarracenia purpurea host diverse eukaryotic and bacterial communities which aid in insect prey digestion, but little is known about the functional processes mediated by the microbial communities. This study aimed to connect pitcher community diversity with functional nutrient transformation processes, identifying bacterial taxa, and measuring regulation of hydrolytic enzyme activity in response to prey and alternative nutrient sources. Genetic analysis identified diverse bacterial taxa known to produce hydrolytic enzyme activities. Chitinase, protease, and phosphatase activities were measured using fluorometric assays. Enzyme activity in field pitchers was positively correlated with bacterial abundance, and activity was suppressed by antibiotics suggesting predominantly bacterial sources of chitinase and protease activity. Fungi, algae, and rotifers observed could also contribute enzyme activity, but fresh insect prey released minimal chitinase activity. Activity of chitinase and proteases was upregulated in response to insect additions, and phosphatase activity was suppressed by phosphate additions. Particulate organic P in prey was broken down, appearing as increasing dissolved organic and inorganic P pools within 14 days. Chitinase and protease were not significantly suppressed by availability of dissolved organic substrates, though organic C and N stimulated bacterial growth, resulting in elevated enzyme activity. This comprehensive field and experimental study show that pitcher plant microbial communities dynamically regulate hydrolytic enzyme activity, to digest prey nutrients to simpler forms, mediating biogeochemical nutrient transformations and release of nutrients for microbial and host plant uptake.

Evidence for the functional significance of diazotroph community structure in soil.

PubMed

Hsu, Shi-Fang; Buckley, Daniel H

2009-01-01

Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.

Proteomic profile of the Bradysia odoriphaga in response to the microbial secondary metabolite benzothiazole.

PubMed

Zhao, Yunhe; Cui, Kaidi; Xu, Chunmei; Wang, Qiuhong; Wang, Yao; Zhang, Zhengqun; Liu, Feng; Mu, Wei

2016-11-24

Benzothiazole, a microbial secondary metabolite, has been demonstrated to possess fumigant activity against Sclerotinia sclerotiorum, Ditylenchus destructor and Bradysia odoriphaga. However, to facilitate the development of novel microbial pesticides, the mode of action of benzothiazole needs to be elucidated. Here, we employed iTRAQ-based quantitative proteomics analysis to investigate the effects of benzothiazole on the proteomic expression of B. odoriphaga. In response to benzothiazole, 92 of 863 identified proteins in B. odoriphaga exhibited altered levels of expression, among which 14 proteins were related to the action mechanism of benzothiazole, 11 proteins were involved in stress responses, and 67 proteins were associated with the adaptation of B. odoriphaga to benzothiazole. Further bioinformatics analysis indicated that the reduction in energy metabolism, inhibition of the detoxification process and interference with DNA and RNA synthesis were potentially associated with the mode of action of benzothiazole. The myosin heavy chain, succinyl-CoA synthetase and Ca + -transporting ATPase proteins may be related to the stress response. Increased expression of proteins involved in carbohydrate metabolism, energy production and conversion pathways was responsible for the adaptive response of B. odoriphaga. The results of this study provide novel insight into the molecular mechanisms of benzothiazole at a large-scale translation level and will facilitate the elucidation of the mechanism of action of benzothiazole.

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

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

Classen, Aimee T; Overby, Stephen; Hart, Stephen C

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality entering an ecosystem or indirectly by affecting a shift in the microbial community that mediate nutrient processes. We examine herbivore susceptibility and resistance effects on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore driven changes in litter inputs will feedback to the microbial community. Our study population consisted of individual trees that are susceptible or resistant to the stem-boring moth (Dioryctria albovittella) and trees that herbivores have been manually removed since 1982. Moth herbivory increased pi on litter nitrogen concentrations (16%) and canopy precipitation infiltrationmore » (28%), both significant factors influencing litter and soil microbial populations. Our research resulted in three major conclusions: 1) In spite of an increase in litter quality, herbivory does not change litter microarthropod abundance or species richness. 2) Herbivore susceptibility alters bulk soil microbial communities, but not soil properties. 3) Season has a strong influence on microbial communities, and their response to herbivore inputs, in this semi-arid ecosystem.« less

Effects of organic loading rates on reactor performance and microbial community changes during thermophilic aerobic digestion process of high-strength food wastewater.

PubMed

Jang, Hyun Min; Lee, Jae Won; Ha, Jeong Hyub; Park, Jong Moon

2013-11-01

To evaluate the applicability of single-stage thermophilic aerobic digestion (TAD) process treating high-strength food wastewater (FWW), TAD process was operated at four organic loading rates (OLRs) from 9.2 to 37.2 kg COD/m(3)d. The effects of OLRs on microbial community changes were also examined. The highest volumetric removal rate (13.3 kg COD/m(3)d) and the highest thermo-stable protease activity (0.95 unit/mL) were detected at OLR=18.6 kg COD/m(3)d. Denaturing gradient gel electrophoresis (DGGE) profiles and quantitative PCR (qPCR) results showed significant microbial community shifts in response to changes in OLR. In particular, DGGE and phylogenetic analysis demonstrate that the presence of Bacillus sp. (phylum of Firmicutes) was strongly correlated with efficient removal of organic particulates from high-strength food wastewater. Copyright © 2013 Elsevier Ltd. All rights reserved.

The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands

DOE PAGES

Yue, Haowei; Wang, Mengmeng; Wang, Shiping; ...

2015-02-17

Warming has been shown to cause soil carbon (C) loss in northern grasslands owing to accelerated microbial decomposition that offsets increased grass productivity. Yet, a multi-decadal survey indicated that the surface soil C stock in Tibetan alpine grasslands remained relatively stable. To investigate this inconsistency, we analyzed the feedback responses of soil microbial communities to simulated warming by soil transplant in Tibetan grasslands. Microbial functional diversity decreased in response to warming, whereas microbial community structure did not correlate with changes in temperature. The relative abundance of catabolic genes associated with nitrogen (N) and C cycling decreased with warming, most notablymore » in genes encoding enzymes associated with more recalcitrant C substrates. By contrast, genes associated with C fixation increased in relative abundance. The relative abundance of genes associated with urease, glutamate dehydrogenase and ammonia monoxygenase ( ureC, gdh and amoA) were significantly correlated with N 2O efflux. These results suggest that unlike arid/semiarid grasslands, Tibetan grasslands maintain negative feedback mechanisms that preserve terrestrial C and N pools. To examine whether these trends were applicable to the whole plateau, we included these measurements in a model and verified that topsoil C stocks remained relatively stable. Thus, by establishing linkages between microbial metabolic potential and soil biogeochemical processes, we conclude that long-term C loss in Tibetan grasslands is ameliorated by a reduction in microbial decomposition of recalcitrant C substrates.« less

Microbial Genetic Memory to Study Heterogeneous Soil Processes

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Multiple-pass high-pressure homogenization of milk for the development of pasteurization-like processing conditions.

PubMed

Ruiz-Espinosa, H; Amador-Espejo, G G; Barcenas-Pozos, M E; Angulo-Guerrero, J O; Garcia, H S; Welti-Chanes, J

2013-02-01

Multiple-pass ultrahigh pressure homogenization (UHPH) was used for reducing microbial population of both indigenous spoilage microflora in whole raw milk and a baroresistant pathogen (Staphylococcus aureus) inoculated in whole sterile milk to define pasteurization-like processing conditions. Response surface methodology was followed and multiple response optimization of UHPH operating pressure (OP) (100, 175, 250 MPa) and number of passes (N) (1-5) was conducted through overlaid contour plot analysis. Increasing OP and N had a significant effect (P < 0·05) on microbial reduction of both spoilage microflora and Staph. aureus in milk. Optimized UHPH processes (five 202-MPa passes; four 232-MPa passes) defined a region where a 5-log(10) reduction of total bacterial count of milk and a baroresistant pathogen are attainable, as a requisite parameter for establishing an alternative method of pasteurization. Multiple-pass UHPH optimized conditions might help in producing safe milk without the detrimental effects associated with thermal pasteurization. © 2012 The Society for Applied Microbiology.

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

Muscles provide protection during microbial infection by activating innate immune response pathways in Drosophila and zebrafish.

PubMed

Chatterjee, Arunita; Roy, Debasish; Patnaik, Esha; Nongthomba, Upendra

2016-06-01

Muscle contraction brings about movement and locomotion in animals. However, muscles have also been implicated in several atypical physiological processes including immune response. The role of muscles in immunity and the mechanism involved has not yet been deciphered. In this paper, using Drosophila indirect flight muscles (IFMs) as a model, we show that muscles are immune-responsive tissues. Flies with defective IFMs are incapable of mounting a potent humoral immune response. Upon immune challenge, the IFMs produce anti-microbial peptides (AMPs) through the activation of canonical signaling pathways, and these IFM-synthesized AMPs are essential for survival upon infection. The trunk muscles of zebrafish, a vertebrate model system, also possess the capacity to mount an immune response against bacterial infections, thus establishing that immune responsiveness of muscles is evolutionarily conserved. Our results suggest that physiologically fit muscles might boost the innate immune response of an individual. © 2016. Published by The Company of Biologists Ltd.

Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE.

PubMed

Liu, Tengfei; Jia, Tianzhu; Chen, Jiangning; Liu, Xiaoyu; Zhao, Minjie; Liu, Pengpeng

Shenqu is a fermented product that is widely used in traditional Chinese medicine (TCM) to treat indigestion; however, the microbial strains in the fermentation process are still unknown. The aim of this study was to investigate microbial diversity in Shenqu using different fermentation time periods. DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) profiles indicated that a strain of Pediococcus acidilactici (band 9) is the predominant bacteria during fermentation and that the predominant fungi were uncultured Rhizopus, Aspergillus oryzae, and Rhizopus oryzae. In addition, pathogenic bacteria, such as Enterobacter cloacae, Klebsiella oxytoca, Erwinia billingiae, and Pantoea vagan were detected in Shenqu. DGGE analysis showed that bacterial and fungal diversity declined over the course of fermentation. This determination of the predominant bacterial and fungal strains responsible for fermentation may contribute to further Shenqu research, such as optimization of the fermentation process. Copyright © 2017. Published by Elsevier Editora Ltda.

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

USGS Publications Warehouse

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

2017-01-01

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

Sub-soil microbial activity under rotational cotton crops in Australia

NASA Astrophysics Data System (ADS)

Polain, Katherine; Knox, Oliver; Wilson, Brian; Pereg, Lily

2016-04-01

Soil microbial communities contribute significantly to soil organic matter formation, stabilisation and destabilisation, through nutrient cycling and biodegradation. The majority of soil microbial research examines the processes occurring in the top 0 cm to 30 cm of the soil, where organic nutrients are easily accessible. In soils such as Vertosols, the high clay content causes swelling and cracking. When soil cracking is coupled with rain or an irrigation event, a flush of organic nutrients can move down the soil profile, becoming available for subsoil microbial community use and potentially making a significant contribution to nutrient cycling and biodegradation in soils. At present, the mechanisms and rates of soil nutrient turnover (such as carbon and nitrogen) at depth under cotton rotations are mostly speculative and the process-response relationships remain unclear, although they are undoubtedly underpinned by microbial activity. Our research aims to determine the contribution and role of soil microbiota to the accumulation, cycling and mineralisation of carbon and nitrogen through the whole root profile under continuous cotton (Gossypium hirsutum) and cotton-maize rotations in regional New South Wales, Australia. Through seasonal work, we have established both baseline and potential microbial activity rates from 0 cm to 100 cm down the Vertosol profile, using respiration and colourimetric methods. Further whole soil profile analyses will include determination of microbial biomass and isotopic carbon signatures using phospholipid fatty acid (PLFA) methodology, identification of microbial communities (sequencing) and novel experiments to investigate potential rates of nitrogen mineralisation and quantification of associated genes. Our preliminary observations and the hypotheses tested in this three-year study will be presented.

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

Zhang, Ping; Van Nostrand, Joy D.; He, Zhili

Cr(VI) is a widespread environmental contaminant that is highly toxic and soluble. Previous work indicated that a one-time amendment of polylactate hydrogen-release compound (HRC) reduced groundwater Cr(VI) concentrations for >3.5 years at a contaminated aquifer; however, microbial communities responsible for Cr(VI) reduction are poorly understood. Here in this study, we hypothesized that HRC amendment would significantly change the composition and structure of groundwater microbial communities, and that the abundance of key functional genes involved in HRC degradation and electron acceptor reduction would increase long-term in response to this slowly degrading, complex substrate. To test these hypotheses, groundwater microbial communities weremore » monitored after HRC amendment for >1 year using a comprehensive functional gene microarray. The results showed that the overall functional composition and structure of groundwater microbial communities underwent sequential shifts after HRC amendment. Particularly, the abundance of functional genes involved in acetate oxidation, denitrification, dissimilatory nitrate reduction, metal reduction, and sulfate reduction significantly increased. The overall community dynamics was significantly correlated with changes in groundwater concentrations of microbial biomass, acetate, NO 3 -, Cr(VI), Fe(II) and SO 4 2-. Finally, our results suggest that HRC amendment primarily stimulated key functional processes associated with HRC degradation and reduction of multiple electron acceptors in the aquifer toward long-term Cr(VI) reduction.« less

Application of response surface methodology to optimise microbial inactivation of shrimp and conch by supercritical carbon dioxide.

PubMed

Chen, Manhua; Sui, Xiao; Ma, Xixiu; Feng, Xiaomei; Han, Yuqian

2015-03-30

Supercritical carbon dioxide (SC-CO2 ) has been shown to have a good pasteurising effect on food. However, very few research papers have investigated the possibility to exploit this treatment for solid foods, particularly for seafood. Considering the microbial safety of raw seafood consumption, the study aimed to explore the feasibility of microbial inactivation of shrimp (Metapenaeus ensis) and conch (Rapana venosa) by SC-CO2 treatment. Response surface methodology (RSM) models were established to predict and analyse the SC-CO2 process. A 3.69-log reduction in the total aerobic plate count (TPC) of shrimp was observed by SC-CO2 treatment at 53°C, 15 MPa for 40 min, and the logarithmic reduction in TPC of conch was 3.31 at 55°C, 14 MPa for 42 min. Sensory scores of the products achieved approximately 8 (desirable). The optimal parameters for microbial inactivation of shrimp and conch by SC-CO2 might be 55°C, 15 MPa and 40 min. SC-CO2 exerted a strong bactericidal effect on the TPC of shrimp and conch, and the products maintained good organoleptic properties. This study verified the feasibility of microbial inactivation of shrimp and conch by SC-CO2 treatment. © 2014 Society of Chemical Industry.

Microbial community dynamics during assays of harbour oil spill bioremediation: a microscale simulation study.

PubMed

Cappello, S; Caruso, G; Zampino, D; Monticelli, L S; Maimone, G; Denaro, R; Tripodo, B; Troussellier, M; Yakimov, M; Giuliano, L

2007-01-01

Microcosm experiments simulating an oil spill event were performed to evaluate the response of the natural microbial community structure of Messina harbour seawater following the accidental load of petroleum. An experimental harbour seawater microcosm, supplemented with nutrients and crude oil, was monitored above 15 days in comparison with unpolluted ones (control microcosms). Bacterial cells were counted with a Live/Dead BacLight viability kit; leucine aminopeptidase, beta-glucosidase, alkaline phosphatase, lipase and esterase enzymes were measured using fluorogenic substrates. The microbial community dynamic was monitored by isolation of total RNA, RT-PCR amplification of 16S rRNA, cloning and sequencing. Oil addition stimulated an increase of the total bacterial abundance, leucine aminopeptidase and phosphatase activity rates, as well as a change in the community structure. This suggested a prompt response of micro-organisms to the load of petroleum hydrocarbons. The present study on the viability, specific composition and metabolic characteristics of the microbial community allows a more precise assessment of oil pollution. Both structural and functional parameters offer interesting perspectives as indicators to monitor changes caused by petroleum hydrocarbons. A better knowledge of microbial structural successions at oil-polluted sites is essential for environmental bioremediation. Data obtained in microcosm studies improve our understanding of natural processes occurring during oil spills.

Microbial communities associated with wet flue gas desulfurization systems

PubMed Central

Brown, Bryan P.; Brown, Shannon R.; Senko, John M.

2012-01-01

Flue gas desulfurization (FGD) systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems. PMID:23226147

Microbial Response to Experimentally Controlled Redox Transitions at the Sediment Water Interface.

PubMed

Frindte, Katharina; Allgaier, Martin; Grossart, Hans-Peter; Eckert, Werner

2015-01-01

The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface.

Optimisation of surfactant decontamination and pre-treatment of waste chicken feathers by using response surface methodology.

PubMed

Tesfaye, Tamrat; Sithole, Bruce; Ramjugernath, Deresh; Ndlela, Luyanda

2018-02-01

Commercially processed, untreated chicken feathers are biologically hazardous due to the presence of blood-borne pathogens. Prior to valorisation, it is crucial that they are decontaminated to remove the microbial contamination. The present study focuses on evaluating the best technologies to decontaminate and pre-treat chicken feathers in order to make them suitable for valorisation. Waste chicken feathers were washed with three surfactants (sodium dodecyl sulphate) dimethyl dioctadecyl ammonium chloride, and polyoxyethylene (40) stearate) using statistically designed experiments. Process conditions were optimised using response surface methodology with a Box-Behnken experimental design. The data were compared with decontamination using an autoclave. Under optimised conditions, the microbial counts of the decontaminated and pre-treated chicken feathers were significantly reduced making them safe for handling and use for valorisation applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Carbon and hydrogen isotopic evidence for the origin of combustible gases in water-supply wells in north-central Pennsylvania

USGS Publications Warehouse

Révész, K. M.; Breen, K.J.; Baldassare, A.J.; Burruss, R.C.

2010-01-01

The origin of the combustible gases in groundwater from glacial-outwash and fractured-bedrock aquifers was investigated in northern Tioga County, Pennsylvania. Thermogenic methane (CH4) and ethane (C2H6) and microbial CH4 were found. Microbial CH4 is from natural in situ processes in the shale bedrock and occurs chiefly in the bedrock aquifer. The δ13C values of CH4 and C2H6 for the majority of thermogenic gases from water wells either matched or were between values for the samples of non-native storage-field gas from injection wells and the samples of gas from storage-field observation wells. Traces of C2H6 with microbial CH4 and a range of C and H isotopic compositions of CH4 indicate gases of different origins are mixing in sub-surface pathways; gas mixtures are present in groundwater. Pathways for gas migration and a specific source of the gases were not identified. Processes responsible for the presence of microbial gases in groundwater could be elucidated with further geochemical study.

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.

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

PubMed

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

2016-03-22

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

Changes in microbial communities associated with the sea anemone Anemonia viridis in a natural pH gradient.

PubMed

Meron, Dalit; Buia, Maria-Cristina; Fine, Maoz; Banin, Ehud

2013-02-01

Ocean acidification, resulting from rising atmospheric carbon dioxide concentrations, is a pervasive stressor that can affect many marine organisms and their symbionts. Studies which examine the host physiology and microbial communities have shown a variety of responses to the ocean acidification process. Recently, several studies were conducted based on field experiments, which take place in natural CO(2) vents, exposing the host to natural environmental conditions of varying pH. This study examines the sea anemone Anemonia viridis which is found naturally along the pH gradient in Ischia, Italy, with an aim to characterize whether exposure to pH impacts the holobiont. The physiological parameters of A. viridis (Symbiodinium density, protein, and chlorophyll a+c concentration) and its microbial community were monitored. Although reduction in pH was seen to have had an impact on composition and diversity of associated microbial communities, no significant changes were observed in A. viridis physiology, and no microbial stress indicators (i.e., pathogens, antibacterial activity, etc.) were detected. In light of these results, it appears that elevated CO(2) does not have a negative influence on A. viridis that live naturally in the site. This suggests that natural long-term exposure and dynamic diverse microbial communities may contribute to the acclimation process of the host in a changing pH environment.

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

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

Song, Hyun-Seob; Thomas, Dennis G.; Stegen, James C.

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accountedmore » for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators.« less

Response of soil microbial and invertebrate communities to tracked vehicle disturbance in tallgrass prairie

Treesearch

P.S. Althoff; T.C. Todd; S.J. Thien; M.A. Callaham

2009-01-01

Soil biota drive fundamental ecosystem processes such as decomposition, nutrient cycling, and maintenance of soil structure. They are especially active in grassland ecosystems such as the tallgrass by heterotrophic soil organisms. Because both soil microbes and soil fauna display perturbation responses that integrate the physical, chemical, and biological changes to...

Biogeochemical Controls on Microbial CO2 and CH4 Production in Polygonal Soils From the Barrow Environmental Observatory

NASA Astrophysics Data System (ADS)

Graham, D. E.; Roy Chowdhury, T.; Herndon, E.; Gu, B.; Liang, L.; Wullschleger, S. D.

2014-12-01

Organic matter buried in Arctic soils and permafrost will become accessible to increased microbial degradation as the ground warms due to climate change. The rates of organic matter degradation and the proportion of CH4 and CO2 greenhouse gasses released in a potential warming feedback cycle depend on the microbial response to warming, organic carbon structure and availability, the pore-water quantity and geochemistry, and available electron acceptors. Significant amounts of iron(II) ions in organic and mineral soils of the active layer in low-centered ice wedge polygons indicate anoxic conditions in most soil horizons. To adapt and improve the representation of these Arctic subsurface processes in terrestrial ecosystem models for the NGEE Arctic project, we examined soil organic matter transformations from elevated and subsided areas of low- and high-centered polygons from interstitial tundra on the Barrow Environmental Observatory (Barrow, AK). Using microcosm incubations at fixed temperatures and controlled thawing systems for frozen soil cores, we investigated the microbiological processes and rates of soil organic matter degradation and greenhouse gas production under anoxic conditions, at ecologically relevant temperatures of -2, +4 or +8 °C. In contrast to the low-centered polygon incubations representing in situ water-saturated conditions, microcosms with unsaturated high-centered polygon samples displayed lower carbon mineralization as either CH4 or CO2. Substantial differences in CH4 and CO2 response curves from different microtopographic samples separate the thermodynamic controls on biological activity from the kinetic controls of microbial growth and migration that together determine the temperature response for greenhouse gas emissions in a warming Arctic.

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.

Using data to inform soil microbial carbon model structure and parameters

NASA Astrophysics Data System (ADS)

Hagerty, S. B.; Schimel, J.

2016-12-01

There is increasing consensus that explicitly representing microbial mechanisms in soil carbon models can improve model predictions of future soil carbon stocks. However, which microbial mechanisms must be represented in these new models and how remains under debate. One of the major challenges in developing microbially explicit soil carbon models is that there is little data available to validate model structure. Empirical studies of microbial mechanisms often fail to capture the full range of microbial processes; from the cellular processes that occur within minutes to hours of substrate consumption to community turnover which may occur over weeks or longer. We added isotopically labeled 14C-glucose to soil incubated in the lab and traced its movement into the microbial biomass, carbon dioxide, and K2SO4 extractable carbon pool. We measured the concentration of 14C in each of these pools at 1, 3, 6, 24, and 72 hours and at 7, 14, and 21 days. We used this data to compare data fits among models that match our conceptual understanding of microbial carbon transformations and to estimate microbial parameters that control the fate of soil carbon. Over 90% of the added glucose was consumed within the first hour after it was added and concentration of the label was highest in biomass at this time. After the first hour, the label in biomass declined, with the rate that the label moved from the biomass slowing after 24hours, because of this models representing the microbial biomass as two pools fit best. Recovery of the label decreased with incubation time, from nearly 80% in the first hour to 67% after three weeks, indicating that carbon is moving into unextractable pools in the soil likely as microbial products and necromass sorb to soil particles and that these mechanisms must be represented in microbial models. This data fitting exercise demonstrates how isotopic data can be useful in validating model structure and estimating microbial model parameters. Future studies can apply this inverse modeling approach to compare the response of microbial parameters to changes in environmental conditions.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil.

PubMed

Yuan, Mengting M; Zhang, Jin; Xue, Kai; Wu, Liyou; Deng, Ye; Deng, Jie; Hale, Lauren; Zhou, Xishu; He, Zhili; Yang, Yunfeng; Van Nostrand, Joy D; Schuur, Edward A G; Konstantinidis, Konstantinos T; Penton, Christopher R; Cole, James R; Tiedje, James M; Luo, Yiqi; Zhou, Jizhong

2018-01-01

Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming-induced environmental changes is critical to evaluating their influences on soil biogeochemical cycles. In this study, a functional gene array (i.e., geochip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately, and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25% and 5%, while the community functional gene β-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw-related soil and plant changes and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems. © 2017 John Wiley & Sons Ltd.

Eicosanoid-mediated immunity in insects

USDA-ARS?s Scientific Manuscript database

Eicosanoid is a collective term for oxygenated metabolites of C20 polyunsaturated fatty acids. As seen in mammals, eicosanoids play crucial roles in mediating various physiological processes, including immune responses, in insects. Upon microbial pathogen infection, non-self recognition signals are ...

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

A Plethora of Virulence Strategies Hidden Behind Nuclear Targeting of Microbial Effectors

PubMed Central

Rivas, Susana; Genin, Stéphane

2011-01-01

Plant immune responses depend on the ability to couple rapid recognition of the invading microbe to an efficient response. During evolution, plant pathogens have acquired the ability to deliver effector molecules inside host cells in order to manipulate cellular and molecular processes and establish pathogenicity. Following translocation into plant cells, microbial effectors may be addressed to different subcellular compartments. Intriguingly, a significant number of effector proteins from different pathogenic microorganisms, including viruses, oomycetes, fungi, nematodes, and bacteria, is targeted to the nucleus of host cells. In agreement with this observation, increasing evidence highlights the crucial role played by nuclear dynamics, and nucleocytoplasmic protein trafficking during a great variety of analyzed plant–pathogen interactions. Once in the nucleus, effector proteins are able to manipulate host transcription or directly subvert essential host components to promote virulence. Along these lines, it has been suggested that some effectors may affect histone packing and, thereby, chromatin configuration. In addition, microbial effectors may either directly activate transcription or target host transcription factors to alter their regular molecular functions. Alternatively, nuclear translocation of effectors may affect subcellular localization of their cognate resistance proteins in a process that is essential for resistance protein-mediated plant immunity. Here, we review recent progress in our field on the identification of microbial effectors that are targeted to the nucleus of host plant cells. In addition, we discuss different virulence strategies deployed by microbes, which have been uncovered through examination of the mechanisms that guide nuclear localization of effector proteins. PMID:22639625

Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse

DOE PAGES

Liu, Chi; Yao, Minjie; Stegen, James C.; ...

2017-12-13

How press disturbance (long-term) influences the phylogenetic turnover of soil microbial communities responding to pulse disturbances (short-term) is not fully known. Understanding the complex connections between the history of environmental conditions, assembly processes and microbial community dynamics is necessary to predict microbial response to perturbation. Here, we started by investigating phylogenetic spatial turnover (based on DNA) of soil prokaryotic communities after long-term nitrogen (N) deposition and temporal turnover (based on RNA) of communities responding to pulse by conducting short-term rewetting experiments. The results showed that moderate N addition increased ecological stochasticity and phylogenetic diversity. In contrast, high N addition slightlymore » increased homogeneous selection and decreased phylogenetic diversity. Examining the system with higher phylogenetic resolution revealed a moderate contribution of variable selection across the whole N gradient. The moisture pulse experiment showed that high N soils had higher rates of phylogenetic turnover across short phylogenetic distances and significant changes in community compositions through time. Long-term N input history influenced spatial turnover of microbial communities, but the dominant community assembly mechanisms differed across different N deposition gradients. We further revealed an interaction between press and pulse disturbances whereby deterministic processes were particularly important following pulse disturbances in high N soils.« less

Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse

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

Liu, Chi; Yao, Minjie; Stegen, James C.

How press disturbance (long-term) influences the phylogenetic turnover of soil microbial communities responding to pulse disturbances (short-term) is not fully known. Understanding the complex connections between the history of environmental conditions, assembly processes and microbial community dynamics is necessary to predict microbial response to perturbation. Here, we started by investigating phylogenetic spatial turnover (based on DNA) of soil prokaryotic communities after long-term nitrogen (N) deposition and temporal turnover (based on RNA) of communities responding to pulse by conducting short-term rewetting experiments. The results showed that moderate N addition increased ecological stochasticity and phylogenetic diversity. In contrast, high N addition slightlymore » increased homogeneous selection and decreased phylogenetic diversity. Examining the system with higher phylogenetic resolution revealed a moderate contribution of variable selection across the whole N gradient. The moisture pulse experiment showed that high N soils had higher rates of phylogenetic turnover across short phylogenetic distances and significant changes in community compositions through time. Long-term N input history influenced spatial turnover of microbial communities, but the dominant community assembly mechanisms differed across different N deposition gradients. We further revealed an interaction between press and pulse disturbances whereby deterministic processes were particularly important following pulse disturbances in high N soils.« less

Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse.

PubMed

Liu, Chi; Yao, Minjie; Stegen, James C; Rui, Junpeng; Li, Jiabao; Li, Xiangzhen

2017-12-13

How press disturbance (long-term) influences the phylogenetic turnover of soil microbial communities responding to pulse disturbances (short-term) is not fully known. Understanding the complex connections between the history of environmental conditions, assembly processes and microbial community dynamics is necessary to predict microbial response to perturbation. We started by investigating phylogenetic spatial turnover (based on DNA) of soil prokaryotic communities after long-term nitrogen (N) deposition and temporal turnover (based on RNA) of communities responding to pulse by conducting short-term rewetting experiments. The results showed that moderate N addition increased ecological stochasticity and phylogenetic diversity. In contrast, high N addition slightly increased homogeneous selection and decreased phylogenetic diversity. Examining the system with higher phylogenetic resolution revealed a moderate contribution of variable selection across the whole N gradient. The moisture pulse experiment showed that high N soils had higher rates of phylogenetic turnover across short phylogenetic distances and significant changes in community compositions through time. Long-term N input history influenced spatial turnover of microbial communities, but the dominant community assembly mechanisms differed across different N deposition gradients. We further revealed an interaction between press and pulse disturbances whereby deterministic processes were particularly important following pulse disturbances in high N soils.

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat.

PubMed

Perazzolli, Michele; Herrero, Noemí; Sterck, Lieven; Lenzi, Luisa; Pellegrini, Alberto; Puopolo, Gerardo; Van de Peer, Yves; Pertot, Ilaria

2016-10-27

Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms. A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of A. mellea. This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic or neutral intruders.

Microbial interactions: ecology in a molecular perspective.

PubMed

Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

2016-12-01

The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

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

De Filippis, Francesca; Genovese, Alessandro; Ferranti, Pasquale

Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipidmore » catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. Finally, the results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality.« less

Effects of shearing on biogas production and microbial community structure during anaerobic digestion with recuperative thickening.

PubMed

Yang, Shufan; Phan, Hop V; Bustamante, Heriberto; Guo, Wenshan; Ngo, Hao H; Nghiem, Long D

2017-06-01

Recuperative thickening can intensify anaerobic digestion to produce more biogas and potentially reduce biosolids odour. This study elucidates the effects of sludge shearing during the thickening process on the microbial community structure and its effect on biogas production. Medium shearing resulted in approximately 15% increase in biogas production. By contrast, excessive or high shearing led to a marked decrease in biogas production, possibly due to sludge disintegration and cell lysis. Microbial analysis using 16S rRNA gene amplicon sequencing showed that medium shearing increased the evenness and diversity of the microbial community in the anaerobic digester, which is consistent with the observed improved biogas production. By contrast, microbial diversity decreased under either excessive shearing or high shearing condition. In good agreement with the observed decrease in biogas production, the abundance of Bacteroidales and Syntrophobaterales (which are responsible for hydrolysis and acetogenesis) decreased due to high shearing during recuperative thickening. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

DOE PAGES

De Filippis, Francesca; Genovese, Alessandro; Ferranti, Pasquale; ...

2016-02-25

Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipidmore » catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. Finally, the results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality.« less

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.

Soil nitrate reducing processes – drivers, mechanisms for spatial variation, and significance for nitrous oxide production

PubMed Central

Giles, Madeline; Morley, Nicholas; Baggs, Elizabeth M.; Daniell, Tim J.

2012-01-01

The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate (NO3−) and production of the potent greenhouse gas, nitrous oxide (N2O). A number of factors are known to control these processes, including O2 concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N2O production from soils. PMID:23264770

Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production.

PubMed

Giles, Madeline; Morley, Nicholas; Baggs, Elizabeth M; Daniell, Tim J

2012-01-01

The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate ([Formula: see text]) and production of the potent greenhouse gas, nitrous oxide (N(2)O). A number of factors are known to control these processes, including O(2) concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N(2)O production from soils.

Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates.

PubMed

Ercan, Onur; Bisschops, Markus M M; Overkamp, Wout; Jørgensen, Thomas R; Ram, Arthur F; Smid, Eddy J; Pronk, Jack T; Kuipers, Oscar P; Daran-Lapujade, Pascale; Kleerebezem, Michiel

2015-09-01

The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial growth rates in such settings can be extremely slow and even approach zero. Furthermore, uncoupling microbial growth from product formation, while cellular integrity and activity are maintained, offers perspectives that are economically highly interesting. Retentostat cultures have been employed to investigate microbial physiology at (near-)zero growth rates. This minireview compares information from recent physiological and gene expression studies on retentostat cultures of the industrially relevant microorganisms Lactobacillus plantarum, Lactococcus lactis, Bacillus subtilis, Saccharomyces cerevisiae, and Aspergillus niger. Shared responses of these organisms to (near-)zero growth rates include increased stress tolerance and a downregulation of genes involved in protein synthesis. Other adaptations, such as changes in morphology and (secondary) metabolite production, were species specific. This comparison underlines the industrial and scientific significance of further research on microbial (near-)zero growth physiology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

PubMed Central

Hemme, Christopher L.; Green, Stefan J.; Rishishwar, Lavanya; Prakash, Om; Pettenato, Angelica; Chakraborty, Romy; Deutschbauer, Adam M.; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Jordan, I. King; Arkin, Adam P.; Kostka, Joel E.

2016-01-01

ABSTRACT Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe2+/Pb2+ permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co2+/Zn2+/Cd2+ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. PMID:27048805

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.

Microbial transformation of the Deepwater Horizon oil spill—past, present, and future perspectives

PubMed Central

Kimes, Nikole E.; Callaghan, Amy V.; Suflita, Joseph M.; Morris, Pamela J.

2014-01-01

The Deepwater Horizon blowout, which occurred on April 20, 2010, resulted in an unprecedented oil spill. Despite a complex effort to cap the well, oil and gas spewed from the site until July 15, 2010. Although a large proportion of the hydrocarbons was depleted via natural processes and human intervention, a substantial portion of the oil remained unaccounted for and impacted multiple ecosystems throughout the Gulf of Mexico. The depth, duration and magnitude of this spill were unique, raising many questions and concerns regarding the fate of the hydrocarbons released. One major question was whether or not microbial communities would be capable of metabolizing the hydrocarbons, and if so, by what mechanisms and to what extent? In this review, we summarize the microbial response to the oil spill as described by studies performed during the past four years, providing an overview of the different responses associated with the water column, surface waters, deep-sea sediments, and coastal sands/sediments. Collectively, these studies provide evidence that the microbial response to the Deepwater Horizon oil spill was rapid and robust, displaying common attenuation mechanisms optimized for low molecular weight aliphatic and aromatic hydrocarbons. In contrast, the lack of evidence for the attenuation of more recalcitrant hydrocarbon components suggests that future work should focus on both the environmental impact and metabolic fate of recalcitrant compounds, such as oxygenated oil components. PMID:25477866

Microbial mitigation-exacerbation continuum: a novel framework for microbiome effects on hosts in the face of stress.

PubMed

David, Aaron S; Thapa-Magar, Khum B; Afkhami, Michelle E

2018-03-01

A key challenge to understanding microbiomes and their role in ecological processes is contextualizing their effects on host organisms, particularly when faced with environmental stress. One influential theory, the Stress Gradient Hypothesis, might predict that the frequency of positive interactions increases with stressful conditions such that microbial taxa would mitigate harmful effects on host performance. Yet, equally plausible is that microbial taxa could exacerbate these effects. Here, we introduce the Mitigation-Exacerbation Continuum as a novel framework to conceptualize microbial mediation of stress. We (1) use this continuum to quantify microbial mediation of stress for six plant species and (2) test the association between these continuum values and natural species' abundance. We factorially manipulated a common stress (allelopathy) and the presence of soil microbes to quantify microbial effects in benign and stressed environments for two critical early life-history metrics, seed germination and seedling biomass. Although we found evidence of both mitigation and exacerbation among the six species, exacerbation was more common. Across species, the degree of microbial-mediated effects on germination explained >80% of the variation of natural field abundances. Our results suggest a critical role of soil microbes in mediating plant stress responses, and a potential microbial mechanism underlying species abundance. © 2018 by the Ecological Society of America.

Following The Money: Characterizing the Dynamics of Microbial Ecosystems and Labile Organic Matter in Grassland Soils

NASA Astrophysics Data System (ADS)

Herbert, B. E.; McNeal, K. S.

2006-12-01

The dynamics of soil microbial ecosystems and labile fractions of soil organic matter in grasslands have important implications for the response of these critical ecosystems to perturbations. Organic, inorganic and genetic biomarkers in the solid (e.g. lipids, microbial DNA), liquid (e.g. porewater ions) or gaseous phases (e.g. carbon dioxide) have been used to characterize carbon cycling and soil microbial ecology. These proxies are generally limited in the amount of temporal information that they can provide (i.e., solid-phase proxies) or the amount of specific information they can provide about carbon sources or microbial community processes (e.g. inorganic gases). It is the aim of this research to validate the use of soil volatile organic carbon emissions (VOCs) as useful indicators of subsurface microbial community shifts and processes as a function of ecosystem perturbations. We present results of method validation using laboratory microcosm, where VOC metabolites as characterized by gas chromatography and mass spectrometry (GC-MS), were related to other proxies including carbon dioxide (CO2) via infra-red technology, and microbial community shifts as measured by Biolog© and fatty acid methyl ester (FAME) techniques. Experiments with soil collected from grasslands along the coastal margin region in southern Texas were preformed where environmental factors such as soil water content, soil type, and charcoal content are manipulated. Results indicate that over fifty identifiable VOC metabolites are produced from the soils, where many (~15) can be direct indicators of microbial ecology. Principle component analysis (PCA) evidences these trends through similar cluster patterns for the VOC results, the Biolog© results, and FAME. Regression analysis further shows that VOCs are significant (p < 0.05) indicators of microbial stress. Our results are encouraging that characterizing VOCs production in grassland soils are easy to measure, relatively inexpensive method, and useful proxies of subsurface microbial ecosystems and the dynamics of labile carbon in these systems.

The changes of bacterial communities and antibiotic resistance genes in microbial fuel cells during long-term oxytetracycline processing.

PubMed

Yan, Weifu; Guo, Yunyan; Xiao, Yong; Wang, Shuhua; Ding, Rui; Jiang, Jiaqi; Gang, Haiyin; Wang, Han; Yang, Jun; Zhao, Feng

2018-05-28

Microbial fuel cell (MFC) is regarded as a promising alternative for enhancing the removal of antibiotic pollutants. In this study, oxytetracycline served as an electron donor in the anode chamber of MFCs, and after continuous operation for 330 days, the efficiency of removal of 10 mg/L oxytetracycline in MFCs increased to 99.00% in 78 h, whereas removal efficiency of only 58.26% was achieved in microbial controls. Compared to microbial controls, higher ATP concentration and persistent electrical stimulation mainly contributed to bioelectrochemical reactions more rapidly to enhance oxytetracycline removal in MFCs. In addition, the analysis of bacterial communities revealed that Eubacterium spp.-as the main functional bacterial genus responsible for oxytetracycline biodegradation-flourished starting from merely 0.00%-91.69% ± 0.27% (mean ± SD) in MFCs. High-throughput quantitative PCR showed that the normalized copy numbers of total antibiotic resistance genes (ARGs) and mobile genetic elements in MFCs were 1.7364 and 0.0065 copies/cell respectively, which were markedly lower than those in the microbial controls. Furthermore, there was no significant correlation between oxytetracycline concentration in the influent and abundance of ARGs in effluent from MFCs. Nevertheless, Tp614, a transposase gene, was found to be enriched in both MFCs and microbial reactors, suggesting that it may be a common challenge for different biological processes for wastewater treatment. This study therefore showed a lower probability of upregulation and transmission of ARGs in MFCs when compared to a traditional anaerobic microbial treatment. Copyright © 2018. Published by Elsevier Ltd.

Fundamentals of Microbial Community Resistance and Resilience

PubMed Central

Shade, Ashley; Peter, Hannes; Allison, Steven D.; Baho, Didier L.; Berga, Mercè; Bürgmann, Helmut; Huber, David H.; Langenheder, Silke; Lennon, Jay T.; Martiny, Jennifer B. H.; Matulich, Kristin L.; Schmidt, Thomas M.; Handelsman, Jo

2012-01-01

Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives – informed by meta-omics data – may provide about microbial community stability. PMID:23267351

Long-term performance of anaerobic digestion for crop residues containing heavy metals and response of microbial communities.

PubMed

Lee, Jongkeun; Kim, Joonrae Roger; Jeong, Seulki; Cho, Jinwoo; Kim, Jae Young

2017-01-01

In order to investigate the long-term stability on the performance of the anaerobic digestion process, a laboratory-scale continuous stirred-tank reactor (CSTR) was operated for 1100 days with sunflower harvested in a heavy metal contaminated site. Changes of microbial communities during digestion were identified using pyrosequencing. According to the results, soluble heavy metal concentrations were lower than the reported inhibitory level and the reactor performance remained stable up to OLR of 2.0g-VS/L/day at HRT of 20days. Microbial communities commonly found in anaerobic digestion for cellulosic biomass were observed and stably established with respect to the substrate. Thus, the balance of microbial metabolism was maintained appropriately and anaerobic digestion seems to be feasible for disposal of heavy metal-containing crop residues from phytoremediation sites. Copyright © 2016 Elsevier Ltd. All rights reserved.

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

PubMed

Schirmer, Melanie; Smeekens, Sanne P; Vlamakis, Hera; Jaeger, Martin; Oosting, Marije; Franzosa, Eric A; Ter Horst, Rob; Jansen, Trees; Jacobs, Liesbeth; Bonder, Marc Jan; Kurilshikov, Alexander; Fu, Jingyuan; Joosten, Leo A B; Zhernakova, Alexandra; Huttenhower, Curtis; Wijmenga, Cisca; Netea, Mihai G; Xavier, Ramnik J

2016-11-03

Gut microbial dysbioses are linked to aberrant immune responses, which are often accompanied by abnormal production of inflammatory cytokines. As part of the Human Functional Genomics Project (HFGP), we investigate how differences in composition and function of gut microbial communities may contribute to inter-individual variation in cytokine responses to microbial stimulations in healthy humans. We observe microbiome-cytokine interaction patterns that are stimulus specific, cytokine specific, and cytokine and stimulus specific. Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism and tryptophan degradation to tryptophol. Besides providing a resource of predicted microbially derived mediators that influence immune phenotypes in response to common microorganisms, these data can help to define principles for understanding disease susceptibility. The three HFGP studies presented in this issue lay the groundwork for further studies aimed at understanding the interplay between microbial, genetic, and environmental factors in the regulation of the immune response in humans. PAPERCLIP. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Reorganisation of a mesophilic biogas microbiome as response to a stepwise increase of ammonium nitrogen induced by poultry manure supply.

PubMed

Alsouleman, Khulud; Linke, Bernd; Klang, Johanna; Klocke, Michael; Krakat, Niclas; Theuerl, Susanne

2016-05-01

An anaerobic digestion experiment was investigated to evaluate the impact of increasing amounts of ammonium nitrogen due to poultry manure addition on the reactor performance, especially on the microbiome response. The microbial community structure was assessed by using a 16S rRNA gene approach, which was further correlated with the prevalent environmental conditions by using statistical analyses. The addition of 50% poultry manure led to a process disturbance indicated by a high VFA content (almost 10 g(HAc-Eq) L(-1)) in combination with elevated concentrations of ammonium nitrogen (5.9 g NH4(+)-N kg(FM)(-1)) and free ammonia (0.5 g NH3 kg(FM)(-1)). Simultaneously the microbiome, changed from a Bacteroidetes-dominated to a Clostridiales-dominated community accompanied by a shift from the acetoclastic to the hydrogenotrophic pathway. The "new" microbial community was functional redundant as the overall process rates were similar to the former one. A further increase of poultry manure resulted in a complete process failure. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rapid Shifts in Soil and Forest Floor Microbial Communities with Changes in Vegetation during Secondary Tropical Forest Succession

NASA Astrophysics Data System (ADS)

Smith, A.; Marin-Spiotta, E.; Balser, T. C.

2012-12-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. In order to predict how disturbance affects belowground carbon storage, it is important to understand how the forest floor and soil microbial community respond to changes in land cover, and the consequences on SOM formation and stabilization. We are measuring microbial functional diversity and activity across a long-term successional chronosequence of secondary forests regrowing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Here we report intra- and interannual data on soil and litter microbial community composition (via phospholipid fatty acid analysis, PLFA) and microbial activity (via extracellular enzyme activity) from active pastures, secondary forests aged 20, 30, 40, 70, and 90-years, and primary forests. Microbial community composition and extracellular enzyme activity differed significantly by season in these wet subtropical ecosystems, even though differences in mean monthly precipitation between the middle of the dry season (January) and the wet season (July) is only 30mm. Despite seasonal differences, there was a persistent strong effect of land cover type and forest successional stage, or age, on overall microbial community PLFA structure. Using principal component analysis, we found differences in microbial community structure among active pastures, early, and late successional forests. The separation of soil microbes into early and late successional communities parallels the clustering of tree composition data. While the successional patterns held across seasons, the importance of different microbial groups driving these patterns differed seasonally. Biomarkers for gram-positive and actinobacteria (i15:0 and 16:0 10Me) were associated with early (20, 30 & 40 year old) secondary forests in the dry season. These younger forest communities were identified by the biomarker for anaerobic gram-negative bacteria (c19:0) in the wet season, which suggests the presence of anaerobic microsites in these very clayey Oxisols. Enzymatic activity did not differ with succession but was highest in the dry season. We expect this may be due to decreased turnover of enzymes with low soil moisture. Interannual sampling has revealed a very rapid microbial response to changes in aboveground cover. Within a year following woody biomass encroachment, we detected a shift in the soil microbial community from a pasture-associated community to an early secondary forest community in one of our replicate pasture sites. This very rapid response in the belowground microbial community structure to changes in vegetation has not been strongly documented in the literature. This data supports a direct link between aboveground and belowground biotic community structures and highlights the importance of long-term repeated sampling of microbial communities in dynamic ecosystems. Our findings have implications for predicting rapid ecological responses to land-cover change.

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.

A network model shows the importance of coupled processes in the microbial N cycle in the Cape Fear River Estuary

NASA Astrophysics Data System (ADS)

Hines, David E.; Lisa, Jessica A.; Song, Bongkeun; Tobias, Craig R.; Borrett, Stuart R.

2012-06-01

Estuaries serve important ecological and economic functions including habitat provision and the removal of nutrients. Eutrophication can overwhelm the nutrient removal capacity of estuaries and poses a widely recognized threat to the health and function of these ecosystems. Denitrification and anaerobic ammonium oxidation (anammox) are microbial processes responsible for the removal of fixed nitrogen and diminish the effects of eutrophication. Both of these microbial removal processes can be influenced by direct inputs of dissolved inorganic nitrogen substrates or supported by microbial interactions with other nitrogen transforming pathways such as nitrification and dissimilatory nitrate reduction to ammonium (DNRA). The coupling of nitrogen removal pathways to other transformation pathways facilitates the removal of some forms of inorganic nitrogen; however, differentiating between direct and coupled nitrogen removal is difficult. Network modeling provides a tool to examine interactions among microbial nitrogen cycling processes and to determine the within-system history of nitrogen involved in denitrification and anammox. To examine the coupling of nitrogen cycling processes, we built a nitrogen budget mass balance network model in two adjacent 1 cm3 sections of bottom water and sediment in the oligohaline portion of the Cape Fear River Estuary, NC, USA. Pathway, flow, and environ ecological network analyses were conducted to characterize the organization of nitrogen flow in the estuary and to estimate the coupling of nitrification to denitrification and of nitrification and DNRA to anammox. Centrality analysis indicated NH4+ is the most important form of nitrogen involved in removal processes. The model analysis further suggested that direct denitrification and coupled nitrification-denitrification had similar contributions to nitrogen removal while direct anammox was dominant to coupled forms of anammox. Finally, results also indicated that partial nitrification-anammox may play an important role in anammox nitrogen removal in the Cape Fear River Estuary.

Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments

PubMed Central

Stagars, Marion H.; Mishra, Sonakshi; Treude, Tina; Amann, Rudolf; Knittel, Katrin

2017-01-01

Anaerobic microbial hydrocarbon degradation is a major biogeochemical process at marine seeps. Here we studied the response of the microbial community to petroleum seepage simulated for 190 days in a sediment core from the Caspian Sea using a sediment-oil-flow-through (SOFT) system. Untreated (without simulated petroleum seepage) and SOFT sediment microbial communities shared 43% bacterial genus-level 16S rRNA-based operational taxonomic units (OTU0.945) but shared only 23% archaeal OTU0.945. The community differed significantly between sediment layers. The detection of fourfold higher deltaproteobacterial cell numbers in SOFT than in untreated sediment at depths characterized by highest sulfate reduction rates and strongest decrease of gaseous and mid-chain alkane concentrations indicated a specific response of hydrocarbon-degrading Deltaproteobacteria. Based on an increase in specific CARD-FISH cell numbers, we suggest the following groups of sulfate-reducing bacteria to be likely responsible for the observed decrease in aliphatic and aromatic hydrocarbon concentration in SOFT sediments: clade SCA1 for propane and butane degradation, clade LCA2 for mid- to long-chain alkane degradation, clade Cyhx for cycloalkanes, pentane and hexane degradation, and relatives of Desulfobacula for toluene degradation. Highest numbers of archaea of the genus Methanosarcina were found in the methanogenic zone of the SOFT core where we detected preferential degradation of long-chain hydrocarbons. Sequencing of masD, a marker gene for alkane degradation encoding (1-methylalkyl)succinate synthase, revealed a low diversity in SOFT sediment with two abundant species-level MasD OTU0.96. PMID:28503173

Effects of dissolved oxygen on performance and microbial community structure in a micro-aerobic hydrolysis sludge in situ reduction process.

PubMed

Niu, Tianhao; Zhou, Zhen; Shen, Xuelian; Qiao, Weimin; Jiang, Lu-Man; Pan, Wei; Zhou, Jijun

2016-03-01

A sludge process reduction activated sludge (SPRAS), with a sludge process reduction module composed of a micro-aerobic tank and a settler positioned before conventional activated sludge process, showed good performance of pollutant removal and sludge reduction. Two SPRAS systems were operated to investigate effects of micro-aeration on sludge reduction performance and microbial community structure. When dissolved oxygen (DO) concentration in the micro-aerobic tank decreased from 2.5 (SPH) to 0.5 (SPL) mg/L, the sludge reduction efficiency increased from 42.9% to 68.3%. Compared to SPH, activated sludge in SPL showed higher contents of extracellular polymeric substances and dissolved organic matter. Destabilization of floc structure in the settler, and cell lysis in the sludge process reduction module were two major reasons for sludge reduction. Illumina-MiSeq sequencing showed that microbial diversity decreased under high DO concentration. Proteobacteria, Bacteroidetes and Chloroflexi were the most abundant phyla in the SPRAS. Specific comparisons down to the class and genus level showed that fermentative, predatory and slow-growing bacteria in SPL community were more abundant than in SPH. The results revealed that micro-aeration in the SPRAS improved hydrolysis efficiency and enriched fermentative and predatory bacteria responsible for sludge reduction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Wine microbiome: A dynamic world of microbial interactions.

PubMed

Liu, Youzhong; Rousseaux, Sandrine; Tourdot-Maréchal, Raphaëlle; Sadoudi, Mohand; Gougeon, Régis; Schmitt-Kopplin, Philippe; Alexandre, Hervé

2017-03-04

Most fermented products are generated by a mixture of microbes. These microbial consortia perform various biological activities responsible for the nutritional, hygienic, and aromatic qualities of the product. Wine is no exception. Substantial yeast and bacterial biodiversity is observed on grapes, and in both must and wine. The diverse microorganisms present interact throughout the winemaking process. The interactions modulate the hygienic and sensorial properties of the wine. Many studies have been conducted to elucidate the nature of these interactions, with the aim of establishing better control of the two fermentations occurring during wine processing. However, wine is a very complex medium making such studies difficult. In this review, we present the current state of research on microbial interactions in wines. We consider the different kinds of interactions between different microorganisms together with the consequences of these interactions. We underline the major challenges to obtaining a better understanding of how microbes interact. Finally, strategies and methodologies that may help unravel microbe interactions in wine are suggested.

Microbiological risk from minimally processed packaged salads in the Dutch food chain.

PubMed

Pielaat, Annemarie; van Leusden, Frans M; Wijnands, Lucas M

2014-03-01

The objective of this study was to evaluate the microbial hazard associated with the consumption of mixed salads produced under standard conditions. The presence of Salmonella, Campylobacter spp., and Escherichia coli O157 in the Dutch production chain of mixed salads was determined. Microbial prevalence and concentration data from a microbiological surveillance study were used as inputs for the quantitative microbial risk assessment. Chain logistics, production figures, and consumption patterns were combined with the survey data for the risk assessment chain approach. The results of the sample analysis were used to track events from contamination through human illness. Wide 95% confidence intervals around the mean were found for estimated annual numbers of illnesses resulting from the consumption of mixed salads contaminated with Salmonella Typhimurium DT104 (0 to 10,300 cases), Campylobacter spp. (0 to 92,000 cases), or E. coli (0 to 800 cases). The main sources of uncertainty are the lack of decontamination data (i.e., produce washing during processing) and an appropriate dose-response relationship.

Microbial community structure and dynamics in a mixotrophic nitrogen removal process using recycled spent caustic under different loading conditions.

PubMed

Park, Sora; Yu, Jaecheul; Byun, Imgyu; Cho, Sunja; Park, Taejoo; Lee, Taeho

2011-08-01

A laboratory-scale Bardenpho process was established to investigate the proper nitrogen loading rate (NLR) when modified spent caustic (MSC) is applied as electron donor and alkalinity source for denitrification. MSC injection induced autotrophic nitrogen removal with sulfur as electron donor and heterotrophic denitrification. The nitrogen removal rate (NRR) did not increase proportionally to NLR. Based on the total nitrogen concentration in the effluent observed in the trials with MSC, the NLR in the influent should not exceed 0.15 kg N/m(3)d in order to satisfy water quality regulations. Microbial communities in the anoxic reactors were characterized by pyrosequencing of 16S rRNA gene sequences amplified by the polymerase chain reaction of DNA extracted from sludge samples. Microbial diversity was lower as MSC dosage was increased, and the injection of MSC caused an increase in SOB belonging to the genus Thiobacillus which is responsible for denitrification using sulfur. Copyright © 2011 Elsevier Ltd. All rights reserved.

Stronger warming effects on microbial abundances in colder regions

DOE PAGES

Chen, Ji; Luo, Yiqi; Xia, Jianyang; ...

2015-12-10

Soil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal, and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra,more » and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our results therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions.« less

Stronger warming effects on microbial abundances in colder regions

PubMed Central

Chen, Ji; Luo, Yiqi; Xia, Jianyang; Jiang, Lifen; Zhou, Xuhui; Lu, Meng; Liang, Junyi; Shi, Zheng; Shelton, Shelby; Cao, Junji

2015-01-01

Soil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal, and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra, and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our findings therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions. PMID:26658882

Solving Microbial Spoilage Problems in Processed Foods

NASA Astrophysics Data System (ADS)

Clavero, Rocelle

This chapter surveys common microbial food spoilage processes. The chapter is organized by food products and includes sections addressing spoilage in meat, poultry, fish; dairy products (milk, butter, cheese); beverage products; bakery products; canned foods; fruit and confectionery products; and emulsions. It addresses the isolation and identification of spoilage organisms and provides several case studies as examples. It introduces various organisms responsible for spoilage including Gram-positive lactic acid bacteria, Gram-negative aerobic bacteria, yeasts, molds, and fungal contaminants. Throughout the chapter, attention is given to when, where, and how spoilage organisms enter the food processing chain. Troubleshooting techniques are suggested. The effect (or lack of effect) of heating, dehydration, pH change, cooling, and sealing on various organisms is explained throughout. The chapter contains four tables that connect specific organisms to various spoilage manifestations in a variety of food products.

Rhizosphere Processes Are Quantitatively Important Components of Terrestrial Biogeochemical Cycles: Data & Models

NASA Astrophysics Data System (ADS)

Finzi, A.

2016-12-01

The rhizosphere is a hot spot and hot moment for biogeochemical cycles. Microbial activity, extracellular enzyme activity and element cycles are greatly enhanced by root derived carbon inputs. As such the rhizosphere may be an important driver of ecosystem responses to global changes such as rising temperatures and atmospheric CO2 concentrations. Empirical research on the rhizosphere is extensive but extrapolation of rhizosphere processes to large spatial and temporal scales is largely uninterrogated. Using a combination of field studies, meta-analysis and numerical models we have found good reason to think that scaling is possible. In this talk I discuss the results of this research and focus on the results of a new modeling effort that explicitly links root distribution and architecture with a model of microbial physiology to assess the extent to which rhizosphere processes may affect ecosystem responses to global change. Results to date suggest that root inputs of C and possibly nutrients (ie, nitrogen) impact the fate of new C inputs to the soil (ie, accumulation or loss) in response to warming and enhanced productivity at elevated CO2. The model also provides qualitative guidance on incorporating the known effects of ectomycorrhizal fungi on decomposition and rates of soil C and N cycling.

Modeling the survival responses of a multi-component biofilm to environmental stress

NASA Astrophysics Data System (ADS)

Carles Brangarí, Albert; Manzoni, Stefano; Sanchez-Vila, Xavier; Fernàndez-Garcia, Daniel

2017-04-01

Biofilms are consortia of microorganisms embedded in self-produced matrices of biopolymers. The survival of such communities depends on their capacity to improve the environmental conditions of their habitat by mitigating, or even benefitting from some adverse external factors. The mechanisms by which the microbial habitat is regulated remain mostly unknown. However, many studies have reported physiological responses to environmental stresses that include the release of extracellular polymeric substances (EPS) and the induction of a dormancy state. A sound understanding of these capacities is required to enhance the knowledge of the microbial dynamics in soils and its potential role in the carbon cycle, with significant implications for the degradation of contaminants and the emission of greenhouse gases, among others. We present a numerical analysis of the dynamics of soil microbes and their responses to environmental stresses. The conceptual model considers a multi-component heterotrophic biofilm made up of active cells, dormant cells, EPS, and extracellular enzymes. Biofilm distribution and properties are defined at the pore-scale and used to determine nutrient availability and water saturation via feedbacks of biofilm on soil hydraulic properties. The pore space micro-habitat is modeled as a simplified pore-network of cylindrical tubes in which biofilms proliferate. Microbial compartments and most of the carbon fluxes are defined at the bulk level. Microbial processes include the synthesis, decay and detachment of biomass, the activation/deactivation of cells, and the release and reutilization of EPS. Results suggest that the release of EPS and the capacity to enter a dormant state offer clear evolutionary advantages in scenarios characterized by environmental stress. On the contrary, when the conditions are favorable, the diversion of carbon into the production of the aforementioned survival mechanisms does not confer any additional benefit and the population of active cells decline. The proposed model (including complex relations between active biomass and biofilm) has been proved useful to capture the most relevant processes involved in biofilm proliferation and its adaptation to environmental conditions. These aspects are largely neglected in biogeochemical models, but could be relevant in soils where strong feedbacks of microbial activity on hydraulic properties emerge.

Investigating the initial stages of soil formation in glacier forefields using the new biogeochemical model: SHIMMER

NASA Astrophysics Data System (ADS)

Bradley, James; Anesio, Alexandre; Arndt, Sandra; Sabacka, Marie; Barker, Gary; Benning, Liane; Blacker, Joshua; Singarayer, Joy; Tranter, Martyn; Yallop, Marian

2016-04-01

Glaciers and ice sheets in Polar and alpine regions are retreating in response to recent climate warming, exposing terrestrial ecosystems that have been locked under the ice for thousands of years. Exposed soils exhibit successional characteristics that can be characterised using a chronosequence approach. Decades of empirical research in glacier forefields has shown that soils are quickly colonised by microbes which drive biogeochemical cycling of elements and affect soil properties including nutrient concentrations, carbon fluxes and soil stability (Bradley et al, 2014). The characterisation of these soils is important for our understanding of the cycling of organic matter under extreme environmental and nutrient limiting conditions, and their potential contribution to global biogeochemical cycles. This is particularly important as these new areas will become more geographically expansive with continued ice retreat. SHIMMER (Soil biogeocHemIcal Model of Microbial Ecosystem Response) (Bradley et al, 2015) is a new mathematical model that simulates biogeochemical and microbial dynamics in glacier forefields. The model captures, explores and predicts the growth of different microbial groups (classified by function), and the associated cycling of carbon, nitrogen and phosphorus along a chronosequence. SHIMMER improves typical soil model formulations by including explicit representation of microbial dynamics, and those processes which are shown to be important for glacier forefields. For example, we categorise microbial groups by function to represent the diversity of soil microbial communities, and include the different metabolic needs and physiological pathways of microbial organisms commonly found in glacier forefields (e.g. microbes derived from underneath the glacier, typical soil bacteria, and microbes that can fix atmospheric nitrogen and assimilate soil nitrogen). Here, we present data from a study where we integrated modelling using SHIMMER with empirical observations from chronosequences from the forefield of Midtre Lovénbreen, Svalbard (78°N), to investigate the first 120 years of soil development. We carried out an in depth analysis of the model dynamics and determined the most sensitive parameters. We then used laboratory measurements to derive values for those parameters: bacterial growth rate, growth efficiency and temperature dependency. By applying the model to the High-Arctic forefield and integrating the measured parameter values, we could refine the model and easily predict the rapid accumulation of microbial biomass that was observed in our field data. Furthermore, we show that the bacterial production is dominated by autotrophy (rather than heterotrophy). Heterotrophic production in young soils (0-20 years) is supported by labile substrate, whereas carbon stocks in older soils (60-120 years) are more refractory. Nitrogen fixing organisms are responsible for the initial accumulation of available nitrates in the soil. However, microbial processes alone do not explain the build-up of organic matter observed in the field data record. Consequently, the model infers that allochthonous deposition of organic material may play a significant contributory role that could accelerate or facilitate further microbial growth. SHIMMER provides a quantitative evaluation on the dynamics of glacier forefield systems that have previously largely been explored through qualitative interpretation of datasets. References Bradley J.A., Singarayer J.S., Anesio A.M. (2014) Microbial community dynamics in the forefield of glaciers. Proceedings Biological sciences / The Royal Society 281(1795), 2793-2802. (doi:10.1098/rspb.2014.0882). Bradley J.A., Anesio A.M., Singarayer J.S., Heath M.R., Arndt S. (2015) SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems. Geosci Model Dev 8(10), 3441-3470. (doi:10.5194/gmd-8-3441-2015).

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

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

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

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.

Insights on Microbial Activity from Reduction Potential: Electrochemical Noise Analysis of a Pristine Aquifer

NASA Astrophysics Data System (ADS)

Enright, A. M.; Shirokova, V.; Ferris, G.

2012-12-01

Reduction potential was measured in a shallow, till-hosted, pristine aquifer. A previous study* characterized the microbial community of the aquifer, and geochemical analysis of water from the aquifer from 2010, 2011, and 2012 indicates persistent localized geochemical gradients of ferrous, ferric, sulphate, and sulphide ions. The chemical plume changes oxidation state from a reduced centre to oxidized outer boundaries, and microbial activity is responsible for the shift in redox state. Analysis of reduction potential as electrochemical noise in both the frequency and time domains provides insight into the manipulation of dissolved ions by the microbial community. Analysis of electrochemical noise is sensitive enough to distinguish the rates and magnitude of influence of the mechanisms which contribute to the redox state of a system. Self-similarity has been suggested to arise in any system where electrochemical noise is the result of a multitude of contributory processes, and this type of noise signature has been reported for many biological and abiotic natural processes. This observed ubiquity is not well understood. Reduction potential data is analyzed using detrended fluctuation analysis in the frequency domain and detrended moving average analysis in the time domain to characterize the Hurst exponent and fractal dimension of this physiological time series. *V.L. Shirokova and F.G. Ferris. (2012). Microbial Diversity and Biogeochemistry of a Pristine Canadian Shield Groundwater System. Geomicrobiology Journal.

Measuring and modeling C flux rates through the central metabolic pathways in microbial communities using position-specific 13C-labeled tracers

NASA Astrophysics Data System (ADS)

Dijkstra, P.; van Groenigen, K.; Hagerty, S.; Salpas, E.; Fairbanks, D. E.; Hungate, B. A.; KOCH, G. W.; Schwartz, E.

2012-12-01

The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We use position-specific 13C-labeled metabolic tracers, combined with models of microbial metabolic organization, to analyze the response of microbial community energy production, biosynthesis, and C use efficiency (CUE) in soils, decomposing litter, and aquatic communities. The method consists of adding position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through the various metabolic pathways. A simplified metabolic model consisting of 23 reactions is solved using results of the metabolic tracer experiments and assumptions of microbial precursor demand. This new method enables direct estimation of fundamental aspects of microbial energy production, CUE, and soil organic matter formation in relatively undisturbed microbial communities. We will present results showing the range of metabolic patterns observed in these communities and discuss results from testing metabolic models.

Optimization of biomass composition explains microbial growth-stoichiometry relationships

USGS Publications Warehouse

Franklin, O.; Hall, E.K.; Kaiser, C.; Battin, T.J.; Richter, A.

2011-01-01

Integrating microbial physiology and biomass stoichiometry opens far-reaching possibilities for linking microbial dynamics to ecosystem processes. For example, the growth-rate hypothesis (GRH) predicts positive correlations among growth rate, RNA content, and biomass phosphorus (P) content. Such relationships have been used to infer patterns of microbial activity, resource availability, and nutrient recycling in ecosystems. However, for microorganisms it is unclear under which resource conditions the GRH applies. We developed a model to test whether the response of microbial biomass stoichiometry to variable resource stoichiometry can be explained by a trade-off among cellular components that maximizes growth. The results show mechanistically why the GRH is valid under P limitation but not under N limitation. We also show why variability of growth rate-biomass stoichiometry relationships is lower under P limitation than under N or C limitation. These theoretical results are supported by experimental data on macromolecular composition (RNA, DNA, and protein) and biomass stoichiometry from two different bacteria. In addition, compared to a model with strictly homeostatic biomass, the optimization mechanism we suggest results in increased microbial N and P mineralization during organic-matter decomposition. Therefore, this mechanism may also have important implications for our understanding of nutrient cycling in ecosystems.

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

Examining seasonal variations in microbial community composition and metabolism in Lake Tahoe, Sierra Nevada, California to gain insight into the role of spring freshet and lake mixing on lake microbial ecology and biogeochemistry

NASA Astrophysics Data System (ADS)

Aluwihare, L.

2016-12-01

The 2016 "State of the Lake Report" for Lake Tahoe notes that surface waters of have warmed 15 times faster in the last four years as compared to the long trend. Lake mixing depth has decreased with only 4 instances of full-lake mixing ( 450 m) recorded since 2000, none since 2011, and the shallowest depth of mixing on record, 80 m, was observed in 2015. Snowpack in the region shows a long-term decline, and April snowpack in 2015 was the lowest recorded in nearly 100 years. Lake biomass peaks shortly after mixing occurs, which demonstrates the dependence of lake primary production on this process. Lake mixing also oxygenates deep waters of the lake. Mixing, organic matter production, and vertical gradients in nutrient and oxygen concentrations profoundly impact the depth distribution of microbial communities and metabolisms. Spring melt also brings nutrients into the lake including organic matter; and in other high elevation lake systems it has been shown that streamflow seeds the lake's microbiome. Here we present data from an year long observation of monthly changes in microbial (including phytoplankton) community composition to examine how the seasonally segregated processes of runoff, lake mixing, and surface primary production affect Lake Tahoe's microbial ecology. Members of certain phylogenetic groups showed trends that we are currently exploring in the context of their metabolic capabilities. For example, Chlorobi and Chloroflexi primarily appear in surface waters during deep mixing, consistent with some of them being sensitive to oxygen. Similarly, common but poorly characterized clades of Actinobacteria exhibited negative responses to discharge, while certain clades of Betaproteobacteria exhibited a positive response during and following discharge events at LT. Actinobacteria have been found to be abundant in numerous lake systems suggesting that their metabolic capabilities maybe particularly telling of the dominant species sorting mechanisms at play in large lakes. Some members of the lake's microbial community appeared sensitive to the loading of terrestrial DOM. However, other members were abundant during times of high primary production. These latter populations may be more vulnerable to processes that decrease overall lake productivity.

2012 Gordon Research Conference on Microbial Stress Response, Schedule and Speaker/Poster Program

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

Donohue, Timothy J.

2012-07-20

The Gordon Research Conference on Microbial Stress Response was held at Mount Holyoke College, South Hadley, Massachusetts, July 15-20, 2012. The Conference was well-attended with 180 participants. The 2012 Microbial Stress Responses Gordon Research Conference will provide a forum for the open reporting of recent discoveries on the diverse mechanisms employed by microbes to respond to stress. Approaches range from analysis at the molecular level (how are signals perceived and transmitted to change gene expression or function) to cellular and microbial community responses. Attached is a copy of the formal schedule and speaker program and the poster program.

Non-microbial methane emissions from soils

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Accelerated rates of in situ microbial activity after permafrost collapse estimated from a porewater isotope model

NASA Astrophysics Data System (ADS)

Waldrop, M. P.; Neumann, R. B.; Jones, M.; Manies, K.; Mcfarland, J. W.; Blazewicz, S.; Turetsky, M. R.

2016-12-01

Permafrost thaw is expected to become widespread in interior Alaska over the coming century, resulting in increased CO2 and CH4 fluxes from soils and a positive feedback to global warming. However much of our understanding of the microbial response to thaw is predicated on simple laboratory incubations that preclude the multitude of interactions occurring in soils under field situations. Here, we utilize a time series of 13CO2 and 13CH4 measured in porewater collected from thermokarst bogs of different ages to estimate in-situ reaction rates of microbial respiration, methanogenesis from acetate, methanogenesis from CO2, homoacetogenesis, and methane oxidation from porewater concentrations and 13CO2 and 13CH4. We utilized this modeling technique to test the hypothesis that microbial activities are stimulated soon after permafrost thaw and this effect declines over time. Our field site is a chronosequence of thermokarst bogs at the Alaska Peatland Experiment (APEX) in interior AK where we have observed significant losses of peatland carbon since permafrost collapse over the last half century. Concentrations of dissolved CO2 and CH4 in porewater increased with depth, and were higher in the youngest bog compared to the older bogs. With increasing depth 13CH4 became more depleted while 13CO2 became more enriched. Preliminary modeling results, based upon these porewater gas concentrations and isotope values, indicate that microbial activities are higher in the youngest bogs compared to the older bogs, supporting the hypothesis that accelerated rates of microbial activities in young thermokarst features are responsible for high rates of C losses from these systems. Additionally, model results will be compared to variation in the abundance of methanogens, methane oxidizers, and acetogens as well as process rates measured in lab incubations, providing insights into the mechanisms responsible for these losses.

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem

PubMed Central

Wang, Yuanqi; Hatt, Janet K.; Tsementzi, Despina; Rodriguez-R, Luis M.; Ruiz-Pérez, Carlos A.; Kizer, Heidi; Maresca, Gina; Krishnan, Raj; Poretsky, Rachel; Spain, Jim C.

2017-01-01

ABSTRACT A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called “rare biosphere.” How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species. IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants. PMID:28258138

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

PubMed

Wang, Yuanqi; Hatt, Janet K; Tsementzi, Despina; Rodriguez-R, Luis M; Ruiz-Pérez, Carlos A; Weigand, Michael R; Kizer, Heidi; Maresca, Gina; Krishnan, Raj; Poretsky, Rachel; Spain, Jim C; Konstantinidis, Konstantinos T

2017-04-15

A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species. IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants. Copyright © 2017 American Society for Microbiology.

The role of lipids in host microbe interactions.

PubMed

Lang, Roland; Mattner, Jochen

2017-06-01

Lipids are one of the major subcellular constituents and serve as signal molecules, energy sources, metabolic precursors and structural membrane components in various organisms. The function of lipids can be modified by multiple biochemical processes such as (de-)phosphorylation or (de-)glycosylation, and the organization of fatty acids into distinct cellular pools and subcellular compartments plays a pivotal role for the morphology and function of various cell populations. Thus, lipids regulate, for example, phagosome formation and maturation within host cells and thus, are critical for the elimination of microbial pathogens. Vice versa, microbial pathogens can manipulate the lipid composition of phagosomal membranes in host cells, and thus avoid their delivery to phagolysosomes. Lipids of microbial origin belong also to the strongest and most versatile inducers of mammalian immune responses upon engagement of distinct receptors on myeloid and lymphoid cells. Furthermore, microbial lipid toxins can induce membrane injuries and cell death. Thus, we will review here selected examples for mutual host-microbe interactions within the broad and divergent universe of lipids in microbial defense, tissue injury and immune evasion.

Assessing the impact of nano- and micro-scale zerovalent iron particles on soil microbial activities: particle reactivity interferes with assay conditions and interpretation of genuine microbial effects.

PubMed

Cullen, Laurence G; Tilston, Emma L; Mitchell, Geoff R; Collins, Chris D; Shaw, Liz J

2011-03-01

The effects of nano-scale and micro-scale zerovalent iron (nZVI and mZVI) particles on general (dehydrogenase and hydrolase) and specific (ammonia oxidation potential, AOP) activities mediated by the microbial community in an uncontaminated soil were examined. nZVI (diameter 12.5 nm; 10 mg g⁻¹ soil) apparently inhibited AOP and nZVI and mZVI apparently stimulated dehydrogenase activity but had minimal influence on hydrolase activity. Sterile experiments revealed that the apparent inhibition of AOP could not be interpreted as such due to the confounding action of the particles, whereas, the nZVI-enhanced dehydrogenase activity could represent the genuine response of a stimulated microbial population or an artifact of ZVI reactivity. Overall, there was no evidence for negative effects of nZVI or mZVI on the processes studied. When examining the impact of redox active particles such as ZVI on microbial oxidation-reduction reactions, potential confounding effects of the test particles on assay conditions should be considered. Copyright © 2010 Elsevier Ltd. All rights reserved.

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.

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

PubMed

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

2016-01-01

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

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

PubMed Central

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

2016-01-01

Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability. PMID:27486444

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

PubMed

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

2014-09-04

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

LABORATORY AND FIELD RESULTS LINKING HIGH CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

EPA Science Inventory

The results of a l6-month field and l6-month meso-scale laboratory investigation of unconsolidated sandy environments contaminated by petroleum hydrocarbons that are undergoing natural biodegradation is presented. The purpose was to understand the processes responsible for causin...

Complex conductivity response to microbial growth and biofilm formation on phenanthrene spiked medium

NASA Astrophysics Data System (ADS)

Albrecht, Remy; Gourry, Jean Christophe; Simonnot, Marie-Odile; Leyval, Corinne

2011-11-01

Several laboratory studies have recently demonstrated the utility of geophysical methods for the investigation of microbial-induced changes over contaminated sites. However, it remains difficult to distinguish the effects due to the new physical properties imparted by microbial processes, to bacterial growth, or to the development of bacterial biofilm. We chose to study the influence of biofilm formation on geophysical response using complex conductivity measurements (0.1-1000 Hz) in phenanthrene-contaminated media. Biotic assays were conducted with two phenanthrene (PHE) degrading bacterial strains: Burkholderia sp (NAH1), which produced biofilm and Stenophomonas maltophilia (MATE10), which did not, and an abiotic control. Results showed that bacterial densities for NAH1 and MATE10 strains continuously increased at the same rate during the experiment. However, the complex conductivity signature showed noticeable differences between the two bacteria, with a phase shift of 50 mrad at 4 Hz for NAH1, which produced biofilm. Biofilm volume was quantified by Scanning Confocal Laser Microscopy (SCLM). Significant correlations were established between phase shift decrease and biofilm volume for NAH1 assays. Results suggest that complex conductivity measurements, specifically phase shift, can be a useful indicator of biofilm formation inside the overall signal of microbial activity on contaminated sites.

Validation of high throughput sequencing and microbial forensics applications

PubMed Central

2014-01-01

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security. PMID:25101166

Validation of high throughput sequencing and microbial forensics applications.

PubMed

Budowle, Bruce; Connell, Nancy D; Bielecka-Oder, Anna; Colwell, Rita R; Corbett, Cindi R; Fletcher, Jacqueline; Forsman, Mats; Kadavy, Dana R; Markotic, Alemka; Morse, Stephen A; Murch, Randall S; Sajantila, Antti; Schmedes, Sarah E; Ternus, Krista L; Turner, Stephen D; Minot, Samuel

2014-01-01

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.

Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation.

PubMed

Chojnacka, Aleksandra; Szczęsny, Paweł; Błaszczyk, Mieczysław K; Zielenkiewicz, Urszula; Detman, Anna; Salamon, Agnieszka; Sikora, Anna

2015-01-01

Anaerobic digestion is a complex process involving hydrolysis, acidogenesis, acetogenesis and methanogenesis. The separation of the hydrogen-yielding (dark fermentation) and methane-yielding steps under controlled conditions permits the production of hydrogen and methane from biomass. The characterization of microbial communities developed in bioreactors is crucial for the understanding and optimization of fermentation processes. Previously we developed an effective system for hydrogen production based on long-term continuous microbial cultures grown on sugar beet molasses. Here, the acidic effluent from molasses fermentation was used as the substrate for methanogenesis in an upflow anaerobic sludge blanket bioreactor. This study focused on the molecular analysis of the methane-yielding community processing the non-gaseous products of molasses fermentation. The substrate for methanogenesis produces conditions that favor the hydrogenotrophic pathway of methane synthesis. Methane production results from syntrophic metabolism whose key process is hydrogen transfer between bacteria and methanogenic Archaea. High-throughput 454 pyrosequencing of total DNA isolated from the methanogenic microbial community and bioinformatic sequence analysis revealed that the domain Bacteria was dominated by Firmicutes (mainly Clostridia), Bacteroidetes, δ- and γ-Proteobacteria, Cloacimonetes and Spirochaetes. In the domain Archaea, the order Methanomicrobiales was predominant, with Methanoculleus as the most abundant genus. The second and third most abundant members of the Archaeal community were representatives of the Methanomassiliicoccales and the Methanosarcinales. Analysis of the methanogenic sludge by scanning electron microscopy with Energy Dispersive X-ray Spectroscopy and X-ray diffraction showed that it was composed of small highly heterogeneous mineral-rich granules. Mineral components of methanogenic granules probably modulate syntrophic metabolism and methanogenic pathways. A rough functional analysis from shotgun data of the metagenome demonstrated that our knowledge of methanogenesis is poor and/or the enzymes responsible for methane production are highly effective, since despite reasonably good sequencing coverage, the details of the functional potential of the microbial community appeared to be incomplete.

Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation

PubMed Central

Chojnacka, Aleksandra; Szczęsny, Paweł; Błaszczyk, Mieczysław K.; Zielenkiewicz, Urszula; Detman, Anna; Salamon, Agnieszka; Sikora, Anna

2015-01-01

Anaerobic digestion is a complex process involving hydrolysis, acidogenesis, acetogenesis and methanogenesis. The separation of the hydrogen-yielding (dark fermentation) and methane-yielding steps under controlled conditions permits the production of hydrogen and methane from biomass. The characterization of microbial communities developed in bioreactors is crucial for the understanding and optimization of fermentation processes. Previously we developed an effective system for hydrogen production based on long-term continuous microbial cultures grown on sugar beet molasses. Here, the acidic effluent from molasses fermentation was used as the substrate for methanogenesis in an upflow anaerobic sludge blanket bioreactor. This study focused on the molecular analysis of the methane-yielding community processing the non-gaseous products of molasses fermentation. The substrate for methanogenesis produces conditions that favor the hydrogenotrophic pathway of methane synthesis. Methane production results from syntrophic metabolism whose key process is hydrogen transfer between bacteria and methanogenic Archaea. High-throughput 454 pyrosequencing of total DNA isolated from the methanogenic microbial community and bioinformatic sequence analysis revealed that the domain Bacteria was dominated by Firmicutes (mainly Clostridia), Bacteroidetes, δ- and γ-Proteobacteria, Cloacimonetes and Spirochaetes. In the domain Archaea, the order Methanomicrobiales was predominant, with Methanoculleus as the most abundant genus. The second and third most abundant members of the Archaeal community were representatives of the Methanomassiliicoccales and the Methanosarcinales. Analysis of the methanogenic sludge by scanning electron microscopy with Energy Dispersive X-ray Spectroscopy and X-ray diffraction showed that it was composed of small highly heterogeneous mineral-rich granules. Mineral components of methanogenic granules probably modulate syntrophic metabolism and methanogenic pathways. A rough functional analysis from shotgun data of the metagenome demonstrated that our knowledge of methanogenesis is poor and/or the enzymes responsible for methane production are highly effective, since despite reasonably good sequencing coverage, the details of the functional potential of the microbial community appeared to be incomplete. PMID:26000448

Spectral Characteristics of Salinized Soils during Microbial Remediation Processes.

PubMed

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

2015-09-01

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

Soil microbial responses to warming and increased precipitation and their implications for ecosystem C cycling.

PubMed

Zhang, Naili; Liu, Weixing; Yang, Haijun; Yu, Xingjun; Gutknecht, Jessica L M; Zhang, Zhe; Wan, Shiqiang; Ma, Keping

2013-11-01

A better understanding of soil microbial ecology is critical to gaining an understanding of terrestrial carbon (C) cycle-climate change feedbacks. However, current knowledge limits our ability to predict microbial community dynamics in the face of multiple global change drivers and their implications for respiratory loss of soil carbon. Whether microorganisms will acclimate to climate warming and ameliorate predicted respiratory C losses is still debated. It also remains unclear how precipitation, another important climate change driver, will interact with warming to affect microorganisms and their regulation of respiratory C loss. We explore the dynamics of microorganisms and their contributions to respiratory C loss using a 4-year (2006-2009) field experiment in a semi-arid grassland with increased temperature and precipitation in a full factorial design. We found no response of mass-specific (per unit microbial biomass C) heterotrophic respiration to warming, suggesting that respiratory C loss is directly from microbial growth rather than total physiological respiratory responses to warming. Increased precipitation did stimulate both microbial biomass and mass-specific respiration, both of which make large contributions to respiratory loss of soil carbon. Taken together, these results suggest that, in semi-arid grasslands, soil moisture and related substrate availability may inhibit physiological respiratory responses to warming (where soil moisture was significantly lower), while they are not inhibited under elevated precipitation. Although we found no total physiological response to warming, warming increased bacterial C utilization (measured by BIOLOG EcoPlates) and increased bacterial oxidation of carbohydrates and phenols. Non-metric multidimensional scaling analysis as well as ANOVA testing showed that warming or increased precipitation did not change microbial community structure, which could suggest that microbial communities in semi-arid grasslands are already adapted to fluctuating climatic conditions. In summary, our results support the idea that microbial responses to climate change are multifaceted and, even with no large shifts in community structure, microbial mediation of soil carbon loss could still occur under future climate scenarios.

Fermented functional foods based on probiotics and their biogenic metabolites.

PubMed

Stanton, Catherine; Ross, R Paul; Fitzgerald, Gerald F; Van Sinderen, Douwe

2005-04-01

The claimed health benefits of fermented functional foods are expressed either directly through the interaction of ingested live microorganisms, bacteria or yeast with the host (probiotic effect) or indirectly as a result of ingestion of microbial metabolites produced during the fermentation process (biogenic effect). Although still far from fully understood, several probiotic mechanisms of action have been proposed, including competitive exclusion, competition for nutrients and/or stimulation of an immune response. The biogenic properties of fermented functional foods result from the microbial production of bioactive metabolites such as certain vitamins, bioactive peptides, organic acids or fatty acids during fermentation.

Patterns and Processes of Microbial Community Assembly

PubMed Central

Schmidt, Steven K.; Fukami, Tadashi; O'Neill, Sean P.; Bilinski, Teresa M.; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott

2013-01-01

SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity. PMID:24006468

Rice rhizosphere soil and root surface bacterial community response to water management changes

USDA-ARS?s Scientific Manuscript database

Different water management practices could affect microbial populations in the rice rhizosphere. A field-scale study was conducted to evaluate microbial populations in the root plaque and rhizosphere of rice in response to continuous and intermittent flooding conditions. Microbial populations in rhi...

Response of microbial communities to experimental warming and precipitation decrease in Rzecin peatland (Poland)

NASA Astrophysics Data System (ADS)

Basińska, Anna M.; Gąbka, Maciej; Reczuga, Monika; Łuców, Dominika; Stróżecki, Marcin; Samson, Mateusz; Józefczyk, Damian; Chojnicki, Bogdan; Urbaniak, Marek; Leśny, Jacek; Olejnik, Janusz; Gilbert, Daniel; Silvennoinen, Hanna; Juszczak, Radosław; Lamentowicz, Mariusz

2017-04-01

In the last decade researchers are intensively testing the consequences of different climate change scenarios. Due to high biodiversity, huge amount of stored carbon and their sensitivity to environmental changes, peatlands became important for the temperature increase and drought experiments. Analyses showed that mosses, vascular plants and microbial communities were affected by warming or drought, but still not all effects are clear. Studying the response of microbial groups and indicators (e.g. mixotrophic species of testate amoeba) to warming in combination with decrease of precipitation will allow to better understand the future environmental changes. To recognize the inflow of organic matter and the carbon fixing processes in disturbed environment, we need to analyse the structure and biomass of main groups living in peatlands and the response of those groups to disturbances. The Polish - Norway "WETMAN" project was designed to recognize biotic and abiotic components of ecosystem response to active warming and decrease of precipitation. In this study we present the response of microbial communities and chosen testate amoeba species (TA) to different treatments: warming, warming and decreased precipitation and only decreased precipitation, in relation to control plots. The microbial biomass of upper and lower Sphagnum segments were analysed separately. Particular microbial groups were positively correlated with manipulations e. g. microalgae and rotifers, and other were negatively affected by combination of drought and warming e.g. cyanobacteria and testate amoeba. The structure of community was modified by manipulations, and differed in the case of upper and lower segment of Sphagnum. RDA analyses showed that different factors were crucial for the biomass of microbial groups in upper (conductivity, temperature and phosphorus) and lower (nitrates and sodium) segment. Considering higher taxonomic resolution we found that at the beginning of the experiment TA community was characterised by higher abundance of mixotrophic species (Hyalosphenia papilio, Archerella flavum, Heleopera sphagni) in all plots, after half year of warming and decreased precipitation we found significant decrease of mixotrophic species biomass. Redundancy analysis showed that TA species distribution (in first year of manipulation) was significantly affected by the treatment type and upper and lower Sphagnum segment. The combination of warming and decreased precipitation led to significant testate amoeba biomass decrease (especially of mixotrophic dominant Hyalosphenia papilio). For less abundant species like Nebela tincta we found an increase of biomass in all treatments, compared to control plots. Changes in microbial communities structure, caused by the combination of drought and warming can influence peatland functioning. For instance, reduction of microbial primary production and intensified consumption may modify physicochemical water parameters as well as carbon dynamics. Project financed by the Polish-Norwegian Research Programme operated by the National Centre for Research and Development under the Norwegian Financial Mechanism (No. Pol-Nor/203258/31/2013, WETMAN). Anna M. Basinska acknowledges support from Franche-Comté regional council and Université Bourgogne Franche-Comté.

Effects of nitrogen deposition and cattle grazing on productivity, invasion impact, and soil microbial processes in a serpentine grassland

NASA Astrophysics Data System (ADS)

Pasari, J.; Hernandez, D.; Selmants, P. C.; Keck, D.

2010-12-01

In recent decades, human activities have vastly increased the amount of biologically available nitrogen (N) in the biosphere. The resulting increase in N availability has broadly affected ecosystems through increased productivity, changes in species composition, altered nutrient cycles, and increases in invasion by exotic plant species, especially in systems that were historically low in N. California serpentine grasslands are N-limited ecosystems historically dominated by native species including several threatened and endangered plants and animals. Cattle grazing has emerged as the primary tool for controlling the impact of nitrophilic exotic grasses whose increased abundance has paralleled the regional traffic-derived increase in atmospheric N deposition. We examined the interactive effects of cattle grazing and N deposition on plant community composition, productivity, invasion resistance, and microbial processes in the Bay Area's largest serpentine grassland to determine the efficacy of current management strategies as well as the biogeochemical consequences of exotic species invasion. In the first two years of the study, aboveground net primary productivity decreased in response to grazing and increased in response to nitrogen addition. However, contrary to our hypotheses the change in productivity was not due to an increase in exotic species cover as there was little overall effect of grazing or N addition on species composition. Microbial activity was more responsive to grazing and N. Potential net N mineralization rates increased with N addition, but were not affected by grazing. In contrast, soil respiration rates were inhibited by grazing, but were not affected by N addition; suggesting strong carbon-limitation of soil microbial activity, particularly under grazing. Site differences in soil depth and grazing intensity were often more important than treatment effects. We suspect that the unusually dry conditions in the first two growing seasons inhibited the growth of exotic species and minimized the effects of cattle exclusion and N addition on species composition.

Human host defense peptides - role in maintaining human homeostasis and pathological processes.

PubMed

Dawgul, Malgorzata Anna; Greber, Katarzyna Ewa; Sawicki, Wieslaw; Kamysz, Wojciech

2016-12-12

The human body expresses over 100 host defense peptides and proteins (antimicrobial peptides, AMPs). The compounds are produced by tissues and mucosal surfaces, e.g. skin, the digestive and urinary tract, the ocular surface and neutrophils, and are believed to play a crucial role in defense from microbial infection. They are considered to protect the human body against microbial infections due to their antimicrobial and immunomodulatory activities. As well as having strong antimicrobial activity towards a broad spectrum of microorganisms, AMPs have been found to interact with neutrophils, monocytes and T-cells and promote the production of cytokines. They also neutralize the action of lipopolysaccharide (LPS) and play a crucial role in wound healing processes. In response to the microbial stimuli the AMPs are released in order to fight the infection, however there are several microorganisms evading the human immune system by downregulation of AMPs. Decreased or elevated expression of AMPs is associated also with several non-infectious diseases. Despite numerous studies conducted in the field of AMPs over the last few decades, their exact role in physiological and pathological processes remains to be explained. In this paper, we review the most significant human AMPs and their potential roles in maintaining human homeostasis as well as in pathological processes.

Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies.

PubMed

Jiménez, Núria; Richnow, Hans H; Vogt, Carsten; Treude, Tina; Krüger, Martin

2016-01-01

Microbial transformation of hydrocarbons to methane is an environmentally relevant process taking place in a wide variety of electron acceptor-depleted habitats, from oil reservoirs and coal deposits to contaminated groundwater and deep sediments. Methanogenic hydrocarbon degradation is considered to be a major process in reservoir degradation and one of the main processes responsible for the formation of heavy oil deposits and oil sands. In the absence of external electron acceptors such as oxygen, nitrate, sulfate or Fe(III), fermentation and methanogenesis become the dominant microbial metabolisms. The major end product under these conditions is methane, and the only electron acceptor necessary to sustain the intermediate steps in this process is CO2, which is itself a net product of the overall reaction. We are summarizing the state of the art and recent advances in methanogenic hydrocarbon degradation research. Both the key microbial groups involved as well as metabolic pathways are described, and we discuss the novel insights into methanogenic hydrocarbon-degrading populations studied in laboratory as well as environmental systems enabled by novel cultivation-based and molecular approaches. Their possible implications on energy resources, bioremediation of contaminated sites, deep-biosphere research, and consequences for atmospheric composition and ultimately climate change are also addressed. © 2016 S. Karger AG, Basel.

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes.

PubMed

Wei, Shiping; Cui, Hongpeng; Zhu, Youhai; Lu, Zhenquan; Pang, Shouji; Zhang, Shuai; Dong, Hailiang; Su, Xin

2018-05-01

Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.

Closed nutrient recycling via microbial catabolism in an eco-engineered self regenerating mixed anaerobic microbiome for hydrogenotrophic methanogenesis.

PubMed

Savvas, Savvas; Donnelly, Joanne; Patterson, Tim P; Dinsdale, Richard; Esteves, Sandra R

2017-03-01

A novel eco-engineered mixed anaerobic culture was successfully demonstrated for the first time to be capable of continuous regeneration in nutrient limiting conditions. Microbial catabolism has been found to support a closed system of nutrients able to enrich a culture of lithotrophic methanogens and provide microbial cell recycling. After enrichment, the hydrogenotrophic species was the dominating methanogens while a bacterial substratum was responsible for the redistribution of nutrients. q-PCR results indicated that 7% of the total population was responsible for the direct conversion of the gases. The efficiency of H 2 /CO 2 conversion to CH 4 reached 100% at a gassing rate of above 60v/v/d. The pH of the culture media was effectively sustained at optimal levels (pH 7-8) through a buffering system created by the dissolved CO 2 . The novel approach can reduce the process nutrient/metal requirement and enhance the environmental and financial performance of hydrogenotrophic methanogenesis for renewable energy storage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

PubMed

Saleem, Muhammad; Moe, Luke A

2014-10-01

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial ecology to manage processes in environmental biotechnology.

PubMed

Rittmann, Bruce E

2006-06-01

Microbial ecology and environmental biotechnology are inherently tied to each other. The concepts and tools of microbial ecology are the basis for managing processes in environmental biotechnology; and these processes provide interesting ecosystems to advance the concepts and tools of microbial ecology. Revolutionary advancements in molecular tools to understand the structure and function of microbial communities are bolstering the power of microbial ecology. A push from advances in modern materials along with a pull from a societal need to become more sustainable is enabling environmental biotechnology to create novel processes. How do these two fields work together? Five principles illuminate the way: (i) aim for big benefits; (ii) develop and apply more powerful tools to understand microbial communities; (iii) follow the electrons; (iv) retain slow-growing biomass; and (v) integrate, integrate, integrate.

Biosignature Preservation Vulnerability Associated with Stress Response Metabolic Redox Mode Switching in a Mars Analogue Coupled Microbial Mat Transiting Near-Space

NASA Astrophysics Data System (ADS)

Archer, R.; Ralat, A.

2016-05-01

Examination of a coupled microbial mat recovered from Death Valley failed to detect rosickyte, both before and after exposure to near-space conditions; associated redox proxies suggest diagenesis caused by rapid adaptive microbial stress response.

Injury enhances TLR2 function and antimicrobial peptide expression through a vitamin D–dependent mechanism

PubMed Central

Schauber, Jürgen; Dorschner, Robert A.; Coda, Alvin B.; Büchau, Amanda S.; Liu, Philip T.; Kiken, David; Helfrich, Yolanda R.; Kang, Sewon; Elalieh, Hashem Z.; Steinmeyer, Andreas; Zügel, Ulrich; Bikle, Daniel D.; Modlin, Robert L.; Gallo, Richard L.

2007-01-01

An essential element of the innate immune response to injury is the capacity to recognize microbial invasion and stimulate production of antimicrobial peptides. We investigated how this process is controlled in the epidermis. Keratinocytes surrounding a wound increased expression of the genes coding for the microbial pattern recognition receptors CD14 and TLR2, complementing an increase in cathelicidin antimicrobial peptide expression. These genes were induced by 1,25(OH)2 vitamin D3 (1,25D3; its active form), suggesting a role for vitamin D3 in this process. How 1,25D3 could participate in the injury response was explained by findings that the levels of CYP27B1, which converts 25OH vitamin D3 (25D3) to active 1,25D3, were increased in wounds and induced in keratinocytes in response to TGF-β1. Blocking the vitamin D receptor, inhibiting CYP27B1, or limiting 25D3 availability prevented TGF-β1 from inducing cathelicidin, CD14, or TLR2 in human keratinocytes, while CYP27B1-deficient mice failed to increase CD14 expression following wounding. The functional consequence of these observations was confirmed by demonstrating that 1,25D3 enabled keratinocytes to recognize microbial components through TLR2 and respond by cathelicidin production. Thus, we demonstrate what we believe to be a previously unexpected role for vitamin D3 in innate immunity, enabling keratinocytes to recognize and respond to microbes and to protect wounds against infection. PMID:17290304

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

PubMed Central

Walsh, Aaron M.; Crispie, Fiona; Kilcawley, Kieran; O’Sullivan, Orla; O’Sullivan, Maurice G.; Claesson, Marcus J.

2016-01-01

ABSTRACT Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. Author Video: An author video summary of this article is available. PMID:27822552

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

PubMed

Walsh, Aaron M; Crispie, Fiona; Kilcawley, Kieran; O'Sullivan, Orla; O'Sullivan, Maurice G; Claesson, Marcus J; Cotter, Paul D

2016-01-01

Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides . Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods.

Nitrogen cycle in microbial mats: completely unknown?

NASA Astrophysics Data System (ADS)

Coban, O.; Bebout, B.

2015-12-01

Microbial mats are thought to have originated around 3.7 billion years ago, most likely in the areas around submarine hydrothermal vents, which supplied a source of energy in the form of reduced chemical species from the Earth's interior. Active hydrothermal vents are also believed to exist on Jupiter's moon Europa, Saturn's moon Enceladus, and on Mars, earlier in that planet's history. Microbial mats have been an important force in the maintenance of Earth's ecosystems and the first photosynthesis was also originated there. Microbial mats are believed to exhibit most, if not all, biogeochemical processes that exist in aquatic ecosystems, due to the presence of different physiological groups of microorganisms therein. While most microbially mediated biogeochemical transformations have been shown to occur within microbial mats, the nitrogen cycle in the microbial mats has received very little study in spite of the fact that nitrogen usually limits growth in marine environments. We will present the first results in the determination of a complete nitrogen budget for a photosynthetic microbial mat. Both in situ sources and sinks of nitrogen in photosynthetic microbial mats are being measured using stable isotope techniques. Our work has a particular focus on recently described, but poorly understood, processes, e.g., anammox and dissimilatory nitrate reduction, and an emphasis on understanding the role that nitrogen cycling may play in generating biogenic nitrogen isotopic signatures and biomarker molecules. Measurements of environmental controls on nitrogen cycling should offer insight into the nature of co-evolution of these microbial communities and their planets of origin. Identifying the spatial (microscale) as well as temporal (diel and seasonal) distribution of nitrogen transformations, e.g., rates of nitrification and denitrification, within mats, particularly with respect to the distribution of photosynthetically-produced oxygen, is anticipated. The results of this research, the first results of which will be presented here, will help us to improve our understanding of the cycle of the element most responsible for limiting the production of biomass on Earth and improved an ability to use stable isotopes of nitrogen, and nitrogen containing compounds, in our search for life elsewhere.

Noninvasive methods for dynamic mapping of microbial populations across the landscape

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Sengupta, A.; Troch, P. A.; Volkmann, T. H. M.

2017-12-01

Soil microorganisms drive key ecosystem processes, and yet characterizing their distribution and activity in soil has been notoriously difficult. This is due, in part, to the heterogeneous nature of their response to changing environmental and nutrient conditions across time and space. These dynamics are challenging to constrain in both natural and experimental systems because of sampling difficulty and constraints. For example, soil microbial sampling at the Landscape Evolution Observatory (LEO) infrastructure in Biosphere 2 is limited in efforts to minimize soil disruption to the long term experiment that aims to characterize the interacting biological, hydrological, and geochemical processes driving soil evolution. In this and other systems, new methods are needed to monitor soil microbial communities and their genetic potential over time. In this study, we take advantage of the well-defined boundary conditions on hydrological flow at LEO to develop a new method to nondestructively characterize in situ microbial populations. In our approach, we sample microbes from the seepage flow at the base of each of three replicate LEO hillslopes and use hydrological models to `map back' in situ microbial populations. Over the course of a 3-month periodic rainfall experiment we collected samples from the LEO outflow for DNA and extraction and microbial community composition analysis. These data will be used to describe changes in microbial community composition over the course of the experiment. In addition, we will use hydrological flow models to identify the changing source region of discharge water over the course of periodic rainfall pulses, thereby mapping back microbial populations onto their geographic origin in the slope. These predictions of in situ microbial populations will be ground-truthed against those derived from destructive soil sampling at the beginning and end of the rainfall experiment. Our results will show the suitability of this method for long-term, non-destructive monitoring of the microbial communities that contribute to soil evolution in this large-scale model system. Furthermore, this method may be useful for other study systems with limitations to destructive sampling including other model infrastructures and natural landscapes.

Effects of spaceflight and simulated microgravity on microbial growth and secondary metabolism.

PubMed

Huang, Bing; Li, Dian-Geng; Huang, Ying; Liu, Chang-Ting

2018-05-14

Spaceflight and ground-based microgravity analog experiments have suggested that microgravity can affect microbial growth and metabolism. Although the effects of microgravity and its analogs on microorganisms have been studied for more than 50 years, plausible conflicting and diverse results have frequently been reported in different experiments, especially regarding microbial growth and secondary metabolism. Until now, only the responses of a few typical microbes to microgravity have been investigated; systematic studies of the genetic and phenotypic responses of these microorganisms to microgravity in space are still insufficient due to technological and logistical hurdles. The use of different test strains and secondary metabolites in these studies appears to have caused diverse and conflicting results. Moreover, subtle changes in the extracellular microenvironments around microbial cells play a key role in the diverse responses of microbial growth and secondary metabolisms. Therefore, "indirect" effects represent a reasonable pathway to explain the occurrence of these phenomena in microorganisms. This review summarizes current knowledge on the changes in microbial growth and secondary metabolism in response to spaceflight and its analogs and discusses the diverse and conflicting results. In addition, recommendations are given for future studies on the effects of microgravity in space on microbial growth and secondary metabolism.

Downstream reactions and engineering in the microbially reconstituted pathway for Taxol.

PubMed

Jiang, Ming; Stephanopoulos, Gregory; Pfeifer, Blaine A

2012-05-01

Taxol (a trademarked product of Bristol-Myers Squibb) is a complex isoprenoid natural product which has displayed potent anticancer activity. Originally isolated from the Pacific yew tree (Taxus brevifolia), Taxol has been mass-produced through processes reliant on plant-derived biosynthesis. Recently, there have been alternative efforts to reconstitute the biosynthetic process through technically convenient microbial hosts, which offer unmatched growth kinetics and engineering potential. Such an approach is made challenging by the need to successfully introduce the significantly foreign enzymatic steps responsible for eventual biosynthesis. Doing so, however, offers the potential to engineer more efficient and economical production processes and the opportunity to design and produce tailored analog compounds with enhanced properties. This mini review will specifically focus on heterologous biosynthesis as it applies to Taxol with an emphasis on the challenges associated with introducing and reconstituting the downstream reaction steps needed for final bioactivity.

Microbial quantification in activated sludge: the hits and misses.

PubMed

Hall, S J; Keller, J; Blackall, L L

2003-01-01

Since the implementation of the activated sludge process for treating wastewater, there has been a reliance on chemical and physical parameters to monitor the system. However, in biological nutrient removal (BNR) processes, the microorganisms responsible for some of the transformations should be used to monitor the processes with the overall goal to achieve better treatment performance. The development of in situ identification and rapid quantification techniques for key microorganisms involved in BNR are required to achieve this goal. This study explored the quantification of Nitrospira, a key organism in the oxidation of nitrite to nitrate in BNR. Two molecular genetic microbial quantification techniques were evaluated: real-time polymerase chain reaction (PCR) and fluorescence in situ hybridisation (FISH) followed by digital image analysis. A correlation between the Nitrospira quantitative data and the nitrate production rate, determined in batch tests, was attempted. The disadvantages and advantages of both methods will be discussed.

Responses of two nonlinear microbial models to warming and increased carbon input

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

Wang, Y. P.; Jiang, J.; Chen-Charpentier, Benito

A number of nonlinear microbial models of soil carbon decomposition have been developed. Some of them have been applied globally but have yet to be shown to realistically represent soil carbon dynamics in the field. A thorough analysis of their key differences is needed to inform future model developments. In this paper, we compare two nonlinear microbial models of soil carbon decomposition: one based on reverse Michaelis–Menten kinetics (model A) and the other on regular Michaelis–Menten kinetics (model B). Using analytic approximations and numerical solutions, we find that the oscillatory responses of carbon pools to a small perturbation in theirmore » initial pool sizes dampen faster in model A than in model B. Soil warming always decreases carbon storage in model A, but in model B it predominantly decreases carbon storage in cool regions and increases carbon storage in warm regions. For both models, the CO 2 efflux from soil carbon decomposition reaches a maximum value some time after increased carbon input (as in priming experiments). This maximum CO 2 efflux (F max) decreases with an increase in soil temperature in both models. However, the sensitivity of F max to the increased amount of carbon input increases with soil temperature in model A but decreases monotonically with an increase in soil temperature in model B. These differences in the responses to soil warming and carbon input between the two nonlinear models can be used to discern which model is more realistic when compared to results from field or laboratory experiments. Lastly, these insights will contribute to an improved understanding of the significance of soil microbial processes in soil carbon responses to future climate change.« less

Permafrost soil characteristics and microbial community structure across a boreal forest watershed vary over short spatial scales and dictate community responses to thaw.

NASA Astrophysics Data System (ADS)

Stegen, J.; Bottos, E. M.; Kennedy, D.; Romero, E. B.; Fansler, S.; Chu, R. K.; Tfaily, M.; Jansson, J.; Bernstein, H. C.; Brown, J. M.; Markillie, L. M.

2017-12-01

Understanding drivers of permafrost microbial community structure and function is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw; however, studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from the selective factors that influence non-permafrost soil communities, but that pre-thaw environmental and community characteristics will be strong determinants of community structure and function post-thaw. We characterized patterns of environmental variation and microbial community composition in sixty permafrost samples spanning landscape gradients in a boreal forest watershed, and monitored community responses to thaw. Consistent with our hypothesis, we found that, proportionally, the strongest process influencing permafrost community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21) and variable selection (0.16), and that deterministic selection arose primarily from energetic constraints of the permafrost environment. Our data supported a structural equation model in which organic carbon thermodynamics and organic acid content, influenced redox conditions and total selection. Post-thaw community composition was found to be driven primarily by pre-thaw community composition, indicating a strong influence of historical conditions. Together, these results suggest that community responses to thaw may be highly varied over short distances and that changes in community structure and function are likely to be drastic, as changes to system hydrology mobilize organisms and nutrients, thereby relieving the primary constraints on the system. These findings are being integrated with metabolomic and metatranscriptomic analyses to improve understanding of how pre-thaw conditions can be used to predict microbial activity post-thaw.

Responses of two nonlinear microbial models to warming and increased carbon input

DOE PAGES

Wang, Y. P.; Jiang, J.; Chen-Charpentier, Benito; ...

2016-02-18

A number of nonlinear microbial models of soil carbon decomposition have been developed. Some of them have been applied globally but have yet to be shown to realistically represent soil carbon dynamics in the field. A thorough analysis of their key differences is needed to inform future model developments. In this paper, we compare two nonlinear microbial models of soil carbon decomposition: one based on reverse Michaelis–Menten kinetics (model A) and the other on regular Michaelis–Menten kinetics (model B). Using analytic approximations and numerical solutions, we find that the oscillatory responses of carbon pools to a small perturbation in theirmore » initial pool sizes dampen faster in model A than in model B. Soil warming always decreases carbon storage in model A, but in model B it predominantly decreases carbon storage in cool regions and increases carbon storage in warm regions. For both models, the CO 2 efflux from soil carbon decomposition reaches a maximum value some time after increased carbon input (as in priming experiments). This maximum CO 2 efflux (F max) decreases with an increase in soil temperature in both models. However, the sensitivity of F max to the increased amount of carbon input increases with soil temperature in model A but decreases monotonically with an increase in soil temperature in model B. These differences in the responses to soil warming and carbon input between the two nonlinear models can be used to discern which model is more realistic when compared to results from field or laboratory experiments. Lastly, these insights will contribute to an improved understanding of the significance of soil microbial processes in soil carbon responses to future climate change.« less

Microbial Community Activity is Insensitive to Passive Warming in a Semiarid Ecosystem

NASA Astrophysics Data System (ADS)

Espinosa, N. J.; Gallery, R. E.; Fehmi, J. S.

2016-12-01

Soil microorganisms drive ecosystem nutrient cycling through the production of extracellular enzymes, which facilitate organic matter decomposition, and the flux of large amounts of carbon dioxide to the atmosphere. Although aird and semiarid ecosystems occupy over 40% of land cover and are projected to expand due to climate change, much of our current understanding of these processes comes from mesic temperate ecosystems. Semiarid ecosystems have added complexity due to the widespread biological adaptations to infrequent and discreet precipitation pulses, which enable biological activity to persist throughout dry periods and thrive following seasonal precipitation events. Additionally, the intricacies of plant-microbe interactions and the response of these interactions to a warmer climate and increased precipitation variability in semiarid ecosystems present a continued challenge for climate change research. In this study, we used a passive warming experiment with added plant debris as either woodchip or biochar, to simulate different long-term carbon additions to two common semiarid soils. The response of soil respiration, plant biomass, and microbial activity was monitored bi-annually. We hypothesized that microbial activity would increase with temperature manipulations when soil moisture limitation was alleviated by summer precipitation. The passive warming treatment was most pronounced during periods of daily and seasonal temperature maxima. For all seven hydrolytic enzymes examined, there was no significant response to experimental warming, regardless of seasonal climatic and soil moisture variation. Surprisingly, soil respiration responded positively to warming for certain carbon additions and seasons, which did not correspond with a similar response in plant biomass. The enzyme results observed here are consistent with the few other experimental results for warming in semiarid ecosystems and indicate that the soil microbial community activity of semiarid ecosystems is potentially resilient to a warmer environment.

Cell-autonomous defense, re-organization and trafficking of membranes in plant-microbe interactions.

PubMed

Dörmann, Peter; Kim, Hyeran; Ott, Thomas; Schulze-Lefert, Paul; Trujillo, Marco; Wewer, Vera; Hückelhoven, Ralph

2014-12-01

Plant cells dynamically change their architecture and molecular composition following encounters with beneficial or parasitic microbes, a process referred to as host cell reprogramming. Cell-autonomous defense reactions are typically polarized to the plant cell periphery underneath microbial contact sites, including de novo cell wall biosynthesis. Alternatively, host cell reprogramming converges in the biogenesis of membrane-enveloped compartments for accommodation of beneficial bacteria or invasive infection structures of filamentous microbes. Recent advances have revealed that, in response to microbial encounters, plasma membrane symmetry is broken, membrane tethering and SNARE complexes are recruited, lipid composition changes and plasma membrane-to-cytoskeleton signaling is activated, either for pre-invasive defense or for microbial entry. We provide a critical appraisal on recent studies with a focus on how plant cells re-structure membranes and the associated cytoskeleton in interactions with microbial pathogens, nitrogen-fixing rhizobia and mycorrhiza fungi. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production.

PubMed

Gallagher, Daniella; Parker, David; Allen, Damian J; Tsesmetzis, Nicolas

2018-05-23

Significant low-cost biofuel production volumes could be achieved from commercial-scale silage by redirecting lactic acid fermentation to ethanol production. A temporal metagenomic analysis on ensiled sweet sorghum inoculated with an ethanologenic yeast has been conducted to understand the underlying microbial processes during bioethanol production. Individual silage buckets approximating silage piles were prepared with freshly harvested material and supplemented with ethanologenic yeast, sulfuric acid or both. The ensiling progress was assessed using high performance liquid chromatography, microbial taxonomic identification and abundance. The combined treatment with Saccharomyces and acid led to a steady reduction of bacterial abundance and microbial diversity with Lactobacillus becoming the dominant genus during the late timepoints. Furthermore, the addition of acid to inhibit bacterial growth hindered Saccharomyces ability to compete with native yeasts like Candida. Knowledge of the response of the in-situ microbial community to the various treatments during ensiling will help improve current methodologies for bioethanol production. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Effect of the length of the cycle on biodegradable polymer production and microbial community selection in a sequencing batch reactor.

PubMed

Dionisi, Davide; Majone, Mauro; Vallini, Giovanni; Gregorio, Simona Di; Beccari, Mario

2007-01-01

The effect of the length of the cycle on the enrichment and selection of mixed cultures in sequencing batch reactors (SBRs) has been studied, with the aim of biodegradable polymers (namely, polyhydroxyalkanoates (PHAs)) production from organic wastes. At a fixed feed concentration (20 gCOD/L) and organic loading rate (20 gCOD/L/day), the SBR was operated at different lengths of the cycle, in the range 1-8 h. Process performance was measured by considering the rates and yields of polymer storage and of the competing phenomenon of growth. The selected biomass was enriched with microorganisms that were able to store PHAs at high rates and yields only when the length of the cycle was 2 or 4 h, even though in these conditions the process was unstable. On the other hand, when the length of the cycle was 1 or 8 h, the dynamic response of the selected microorganisms was dominated by growth. The best process performance was characterized by storage rates in the range 500-600 mgCOD/gCOD/h and storage yields of 0.45-0.55 COD/COD. The corresponding productivity of the process was in the range 0.25-0.30 gPHA/L/h, the highest values obtained until now for mixed cultures. The microbial composition of the selected biomasses was analyzed through denaturing gradient gel electrophoresis (DGGE) and reverse-transcriptase denaturing gradient gel electrophoresis (RT-DGGE). The instability of the runs characterized by high storage rate was associated with a higher microbial heterogeneity compared to the runs with a stable growth response.

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

NASA Astrophysics Data System (ADS)

Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

2015-08-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass, and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter are identified as important in sustaining this productivity. Microbial production in young soils is supported by labile organic matter, whereas carbon stocks in older soils are more refractory. Nitrogen fixing bacteria are responsible for the initial accumulation of available nitrates in the soil. Biogeochemical rates are highly seasonal, as observed in experimental data. The development and application of SHIMMER not only provides important new insights into forefield dynamics, but also highlights aspects of these systems that require further field and laboratory research. The most pressing advances need to come in quantifying nutrient budgets and biogeochemical rates, in exploring seasonality, the fate of allochthonous deposition in relation to autochthonous production, and empirical studies of microbial growth and cell death, to increase understanding of how glacier forefield development contributes to the global biogeochemical cycling and climate in the future.

Ecosystem and physiological scales of microbial responses to nutrients in a detritus-based stream: results of a 5-year continuous enrichment

Treesearch

Keller Suberkropp; Vladislav Gulis; Amy D. Rosemond; Jonathan Benstead

2010-01-01

Our study examined the response of leaf detritus–associated microorganisms (both bacteria and fungi) to a 5-yr continuous nutrient enrichment of a forested headwater stream. Leaf litter dominates detritus inputs to such streams and, on a system wide scale, serves as the key substrate for microbial colonization. We determined physiological responses as microbial biomass...

Environmental context affects microbial ecophysiological mechanisms underpinning soil carbon storage under different land use

NASA Astrophysics Data System (ADS)

Malik, A. A.; Puissant, J.; Buckeridge, K. M.; Goodall, T.; Jehmlich, N.; Chowdhury, S.; Gleixner, G.; Griffiths, R.

2017-12-01

Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of organic matter in soil. Increasing evidence now exists to suggest that microbial biomass contributes significantly to soil organic carbon formation. However, we do not fully understand the microbial mechanisms of organic matter processing and this hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically link key microbial ecophysiological traits to soil carbon storage in temperate grassland habitats ranging in land use from pristine species-rich grasslands to intensive croplands in 56 different soils across Britain. Physiological mechanisms of soil microorganisms were assessed using stable carbon isotope tracing and soil proteomics. Through spatial patterns and path analysis of structural equation modeling we discern two distinct pH-related mechanisms of soil carbon storage and highlight that the response of these mechanistic indicators is shaped by the environmental context. Land use intensification in low pH soils that increases soil pH above a threshold value ( 6.2) leads to loss of carbon due to increased microbial degradation as a result of lower acid retardation of organic matter decomposition. On the contrary, the loss of carbon through intensification in high pH (> 6.2) soils was linked to decreased microbial biomass and reduced carbon use efficiency that was linked to tradeoffs with stress alleviation and resource acquisition. We conclude that land use intensification-induced changes in soil pH can be used as a proxy to determine the effect of land management strategies on microbial soil carbon cycling processes and emphasize that more extensive land management practices at higher soil pH have greater potential for soil carbon storage through increased microbial metabolic efficiency, whereas in acidic soils abiotic factors exert a greater influence on the fate of soil carbon.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.

PubMed

Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

2015-03-01

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model

PubMed Central

Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

2015-01-01

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs. PMID:26074626

Enhanced microbial coalbed methane generation: A review of research, commercial activity, and remaining challenges

USGS Publications Warehouse

Ritter, Daniel J.; Vinson, David S.; Barnhart, Elliott P.; Akob, Denise M.; Fields, Matthew W.; Cunningham, Al B.; Orem, William H.; McIntosh, Jennifer C.

2015-01-01

Coalbed methane (CBM) makes up a significant portion of the world’s natural gas resources. The discovery that approximately 20% of natural gas is microbial in origin has led to interest in microbially enhanced CBM (MECoM), which involves stimulating microorganisms to produce additional CBM from existing production wells. This paper reviews current laboratory and field research on understanding processes and reservoir conditions which are essential for microbial CBM generation, the progress of efforts to stimulate microbial methane generation in coal beds, and key remaining knowledge gaps. Research has been primarily focused on identifying microbial communities present in areas of CBM generation and attempting to determine their function, in-situ reservoir conditions that are most favorable for microbial CBM generation, and geochemical indicators of metabolic pathways of methanogenesis (i.e., acetoclastic or hydrogenotrophic methanogenesis). Meanwhile, researchers at universities, government agencies, and companies have focused on four primary MECoM strategies: 1) microbial stimulation (i.e., addition of nutrients to stimulate native microbes); 2) microbial augmentation (i.e., addition of microbes not native to or abundant in the reservoir of interest); 3) physically increasing microbial access to coal and distribution of amendments; and 4) chemically increasing the bioavailability of coal organics. Most companies interested in MECoM have pursued microbial stimulation: Luca Technologies, Inc., successfully completed a pilot scale field test of their stimulation strategy, while two others, Ciris Energy and Next Fuel, Inc., have undertaken smaller scale field tests. Several key knowledge gaps remain that need to be addressed before MECoM strategies can be implemented commercially. Little is known about the bacterial community responsible for coal biodegradation and how these microorganisms may be stimulated to enhance microbial methanogenesis. In addition, research is needed to understand what fraction of coal is available for biodegradation, and methods need to be developed to determine the extent of in-situ coal biodegradation by MECoM processes for monitoring changes to coal quality. Questions also remain about how well field-scale pilot tests will scale to commercial production, how often amendments will need to be added to maintain new methane generation, and how well MECoM strategies transfer between coal basins with different formation water geochemistries and coal ranks. Addressing these knowledge gaps will be key in determining the feasibility and commercial viability of MECoM technology.

Methane dynamics regulated by microbial community response to permafrost thaw.

PubMed

McCalley, Carmody K; Woodcroft, Ben J; Hodgkins, Suzanne B; Wehr, Richard A; Kim, Eun-Hae; Mondav, Rhiannon; Crill, Patrick M; Chanton, Jeffrey P; Rich, Virginia I; Tyson, Gene W; Saleska, Scott R

2014-10-23

Permafrost contains about 50% of the global soil carbon. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ(13)C signature (10-15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus 'Methanoflorens stordalenmirensis' is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.

Use of PCR-DGGE Based Molecular Methods to Analyse Microbial Community Diversity and Stability during the Thermophilic Stages of an ATAD Wastewater Sludge Treatment Process as an Aid to Performance Monitoring

PubMed Central

Piterina, Anna V.; Pembroke, J. Tony

2013-01-01

PCR and PCR-DGGE techniques have been evaluated to monitor biodiversity indexes within an ATAD (autothermal thermophilic aerobic digestion) system treating domestic sludge for land spread, by examining microbial dynamics in response to elevated temperatures during treatment. The ATAD process utilises a thermophilic population to generate heat and operates at elevated pH due to degradation of sludge solids, thus allowing pasteurisation and stabilisation of the sludge. Genera-specific PCR revealed that Archaea, Eukarya and Fungi decline when the temperature reaches 59°C, while the bacterial lineage constitutes the dominant group at this stage. The bacterial community at the thermophilic stage, its similarity index to the feed material, and the species richness present were evaluated by PCR-DGGE. Parameters such as choice of molecular target (16S rDNA or rpoB genes), and electrophoresis condition, were optimised to maximise the resolution of the method for ATAD. Dynamic analysis of microbial communities was best observed utilising PCR-DGGE analysis of the V6-V8 region of 16S rDNA, while rpoB gene profiles were less informative. Unique thermophilic communities were shown to quickly adapt to process changes, and shown to be quite stable during the process. Such techniques may be used as a monitoring technique for process health and efficiency. PMID:25937969

Microbial diversity associated with odor modification for production of fertilizers from chicken litter.

PubMed

Enticknap, Julie J; Nonogaki, Hirofumi; Place, Allen R; Hill, Russell T

2006-06-01

Litter from the chicken industry can present several environmental challenges, including offensive odors and runoff into waterways leading to eutrophication. An economically viable solution to the disposal of waste from chicken houses is treatment to produce a natural, granulated fertilizer that can be commercially marketed for garden and commercial use. Odor of the final product is important in consumer acceptance, and an earthy odor is desirable. By understanding and manipulating the microbial processes occurring during this process, it may be possible to modify the odors produced. Geosmin and related volatiles produced by soil actinomycetes are responsible for earthy odors, and actinomycetes are likely to be present in the composting manure. Bacterial communities at each stage of the process were analyzed by culturing studies and denaturing gradient gel electrophoresis (DGGE). The processing steps changed the culturable bacterial community, but the total community was shown by DGGE to be stable throughout the process. A local agricultural soil was analyzed in parallel as a potential source of geosmin-producing actinomycetes. This agricultural soil had higher microbial diversity than the compost at both the culturable and the molecular levels. Actinomycete bacteria were isolated and analyzed by AromaTrax, a gas chromatography-olfactometry system. This system enables the odor production of individual isolates to be monitored, allowing for rational selection of strains for augmentation experiments to improve the odor of the final fertilizer product.

Microbial Diversity Associated with Odor Modification for Production of Fertilizers from Chicken Litter†

PubMed Central

Enticknap, Julie J.; Nonogaki, Hirofumi; Place, Allen R.; Hill, Russell T.

2006-01-01

Litter from the chicken industry can present several environmental challenges, including offensive odors and runoff into waterways leading to eutrophication. An economically viable solution to the disposal of waste from chicken houses is treatment to produce a natural, granulated fertilizer that can be commercially marketed for garden and commercial use. Odor of the final product is important in consumer acceptance, and an earthy odor is desirable. By understanding and manipulating the microbial processes occurring during this process, it may be possible to modify the odors produced. Geosmin and related volatiles produced by soil actinomycetes are responsible for earthy odors, and actinomycetes are likely to be present in the composting manure. Bacterial communities at each stage of the process were analyzed by culturing studies and denaturing gradient gel electrophoresis (DGGE). The processing steps changed the culturable bacterial community, but the total community was shown by DGGE to be stable throughout the process. A local agricultural soil was analyzed in parallel as a potential source of geosmin-producing actinomycetes. This agricultural soil had higher microbial diversity than the compost at both the culturable and the molecular levels. Actinomycete bacteria were isolated and analyzed by AromaTrax, a gas chromatography-olfactometry system. This system enables the odor production of individual isolates to be monitored, allowing for rational selection of strains for augmentation experiments to improve the odor of the final fertilizer product. PMID:16751521

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Metabolome-mediated biocryomorphic evolution promotes carbon fixation in Greenlandic cryoconite holes.

PubMed

Cook, Joseph M; Edwards, Arwyn; Bulling, Mark; Mur, Luis A J; Cook, Sophie; Gokul, Jarishma K; Cameron, Karen A; Sweet, Michael; Irvine-Fynn, Tristram D L

2016-12-01

Microbial photoautotrophs on glaciers engineer the formation of granular microbial-mineral aggregates termed cryoconite which accelerate ice melt, creating quasi-cylindrical pits called 'cryoconite holes'. These act as biogeochemical reactors on the ice surface and provide habitats for remarkably active and diverse microbiota. Evolution of cryoconite holes towards an equilibrium depth is well known, yet interactions between microbial activity and hole morphology are currently weakly addressed. Here, we experimentally perturbed the depths and diameters of cryoconite holes on the Greenland Ice Sheet. Cryoconite holes responded by sensitively adjusting their shapes in three dimensions ('biocryomorphic evolution') thus maintaining favourable conditions for net autotrophy at the hole floors. Non-targeted metabolomics reveals concomitant shifts in cyclic AMP and fucose metabolism consistent with phototaxis and extracellular polymer synthesis indicating metabolomic-level granular changes in response to perturbation. We present a conceptual model explaining this process and suggest that it results in remarkably robust net autotrophy on the Greenland Ice Sheet. We also describe observations of cryoconite migrating away from shade, implying a degree of self-regulation of carbon budgets over mesoscales. Since cryoconite is a microbe-mineral aggregate, it appears that microbial processes themselves form and maintain stable autotrophic habitats on the surface of the Greenland ice sheet. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial exopolysaccharide-mediated synthesis and stabilization of metal nanoparticles.

PubMed

Sathiyanarayanan, Ganesan; Dineshkumar, Krishnamoorthy; Yang, Yung-Hun

2017-11-01

Exopolysaccharides (EPSs) are structurally and functionally valuable biopolymer secreted by different prokaryotic and eukaryotic microorganisms in response to biotic/abiotic stresses and to survive in extreme environments. Microbial EPSs are fascinating in various industrial sectors due to their excellent material properties and less toxic, highly biodegradable, and biocompatible nature. Recently, microbial EPSs have been used as a potential template for the rapid synthesis of metallic nanoparticles and EPS-mediated metal reduction processes are emerging as simple, harmless, and environmentally benign green chemistry approaches. EPS-mediated synthesis of metal nanoparticles is a distinctive metabolism-independent bio-reduction process due to the formation of interfaces between metal cations and the polyanionic functional groups (i.e. hydroxyl, carboxyl and amino groups) of the EPS. In addition, the range of physicochemical features which facilitates the EPS as an efficient stabilizing or capping agents to protect the primary structure of the metal nanoparticles with an encapsulation film in order to separate the nanoparticle core from the mixture of composites. The EPS-capping also enables the further modification of metal nanoparticles with expected material properties for multifarious applications. The present review discusses the microbial EPS-mediated green synthesis/stabilization of metal nanoparticles, possible mechanisms involved in EPS-mediated metal reduction, and application prospects of EPS-based metal nanoparticles.

Molecular Adaptation Mechanisms Employed by Ethanologenic Bacteria in Response to Lignocellulose-derived Inhibitory Compounds

PubMed Central

Ibraheem, Omodele; Ndimba, Bongani K.

2013-01-01

Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of 'intelligent' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains. PMID:23847442

Study of the diversity of microbial communities in a sequencing batch reactor oxic-settling-anaerobic process and its modified process.

PubMed

Sun, Lianpeng; Chen, Jianfan; Wei, Xiange; Guo, Wuzhen; Lin, Meishan; Yu, Xiaoyu

2016-05-01

To further reveal the mechanism of sludge reduction in the oxic-settling-anaerobic (OSA) process, the polymerase chain reaction - denaturing gradient gel electrophoresis protocol was used to study the possible difference in the microbial communities between a sequencing batch reactor (SBR)-OSA process and its modified process, by analyzing the change in the diversity of the microbial communities in each reactor of both systems. The results indicated that the structure of the microbial communities in aerobic reactors of the 2 processes was very different, but the predominant microbial populations in anaerobic reactors were similar. The predominant microbial population in the aerobic reactor of the SBR-OSA belonged to Burkholderia cepacia, class Betaproteobacteria, while those of the modified process belonged to the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. These 3 types of microbes had a cryptic growth characteristic, which was the main cause of a greater sludge reduction efficiency achieved by the modified process.

New insights into microbial responses to oil spills from the Deepwater Horizon incident

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

Mason, O.U.; Hazen, T.C.

2011-06-15

On April 20, 2010, a catastrophic eruption of methane caused the Deepwater Horizon exploratory drill rig drilling the Macondo Well in Mississippi Canyon Block 252 (MC252) to explode. The Deepwater Horizon oil spill was unprecendeted for several reasons: the volume of oil released; the spill duration; the well depth; the distance from the shore-line (77 km or about 50 miles); the type of oil (light crude); and the injection of dispersant directly at the wellhead. This study clearly demonstrated that there was a profound and significant response by certain members of the in situ microbial community in the deep-sea inmore » the Gulf of Mexico. In particular putative hydrocarbon degrading Bacteria appeared to bloom in response to the Deepwater Horizon oil spill, even though the temperature at these depths is never >5 C. As the plume aged the shifts in the microbial community on a temporal scale suggested that different, yet metabolically important members of the community were able to respond to a myriad of plume constituents, e.g. shifting from propane/ethane to alkanes and finally to methane. Thus, the biodegradation of hydrocarbons in the plume by Bacteria was a highly significant process in the natural attenuation of many compounds released during the Deepwater Horizon oil spill.« less

Role of Law Enforcement Response and Microbial Forensics in Investigation of Bioterrorism

PubMed Central

Budowle, Bruce; Beaudry, Jodi A.; Barnaby, Neel G.; Giusti, Alan M.; Bannan, Jason D.; Keim, Paul

2007-01-01

The risk and threat of bioterrorism and biocrime have become a large concern and challenge for governments and society to enhance biosecurity. Law enforcement plays an important role in assessing and investigating activities involved in an event of bioterrorism or biocrime. Key to a successful biosecurity program is increased awareness and early detection of threats facilitated by an integrated network of responsibilities and capabilities from government, academic, private, and public assets. To support an investigation, microbial forensic sciences are employed to analyze and characterize forensic evidence with the goal of attribution or crime scene reconstruction. Two different molecular biology-based assays – real time polymerase chain reaction (PCR) and repetitive element PCR – are described and demonstrate how molecular biology tools may be utilized to aid in the investigative process. Technologies relied on by microbial forensic scientists need to be properly validated so that the methods used are understood and so that interpretation of results is carried out within the limitations of the assays. The three types of validation are preliminary, developmental, and internal. The first is necessary for rapid response when a threat is imminent or an attack has recently occurred. The latter two apply to implementation of routinely used procedures. PMID:17696298

Microbial response to modified precipitation patterns in tallgrass prairie soil: molecular mechanisms, activity rates and organic matter dynamics

NASA Astrophysics Data System (ADS)

Zeglin, L. H.; David, M.; Bottomley, P.; Hettich, R. L.; Jansson, J.; Jumpponen, A.; Rice, C. W.; Tringe, S.; VerBerkmoes, N. C.; Myrold, D.

2011-12-01

A significant amount of carbon (C) is processed and stored in prairie soils: grasslands cover 6.1-7.4% of the earth's land surface and hold 7.3-11.4% of global soil C. Global change models predict that the future precipitation regime across the North American Great Plains will entail less frequent but larger rainfall events. The response of prairie soil microbial C processing and allocation to this scenario of higher hydrologic variability is not known, but will be a key determiner of the future capacity for prairie soil C sequestration. We are approaching this problem by assessing soil microbial function (respiration, C utilization efficiency, extracellular enzyme activity) and molecular indicators of dominant C allocation pathways (soil transcriptome, proteome and metabolome) under ambient and experimentally modified precipitation regimes. The rainfall manipulation plots (RaMPs) at the Konza Prairie Long-Term Ecological Research (LTER) site in eastern Kansas, USA is a replicated field manipulation of the magnitude and frequency of natural precipitation that was established in 1998. We collected soil before, during and after a rainfall event in both ambient and modified precipitation treatments and measured the microbial response. Microbial respiration doubled in both treatments during the water addition, and cellobiohydrolase enzyme potential activity (a catalyst of cellulose hydrolysis) increased slightly, but no significant effect of altered precipitation treatment has emerged. The fungal and bacterial ribosomal gene composition was also similar between precipitation treatments. Although pools of genes and extracellular enzymes may be relatively static during short-term dynamic conditions, transcript and intracellular protein abundances may be more indicative of the active microbial metabolic response to rapid shifts in soil moisture. Thus, analysis of transcript and protein composition is underway. In addition, we have implemented a series of lab experiments to optimize and link transcript and protein recovery and analysis procedures using the model soil bacterium Arthrobacter chlorophenicolus strain A6 (ArtchA6). Konza prairie soil was inoculated with ArchA6 and incubated for 72 h with no supplemental C, with acetate or with 4-chlorophenol (a xenobiotic compound that ArtchA6 can utilize as its sole C source), then RNA and protein were extracted from the soil. Quantitatively representative recovery of ArtchA6 genes, rRNA, mRNA and protein was successful. The ratio of ArtchA6 isocitrate lyase (icl, indicative of 2-C metabolism) to succinyl CoA synthetase (suCAB, indicative of total respiratory activity) transcript was highest in soils amended with acetate. Proteomic signatures were distinct in soils with different supplemental C sources. This experiment confirms our capability of recovering transcript and protein from the study soil and of identifying the functional molecules representative of distinct C metabolism pathways.

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.

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.

2010 MICROBIAL STRESS RESPONSE GORDON RESEARCH CONFERENCE, JULY 18-23, 2010

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

Sarah Ades

2011-07-23

The 2010 Gordon Research Conference on Microbial Stress Responses provides an open and exciting forum for the exchange of scientific discoveries on the remarkable mechanisms used by microbes to survive in nearly every niche on the planet. Understanding these stress responses is critical for our ability to control microbial survival, whether in the context of biotechnology, ecology, or pathogenesis. From its inception in 1994, this conference has traditionally employed a very broad definition of stress in microbial systems. Sessions will cover the major steps of stress responses from signal sensing to transcriptional regulation to the effectors that mediate responses. Amore » wide range of stresses will be represented. Some examples include (but are not limited to) oxidative stress, protein quality control, antibiotic-induced stress and survival, envelope stress, DNA damage, and nutritional stress. The 2010 meeting will also focus on the role of stress responses in microbial communities, applied and environmental microbiology, and microbial development. This conference brings together researchers from both the biological and physical sciences investigating stress responses in medically- and environmentally relevant microbes, as well as model organisms, using cutting-edge techniques. Computational, systems-level, and biophysical approaches to exploring stress responsive circuits will be integrated throughout the sessions alongside the more traditional molecular, physiological, and genetic approaches. The broad range of excellent speakers and topics, together with the intimate and pleasant setting at Mount Holyoke College, provide a fertile ground for the exchange of new ideas and approaches.« less

Electrolyte selection and microbial toxicity for electrochemical oxidative water treatment using a boron-doped diamond anode to support site specific contamination incident response.

PubMed

Phillips, Rebecca B; James, Ryan R; Magnuson, Matthew L

2018-04-01

Intentional and unintentional contamination incidents, such as terrorist attacks, natural disasters, and accidental spills, can result in large volumes of contaminated water. These waters may require pre-treatment before disposal and assurances that treated waters will not adversely impact biological processes at wastewater treatment facilities, or receiving waters. Based on recommendations of an industrial workgroup, this study addresses such concerns by studying electrochemical advanced oxidation process (EAOP) pre-treatment for contaminated waters, using a boron-doped diamond (BDD) anode, prior to discharge to wastewater treatment facilities. Reaction conditions were investigated, and microbial toxicity was assessed using the Microtox ® toxicity assay and the Nitrification Inhibition test. A range of contaminants were studied including herbicides, pesticides, pharmaceuticals and flame retardants. Resulting toxicities varied with supporting electrolyte from 5% to 92%, often increasing, indicating that microbial toxicity, in addition to parent compound degradation, should be monitored during treatment. These toxicity results are particularly novel because they systematically compare the microbial toxicity effects of a variety of supporting electrolytes, indicating some electrolytes may not be appropriate in certain applications. Further, these results are the first known report of the use of the Nitrification Inhibition test for this application. Overall, these results systematically demonstrate that anodic oxidation using the BDD anode is useful for addressing water contaminated with refractory organic contaminants, while minimizing impacts to wastewater plants or receiving waters accepting EAOP-treated effluent. The results of this study indicate nitrate can be a suitable electrolyte for incident response and, more importantly, serve as a baseline for site specific EAOP usage. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus predominate during well-performed Malaysian cocoa bean box fermentations, underlining the importance of these microbial species for a successful cocoa bean fermentation process.

PubMed

Papalexandratou, Zoi; Lefeber, Timothy; Bahrim, Bakhtiar; Lee, Ong Seng; Daniel, Heide-Marie; De Vuyst, Luc

2013-09-01

Two spontaneous Malaysian cocoa bean box fermentations (one farm, two plantation plots) were investigated. Physical parameters, microbial community dynamics, yeast and bacterial species diversity [mainly lactic acid bacteria (LAB) and acetic acid bacteria (AAB)], and metabolite kinetics were monitored, and chocolates were produced from the respective fermented dry cocoa beans. Similar microbial growth and metabolite profiles were obtained for the two fermentations. Low concentrations of citric acid were found in the fresh pulp, revealing low acidity of the raw material. The main end-products of the catabolism of the pulp substrates glucose, fructose, and citric acid by yeasts, LAB, and AAB were ethanol, lactic acid, acetic acid, and/or mannitol. Hanseniaspora opuntiae, Lactobacillus fermentum, and Acetobacter pasteurianus were the prevalent species of the two fermentations. Saccharomyces cerevisiae, Lactobacillus plantarum, Lactobacillus pentosus, and Acetobacter ghanensis were also found during the mid-phase of the fermentation processes. Leuconostoc pseudomesenteroides and Acetobacter senegalensis were among the prevailing species during the initial phase of the fermentations. Tatumella saanichensis and Enterobacter sp. were present in the beginning of the fermentations and they could be responsible for the degradation of citric acid and/or the production of gluconic acid and lactic acid, respectively. The presence of facultative heterofermentative LAB during the fermentations caused a high production of lactic acid. Finally, as these fermentations were carried out with high-quality raw material and were characterised by a restricted microbial species diversity, resulting in successfully fermented dry cocoa beans and good chocolates produced thereof, it is likely that the prevailing species H. opuntiae, S. cerevisiae, Lb. fermentum, and A. pasteurianus were responsible for it. Copyright © 2013 Elsevier Ltd. All rights reserved.

Regulation of pesticide degradation in the detritusphere

NASA Astrophysics Data System (ADS)

Pagel, Holger; Poll, Christian; Ingwersen, Joachim; Ditterich, Franziska; Gebala, Aurelia; Kandeler, Ellen; Streck, Thilo

2015-04-01

The detritusphere is a microbial hot spot of C turnover and degradation of pesticides in soils. We aimed at an improved understanding of the regulation mechanisms, which are responsible for stimulated degradation of the herbicide MCPA (2-Methyl-4-chlorophenoxyacetic acid) in response to increased C availability in the detritusphere. We combined a microcosm experiment with biogeochemical modeling and linked genetic information on abundances of total bacteria, fungi and specific pesticide degraders in soil to the coupled biogeochemical dynamics of C and MCPA. As a result of diffusive and convective C transport from litter into the adjacent soil we found increased dissolved organic C (DOC) in soil up to a 6 mm distance to litter (detritusphere). In the detritusphere, we observed increased microbial C and accelerated MCPA degradation. These dynamics were accurately reproduced by the model. Whereas the observed increase of bacteria and pesticide degrader populations in the detritusphere was simulated satisfactorily, the model could not reproduce the steep increase of fungi indicated by the fungal marker gene. Our simulations suggest that bacterial MCPA degraders mostly benefited from high-quality DOC, whereas fungal activity and growth were specifically stimulated by low-quality DOC. According to the simulations, MCPA was predominantly degraded via fungal co-metabolism. Our study demonstrates that biogeochemical processes in soil hotspots are regulated by the interaction of transport processes and microbial dynamics. It further reveals that mathematical modelling is as powerful tool to gain comprehensive insight into the microbial regulation of matter cycling in soil. Genetic information has a high potential to parameterize and evaluate complex mechanistic models, but model approaches must be improved based on extended information on gene dynamics at the cellular level.

Modern Microbial Fossilization Processes as Signatures for Interpreting Ancient Terrestrial and Extraterrestrial Microbial Forms

NASA Technical Reports Server (NTRS)

Morris, Penny A.; Wentworth, Susan J.; Nelman, Mayra; Byrne, Monica; Longazo, Teresa; Galindo, Charles; McKay, David S.; Sams, Clarence

2003-01-01

Terrestrial biotas from microbially dominated hypersaline environments will help us understand microbial fossilization processes. Hypersaline tolerant biota from Storr's Lake, San Salvador Island (Bahamas), Mono Lake (California), and the Dead Sea (Israel) represent marine and nonmarine sites for comparative studies of potential analogs for interpreting some Mars meteorites and Mars sample return rocks [1,2,3,4,5,6]. The purpose of this study is to compare microbial fossilization processes, the dominant associated minerals, and potential diagenic implications.

Reprint of Design of synthetic microbial communities for biotechnological production processes.

PubMed

Jagmann, Nina; Philipp, Bodo

2014-12-20

In their natural habitats microorganisms live in multi-species communities, in which the community members exhibit complex metabolic interactions. In contrast, biotechnological production processes catalyzed by microorganisms are usually carried out with single strains in pure cultures. A number of production processes, however, may be more efficiently catalyzed by the concerted action of microbial communities. This review will give an overview of organismic interactions between microbial cells and of biotechnological applications of microbial communities. It focuses on synthetic microbial communities that consist of microorganisms that have been genetically engineered. Design principles for such synthetic communities will be exemplified based on plausible scenarios for biotechnological production processes. These design principles comprise interspecific metabolic interactions via cross-feeding, regulation by interspecific signaling processes via metabolites and autoinducing signal molecules, and spatial structuring of synthetic microbial communities. In particular, the implementation of metabolic interdependencies, of positive feedback regulation and of inducible cell aggregation and biofilm formation will be outlined. Synthetic microbial communities constitute a viable extension of the biotechnological application of metabolically engineered single strains and enlarge the scope of microbial production processes. Copyright © 2014 Elsevier B.V. All rights reserved.

The use of microbial gene abundance in the development of fuel remediation guidelines in polar soils.

PubMed

Richardson, Elizabeth L; King, Catherine K; Powell, Shane M

2015-04-01

Terrestrial fuel spills in Antarctica commonly occur on ice-free land around research stations as the result of human activities. Successful spill clean-ups require appropriate targets that confirm contaminated sites are no longer likely to pose environmental risk following remediation. These targets are based on knowledge of the impacts of contaminants on the soil ecosystem and on the response of native biota to contamination. Our work examined the response of soil microbial communities to fuel contamination by measuring the abundance of genes involved in critical soil processes, and assessed the use of this approach as an indicator of soil health in the presence of weathered and fresh fuels. Uncontaminated and contaminated soils were collected from the site of remediation treatment of an aged diesel spill at Casey Station, East Antarctica in December 2012. Uncontaminated soil was spiked with fresh Special Antarctic Blend (SAB) diesel to determine the response of the genes to fresh fuel. Partly remediated soil containing weathered SAB diesel was diluted with uncontaminated soil to simulate a range of concentrations of weathered fuel and used to determine the response of the genes to aged fuel. Quantitative PCR (qPCR) was used to measure the abundance of rpoB, alkB, cat23, and nosZ in soils containing SAB diesel. Differences were observed between the abundance of genes in control soils versus soils containing weathered and fresh fuels. Typical dose-response curves were generated for genes in response to the presence of fresh fuel. In contrast, the response of these genes to the range of weathered fuel appeared to be due to dilution, rather than to the effect of the fuel on the microbial community. Changes in microbial genes in response to fresh contamination have potential as a sensitive measure of soil health and for assessments of the effect of fuel spills in polar soils. This will contribute to the development of remediation guidelines to assist in management decisions on when the impact of a fuel spill warrants remediation. © 2014 SETAC.

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.

Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates.

PubMed

Hu, Hang-Wei; Chen, Deli; He, Ji-Zheng

2015-09-01

The continuous increase of the greenhouse gas nitrous oxide (N2O) in the atmosphere due to increasing anthropogenic nitrogen input in agriculture has become a global concern. In recent years, identification of the microbial assemblages responsible for soil N2O production has substantially advanced with the development of molecular technologies and the discoveries of novel functional guilds and new types of metabolism. However, few practical tools are available to effectively reduce in situ soil N2O flux. Combating the negative impacts of increasing N2O fluxes poses considerable challenges and will be ineffective without successfully incorporating microbially regulated N2O processes into ecosystem modeling and mitigation strategies. Here, we synthesize the latest knowledge of (i) the key microbial pathways regulating N2O production and consumption processes in terrestrial ecosystems and the critical environmental factors influencing their occurrence, and (ii) the relative contributions of major biological pathways to soil N2O emissions by analyzing available natural isotopic signatures of N2O and by using stable isotope enrichment and inhibition techniques. We argue that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions. We further propose a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N2O emissions. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Seasonal variability of microbial biomass phosphorus in urban soils.

PubMed

Halecki, W; Gąsiorek, M

2015-01-01

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

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

PubMed

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

2017-12-01

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

The importance of anabolism in microbial control over soil carbon storage

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

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

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

Detection of microbial biofilms on food processing surfaces: hyperspectral fluorescence imaging study

NASA Astrophysics Data System (ADS)

Jun, Won; Kim, Moon S.; Chao, Kaunglin; Lefcourt, Alan M.; Roberts, Michael S.; McNaughton, James L.

2009-05-01

We used a portable hyperspectral fluorescence imaging system to evaluate biofilm formations on four types of food processing surface materials including stainless steel, polypropylene used for cutting boards, and household counter top materials such as formica and granite. The objective of this investigation was to determine a minimal number of spectral bands suitable to differentiate microbial biofilm formation from the four background materials typically used during food processing. Ultimately, the resultant spectral information will be used in development of handheld portable imaging devices that can be used as visual aid tools for sanitation and safety inspection (microbial contamination) of the food processing surfaces. Pathogenic E. coli O157:H7 and Salmonella cells were grown in low strength M9 minimal medium on various surfaces at 22 +/- 2 °C for 2 days for biofilm formation. Biofilm autofluorescence under UV excitation (320 to 400 nm) obtained by hyperspectral fluorescence imaging system showed broad emissions in the blue-green regions of the spectrum with emission maxima at approximately 480 nm for both E. coli O157:H7 and Salmonella biofilms. Fluorescence images at 480 nm revealed that for background materials with near-uniform fluorescence responses such as stainless steel and formica cutting board, regardless of the background intensity, biofilm formation can be distinguished. This suggested that a broad spectral band in the blue-green regions can be used for handheld imaging devices for sanitation inspection of stainless, cutting board, and formica surfaces. The non-uniform fluorescence responses of granite make distinctions between biofilm and background difficult. To further investigate potential detection of the biofilm formations on granite surfaces with multispectral approaches, principal component analysis (PCA) was performed using the hyperspectral fluorescence image data. The resultant PCA score images revealed distinct contrast between biofilms and granite surfaces. This investigation demonstrated that biofilm formations on food processing surfaces, even for background materials with heterogeneous fluorescence responses, can be detected. Furthermore, a multispectral approach in developing handheld inspection devices may be needed to inspect surface materials that exhibit non-uniform fluorescence.

Analysis of extracellular polymeric substances (EPS) and ciprofloxacin-degrading microbial community in the combined Fe-C micro-electrolysis-UBAF process for the elimination of high-level ciprofloxacin.

PubMed

Zhang, Longlong; Yue, Qinyan; Yang, Kunlun; Zhao, Pin; Gao, Baoyu

2018-02-01

Extracellular polymeric substances (EPS) and ciprofloxacin-degrading microbial community in the combined Fe-C micro-electrolysis and up-flow biological aerated filter (UBAF) process for the treatment of high-level ciprofloxacin (CIP) were analyzed. The research demonstrated a great potential of Fe-C micro-electrolysis-UBAF for the elimination of high-level CIP. Above 90% of CIP removal was achieved through the combined process at 100 mg L -1 of CIP loading. In UBAF, the pollutants were mainly removed at 0-70 cm heights. Three-dimensional fluorescence spectrum (3D-EEM) was used to characterize the chemical structural of loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) extracted from biofilm sample in UBAF. The results showed that the protein-like substances in LB-EPS and TB-EPS had no clear change in the study. Nevertheless, an obvious release of polysaccharides in EPSs was observed during long-term exposure to CIP, which was considered as a protective response of microbial to CIP toxic. The high-throughput sequencing results revealed that the biodiversity of bacteria community became increasingly rich with gradual ciprofloxacin biodegradation in UBAF. The ciprofloxacin-degrading microbial community was mainly dominated by Proteobacteria and Bacteroidetes. Microorganisms from genera Dechloromonas, Brevundimonas, Flavobacterium, Sphingopyxis and Bosea might take a major role in ciprofloxacin degradation. This study provides deep theoretical guidance for real CIP wastewater treatment. Copyright © 2017. Published by Elsevier Ltd.

Ecological Succession Pattern of Fungal Community in Soil along a Retreating Glacier

PubMed Central

Tian, Jianqing; Qiao, Yuchen; Wu, Bing; Chen, Huai; Li, Wei; Jiang, Na; Zhang, Xiaoling; Liu, Xingzhong

2017-01-01

Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2–188 years of deglaciation. Shannon diversity and evenness peaked at a distance of 370 m and declined afterwards. The response of fungal diversity to distance varied in different phyla. Basidiomycota Shannon diversity significantly decreased with distance, while the pattern of Rozellomycota Shannon diversity was unimodal. Abundance of most frequencies OTU2 (Cryptococcus terricola) increased with successional distance, whereas that of OTU65 (Tolypocladium tundrense) decreased. Based on null deviation analyses, composition of the fungal community was initially governed by deterministic processes strongly but later less deterministic processes. Our results revealed that distance, altitude, soil microbial biomass carbon, soil microbial biomass nitrogen and NH4+–N significantly correlated with fungal community composition along the chronosequence. These results suggest that the drivers of fungal community are dynamics in a glacier chronosequence, that may relate to fungal ecophysiological traits and adaptation in an evolving ecosystem. The information will provide understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession under different scales and scenario. PMID:28649234

Ecological Succession Pattern of Fungal Community in Soil along a Retreating Glacier.

PubMed

Tian, Jianqing; Qiao, Yuchen; Wu, Bing; Chen, Huai; Li, Wei; Jiang, Na; Zhang, Xiaoling; Liu, Xingzhong

2017-01-01

Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2-188 years of deglaciation. Shannon diversity and evenness peaked at a distance of 370 m and declined afterwards. The response of fungal diversity to distance varied in different phyla. Basidiomycota Shannon diversity significantly decreased with distance, while the pattern of Rozellomycota Shannon diversity was unimodal. Abundance of most frequencies OTU2 ( Cryptococcus terricola ) increased with successional distance, whereas that of OTU65 ( Tolypocladium tundrense ) decreased. Based on null deviation analyses, composition of the fungal community was initially governed by deterministic processes strongly but later less deterministic processes. Our results revealed that distance, altitude, soil microbial biomass carbon, soil microbial biomass nitrogen and [Formula: see text]-N significantly correlated with fungal community composition along the chronosequence. These results suggest that the drivers of fungal community are dynamics in a glacier chronosequence, that may relate to fungal ecophysiological traits and adaptation in an evolving ecosystem. The information will provide understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession under different scales and scenario.

Characterizing the microbial colonization of a dolostone quarry: implications for stone biodeterioration and response to biocide treatments.

PubMed

Cámara, Beatriz; De los Ríos, Asuncion; Urizal, Marta; de Buergo, Mónica Alvarez; Varas, Maria Jose; Fort, Rafael; Ascaso, Carmen

2011-08-01

This study examines the microbial colonization of three fronts of an abandoned dolostone quarry (Redueña, Madrid, Spain) exposed to atmospheric conditions for different time periods since Roman times to the present. Through scanning electron microscopy in backscattered electron mode (SEM-BSE), endolithic colonization was predominantly detected in the most recently exposed front, while in the longer exposed quarry fronts, epilithic forms of growth were most often observed. These observations were confirmed by denaturing gradient gel electrophoresis (DGGE) analysis. Based on the distribution pattern of microbial colonization in the different quarry fronts, we then established a sequence of colonization events that took place over this long time frame. Bioalteration processes related to this sequential colonization were also identified. Characterizing these sequential processes can be useful for interpreting biodeterioration processes in historic dolostone monuments, especially those affecting constructions in the area of the Redueña stone quarry. In a second experimental stage, different biocide treatments were tested on this quarry rock to find the best way to avoid the microbial colonization effects identified. Through combined SEM-BSE/DGGE analysis, the efficacy of several biocides against the microorganisms inhabiting the dolostones was assessed after 4 and 16 months treatment. In general, all treatments were effective at reducing around 80% of the lichen cover, although effects on endolithic lithobiontic communities were dependent on how well the rock surface had been mechanically cleaned prior to treatment and gradually disappeared over time.

Trajectories of Microbial Community Function in Response to Accelerated Remediation of Subsurface Metal Contaminants

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

Firestone, Mary

Objectives of proposed research were to; Determine if the trajectories of microbial community composition and function following organic carbon amendment can be related to, and predicted by, key environmental determinants; Assess the relative importance of the characteristics of the indigenous microbial community, sediment, groundwater, and concentration of organic carbon amendment as the major determinants of microbial community functional response and bioremediation capacity; and Provide a fundamental understanding of the microbial community ecology underlying subsurface metal remediation requisite to successful application of accelerated remediation and long-term stewardship of DOE-IFC sites.

Influence of altered precipitation pattern on greenhouse gas emissions and soil enzyme activities in Pannonian soils

NASA Astrophysics Data System (ADS)

Forstner, Stefan Johannes; Michel, Kerstin; Berthold, Helene; Baumgarten, Andreas; Wanek, Wolfgang; Zechmeister-Boltenstern, Sophie; Kitzler, Barbara

2013-04-01

Precipitation patterns are likely to be altered due to climate change. Recent models predict a reduction of mean precipitation during summer accompanied by a change in short-term precipitation variability for central Europe. Correspondingly, the risk for summer drought is likely to increase. This may especially be valid for regions which already have the potential for rare, but strong precipitation events like eastern Austria. Given that these projections hold true, soils in this area will receive water irregularly in few, heavy rainfall events and be subjected to long-lasting dry periods in between. This pattern of drying/rewetting can alter soil greenhouse gas fluxes, creating a potential feedback mechanism for climate change. Microorganisms are the key players in most soil carbon (C) and nitrogen (N) transformation processes including greenhouse gas exchange. A conceptual model proposed by Schimel and colleagues (2007) links microbial stress-response physiology to ecosystem-scale biogeochemical processes: In order to cope with decreasing soil water potential, microbes modify resource allocation patterns from growth to survival. However, it remains unclear how microbial resource acquisition via extracellular enzymes and microbial-controlled greenhouse gas fluxes respond to water stress induced by soil drying/rewetting. We designed a laboratory experiment to test for effects of multiple drying/rewetting cycles on soil greenhouse gas fluxes (CO2, CH4, N2O, NO), microbial biomass and extracellular enzyme activity. Three soils representing the main soil types of eastern Austria were collected in June 2012 at the Lysimeter Research Station of the Austrian Agency for Health and Food Safety (AGES) in Vienna. Soils were sieved to 2mm, filled in steel cylinders and equilibrated for one week at 50% water holding capacity (WHC) for each soil. Then soils were separated into two groups: One group received water several times per week (C=control), the other group received water only once in two weeks (D=dry). Both groups received same water totals for each soil. At the end of each two week drying period, greenhouse gas fluxes were measured via an open-chamber-system (CO2, NO) and a closed-chamber-approach (CH4, N2O, CO2). Additional cylinders were harvested destructively to quantify inorganic N forms, microbial biomass C, N and extracellular enzyme activity (Cellulase, Xylanase, Protease, Phenoloxidase, Peroxidase). We hypothesize that after rewetting (1) rates of greenhouse gas fluxes will generally increase, as well as (2) extracellular enzyme activity indicating enhanced microbial activity. However, response may be different for gases and enzymes involved in the C and N cycle, respectively, as drying/rewetting stress may uncouple microbial mediated biogeochemical cycles. Results will be presented at the EGU General Assembly. Reference: Schimel, J., Balser, T.C., and Wallenstein, M. (2007). Microbial stress-response physiology and its implications for ecosystem function. Ecology 88, 1386-1394.

Spatial and Temporal Scales of Surface Water-Groundwater Interactions

NASA Astrophysics Data System (ADS)

Boano, F.

2016-12-01

The interfaces between surface water and groundwater (i.e., river and lake sediments) represent hotspots for nutrient transformation in watersheds. This intense biochemical activity stems from the peculiar physicochemical properties of these interface areas. Here, the exchange of water and nutrients between surface and subsurface environments creates an ecotone region that can support the presence of different microbial species responsible for nutrient transformation. Previous studies have elucidated that water exchange between rivers and aquifers is organized in a complex system of nested flow cells. Each cell entails a range of residence timescales spanning multiple order of magnitudes, providing opportunities for different biochemical reactions to occur. Physically-bases models represent useful tools to deal with the wide range of spatial and temporal scales that characterize surface-subsurface water exchange. This contribution will present insights about how hydrodynamic processes control scale organization for surface water - groundwater interactions. The specific focus will be the influence of exchange processes on microbial activity and nutrient transformation, discussing how groundwater flow at watershed scale controls flow conditions and hence constrain microbial reactions at much smaller scales.

Electro-peroxone pretreatment for enhanced simulated hospital wastewater treatment and antibiotic resistance genes reduction.

PubMed

Zheng, He-Shan; Guo, Wan-Qian; Wu, Qu-Li; Ren, Nan-Qi; Chang, Jo-Shu

2018-06-01

Hospital wastewater is one of the possible sources responsible for antibiotic resistant bacteria spread into the environment. This study proposed a promising strategy, electro-peroxone (E-peroxone) pretreatment followed by a sequencing batch reactor (SBR) for simulated hospital wastewater treatment, aiming to enhance the wastewater treatment performance and to reduce antibiotic resistance genes production simultaneously. The highest chemical oxygen demand (COD) and total organic carbon (TOC) removal efficiency of 94.3% and 92.8% were obtained using the E-peroxone-SBR process. The microbial community analysis through high-throughput sequencing showed that E-peroxone pretreatment could guarantee microbial richness and diversity in SBR, as well as reduce the microbial inhibitions caused by antibiotic and raise the amount of nitrification and denitrification genera. Specially, quantitative real-time PCRs revealed that E-peroxone pretreatment could largely reduce the numbers and contents of antibiotic resistance genes (ARGs) production in the following biological treatment unit. It was indicated that E-peroxone-SBR process may provide an effective way for hospital wastewater treatment and possible ARGs reduction. Copyright © 2018 Elsevier Ltd. All rights reserved.

Competition between autotrophic and heterotrophic microbial plankton for inorganic nutrients induced by variability in estuarine biophysicochemical conditions

NASA Astrophysics Data System (ADS)

Williams, A.; Quigg, A.

2016-02-01

Competition for inorganic nutrients between autotrophic and heterotrophic fractions of microbial plankton (0.2-20μm) was investigated at two stations in a sub-tropical estuary, Galveston Bay, Texas. Competition potential between these groups is enhanced because individuals are similar in size, reducing variability among their nutrient uptake efficiencies. Further, in estuaries, allochthonous supplements to autochthonous carbon may satisfy heterotrophic requirements, allowing alternative factors to limit abundance. The relative abundance of autotrophs and heterotrophs stained with SYBR Green I and enumerated on a Beckman Coulter Gallios flow cytometer were evaluated monthly during a year-long study. Shifts in the relative in situ abundance were significantly related to temperature, dissolved inorganic nitrogen (DIN), phosphorous (Pi), and total organic carbon (TOC) concentrations revealing opposing gradients of limitation by different abiotic factors. In corresponding in vitro nutrient enrichment bioassays the relative contribution of autotrophic or heterotrophic microbial plankton to significant enrichment responses varied. Only during macro- (>20μm) phytoplankton blooms do autotrophic microbial plankton respond to nutrient enrichment. Contrastingly, the heterotrophic microbial plankton responded to nutrient enrichment primarily when temperature limitation was alleviated. Therefore, the potential for autotrophic and heterotrophic microbial plankton competition for limiting nutrients is highest when autotrophic microbial plankton are also competing with larger phytoplankton during bloom events. Based on this evidence, we hypothesize that the autotrophic microbial fraction has a competitive advantage over the heterotrophs for inorganic nutrients in Galveston Bay. The observed microbial competition during estuarine phytoplankton blooms may have important consequences on biogeochemical processes including carbon and nutrient cycling.

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.

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

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

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

PubMed

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

2015-07-21

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

Microbially mediated carbon cycling as a control on the δ 13C of sedimentary carbon in eutrophic Lake Mendota (USA): new models for interpreting isotopic excursions in the sedimentary record

NASA Astrophysics Data System (ADS)

Hollander, David J.; Smith, Michael A.

2001-12-01

An isotopic study of various carbon phases in eutrophic Lake Mendota (Wisconsin, USA) indicates that the δ13C composition of sedimentary organic and inorganic carbon has become more negative in response to increasing microbially mediated carbon cycling and processes associated with the intensification of seasonal and long-term eutrophication. Progressive increases in the contributions of isotopically depleted chemoautotrophic and methanotrophic biomass (reflected in the -40 to -90‰ values of hopanols and FAMES), attributed to seasonal and long-term increases in production and expansion of the anaerobic water mass, accounts for carbon isotopic trends towards depleted δ13C values observed in both seasonal varves and over the past 100 years. Changes in the intensities of certain microbial processes are also evident in the sedimentary geochemical record. During the period of most intense cultural eutrophication, when the oxic-anoxic interface was located close to the surface, methanogenesis/methanotrophy and the oxidation of biogenic methane increased to the extent that significant quantities of 13C-depleted CO2 were added into the epilimnion. This depleted CO2 was subsequently utilized by phytoplankton and incorporated into CaCO3 during biogenically induced calcite precipitation. A comparative study between eutrophic Lakes Mendota and Greifen, further indicate that the extent of nutrient loading in the epilimnion determines whether the δ13C record of sedimentary organic carbon reflects intensification of microbial processes in the hypolimnion and sediments, or changes in the primary productivity in the photic zone. From this comparison, a series of eutrophication models are developed to describe progressive transitions through thresholds of microbial and eukaryotic productivity and their influence on the δ13C record of sedimentary carbon. With increasing eutrophication, the models initially predict a negative and then a subsequent positive carbon isotopic excursion reflecting the changing influence of 13C-deleted microbial biomass relative to 13C-enriched photoautrophic biomass. These eutrophication models provide a framework to evaluate carbon cycling processes in modern environments and have significant implications for interpreting carbon isotopic excursions in the sedimentary record.

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.

Microbial enhanced oil recovery: Entering the log phase

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

Bryant, R.S.

1995-12-31

Microbial enhanced oil recovery (MEOR) technology has advanced internationally since 1980 from a laboratory-based evaluation of microbial processes to field applications. In order to adequately support the decline in oil production in certain areas, research on cost-effective technologies such as microbial enhanced oil recovery processes must focus on both near-term and long-term applications. Many marginal wells are desperately in need of an inexpensive improved oil recovery technology today that can assist producers in order to prevent their abandonment. Microbial enhanced waterflooding technology has also been shown to be an economically feasible technology in the United States. Complementary environmental research andmore » development will also be required to address any potential environmental impacts of microbial processes. In 1995 at this conference, the goal is to further document and promote microbial processes for improved oil recovery and related technology for solving environmental problems.« less

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.

PubMed

Cao, Peng; Wang, Jun-Tao; Hu, Hang-Wei; Zheng, Yuan-Ming; Ge, Yuan; Shen, Ju-Pei; He, Ji-Zheng

2016-07-01

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

Using a Microbial Physiologic and Genetic Approach to Investigate How Bacteria Sense Physical Stimuli

ERIC Educational Resources Information Center

Mussi, María Alejandra; Actis, Luis A.; de Mendoza, Diego; Cybulski, Larisa E.

2014-01-01

A laboratory exercise was designed to illustrate how physical stimuli such as temperature and light are sensed and processed by bacteria to elaborate adaptive responses. In particular, we use the well-characterized Des pathway of "Bacillus subtilis" to show that temperature modulates gene expression, resulting ultimately in modification…

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

USDA-ARS?s Scientific Manuscript database

Despite decades of study, the underlying mechanisms by which soil microbes respond to rising atmospheric CO2 and ozone remain poorly understood. A prevailing hypothesis, which states that changes in C availability induced by elevated CO2 and ozone drive alterations in soil microbes and the processe...

Evaluating the influence of process parameters on soluble microbial products formation using response surface methodology coupled with grey relational analysis.

PubMed

Xu, Juan; Sheng, Guo-Ping; Luo, Hong-Wei; Fang, Fang; Li, Wen-Wei; Zeng, Raymond J; Tong, Zhong-Hua; Yu, Han-Qing

2011-01-01

Soluble microbial products (SMPs) present a major part of residual chemical oxygen demand (COD) in the effluents from biological wastewater treatment systems, and the SMP formation is greatly influenced by a variety of process parameters. In this study, response surface methodology (RSM) coupled with grey relational analysis (GRA) method was used to evaluate the effects of substrate concentration, temperature, NH(4)(+)-N concentration and aeration rate on the SMP production in batch activated sludge reactors. Carbohydrates were found to be the major component of SMP, and the influential priorities of these factors were: temperature>substrate concentration > aeration rate > NH(4)(+)-N concentration. On the basis of the RSM results, the interactive effects of these factors on the SMP formation were evaluated, and the optimal operating conditions for a minimum SMP production in such a batch activated sludge system also were identified. These results provide useful information about how to control the SMP formation of activated sludge and ensure the bioreactor high-quality effluent. Copyright © 2010 Elsevier 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.

Microbial community response reveals underlying mechanism of industrial-scale manganese sand biofilters used for the simultaneous removal of iron, manganese and ammonia from groundwater.

PubMed

Zhang, Yu; Sun, Rui; Zhou, Aijuan; Zhang, Jiaguang; Luan, Yunbo; Jia, Jianna; Yue, Xiuping; Zhang, Jie

2018-01-08

Most studies have employed aeration-biofiltration process for the simultaneous removal of iron, manganese and ammonia in groundwater. However, what's inside the "black box", i.e., the potential contribution of functional microorganisms behavior and interactions have seldom been investigated. Moreover, little attention has been paid to the correlations between environmental variables and functional microorganisms. In this study, the performance of industrial-scale biofilters for the contaminated groundwater treatment was studied. The effluent were all far below the permitted concentration level in the current drinking water standard. Pyrosequencing illustrated that shifts in microbial community structure were observed in the microbial samples from different depths of filter. Microbial networks showed that the microbial community structure in the middle- and deep-layer samples was similar, in which a wide range of manganese-oxidizing bacteria was identified. By contrast, canonical correlation analysis showed that the bacteria capable of ammonia-oxidizing and nitrification was enriched in the upper-layer, i.e., Propionibacterium, Nitrosomonas, Nitrosomonas and Candidatus Nitrotoga. The stable biofilm on the biofilter media, created by certain microorganisms from the groundwater microflora, played a crucial role in the simultaneous removal of the three pollutants.

Interactions Between Mineral Surfaces, Substrates, Enzymes, and Microbes Result in Hysteretic Temperature Sensitivities and Microbial Carbon Use Efficiencies and Weaker Predicted Carbon-Climate Feedbacks

NASA Astrophysics Data System (ADS)

Riley, W. J.; Tang, J.

2014-12-01

We hypothesize that the large observed variability in decomposition temperature sensitivity and carbon use efficiency arises from interactions between temperature, microbial biogeochemistry, and mineral surface sorptive reactions. To test this hypothesis, we developed a numerical model that integrates the Dynamic Energy Budget concept for microbial physiology, microbial trait-based community structure and competition, process-specific thermodynamically ­­based temperature sensitivity, a non-linear mineral sorption isotherm, and enzyme dynamics. We show, because mineral surfaces interact with substrates, enzymes, and microbes, both temperature sensitivity and microbial carbon use efficiency are hysteretic and highly variable. Further, by mimicking the traditional approach to interpreting soil incubation observations, we demonstrate that the conventional labile and recalcitrant substrate characterization for temperature sensitivity is flawed. In a 4 K temperature perturbation experiment, our fully dynamic model predicted more variable but weaker carbon-climate feedbacks than did the static temperature sensitivity and carbon use efficiency model when forced with yearly, daily, and hourly variable temperatures. These results imply that current earth system models likely over-estimate the response of soil carbon stocks to global warming.

Weaker soil carbon-climate feedbacks resulting from microbial and abiotic interactions

NASA Astrophysics Data System (ADS)

Tang, Jinyun; Riley, William J.

2015-01-01

The large uncertainty in soil carbon-climate feedback predictions has been attributed to the incorrect parameterization of decomposition temperature sensitivity (Q10; ref. ) and microbial carbon use efficiency. Empirical experiments have found that these parameters vary spatiotemporally, but such variability is not included in current ecosystem models. Here we use a thermodynamically based decomposition model to test the hypothesis that this observed variability arises from interactions between temperature, microbial biogeochemistry, and mineral surface sorptive reactions. We show that because mineral surfaces interact with substrates, enzymes and microbes, both Q10 and microbial carbon use efficiency are hysteretic (so that neither can be represented by a single static function) and the conventional labile and recalcitrant substrate characterization with static temperature sensitivity is flawed. In a 4-K temperature perturbation experiment, our fully dynamic model predicted more variable but weaker soil carbon-climate feedbacks than did the static Q10 and static carbon use efficiency model when forced with yearly, daily and hourly variable temperatures. These results imply that current Earth system models probably overestimate the response of soil carbon stocks to global warming. Future ecosystem models should therefore consider the dynamic interactions between sorptive mineral surfaces, substrates and microbial processes.

Growth and element flux at fine taxonomic resolution in natural microbial communities

NASA Astrophysics Data System (ADS)

Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

2015-04-01

Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

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.

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.

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

USGS Publications Warehouse

MacKelprang, R.; Waldrop, M.P.; Deangelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

2011-01-01

Permafrost contains an estimated 1672????????Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 ??C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost. ?? 2011 Macmillan Publishers Limited. 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

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.

Optimization of supercritical carbon dioxide treatment for the inactivation of the natural microbial flora in cubed cooked ham.

PubMed

Ferrentino, Giovanna; Balzan, Sara; Spilimbergo, Sara

2013-02-15

This study aims to investigate the effects of supercritical carbon dioxide (SC-CO₂) treatment on the inactivation of the natural microbial flora in cubed cooked ham. Response surface methodology with a central composite design was applied to determine the optimal process conditions and investigate the effect of three independent variables (pressure, temperature and treatment time). Additionally, analyses of texture, pH and color together with a storage study of the product were performed to determine its microbial and qualitative stability. Response surface analysis revealed that 12 MPa, 50 °C, 5 min were the optimal conditions to obtain about 3.0, 1.6, and 2.5 Log(CFU/g) reductions of mesophilic aerobic bacteria, psychrophilic bacteria and lactic acid bacteria respectively. Inactivation to undetectable levels of yeasts and molds and coliforms was also obtained. A storage study of 30 days at 4 °C was carried out on the treated product (12 MPa, 50 °C, 5 min) monitoring microbial growth, pH, texture, and color parameters (L*, a*, b* and ΔE). Microbial loads slightly increased and after 30 days of storage reached the same levels detected in the fresh product. Color parameters (L*, a*, b*) showed slight variations while pH and texture did not change significantly. On the basis of the results obtained, SC-CO₂ can be considered a promising technique to microbiologically stabilize cubed cooked ham and, in general, cut/sliced meat products without affecting its quality attributes. Copyright © 2012 Elsevier B.V. All rights reserved.

Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

NASA Astrophysics Data System (ADS)

Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

2014-12-01

Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

Frozen peatlands: carbon store and the climate change

NASA Astrophysics Data System (ADS)

Ogneva, Olga; Matyshak, George; Tarkhov, Matvey

2017-04-01

Peatlands soils in the northern permafrost region store approximately 40% of total Earth's soils carbon. These soils develop under the influence of cryogenic processes especially such as freeze-thaw and cryoturbations. Climate change predictions suggest that the frequency of soil freeze-thaw cycles (FTCs) will increase in cool temperate and other high-latitude regions. This trend may cause a response in organic matter decomposition rate - that will result in significant changes of greenhouse gases emission (CO2, CH4). For further predictions improvement of soils response to global climate changes it is necessary to estimate the impact of FTCs in permafrost soils on organic matter decomposition. We investigated the effects of FTCs on microbial biomass, basal respiration, metabolic quotient and dissolved organic matter (DOM) content (carbon - DOC and nitrogen - DON) in frozen peatlands soils by laboratory modelling experiment. Frozen peatlands from the north of Western Siberia in Nadym area (N65°19', E72°53'), in a zone of discontinuous permafrost were studied. The soil cover of these formations is represented by a complex of Typic Histoturbels (Turbic Cryosol) and Typic Historthels (Cryic Histosols). Peat profiles of both soil types were divided into horizons due to decomposition degree (from 15 to 55-60%), age (from 1000 to 5700 yrs) and botanic composition (oligotrophic, mesotrophic, eutrophic). During the experiment, first group of samples of peat horizons (field moisture content) were subjected for 10 times to 3-day FTCs at the temperature of -10 and +4 ° C. In the second group of peat samples were incubated at +4 ° C (with no freeze-thaw). It was established that all studied microbial properties were inversely proportional with decomposition degree of peat, except metabolic quotient. Our results illustrate that microbial activity, estimated by BR, shows resistance to FTCs and doesn't significantly differ after FTCs an average. Microbial biomass (carbon and nitrogen) as well as BR doesn't differ too. The most intensive response to FTCs shows DOM content value which was 1.5 times higher on average in samples after FTCs in comparison with control samples. We suppose that increase of FTCs frequency in soil will result in significant acceleration mineralization of peat. Because these processes exert disruptive effects on soil organic matter, provide converting carbon from pool into forms available for microbial communities, thus involving stored carbon into the carbon turnover.

Patterns and Controls of Nutrient Concentrations in a Southeastern United States Tidal Creek

DTIC Science & Technology

2013-09-01

which the Duplm’s salinity was controlled solely by mixing between Altamaha River and Atlantic Ocean water . Marine end-membei composition was...ix’iiirrint; within the water - shed must hove been responsible. SEDIMENT AND WATER COLUMN MICROBIAL PROCESSES There was a great deal ot...subsequent processes transform these nutrients in the land-ocean transition zone. Here, we describe spatial and temporal patterns in surface water

Long-term high-solids anaerobic digestion of food waste: Effects of ammonia on process performance and microbial community.

PubMed

Peng, Xuya; Zhang, ShangYi; Li, Lei; Zhao, Xiaofei; Ma, Yao; Shi, Dezhi

2018-04-22

A long-term high solids anaerobic digestion of food waste was conducted to identify microbial mechanisms of ammonia inhibition during digestion and to clarify correlations between ammonia accumulation, microbial community dynamics (diversity, composition, and interactions), and process stability. Results show that the effects of ammonia on process performance and microbial community were indirectly caused by volatile fatty acid accumulation. Excess free ammonia blocked acetate metabolism, leading to process instability. Accumulated acetate caused feedback inhibition at the acetogenesis stage, which resulted in considerable accumulation of propionate, valerate, and other long-chain fatty acids. This high concentration of volatile fatty acids reduced the abundance of syntrophic acetogenic bacteria and allowed hydrolytic fermentative bacteria to dominate. The normally interactive and orderly metabolic network was broken, which further exacerbated the process instability. These results improve the understanding of microbial mechanisms which contribute to process instability and provide guidance for the microbial management of anaerobic digesters. Copyright © 2018 Elsevier Ltd. All rights reserved.

Synergy of SOCS-1 Inhibition and Microbial-Based Cancer Vaccines

DTIC Science & Technology

2014-11-01

response without causing additional risk to the patient. The goal of our proposal is to modify a live- attenuated vaccine vector based on the food -borne...response after vaccination with a live-­‐‑attenuated L. monocytogenes. Aim 3: Test the hypothesis that secretion of a SOCS-­‐‑1 small peptide ...efficient internalization of pathogens and dying cells, processing of this material into peptide antigens that are presented in the context of major

Memory T cells and vaccines.

PubMed

Esser, Mark T; Marchese, Rocio D; Kierstead, Lisa S; Tussey, Lynda G; Wang, Fubao; Chirmule, Narendra; Washabaugh, Michael W

2003-01-17

T lymphocytes play a central role in the generation of a protective immune response in many microbial infections. After immunization, dendritic cells take up microbial antigens and traffic to draining lymph nodes where they present processed antigens to naïve T cells. These naïve T cells are stimulated to proliferate and differentiate into effector and memory T cells. Activated, effector and memory T cells provide B cell help in the lymph nodes and traffic to sites of infection where they secrete anti-microbial cytokines and kill infected cells. At least two types of memory cells have been defined in humans based on their functional and migratory properties. T central-memory (T(CM)) cells are found predominantly in lymphoid organs and can not be immediately activated, whereas T effector-memory (T(EM)) cells are found predominantly in peripheral tissue and sites of inflammation and exhibit rapid effector function. Most currently licensed vaccines induce antibody responses capable of mediating long-term protection against lytic viruses such as influenza and small pox. In contrast, vaccines against chronic pathogens that require cell-mediated immune responses to control, such as malaria, Mycobacterium tuberculosis (TB), human immunodeficiency virus (HIV) and hepatitis C virus (HCV), are currently not available or are ineffective. Understanding the mechanisms by which long-lived cellular immune responses are generated following vaccination should facilitate the development of safe and effective vaccines against these emerging diseases. Here, we review the current literature with respect to memory T cells and their implications to vaccine development.

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.

Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities

PubMed Central

Bridier, Arnaud; Piard, Jean-Christophe; Pandin, Caroline; Labarthe, Simon; Dubois-Brissonnet, Florence; Briandet, Romain

2017-01-01

Biofilms are dynamic habitats which constantly evolve in response to environmental fluctuations and thereby constitute remarkable survival strategies for microorganisms. The modulation of biofilm functional properties is largely governed by the active remodeling of their three-dimensional structure and involves an arsenal of microbial self-produced components and interconnected mechanisms. The production of matrix components, the spatial reorganization of ecological interactions, the generation of physiological heterogeneity, the regulation of motility, the production of actives enzymes are for instance some of the processes enabling such spatial organization plasticity. In this contribution, we discussed the foundations of architectural plasticity as an adaptive driver of biofilms through the review of the different microbial strategies involved. Moreover, the possibility to harness such characteristics to sculpt biofilm structure as an attractive approach to control their functional properties, whether beneficial or deleterious, is also discussed. PMID:28775718

Native soil organic matter conditions the response of microbial communities to organic inputs with different stability

NASA Astrophysics Data System (ADS)

Yanardaǧ, Ibrahim H.; Zornoza, Raúl; Bastida, Felipe; Büyükkiliç-Yanardaǧ, Asuman; Acosta, Jose A.; García, Carlos; Faz, Ángel; Mermut, Ahmet R.

2017-04-01

The response of soil microbial communities from soils with different soil organic matter (SOM) content to organic inputs with different stability is still poorly understood. Thus, an incubation experiment was designed to study how the addition of pig slurry (PS), its manure (M) and its biochar (BC) affect soil microbial community and activity in three soils differing in SOM content (Regosol, Luvisol and Kastanozem). The evolution of different C and N fractions, microbial biomass C and N, enzyme activities and microbial community structure by the use of phospholipid fatty acid (PLFA) analysis was assessed for 60 days. Results showed that the different amendments had different effect on microbial properties depending on the soil type. The addition of M caused the highest increase in all microbial properties in the three soils, followed by PS. These changes were more intense in the soil with the lowest SOM (Regosol). The addition of M and PS caused changes in the microbial community structure in all soils, which were more related to the presence of available sources of N than to the labile fractions of C. The addition of BC was followed by increases in the proportions of fungi and Gram positive bacteria in the Regosol, while enhanced the proportion of actinobacteria in all soil types, related to increments in pH and soil C recalcitrance. Thus, native SOM determined the response of microbial communities to external inputs with different stability, soils with low SOM being more prone to increase microbial biomass and activity and change microbial community structure.

Microbial Influences on Trace Metal Cycling in a Meromictic Lake, Fayetteville Green Lake, NY

NASA Astrophysics Data System (ADS)

Zerkle, A. L.; House, C.; Kump, L.

2002-12-01

Microorganisms can exist in aquatic environments at very high cell densities of up to 1011 cells/L, and can accumulate significant quantities of trace metals. Bacteria actively take up bioactive trace metals, including Fe, Zn, Mn, Co, Ni, Cu, and Mo, which function as catalytic centers in metalloproteins and metal-activated enzymes involved in virtually all cellular functions. In addition, bacteria may catalyze the release of trace metals from inorganic substrates by processes such as the reduction of iron and manganese oxides, suggesting that trace metal distributions within a natural environment dominated by microbial processes may be controlled primarily by microbial ecology. Fayetteville Green Lake (FGL), NY, is a permanently stratified meromictic lake that has a well-oxygenated surface water mass (mixolimnion) overlying a relatively stagnant, anoxic deep water mass (monimolimnion). A chemocline separates the water masses at around 20m depth, where oxygen concentrations decrease and sulfate and methane concentrations increase. In addition, previous studies have indicated that trace metals such as V, Cr, Co, Mn, and Fe reach elevated concentrations at the chemocline. Using fluorescent in situ hybridization (FISH) of FGL samples from depths of up to 40m with bacterial and archaeal probes, we have shown that fluctuating redox conditions within the FGL water column correlate with significant variations in the composition and distribution of microbial populations with depth. The mixolimnion is dominated by Eubacteria, with increasing concentrations of Archaea in the lower anoxic zone. Increases in microbial cell densities coincide with increases in trace metals at the chemocline, suggesting microbial activity may be responsible for trace metal release at this boundary. 16S rRNA PCR cloning techniques are currently being used to identify dominant microbial populations at various levels within the FGL water column. Future studies will focus on the potential for these dominant microorganisms to influence trace metal cycling and bioavailability in the FGL water column.

The gut microbiota and its role in the development of allergic disease: a wider perspective.

PubMed

West, C E; Jenmalm, M C; Prescott, S L

2015-01-01

The gut microbiota are critical in the homoeostasis of multiple interconnected host metabolic and immune networks. If early microbial colonization is delayed, the gut-associated lymphoid tissues (GALT) fail to develop, leading to persistent immune dysregulation in mice. Microbial colonization has also been proposed as a major driver for the normal age-related maturation of both Th1 and T regulatory (Treg) pathways that appear important in suppressing early propensity for Th2 allergic responses. There is emerging evidence that resident symbionts induce tolerogenic gut-associated Treg cells and dendritic cells that ensure the preferential growth of symbionts; keeping pathogenic strains in check and constraining proinflammatory Th1, Th2, and Th17 clones. Some effects of symbionts are mediated by short-chain fatty acids, which play a critical role in mucosal integrity and local and systemic metabolic function and stimulate the regulatory immune responses. The homoeostatic IL-10/TGF-β dominated tolerogenic response within the GALT also signals the production of secretory IgA, which have a regulating role in mucosal integrity. Contrary to the 'sterile womb' paradigm, recent studies suggest that maternal microbial transfer to the offspring begins during pregnancy, providing a pioneer microbiome. It is likely that appropriate microbial stimulation both pre- and postnatally is required for optimal Th1 and Treg development to avoid the pathophysiological processes leading to allergy. Disturbed gut colonization patterns have been associated with allergic disease, but whether microbial variation is the cause or effect of these diseases is still under investigation. We are far from understanding what constitutes a 'healthy gut microbiome' that promotes tolerance. This remains a major limitation and might explain some of the inconsistency in human intervention studies with prebiotics and probiotics. Multidisciplinary integrative approaches with researchers working in networks, using harmonized outcomes and methodologies, are needed to advance our understanding in this field. © 2014 John Wiley & Sons Ltd.

The Role of Reactive-Oxygen-Species in Microbial Persistence and Inflammation

PubMed Central

Spooner, Ralee; Yilmaz, Özlem

2011-01-01

The mechanisms of chronic infections caused by opportunistic pathogens are of keen interest to both researchers and health professionals globally. Typically, chronic infectious disease can be characterized by an elevation in immune response, a process that can often lead to further destruction. Reactive-Oxygen-Species (ROS) have been strongly implicated in the aforementioned detrimental response by host that results in self-damage. Unlike excessive ROS production resulting in robust cellular death typically induced by acute infection or inflammation, lower levels of ROS produced by host cells are increasingly recognized to play a critical physiological role for regulating a variety of homeostatic cellular functions including growth, apoptosis, immune response, and microbial colonization. Sources of cellular ROS stimulation can include “danger-signal-molecules” such as extracellular ATP (eATP) released by stressed, infected, or dying cells. Particularly, eATP-P2X7 receptor mediated ROS production has been lately found to be a key modulator for controlling chronic infection and inflammation. There is growing evidence that persistent microbes can alter host cell ROS production and modulate eATP-induced ROS for maintaining long-term carriage. Though these processes have yet to be fully understood, exploring potential positive traits of these “injurious” molecules could illuminate how opportunistic pathogens maintain persistence through physiological regulation of ROS signaling. PMID:21339989

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

A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom

NASA Astrophysics Data System (ADS)

Yang, Caiyun; Li, Yi; Zhou, Yanyan; Lei, Xueqian; Zheng, Wei; Tian, Yun; van Nostrand, Joy D.; He, Zhili; Wu, Liyou; Zhou, Jizhong; Zheng, Tianling

2016-10-01

Phytoplankton blooms are a worldwide problem and can greatly affect ecological processes in aquatic systems, but its impacts on the functional potential of microbial communities are limited. In this study, a high-throughput microarray-based technology (GeoChip) was used to profile the functional potential of free-living microbes from the Xiamen Sea Area in response to a 2011 Akashiwo sanguinea bloom. The bloom altered the overall community functional structure. Genes that were significantly (p < 0.05) increased during the bloom included carbon degradation genes and genes involved in nitrogen (N) and/or phosphorus (P) limitation stress. Such significantly changed genes were well explained by chosen environmental factors (COD, nitrite-N, nitrate-N, dissolved inorganic phosphorus, chlorophyll-a and algal density). Overall results suggested that this bloom might enhance the microbial converting of nitrate to N2 and ammonia nitrogen, decrease P removal from seawater, activate the glyoxylate cycle, and reduce infection activity of bacteriophage. This study presents new information on the relationship of algae to other microbes in aquatic systems, and provides new insights into our understanding of ecological impacts of phytoplankton blooms.

Electron acceptor redox potential globally regulates transcriptomic profiling in Shewanella decolorationis S12

NASA Astrophysics Data System (ADS)

Lian, Yingli; Yang, Yonggang; Guo, Jun; Wang, Yan; Li, Xiaojing; Fang, Yun; Gan, Lixia; Xu, Meiying

2016-08-01

Electron acceptor redox potential (EARP) was presumed to be a determining factor for microbial metabolism in many natural and engineered processes. However, little is known about the potentially global effects of EARP on bacteria. In this study, we compared the physiological and transcriptomic properties of Shewanella decolorationis S12 respiring with different EARPs in microbial electrochemical systems to avoid the effects caused by the other physicochemical properties of real electron acceptor. Results showed that the metabolic activities of strain S12 were nonlinear responses to EARP. The tricarboxylic acid cycle for central carbon metabolism was down-regulated while glyoxylate shunt was up-regulated at 0.8 V compared to 0.2 and -0.2 V, which suggested that EARP is an important but not the only determinant for metabolic pathways of strain S12. Moreover, few cytochrome c genes were differentially expressed at different EARPs. The energy intensive flagella assembly and assimilatory sulfur metabolism pathways were significantly enriched at 0.8 V, which suggested strain S12 had stronger electrokinesis behavior and oxidative stress-response at high EARP. This study provides the first global information of EARP regulations on microbial metabolism, which will be helpful for understanding microorganism respiration.

The Modulation of Adaptive Immune Responses by Bacterial Zwitterionic Polysaccharides

PubMed Central

Stephen, Tom Li; Groneck, Laura; Kalka-Moll, Wiltrud Maria

2010-01-01

The detection of pathogen-derived molecules as foreign particles by adaptive immune cells triggers T and B lymphocytes to mount protective cellular and humoral responses, respectively. Recent immunological advances elucidated that proteins and some lipids are the principle biological molecules that induce protective T cell responses during microbial infections. Polysaccharides are important components of microbial pathogens and many vaccines. However, research concerning the activation of the adaptive immune system by polysaccharides gained interest only recently. Traditionally, polysaccharides were considered to be T cell-independent antigens that did not directly activate T cells or induce protective immune responses. Here, we review several recent advances in “carbohydrate immunobiology”. A group of bacterial polysaccharides that are known as “zwitterionic polysaccharides (ZPSs)” were recently identified as potent immune modulators. The immunomodulatory effect of ZPSs required antigen processing and presentation by antigen presenting cells, the activation of CD4 T cells and subpopulations of CD8 T cells and the modulation of host cytokine responses. In this review, we also discuss the potential use of these unique immunomodulatory ZPSs in new vaccination strategies against chronic inflammatory conditions, autoimmunity, infectious diseases, allergies and asthmatic conditions. PMID:21234388

Microbiota as a mediator of cancer progression and therapy.

PubMed

Pope, Jillian L; Tomkovich, Sarah; Yang, Ye; Jobin, Christian

2017-01-01

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbiota as a mediator of cancer progression and therapy

PubMed Central

Pope, Jillian L.; Tomkovich, Sarah; Yang, Ye; Jobin, Christian

2017-01-01

Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis. PMID:27554797

Using a trait-based approach to link microbial community composition and functioning to soil salinity

NASA Astrophysics Data System (ADS)

Rath, Kristin; Fierer, Noah; Rousk, Johannes

2017-04-01

Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared through 16S rRNA gene amplicon sequencing. Microbial community composition changed greatly along the salinity gradients. Using the salt-tolerance assessments to estimate bacterial trait-distributions we could determine substantial differences in tolerance to salt revealing a strong causal connection between environment and trait distributions. By constraining the community composition with salinity tolerance in ordinations, we could assign which community differences were directly due to a shift in community trait distributions. These analyses revealed that a substantial part (up to 30%) of the community composition differences were directly driven by environmental salt concentrations.. Even though communities in saline soils had trait-distributions aligned to their environment, their performance (respiration, growth rates) was lower than those in non-saline soils and remained low even after input of organic material. Using a trait-based approach we could connect filtered trait distributions along environmental gradients, to the composition of the microbial community. We show that soil salinity played an important role in shaping microbial community composition by selecting for communities with higher salt tolerance. The shift toward bacterial communities with trait distributions matched to salt environments probably compensated for much of the potential loss of function induced by salinity, resulting in a degree of apparent functional redundancy for decomposition. However, more tolerant communities still showed reduced functioning, suggesting a trade-off between salt tolerance and performance.

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem.

PubMed

Zhou, Jizhong; Deng, Ye; Zhang, Ping; Xue, Kai; Liang, Yuting; Van Nostrand, Joy D; Yang, Yunfeng; He, Zhili; Wu, Liyou; Stahl, David A; Hazen, Terry C; Tiedje, James M; Arkin, Adam P

2014-03-04

Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.

Balancing macronutrient stoichiometry to alleviate eutrophication.

PubMed

Stutter, M I; Graeber, D; Evans, C D; Wade, A J; Withers, P J A

2018-09-01

Reactive nitrogen (N) and phosphorus (P) inputs to surface waters modify aquatic environments, affect public health and recreation. Source controls dominate eutrophication management, whilst biological regulation of nutrients is largely neglected, although aquatic microbial organisms have huge potential to process nutrients. The stoichiometric ratio of organic carbon (OC) to N to P atoms should modulate heterotrophic pathways of aquatic nutrient processing, as high OC availability favours aquatic microbial processing. Heterotrophic microbial processing removes N by denitrification and captures N and P as organically-complexed, less eutrophying forms. With a global data synthesis, we show that the atomic ratios of bioavailable dissolved OC to either N or P in rivers with urban and agricultural land use are often distant from a "microbial optimum". This OC-deficiency relative to high availabilities of N and P likely overwhelms within-river heterotrophic processing. We propose that the capability of streams and rivers to retain N and P may be improved by active stoichiometric rebalancing. Although autotrophic OC production contributes to heterotrophic rates substantial control on nutrient processing from allochthonous OC is documented for N and an emerging field for P. Hence, rebalancing should be done by reconnecting appropriate OC sources such as wetlands and riparian forests that have become disconnected from rivers concurrent with agriculture and urbanisation. However, key knowledge gaps require research prior to the safe implementation of this approach in management: (i) to evaluate system responses to catchment inputs of dissolved OC forms and amounts relative to internal production of autotrophic dissolved OC and aquatic and terrestrial particulate OC and (ii) evaluate risk factors in anoxia-mediated P desorption with elevated OC scenarios. Still, we find stoichiometric rebalancing through reconnecting landscape beneficial OC sources has considerable potential for river management to alleviate eutrophication, improve water quality and aquatic ecosystem health, if augmenting nutrient source control. Copyright © 2018 Elsevier B.V. All rights reserved.

Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition

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

Bouskill, Nicholas J.; Wood, Tana E.; Baran, Richard

Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however, the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the productionmore » of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO 2 efflux following wet-up in drought plots relative to control plots.« less

Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition

PubMed Central

Bouskill, Nicholas J.; Wood, Tana E.; Baran, Richard; Hao, Zhao; Ye, Zaw; Bowen, Ben P.; Lim, Hsiao Chien; Nico, Peter S.; Holman, Hoi-Ying; Gilbert, Benjamin; Silver, Whendee L.; Northen, Trent R.; Brodie, Eoin L.

2016-01-01

Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however, the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the production of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO2 efflux following wet-up in drought plots relative to control plots. PMID:27014243

Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition

DOE PAGES

Bouskill, Nicholas J.; Wood, Tana E.; Baran, Richard; ...

2016-03-15

Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however, the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the productionmore » of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO 2 efflux following wet-up in drought plots relative to control plots.« less

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health.

PubMed

Ha, Connie W Y; Lam, Yan Y; Holmes, Andrew J

2014-11-28

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging.

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

PubMed Central

Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

2014-01-01

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

Human System Risk Management - Tools of our Trade

NASA Technical Reports Server (NTRS)

Ott, C. Mark

2009-01-01

The risk of infectious disease to select individuals has historically been difficult to predict in either spaceflight or on Earth with health care efforts relying on broad-based prevention and post-infection treatment. Over the past 10 years, quantitative microbial risk assessment evaluations have evolved to formalize the assessment process and quantify the risk. This process of hazard identification, exposure assessment, dose-response assessment, and risk characterization has been applied by the water and food safety industries to address the public health impacts associated with the occurrence of and human exposure to pathogens in water and food for the development of preventive strategies for microbial disease. NASA is currently investigating the feasibility of using these techniques to better understand the risks to astronauts and refine their microbiological requirements. To assess these techniques, NASA began an evaluation of the potable water system on the International Space Station to determine how the microbial risk from water consumption during flight differed from terrestrial sources, such as municipal water systems. The ultimate goal of this work is to optimize microbial requirements which would minimize unnecessary cargo and use of crew time, while still protecting the health of the crew. Successful demonstration of this risk assessment framework with the water system holds the potential to maximize the use of available resources during spaceflight missions and facilitate investigations into the evaluation of other routes of infection, such as through the spaceflight foods system.

Responses of microbial respiration in grazed and ungrazed grasslands to glucose addition

NASA Astrophysics Data System (ADS)

Xu, Xingliang; Liu, Qianyuan; Pang, Rui

2017-04-01

Grazing can change species composition, alter soil properties, and thus modify microbial activities, affecting biogeochemical processes in grasslands. However, it remains unclear how microbial respiration in grazed and ungrazed grasslands responds to glucose addition. Here we hypothesize that microbial respiration in grazed grasslands will respond more strongly to glucose addition than in ungrazed grasslands because moderate grazing can enhance microbial activity. To examine the hypothesis above, we collected the upper 10 cm soil from grazed and ungrazed grasslands at five sites of China. Three sites (Hulunbuir 1, Hulunbuir 2 and Xielingele) were located in Inner Mongolia and two in the Tibet Plateau) Soils were incubated with low glucose input (50% MBC), high glucose input (150% MBC), and water for 60 days in 21oC. CO2 released from soil was trapped with 1 M NaOH. The results showed that the effect of grazing on microbial respiration has two distinct patterns, depending on soil types and addition amount. After glucose addition, cumulative CO2 efflux from grazed soils was significantly higher than from ungrazed soils in two temperate grasslands (Hulunbuir 1 and Xielingele). This may be ascribed to that moderate grazing promoted microbial activity. On the contrary, microbial respirations from grazed soils were lower than ungrazed soils in two alpine meadows of Haibei and Dangxiong and in Hulunbuir 2. This effect of grazing was not obvious in Hulunbeier 2 soils at low carbon addition level. Grazing may decrease soil organic carbon, nitrogen availability and thus microbial activity in alpine grasslands. These findings indicate that soil microorganisms could have different adaptation mechanisms to grazing in temperate and alpine grasslands.

Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland.

PubMed

Yang, Yunfeng; Wu, Linwei; Lin, Qiaoyan; Yuan, Mengting; Xu, Depeng; Yu, Hao; Hu, Yigang; Duan, Jichuang; Li, Xiangzhen; He, Zhili; Xue, Kai; van Nostrand, Joy; Wang, Shiping; Zhou, Jizhong

2013-02-01

Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH4 (+) -N. In-depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N-reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land-use and/or climate changes. © 2012 Blackwell Publishing Ltd.

Microbial models with data-driven parameters predict stronger soil carbon responses to climate change.

PubMed

Hararuk, Oleksandra; Smith, Matthew J; Luo, Yiqi

2015-06-01

Long-term carbon (C) cycle feedbacks to climate depend on the future dynamics of soil organic carbon (SOC). Current models show low predictive accuracy at simulating contemporary SOC pools, which can be improved through parameter estimation. However, major uncertainty remains in global soil responses to climate change, particularly uncertainty in how the activity of soil microbial communities will respond. To date, the role of microbes in SOC dynamics has been implicitly described by decay rate constants in most conventional global carbon cycle models. Explicitly including microbial biomass dynamics into C cycle model formulations has shown potential to improve model predictive performance when assessed against global SOC databases. This study aimed to data-constrained parameters of two soil microbial models, evaluate the improvements in performance of those calibrated models in predicting contemporary carbon stocks, and compare the SOC responses to climate change and their uncertainties between microbial and conventional models. Microbial models with calibrated parameters explained 51% of variability in the observed total SOC, whereas a calibrated conventional model explained 41%. The microbial models, when forced with climate and soil carbon input predictions from the 5th Coupled Model Intercomparison Project (CMIP5), produced stronger soil C responses to 95 years of climate change than any of the 11 CMIP5 models. The calibrated microbial models predicted between 8% (2-pool model) and 11% (4-pool model) soil C losses compared with CMIP5 model projections which ranged from a 7% loss to a 22.6% gain. Lastly, we observed unrealistic oscillatory SOC dynamics in the 2-pool microbial model. The 4-pool model also produced oscillations, but they were less prominent and could be avoided, depending on the parameter values. © 2014 John Wiley & Sons Ltd.

Thin-layer heap bioleaching of copper flotation tailings containing high levels of fine grains and microbial community succession analysis

NASA Astrophysics Data System (ADS)

Hao, Xiao-dong; Liang, Yi-li; Yin, Hua-qun; Liu, Hong-wei; Zeng, Wei-min; Liu, Xue-duan

2017-04-01

Thin-layer heap bioleaching of copper flotation tailings containing high levels of fine grains was carried out by mixed cultures on a small scale over a period of 210 d. Lump ores as a framework were loaded at the bottom of the ore heap. The overall copper leaching rates of tailings and lump ores were 57.10wt% and 65.52wt%, respectively. The dynamic shifts of microbial community structures about attached microorganisms were determined using the Illumina MiSeq sequencing platform based on 16S rRNA amplification strategy. The results indicated that chemolithotrophic genera Acidithiobacillus and Leptospirillum were always detected and dominated the microbial community in the initial and middle stages of the heap bioleaching process; both genera might be responsible for improving the copper extraction. However, Thermogymnomonas and Ferroplasma increased gradually in the final stage. Moreover, the effects of various physicochemical parameters and microbial community shifts on the leaching efficiency were further investigated and these associations provided some important clues for facilitating the effective application of bioleaching.

Inorganic polyphosphate in the microbial world. Emerging roles for a multifaceted biopolymer.

PubMed

Albi, Tomás; Serrano, Aurelio

2016-02-01

Inorganic polyphosphates (polyP) are linear polymers of tens to hundreds orthophosphate residues linked by phosphoanhydride bonds. These fairly abundant biopolymers occur in all extant forms of life, from prokaryotes to mammals, and could have played a relevant role in prebiotic evolution. Since the first identification of polyP deposits as metachromatic or volutin granules in yeasts in the nineteenth century, an increasing number of varied physiological functions have been reported. Due to their "high energy" bonds analogous to those in ATP and their properties as polyanions, polyP serve as microbial phosphagens for a variety of biochemical reactions, as a buffer against alkalis, as a storage of Ca(2+) and as a metal-chelating agent. In addition, recent studies have revealed polyP importance in signaling and regulatory processes, cell viability and proliferation, pathogen virulence, as a structural component and chemical chaperone, and as modulator of microbial stress response. This review summarizes the current status of knowledge and future perspectives of polyP functions and their related enzymes in the microbial world.

Microbial production of metabolites and associated enzymatic reactions under high pressure.

PubMed

Dong, Yongsheng; Jiang, Hua

2016-11-01

High environmental pressure exerts an external stress on the survival of microorganisms that are commonly found under normal pressure. In response, many growth traits alter, including cell morphology and physiology, cellular structure, metabolism, physical and chemical properties, the reproductive process, and defense mechanisms. The high-pressure technology (HP) has been industrially utilized in pressurized sterilization, synthesis of stress-induced products, and microbial/enzymatic transformation of chemicals. This article reviews current research on pressure-induced production of metabolites in normal-pressure microbes and their enzymatic reactions. Factors that affect the production of such metabolites are summarized, as well as the effect of pressure on the performance of microbial fermentation and the yield of flavoring compounds, different categories of induced enzymatic reactions and their characteristics in the supercritical carbon dioxide fluid, effects on enzyme activity, and the selection of desirable bacterial strains. Technological challenges are discussed, and future research directions are proposed. Information presented here will benefit the research, development, and application of the HP technology to improve microbial fermentation and enzymatic production of biologically active substances, thereby help to meet their increasing demand from the ever-expanding market.

Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment

PubMed Central

Dang, Hongyue; Chen, Chen-Tung A.

2017-01-01

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field. PMID:28769878

RESISTANCE OF MICROBIAL COMMUNITIES FROM ECUADOR ECOSYSTEMS TO REPRESENTATIVE TOXIC METALS - CrO4(2-), Co2+, Ni2+, Cu2+, Hg2+.

PubMed

Tashyrev, O B; Prekrasna, Ie P; Tashyreva, G O; Bielikova, O Iu

2015-01-01

Microbial communities of the Ecuadorian Andes and volcano Tungurahua were shown to be super resistant to representative toxic metals. Maximum permissible concentrations of toxic metals were 100 ppm of Hg2+, 500 ppm of Co2+ and Ni2+, 1000 and 1500 ppm of Cr(VI), 10000 and 20000 ppm of Cu2+. The effect of metal concentration increasing on the biomass growth, CO2 and H2 synthesis was investigated. Two types of response of microbial communities on the increasing of toxic metals concentrations were discovered. The first type of response is the catastrophic inhibition of microbial growth. The second type of response is the absence of microbial growth inhibition at certain metal concentration gradient. The succession of qualitative structure of Ecuadorian microbial communities was shown for the first time. Bacteria, yeasts and finally fungi consistently dominate in the microbial community at the Cu2+ concentration raising. Microorganisms resistant to ultra-high concentrations of toxic metals (e.g., 3000 ... 20000 ppm of Cu2+) were isolated from Ecuadorian ecosystems. These microorganisms are able to accumulate toxic metals.

Short-term belowground responses to thinning and burning treatments in southwestern ponderosa pine forests of the USA

Treesearch

Steven T. Overby; Stephen C. Hart

2016-01-01

Microbial-mediated decomposition and nutrient mineralization are major drivers of forest productivity. As landscape-scale fuel reduction treatments are being implemented throughout the fire-prone western United States of America, it is important to evaluate operationally how these wildfire mitigation treatments alter belowground processes. We quantified these important...

Low-to-moderate nitrogen and phosphorus concentrations accelerate microbially driven litter breakdown rates

Treesearch

John S. Kominoski; Amy D. Rosemond; Jonathan P. Benstead; Vladislav Gulis; John C. Maerz; David Manning

2015-01-01

Particulate organic matter (POM) processing is an important driver of aquatic ecosystem productivity that is sensitive to nutrient enrichment and drives ecosystem carbon (C) loss. Although studies of single concentrations of nitrogen (N) or phosphorus (P) have shown effects at relatively low concentrations, responses of litter breakdown rates along gradients of low-to-...

Lipidomic profiling of bioactive lipids by mass spectrometry during microbial infections.

PubMed

Tam, Vincent C

2013-10-31

Bioactive lipid mediators play crucial roles in promoting the induction and resolution of inflammation. Eicosanoids and other related unsaturated fatty acids have long been known to induce inflammation. These signaling molecules can modulate the circulatory system and stimulate immune cell infiltration into the site of infection. Recently, DHA- and EPA-derived metabolites have been discovered to promote the resolution of inflammation, an active process. Not only do these molecules stop the further infiltration of immune cells, they prompt non-phlogistic phagocytosis of apoptotic neutrophils, stimulating the tissue to return to homeostasis. After the rapid release of lipid precursors from the plasma membrane upon stimulation, families of enzymes in a complex network metabolize them to produce a large array of lipid metabolites. With current advances in mass spectrometry, the entire lipidome can be accurately quantified to assess the immune response upon microbial infection. In this review, we discuss the various lipid metabolism pathways in the context of the immune response to microbial pathogens, as well as their complex network interactions. With the advancement of mass spectrometry, these approaches have also been used to characterize the lipid mediator response of macrophages and neutrophils upon immune stimulation in vitro. Lastly, we describe the recent efforts to apply systems biology approaches to dissect the role of lipid mediators during bacterial and viral infections in vivo. Copyright © 2013 Elsevier Ltd. All rights reserved.

Changes in the ginsenoside content during the fermentation process using microbial strains.

PubMed

Lee, So Jin; Kim, Yunjeong; Kim, Min-Gul

2015-10-01

Red ginseng (RG) is processed from Panax ginseng via several methods including heat treatment, mild acid hydrolysis, and microbial conversion to transform the major ginsenosides into minor ginsenosides, which have greater pharmaceutical activities. During the fermentation process using microbial strains in a machine for making red ginseng, a change of composition occurs after heating. Therefore, we confirmed that fermentation had occurred using only microbial strains and evaluated the changes in the ginsenosides and their chemical composition. To confirm the fermentation by microbial strains, the fermented red ginseng was made with microbial strains (w-FRG) or without microbial strains (n-FRG), and the fermentation process was performed to tertiary fermentation. The changes in the ginsenoside composition of the self-manufactured FRG using the machine were evaluated using HPLC, and the 20 ginsenosides were analyzed. Additionally, we investigated changes of the reducing sugar and polyphenol contents during fermentation process. In the fermentation process, ginsenosides Re, Rg1, and Rb1 decreased but ginsenosides Rh1, F2, Rg3, and Compound Y (C.Y) increased in primary FRG more than in the raw ginseng and RG. The content of phenolic compounds was high in FRG and the highest in the tertiary w-FRG. Moreover, the reducing sugar content was approximately three times higher in the tertiary w-FRG than in the other n-FRG. As the results indicate, we confirmed the changes in the ginsenoside content and the role of microbial strains in the fermentation process.

Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study.

PubMed

Crowther, Thomas W; Maynard, Daniel S; Leff, Jonathan W; Oldfield, Emily E; McCulley, Rebecca L; Fierer, Noah; Bradford, Mark A

2014-09-01

The consequences of deforestation for aboveground biodiversity have been a scientific and political concern for decades. In contrast, despite being a dominant component of biodiversity that is essential to the functioning of ecosystems, the responses of belowground biodiversity to forest removal have received less attention. Single-site studies suggest that soil microbes can be highly responsive to forest removal, but responses are highly variable, with negligible effects in some regions. Using high throughput sequencing, we characterize the effects of deforestation on microbial communities across multiple biomes and explore what determines the vulnerability of microbial communities to this vegetative change. We reveal consistent directional trends in the microbial community response, yet the magnitude of this vegetation effect varied between sites, and was explained strongly by soil texture. In sandy sites, the difference in vegetation type caused shifts in a suite of edaphic characteristics, driving substantial differences in microbial community composition. In contrast, fine-textured soil buffered microbes against these effects and there were minimal differences between communities in forest and grassland soil. These microbial community changes were associated with distinct changes in the microbial catabolic profile, placing community changes in an ecosystem functioning context. The universal nature of these patterns allows us to predict where deforestation will have the strongest effects on soil biodiversity, and how these effects could be mitigated. © 2014 John Wiley & Sons Ltd.

Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective.

PubMed

García-Palacios, Pablo; Vandegehuchte, Martijn L; Shaw, E Ashley; Dam, Marie; Post, Keith H; Ramirez, Kelly S; Sylvain, Zachary A; de Tomasel, Cecilia Milano; Wall, Diana H

2015-04-01

In recent years, there has been an increase in research to understand how global changes' impacts on soil biota translate into altered ecosystem functioning. However, results vary between global change effects, soil taxa, and ecosystem processes studied, and a synthesis of relationships is lacking. Therefore, here we initiate such a synthesis to assess whether the effect size of global change drivers (elevated CO2, N deposition, and warming) on soil microbial abundance is related with the effect size of these drivers on ecosystem functioning (plant biomass, soil C cycle, and soil N cycle) using meta-analysis and structural equation modeling. For N deposition and warming, the global change effect size on soil microbes was positively associated with the global change effect size on ecosystem functioning, and these relationships were consistent across taxa and ecosystem processes. However, for elevated CO2, such links were more taxon and ecosystem process specific. For example, fungal abundance responses to elevated CO2 were positively correlated with those of plant biomass but negatively with those of the N cycle. Our results go beyond previous assessments of the sensitivity of soil microbes and ecosystem processes to global change, and demonstrate the existence of general links between the responses of soil microbial abundance and ecosystem functioning. Further we identify critical areas for future research, specifically altered precipitation, soil fauna, soil community composition, and litter decomposition, that are need to better quantify the ecosystem consequences of global change impacts on soil biodiversity. © 2014 John Wiley & Sons Ltd.

Soil microbial responses to nitrogen addition in arid ecosystems

DOE PAGES

Sinsabaugh, Robert L.; Belnap, Jayne; Rudgers, Jennifer; ...

2015-08-14

The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO 3-NH 4 mix at 0, 7, and 15 kg N ha -1 y -1 from March 2012 to March 2013. In March 2013, biocrust (0–0.5 cm) and bulk soils (0–10 cm) were collected beneath Ambrosia canopies andmore » in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. By most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha -1 y -1 and 159 kg ha -1, respectively, for biomass, and 70 kg ha -1 y -1 and 114 kg ha -1, respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration reported in broader meta-analyses of N amendment effects in mesic ecosystems. As a result, large effect sizes at low N addition rates indicate that arid ecosystems are sensitive to modest increments in anthropogenic N deposition.« less

Microbial communities in the functional areas of a biofilm reactor with anaerobic-aerobic process for oily wastewater treatment.

PubMed

Li, Jianhua; Sun, Shanshan; Yan, Ping; Fang, Li; Yu, Yang; Xiang, Yangdong; Wang, Di; Gong, Yejing; Gong, Yanjun; Zhang, Zhongzhi

2017-08-01

Microbial communities in the functional areas of biofilm reactors with large height-diameter ratio using the anaerobic-aerobic (A/O) reflux process was investigated to treat heavy oil refinery wastewater without pretreatment. In the process, chemical oxygen demand (COD) and total nitrogen (TN) removal reached 93.2% and 82.8%, and the anaerobic biofilm reactor was responsible for 95% and 99%, respectively. Areas for hydrolysis acidification and acetic acid production, methane production, and COD recovery were obvious in the anaerobic reactor. Among all areas, area for hydrolysis acidification and acetic acid production was the key factor to improve COD removal efficiency. High throughput sequencing of 16S rDNA gene showed that the native community was mainly composed of functional groups for hydrocarbon degradation, syntrophic bacteria union body, methanogenesis, nitrification, denitrification, and sulfate reduction. The deviations between predicted values and actual COD and TN removal were less than 5% in the optimal prediction model. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Rain increases methane production and methane oxidation in a boreal thermokarst bog

NASA Astrophysics Data System (ADS)

Neumann, R. B.; Moorberg, C.; Turner, J.; Wong, A.; Waldrop, M. P.; Euskirchen, E. S.; Edgar, C.; Turetsky, M. R.

2017-12-01

Bottom-up biogeochemical models of wetland methane emissions simulate the response of methane production, oxidation and transport to wetland conditions and environmental forcings. One reason for mismatches between bottom-up and top-down estimates of emissions is incomplete knowledge of factors and processes that control microbial rates and methane transport. To advance mechanistic understanding of wetland methane emissions, we conducted a multi-year field investigation and plant manipulation experiment in a thermokarst bog located near Fairbanks, Alaska. The edge of the bog is experiencing active permafrost thaw, while the center of the bog thawed 50 to 100 years ago. Our study, which captured both an average year and two of the wettest years on record, revealed how rain interacts with vascular vegetation and recently thawed permafrost to affect methane emissions. In the floating bog, rain water warmed and oxygenated the subsurface, but did not alter soil saturation. The warmer peat temperatures increased both microbial methane production and plant productivity at the edge of the bog near the actively thawing margin, but minimally altered microbial and plant activity in the center of the bog. These responses indicate processes at the edge of the bog were temperature limited while those in the center were not. The compounding effect of increased microbial activity and plant productivity at the edge of the bog doubled methane emissions from treatments with vascular vegetation during rainy years. In contrast, methane emissions from vegetated treatments in the center of the bog did not change with rain. The oxygenating influence of rain facilitated greater methane oxidation in treatments without vascular vegetation, which offset warming-induced increases in methane production at the edge of the bog and decreased methane emissions in the center of the bog. These results elucidate the complex and spatially variable response of methane production and oxidation in thermokarst bogs to energy and oxygen inputs from rain, and have implications for how boreal wetland methane emissions may respond in the future to altered precipitation patterns. Advective delivery of energy and oxygen to wetland subsoils via rainwater is not currently a mechanism included in bottom-up wetland methane models.

Role of vegetation and edaphic factors in controlling diversity and use of different carbon sources in semi-arid ecosystems

NASA Astrophysics Data System (ADS)

Lohse, K. A.; McLain, J. E.; Harman, C. J.; Sivapalan, M.; Troch, P. A.

2010-12-01

Microbially-mediated soil carbon cycling is closely linked to soil moisture and temperature. Climate change is predicted to increase intra-annual precipitation variability (i.e. less frequent yet more intense precipitation events) and alter biogeochemical processes due to shifts in soil moisture dynamics and inputs of carbon. However, the responses of soil biology and chemistry to predicted climate change, and their concomitant feedbacks on ecosystem productivity and biogeochemical processes are poorly understood. We collected soils at three different elevations in the Santa Catalina Mountains, AZ and quantified carbon utilization during pre-monsoon precipitation conditions. Contrasting parent materials (schist and granite) were paired at each elevation. We expected climate to determine the overall activity of soil fungal and bacterial communities and diversity of soil C utilization, and differences in parent material to modify these responses through controls on soil physical properties. We used EcoPlateTM C utilization assays to determine the relative abundance of soil bacterial and fungal populations and rate and diversity of carbon utilization. Additional plates were incubated with inhibitors selective to fungal or bacterial activity to assess relative contribution of these microbial groups to overall C utilization. We analyzed soils for soil organic matter, total C and N, particle size analysis and soil moisture content via both gravimetric and volumetric methods to assess the influences of soil physical and chemical properties on the measured biological responses. Consistent with our expectations, overall microbial activity was highest at the uppermost conifer elevation sites compared to the middle and lower elevation sites. In contrast to our expectations, however, overall activity was lower at the mid elevation oak woodland sites compared to the low elevation desert sites. Also consistent with our expectations was the observation that overall activities were consistently higher in schist parent material compared to granite. Though differences between canopy and intercanopy carbon utilization were subtle, the diversity of carbon utilization differed, suggesting a potential role of root exudates in governing C utilization in these semiarid soils. Findings from this study suggest that soil physical properties due to parent material have primary impacts in constraining microbial growth and carbon utilization under changing climate conditions.

Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor.

PubMed

Stern, Noah; Ginder-Vogel, Matthew; Stegen, James C; Arntzen, Evan; Kennedy, David W; Larget, Bret R; Roden, Eric E

2017-08-15

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities ( in situ colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to "cross-feeding" with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during in situ colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCE The influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were "cross-fed" with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors. Copyright © 2017 American Society for Microbiology.

Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

NASA Technical Reports Server (NTRS)

Grace, Joseph M.; Verseux, Cyprien; Gentry, Diana; Moffet, Amy; Thayabaran, Ramanen; Wong, Nathan; Rothschild, Lynn

2013-01-01

The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the number or growth rate of surviving cells. We are on our second prototype iteration, with demonstrated functions of microbial growth monitoring and dynamic exposure to UV-C radiation and temperature. We plan to add functionality for general chemical presence or absence by Nov. 2013. By making the project low-cost and open-source, we hope to encourage others to use it as a basis for future development of a common microbial environmental adaptation testbed.

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community.

PubMed

Peces, M; Astals, S; Jensen, P D; Clarke, W P

2018-05-17

The impact of the starting inoculum on long-term anaerobic digestion performance, process functionality and microbial community composition remains unclear. To understand the impact of starting inoculum, active microbial communities from four different full-scale anaerobic digesters were each used to inoculate four continuous lab-scale anaerobic digesters, which were operated identically for 295 days. Digesters were operated at 15 days solid retention time, an organic loading rate of 1 g COD L r -1 d -1 (75:25 - cellulose:casein) and 37 °C. Results showed that long-term process performance, metabolic rates (hydrolytic, acetogenic, and methanogenic) and microbial community are independent of the inoculum source. Digesters process performance converged after 80 days, while metabolic rates and microbial communities converged after 120-145 days. The convergence of the different microbial communities towards a core-community proves that the deterministic factors (process operational conditions) were a stronger driver than the initial microbial community composition. Indeed, the core-community represented 72% of the relative abundance among the four digesters. Moreover, a number of positive correlations were observed between higher metabolic rates and the relative abundance of specific microbial groups. These correlations showed that both substrate consumers and suppliers trigger higher metabolic rates, expanding the knowledge of the nexus between microorganisms and functionality. Overall, these results support that deterministic factors control microbial communities in bioreactors independently of the inoculum source. Hence, it seems plausible that a desired microbial composition and functionality can be achieved by tuning process operational conditions. Copyright © 2018. Published by Elsevier Ltd.

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

PubMed

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

2015-05-01

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

Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

USDA-ARS?s Scientific Manuscript database

Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that el...

Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

USDA-ARS?s Scientific Manuscript database

Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that eli...

Effects of microbial inoculum composition on rumen microbial ecology of dairy calves

USDA-ARS?s Scientific Manuscript database

The objective of this study was to determine if microbial inoculum composition affects dairy calf rumen microbial ecology. Holstein bull calves (n=20) were removed from their dam at birth and individually housed in calf hutches with sand bedding. Responses were studied using a randomized complete bl...

Modeling the Response of Soil Organic Matter Decomposition to Warming: Effects of Dynamical Enzyme Productivity and Nuanced Representation of Respiration.

NASA Astrophysics Data System (ADS)

Sihi, D.; Gerber, S.; Inglett, K. S.; Inglett, P.

2014-12-01

Recent development in modeling soil organic carbon (SOC) decomposition includes the explicit incorporation of enzyme and microbial dynamics. A characteristic of these models is a feedback between substrate and consumers which is absent in traditional first order decay models. Second, microbial decomposition models incorporate carbon use efficiency (CUE) as a function of temperature which proved to be critical to prediction of SOC with warming. Our main goal is to explore microbial decomposition models with respect to responses of microbes to enzyme activity, costs to enzyme production, and to incorporation of growth vs. maintenance respiration. In order to simplify the modeling setup we assumed quick adjustment of enzyme activity and depolymerized carbon to microbial and SOC pools. Enzyme activity plays an important role to decomposition if its production is scaled to microbial biomass. In fact if microbes are allowed to optimize enzyme productivity the microbial enzyme model becomes unstable. Thus if the assumption of enzyme productivity is relaxed, other limiting factors must come into play. To stabilize the model, we account for two feedbacks that include cost of enzyme production and diminishing return of depolymerization with increasing enzyme concentration and activity. These feedback mechanisms caused the model to behave in a similar way to traditional, first order decay models. Most importantly, we found, that under warming, the changes in SOC carbon were more severe in enzyme synthesis is costly. In turn, carbon use efficiency (CUE) and its dynamical response to temperature is mainly determined by 1) the rate of turnover of microbes 2) the partitioning of dead microbial matter into different quality pools, and 3) and whether growth, maintenance respiration and microbial death rate have distinct responses to changes in temperature. Abbreviations: p: decay of enzyme, g: coefficient for growth respiration, : fraction of material from microbial turnover that enters the DOC pool, loss of C scaled to microbial mass, half saturation constant.

Optimization of hot water treatment for removing microbial colonies on fresh blueberry surface.

PubMed

Kim, Tae Jo; Corbitt, Melody P; Silva, Juan L; Wang, Dja Shin; Jung, Yean-Sung; Spencer, Barbara

2011-08-01

Blueberries for the frozen market are washed but this process sometimes is not effective or further contaminates the berries. This study was designed to optimize conditions for hot water treatment (temperature, time, and antimicrobial concentration) to remove biofilm and decrease microbial load on blueberries. Scanning electron microscopy (SEM) image showed a well-developed microbial biofilm on blueberries dipped in room temperature water. The biofilm consisted of yeast and bacterial cells attached to the berry surface in the form of microcolonies, which produced exopolymer substances between or upon the cells. Berry exposure to 75 and 90 °C showed little to no microorganisms on the blueberry surface; however, the sensory quality (wax/bloom) of berries at those temperatures was unacceptable. Response surface plots showed that increasing temperature was a significant factor on reduction of aerobic plate counts (APCs) and yeast/mold counts (YMCs) while adding Boxyl® did not have significant effect on APC. Overlaid contour plots showed that treatments of 65 to 70 °C for 10 to 15 s showed maximum reductions of 1.5 and 2.0 log CFU/g on APCs and YMCs, respectively; with acceptable level of bloom/wax score on fresh blueberries. This study showed that SEM, response surface, and overlaid contour plots proved successful in arriving at optima to reduce microbial counts while maintaining bloom/wax on the surface of the blueberries. Since chemical sanitizing treatments such as chlorine showed ineffectiveness to reduce microorganisms loaded on berry surface (Beuchat and others 2001, Sapers 2001), hot water treatment on fresh blueberries could maximize microbial reduction with acceptable quality of fresh blueberries. © 2011 Institute of Food Technologists®

Response of soil microbial communities to roxarsone pollution along a concentration gradient.

PubMed

Liu, Yaci; Zhang, Zhaoji; Li, Yasong; Wen, Yi; Fei, Yuhong

2017-07-29

The extensive use of roxarsone (3-nitro-4-hydroxyphenylarsonic acid) as a feed additive in the broiler poultry industry can lead to environmental arsenic contamination. This study was conducted to reveal the response of soil microbial communities to roxarsone pollution along a concentration gradient. To explore the degradation process and degradation kinetics of roxarsone concentration gradients in soil, the concentration shift of roxarsone at initial concentrations of 0, 50, 100, and 200 mg/kg, as well as that of the arsenic derivatives, was detected. The soil microbial community composition and structure accompanying roxarsone degradation were investigated by high-throughput sequencing. The results showed that roxarsone degradation was inhibited by a biological inhibitor, confirming that soil microbes were absolutely essential to its degradation. Moreover, soil microbes had considerable potential to degrade roxarsone, as a high initial concentration of roxarsone resulted in a substantially increased degradation rate. The concentrations of the degradation products HAPA (3-amino-4-hydroxyphenylarsonic acid), AS(III), and AS(V) in soils were significantly positively correlated. The soil microbial community composition and structure changed significantly across the roxarsone contamination gradient, and the addition of roxarsone decreased the microbial diversity. Some bacteria tended to be inhibited by roxarsone, while Bacillus, Paenibacillus, Arthrobacter, Lysobacter, and Alkaliphilus played important roles in roxarsone degradation. Moreover, HAPA, AS(III), and AS(V) were significantly positively correlated with Symbiobacterium, which dominated soils containing roxarsone, and their abundance increased with increasing initial roxarsone concentration. Accordingly, Symbiobacterium could serve as indicator of arsenic derivatives released by roxarsone as well as the initial roxarsone concentration. This is the first investigation of microbes closely related to roxarsone degradation.

Carbon nanotubes as antimicrobial agents for water disinfection and pathogen control.

PubMed

Liu, Dan; Mao, Yiqin; Ding, Lijun

2018-04-01

Waterborne diseases significantly affect human health and are responsible for high mortality rates worldwide. Antibiotics have been known for decades for treatment of bacterial strains and their overuse and irrational applications are causing increasing bacteria resistance. Therefore, there is a strong need to find alternative ways for efficient water disinfection and microbial control. Carbon nanotubes (CNTs) have demonstrated strong antimicrobial properties due to their remarkable structure. This paper reviews the antimicrobial properties of CNTs, discusses diverse mechanisms of action against microorganisms as well as their applicability for water disinfection and microbial control. Safety concerns, challenges of CNTs as antimicrobial agents and future opportunities for their application in the water remediation process are also highlighted.

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.

Effects of 4-chlorophenol wastewater treatment on sludge acute toxicity, microbial diversity and functional genes expression in an activated sludge process.

PubMed

Zhao, Jianguo; Li, Yahe; Li, Yu; Yu, Zeya; Chen, Xiurong

2018-05-31

In this study, the effects of 4-chlorophenol (4-CP) wastewater treatment on sludge acute toxicity of luminescent bacteria, microbial diversity and functional genes expression of Pseudomonas were explored. Results showed that in the entire operational process, the sludge acute toxicity acclimated by 4-CP in a sequencing batch bioreactor (SBR) was significantly higher than the control SBR without 4-CP. The dominant phyla in acclimated SBR were Proteobacteria and Firmicutes, which also existed in control SBR. Some identified genera in acclimated SBR were responsible for 4-CP degradation. At the stable operational stages, the functional genes expression of Pseudomonas in acclimated SBR was down-regulated at the end of SBR cycle, and their expression mechanisms needed further research. This study provides a theoretical support to comprehensively understand the sludge performance in industrial wastewater treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Graphene oxide and H2 production from bioelectrochemical graphite oxidation.

PubMed

Lu, Lu; Zeng, Cuiping; Wang, Luda; Yin, Xiaobo; Jin, Song; Lu, Anhuai; Jason Ren, Zhiyong

2015-11-17

Graphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy consumption and hazardous chemicals. In this study, we reported a new bioelectrochemical method to produce GO from graphite under ambient conditions without chemical amendments, value-added organic compounds and high rate H2 were also produced. Compared with abiotic electrochemical electrolysis control, the microbial assisted graphite oxidation produced high rate of graphite oxide and graphene oxide (BEGO) sheets, CO2, and current at lower applied voltage. The resultant electrons are transferred to a biocathode, where H2 and organic compounds are produced by microbial reduction of protons and CO2, respectively, a process known as microbial electrosynthesis (MES). Pseudomonas is the dominant population on the anode, while abundant anaerobic solvent-producing bacteria Clostridium carboxidivorans is likely responsible for electrosynthesis on the cathode. Oxygen production through water electrolysis was not detected on the anode due to the presence of facultative and aerobic bacteria as O2 sinkers. This new method provides a sustainable route for producing graphene materials and renewable H2 at low cost, and it may stimulate a new area of research in MES.

Graphene oxide and H2 production from bioelectrochemical graphite oxidation

PubMed Central

Lu, Lu; Zeng, Cuiping; Wang, Luda; Yin, Xiaobo; Jin, Song; Lu, Anhuai; Jason Ren, Zhiyong

2015-01-01

Graphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy consumption and hazardous chemicals. In this study, we reported a new bioelectrochemical method to produce GO from graphite under ambient conditions without chemical amendments, value-added organic compounds and high rate H2 were also produced. Compared with abiotic electrochemical electrolysis control, the microbial assisted graphite oxidation produced high rate of graphite oxide and graphene oxide (BEGO) sheets, CO2, and current at lower applied voltage. The resultant electrons are transferred to a biocathode, where H2 and organic compounds are produced by microbial reduction of protons and CO2, respectively, a process known as microbial electrosynthesis (MES). Pseudomonas is the dominant population on the anode, while abundant anaerobic solvent-producing bacteria Clostridium carboxidivorans is likely responsible for electrosynthesis on the cathode. Oxygen production through water electrolysis was not detected on the anode due to the presence of facultative and aerobic bacteria as O2 sinkers. This new method provides a sustainable route for producing graphene materials and renewable H2 at low cost, and it may stimulate a new area of research in MES. PMID:26573014

Metagenomics reveals flavour metabolic network of cereal vinegar microbiota.

PubMed

Wu, Lin-Huan; Lu, Zhen-Ming; Zhang, Xiao-Juan; Wang, Zong-Min; Yu, Yong-Jian; Shi, Jin-Song; Xu, Zheng-Hong

2017-04-01

Multispecies microbial community formed through centuries of repeated batch acetic acid fermentation (AAF) is crucial for the flavour quality of traditional vinegar produced from cereals. However, the metabolism to generate and/or formulate the essential flavours by the multispecies microbial community is hardly understood. Here we used metagenomic approach to clarify in situ metabolic network of key microbes responsible for flavour synthesis of a typical cereal vinegar, Zhenjiang aromatic vinegar, produced by solid-state fermentation. First, we identified 3 organic acids, 7 amino acids, and 20 volatiles as dominant vinegar metabolites. Second, we revealed taxonomic and functional composition of the microbiota by metagenomic shotgun sequencing. A total of 86 201 predicted protein-coding genes from 35 phyla (951 genera) were involved in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of Metabolism (42.3%), Genetic Information Processing (28.3%), and Environmental Information Processing (10.1%). Furthermore, a metabolic network for substrate breakdown and dominant flavour formation in vinegar microbiota was constructed, and microbial distribution discrepancy in different metabolic pathways was charted. This study helps elucidating different metabolic roles of microbes during flavour formation in vinegar microbiota. Copyright © 2016 Elsevier Ltd. All rights reserved.

Uranium reduction and microbial community development in response to stimulation with different electron donors.

PubMed

Barlett, Melissa; Moon, Hee Sun; Peacock, Aaron A; Hedrick, David B; Williams, Kenneth H; Long, Philip E; Lovley, Derek; Jaffe, Peter R

2012-07-01

Stimulating microbial reduction of soluble U(VI) to less soluble U(IV) shows promise as an in situ bioremediation strategy for uranium contaminated groundwater, but the optimal electron donors for promoting this process have yet to be identified. The purpose of this study was to better understand how the addition of various electron donors to uranium-contaminated subsurface sediments affected U(VI) reduction and the composition of the microbial community. The simple electron donors, acetate or lactate, or the more complex donors, hydrogen-release compound (HRC) or vegetable oil, were added to the sediments incubated in flow-through columns. The composition of the microbial communities was evaluated with quantitative PCR probing specific 16S rRNA genes and functional genes, phospholipid fatty acid analysis, and clone libraries. All the electron donors promoted U(VI) removal, even though the composition of the microbial communities was different with each donor. In general, the overall biomass, rather than the specific bacterial species, was the factor most related to U(VI) removal. Vegetable oil and HRC were more effective in stimulating U(VI) removal than acetate. These results suggest that the addition of more complex organic electron donors could be an excellent option for in situ bioremediation of uranium-contaminated groundwater.

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.

Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients

PubMed Central

Sun, Weimin; Sun, Min; Dong, Yiran; Ning, Zengping; Xiao, Enzong; Tang, Song; Li, Jiwei

2015-01-01

Located in southwest China, the Aha watershed is continually contaminated by acid mine drainage (AMD) produced from upstream abandoned coal mines. The watershed is fed by creeks with elevated concentrations of aqueous Fe (total Fe > 1 g/liter) and SO42− (>6 g/liter). AMD contamination gradually decreases throughout downstream rivers and reservoirs, creating an AMD pollution gradient which has led to a suite of biogeochemical processes along the watershed. In this study, sediment samples were collected along the AMD pollution sites for geochemical and microbial community analyses. High-throughput sequencing found various bacteria associated with microbial Fe and S cycling within the watershed and AMD-impacted creek. A large proportion of Fe- and S-metabolizing bacteria were detected in this watershed. The dominant Fe- and S-metabolizing bacteria were identified as microorganisms belonging to the genera Metallibacterium, Aciditerrimonas, Halomonas, Shewanella, Ferrovum, Alicyclobacillus, and Syntrophobacter. Among them, Halomonas, Aciditerrimonas, Metallibacterium, and Shewanella have previously only rarely been detected in AMD-contaminated environments. In addition, the microbial community structures changed along the watershed with different magnitudes of AMD pollution. Moreover, the canonical correspondence analysis suggested that temperature, pH, total Fe, sulfate, and redox potentials (Eh) were significant factors that structured the microbial community compositions along the Aha watershed. PMID:25979900

Bioaerosol assessment in naturally ventilated historical library building with restricted personnel access.

PubMed

Harkawy, Aleksander; Górny, Rafał L; Ogierman, Leonard; Wlazło, Agnieszka; Ławniczek-Wałczyk, Anna; Niesler, Anna

2011-01-01

The aim of this study was to check the degree and identify the sources of microbial contamination of the Jasna Gora (Bright Hill) monastery library 10 years after disinfection of the incunabula collection. The registered maximum viable indoor microbial concentrations were 1,875 and 7,100 cfu/m³ for stationary and personal measurements, whereas respective total concentrations were 71,000 and 100,000 counts/m3. There was no statistically significant difference between the concentrations of viable microorganisms measured in the stationary using Andersen, GSP, and Button samplers. Moreover, GSP and Button samplers can be interchangeably applied when viable or total microbial levels are stationary or personally measured. The culturable microorganisms constituted 0.5 - 3.9% of the total microflora only. Filamentous fungi were the most prevalent outdoors, whereas Gram-positive cocci and endospore forming Gram-positive rods dominated indoors in the air and settled dust, respectively. Hence, an unrestrained infiltration of ambient air through the draughtiness of the building envelope is probably the main process responsible for indoor fungal pollution, whereas bacterial contaminants have their major sources in the indoor environment. Moreover, even a chemically cleansed library collection, having a restricted personnel access, but under the influence of ambient air, can undergo microbial contamination and becomes an important microbial emission source.

A Generalized QMRA Beta-Poisson Dose-Response Model.

PubMed

Xie, Gang; Roiko, Anne; Stratton, Helen; Lemckert, Charles; Dunn, Peter K; Mengersen, Kerrie

2016-10-01

Quantitative microbial risk assessment (QMRA) is widely accepted for characterizing the microbial risks associated with food, water, and wastewater. Single-hit dose-response models are the most commonly used dose-response models in QMRA. Denoting PI(d) as the probability of infection at a given mean dose d, a three-parameter generalized QMRA beta-Poisson dose-response model, PI(d|α,β,r*), is proposed in which the minimum number of organisms required for causing infection, K min , is not fixed, but a random variable following a geometric distribution with parameter 0

Key factors controlling microbial community response after a fire: importance of severity and recurrence

NASA Astrophysics Data System (ADS)

Lombao, Alba; Barreiro, Ana; Martín, Ángela; Díaz-Raviña, Montserrat

2015-04-01

Microorganisms play an important role in forest ecosystems, especially after fire when vegetation is destroyed and soil is bared. Fire severity and recurrence might be one of main factors controlling the microbial response after a wildfire but information about this topic is scarce. The aim of this study is to evaluate the influence of fire regimen (recurrence and severity) on soil microbial community structure by means of the analysis of phospholipid fatty acid (PLFA). The study was performed with unburned and burned samples collected from the top layer of a soil affected by a high severity fire (Laza, NW Spain) heated under laboratory conditions at different temperatures (50°C, 75°C, 100°C, 125°C, 150°C, 175°C, 200°C, 300°C) to simulate different fire intensities; the process was repeated after further soil recovery (1 month incubation) to simulate fire recurrence. The soil temperature was measured with thermocouples and used to calculate the degree-hours as estimation of the amount of heat supplied to the samples (fire severity). The PLFA analysis was used to estimate total biomass and the biomass of specific groups (bacteria, fungi, gram-positive bacteria and gram-negative bacteria) as well as microbial community structure (PLFA pattern) and PLFA data were analyzed by means of principal component analysis (PCA) in order to identify main factors determining microbial community structure. The results of PCA, performed with the whole PLFA data set, showed that first component explained 35% of variation and clearly allow us to differentiate unburned samples from the corresponding burned samples, while the second component, explaining 16% of variation, separated samples according the heating temperature. A marked impact of fire regimen on soil microorganisms was detected; the microbial community response varied depending on previous history of soil heating and the magnitude of changes in the PLFA pattern was related to the amount of heat supplied to the samples. Thus, wildfire was the main factor determining the microbial community structure followed, in less extent, by fire severity. The total biomass and the biomass of specifics microbial groups decreased notably as consequence of wildfire and minor changes were detected due to soil heating under laboratory conditions. The results clearly showed the usefulness of PLFA pattern combined with PCA to study the relationships between fire regimen (recurrence and severity) and associated direct and indirect changes in soil microorganisms. The data also indicated that degree-hours methodology rather than temperature is adequate for evaluating the impact of soil heating on microbial communities. Keywords: wildfire, heating temperature, degree-hours, PLFA pattern, microbial biomass Acknowledgements. This study was supported by the Ministerio Español de Economía y Competitividad (AGL2012-39688-C02-01). A Lombao is recipient of FPU grant from Ministerio Español de Educación.

Microbial Invasion vs. Tick Immune Regulation.

PubMed

Sonenshine, Daniel E; Macaluso, Kevin R

2017-01-01

Ticks transmit a greater variety of pathogenic agents that cause disease in humans and animals than any other haematophagous arthropod, including Lyme disease, Rocky Mountain spotted fever, human granulocytic anaplasmosis, babesiosis, tick-borne encephalitis, Crimean Congo haemorhagic fever, and many others (Gulia-Nuss et al., 2016). Although diverse explanations have been proposed to explain their remarkable vectorial capacity, among the most important are their blood feeding habit, their long term off-host survival, the diverse array of bioactive molecules that disrupt the host's natural hemostatic mechanisms, facilitate blood flow, pain inhibitors, and minimize inflammation to prevent immune rejection (Hajdušek et al., 2013). Moreover, the tick's unique intracellular digestive processes allow the midgut to provide a relatively permissive microenvironment for survival of invading microbes. Although tick-host-pathogen interactions have evolved over more than 300 million years (Barker and Murrell, 2008), few microbes have been able to overcome the tick's innate immune system, comprising both humoral and cellular processes that reject them. Similar to most eukaryotes, the signaling pathways that regulate the innate immune response, i.e., the Toll, IMD (Immunodeficiency) and JAK-STAT (Janus Kinase/ Signal Transducers and Activators of Transcription) also occur in ticks (Gulia-Nuss et al., 2016). Recognition of pathogen-associated molecular patterns (PAMPs) on the microbial surface triggers one or the other of these pathways. Consequently, ticks are able to mount an impressive array of humoral and cellular responses to microbial challenge, including anti-microbial peptides (AMPs), e.g., defensins, lysozymes, microplusins, etc., that directly kill, entrap or inhibit the invaders. Equally important are cellular processes, primarily phagocytosis, that capture, ingest, or encapsulate invading microbes, regulated by a primordial system of thioester-containing proteins, fibrinogen-related lectins and convertase factors (Hajdušek et al., 2013). Ticks also express reactive oxygen species (ROS) as well as glutathione-S-transferase, superoxide dismutase, heat shock proteins and even protease inhibitors that kill or inhibit microbes. Nevertheless, many tick-borne microorganisms are able to evade the tick's innate immune system and survive within the tick's body. The examples that follow describe some of the many different strategies that have evolved to enable ticks to transmit the agents of human and/or animal disease.

When microbial conversations get physical

PubMed Central

Reguera, Gemma

2011-01-01

It is widely accepted that microorganisms are social beings. Whereas communication via chemical signals (e.g. quorum sensing) has been the focus of most investigations, the use of physical signals for microbial cell-cell communication has received only limited attention. Here, I argue that physical modes of microbial communication could be widespread in nature. This is based on experimental evidence on the microbial emission and response to three physical signals: sound waves, electromagnetic radiation, and electric currents. These signals propagate rapidly and, even at very low intensities, they provide useful mechanisms when a rapid response is required. I also make some suggestions for promising future research avenues that could bring novel and unsuspected insights into the physical nature of microbial signaling networks. PMID:21239171

Good Manufacturing Practices and Microbial Contamination Sources in Orange Fleshed Sweet Potato Puree Processing Plant in Kenya

PubMed Central

Abong', George Ooko

2018-01-01

Limited information exists on the status of hygiene and probable sources of microbial contamination in Orange Fleshed Sweet Potato (OFSP) puree processing. The current study is aimed at determining the level of compliance to Good Manufacturing Practices (GMPs), hygiene, and microbial quality in OFSP puree processing plant in Kenya. Intensive observation and interviews using a structured GMPs checklist, environmental sampling, and microbial analysis by standard microbiological methods were used in data collection. The results indicated low level of compliance to GMPs with an overall compliance score of 58%. Microbial counts on food equipment surfaces, installations, and personnel hands and in packaged OFSP puree were above the recommended microbial safety and quality legal limits. Steaming significantly (P < 0.05) reduced microbial load in OFSP cooked roots but the counts significantly (P < 0.05) increased in the puree due to postprocessing contamination. Total counts, yeasts and molds, Enterobacteriaceae, total coliforms, and E. coli and S. aureus counts in OFSP puree were 8.0, 4.0, 6.6, 5.8, 4.8, and 5.9 log10 cfu/g, respectively. In conclusion, equipment surfaces, personnel hands, and processing water were major sources of contamination in OFSP puree processing and handling. Plant hygiene inspection, environmental monitoring, and food safety trainings are recommended to improve hygiene, microbial quality, and safety of OFSP puree. PMID:29808161

Good Manufacturing Practices and Microbial Contamination Sources in Orange Fleshed Sweet Potato Puree Processing Plant in Kenya.

PubMed

Malavi, Derick Nyabera; Muzhingi, Tawanda; Abong', George Ooko

2018-01-01

Limited information exists on the status of hygiene and probable sources of microbial contamination in Orange Fleshed Sweet Potato (OFSP) puree processing. The current study is aimed at determining the level of compliance to Good Manufacturing Practices (GMPs), hygiene, and microbial quality in OFSP puree processing plant in Kenya. Intensive observation and interviews using a structured GMPs checklist, environmental sampling, and microbial analysis by standard microbiological methods were used in data collection. The results indicated low level of compliance to GMPs with an overall compliance score of 58%. Microbial counts on food equipment surfaces, installations, and personnel hands and in packaged OFSP puree were above the recommended microbial safety and quality legal limits. Steaming significantly ( P < 0.05) reduced microbial load in OFSP cooked roots but the counts significantly ( P < 0.05) increased in the puree due to postprocessing contamination. Total counts, yeasts and molds, Enterobacteriaceae, total coliforms, and E. coli and S. aureus counts in OFSP puree were 8.0, 4.0, 6.6, 5.8, 4.8, and 5.9 log 10 cfu/g, respectively. In conclusion, equipment surfaces, personnel hands, and processing water were major sources of contamination in OFSP puree processing and handling. Plant hygiene inspection, environmental monitoring, and food safety trainings are recommended to improve hygiene, microbial quality, and safety of OFSP puree.

Microbial Biomass and Activity in Geomorphic Features in Forested and Urban Restored and Degraded Streams

EPA Science Inventory

Geomorphic spatial heterogeneity affects sediment denitrification, an anaerobic microbial process that results in the loss of nitrogen (N), and other anaerobic microbial processes such as methanogenesis in urban streams. We measured sediment denitrification potential (DEA), metha...

Integrating ecological and engineering concepts of resilience in microbial communities

DOE PAGES

Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; ...

2015-12-01

We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the twomore » concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.« less

The Importance of TLR2 and Macrophages in Modulating a Humoral Response after Encountering Streptococcus pneumoniae

DTIC Science & Technology

2008-03-26

Response after Encountering Streptococcus Pneumoniae" Brian Schae:5 ,Ph.D. Department of Microbi ogy & Immunology Committee Chairperson Masters...presenting cells (APCs), such as macrophages (M ) and dendritic cells (DC) recognize microbial surface components via cell surface receptors (i.e...stimulating factor (GM-CSF). TH1 cells are able to secrete IFN- , which is important in activating M to produce mediators important for microbial

Sensing technologies to measure metabolic activities in soil and assess its health conditions

NASA Astrophysics Data System (ADS)

De Cesare, Fabrizio; Macagnano, Antonella

2013-04-01

Soil is a complex ecosystem comprised of several and mutually interacting components, both abiotic (organo-mineral associations) and biotic (microbial and pedofaunal populations and plants), where a single parameter depends on other factors and affects the same and other factors, so that a network of influences among organisms coexists with the reciprocal actions between organisms and their environment. Therefore, it is difficult to undoubtedly determine what is the cause and what the effect within relationships between factors and processes. Soil is commonly studied through the evaluation and measurement of single parameters (e.g. the content of soil organic matter (SOM), microbial biomass, enzyme activities, pH, etc.), events (e.g. soil erosion, compaction, etc.) and processes (e.g. soil respiration, carbon fluxes, nitrification/denitrification, etc.), often carried out in laboratory conditions in order to limit the number of factors acting within the ecosystem under study, but missing the information about the global soil environment that way. In the last decade, several scientists have proposed and suggested the need for a holistic approach to soil ecosystems in different contexts. Recently, we have applied a sensing system developed in the last decades and capable of analysing complex mixtures of gases and volatiles (odours or aromas) in atmospheres, namely called electronic nose (EN). Typically, ENs are devices consisting of an array of differentially and partially specific, despite selective, sensors upon diverse coatings of sensitive films, i.e. interacting with single analytes of the same chemical class, despite not highly specific for a single substance, only, but showing also lower extent of cross-selectivity towards compounds of other chemical classes. ENs can be used in the classifications of odours by processing the collected responses of all sensors in the array through pattern recognition analyses, in order to obtain a chemical fingerprint (olfactory fingerprint) typical of the analysed air sample. Due to these features, we decided to apply such a sensing technology to the analyses of soil atmospheres, because several processes in soil, both abiotic and biotic, result in gas and/or volatile production and the dynamics of such releases may also be affected by several additional environmental factors, such as soil moisture, temperature, gas exchange rates with outer atmosphere, adsorption/desorption processes, etc. Then, the analysis of soil atmosphere may provide information about global soil conditions (e.g. soil quality and health), according to a holistic approach, where several factors are contemporarily taken into account. At the same time, the use of such a technology, if adequately trained on purpose, can supply information about a single or a pool of processes sharing similar features, which occur in soil over a certain period of time and mostly affecting soil atmosphere. According to these premises and hypotheses, we demonstrated that EN is an useful technology to measure soil microbial activity, through its correlation to specific metabolic activities occurring in soil (i.e. global and specific respiration and some enzyme activities), but also soil microbial biomass. On the basis of such evidences, we also were able to use this technology to assess the quality and health conditions of soil ecosystems in terms of metabolic indices previously identified, according to some metabolic parameters and biomass quantification of microbial populations. In other studies, we also applied EN technology, despite using a different set of sensors in the array, to analyse the atmosphere of soil ecosystems in order to assess their environmental conditions after contamination with polycyclic aromatic hydrocarbons (PAHs) (i.e. semivolatile - SVOCs - organic pollutants). In this case, EN technology resulted capable of distinguishing between contaminated and uncontaminated soils, according to the differences in a list of substances, occurring in the atmospheres of differently treated soils, which were identified through SPME-GC/MS analyses and then suggested to be responsible for the different classification. Analysing the EN responses, it was also possible to follow the degradation process of pollutants by resident microbial populations over time, on the basis of the contemporary decrease of contaminant and the increased release of CO2. Then, we suggest that EN technology may be usefully employed in the analyses of soil ecosystems in order to both supply information about global soil environment, according to the holistic approach, and about specific processes occurring therein. Furthermore, since EN technology resulted to be effective and successful in detecting processes in soil, in both natural and perturbed conditions, involving microbial populations, which are commonly considered as the most sensitive and responsive to soil environmental modifications, we suggest it might be reasonably employed in analyses concerning the assessment of soil quality and health. Consequently, such a technology may also be used to study several processes involving soil ecosystems, such as soil management practices, soil restoration, soil contamination and remediation, soil fertility, etc.

Experimental evidence of two mechanisms coupling leaf-level C assimilation to rhizosphere CO2 release

Treesearch

Zachary Kayler; Claudia Keitel; Kirstin Jansen; Arthur Gessler

2017-01-01

The time span needed for carbon fixed by plants to induce belowground responses of root and rhizosphere microbial metabolic processing is of high importance for quantifying the coupling between plant canopy physiology and soil biogeochemistry, but recent observations of a rapid link cannot be explained by new assimilate transport by phloem mass flow alone. We performed...

Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment.

PubMed

Valentín-Vargas, Alexis; Root, Robert A; Neilson, Julia W; Chorover, Jon; Maier, Raina M

2014-12-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings. Copyright © 2014 Elsevier B.V. All rights reserved.

Modeling the unmeasurable: scaling soil physiology from microns to meters and seconds to centuries (Invited)

NASA Astrophysics Data System (ADS)

Schimel, J.; Xu, X.; Lawrence, C. R.

2013-12-01

Models are essential tools for linking microbial dynamics to their manifestations at large scales. Yet, developing mechanistically accurate models requires data that we often don't have and may not be able to get, such as the functional life-span of an extracellular enzyme. Yet there are approaches to condense complex microbial dynamics into 'workable' models. One example is in describing soil responses to moisture pulses. We developed a family of five separate models to capture microbial dynamics through dry/wet cycles. The simplest was a straight multi-pool, 1st-order decomposition model, with versions adding levels of microbial mechanism, culminating in one that included exoenzyme-breakdown of detritus. However, this identified the critical mechanism, not as exoenzymes, but as the production of a bioavailable C pool that accumulates in dry soil and is rapidly metabolized on rewetting. A final version of the model therefore stripped out explicit enzymes but retained separate polymer breakdown and substrate use; this model was the most robust. A second pervasive question in soil biology has been what controls the size of the microbial biomass across biomes? We approached this through a physiological model that regulated microbial C assimilation into biomass by two processes: initial assimilation followed by ongoing maintenance. Assimilation is a function of substrate quality, while maintenance is regulated by climate--notably the period of the year during which microbes are active. This model was tested against a global dataset of microbial biomass. It explains why, for example, deserts and tundra have relatively high proportions of their organic matter in microbial biomass, while the low substrate quality and long active periods common in temperate conifer forests lead to low biomass levels.

Environmental Factors Influencing the Structural Dynamics of Soil Microbial Communities During Assisted Phytostabilization of Acid-Generating Mine Tailings: a Mesocosm Experiment

PubMed Central

Valentín-Vargas, Alexis; Root, Robert A.; Neilson, Julia W; Chorover, Jon; Maier, Raina M.

2014-01-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings. PMID:25237788

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.

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

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

PubMed

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

2011-03-01

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

Insights from intercomparison of microbial and conventional soil models

NASA Astrophysics Data System (ADS)

Allison, S. D.; Li, J.; Luo, Y.; Mayes, M. A.; Wang, G.

2014-12-01

Changing the structure of soil biogeochemical models to represent coupling between microbial biomass and carbon substrate pools could improve predictions of carbon-climate feedbacks. So-called "microbial models" with this structure make very different predictions from conventional models based on first-order decay of carbon substrate pools. Still, the value of microbial models is uncertain because microbial physiological parameters are poorly constrained and model behaviors have not been fully explored. To address these issues, we developed an approach for inter-comparing microbial and conventional models. We initially focused on soil carbon responses to microbial carbon use efficiency (CUE) and temperature. Three scenarios were implemented in all models at a common reference temperature (20°C): constant CUE (held at 0.31), varied CUE (-0.016°C-1), and 50% acclimated CUE (-0.008°C-1). Whereas the conventional model always showed soil carbon losses with increasing temperature, the microbial models each predicted a temperature threshold above which warming led to soil carbon gain. The location of this threshold depended on CUE scenario, with higher temperature thresholds under the acclimated and constant scenarios. This result suggests that the temperature sensitivity of CUE and the structure of the soil carbon model together regulate the long-term soil carbon response to warming. Compared to the conventional model, all microbial models showed oscillatory behavior in response to perturbations and were much less sensitive to changing inputs. Oscillations were weakest in the most complex model with explicit enzyme pools, suggesting that multi-pool coupling might be a more realistic representation of the soil system. This study suggests that model structure and CUE parameterization should be carefully evaluated when scaling up microbial models to ecosystems and the globe.

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery

PubMed Central

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery. PMID:26925051

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery.

PubMed

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery.

Investigating the legacy effect of drought on microbial responses to drying and rewetting along a Texan precipitation gradient

NASA Astrophysics Data System (ADS)

Hicks, Lettice; Leizeaga, Ainara; Hawkes, Christine; Rousk, Johannes

2017-04-01

Hydrological regimes will intensify due to climate change, thus increasing the duration and intensity of drought and rainfall events. Rewetting of dry soil is known to stimulate dramatic CO2 releases. A clear understanding of the mechanisms that determine the dynamics of CO2 loss upon rewetting is therefore required to characterise ecosystem C-budgets and predict responses to climate change. Laboratory studies have identified two distinct responses upon rewetting; bacterial growth either increases linearly immediately, with maximal respiration also occurring immediately and decreasing exponentially with time ("Type 1"), or bacterial growth increases exponentially after a period of near-zero growth, with a sustained period of elevated respiration, sometimes followed by a secondary increase in respiration coinciding with the onset of bacterial growth ("Type 2"). A shift from a Type 1 to a Type 2 response has been observed with increasing duration and intensity of drying prior to rewetting. The size of the surviving microbial community after drying, relative to resources available after rewetting, is suggested to dictate whether a Type 1 or 2 response occurs, with more 'harsh' (i.e. longer or more severe) drying reducing microbial biomass such that carbon available upon rewetting is sufficient to support exponential growth (leading to Type 2 response). However, this is yet to be tested in intact ecosystems. We investigated the legacy of drought on microbial responses to drying and rewetting using grassland soils from a natural precipitation gradient in Texas. Mean annual precipitation spanned a 500 mm range (400-900 mm year-1) across the 400 km gradient, while mean annual temperature was constant. Soil properties (pH, SOM) did not vary systematically across the gradient, with differences reflecting land-use history rather than rainfall. Air dried soils from 18 sites were rewetted to 50 % water holding capacity with bacterial growth, fungal growth and respiration measured at high temporal resolution over 7 days. We predicted that there would be a shift in the type of response to rewetting (Type 1 to Type 2) across the gradient, as a consequence of exposure to harsher drying. Further, given the lack of systematic variation in other factors with rainfall, we expected levels of maximal growth and respiration as well as the level of steady state growth and respiration to be similar across the gradient. All soils exhibited a Type 1 response, with respiration, bacterial and fungal growth increasing immediately upon rewetting and typically stabilising after c. 20 hours. There were, however, differences in the magnitude of CO2 release and microbial growth among soils, whereby rewetting of historically wetter soils stimulated higher rates of microbial growth and a greater release of CO2, compared to rewetting of historically drier soils. Contrary to expectations, there was no difference in the type of microbial response to rewetting, but instead a systematic dependence of overall microbial rates, depending on the legacy of drought. This contrasted with previous laboratory studies, suggesting that exposure to drought across the natural gradient was not perceived as 'harsh' by the microbial communities. This may be explained by either (i) differences in resource availability (i.e. plant input) mitigating the microbial susceptibility to drought in intact ecosystems or (ii) microbial tolerance to drought.

Microbial denitrogenation of fossil fuels.

PubMed

Benedik, M J; Gibbs, P R; Riddle, R R; Willson, R C

1998-09-01

The microbial degradation of nitrogen compounds from fossil fuels is important because of the contribution these contaminants make to the formation of nitrogen oxides (NOx) and hence to air pollution and acid rain. They also contribute to catalyst poisoning during the refining of crude oil, thus reducing process yields. We review the current status of microbial degradation of aromatic nitrogen compounds and discuss the potential of microbial processes to alleviate these problems.

Fluidized-bed bioreactor process for the microbial solubiliztion of coal

DOEpatents

Scott, Charles D.; Strandberg, Gerald W.

1989-01-01

A fluidized-bed bioreactor system for the conversion of coal into microbially solubilized coal products. The fluidized-bed bioreactor continuously or periodically receives coal and bio-reactants and provides for the production of microbially solubilized coal products in an economical and efficient manner. An oxidation pretreatment process for rendering coal uniformly and more readily susceptible to microbial solubilization may be employed with the fluidized-bed bioreactor.

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

PubMed Central

Zhou, Jizhong; Deng, Ye; Zhang, Ping; Xue, Kai; Liang, Yuting; Van Nostrand, Joy D.; Yang, Yunfeng; He, Zhili; Wu, Liyou; Stahl, David A.; Hazen, Terry C.; Tiedje, James M.; Arkin, Adam P.

2014-01-01

Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession. PMID:24550501

Microbial responses to microgravity and other low-shear environments.

PubMed

Nickerson, Cheryl A; Ott, C Mark; Wilson, James W; Ramamurthy, Rajee; Pierson, Duane L

2004-06-01

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

Microbial Responses to Microgravity and Other Low-Shear Environments

NASA Technical Reports Server (NTRS)

Nickerson, Cheryl A.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

2004-01-01

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

Drivers of decomposition in forest soils: Insights from a trans-European experiment.

NASA Astrophysics Data System (ADS)

Hood-Nowotny, Rebecca

2017-04-01

Meta-data analyses and the model based hypotheses state that global soil C storage is controlled by microbial scale processes of fungal competition for available nitrogen (N). The details of these microbe-dependent feedback mechanisms on N and C dynamics in European soils are largely unknown and contentious. Global trends of increasing atmospheric N deposition and the continuing use of inorganic N fertilizer in both agriculture and forestry mean that the soils vital function as a carbon sink is potentially under threat. We set out to experimentally investigate these hypotheses across a Trans-European gradient of forest soils and provide reliable information on soil microbial responses to nitrogen inputs for predictive climate change models. Changes in nutrient status could result in a chain reaction of interacting microbial mechanisms which in turn could lead to the shifts in underlying ecosystem biogeochemical process rates. Recent meta-analysis has shown that plant fungal symbiont community structure, exerts a greater fundamental control over soil C storage than temperature, precipitation or net primary production. Based on the hypothesis that plant associated fungi effectively scavenge all available organic and inorganic N leaving little N for the growth of the free-living decomposer microbial community and preventing further breakdown of SOM. To investigate these possible effects we have sampled forest soils across a trans European gradient (ALTER-net-MSII network) which have received additional inputs of inorganic nitrogen fertilizer or carbon in the form of sugar, over a three year period. We have studied both nitrogen and carbon dynamics in these systems using a tool box of stable isotopes, high through-put sequencing for microbial community analysis and be-spoke litter bags to tease out the dominant drivers of decomposition. The results and conclusions from these analyses will be presented.

Flow-through SIP - A novel stable isotope probing approach limiting cross-feeding

NASA Astrophysics Data System (ADS)

Mooshammer, Maria; Kitzinger, Katharina; Schintlmeister, Arno; Kjedal, Henrik; Nielsen, Jeppe Lund; Nielsen, Per; Wagner, Michael

2017-04-01

Stable isotope probing (SIP) is a widely applied tool to link specific microbial populations to metabolic processes in the environment without the prerequisite of cultivation, which has greatly advanced our understanding of the role of microorganisms in biogeochemical cycling. SIP relies on tracing specific isotopically labeled substrates (e.g., 13C, 15N, 18O) into cellular biomarkers, such as DNA, RNA or phospholipid fatty acids, and is considered to be a robust technique to identify microbial populations that assimilate the labeled substrate. However, cross-feeding can occur when labeled metabolites are released from a primary consumer and then used by other microorganisms. This leads to erroneous identification of organisms that are not directly responsible for the process of interest, but are rather connected to primary consumers via a microbial food web. Here, we introduce a new approach that has the potential to eliminate the effect of cross-feeding in SIP studies and can thus also be used to distinguish primary consumers from other members of microbial food webs. In this approach, a monolayer of microbial cells are placed on a filter membrane, and labeled substrates are supplied by a continuous flow. By means of flow-through, labeled metabolites and degradation products are constantly removed, preventing secondary consumption of the substrate. We present results from a proof-of-concept experiment using nitrifiers from activated sludge as model system, in which we used fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes for identification of nitrifiers in combination with nanoscale secondary ion mass spectrometry (NanoSIMS) for visualization of isotope incorporation at the single-cell level. Our results show that flow-through SIP is a promising approach to significantly reduce cross-feeding and secondary substrate consumption in SIP experiments.

Changes in optical characteristics of surface microlayers hint to photochemically and microbially-mediated DOM turnover in the upwelling region off Peru

NASA Astrophysics Data System (ADS)

Galgani, L.; Engel, A.

2015-12-01

The coastal upwelling system off Peru is characterized by high biological activity and a pronounced subsurface oxygen minimum zone, as well as associated emissions of atmospheric trace gases such as N2O, CH4 and CO2. During the Meteor (M91) cruise to the Peruvian upwelling system in 2012, we investigated the composition of the sea-surface microlayer (SML), the oceanic uppermost boundary directly subject to high solar radiation, often enriched in specific organic compounds of biological origin like Chromophoric Dissolved Organic Matter (CDOM) and marine gels. In the SML, the continuous photochemical and microbial recycling of organic matter may strongly influence gas exchange between marine systems and the atmosphere. In order to understand organic matter cycling in surface films, we analyzed SML and underlying water samples at 38 stations determining DOC concentration, amino acid composition, marine gels, CDOM and bacterial and phytoplankton abundance as indicators of photochemical and microbial alteration processes. CDOM composition was characterized by spectral slope (S) values and Excitation-Emission Matrix fluorescence (EEMs), which allow to track changes in molecular weight (MW) of DOM, and to determine potential DOM sources and sinks. We identified five fluorescent components of the CDOM pool, of which two had excitation/emission characteristics of protein-like fluorophores and were highly enriched in the SML. CDOM composition and changes in spectral slope properties suggested a local microbial release of HMW DOM directly in the SML as a response to light exposure in this extreme environment. Our results suggest that microbial and photochemical processes play an important role for the production, alteration and loss of optically active substances in the SML.

Ciliated protists from the nepheloid layer and water column of sites affected by the Deepwater Horizon oil spill in the Northeastern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Moss, Joseph A.; McCurry, Chelsea; Tominack, Sarah; Romero, Isabel C.; Hollander, David; Jeffrey, Wade H.; Snyder, Richard A.

2015-12-01

Benthic marine protists have been well documented from shallow marine benthic habitats but remain understudied in deeper habitats on continental shelves and slopes, particularly in the Northeastern Gulf of Mexico (NEGOM). This region was affected by a deep water oil well failure (BP-Deepwater Horizon, 2010). The combination of a lack of information on deep sea microbenthic communities and the potential for benthic microbial petroleum mineralization prompted this investigation. Water column and nepheloid layer samples were obtained via Niskin bottles and a multicorer respectively at stations across the NEGOM to: (1) determine whether nepheloid and water column communities are distinct and (2) assess benthic species richness relative to sediment PAH contamination. Phylum specific 18S rRNA gene amplification was used to construct clone libraries of ciliate assemblages. BLAST searches in the NCBI database indicated that a majority (~75%) of the clone sequences corresponded (94-100% similarity) with listed, yet unclassified sequences. Several putative species were common at most site locations and depths. Many known benthic ciliates, such as Uronychia transfuga, Uronychia setigera, and Spirotrachelostyla tani, were common in the nepheloid layer samples and not recovered in water column samples. Ciliated protist species richness increased with PAH levels found in surface sediments, suggesting a positive microbial response to petroleum enrichment of the benthos. The presence of previously unknown microbenthic communites in the nephaloid layer over oceanic clay-silt muds alters our view of microbial processes in the deep sea and merits investigation of the microbial processes and rates of microbial mineralization and biomass production important to global biogeochemistry.

Genomic perspectives in microbial oceanography.

PubMed

DeLong, Edward F; Karl, David M

2005-09-15

The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine microbial evolution, metabolism and ecology. Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers.

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents.

PubMed

Reed, Daniel C; Breier, John A; Jiang, Houshuo; Anantharaman, Karthik; Klausmeier, Christopher A; Toner, Brandy M; Hancock, Cathrine; Speer, Kevin; Thurnherr, Andreas M; Dick, Gregory J

2015-08-01

Submarine hydrothermal vents perturb the deep-ocean microbiome by injecting reduced chemical species into the water column that act as an energy source for chemosynthetic organisms. These systems thus provide excellent natural laboratories for studying the response of microbial communities to shifts in marine geochemistry. The present study explores the processes that regulate coupled microbial-geochemical dynamics in hydrothermal plumes by means of a novel mathematical model, which combines thermodynamics, growth and reaction kinetics, and transport processes derived from a fluid dynamics model. Simulations of a plume located in the ABE vent field of the Lau basin were able to reproduce metagenomic observations well and demonstrated that the magnitude of primary production and rate of autotrophic growth are largely regulated by the energetics of metabolisms and the availability of electron donors, as opposed to kinetic parameters. Ambient seawater was the dominant source of microbes to the plume and sulphur oxidisers constituted almost 90% of the modelled community in the neutrally-buoyant plume. Data from drifters deployed in the region allowed the different time scales of metabolisms to be cast in a spatial context, which demonstrated spatial succession in the microbial community. While growth was shown to occur over distances of tens of kilometers, microbes persisted over hundreds of kilometers. Given that high-temperature hydrothermal systems are found less than 100 km apart on average, plumes may act as important vectors between different vent fields and other environments that are hospitable to similar organisms, such as oil spills and oxygen minimum zones.

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents

PubMed Central

Reed, Daniel C; Breier, John A; Jiang, Houshuo; Anantharaman, Karthik; Klausmeier, Christopher A; Toner, Brandy M; Hancock, Cathrine; Speer, Kevin; Thurnherr, Andreas M; Dick, Gregory J

2015-01-01

Submarine hydrothermal vents perturb the deep-ocean microbiome by injecting reduced chemical species into the water column that act as an energy source for chemosynthetic organisms. These systems thus provide excellent natural laboratories for studying the response of microbial communities to shifts in marine geochemistry. The present study explores the processes that regulate coupled microbial-geochemical dynamics in hydrothermal plumes by means of a novel mathematical model, which combines thermodynamics, growth and reaction kinetics, and transport processes derived from a fluid dynamics model. Simulations of a plume located in the ABE vent field of the Lau basin were able to reproduce metagenomic observations well and demonstrated that the magnitude of primary production and rate of autotrophic growth are largely regulated by the energetics of metabolisms and the availability of electron donors, as opposed to kinetic parameters. Ambient seawater was the dominant source of microbes to the plume and sulphur oxidisers constituted almost 90% of the modelled community in the neutrally-buoyant plume. Data from drifters deployed in the region allowed the different time scales of metabolisms to be cast in a spatial context, which demonstrated spatial succession in the microbial community. While growth was shown to occur over distances of tens of kilometers, microbes persisted over hundreds of kilometers. Given that high-temperature hydrothermal systems are found less than 100 km apart on average, plumes may act as important vectors between different vent fields and other environments that are hospitable to similar organisms, such as oil spills and oxygen minimum zones. PMID:25658053

Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture

PubMed Central

Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S.

2016-01-01

Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (tlag) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h−1 of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced tlag, indicating that favorable abiotic conditions activated soil microorganisms. We conclude that soil respiratory responses to short-term changes in environmental conditions are better explained by changes in AMB than in TMB. These results suggest that decomposition models that explicitly represent microbial carbon pools should take into account the active microbial pool, and researchers should be cautious in comparing modeled microbial pool sizes with measurements of TMB. PMID:27148213

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes.

PubMed

Kumar, Amit; Ng, Daphne H P; Wu, Yichao; Cao, Bin

2018-05-28

Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.

Ecological and soil hydraulic implications of microbial responses to stress - A modeling analysis

NASA Astrophysics Data System (ADS)

Brangarí, Albert C.; Fernàndez-Garcia, Daniel; Sanchez-Vila, Xavier; Manzoni, Stefano

2018-06-01

A better understanding of microbial dynamics in porous media may lead to improvements in the design and management of a number of technological applications, ranging from the degradation of contaminants to the optimization of agricultural systems. To this aim, there is a recognized need for predicting the proliferation of soil microbial biomass (often organized in biofilms) under different environments and stresses. We present a general multi-compartment model to account for physiological responses that have been extensively reported in the literature. The model is used as an explorative tool to elucidate the ecological and soil hydraulic consequences of microbial responses, including the production of extracellular polymeric substances (EPS), the induction of cells into dormancy, and the allocation and reuse of resources between biofilm compartments. The mechanistic model is equipped with indicators allowing the microorganisms to monitor environmental and biological factors and react according to the current stress pressures. The feedbacks of biofilm accumulation on the soil water retention are also described. Model runs simulating different degrees of substrate and water shortage show that adaptive responses to the intensity and type of stress provide a clear benefit to microbial colonies. Results also demonstrate that the model may effectively predict qualitative patterns in microbial dynamics supported by empirical evidence, thereby improving our understanding of the effects of pore-scale physiological mechanisms on the soil macroscale phenomena.

Microbial response to environmental gradients in a ceramic-based diffusion system.

PubMed

Wolfaardt, G M; Hendry, M J; Birkham, T; Bressel, A; Gardner, M N; Sousa, A J; Korber, D R; Pilaski, M

2008-05-01

A solid, porous matrix was used to establish steady-state concentration profiles upon which microbial responses to concentration gradients of nutrients or antimicrobial agents could be quantified. This technique relies on the development of spatially defined concentration gradients across a ceramic plate resulting from the diffusion of solutes through the porous ceramic matrix. A two-dimensional, finite-element numerical transport model was used to predict the establishment of concentration profiles, after which concentration profiles of conservative tracers were quantified fluorometrically and chemically at the solid-liquid interface to verify the simulated profiles. Microbial growth responses to nutrient, hypochloride, and antimicrobial concentration gradients were then quantified using epifluorescent or scanning confocal laser microscopy. The observed microbial response verified the establishment and maintenance of stable concentration gradients along the solid-liquid interface. These results indicate the ceramic diffusion system has potential for the isolation of heterogeneous microbial communities as well as for testing the efficacy of antimicrobial agents. In addition, the durability of the solid matrix allowed long-term investigations, making this approach preferable to conventional gel-stabilized systems that are impeded by erosion as well as expansion or shrinkage of the gel. Copyright 2008 Wiley Periodicals, Inc.

[Microbial Processes and Genesis of Methane Gas Jets in the Coastal Areas of the Crimea Peninsula].

PubMed

Malakhova, T V; Kanapatskii, T A; Egorov, V N; Malakhova, L V; Artemov, Yu G; Evtushenko, D B; Gulin, S B; Pimenov, N V

2015-01-01

Hydroasoustic techniques were used for detection and mapping of gas jet areas in the coastal regions of the Crimean peninsula. Gas seep areas in the bays Laspi, Khersones, and Kazach'ya were chosen for detailed microbiological investigation. The first type of gas jets, observed in the Laspi Bay, was probably associated with discarge of deep thermogenic methane along the faults. Methane isotopic composition was char- acterized by Δ13C of -35.3 degrees. While elevated rates of aerobic methane oxidation were revealed in the sandy sediments adjacent to the methane release site, no evidence of bacterial mats was found. The second type of gas emission, observed in the Khersones Bay, was accompanied by formation of bacterial biofilms of the "Thiodendron" microbial community type, predominated by filamentous, spirochete-like organisms, in the areas of gas seepage. The isotopic composition of methane was there considerably lower (-60.4 degrees), indicating a considerable contribution of modern microbial methane to the gas bubbles discharged in this bay. Activity of the third type of gas emission, the seeps of the Kazach'ya Bay, probably depended directly on modern microbial processes of organic matter degradation in the upper sediment layers. The rates of sulfate reduction and methanogenesis were 260 and 34 μmol dm(-3) day(-1), respectively. Our results indicate different mechanisms responsible for formation of methane jets in the Laspi Bay and in the coastal areas of the Heracles Peninsula, where the bays Kazach'ya and Khersones are located.

Health benefits of fermented foods.

PubMed

Şanlier, Nevin; Gökcen, Büşra Başar; Sezgin, Aybüke Ceyhun

2017-09-25

In the past, the beneficial effects of fermented foods on health were unknown, and so people primarily used fermentation to preserve foods, enhance shelf life, and improve flavour. Fermented foods became an important part of the diet in many cultures, and over time fermentation has been associated with many health benefits. Because of this, the fermentation process and the resulting fermented products have recently attracted scientific interest. In addition, microorganisms contributing to the fermentation process have recently been associated with many health benefits, and so these microorganisms have become another focus of attention. Lactic acid bacteria (LAB) have been some of the most studied microorganisms. During fermentation, these bacteria synthesize vitamins and minerals, produce biologically active peptides with enzymes such as proteinase and peptidase, and remove some non-nutrients. Compounds known as biologically active peptides, which are produced by the bacteria responsible for fermentation, are also well known for their health benefits. Among these peptides, conjugated linoleic acids (CLA) have a blood pressure lowering effect, exopolysaccharides exhibit prebiotic properties, bacteriocins show anti-microbial effects, sphingolipids have anti-carcinogenic and anti-microbial properties, and bioactive peptides exhibit anti-oxidant, anti-microbial, opioid antagonist, anti-allergenic, and blood pressure lowering effects. As a result, fermented foods provide many health benefits such as anti-oxidant, anti-microbial, anti-fungal, anti-inflammatory, anti-diabetic and anti-atherosclerotic activity. However, some studies have shown no relationship between fermented foods and health benefits. Therefore, this paper aims to investigate the health effects of fermented foods.

Nutrient Limitation of Microbial Mediated Decomposition and Arctic Soil Chronology

NASA Astrophysics Data System (ADS)

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

2012-12-01

Soils of northern permafrost regions currently contain twice as much carbon as the entire Earth's atmosphere. Traditionally, environmental constraints have limited microbial activity resulting in restricted decomposition of soil organic matter in these systems and accumulation of massive amounts of soil organic carbon (SOC), however climate change is reducing the constraints of decomposition in arctic permafrost regions. Carbon cycling in nutrient poor, arctic ecosystems is tightly coupled to other biogeochemical cycles. Several studies have suggested strong nitrogen limitations of primary productivity and potentially warm-season microbial activity in these nutrient deficient soils. Nitrogen is required for microbial extracellular enzyme production which drives the decomposition of soil organic matter (SOM). Nitrogen limited arctic soils may also experience limitation via labile carbon availability despite the SOM rich environment due to low extracellular enzyme production. Few studies have directly addressed nutrient induced microbial limitation in SOC rich arctic tundra soils, and even less is known about the potential for nutrient co-limitation. Additionally, through the process of becoming deglaciated, sites within close proximity to one another may have experienced drastic differences in their effective soil ages due to the varied length of their active histories. Many soil properties and nutrient deficiencies are directly related to soil age, however this chronology has not previously been a focus of research on nutrient limitation of arctic soil microbial activity. Understanding of nutrient limitations, as well as potential co-limitation, on arctic soil microbial activity has important implications for carbon cycling and the ultimate fate of the current arctic SOC reservoir. Analyses of nutrient limitation on soils of a single site are not adequate for fully understanding the controls on soil microbial activity across a vast land mass with large variation in effective soil age. My research is focused on addressing the questions of the extent of microbial N limitation in arctic tundra soils, the potential for co-limitation of labile C despite a high SOC environment, and the dependence, if any, nutrient limitation may have on the effective age of the soil. I have addressed these questions by conducting a laboratory soil incubation of factorial design with treatments of amended glucose, amended ammonium nitrate, and a control consisting of an addition of an equivalent volume of deionized water. Moist acid tundra soils possessing similar soil properties from two arctic sites of close proximity yet with varying deglaciation chronologies were utilized in my study. Soil properties of C-mineralization via respiration, microbial biomass, and nitrogen content in the forms of ammonium, nitrate, and total free amino acids and microbial extra-cellular enzyme production were assayed to determine the microbial response to the experimental treatments. Through the results of this work, I hope to better our understanding of biogeochemical cycling within arctic tundra ecosystems and the response to climate change by contributing to existing knowledge of nutrient limitation on microbial mediated decomposition of SOC in the arctic and how this may differ in soils of varying effective age.

Oriented acidification of wasted activated sludge (WAS) focused on odd-carbon volatile fatty acid (VFA): Regulation strategy and microbial community dynamics.

PubMed

Huang, Long; Chen, Zhiqiang; Xiong, Dandan; Wen, Qinxue; Ji, Ye

2018-06-01

As the main intermediate metabolite in anaerobic digestion of wasted activated sludge (WAS), volatile fatty acids (VFAs) are proper substrate for mixed culture (MC) polyhydroxyalkanoate (PHA) synthesis. To further optimize the performance of MC PHA production process, VFA _odd (i.e., VFA with odd carbon atoms) oriented acidification process was proposed and conducted in this study. Three regulation factors including reaction pH, fraction of added β-cyclodextrin (β-CD) and glycerol were selected and response surface methodology (RSM) was used to enhance and effectively regulate the VFA _odd production while maintaining enough acidification degree in the WAS acidification. High percentage of VFA _odd (larger than 60% and dominated by propionic acid) can be obtained in the operating condition area with glycerol addition ratio (quantified by C/N) ranging from 15 to 20 and reaction pH ranging from 8.0 to 9.5 when β-CD addition was held at zero level (0.2 g/gTSS) according to the RSM. Semi-continuous acidification and MC PHA production assays further verified the reliability and effectiveness of the VFA _odd oriented acidification strategy. Microbial function group related to propionic acid production (G prop ) was defined based on the relationships between system function and microbial community structure, and 13 frequent species were found being involved in the G prop . Roles of the group members in the oriented acidification were analyzed to understand the mechanisms of the regulation of VFA _odd production at microbial ecological level. A synergistic effect of WAS and glycerol on the VFA _odd production in the acidification process was revealed based on the ecological analysis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Methane related changes in prokaryotic activity along geochemical profiles in sediments of Lake Kinneret (Israel)

NASA Astrophysics Data System (ADS)

Bar Or, I.; Ben-Dov, E.; Kushmaro, A.; Eckert, W.; Sivan, O.

2014-06-01

Microbial methane oxidation process (methanotrophy) is the primary control on the emission of the greenhouse gas methane (CH4) to the atmosphere. In terrestrial environments, aerobic methanotrophic bacteria are mainly responsible for oxidizing the methane. In marine sediments the coupling of the anaerobic oxidation of methane (AOM) with sulfate reduction, often by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria, was found to consume almost all the upward diffusing methane. Recently, we showed geochemical evidence for AOM driven by iron reduction in Lake Kinneret (LK) (Israel) deep sediments and suggested that this process can be an important global methane sink. The goal of the present study was to link the geochemical gradients found in the porewater (chemical and isotope profiles) with possible changes in microbial community structure. Specifically, we examined the possible shift in the microbial community in the deep iron-driven AOM zone and its similarity to known sulfate driven AOM populations. Screening of archaeal 16S rRNA gene sequences revealed Thaumarchaeota and Euryarchaeota as the dominant phyla in the sediment. Thaumarchaeota, which belongs to the family of copper containing membrane-bound monooxgenases, increased with depth while Euryarchaeota decreased. This may indicate the involvement of Thaumarchaeota, which were discovered to be ammonia oxidizers but whose activity could also be linked to methane, in AOM in the deep sediment. ANMEs sequences were not found in the clone libraries, suggesting that iron-driven AOM is not through sulfate. Bacterial 16S rRNA sequences displayed shifts in community diversity with depth. Proteobacteria and Chloroflexi increased with depth, which could be connected with their different dissimilatory anaerobic processes. The observed changes in microbial community structure suggest possible direct and indirect mechanisms for iron-driven AOM in deep sediments.

Evidence of a dynamic microbial community structure and predation through combined microbiological and stable isotope characterization

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Bill, M.; Lim, H. C.; Wu, C.; Conrad, M. E.; Williams, K. H.; DePaolo, D. J.; Brodie, E.

2014-12-01

The speciation, reactivity and mobility of carbon in the near surface environment is intimately linked to the prevalence, diversity and dynamics of native microbial populations. We utilize this relationship by introducing 13C-labeled acetate to sediments recovered from a shallow aquifer system to track both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Results demonstrate a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples analyzed weekly for microbial composition by pyrosequencing of ribosomal RNA genes showed a transient microbial community structure, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identifiable in the partitioning of carbon isotopes. The impact of predator-prey relationships on subsurface microbial community dynamics and therefore the flux of carbon through a system via the microbial biomass pool suggests a diversity of processes that should be considered for inclusion in reactive transport models that aim to predict carbon turnover, nutrient flux, and redox reactions in natural and stimulated subsurface systems.

Phosphorus cycling in natural and low input soil/plant systems: the role of soil microorganisms

NASA Astrophysics Data System (ADS)

Tamburini, F.; Bünemann, E. K.; Oberson, A.; Bernasconi, S. M.; Frossard, E.

2011-12-01

Availability of phosphorus (as orthophosphate, Pi) limits biological production in many terrestrial ecosystems. During the first phase of soil development, weathering of minerals and leaching of Pi are the processes controlling Pi concentrations in the soil solution, while in mature soils, Pi is made available by desorption of mineral Pi and mineralization of organic compounds. In agricultural soils additional Pi is supplied by fertilization, either with mineral P and/or organic inputs (animal manure or plant residues). Soil microorganisms (bacteria and fungi) mediate several processes, which are central to the availability of Pi to plants. They play a role in the initial release of Pi from the mineral phase, and through extracellular phosphatase enzymes, they decompose and mineralize organic compounds, releasing Pi. On the other hand, microbial immobilization and internal turnover of Pi can decrease the soil available Pi pool, competing in this way with plants. Using radio- and stable isotopic approaches, we show evidence from different soil/plant systems which points to the central role of the microbial activity. In the presented case studies, P contained in the soil microbial biomass is a larger pool than available Pi. In a soil chronosequence after deglaciation, stable isotopes of oxygen associated to phosphate showed that even in the youngest soils microbial activity highly impacted the isotopic signature of available Pi. These results suggested that microorganisms were rapidly taking up and cycling Pi, using it to sustain their community. Microbial P turnover time was faster in the young (about 20 days) than in older soils (about 120 days), reflecting a different functioning of the microbial community. Microbial community crashes, caused by drying/rewetting and freezing/thawing cycles, were most likely responsible for microbial P release to the available P pool. In grassland fertilization experiments with mineral NK and NPK amendments, microbial P turnover was faster in the P-free treatment. Laboratory incubation also showed a more rapid P uptake by microbial biomass in the NK than in the NPK treatment (37% and 6% of added 33P recovered in microbial P after 100 minutes in NK and NPK, respectively). The seasonal microbial P flux in both treatments was 1.5-4 times larger than the annual plant P uptake. In field studies carried out on highly weathered low P soils in Colombia, the comparison between grass-legume and grass-only pastures showed that the presence of legumes had an impact on the overall biological activity. In fact, microbial biomass and phosphatase activity were significantly larger in grass-legume pastures than in the legume-free experiments. Larger release of Pi from the organic P pool improved P availability to plants and pointed at a modified C:N:P stoichiometry along pathways of the nutrient cycle in the soil/plant system. All these data are evidence of a highly dynamic microbial P pool, which controls Pi concentration and, hence, availability for plants in natural and low input agricultural ecosystems.

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.

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes.

PubMed

Docherty, Kathryn M; Borton, Hannah M; Espinosa, Noelle; Gebhardt, Martha; Gil-Loaiza, Juliana; Gutknecht, Jessica L M; Maes, Patrick W; Mott, Brendon M; Parnell, John Jacob; Purdy, Gayle; Rodrigues, Pedro A P; Stanish, Lee F; Walser, Olivia N; Gallery, Rachel E

2015-01-01

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

PubMed Central

Borton, Hannah M.; Espinosa, Noelle; Gebhardt, Martha; Gil-Loaiza, Juliana; Gutknecht, Jessica L. M.; Maes, Patrick W.; Mott, Brendon M.; Parnell, John Jacob; Purdy, Gayle; Rodrigues, Pedro A. P.; Stanish, Lee F.; Walser, Olivia N.

2015-01-01

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers. PMID:26536666

Hyperosmotic nanoemulsions: Development and application of a new antimicrobial treatment for wound care

NASA Astrophysics Data System (ADS)

Connell, Sean

Wound healing is the intricate process that restores function to damaged skin. The process consists of the inflammatory, proliferative and remodeling phases that orchestrate dynamic cellular responses to regenerate the cutaneous barrier. However, microbial contamination of the wound site stimulates a deleterious inflammatory response with the production of endotoxins, exotoxins and proteases that result in secondary injury. The end result is delayed healing, protracted debilitation and increased health care costs. Controlling contamination is critical for proper wound management and reduced burden on the healthcare system. Based on this concern, we developed and applied a new antimicrobial therapeutic that relies on hyperosmotic nanoemulsions (HNE). The biomechanical process consists of a high-energy nanoemulsion component that permeates the protective microbial membrane and a (ii) nonionic hyperosmoticum that facilitates intracellular water extraction to critically dehydrate the pathogen. HNE was shown to be effective against a multitude of pathogens including bacteria, antibiotic-resistant variants, fungi and viruses. Reported non-clinical studies demonstrate that the membrane disrupting nanoemulsion and hyperosmotic component act synergistically to enhance microbicidal activity. Further, results illustrate that pathogen inactivation was rapid as determined by ion and macromolecule leakage assays. Application of HNE in a pre-clinical animal model of wound healing demonstrated the treatment actively promoted healing to reduce treatment times. HNE mitigated wound infection to reduce the inflammatory response and mechanically debrided the wound to facilitate wound closure. Recent work further enhanced the stability of the nanoemulsion component with the addition of surfactant stabilizers using a low-energy spontaneous emulsification process. The refined nanoemulsion composition was stable against physical stressors and long-term storage without disrupting the intrinsic antimicrobial attributes. The reported findings have key implications for the development and application of a new antimicrobial therapeutic platform for wound management.

Connecting Taxon-Specific Microbial Activities to Carbon Cycling in the Rhizosphere

NASA Astrophysics Data System (ADS)

Hungate, B. A.; Morrissey, E.; Schwartz, E.; Dijkstra, P.; Blazewicz, S.; Pett-Ridge, J.; Koch, G. W.; Marks, J.; Koch, B.; McHugh, T. A.; Mau, R. L.; Hayer, M.

2016-12-01

Plant carbon inputs influence microbial growth in the rhizosphere, but the quantitative details of these effects are not well understood, nor are their consequences for carbon cycling in the rhizosphere. With a new pulse of carbon input to soil, which microbial taxa increase their growth rates, and by how much? Do any microbial taxa respond negatively? And how does the extra carbon addition alter the utilization of other resources, including other carbon sources, as well as inorganic nitrogen? This talk will present new research using quantitative stable isotope probing that reveals the distribution of growth responses among microbial taxa, from positive to neutral to negative, and how these growth responses are associated with various substrates. For example, decomposition of soil C in response to added labile carbon occurred as a phylogenetically-diverse majority of taxa shifted toward soil C use for growth. In contrast, bacteria with suppressed growth or that relied directly on glucose for growth clustered strongly by phylogeny. These results suggest that priming is a prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the priming effect in nature. These results also illustrate the potential power of molecular tools and models that seek to estimate metrics directly relevant to quantitative ecology and biogeochemistry, moreso than is the standard currently in microbial ecology. Tools that estimate growth rate, mortality rate, and rates of substrate use - all quantified with the taxonomic precision afforded by modern sequencing - provide a foundation for quantifying the biogeochemical significance of microbial biodiversity, and a more complete understanding of the rich ecosystem of the rhizosphere.

Responses of soluble microbial products and extracellular polymeric substances to the presence of toxic 2,6-dichlorophenol in aerobic granular sludge system.

PubMed

Li, Kai; Wei, Dong; Yan, Tao; Du, Bin; Wei, Qin

2016-12-01

The objective of this study was to evaluate the responses of soluble microbial products (SMP) and extracellular polymeric substances (EPS) to the presence of toxic 2,6-dichlorophenol (2,6-DCP) in aerobic granular sludge (AGS) system. Batch experiment showed that NH 4 + -N removal efficiency significantly decreased from 99.6% to 47.2% in the toxic 2,6-DCP of 20 mg/L. Moreover, the inhibition degrees of 2,6-DCP on (SOUR) H , [Formula: see text] and [Formula: see text] were 7.8%, 32.1% and 9.5%, respectively. The main components of SMP, including protein (PN) and polysaccharide (PS) increased from 2.3 ± 0.74 and 16.8 ± 0.12 mg/L to 66.4 ± 0.56 and 18.0 ± 0.19 mg/L in the presence of 2,6-DCP. Three-dimensional excitation-emission matrix (3D-EEM) spectroscopy identified tryptophan PN-like, humic acid-like and fulvic acid-like substances in the control SMP, and their fluorescence intensities increased after exposure to 2,6-DCP. Synchronous fluorescence spectra suggested that the fluorescence quenching between EPS and 2,6-DCP was a static quenching process. The obtained results could provide insightful information on the responses of microbial products to AGS in the presence of toxic chlorophenols. Copyright © 2016 Elsevier Ltd. All rights reserved.

40 CFR 172.52 - Notification exemption process.

Code of Federal Regulations, 2011 CFR

2011-07-01

... EXPERIMENTAL USE PERMITS Notification for Certain Genetically Modified Microbial Pesticides § 172.52... notification requirements of this subpart for a specific microbial pesticide or class of microbial pesticides...' Document Processing Desk at the appropriate address as set forth in 40 CFR 150.17(a) or (b). (3) Content of...

40 CFR 172.52 - Notification exemption process.

Code of Federal Regulations, 2010 CFR

2010-07-01

... EXPERIMENTAL USE PERMITS Notification for Certain Genetically Modified Microbial Pesticides § 172.52... notification requirements of this subpart for a specific microbial pesticide or class of microbial pesticides...' Document Processing Desk at the appropriate address as set forth in 40 CFR 150.17(a) or (b). (3) Content of...

Microbial Shifts in the Intestinal Microbiota of Salmonella Infected Chickens in Response to Enrofloxacin

PubMed Central

Li, Jun; Hao, Haihong; Cheng, Guyue; Liu, Chunbei; Ahmed, Saeed; Shabbir, Muhammad A. B.; Hussain, Hafiz I.; Dai, Menghong; Yuan, Zonghui

2017-01-01

Fluoroquinolones (FQs) are important antibiotics used for treatment of Salmonella infection in poultry in many countries. However, oral administration of fluoroquinolones may affect the composition and abundance of a number of bacterial taxa in the chicken intestine. Using 16S rRNA gene sequencing, the microbial shifts in the gut of Salmonella infected chickens in response to enrofloxacin treatments at different dosages (0, 0.1, 4, and 100 mg/kg b.w.) were quantitatively evaluated. The results showed that the shedding levels of Salmonella were significantly reduced in the high dosage group as demonstrated by both the culturing method and 16S rRNA sequencing method. The average values of diversity indices were higher in the control group than in the three medicated groups. Non-metric multidimensional scaling (NMDS) analysis results showed that the microbial community of high dosage group was clearly separated from the other three groups. In total, 25 genera were significantly enriched (including 6 abundant genera: Lactococcus, Bacillus, Burkholderia, Pseudomonas, Rhizobium, and Acinetobacter) and 23 genera were significantly reduced in the medicated groups than in the control group for the treatment period, but these bacterial taxa recovered to normal levels after therapy withdrawal. Additionally, 5 genera were significantly reduced in both treatment and withdrawal periods (e.g., Blautia and Anaerotruncus) and 23 genera (e.g., Enterobacter and Clostridium) were significantly decreased only in the withdrawal period, indicating that these genera might be the potential targets for the fluoroquinolones antimicrobial effects. Specially, Enterococcus was significantly reduced under high dosage of enrofloxacin treatment, while significantly enriched in the withdrawal period, which was presumably due to the resistance selection. Predicted microbial functions associated with genetic information processing were significantly decreased in the high dosage group. Overall, enrofloxacin at a dosage of 100 mg/kg b.w. significantly altered the microbial community membership and structure, and microbial functions in the chicken intestine during the medication. This study fully investigates the chicken intestinal microbiota in response to enrofloxacin treatment and identifies potential targets against which the fluoroquinolones may have potent antimicrobial effects. These results provide insights into the effects of the usage of enrofloxacin on chicken and will aid in the prudent and rational use of antibiotics in poultry industry. PMID:28943868

Microbial Shifts in the Intestinal Microbiota of Salmonella Infected Chickens in Response to Enrofloxacin.

PubMed

Li, Jun; Hao, Haihong; Cheng, Guyue; Liu, Chunbei; Ahmed, Saeed; Shabbir, Muhammad A B; Hussain, Hafiz I; Dai, Menghong; Yuan, Zonghui

2017-01-01

Fluoroquinolones (FQs) are important antibiotics used for treatment of Salmonella infection in poultry in many countries. However, oral administration of fluoroquinolones may affect the composition and abundance of a number of bacterial taxa in the chicken intestine. Using 16S rRNA gene sequencing, the microbial shifts in the gut of Salmonella infected chickens in response to enrofloxacin treatments at different dosages (0, 0.1, 4, and 100 mg/kg b.w.) were quantitatively evaluated. The results showed that the shedding levels of Salmonella were significantly reduced in the high dosage group as demonstrated by both the culturing method and 16S rRNA sequencing method. The average values of diversity indices were higher in the control group than in the three medicated groups. Non-metric multidimensional scaling (NMDS) analysis results showed that the microbial community of high dosage group was clearly separated from the other three groups. In total, 25 genera were significantly enriched (including 6 abundant genera: Lactococcus , Bacillus , Burkholderia , Pseudomonas , Rhizobium , and Acinetobacter ) and 23 genera were significantly reduced in the medicated groups than in the control group for the treatment period, but these bacterial taxa recovered to normal levels after therapy withdrawal. Additionally, 5 genera were significantly reduced in both treatment and withdrawal periods (e.g., Blautia and Anaerotruncus ) and 23 genera (e.g., Enterobacter and Clostridium ) were significantly decreased only in the withdrawal period, indicating that these genera might be the potential targets for the fluoroquinolones antimicrobial effects. Specially, Enterococcus was significantly reduced under high dosage of enrofloxacin treatment, while significantly enriched in the withdrawal period, which was presumably due to the resistance selection. Predicted microbial functions associated with genetic information processing were significantly decreased in the high dosage group. Overall, enrofloxacin at a dosage of 100 mg/kg b.w. significantly altered the microbial community membership and structure, and microbial functions in the chicken intestine during the medication. This study fully investigates the chicken intestinal microbiota in response to enrofloxacin treatment and identifies potential targets against which the fluoroquinolones may have potent antimicrobial effects. These results provide insights into the effects of the usage of enrofloxacin on chicken and will aid in the prudent and rational use of antibiotics in poultry industry.

Innovative biological approaches for monitoring and improving water quality

PubMed Central

Aracic, Sanja; Manna, Sam; Petrovski, Steve; Wiltshire, Jennifer L.; Mann, Gülay; Franks, Ashley E.

2015-01-01

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages. PMID:26322034

Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure.

PubMed

De Vrieze, Jo; Christiaens, Marlies E R; Walraedt, Diego; Devooght, Arno; Ijaz, Umer Zeeshan; Boon, Nico

2017-03-15

Anaerobic digestion of high-salinity wastewaters often results in process inhibition due to the susceptibility of the methanogenic archaea. The ability of the microbial community to deal with increased salinity levels is of high importance to ensure process perseverance or recovery after failure. The exact strategy of the microbial community to ensure process endurance is, however, often unknown. In this study, we investigated how the microbial community is able to recover process performance following a disturbance through the application of high-salinity molasses wastewater. After a stable start-up, methane production quickly decreased from 625 ± 17 to 232 ± 35 mL CH 4 L -1 d -1 with a simultaneous accumulation in volatile fatty acids up to 20.5 ± 1.4 g COD L -1 , indicating severe process disturbance. A shift in feedstock from molasses wastewater to waste activated sludge resulted in complete process recovery. However, the bacterial and archaeal communities did not return to their original composition as before the disturbance, despite similar process conditions. Microbial community diversity was recovered to similar levels as before disturbance, which indicates that the metabolic potential of the community was maintained. A mild increase in ammonia concentration after process recovery did not influence methane production, indicating a well-balanced microbial community. Hence, given the change in community composition following recovery after salinity disturbance, it can be assumed that microbial community redundancy was the major strategy to ensure the continuation of methane production, without loss of functionality or metabolic flexibility. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community.

PubMed

Posman, Kevin M; DeRito, Christopher M; Madsen, Eugene L

2017-02-15

Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [ 13 C]benzene enabled us to obtain 13 C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities. Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation. Copyright © 2017 American Society for Microbiology.

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community

PubMed Central

Posman, Kevin M.; DeRito, Christopher M.

2016-01-01

ABSTRACT Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [13C]benzene enabled us to obtain 13C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities. IMPORTANCE Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation. PMID:27913419

Identification of the microbial community composition and structure of coal-mine wastewater treatment plants.

PubMed

Ma, Qiao; Qu, Yuan-Yuan; Zhang, Xu-Wang; Shen, Wen-Li; Liu, Zi-Yan; Wang, Jing-Wei; Zhang, Zhao-Jing; Zhou, Ji-Ti

2015-06-01

The wastewater from coal-mine industry varies greatly and is resistant to biodegradation for containing large quantities of inorganic and organic pollutants. Microorganisms in activated sludge are responsible for the pollutants' removal, whereas the microbial community composition and structure are far from understood. In the present study, the sludges from five coal-mine wastewater treatment plants were collected and the microbial communities were analyzed by Illumina high-throughput sequencing. The diversities of these sludges were lower than that of the municipal wastewater treatment systems. The most abundant phylum was Proteobacteria ranging from 63.64% to 96.10%, followed by Bacteroidetes (7.26%), Firmicutes (5.12%), Nitrospira (2.02%), Acidobacteria (1.31%), Actinobacteria (1.30%) and Planctomycetes (0.95%). At genus level, Thiobacillus and Comamonas were the two primary genera in all sludges, other major genera included Azoarcus, Thauera, Pseudomonas, Ohtaekwangia, Nitrosomonas and Nitrospira. Most of these core genera were closely related with aromatic hydrocarbon degradation and denitrification processes. Identification of the microbial communities in coal-mine wastewater treatment plants will be helpful for wastewater management and control. Copyright © 2015 Elsevier GmbH. All rights reserved.

CATALASE FROM A FUNGAL MICROBIAL PESTICIDE INDUCES A UNIQUE IGE RESPONSE.

EPA Science Inventory

BALB/c mice exposed by involuntary aspiration to Metarhizium anisopliae extract (MACA), a microbial pesticide, have shown responses characteristic of human allergic lung disease/asthma. IgE-binding proteins have been identified in MACA by Western blot analysis, 2-dimensio...

Development of Biomarkers for Assessing In Situ RDX Biodegradation Potential

DTIC Science & Technology

2016-06-10

bioremediation .................................................................................................................................. 4 2.1...RDX Degrading Microbial Communities and the Prediction of Microorganisms Responsible for RDX Bioremediation This review chapter was published...Cupples 2013), as follows: Cupples AM. 2013. RDX degrading microbial communities and the prediction of microorganisms responsible for RDX bioremediation

Towards Targeting the Aryl Hydrocarbon Receptor in Cystic Fibrosis

PubMed Central

Paolicelli, Giuseppe; De Luca, Antonella; Renga, Giorgia; Borghi, Monica; Pariano, Marilena; Stincardini, Claudia; Scaringi, Lucia; Ricci, Maurizio; Romani, Luigina

2018-01-01

Tryptophan (trp) metabolism is an important regulatory component of gut mucosal homeostasis and the microbiome. Metabolic pathways targeting the trp can lead to a myriad of metabolites, of both host and microbial origins, some of which act as endogenous low-affinity ligands for the aryl hydrocarbon receptor (AhR), a cytosolic, ligand-operated transcription factor that is involved in many biological processes, including development, cellular differentiation and proliferation, xenobiotic metabolism, and the immune response. Low-level activation of AhR by endogenous ligands is beneficial in the maintenance of immune health and intestinal homeostasis. We have defined a functional node whereby certain bacteria species contribute to host/microbial symbiosis and mucosal homeostasis. A microbial trp metabolic pathway leading to the production of indole-3-aldehyde (3-IAld) by lactobacilli provided epithelial protection while inducing antifungal resistance via the AhR/IL-22 axis. In this review, we highlight the role of AhR in inflammatory lung diseases and discuss the possible therapeutic use of AhR ligands in cystic fibrosis. PMID:29670460

Microbial Transformation of Iodine: From Radioisotopes to Iodine Deficiency.

PubMed

Yeager, Chris M; Amachi, Seigo; Grandbois, Russell; Kaplan, Daniel I; Xu, Chen; Schwehr, Kathy A; Santschi, Peter H

2017-01-01

Iodine is a biophilic element that is important for human health, both as an essential component of several thyroid hormones and, on the other hand, as a potential carcinogen in the form of radioiodine generated by anthropogenic nuclear activity. Iodine exists in multiple oxidation states (-1, 0, +1, +3, +5, and +7), primarily as molecular iodine (I 2 ), iodide (I - ), iodate [Formula: see text] , or organic iodine (org-I). The mobility of iodine in the environment is dependent on its speciation and a series of redox, complexation, sorption, precipitation, and microbial reactions. Over the last 15years, there have been significant advances in iodine biogeochemistry, largely spurred by renewed interest in the fate of radioiodine in the environment. We review the biogeochemistry of iodine, with particular emphasis on the microbial processes responsible for volatilization, accumulation, oxidation, and reduction of iodine, as well as the exciting technological potential of these fascinating microorganisms and enzymes. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Culture-independent quantification of physiologically-active microbial groups in fermented foods using rRNA-targeted oligonucleotide probes: application to pozol, a Mexican lactic acid fermented maize dough.

PubMed

Ampe, F; ben Omar, N; Guyot, J P

1999-07-01

Nine phylogenetic oligonucleotide probes were used to describe at the genus level the microbial community responsible for the spontaneous fermentation of maize, leading to the production of Mexican pozol. Ribosomal RNAs of specific groups and genera, in particular, lactic acid bacteria, were quantified using a culture-independent approach. In the early stage of the fermentation, Lactococcus and Leuconostoc appeared to be the dominant genera. A contrario, these represented minor genera at the end of the fermentation when Lactobacillus dominated the process. In addition, eukaryotes seemed to play a significant role throughout the fermentation and enterobacteria could be detected by this method.

2016 Microbial Stress Response GRC/GRS

DTIC Science & Technology

2016-09-13

Holyoke College South Hadley, MA Chairs: Eduardo A. Groisman & Dianne K. Newman Vice Chairs: Petra A. Levin & William W. Navarre Contributors...by Discussion Leader 9:10 am - 9:35 am Martin Ackermann (ETH Zurich, Switzerland) "History-Dependence in Bacterial Stress Response – Scaling up from...Government. Microbial Stress Response GRC – Registration List Ackermann, Martin ETH Zurich Speaker Registered Andersson, Dan I Uppsala

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

Microbes and associated soluble and volatile chemicals on periodically wet household surfaces.

PubMed

Adams, Rachel I; Lymperopoulou, Despoina S; Misztal, Pawel K; De Cassia Pessotti, Rita; Behie, Scott W; Tian, Yilin; Goldstein, Allen H; Lindow, Steven E; Nazaroff, William W; Taylor, John W; Traxler, Matt F; Bruns, Thomas D

2017-09-26

Microorganisms influence the chemical milieu of their environment, and chemical metabolites can affect ecological processes. In built environments, where people spend the majority of their time, very little is known about how surface-borne microorganisms influence the chemistry of the indoor spaces. Here, we applied multidisciplinary approaches to investigate aspects of chemical microbiology in a house. We characterized the microbial and chemical composition of two common and frequently wet surfaces in a residential setting: kitchen sink and bathroom shower. Microbial communities were studied using culture-dependent and independent techniques, including targeting RNA for amplicon sequencing. Volatile and soluble chemicals from paired samples were analyzed using state-of-the-art techniques to explore the links between the observed microbiota and chemical exudates. Microbial analysis revealed a rich biological presence on the surfaces exposed in kitchen sinks and bathroom shower stalls. Microbial composition, matched for DNA and RNA targets, varied by surface type and sampling period. Bacteria were found to have an average of 25× more gene copies than fungi. Biomass estimates based on qPCR were well correlated with measured total volatile organic compound (VOC) emissions. Abundant VOCs included products associated with fatty acid production. Molecular networking revealed a diversity of surface-borne compounds that likely originate from microbes and from household products. Microbes played a role in structuring the chemical profiles on and emitted from kitchen sinks and shower stalls. Microbial VOCs (mVOCs) were predominately associated with the processing of fatty acids. The mVOC composition may be more stable than that of microbial communities, which can show temporal and spatial variation in their responses to changing environmental conditions. The mVOC output from microbial metabolism on kitchen sinks and bathroom showers should be apparent through careful measurement, even against a broader background of VOCs in homes, some of which may originate from microbes in other locations within the home. A deeper understanding of the chemical interactions between microbes on household surfaces will require experimentation under relevant environmental conditions, with a finer temporal resolution, to build on the observational study results presented here.

Development and Optimization of a Fluorescent Differential Display PCR System for Analyzing the Stress Response in Lactobacillus sakei Strains

PubMed Central

Bonomo, Maria Grazia; Sico, Maria Anna; Grieco, Simona; Salzano, Giovanni

2009-01-01

Lactobacillus sakei is widely used as starter in the production process of Italian fermented sausages and its growth and survival are affected by various factors. We studied the differential expression of genome in response to different stresses by the fluorescent differential display (FDD) technique. This study resulted in the development and optimization of an innovative technique, with a high level of reproducibility and quality, which allows the identification of gene expression changes associated with different microbial behaviours under different growth conditions. PMID:22253979

Microbial Mechanisms Enhancing Soil C Storage

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

Zak, Donald

2015-09-24

Human activity has globally increased the amount of nitrogen (N) entering ecosystems, which could foster higher rates of C sequestration in the N-limited forests of the Northern Hemisphere. Presently, these ecosystems are a large global sink for atmospheric CO2, the magnitude of which could be influenced by the input of human-derived N from the atmosphere. Nevertheless, empirical studies and simulation models suggest that anthropogenic N deposition could have either an important or inconsequential effect on C storage in forests of the Northern Hemisphere, a set of observations that continues to fuel scientific discourse. Although a relatively simple set of physiologicalmore » processes control the C balance of terrestrial ecosystems, we still fail to understand how these processes directly and indirectly respond to greater N availability in the environment. The uptake of anthropogenic N by N-limited forest trees and a subsequent enhancement of net primary productivity have been the primary mechanisms thought to increase ecosystem C storage in Northern Hemisphere forests. However, there are reasons to expect that anthropogenic N deposition could slow microbial activity in soil, decrease litter decay, and increase soil C storage. Fungi dominate the decay of plant detritus in forests and, under laboratory conditions, high inorganic N concentrations can repress the transcription of genes coding for enzymes which depolymerize lignin in plant detritus; this observation presents the possibility that anthropogenic N deposition could elicit a similar effect under field conditions. In our 18-yr-long field experiment, we have been able to document that simulated N deposition, at a rate expected in the near future, resulted in a significant decline in cellulolytic and lignolytic microbial activity, slowed plant litter decay, and increased soil C storage (+10%); this response is not portrayed in any biogeochemical model simulating the effect of atmospheric N deposition on ecosystem C storage. Our preliminary results support the hypothesis that simulated N deposition has down-regulated the transcription of fungal genes encoding lignocellulolytic enzymes, thereby slowing litter decay and substantially increasing soil C storage over a relative short duration. The objective of this study was to understand the molecular mechanisms and metabolic processes by which simulated N deposition has slowed microbial decay of plant detritus, thereby increasing soil C storage in the wide-spread and ecologically important northern forest ecosystem. We addressed our research objective using a combination of transcriptomic and metatranscriptomic approaches in parallel with biogeochemical analyses of soil C cycling. By linking the environmental regulation of microbial genes to biogeochemical processes, we endeavor to understanding the enhanced accumulation of soil C in response to a wide-spread agent of global change.« less

Integrated microbial processes for biofuels and high value-added products: the way to improve the cost effectiveness of biofuel production.

PubMed

da Silva, Teresa Lopes; Gouveia, Luísa; Reis, Alberto

2014-02-01

The production of microbial biofuels is currently under investigation, as they are alternative sources to fossil fuels, which are diminishing and their use has a negative impact on the environment. However, so far, biofuels derived from microbes are not economically competitive. One way to overcome this bottleneck is the use of microorganisms to transform substrates into biofuels and high value-added products, and simultaneously taking advantage of the various microbial biomass components to produce other products of interest, as an integrated process. In this way, it is possible to maximize the economic value of the whole process, with the desired reduction of the waste streams produced. It is expected that this integrated system makes the biofuel production economically sustainable and competitive in the near future. This review describes the investigation on integrated microbial processes (based on bacteria, yeast, and microalgal cultivations) that have been experimentally developed, highlighting the importance of this approach as a way to optimize microbial biofuel production process.

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

PubMed

Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

2016-04-26

Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

The emerging relevance of the gut microbiome in cardiometabolic health

USDA-ARS?s Scientific Manuscript database

Host metabolic pathways and physiological responses are regulated by signals linking the host to the gut microbial community or microbiome. Here, we draw a spotlight on lipid and bile acid metabolism and inflammatory response as they pertain to cardiometabolic dysfunction. Gut microbial dysbiosis al...

Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

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

Stern, Noah; Ginder-Vogel, Matthew; Stegen, James C.

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situcolonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection duringin situcolonization would dictate the responsemore » to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCEThe influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were “cross-fed” with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors.« less

Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica

PubMed Central

Koo, Hyunmin; Mojib, Nazia; Hakim, Joseph A.; Hawes, Ian; Tanabe, Yukiko; Andersen, Dale T.; Bej, Asim K.

2017-01-01

In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1), middle (U2), and inner (U3) decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI) values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance. PMID:28824553

Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica.

PubMed

Koo, Hyunmin; Mojib, Nazia; Hakim, Joseph A; Hawes, Ian; Tanabe, Yukiko; Andersen, Dale T; Bej, Asim K

2017-01-01

In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1), middle (U2), and inner (U3) decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI) values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.

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

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.

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

PubMed

Huang, Qiuyuan; Briggs, Brandon R; Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

Growth-altering microbial interactions are responsive to chemical context

PubMed Central

2017-01-01

Microbial interactions are ubiquitous in nature, and are equally as relevant to human wellbeing as the identities of the interacting microbes. However, microbial interactions are difficult to measure and characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on environmental context. We present a novel workflow for inferring microbial interactions that integrates semi-automated image analysis with a colony stamping mechanism, with the overall effect of improving throughput and reproducibility of colony interaction assays. We apply our approach to infer interactions among bacterial species associated with the normal lung microbiome, and how those interactions are altered by the presence of benzo[a]pyrene, a carcinogenic compound found in cigarettes. We found that the presence of this single compound changed the interaction network, demonstrating that microbial interactions are indeed dynamic and responsive to local chemical context. PMID:28319121

Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

NASA Astrophysics Data System (ADS)

Masum, Shakil A.; Thomas, Hywel R.

2018-06-01

To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

Quantitative Microbial Risk Assessment Tutorial: HSPF Setup, Application, and Calibration of Flows and Microbial Fate and Transport on an Example Watershed

EPA Science Inventory

A Quantitative Microbial Risk Assessment (QMRA) infrastructure that automates the manual process of characterizing transport of pathogens and microorganisms, from the source of release to a point of exposure, has been developed by loosely configuring a set of modules and process-...

Effects of graded levels of microbial phytase on apparent total tract digestibility of calcium and phosphorus and standardized total tract digestibility of phosphorus in four sources of canola meal and in soybean meal fed to growing pigs.

PubMed

She, Y; Liu, Y; Stein, H H

2017-05-01

One hundred twenty pigs were used to determine effects of graded levels of microbial phytase on the apparent total tract digestibility (ATTD) of P and Ca and the standardized total tract digestibility (STTD) of P in 4 sources of canola meal and in 1 source of soybean meal (SBM) fed to growing pigs. The 4 sources of canola meal were produced from 1 source of high-protein canola seeds and 2 sources of conventional canola seeds with 1 of the conventional canola seeds being divided into 2 separate batches before crushing. Pigs (16.2 ± 5.3 kg initial BW) were individually housed in metabolism crates and were randomly allotted to 1 of 20 diets in a 5 × 4 factorial arrangement of treatments with 5 ingredients and 4 levels of phytase. There were 6 replicate pigs per diet. Five basal diets based on high-protein canola meal (CM-HP), high-temperature processed canola meal (CM-HT), low-temperature processed canola meal (CM-LT), conventional canola meal (CM-CV), or SBM were formulated. The basal diets contained no phytase. Fifteen additional diets were prepared by adding approximately 500, 1,500, or 2,500 phytase units/kg to each of the 5 basal diets. Feces were quantitatively collected for 5 d based on the marker-to-marker approach after a 7-d adaptation period. Results indicated that supplementation of microbial phytase increased (linear, < 0.05) the ATTD of Ca in diets containing CM-HP, CM-HT, CM-CV, and SBM but not in diets containing CM-LT. Microbial phytase also increased (linear and quadratic, < 0.05) the ATTD and STTD of P in all 5 ingredients. Compared with the CM-CV diets, the CM-HP diets had greater ( < 0.05) ATTD of Ca. The ATTD of Ca in the SBM diet was greater ( < 0.05) than in all canola meal diets, but no differences were observed in ATTD of Ca between CM-HT and CM-LT diets. The ATTD and the STTD of P were less ( < 0.05) in CM-HP, CM-HT, CM-LT, or CM-CV than in SBM if no microbial phytase was added, but no differences were observed in the ATTD and STTD of P in SBM, CM-HP, CM-HT, or CM-CV if the highest amount of phytase were added (interaction, < 0.05). Regression equations were developed to calculate the response to microbial phytase on the STTD of P in CM-HP, CM-HT, CM-LT, CM-CV, and SBM. In conclusion, inclusion of graded levels of microbial phytase increased the ATTD and STTD of P in CM-HP, CM-HT, CM-LT, CM-CV, and SBM and the response to microbial phytase added to each ingredient can be predicted by regression equations.