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

Modeling biogechemical reactive transport in a fracture zone

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

Molinero, Jorge; Samper, Javier; Yang, Chan Bing, and Zhang, Guoxiang

2005-01-14

A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes inmore » biochemical parameters.« less

Specificity of marine microbial surface interactions.

PubMed Central

Imam, S H; Bard, R F; Tosteson, T R

1984-01-01

The macromolecular surface components involved in intraspecific cell surface interactions of the green microalga Chlorella vulgaris and closely associated bacteria were investigated. The specific surface attachment between this alga and its associated bacteria is mediated by lectin-like macromolecules associated with the surfaces of these cells. The binding activity of these surface polymers was inhibited by specific simple sugars; this suggests the involvement of specific receptor-ligand binding sites on the interactive surfaces. Epifluorescent microscopic evaluation of bacteria-alga interactions in the presence and absence of the macromolecules that mediate these interactions showed that the glycoproteins active in these processes were specific to the microbial sources from which they were obtained. The demonstration and definition of the specificity of these interactions in mixed microbial populations may play an important role in our understanding of the dynamics of marine microbial populations in the sea. PMID:6508293

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.

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

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow.

PubMed

Zhang, Yuguang; Liu, Xiao; Cong, Jing; Lu, Hui; Sheng, Yuyu; Wang, Xiulei; Li, Diqiang; Liu, Xueduan; Yin, Huaqun; Zhou, Jizhong; Deng, Ye

2017-07-01

Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analysed using high-throughput technologies, including Illumina sequencing and geochip functional gene arrays. The soil microbial community structure and diversity were significantly (p < .05) different between alpine meadow and alpine steppe meadow; the microbial ɑ-diversity in alpine steppe meadow was significantly (p < .01) higher than in alpine meadow. Molecular ecological network analysis indicated that the microbial community structure in alpine steppe meadow was more complex and tighter than in the alpine meadow. The relative abundance of soil microbial labile carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g., chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decrease SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition. © 2017 John Wiley & Sons Ltd.

Microbial ecology of hot desert edaphic systems.

PubMed

Makhalanyane, Thulani P; Valverde, Angel; Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Cowan, Don A

2015-03-01

A significant proportion of the Earth's surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

PubMed Central

Zhao, Mengxin; Xue, Kai; Wang, Feng; Liu, Shanshan; Bai, Shijie; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

2014-01-01

Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling. PMID:24694714

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

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

DOE PAGES

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; ...

2017-09-28

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

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

NASA Astrophysics Data System (ADS)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; Zhou, Xiaolu; Wang, Meng; Zhang, Kerou; Wang, Gangsheng

2017-10-01

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 1195 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 by Xu et al. (2014). 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). However, our work represents the first step toward a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.

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

Large-scale controls on potential respiration and denitrification in riverine floodplains

PubMed Central

Welti, Nina; Bondar-Kunze, Elisabeth; Singer, Gabriel; Tritthart, Michael; Zechmeister-Boltenstern, Sophie; Hein, Thomas; Pinay, Gilles

2012-01-01

Restoration measures of deteriorated river ecosystems generally aim at increasing the spatial heterogeneity and connectivity of these systems in order to increase biodiversity and ecosystem stability. While this is believed to benefit overall ecological integrity, consequences of such restoration projects on biogeochemical processes per se (i.e. ecosystem functioning) in fluvial systems are rarely considered. We address these issues by evaluating the characteristics of surface water connection between side arms and the main river channel in a former braided river section and the role and degree of connectivity (i.e. duration of surface water connection) on the sediment biogeochemistry. We hypothesized that potential respiration and denitrification would be controlled by the degree of hydrological connectivity, which was increased after floodplain restoration. We measured potential microbial respiration (SIR) and denitrification (DEA) and compared a degraded floodplain section of the Danube River with a reconnected and restored floodplain in the same river section. Re-establishing surface water connection altered the controls on sediment microbial respiration and denitrification ultimately impacting potential microbial activities. Meta-variables were created to characterize the effects of hydrology, morphology, and the available carbon and nutrient pools on potential microbial processing. Mantel statistics and path analysis were performed and demonstrate a hierarchy where the effects of hydrology on the available substrates and microbial processing are mediated by the morphology of the floodplain. In addition, these processes are highest in the least connected sites. Surface water connection, mediated by morphology regulates the potential denitrification rate and the ratio of N2O to N2 emissions, demonstrating the effects of restoration in floodplain systems. PMID:23565037

Microbial imprint on soil-atmosphere H2, COS, and CO2 fluxes

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Commane, R.; Munger, J. W.; Wofsy, S. C.; Prinn, R. G.

2013-12-01

Microorganisms drive large trace gas fluxes between soil and atmosphere, but the signal can be difficult to detect and quantify in the presence of stronger exchange processes in an ecosystem. Partitioning methods are often needed to estimate trace gas budgets and to develop process-based models to explore the sensitivity of microbe-mediated fluxes. In this study, we test the performance of trace gases with predominantly microbe-mediated soil fluxes as a metric of the soil microbial uptake activity of other trace gases. Using simultaneous, collocated measurements at Harvard Forest, we consider three trace gases with microbe-mediated soil fluxes of various importance relative to their other (mainly plant-mediated) ecosystem fluxes: molecular hydrogen (H2), carbonyl sulfide (COS), and carbon dioxide (CO2). These gases probe different aspects of the soil trace-gas microbiology. Soil H2 uptake is a redox reaction driving the energy metabolism of a portion of the microbial community, while soil CO2 respiration is a partial proxy for the overall soil microbial metabolism. In comparison, very little is understood about the microbiological and environmental drivers of soil COS uptake and emissions. In this study, we find that H2, COS, and CO2 soil uptake rates are often correlated, but the relative soil uptake between gases is not constant, and is influenced by seasonality and local environmental conditions. We also consider how differences in the microbial communities and pathways involved in the soil fluxes may explain differences in the observations. Our results are important for informing previous studies using tracer approaches. For example, H2 has been used to estimate COS soil uptake, which must be accounted for to use COS as a carbon cycle tracer. Furthermore, the global distribution of H2 deposition velocity has been inferred from net primary productivity (CO2). Given that insufficient measurement frequency and spatial distribution exists to partition global net ecosystem fluxes of many climate-relevant trace gases, insight into the use of certain trace gases to estimate rates of more general biogeochemical processes is useful.

Changes in Microbial Nitrogen Across a 100-Year Chronosequence of Upland Hardwood Forests

Treesearch

Travis W. Idol; Phillip E. Pope; Felix, Jr. Ponder

2002-01-01

Soil microorganisms mediate many of the major processes involved in soil N cycling. Also, they are strong competitors with plants for available soil N. Thus, changes in microbial N because of forest harvesting may have significant impacts on N availability and overall forest N cycling. A chronosequence of upland hardwood forest stands in southern Indiana, USA, ranging...

ENVIRONMENTAL CHARACTERISTICS AFFECTING REDUCTIVE TRANSFORMATION OF ORGANIC POLLUTANTS IN ANOXIC SEDIMENTS

EPA Science Inventory

Reductive transformations are important processes for determining the fate of organic pollutants in anoxic environments. These processes are most often microbially mediated by both direct and indirect means. For example, specific bacteria transform organic pollutants directly as ...

Microbial community assembly and metabolic function during mammalian corpse decomposition

USGS Publications Warehouse

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Microbial community assembly and metabolic function during mammalian corpse decomposition

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

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in lowmore » abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.« less

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events

PubMed Central

Mooshammer, Maria; Hofhansl, Florian; Frank, Alexander H.; Wanek, Wolfgang; Hämmerle, Ieda; Leitner, Sonja; Schnecker, Jörg; Wild, Birgit; Watzka, Margarete; Keiblinger, Katharina M.; Zechmeister-Boltenstern, Sophie; Richter, Andreas

2017-01-01

Predicted changes in the intensity and frequency of climate extremes urge a better mechanistic understanding of the stress response of microbially mediated carbon (C) and nutrient cycling processes. We analyzed the resistance and resilience of microbial C, nitrogen (N), and phosphorus (P) cycling processes and microbial community composition in decomposing plant litter to transient, but severe, temperature disturbances, namely, freeze-thaw and heat. Disturbances led temporarily to a more rapid cycling of C and N but caused a down-regulation of P cycling. In contrast to the fast recovery of the initially stimulated C and N processes, we found a slow recovery of P mineralization rates, which was not accompanied by significant changes in community composition. The functional and structural responses to the two distinct temperature disturbances were markedly similar, suggesting that direct negative physical effects and costs associated with the stress response were comparable. Moreover, the stress response of extracellular enzyme activities, but not that of intracellular microbial processes (for example, respiration or N mineralization), was dependent on the nutrient content of the resource through its effect on microbial physiology and community composition. Our laboratory study provides novel insights into the mechanisms of microbial functional stress responses that can serve as a basis for field studies and, in particular, illustrates the need for a closer integration of microbial C-N-P interactions into climate extremes research. PMID:28508070

Extracellular enzymes facilitate electron uptake in biocorrosion and bioelectrosynthesis.

PubMed

Deutzmann, Jörg S; Sahin, Merve; Spormann, Alfred M

2015-04-21

Direct, mediator-free transfer of electrons between a microbial cell and a solid phase in its surrounding environment has been suggested to be a widespread and ecologically significant process. The high rates of microbial electron uptake observed during microbially influenced corrosion of iron [Fe(0)] and during microbial electrosynthesis have been considered support for a direct electron uptake in these microbial processes. However, the underlying molecular mechanisms of direct electron uptake are unknown. We investigated the electron uptake characteristics of the Fe(0)-corroding and electromethanogenic archaeon Methanococcus maripaludis and discovered that free, surface-associated redox enzymes, such as hydrogenases and presumably formate dehydrogenases, are sufficient to mediate an apparent direct electron uptake. In genetic and biochemical experiments, we showed that these enzymes, which are released from cells during routine culturing, catalyze the formation of H2 or formate when sorbed to an appropriate redox-active surface. These low-molecular-weight products are rapidly consumed by M. maripaludis cells when present, thereby preventing their accumulation to any appreciable or even detectable level. Rates of H2 and formate formation by cell-free spent culture medium were sufficient to explain the observed rates of methane formation from Fe(0) and cathode-derived electrons by wild-type M. maripaludis as well as by a mutant strain carrying deletions in all catabolic hydrogenases. Our data collectively show that cell-derived free enzymes can mimic direct extracellular electron transfer during Fe(0) corrosion and microbial electrosynthesis and may represent an ecologically important but so far overlooked mechanism in biological electron transfer. The intriguing trait of some microbial organisms to engage in direct electron transfer is thought to be widespread in nature. Consequently, direct uptake of electrons into microbial cells from solid surfaces is assumed to have a significant impact not only on fundamental microbial and biogeochemical processes but also on applied bioelectrochemical systems, such as microbial electrosynthesis and biocorrosion. This study provides a simple mechanistic explanation for frequently observed fast electron uptake kinetics in microbiological systems without a direct transfer: free, cell-derived enzymes can interact with cathodic surfaces and catalyze the formation of intermediates that are rapidly consumed by microbial cells. This electron transfer mechanism likely plays a significant role in various microbial electron transfer reactions in the environment. Copyright © 2015 Deutzmann et al.

Microbial community assembly and metabolic function during mammalian corpse decomposition.

PubMed

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-08

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations. Copyright © 2016, American Association for the Advancement of Science.

Models of microbiome evolution incorporating host and microbial selection.

PubMed

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong parental contribution, when host-mediated selection acts on microbes concomitantly. We present a computational framework that integrates different selective processes acting on the evolution of microbiomes. Our framework demonstrates that selection acting on microbes can have a strong effect on microbial diversities and fitnesses, whereas selection on hosts can have weaker outcomes.

Modelling geochemical and microbial consumption of dissolved oxygen after backfilling a high level radiactive waste repository.

PubMed

Yang, Changbing; Samper, Javier; Molinero, Jorge; Bonilla, Mercedes

2007-08-15

Dissolved oxygen (DO) left in the voids of buffer and backfill materials of a deep geological high level radioactive waste (HLW) repository could cause canister corrosion. Available data from laboratory and in situ experiments indicate that microbes play a substantial role in controlling redox conditions near a HLW repository. This paper presents the application of a coupled hydro-bio-geochemical model to evaluate geochemical and microbial consumption of DO in bentonite porewater after backfilling of a HLW repository designed according to the Swedish reference concept. In addition to geochemical reactions, the model accounts for dissolved organic carbon (DOC) respiration and methane oxidation. Parameters for microbial processes were derived from calibration of the REX in situ experiment carried out at the Aspö underground laboratory. The role of geochemical and microbial processes in consuming DO is evaluated for several scenarios. Numerical results show that both geochemical and microbial processes are relevant for DO consumption. However, the time needed to consume the DO trapped in the bentonite buffer decreases dramatically from several hundreds of years when only geochemical processes are considered to a few weeks when both geochemical reactions and microbially-mediated DOC respiration and methane oxidation are taken into account simultaneously.

Extracellular Enzymes Facilitate Electron Uptake in Biocorrosion and Bioelectrosynthesis

PubMed Central

Deutzmann, Jörg S.; Sahin, Merve

2015-01-01

ABSTRACT Direct, mediator-free transfer of electrons between a microbial cell and a solid phase in its surrounding environment has been suggested to be a widespread and ecologically significant process. The high rates of microbial electron uptake observed during microbially influenced corrosion of iron [Fe(0)] and during microbial electrosynthesis have been considered support for a direct electron uptake in these microbial processes. However, the underlying molecular mechanisms of direct electron uptake are unknown. We investigated the electron uptake characteristics of the Fe(0)-corroding and electromethanogenic archaeon Methanococcus maripaludis and discovered that free, surface-associated redox enzymes, such as hydrogenases and presumably formate dehydrogenases, are sufficient to mediate an apparent direct electron uptake. In genetic and biochemical experiments, we showed that these enzymes, which are released from cells during routine culturing, catalyze the formation of H2 or formate when sorbed to an appropriate redox-active surface. These low-molecular-weight products are rapidly consumed by M. maripaludis cells when present, thereby preventing their accumulation to any appreciable or even detectable level. Rates of H2 and formate formation by cell-free spent culture medium were sufficient to explain the observed rates of methane formation from Fe(0) and cathode-derived electrons by wild-type M. maripaludis as well as by a mutant strain carrying deletions in all catabolic hydrogenases. Our data collectively show that cell-derived free enzymes can mimic direct extracellular electron transfer during Fe(0) corrosion and microbial electrosynthesis and may represent an ecologically important but so far overlooked mechanism in biological electron transfer. PMID:25900658

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

PubMed

Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

Linking genes to ecosystem trace gas fluxes in a large-scale model system

NASA Astrophysics Data System (ADS)

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

2017-12-01

Soil microorganisms mediate biogeochemical cycles through biosphere-atmosphere gas exchange with significant impact on atmospheric trace gas composition. Improving process-based understanding of these microbial populations and linking their genomic potential to the ecosystem-scale is a challenge, particularly in soil systems, which are heterogeneous in biodiversity, chemistry, and structure. In oligotrophic systems, such as the Landscape Evolution Observatory (LEO) at Biosphere 2, atmospheric trace gas scavenging may supply critical metabolic needs to microbial communities, thereby promoting tight linkages between microbial genomics and trace gas utilization. This large-scale model system of three initially homogenous and highly instrumented hillslopes facilitates high temporal resolution characterization of subsurface trace gas fluxes at hundreds of sampling points, making LEO an ideal location to study microbe-mediated trace gas fluxes from the gene to ecosystem scales. Specifically, we focus on the metabolism of ubiquitous atmospheric reduced trace gases hydrogen (H2), carbon monoxide (CO), and methane (CH4), which may have wide-reaching impacts on microbial community establishment, survival, and function. Additionally, microbial activity on LEO may facilitate weathering of the basalt matrix, which can be studied with trace gas measurements of carbonyl sulfide (COS/OCS) and carbon dioxide (O-isotopes in CO2), and presents an additional opportunity for gene to ecosystem study. This work will present initial measurements of this suite of trace gases to characterize soil microbial metabolic activity, as well as links between spatial and temporal variability of microbe-mediated trace gas fluxes in LEO and their relation to genomic-based characterization of microbial community structure (phylogenetic amplicons) and genetic potential (metagenomics). Results from the LEO model system will help build understanding of the importance of atmospheric inputs to microorganisms pioneering fresh mineral matrix. Additionally, the measurement and modeling techniques that will be developed at LEO will be relevant for other investigators linking microbial genomics to ecosystem function in more well-developed soils with greater complexity.

Interactive effects of global climate change and pollution on marine microbes: the way ahead.

PubMed

Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Angela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

2013-06-01

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.

Interactive effects of global climate change and pollution on marine microbes: the way ahead

PubMed Central

Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Ângela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

2013-01-01

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future. PMID:23789087

Through the eye of the needle: a review of isotope approaches to quantify microbial processes mediating soil carbon balance.

PubMed

Paterson, Eric; Midwood, Andrew J; Millard, Peter

2009-01-01

For soils in carbon balance, losses of soil carbon from biological activity are balanced by organic inputs from vegetation. Perturbations, such as climate or land use change, have the potential to disrupt this balance and alter soil-atmosphere carbon exchanges. As the quantification of soil organic matter stocks is an insensitive means of detecting changes, certainly over short timescales, there is a need to apply methods that facilitate a quantitative understanding of the biological processes underlying soil carbon balance. We outline the processes by which plant carbon enters the soil and critically evaluate isotopic methods to quantify them. Then, we consider the balancing CO(2) flux from soil and detail the importance of partitioning the sources of this flux into those from recent plant assimilate and those from native soil organic matter. Finally, we consider the interactions between the inputs of carbon to soil and the losses from soil mediated by biological activity. We emphasize the key functional role of the microbiota in the concurrent processing of carbon from recent plant inputs and native soil organic matter. We conclude that quantitative isotope labelling and partitioning methods, coupled to those for the quantification of microbial community substrate use, offer the potential to resolve the functioning of the microbial control point of soil carbon balance in unprecedented detail.

Role of Neurochemicals in the Interaction between the Microbiota and the Immune and the Nervous System of the Host Organism.

PubMed

Oleskin, Alexander V; Shenderov, Boris A; Rogovsky, Vladimir S

2017-09-01

This work is concerned with the role of evolutionary conserved substances, neurotransmitters, and neurohormones, within the complex framework of the microbial consortium-immune system-nervous system axis in the human or animal organism. Although the operation of each of these systems per se is relatively well understood, their combined effects on the host organism still await further research. Drawing on recent research on host-produced and microbial low-molecular-weight neurochemicals such as biogenic amines, amino acids, and short-chain fatty acids (SCFAs), we suggest that these mediators form a part of a universal neurochemical "language." It mediates the whole gamut of harmonious and disharmonious interactions between (a) the intestinal microbial consortium, (b) local and systemic immune cells, and (c) the central and peripheral nervous system. Importantly, the ongoing microbiota-host interactivity is bidirectional. We present evidence that a large number of microbially produced low-molecular-weight compounds are identical or homologous to mediators that are synthesized by immune or nervous cells and, therefore, can bind to the corresponding host receptors. In addition, microbial cells specifically respond to host-produced neuromediators/neurohormones because they have adapted to them during the course of many millions of years of microbiota-host coevolution. We emphasize that the terms "microbiota" and "microbial consortium" are to be used in the broadest sense, so as to include, apart from bacteria, also eukaryotic microorganisms. These are exemplified by the mycobiota whose role in the microbial consortium-immune system-nervous system axis researchers are only beginning to elucidate. In light of the above, it is imperative to reform the current strategies of using probiotic microorganisms and their metabolites for treating and preventing dysbiosis-related diseases. The review demonstrates, in the example of novel probiotics (psychobiotics), that many target-oriented probiotic preparations produce important side effects on a wide variety of processes in the host organism. In particular, we should take into account probiotics' capacity to produce mediators that can considerably modify the operation of the microecological, immune, and nervous system of the human organism.

Biofilm-induced bioclogging produces sharp interfaces in hyporheic flow, redox conditions, and microbial community structure

NASA Astrophysics Data System (ADS)

Caruso, Alice; Boano, Fulvio; Ridolfi, Luca; Chopp, David L.; Packman, Aaron

2017-05-01

Riverbed sediments host important biogeochemical processes that play a key role in nutrient dynamics. Sedimentary nutrient transformations are mediated by bacteria in the form of attached biofilms. The influence of microbial metabolic activity on the hydrochemical conditions within the hyporheic zone is poorly understood. We present a hydrobiogeochemical model to assess how the growth of heterotrophic and autotrophic biomass affects the transport and transformation of dissolved nitrogen compounds in bed form-induced hyporheic zones. Coupling between hyporheic exchange, nitrogen metabolism, and biomass growth leads to an equilibrium between permeability reduction and microbial metabolism that yields shallow hyporheic flows in a region with low permeability and high rates of microbial metabolism near the stream-sediment interface. The results show that the bioclogging caused by microbial growth can constrain rates and patterns of hyporheic fluxes and microbial transformation rate in many streams.

Sniffing on microbes: diverse roles of microbial volatile organic compounds in plant health.

PubMed

Bitas, Vasileios; Kim, Hye-Seon; Bennett, Joan W; Kang, Seogchan

2013-08-01

Secreted proteins and metabolites play diverse and critical roles in organismal and organism-environment interactions. Volatile organic compounds (VOC) can travel far from the point of production through the atmosphere, porous soils, and liquid, making them ideal info-chemicals for mediating both short- and long-distance intercellular and organismal interactions. Critical ecological roles for animal- and plant-derived VOC in directing animal behaviors and for VOC as a language for plant-to-plant communication and regulators of various physiological processes have been well documented. Similarly, microbial VOC appear to be involved in antagonism, mutualism, intra- and interspecies regulation of cellular and developmental processes, and modification of their surrounding environments. However, the available knowledge of how microbial VOC affect other organisms is very limited. Evidence supporting diverse roles of microbial VOC with the focus on their impact on plant health is reviewed here. Given the vast diversity of microbes in nature and the critical importance of microbial communities associated with plants for their ecology and fitness, systematic exploration of microbial VOC and characterization of their biological functions and ecological roles will likely uncover novel mechanisms for controlling diverse biological processes critical to plant health and will also offer tangible practical benefits in addressing agricultural and environmental problems.

Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota

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

Warren, Melissa J.; Lin, Xueju; Gaby, John C.

We present that Microbial N 2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO 2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O 2, CO 2, and CH 4) on potential rates of diazotrophy measured by acetylene (C 2H 2) reduction and 15N 2incorporation. A molecularmore » analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (15N 2 was suppressed 90% by O 2 and 55% by C 2H 2 and was unaffected by CH 4 and CO 2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C 2H 2-sensitive and C 2H 2-insensitive microbes that are more active at low concentrations of O 2 and show similar activity at high and low concentrations of CH 4. Importance: Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. In conclusion, our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.« less

Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota

DOE PAGES

Warren, Melissa J.; Lin, Xueju; Gaby, John C.; ...

2017-06-30

We present that Microbial N 2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO 2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O 2, CO 2, and CH 4) on potential rates of diazotrophy measured by acetylene (C 2H 2) reduction and 15N 2incorporation. A molecularmore » analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (15N 2 was suppressed 90% by O 2 and 55% by C 2H 2 and was unaffected by CH 4 and CO 2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C 2H 2-sensitive and C 2H 2-insensitive microbes that are more active at low concentrations of O 2 and show similar activity at high and low concentrations of CH 4. Importance: Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. In conclusion, our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.« less

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.

Microbial communities mediating algal detritus turnover under anaerobic conditions

PubMed Central

Morrison, Jessica M.; Murphy, Chelsea L.; Baker, Kristina; Zamor, Richard M.; Nikolai, Steve J.; Wilder, Shawn; Elshahed, Mostafa S.

2017-01-01

Background Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored. Results Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O’ the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13–16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genus Clostridium, or family Veillonellaceae within the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched included the uncultured groups VadinBC27 and WCHB1-69 within the Bacteroidetes, genus Spirochaeta and the uncultured group SHA-4 within Spirochaetes, Ruminococcaceae, Lachnospiraceae, Yongiibacter, Geosporobacter, and Acidaminobacter within the Firmicutes, and genera Kluyvera, Pantoea, Edwardsiella and Aeromonas, and Buttiauxella within the Gamma-Proteobaceteria order Enterobacteriales. Conclusions Our results represent the first systematic survey of microbial communities mediating turnover of algal biomass under anaerobic conditions, and highlights the diversity of lineages putatively involved in the degradation process. PMID:28097050

Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico.

PubMed

Breitbart, Mya; Hoare, Ana; Nitti, Anthony; Siefert, Janet; Haynes, Matthew; Dinsdale, Elizabeth; Edwards, Robert; Souza, Valeria; Rohwer, Forest; Hollander, David

2009-01-01

Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Ciénegas, Mexico. Metagenomic sequencing revealed a diverse, redox-dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites.

Harnessing biodiesel-producing microbes: from genetic engineering of lipase to metabolic engineering of fatty acid biosynthetic pathway.

PubMed

Yan, Jinyong; Yan, Yunjun; Madzak, Catherine; Han, Bingnan

2017-02-01

Microbial production routes, notably whole-cell lipase-mediated biotransformation and fatty-acids-derived biosynthesis, offer new opportunities for synthesizing biodiesel. They compare favorably to immobilized lipase and chemically catalyzed processes. Genetically modified whole-cell lipase-mediated in vitro route, together with in vivo and ex vivo microbial biosynthesis routes, constitutes emerging and rapidly developing research areas for effective production of biodiesel. This review presents recent advances in customizing microorganisms for producing biodiesel, via genetic engineering of lipases and metabolic engineering (including system regulation) of fatty-acids-derived pathways. Microbial hosts used include Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Aspergillus oryzae. These microbial cells can be genetically modified to produce lipases under different forms: intracellularly expressed, secreted or surface-displayed. They can be metabolically redesigned and systematically regulated to obtain balanced biodiesel-producing cells, as highlighted in this study. Such genetically or metabolically modified microbial cells can support not only in vitro biotransformation of various common oil feedstocks to biodiesel, but also de novo biosynthesis of biodiesel from glucose, glycerol or even cellulosic biomass. We believe that the genetically tractable oleaginous yeast Yarrowia lipolytica could be developed to an effective biodiesel-producing microbial cell factory. For this purpose, we propose several engineered pathways, based on lipase and wax ester synthase, in this promising oleaginous host.

Anthropogenic N Deposition Slows Decay by Favoring Bacterial Metabolism: Insights from Metagenomic Analyses

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

Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.

Litter decomposition is an enzymatically-complex process that is mediated by a diverse assemblage of saprophytic microorganisms. It is a globally important biogeochemical process that can be suppressed by anthropogenic N deposition. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. Here, we paired extracellular enzyme assays with shotgun metagenomics to assess if anthropogenic N deposition has altered the functional potential of microbial communities inhabiting decaying forest floor. Experimental N deposition significantly reduced the activity of extracellular enzymes mediating plant cell wallmore » decay, which occurred concurrently with changes in the relative abundance of metagenomic functional gene pathways mediating the metabolism of carbohydrates, aromatic compounds, as well as microbial respiration. Moreover, experimental N deposition increased the relative abundance of 50 of the 60 gene pathways, the majority of which were associated with saprotrophic bacteria. Conversely, the relative abundance and composition of fungal genes mediating the metabolism of plant litter was not affected by experimental N deposition. Future rates of atmospheric N deposition have favored saprotrophic soil bacteria, whereas the metabolic potential of saprotrophic fungi appears resilient to this agent of environmental change. Results presented here provide evidence that changes in the functional capacity of saprotrophic soil microorganisms mediate how anthropogenic N deposition increases C storage in soil.« less

Anthropogenic N Deposition Slows Decay by Favoring Bacterial Metabolism: Insights from Metagenomic Analyses

DOE PAGES

Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.; ...

2016-03-02

Litter decomposition is an enzymatically-complex process that is mediated by a diverse assemblage of saprophytic microorganisms. It is a globally important biogeochemical process that can be suppressed by anthropogenic N deposition. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. Here, we paired extracellular enzyme assays with shotgun metagenomics to assess if anthropogenic N deposition has altered the functional potential of microbial communities inhabiting decaying forest floor. Experimental N deposition significantly reduced the activity of extracellular enzymes mediating plant cell wallmore » decay, which occurred concurrently with changes in the relative abundance of metagenomic functional gene pathways mediating the metabolism of carbohydrates, aromatic compounds, as well as microbial respiration. Moreover, experimental N deposition increased the relative abundance of 50 of the 60 gene pathways, the majority of which were associated with saprotrophic bacteria. Conversely, the relative abundance and composition of fungal genes mediating the metabolism of plant litter was not affected by experimental N deposition. Future rates of atmospheric N deposition have favored saprotrophic soil bacteria, whereas the metabolic potential of saprotrophic fungi appears resilient to this agent of environmental change. Results presented here provide evidence that changes in the functional capacity of saprotrophic soil microorganisms mediate how anthropogenic N deposition increases C storage in soil.« less

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

Zhen Li; Rishika Haynes; Eugene Sato

Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopymore » results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.« less

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.

Electricity generation in microbial fuel cells using neutral red as an electronophore

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

Park, D.H.; Zeikus, J.G.

2000-04-01

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. Inmore » microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator was 10-fold more than the amount produced when thionin was the electron mediator. The amount of electrical energy generated and the amount of current produced from glucose in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge was used in the fuel cell, stable and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Their results are discussed in relation to factors that may improve the relatively low electrical efficiencies obtained with microbial fuel cells.« less

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

PubMed Central

Weedon, James T.; Kowalchuk, George A.; Aerts, Rien; Freriks, Stef; Röling, Wilfred F. M.; van Bodegom, Peter M.

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts. PMID:28326062

Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

NASA Astrophysics Data System (ADS)

Kritee, K.; Barkay, Tamar; Blum, Joel D.

2009-03-01

Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg degradation experiments and, based on estimates of the rates of the various steps involved in this mer mediated pathway, suggest which steps in the process could contribute towards the observed extent of fractionation. This framework suggests that at lower cell densities catalysis by MerB was the rate limiting step while at higher cell densities transport into the cell, which does not cause fractionation, became the rate limiting step. In addition to presenting evidence for absence of MIF during mer mediated Hg transformations, based on the nature of Hg compounds and microbe-Hg interactions, we suggest that the nuclear spin dependent MIF (i.e., the magnetic isotope effect) is also unlikely to occur during other non mer mediated 'dark' microbial Hg transformations (e.g., formation of MMHg and oxidative degradation of MMHg). Because of the important implications of the absence of MIF during biological processes on Hg isotope systematics, we discuss theoretical considerations and experimental strategies that could be used to confirm this suggestion.

Reactive Transport Modeling of Microbe-mediated Fe (II) Oxidation for Enhanced Oil Recovery

NASA Astrophysics Data System (ADS)

Surasani, V.; Li, L.

2011-12-01

Microbially Enhanced Oil Recovery (MEOR) aims to improve the recovery of entrapped heavy oil in depleted reservoirs using microbe-based technology. Reservoir ecosystems often contain diverse microbial communities those can interact with subsurface fluids and minerals through a network of nutrients and energy fluxes. Microbe-mediated reactions products include gases, biosurfactants, biopolymers those can alter the properties of oil and interfacial interactions between oil, brine, and rocks. In addition, the produced biomass and mineral precipitates can change the reservoir permeability profile and increase sweeping efficiency. Under subsurface conditions, the injection of nitrate and Fe (II) as the electron acceptor and donor allows bacteria to grow. The reaction products include minerals such as Fe(OH)3 and nitrogen containing gases. These reaction products can have large impact on oil and reservoir properties and can enhance the recovery of trapped oil. This work aims to understand the Fe(II) oxidation by nitrate under conditions relevant to MEOR. Reactive transport modeling is used to simulate the fluid flow, transport, and reactions involved in this process. Here we developed a complex reactive network for microbial mediated nitrate-dependent Fe (II) oxidation that involves both thermodynamic controlled aqueous reactions and kinetic controlled Fe (II) mineral reaction. Reactive transport modeling is used to understand and quantify the coupling between flow, transport, and reaction processes. Our results identify key parameter controls those are important for the alteration of permeability profile under field conditions.

Boosting mediated electron transfer in bioelectrochemical systems with tailored defined microbial cocultures.

PubMed

Schmitz, Simone; Rosenbaum, Miriam A

2018-05-19

Bioelectrochemical systems (BES) hold great promise for sustainable energy generation via a microbial catalyst from organic matter, for example, from wastewater. To improve current generation in BES, understanding the underlying microbiology of the electrode community is essential. Electron mediator producing microorganism like Pseudomonas aeruginosa play an essential role in efficient electricity generation in BES. These microbes enable even nonelectroactive microorganism like Enterobacter aerogenes to contribute to current production. Together they form a synergistic coculture, where both contribute to community welfare. To use microbial co-operation in BES, the physical and chemical environments provided in the natural habitats of the coculture play a crucial role. Here, we show that synergistic effects in defined cocultures of P. aeruginosa and E. aerogenes can be strongly enhanced toward high current production by adapting process parameters, like pH, temperature, oxygen demand, and substrate requirements. Especially, oxygen was identified as a major factor influencing coculture behavior and optimization of its supply could enhance electric current production over 400%. Furthermore, operating the coculture in fed-batch mode enabled us to obtain very high current densities and to harvest electrical energy for 1 month. In this optimized condition, the coulombic efficiency of the process was boosted to 20%, which is outstanding for mediator-based electron transfer. This study lays the foundation for a rationally designed utilization of cocultures in BES for bioenergy generation from specific wastewaters or for bioprocess sensing and for benefiting from their synergistic effects under controlled bioprocess condition. © 2018 Wiley Periodicals, Inc.

Can Microbial Ecology and Mycorrhizal Functioning Inform Climate Change Models?

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

Hofmockel, Kirsten; Hobbie, Erik

Our funded research focused on soil organic matter dynamics and plant-microbe interactions by examining the role of belowground processes and mechanisms across scales, including decomposition of organic molecules, microbial interactions, and plant-microbe interactions associated with a changing climate. Research foci included mycorrhizal mediated priming of soil carbon turnover, organic N use and depolymerization by free-living microbes and mycorrhizal fungi, and the use of isotopes as additional constraints for improved modeling of belowground processes. This work complemented the DOE’s mandate to understand both the consequences of atmospheric and climatic change for key ecosystems and the feedbacks on C cycling.

NIGHTHAWK - A Program for Modeling Saturated Batch and Column Experiments Incorporating Equilibrium and Kinetic Biogeochemistry

EPA Science Inventory

NIGHTHAWK simulates the fate and transport of biogeochemically reactive contaminants in the saturated subsurface. Version 1.2 supports batch and one- dimensional advective-dispersive-reactive transport involving a number of biogeochemical processes, including: microbially-mediate...

Role of biochar as an additive in organic waste composting.

PubMed

Sanchez-Monedero, M A; Cayuela, M L; Roig, A; Jindo, K; Mondini, C; Bolan, N

2018-01-01

The use of biochar in organic waste composting has attracted interest in the last decade due to the environmental and agronomical benefits obtained during the process. Biochar presents favourable physicochemical properties, such as large porosity, surface area and high cation exchange capacity, enabling interaction with major nutrient cycles and favouring microbial growth in the composting pile. The enhanced environmental conditions can promote a change in the microbial communities that can affect important microbially mediated biogeochemical cycles: organic matter degradation and humification, nitrification, denitrification and methanogenesis. The main benefits of the use of biochar in composting are reviewed in this article, with special attention to those related to the process performance, compost microbiology, organic matter degradation and humification, reduction of N losses and greenhouse gas emissions and fate of heavy metals. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

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.

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy.

PubMed

Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis G; De Francisci, Davide; Valle, Giorgio; Angelidaki, Irini

2016-01-01

Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge. In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway. This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.

Inhibitory Effects of Sulfate and Nitrate Reduction on Reductive Dechlorination of PCP in a Flooded Paddy Soil

PubMed Central

Xu, Yan; Xue, Lili; Ye, Qi; Franks, Ashley E.; Zhu, Min; Feng, Xi; Xu, Jianming; He, Yan

2018-01-01

Pentachlorophenol (PCP) is highly toxic and persistent in soils. Bioreduction of PCP often co-occurs with varying concentrations of sulfate and nitrate in flooded paddy soils where each can act as an electron acceptor. Anaerobic soil microcosms were constructed to evaluate the influence of sulfate and nitrate amendments and their redox processes. Microcosms with varying sulfate and nitrate concentrations demonstrated an inhibitory effect on reductive dechlorination of PCP compared to an untreated control. Compared to nitrate, sulfate exhibited a more significant impact on PCP dechlorination, as evidenced by a lower maximum reaction rate and a longer time to reach the maximum reaction rate. Dechlorination of PCP was initiated at the ortho-position, and then at the para- and meta-positions to form 3-CP as the final product in all microcosms. Deep sequencing of microbial communities in the microcosms revealed a strong variation in bacterial taxon among treatments. Specialized microbial groups, such as the genus of Desulfovibrio responding to the addition of sulfate, had a potential to mediate the competitive microbial dechlorination of PCP. Our results provide an insight into the competitive microbial-mediated reductive dechlorination of PCP in natural flooded soil or sediment environments. PMID:29643842

An overview of field-specific designs of microbial EOR

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

Robertson, E.P.; Bala, G.A.; Fox, S.L.

1995-12-31

The selection and design of an MEOR process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (bigenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. This paper discusses the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery processmore » for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated, and field isolates were characterized.« less

Microbial Diversity in Endostromatolites (cf. Fissure Calcretes) and in the Surrounding Permafrost Landscape, Haughton Impact Structure Region, Devon Island, Canada

NASA Astrophysics Data System (ADS)

Pellerin, André; Lacelle, Denis; Fortin, Danielle; Clark, Ian D.; Lauriol, Bernard

2009-11-01

In recent years, endostromatolites, which consist of finely laminated calcite columns that grow orthogonally within millimeter- to centimeter-thick fissures in limestone bedrock outcrops, have been discovered in dolomitic outcrops in the Haughton impact structure region, Devon Island, Canada. The growth mechanism of the endostromatolites is believed to be very slow and possibly intertwined with biotic and abiotic processes. Therefore, to discern how endostromatolites form in this polar desert environment, the composition of the microbial community of endostromatolites was determined by means of molecular phylogenetic analysis and compared to the microbial communities found in the surrounding soils. The microbial community present within endostromatolites can be inferred to be (given the predominant metabolic traits of related organisms) mostly aerobic and chemoheterotrophic, and belongs in large part to the phylum Actinobacteria and the subphylum Alphaproteobacteria. The identification of these bacteria suggests that the conditions within the fissure were mostly oxidizing during the growth of endostromatolite. The DNA sequences also indicate that a number of bacteria that closely resemble Rubrobacter radiotolerans are abundant in the endostromatolites as well as other Actinobacteria and Alphaproteobacteria. Some of these taxa have been associated with calcite precipitation, which suggests that the endostromatolites might in fact be microbially mediated. Bacterial communities from nearby permanently frozen soils were more diverse and harbored all the phyla found in the endostromatolites with additional taxa. This study on the microbial communities preserved in potentially microbially mediated secondary minerals in the Arctic could help in the search for evidence of life-forms near the edge of habitability on other planetary bodies.

BEHAVIOR AND ASSIMILATION OF ORGANIC AND INORGANIC PRIOIRTY POLLUTANTS CODISPOSED WITH MUNICIPAL REFUSE - VOLUME II - APPENDICES

EPA Science Inventory

Organic and inorganic priority pollutants codisposed with municipal solid waste (MSW) in ten pilot-scale simulated landfill columns, operated under single pass leaching or leachate recycle, were capable of being attenuated by microbially-mediated landfill stabilization processes....

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

PubMed

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

2013-08-01

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

Magnesium Isotopic Evidence for Widespread Microbial Dolomite Precipitation in the Geological Record.

NASA Astrophysics Data System (ADS)

Carder, E. A.; Galy, A.; McKenzie, J. A.; Vasconcelos, C.; Elderfield, H.

2005-12-01

The enigma surrounding the `Dolomite Problem' is the relative abundance of dolomite in the geological record versus its very rare occurrence on the surface of the modern Earth despite a particularly favourable modern seawater chemistry. Recent studies of modern dolomite from hypersaline coastal lagoons in Brazil and Pleistocene dolomite from ODP cores collected during ODP Leg 201 on the Peru Margin suggest microbial mediation is an important factor [1]. Indeed, cultures of sulfate-reducing bacteria isolated from the lagoons mediate dolomite precipitation in the laboratory [2, 3]. In this study we report magnesium isotopic analyses of these modern microbial associated dolomites and ancient dolomites of a range of geological ages and environments. The application of stable magnesium isotopes to study dolomite formation and the nature of the processes involved represents a new frontier in isotope geochemistry. Highly accurate determination of the magnesium isotopic composition allows us to distinguish between kinetic and equilibrium isotope fractionation on the basis of the excess of 25Mg. A significant kinetic isotope fractionation is observed in laboratory cultures and surfical microbial mats from the Brazilian lagoons. Older dolomites (<3000 yrs.) taken from cores recovered from the lagoon are much closer to equilibrium. We interpret our data as evidencing an initial microbial mediated nucleation of dolomite that is a kinetic process and a subsequent inorganic addition of dolomite overprinting an equilibrium signature. This is in agreement with a previous major element and crystallographic study of the Brazilian dolomites [1]. The ancient dolomites analysed range in age from Neoproterozoic to Pleistocene and come from diverse geological environments including submarine diagenetic zones, platform carbonates and lagoonal environments. Magnesium isotopic analysis shows evidence of a varying component of kinetic fractionation, smaller than the kinetic end member as typified by the laboratory cultures. The ancient dolomites appear to evidence the same initial kinetic nucleation and subsequent equilibrium growth as the modern. In contrast, hydrothermal dolomite exhibits only equilibrium fractionation. Taken together, our results argue for a strong biological role in magnesium fixation into sedimentary dolomite in both the ancient and modern and suggest microbial processes are important in resolving the `Dolomite Problem'. References [1] Vasconcelos, C. and McKenzie, J.A., (1997), J. Sed. Res., 67, 378-390. [2] Vasconcelos, C., McKenzie, J.A., Bernasconi, S., Grujic, D. and Tien, A.J., (1995), Nature 377, 220-222. [3] Warthmann R., van Lith Y., Vasconcelos C., McKenzie J.A. and Karpoff A.M., (2000), Geology 28, 1091-1094.

Quantitative Relationships between Photosynthetic, Nitrogen Fixing, and Fermentative H2 Metabolism in a Photosynthetic Microbial Mat

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Albert, Daniel B.; Bebout, Brad M.; Turk, Kendra A.; DesMarais, David J.

2004-01-01

The ultimate potential of any microbial ecosystem to contribute chemically to its environment - and therefore, to impact planetary biogeochemistry or to generate recognizable biosignatures - depends not only on the individual metabolic capabilities of constituent organisms, but also on how those capabilities are expressed through interactions with neighboring organisms. This is particularly important for microbial mats, which compress an extremely broad range of metabolic potential into a small and dynamic system. H2 participates in many of these metabolic processes, including the major elemental cycling processes of photosynthesis, nitrogen fixation, sulfate reduction, and fermentation, and may therefore serve as a mediator of microbial interactions within the mat system. Collectively, the requirements of energy, electron transfer, and biomass element stoichiometry suggest quantitative relationships among the major element cycling processes, as regards H2 metabolism We determined experimentally the major contributions to 32 cycling in hypersaline microbial mats from Baja California, Mexico, and compared them to predicted relationships. Fermentation under dark, anoxic conditions is quantitatively the most important mechanism of H2 production, consistent with expectations for non-heterocystous mats such as those under study. Up to 16% of reducing equivalents fixed by photosynthesis during the day may be released by this mechanism. The direct contribution of nitrogen fixation to H2 production is small in comparison, but this process may indirectly stimulate substantial H2 generation, by requiring higher rates of fermentation. Sulfate reduction, aerobic consumption, diffusive and ebulitive loss, and possibly H2-based photoreduction of CO2 serve as the principal H2 sinks. Collectively, these processes interact to create an orders-of-magnitude daily variation in H2 concentrations and fluxes, and thereby in the oxidation-reduction potential that is imposed on microbial processes occuring within the mat matrix.

Metagenomic insights into zooplankton‐associated bacterial communities

PubMed Central

Srivastava, Abhishek; Koski, Marja; Garcia, Juan Antonio L.; Takaki, Yoshihiro; Yokokawa, Taichi; Nunoura, Takuro; Elisabeth, Nathalie H.; Sintes, Eva; Herndl, Gerhard J.

2017-01-01

Summary Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton‐associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton‐associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton‐associated microbiome suggests that this zooplankton‐associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. PMID:28967193

Electricity Generation in Microbial Fuel Cells Using Neutral Red as an Electronophore

PubMed Central

Park, Doo Hyun; Zeikus, J. Gregory

2000-01-01

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. In microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator (3.5 mA) was 10-fold more than the amount produced when thionin was the electron mediator (0.4 mA). The amount of electrical energy generated (expressed in joules per mole of substrate) and the amount of current produced from glucose (expressed in milliamperes) in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge (i.e., a mixed culture of anaerobic bacteria) was used in the fuel cell, stable (for 120 h) and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Our results are discussed in relation to factors that may improve the relatively low electrical efficiencies (1.2 kJ/mol) obtained with microbial fuel cells. PMID:10742202

Molecular characterization of biochars and their influence on microbiological properties of soil

USDA-ARS?s Scientific Manuscript database

The composition and surface chemistry of carbon rich biochar materials is highly uncertain and believed to change with feedstock and biomass conversion process. The tentative connection between the biochar surface chemical properties and their influence on microbially mediated mineralization of C, N...

Process for Biotransformation of Androsta-4-ene-3, 17-Dione (4-AD) to Androsta-1,4-Diene-3,17-Dione (ADD).

PubMed

Prakash, Surya; Bajaj, Abhay

2017-01-01

Androsta-1,4-diene-3,17-dione (androstadienedione, ADD) is key intermediate for the organic synthesis of a variety of female sex hormones such as estrone, estradiol, estriol and other related derivatives. De novo synthesis of this molecule is not yet reported in any form of living system, i.e., microbial, plant, and animal. The structural complexities due to presence of several chiral carbon centers create significant hurdles in chemical synthesis of such molecules. Microbe-mediated biotransformation offer a highly reliable, cost-effective, and relatively non hazardous way for commercial manufacturing of steroidal key intermediates. Currently microbial biotransformations are extensively being exploited for large-scale production of basic intermediates such as androstenedione (AD), ADD, and several types of hydroxylated derivatives of androstane compounds. In this chapter several aspects of microbial biotransformation process of AD to ADD are discussed.

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

Geomicrobiological redox cycling of the transuranic element neptunium.

PubMed

Law, Gareth T W; Geissler, Andrea; Lloyd, Jonathan R; Livens, Francis R; Boothman, Christopher; Begg, James D C; Denecke, Melissa A; Rothe, Jörg; Dardenne, Kathy; Burke, Ian T; Charnock, John M; Morris, Katherine

2010-12-01

Microbial processes can affect the environmental behavior of redox sensitive radionuclides, and understanding these reactions is essential for the safe management of radioactive wastes. Neptunium, an alpha-emitting transuranic element, is of particular importance because of its long half-life, high radiotoxicity, and relatively high solubility as Np(V)O(2)(+) under oxic conditions. Here, we describe experiments to explore the biogeochemistry of Np where Np(V) was added to oxic sediment microcosms with indigenous microorganisms and anaerobically incubated. Enhanced Np removal to sediments occurred during microbially mediated metal reduction, and X-ray absorption spectroscopy showed this was due to reduction to poorly soluble Np(IV) on solids. In subsequent reoxidation experiments, sediment-associated Np(IV) was somewhat resistant to oxidative remobilization. These results demonstrate the influence of microbial processes on Np solubility and highlight the critical importance of radionuclide biogeochemistry in nuclear legacy management.

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

Reactor performances and microbial communities of biogas reactors: effects of inoculum sources.

PubMed

Han, Sheng; Liu, Yafeng; Zhang, Shicheng; Luo, Gang

2016-01-01

Anaerobic digestion is a very complex process that is mediated by various microorganisms, and the understanding of the microbial community assembly and its corresponding function is critical in order to better control the anaerobic process. The present study investigated the effect of different inocula on the microbial community assembly in biogas reactors treating cellulose with various inocula, and three parallel biogas reactors with the same inoculum were also operated in order to reveal the reproducibility of both microbial communities and functions of the biogas reactors. The results showed that the biogas production, volatile fatty acid (VFA) concentrations, and pH were different for the biogas reactors with different inocula, and different steady-state microbial community patterns were also obtained in different biogas reactors as reflected by Bray-Curtis similarity matrices and taxonomic classification. It indicated that inoculum played an important role in shaping the microbial communities of biogas reactor in the present study, and the microbial community assembly in biogas reactor did not follow the niche-based ecology theory. Furthermore, it was found that the microbial communities and reactor performances of parallel biogas reactors with the same inoculum were different, which could be explained by the neutral-based ecology theory and stochastic factors should played important roles in the microbial community assembly in the biogas reactors. The Bray-Curtis similarity matrices analysis suggested that inoculum affected more on the microbial community assembly compared to stochastic factors, since the samples with different inocula had lower similarity (10-20 %) compared to the samples from the parallel biogas reactors (30 %).

Dominance of Saccharomyces cerevisiae in alcoholic fermentation processes: role of physiological fitness and microbial interactions.

PubMed

Albergaria, Helena; Arneborg, Nils

2016-03-01

Winemaking, brewing and baking are some of the oldest biotechnological processes. In all of them, alcoholic fermentation is the main biotransformation and Saccharomyces cerevisiae the primary microorganism. Although a wide variety of microbial species may participate in alcoholic fermentation and contribute to the sensory properties of end-products, the yeast S. cerevisiae invariably dominates the final stages of fermentation. The ability of S. cerevisiae to outcompete other microbial species during alcoholic fermentation processes, such as winemaking, has traditionally been ascribed to its high fermentative power and capacity to withstand the harsh environmental conditions, i.e. high levels of ethanol and organic acids, low pH values, scarce oxygen availability and depletion of certain nutrients. However, in recent years, several studies have raised evidence that S. cerevisiae, beyond its remarkable fitness for alcoholic fermentation, also uses defensive strategies mediated by different mechanisms, such as cell-to-cell contact and secretion of antimicrobial peptides, to combat other microorganisms. In this paper, we review the main physiological features underlying the special aptitude of S. cerevisiae for alcoholic fermentation and discuss the role of microbial interactions in its dominance during alcoholic fermentation, as well as its relevance for winemaking.

Microbial and diagenetic steps leading to the mineralisation of Great Salt Lake microbialites

NASA Astrophysics Data System (ADS)

Pace, Aurélie; Bourillot, Raphaël; Bouton, Anthony; Vennin, Emmanuelle; Galaup, Serge; Bundeleva, Irina; Patrier, Patricia; Dupraz, Christophe; Thomazo, Christophe; Sansjofre, Pierre; Yokoyama, Yusuke; Franceschi, Michel; Anguy, Yannick; Pigot, Léa; Virgone, Aurélien; Visscher, Pieter T.

2016-08-01

Microbialites are widespread in modern and fossil hypersaline environments, where they provide a unique sedimentary archive. Authigenic mineral precipitation in modern microbialites results from a complex interplay between microbial metabolisms, organic matrices and environmental parameters. Here, we combined mineralogical and microscopic analyses with measurements of metabolic activity in order to characterise the mineralisation of microbial mats forming microbialites in the Great Salt Lake (Utah, USA). Our results show that the mineralisation process takes place in three steps progressing along geochemical gradients produced through microbial activity. First, a poorly crystallized Mg-Si phase precipitates on alveolar extracellular organic matrix due to a rise of the pH in the zone of active oxygenic photosynthesis. Second, aragonite patches nucleate in close proximity to sulfate reduction hotspots, as a result of the degradation of cyanobacteria and extracellular organic matrix mediated by, among others, sulfate reducing bacteria. A final step consists of partial replacement of aragonite by dolomite, possibly in neutral to slightly acidic porewater. This might occur due to dissolution-precipitation reactions when the most recalcitrant part of the organic matrix is degraded. The mineralisation pathways proposed here provide pivotal insight for the interpretation of microbial processes in past hypersaline environments.

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.

The importance of plant-soil interactions for N mineralisation in different soil types

NASA Astrophysics Data System (ADS)

Murphy, Conor; Paterson, Eric; Baggs, Elizabeth; Morley, Nicholas; Wall, David; Schulte, Rogier

2013-04-01

The last hundred years has seen major advancements in our knowledge of nitrogen mineralisation in soil, but key drivers and controls remain poorly understood. Due to an increase in the global population there is a higher demand on food production. To accommodate this demand agriculture has increased its use of N based fertilizers, but these pose risks for water quality and GHG emissions as N can be lost through nitrate leaching, ammonia volatilization, and denitrification processes (Velthof, et al., 2009). Therefore, understanding the underlying processes that determine the soils ability to supply N to the plant is vital for effective optimisation of N-fertilisation with crop demand. Carbon rich compounds exuded from plant roots to the rhizosphere, which are utilized by the microbial biomass and support activities including nutrient transformations, may be a key unaccounted for driver of N mineralisation. The main aim of this study was to study the impact of root exudates on turnover of C and N in soil, as mediated by the microbial community. Two soil types, known to contrast in N-mineralisation capacity, were used to determine relationships between C inputs, organic matter mineralisation (priming effects) and N fluxes. 15N and 13C stable isotope approaches were used to quantify the importance of rhizosphere processes on C and N mineralisation. Gross nitrogen mineralisation was measured using 15N pool dilution. Total soil CO2 efflux was measured and 13C isotope partitioning was applied to quantify SOM turnover and microbial biomass respiration. Also, 13C was traced through the microbial biomass (chloroform fumigation) to separate pool-substitution effects (apparent priming) from altered microbial utilisation of soil organic matter (real priming effects). Addition of labile carbon resulted in an increase in N-mineralisation from soil organic matter in both soils. Concurrent with this there was an increase in microbial biomass size, indicating that labile C elicited real priming effects that mobilised N from organic matter. The results from this experiment indicate that rhizosphere processes play an important role in mediating rates of C and N mineralisation and should be accounted for in estimating soil N-supply capacities. Velthof, G.L., Oudendag, D., Witzke, H.P., Asman, W.A.H., Klimont, Z., Oenema, O., 2009. Integrated assessment of nitrogen losses from agriculture in EU-27 using MITERRA-EUROPE. Journal of Environmental Quality 38, 402-417.

Microbial Fe biomineralization in mafic and ultramafic rocks

NASA Astrophysics Data System (ADS)

Templeton, A. S.; Mayhew, L.; McCollom, T.; Trainor, T.

2011-12-01

Fluid-filled microfractures within mafic and ultramafic rocks, such as basalt and peridotite, may be one of the most ubiquitous microbial habitats on the modern and ancient earth. In seafloor and subseafloor systems, one of the dominant energy sources is the oxidation of Fe by numerous potential oxidants under aerobic to anaerobic conditions. In particular, the oxidation of Fe may be directly catalyzed by microbial organisms, or result in the production of molecular hydrogen which can then fuel diverse lithotrophic metabolisms. However, it remains challenging to identify the dominant metabolic activities and unravel the microscale biogeochemical processes occuring within such rock-hosted systems. We are investigating the mechanisms of solid-state Fe-oxidation and biomineralization in basalt, olivine, pyroxenes and basalts, in the presence and absence of microbial organisms that can thrive across the full stability range of water. In this talk we will present synchrotron-based x-ray scattering and spectroscopic analyses of Fe speciation within secondary minerals formed during microbially-mediated vs. abiotic water-rock interactions. Determining the valence state and mineralogy of Fe-bearing phases is critical for determining the water-rock reaction pathways and identifying potential biominerals that may form; therefore, we will highlight new approaches for identifying key Fe transformations within complex geological media. In addition, many of our experimental studies involve the growth of lithotrophic biofilms on well-characterized mineral surfaces in order to determine the chemistry of the microbe-mineral interface during progressive electron-transfer reactions. By coupling x-ray spectroscopy, x-ray diffraction, and electron-microscopy measurements, we will also contrast the evolution of mineral surfaces that undergo microbially-mediated oxidative alteration against minerals surfaces that produce H2 to sustain anaerobic microbial communities.

Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.

PubMed

Ni, Gaofeng; Christel, Stephan; Roman, Pawel; Wong, Zhen Lim; Bijmans, Martijn F M; Dopson, Mark

2016-09-01

Sulfide mineral processing often produces large quantities of wastewaters containing acid-generating inorganic sulfur compounds. If released untreated, these wastewaters can cause catastrophic environmental damage. In this study, microbial fuel cells were inoculated with acidophilic microorganisms to investigate whether inorganic sulfur compound oxidation can generate an electrical current. Cyclic voltammetry suggested that acidophilic microorganisms mediated electron transfer to the anode, and that electricity generation was catalyzed by microorganisms. A cation exchange membrane microbial fuel cell, fed with artificial wastewater containing tetrathionate as electron donor, reached a maximum whole cell voltage of 72 ± 9 mV. Stepwise replacement of the artificial anolyte with real mining process wastewater had no adverse effect on bioelectrochemical performance and generated a maximum voltage of 105 ± 42 mV. 16S rRNA gene sequencing of the microbial consortia resulted in sequences that aligned within the genera Thermoplasma, Ferroplasma, Leptospirillum, Sulfobacillus and Acidithiobacillus. This study opens up possibilities to bioremediate mining wastewater using microbial fuel cell technology. Copyright © 2016 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

NASA Astrophysics Data System (ADS)

Wang, G.; Mayes, M. A.; Gu, L.; Schadt, C. W.

2013-12-01

Experimental observations and modeling efforts have shown that dormancy is likely a common strategy for microorganisms to contend with environmental stress. We review the state-of-the-art in modeling approaches for microbial dormancy and discuss the rationales of these models. We proved that the physiological state index model is not appropriate for describing transformation between active and dormant states. Based on the generally accepted assumptions summarized from ten existing models, we postulated a new synthetic microbial physiology component within the Microbial-ENzyme-mediated Decomposition (MEND) model. Both the steady state active fraction (rss) and substrate saturation level (Øss) positively depend on two physiological indices: α and β. The index α = mR /(μG+ mR), where μG and mR represent the maximum specific growth and maintenance rates, respectively, for active microbes. β denotes the ratio of dormant to active maintenance rate. The rss equals to Øss only under the condition of β→0, and they are identical to α. When substrate availability is the only limiting factor, the maximum rss is ca. 0.5 with α≤0.5 and β ≤0.01. This threshold value (0.5) of rss (not dynamic r) can explain the low active microbial fractions observed in undisturbed soils. The applications of the improved model to a 14C-labeled glucose induced respiration dataset and a batch experimental dataset show satisfactory model performance. We found that the exponential growth respiration rates can only be used to determine μG and initial active microbial biomass (Ba0), thus we suggest using respiration data representing both exponential growth and non-accelerating phases to robustly determine other important parameters such as initial total live microbial biomass (B0), initial active fraction (r0), μG, α, and the half-saturation constant (Ks). Similar improved representations of microbial physiology should be incorporated into existing ecosystem models in order to account for the significance of dormancy in microbially-mediated processes.

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

PubMed Central

Lesniewski, Ryan A; Jain, Sunit; Anantharaman, Karthik; Schloss, Patrick D; Dick, Gregory J

2012-01-01

Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3–4 times) and microbially mediated manganese oxidation rates (15–125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10–20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California. PMID:22695860

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs.

PubMed

Lesniewski, Ryan A; Jain, Sunit; Anantharaman, Karthik; Schloss, Patrick D; Dick, Gregory J

2012-12-01

Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3-4 times) and microbially mediated manganese oxidation rates (15-125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10-20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California.

THE NEAR-EQUILIBRIUM OF MICROBIALLY MEDIATED REDOX COUPLES IN REDUCING GROUNDWATER ENVIRONMENTS

EPA Science Inventory

Redox couples are commonly held to be in disequilibrium among each other in most natural waters. To evaluate this view for microbially mediated, reducing, groundwater environments, monitoring data were examined for several couples under conditions ranging from nitrate-detectable...

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

PubMed

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

2015-08-20

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

Advanced Chemical Design for Efficient Lignin Bioconversion

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

Xie, Shangxian; Sun, Qining; Pu, Yunqiao

Here, lignin depolymerization mainly involves redox reactions relying on the effective electron transfer. Even though electron mediators were previously used for delignification of paper pulp, no study has established a bioprocess to fragment and solubilize the lignin with an effective laccase–mediator system, in particular, for subsequent microbial bioconversion. Efficient lignin depolymerization was achieved by screening proper electron mediators with laccase to attain a nearly 6-fold increase of kraft lignin solubility compared to the control kraft lignin without laccase treatment. Chemical analysis suggested the release of a low molecular weight fraction of kraft lignin into the solution phase. Moreover, NMR analysismore » revealed that an efficient enzyme–mediator system can promote the lignin degradation. More importantly, the fundamental mechanisms guided the development of an efficient lignin bioconversion process, where solubilized lignin from laccase–HBT treatment served as a superior substrate for bioconversion by Rhodococcus opacus PD630. The cell growth was increased by 10 6 fold, and the lipid titer reached 1.02 g/L. Overall, the study has manifested that an efficient enzyme–mediator–microbial system can be exploited to establish a bioprocess to solubilize lignin, cleave lignin linkages, modify the structure, and produce substrates amenable to bioconversion.« less

Advanced Chemical Design for Efficient Lignin Bioconversion

DOE PAGES

Xie, Shangxian; Sun, Qining; Pu, Yunqiao; ...

2017-01-30

Here, lignin depolymerization mainly involves redox reactions relying on the effective electron transfer. Even though electron mediators were previously used for delignification of paper pulp, no study has established a bioprocess to fragment and solubilize the lignin with an effective laccase–mediator system, in particular, for subsequent microbial bioconversion. Efficient lignin depolymerization was achieved by screening proper electron mediators with laccase to attain a nearly 6-fold increase of kraft lignin solubility compared to the control kraft lignin without laccase treatment. Chemical analysis suggested the release of a low molecular weight fraction of kraft lignin into the solution phase. Moreover, NMR analysismore » revealed that an efficient enzyme–mediator system can promote the lignin degradation. More importantly, the fundamental mechanisms guided the development of an efficient lignin bioconversion process, where solubilized lignin from laccase–HBT treatment served as a superior substrate for bioconversion by Rhodococcus opacus PD630. The cell growth was increased by 10 6 fold, and the lipid titer reached 1.02 g/L. Overall, the study has manifested that an efficient enzyme–mediator–microbial system can be exploited to establish a bioprocess to solubilize lignin, cleave lignin linkages, modify the structure, and produce substrates amenable to bioconversion.« less

Strain- and Substrate-Dependent Redox Mediator and Electricity Production by Pseudomonas aeruginosa.

PubMed

Bosire, Erick M; Blank, Lars M; Rosenbaum, Miriam A

2016-08-15

Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm(-2) with ∼150 μg ml(-1) phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions. Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an entire microbial community to access a solid electrode as an alternative electron acceptor. To better understand the ecological relationships between mediator producers and mediator utilizers, we here present a comparison of the phenazine-dependent electroactivities of three Pseudomonas strains. This work forms the foundation for more complex coculture investigations of mediated electron transfer in microbial fuel cells. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Strain- and Substrate-Dependent Redox Mediator and Electricity Production by Pseudomonas aeruginosa

PubMed Central

Bosire, Erick M.; Blank, Lars M.

2016-01-01

ABSTRACT Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa. We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm−2 with ∼150 μg ml−1 phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions. IMPORTANCE Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an entire microbial community to access a solid electrode as an alternative electron acceptor. To better understand the ecological relationships between mediator producers and mediator utilizers, we here present a comparison of the phenazine-dependent electroactivities of three Pseudomonas strains. This work forms the foundation for more complex coculture investigations of mediated electron transfer in microbial fuel cells. PMID:27287325

Activation and Resolution of Periodontal Inflammation and Its Systemic Impact

PubMed Central

Hasturk, Hatice; Kantarci, Alpdogan

2015-01-01

Inflammation is a highly organized event impacting upon organs, tissues and biological systems. Periodontal diseases are characterized by dysregulation or dysfunction of resolution pathways of inflammation resulting in a failure of healing and a dominant chronic, progressive, destructive and predominantly unresolved inflammation. The biological consequences of inflammatory processes may be independent of the etiological agents such as trauma, microbial organisms and stress. The impact of the inflammatory pathological process depends upon the affected tissues or organ system. Whilst mediators are similar, there is a tissue specificity for the inflammatory events. It is plausible that inflammatory processes in one organ could directly lead to pathologies in another organ or tissue. Communication between distant parts of the body and their inflammatory status is also mediated by common signaling mechanisms mediated via cells and soluble mediators. This review focuses on periodontal inflammation, its systemic associations and advances in therapeutic approaches based on mediators acting through orchestration of natural pathway to resolution of inflammation. We also discuss a new treatment concept where natural pathways of resolution of periodontal inflammation can be used to limit systemic inflammation and promote healing and regeneration. PMID:26252412

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

PubMed Central

Momeni, Babak; Xie, Li; Shou, Wenying

2017-01-01

Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

Quorum sensing is a language of chemical signals and plays an ecological role in algal-bacterial interactions

PubMed Central

Zhou, Jin; Lyu, Yihua; Richlen, Mindy; Anderson, Donald M.; Cai, Zhonghua

2017-01-01

Algae are ubiquitous in the marine environment, and the ways in which they interact with bacteria are of particular interest in marine ecology field. The interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape microbial diversity. Although algal-bacterial interactions are well known and studied, information regarding the chemical-ecological role of this relationship remains limited, particularly with respect to quorum sensing (QS), which is a system of stimuli and response correlated to population density. In the microbial biosphere, QS is pivotal in driving community structure and regulating behavioral ecology, including biofilm formation, virulence, antibiotic resistance, swarming motility, and secondary metabolite production. Many marine habitats, such as the phycosphere, harbour diverse populations of microorganisms and various signal languages (such as QS-based autoinducers). QS-mediated interactions widely influence algal-bacterial symbiotic relationships, which in turn determine community organization, population structure, and ecosystem functioning. Understanding infochemicals-mediated ecological processes may shed light on the symbiotic interactions between algae host and associated microbes. In this review, we summarize current achievements about how QS modulates microbial behavior, affects symbiotic relationships, and regulates phytoplankton chemical ecological processes. Additionally, we present an overview of QS-modulated co-evolutionary relationships between algae and bacterioplankton, and consider the potential applications and future perspectives of QS. PMID:28966438

Fire effects on belowground sustainability: A review and synthesis

Treesearch

Daniel G. Neary; Carole C. Klopatek; Leonard F. DeBano; Peter F. Ffolliott

1999-01-01

The overall effects of the fire on ecosystems are complex, ranging from the reduction or elimination of aboveground biomass to impacts on belowground physical, chemical and microbial mediated processes. Since a key component of overall ecosystem sustainability occurs belowground, recovery is tied to the soil's physical, chemical, and biological functions and...

Evidence for polyphosphate accumulating organism (PAO)-mediated phosphorus cycling in stream biofilms under alternating aerobic/anaerobic conditions

USDA-ARS?s Scientific Manuscript database

Phosphorus (P) is often a limiting nutrient in freshwater ecosystems and excessive inputs can lead to eutrophication. In-stream cycling of P involves complex biological, chemical, and physical processes that are not fully understood. Microbial metabolisms are suspected to control oxygen-dependent up...

Seasonal and spatial patterns in coupled nitrification-denitrification rates in a large Great Lakes coastal system: The St. Louis River Estuary

EPA Science Inventory

Anthropogenic inputs of excess nitrogen (N) to aquatic systems are detrimental, but aquatic plants and sediments have the potential to mitigate N-loading. Sediment processes are driven by microbially mediated N-cycling. Coastal embayments purportedly play a significant role in N-...

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.

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

The mechanism of neutral red-mediated microbial electrosynthesis in Escherichia coli: menaquinone reduction

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

Harrington, Timothy D.; Tran, Vi N.; Mohamed, Abdelrhman

The aim of this work was to elucidate the mechanism of mediated microbial electrosynthesis via neutral red from an electrode to fermenting Escherichia coli cultures in a bioelectrochemical system. Chemical reduction of NAD+ by reduced neutral red did not occur as predicted. Instead, neutral red was shown to reduce the menaquinone pool in the inner bacterial membrane. The reduced menaquinone pool altered fermentative metabolite production via the arcB redox-sensing cascade in the absence of terminal electron acceptors. When the acceptors DMSO, fumarate, or nitrate were provided, as many as 19% of the electrons trapped in the reduced acceptors were derivedmore » from the electrode. These results demonstrate the mechanism of neutral red-mediated microbial electrosynthesis during fermentation as well as how neutral red enables microbial electrosynthesis of reduced terminal electron acceptors.« less

Microbial secondary metabolites and their impacts on insect symbioses.

PubMed

Klassen, Jonathan L

2014-10-01

All insects host communities of microbes that interact both with the insect and each other. Secondary metabolites are understood to mediate many of these interactions, although examples having robust genetic, chemical and/or ecological evidence are relatively rare. Here, I review secondary metabolites mediating community interactions in the beewolf, entomopathogenic nematode and fungus-growing ant symbioses, using the logic of Koch's postulates to emphasize well-validated symbiotic functions mediated by these metabolites. I especially highlight how these interaction networks are structured by both ecological and evolutionary processes, and how selection acting on secondary metabolite production can be multidimensional. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

Plant-soil-microbe interactions regulating soil C storage

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.

2016-12-01

Integration across disciplines is required to identify the emergent microbial scale properties that regulate the release or occlusion of plant inputs in soil organic matter. To investigate how micro-scale processes influence soil carbon cycling, we measured microbial community composition and activity within soil aggregates monthly over two growing seasons of a long-term bioenergy field experiment. Using a biologically sensitive sieving technique, soil aggregates were isolated and microbial community activity and composition were measured. This aggregate approach revealed biogeochemical processes regulating C cycling that are not detected using whole soil approaches. Soil aggregation influenced microbe-substrate interactions, where diversified perennial grassland systems supported greater aggregation and reduced severity of aggregate turnover compared to corn systems. Aggregate turnover and concurrent increases in activity resulted in greater microbial biomass and physical protection of soil organic matter in prairie systems, especially fertilized prairies. Fertilized prairie enhanced microbial biomass, enzyme activity, and soil aggregation despite greater root biomass in unfertilized prairie. Independent of ecosystem or sampling date, N-acetyl-glucosaminidase activity and Nitrospirae abundance was greatest in large macroaggregates (>2000 µm), which harbored the highest C:N; cellobiohydrolase activity and Acidobacteria abundance was greatest in microaggregates (<250 µm) which had the lowest C:N. Aggregate fractions differed in microbial community composition (bacteria, archaea, and fungi) and potential enzyme activity, independent of cropping system. Microaggregates harbored significantly greater microbial diversity and richness across all bioenergy cropping systems. Together these results suggest that by mediating access to substrates, soil structure (aggregates) can influence the microbial community composition and extracellular enzyme activity to regulate ecosystem scale decomposition of soil organic matter.

Live microbial cells adsorb Mg2+ more effectively than lifeless organic matter

NASA Astrophysics Data System (ADS)

Qiu, Xuan; Yao, Yanchen; Wang, Hongmei; Duan, Yong

2018-03-01

The Mg2+ content is essential in determining different Mg-CaCO3 minerals. It has been demonstrated that both microbes and the organic matter secreted by microbes are capable of allocating Mg2+ and Ca2+ during the formation of Mg-CaCO3, yet detailed scenarios remain unclear. To investigate the mechanism that microbes and microbial organic matter potentially use to mediate the allocation of Mg2+ and Ca2+ in inoculating systems, microbial mats and four marine bacterial strains ( Synechococcus elongatus, Staphylococcus sp., Bacillus sp., and Desulfovibrio vulgaris) were incubated in artificial seawater media with Mg/Ca ratios ranging from 0.5 to 10.0. At the end of the incubation, the morphology of the microbial mats and the elements adsorbed on them were analyzed using scanning electronic microscopy (SEM) and energy diffraction spectra (EDS), respectively. The content of Mg2+ and Ca2+ adsorbed by the extracellular polysaccharide substances (EPS) and cells of the bacterial strains were analyzed with atomic adsorption spectroscopy (AAS). The functional groups on the surface of the cells and EPS of S. elongatus were estimated using automatic potentiometric titration combined with a chemical equilibrium model. The results show that live microbial mats generally adsorb larger amounts of Mg2+ than Ca2+, while this rarely is the case for autoclaved microbial mats. A similar phenomenon was also observed for the bacterial strains. The living cells adsorb more Mg2+ than Ca2+, yet a reversed trend was observed for EPS. The functional group analysis indicates that the cell surface of S. elongatus contains more basic functional groups (87.24%), while the EPS has more acidic and neutral functional groups (83.08%). These features may be responsible for the different adsorption behavior of Mg2+ and Ca2+ by microbial cells and EPS. Our work confirms the differential Mg2+ and Ca2+ mediation by microbial cells and EPS, which may provide insight into the processes that microbes use to induce Mg-carbonate formation.

Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM).

PubMed

Behrens, Sebastian; Kappler, Andreas; Obst, Martin

2012-11-01

Environmental microbiology research increasingly focuses on the single microbial cell as the defining entity that drives environmental processes. The interactions of individual microbial cells with each other, the environment and with higher organisms shape microbial communities and control the functioning of whole ecosystems. A single-cell view of microorganisms in their natural environment requires analytical tools that measure both cell function and chemical speciation at the submicrometre scale. Here we review the technical capabilities and limitations of high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission (soft) X-ray microscopy (STXM) and give examples of their applications. Whereas NanoSIMS can be combined with isotope-labelling, thereby localizing the distribution of cellular activities (e.g. carbon/nitrogen fixation/turnover), STXM provides information on the location and chemical speciation of metabolites and products of redox reactions. We propose the combined use of both techniques and discuss the technical challenges of their joint application. Both techniques have the potential to enhance our understanding of cellular mechanisms and activities that contribute to microbially mediated processes, such as the biogeochemical cycling of elements, the transformation of contaminants and the precipitation of mineral phases. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

The Effect Of microbial Mats In The Decay Of Anurans With Implications For Understanding Taphonomic Processes In The Fossil Record

PubMed Central

Iniesto, M.; Villalba, I.; Buscalioni, A. D.; Guerrero, M. C.; López-Archilla, A. I.

2017-01-01

The pattern and sequence of the decomposition of the Pipidae African dwarf frog (Hymenochirus boettgeri) is tracked in an experiment with microbial mats in order to explore soft tissue preservation over three years. Frog decay in microbial mats is preceded by rapid entombment (25–30 days) and mediated by the formation of a sarcophagus, which is built by a complex microbial community. The frog carcasses maintained a variety of soft tissues for years. Labile organic structures show greater durability within the mat, cells maintain their general shape (bone marrow cells and adipocytes), and muscles and connective tissues (adipose and fibrous tendons) exhibit their original organic structures. In addition, other soft tissues are promptly mineralized (day 540) in a Ca-rich carbonate phase (encephalic tectum) or enriched in sulphur residues (integumentary system). The result is coherent with a bias in soft-tissue preservation, as some tissues are more likely to be conserved than others. The outcomes support observations of exceptionally preserved fossil anurans (adults and tadpoles). Decomposition in mats shows singular conditions of pH and dissolved oxygen. Mineralization processes could be more diverse than in simple heterotrophic biofilms, opening new taphonomic processes that have yet to be explored. PMID:28338095

Mess management in microbial ecology: Rhetorical processes of disciplinary integration

NASA Astrophysics Data System (ADS)

McCracken, Christopher W.

As interdisciplinary work becomes more common in the sciences, research into the rhetorical processes mediating disciplinary integration becomes more vital. This dissertation, which takes as its subject the integration of microbiology and ecology, combines a postplural approach to rhetoric of science research with Victor Turner's "social drama" analysis and a third-generation activity theory methodological framework to identify conceptual and practical conflicts in interdisciplinary work and describe how, through visual and verbal communication, scientists negotiate these conflicts. First, to understand the conflicting disciplinary principles that might impede integration, the author conducts a Turnerian analysis of a disciplinary conflict that took place in the 1960s and 70s, during which American ecologists and biologists debated whether they should participate in the International Biological Program (IBP). Participation in the IBP ultimately contributed to the emergence of ecology as a discipline distinct from biology, and Turnerian social drama analysis of the debate surrounding participation lays bare the conflicting principles separating biology and ecology. Second, to answer the question of how these conflicting principles are negotiated in practice, the author reports on a yearlong qualitative study of scientists working in a microbial ecology laboratory. Focusing specifically on two case studies from this fieldwork that illustrate the key concept of textually mediated disciplinary integration, the author's analysis demonstrates how scientific objects emerge in differently situated practices, and how these objects manage to cohere despite their multiplicity through textually mediated rhetorical processes of calibration and alignment.

Microbial Life Driving Low-Temperature Basalt Alteration in the Subsurface: Decoupling Abiotic Processes from Biologically-Mediated Rock Alteration

NASA Astrophysics Data System (ADS)

Moore, R.; Lecoeuvre, A.; Stephant, S.; Dupraz, S.; Ranchou-Peyruse, M.; Ranchou-Peyruse, A.; Gérard, E.; Ménez, B.

2017-12-01

Microorganisms are involved with specific rock alteration processes in the deep subsurface. It is a challenge to link any contribution microbial life may have on rock alteration with specific functions or phyla because many alteration features and secondary minerals produced by metabolic processes can also produce abiotically. Here, two flow-through experiments were designed to mimic the circulation of a CO2-rich fluid through crystalline basalt. In order to identify microbially-mediated alteration and be able to link it with specific metabolisms represented in the subsurface, a relatively fresh crystalline basalt substrate was subsampled, sterilized and used as the substrate for both experiments. In one experiment, the substrate was left sterile, and in the other it was inoculated with an enrichment culture derived from the same aquifer as the rock substrate. Initial results show that the inoculum contained Proteobacteria and Firmicutes, which have diverse metabolic potentials. Fluid and rock analyses before, during, and after the experiments show that mineralogy, fluid chemistry, and dissolution processes differ between the sterile and inoculated systems. In the inoculated experiment iron-rich orthopyroxenes were preferentially dissolved while in the sterile system clinopyroxenes and plagioclases both exhibited a higher degree of dissolution. Additionally, the patterns of CO2 consumption and production over the duration of both experiments is different. This suggest that in a low-temperature basalt system with microorganisms CO2 is either consumed to produce biomass, or that carbonates are produced and then subsequently preserved. This suite of results combined with molecular ecology analyses can be used to conclude that in low-temperature basalts microorganisms play an intrinsic role in rock alteration.

Phytoremediation of trichloroethene (TCE) using cottonwood trees

USGS Publications Warehouse

Jones, S.A.; Lee, R.W.; Kuniansky, E.L.; Leeson, Andrea; Alleman, Bruce C.

1999-01-01

Phytoremediation uses the natural ability of plants to degrade contaminants in ground water. A field demonstration designed to remediate aerobic shallow ground water that contains trichloroethene began in April 1996 with the planting of cottonwood trees over an approximately 0.2-hectare area at the Naval Air Station, Fort Worth, Tx. Ground water was sampled in July 1997, November 1997, February 1998, and June 1998. Analyses from samples indicate that tree roots have the potential to create anaerobic conditions in the ground water that will facilitate degradation of trichloroethene by microbially mediated reductive dichlorination. Dissolved oxygen concentrations, which varied across the site, were smallest near a mature cottonwood tree (about-20 years old) 60 meters southwest of the cottonwood plantings. Reduction of dissolved oxygen is the primary microbially mediated reaction occurring in the ground water beneath the planted trees, whereas near the mature cottonwood tree, data indicate that methanogenesis is the most probable reaction occurring. Reductive dichlorination either is not occurring or is not a primary process away from the mature tree. On the basis of isotopic analyses of carbon-13 at locations away from the mature tree, trichloroethene concentration is controlled by volatilization.Phytoremediation uses the natural ability of plants to degrade contaminants in ground water. A field demonstration designed to remediate aerobic shallow ground water that contains trichloroethene began in April 1996 with the planting of cottonwood trees over an approximately 0.2-hectare area at the Naval Air Station, Fort Worth, Tx. Ground water was sampled in July 1997, November 1997, February 1998, and June 1998. Analyses from samples indicate that tree roots have the potential to create anaerobic conditions in the ground water that will facilitate degradation of trichloroethene by microbially mediated reductive dichlorination. Dissolved oxygen concentrations, which varied across the site, were smallest near a mature cottonwood tree (about-20 years old) 60 meters southwest of the cottonwood plantings. Reduction of dissolved oxygen is the primary microbially mediated reaction occurring in the ground water beneath the planted trees, whereas near the mature cottonwood tree, data indicate that methanogenesis is the most probable reaction occurring. Reductive dichlorination either is not occurring or is not a primary process away from the mature tree. On the basis of isotopic analyses of carbon-13 at locations away from the mature tree, trichloroethene concentration is controlled by volatilization.

Electron transfer capacity dependence of quinone-mediated Fe(III) reduction and current generation by Klebsiella pneumoniae L17.

PubMed

Li, Xiaomin; Liu, Liang; Liu, Tongxu; Yuan, Tian; Zhang, Wei; Li, Fangbai; Zhou, Shungui; Li, Yongtao

2013-06-01

Quinone groups in exogenous electron shuttles can accelerate extracellular electron transfer (EET) from bacteria to insoluble terminal electron acceptors, such as Fe(III) oxides and electrodes, which are important in biogeochemical redox processes and microbial electricity generation. However, the relationship between quinone-mediated EET performance and electron-shuttling properties of the quinones remains incompletely characterized. This study investigates the effects of a series of synthetic quinones (SQs) on goethite reduction and current generation by a fermenting bacterium Klebsiella pneumoniae L17. In addition, the voltammetric behavior and electron transfer capacities (ETCs) of SQ, including electron accepting (EAC) and donating (EDC) capacities, is also examined using electrochemical methods. The results showed that SQ can significantly increase both the Fe(III) reduction rates and current outputs of L17. Each tested SQ reversibly accepted and donated electrons as indicated by the cyclic voltammograms. The EAC and EDC results showed that Carmine and Alizarin had low relative capacities of electron transfer, whereas 9,10-anthraquinone-2,6-disulfonic acid (AQDS), 2-hydroxy-1,4-naphthoquinone (2-HNQ), and 5-hydroxy-1,4-naphthoquinone (5-HNQ) showed stronger relative ETC, and 9,10-anthraquinone-2-carboxylic acid (AQC) and 9,10-anthraquinone-2-sulfonic acid (AQS) had high relative ETC. Enhancement of microbial goethite reduction kinetics and current outputs by SQ had a good linear relationship with their ETC, indicating that the effectiveness of quinone-mediated EET may be strongly dependent on the ETC of the quinones. Therefore, the presence of quinone compounds and fermenting microorganisms may increase the diversity of microbial populations that contribute to element transformation in natural environments. Moreover, ETC determination of different SQ would help to evaluate their performance for microbial EET under anoxic conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Biomineralization of U(VI) phosphate promoted by microbially-mediated phytate hydrolysis in contaminated soils

NASA Astrophysics Data System (ADS)

Salome, Kathleen R.; Beazley, Melanie J.; Webb, Samuel M.; Sobecky, Patricia A.; Taillefert, Martial

2017-01-01

The bioreduction of uranium may immobilize a significant fraction of this toxic contaminant in reduced environments at circumneutral pH. In oxic and low pH environments, however, the low solubility of U(VI)-phosphate minerals also makes them good candidates for the immobilization of U(VI) in the solid phase. As inorganic phosphate is generally scarce in soils, the biomineralization of U(VI)-phosphate minerals via microbially-mediated organophosphate hydrolysis may represent the main immobilization process of uranium in these environments. In this study, contaminated sediments were incubated aerobically in two pH conditions to examine whether phytate, a naturally-occurring and abundant organophosphate in soils, could represent a potential phosphorous source to promote U(VI)-phosphate biomineralization by natural microbial communities. While phytate hydrolysis was not evident at pH 7.0, nearly complete hydrolysis was observed both with and without electron donor at pH 5.5, suggesting indigenous microorganisms express acidic phytases in these sediments. While the rate of hydrolysis of phytate generally increased in the presence of uranium, the net rate of inorganic phosphate production in solution was decreased and inositol phosphate intermediates were generated in contrast to similar incubations conducted without uranium. These findings suggest uranium stress enhanced the phytate-metabolism of the microbial community, while simultaneously inhibiting phosphatase production and/or activity by the indigenous population. Finally, phytate hydrolysis drastically decreased uranium solubility, likely due to formation of ternary sorption complexes, U(VI)-phytate precipitates, and U(VI)-phosphate minerals. Overall, the results of this study provide evidence for the ability of natural microbial communities to liberate phosphate from phytate in acidic sediments, possibly as a detoxification mechanism, and demonstrate the potential utility of phytate-promoted uranium immobilization in subsurface environments. These processes should be investigated in more detail with pure cultures isolated from these sediments.

Electron transfer from a solid-state electrode assisted by methyl viologen sustains efficient microbial reductive dechlorination of TCE.

PubMed

Aulenta, Federico; Catervi, Alessandro; Majone, Mauro; Panero, Stefania; Reale, Priscilla; Rossetti, Simona

2007-04-01

The ability to transfer electrons, via an extracellular path, to solid surfaces is typically exploited by microorganisms which use insoluble electron acceptors, such as iron-or manganese-oxides or inert electrodes in microbial fuel cells. The reverse process, i.e., the use of solid surfaces or electrodes as electron donors in microbial respirations, although largely unexplored, could potentially have important environmental applications, particularly for the removal of oxidized pollutants from contaminated groundwater or waste streams. Here we show, for the first time, that an electrochemical cell with a solid-state electrode polarized at -500 mV (vs standard hydrogen electrode), in combination with a low-potential redox mediator (methyl viologen), can efficiently transfer electrochemical reducing equivalents to microorganisms which respire using chlorinated solvents. By this approach, the reductive transformation of trichloroethene, a toxic yet common groundwater contaminant, to harmless end-products such as ethene and ethane could be performed. Furthermore, using a methyl-viologen-modified electrode we could even demonstrate that dechlorinating bacteria were able to accept reducing equivalents directly from the modified electrode surface. The innovative concept, based on the stimulation of dechlorination reactions through the use of solid-state electrodes (we propose for this process the acronym BEARD: Bio-Electrochemically Assisted Reductive Dechlorination), holds promise for in situ bioremediation of chlorinated-solvent-contaminated groundwater, and has several potential advantages over traditional approaches based on the subsurface injection of organic compounds. The results of this study raise the possibility that immobilization of selected redox mediators may be a general strategy for stimulating and controlling a range of microbial reactions using insoluble electrodes as electron donors.

MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection

PubMed Central

Kubinak, Jason L.; Stephens, W. Zac; Soto, Ray; Petersen, Charisse; Chiaro, Tyson; Gogokhia, Lasha; Bell, Rickesha; Ajami, Nadim J.; Petrosino, Joseph F.; Morrison, Linda; Potts, Wayne K.; Jensen, Peter E.; O'Connell, Ryan M.; Round, June L.

2015-01-01

The presentation of protein antigens on the cell surface by major histocompatibility complex (MHC) molecules coordinates vertebrate adaptive immune responses, thereby mediating susceptibility to a variety of autoimmune and infectious diseases. The composition of symbiotic microbial communities (the microbiota) is influenced by host immunity and can have a profound impact on host physiology. Here we use an MHC congenic mouse model to test the hypothesis that genetic variation at MHC genes among individuals mediates susceptibility to disease by controlling microbiota composition. We find that MHC genotype significantly influences antibody responses against commensals in the gut, and that these responses are correlated with the establishment of unique microbial communities. Transplantation experiments in germfree mice indicate that MHC-mediated differences in microbiota composition are sufficient to explain susceptibility to enteric infection. Our findings indicate that MHC polymorphisms contribute to defining an individual's unique microbial fingerprint that influences health. PMID:26494419

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...

Evaluating the Classical Versus an Emerging Conceptual Model of Peatland Methane Dynamics

Treesearch

Wendy H. Yang; Gavin McNicol; Yit Arn Teh; Katerina Estera-Molina; Tana E. Wood; Whendee L. Silver

2017-01-01

Methane (CH4) is a potent greenhouse gas that is both produced and consumed in soils by microbially mediated processes sensitive to soil redox. We evaluated the classical conceptual model of peatland CH4 dynamics—in which the water table position determines the vertical distribution of methanogenesis and methanotrophy—...

The Effect of Elevated CO2 and O3 on Soil Nitrogen Inputs and Losses in a Soybean Agroecosystem in Illinois

USDA-ARS?s Scientific Manuscript database

It has been found that elevated atmospheric carbon dioxide (eCO2) and tropospheric ozone (eO3) affect belowground microbial processes, including N transformations, through plant-mediated changes. Conversely, changes in soil organic carbon sequestration and plant biomass production are constrained by...

Metabolic adaptation and in situ attenuation of chlorinated ethenes by naturally occurring microorganisms in a fractured dolomite aquifer near Niagara Falls, New York

USGS Publications Warehouse

Yager, R.M.; Bilotta, S.E.; Mann, C.L.; Madsen, E.L.

1997-01-01

A combination of hydrogeological, geochemical, and microbiological methods was used to document the biotransformation of trichloroethene (TCE) to ethene, a completely dechlorinated and environmentally benign compound, by naturally occurring microorganisms within a fractured dolomite aquifer. Analyses of groundwater samples showed that three microbially produced TCE breakdown products (cis-1,2-dichloroethene, vinyl chloride, and ethene) were present in the contaminant plume. Hydrogen (H2) concentrations in groundwater indicated that iron reduction was the predominant terminal electron-accepting process in the most contaminated geologic zone of the site. Laboratory microcosms prepared with groundwater demonstrated complete sequential dechlorination of TCE to ethene. Microcosm assays also revealed that reductive dechlorination activity was present in waters from the center but not from the periphery of the contaminant plume. This dechlorination activity indicated that naturally occurring microorganisms have adapted to utilize chlorinated ethenes and suggested that dehalorespiring rather than cometabolic, microbial processes were the cause of the dechlorination. The addition of pulverized dolomite to microcosms enhanced the rate of reductive dechlorination, suggesting that hydrocarbons in the dolomite aquifer may serve as electron donors to drive microbially mediated reductive dechlorination reactions. Biodegradation of the chlorinated ethenes appears to contribute significantly to decontamination of the site.A combination of hydrogeological, geochemical, and microbiological methods was used to document the biotransformation of trichloroethene (TCE) to ethene, a completely dechlorinated and environmentally benign compound, by naturally occurring microorganisms within a fractured dolomite aquifer. Analyses of groundwater samples showed that three microbially produced TCE breakdown products (cis-1,2-dichloroethene, vinyl chloride, and ethene) were present in the contaminant plume. Hydrogen (H2) concentrations in groundwater indicated that iron reduction was the predominant terminal electron-accepting process in the most contaminated geologic zone of the site. Laboratory microcosms prepared with groundwater demonstrated complete sequential dechlorination of TCE to ethene. Microcosm assays also revealed that reductive dechlorination activity was present in waters from the center but not from the periphery of the contaminant plume. This dechlorination activity indicated that naturally occurring microorganisms have adapted to utilize chlorinated ethenes and suggested that dehalorespiring rather than cometabolic, microbial processes were the cause of the dechlorination. The addition of pulverized dolomite to microcosms enhanced the rate of reductive dechlorination, suggesting that hydrocarbons in the dolomite aquifer may serve as electron donors to drive microbially mediated reductive dechlorination reactions. Biodegradation of the chlorinated ethenes appears to contribute significantly to decontamination of the site.

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

PubMed

Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

2016-07-01

Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

Proteomic Characterization of Central Pacific Oxygen Minimum Zone Microbial Communities

NASA Astrophysics Data System (ADS)

Saunders, J. K.; McIlvin, M. M.; Moran, D.; Held, N.; Futrelle, J.; Webb, E.; Santoro, A.; Dupont, C.; Saito, M.

2018-05-01

Microbial proteomic profiles are excellent for surveying vast expanses of pelagic ecosystems for links between microbial communities and the biogeochemical cycles they mediate. Data from the ProteOMZ expedition supports the utility of this method.

Microbially Mediated Glass Alteration in the Geological Record: Textural clues for Microbial Functions.

NASA Astrophysics Data System (ADS)

Staudigel, H.; Furnes, H.; McLoughlin, N.; Banerjee, N.

2007-12-01

Fe and Mn oxidizing microbes interact with their environment through the microbially mediated formation of Fe/Mn oxides and through the corrosion textures they may leave behind in the solids they colonize and from which they extract nutrients. Understanding the geo-biology of Fe and Mn oxidation may focus on the study of the microbes themselves, the mineral products, its biocorrosion features and the relationships between these types of observations. We have reviewed our own data on glass bio-corrosion and in particular the wider literature on microbial mineral tunneling to develop a two stage biocorrosion model for volcanic glass that offers feedback for our understanding of the mechanisms and the dynamics of microbial dissolution. Traces of microbially mediated dissolution of volcanic glass are commonly observed in volcanic glass found in submarine volcanoes on the seafloor, and in uplifted submarine volcanoes of almost any geological age back to the origin of life. Two main bioalteration textures care observed, granular and tubular. Based on a comparison of these features in particular with tunneling by ectomycorrhizal fungi, we propose two distinct types of biocorrosion that affects glass: (1) Granular alteration textures, made up of colonies of microbe-sized, near spherical mineral - filled cavities that form irregular clusters ranging to a tens of micron thick bands at the glas surfaces. These granular textures are interpreted as the result of microbial colonization. accompanied by dissolution of the glass in their contact surface, deposition of authigenic minerals and the formation of a biofilm, that eventually seals the glass from easy access by seawater for hydration, or from microbes accessing Fe (II) in the glass. (2) The most spectacular bioalteration feature, repesented by the formation of tubes cannot be easily formed by the former mechanism because near spherical, individual microbes are likely not to produce the directionality that is required to produce the near linear or sometimes coiled tubes. Instead, we envision the activity of hyphae-like organelles or filaments, that may radiate out from a host body located in direct contact with circulating water, possibly penetrating a biofilm and entering/drilling into the fresh glass. Such microdrilling is well described in soils, where hyphae can slowly drill into silicates, in a process that takes about 1000 years to become visible as tunnels.

Spatial Distribution of Viruses Associated with Planktonic and Attached Microbial Communities in Hydrothermal Environments

PubMed Central

Nunoura, Takuro; Kazama, Hiromi; Noguchi, Takuroh; Inoue, Kazuhiro; Akashi, Hironori; Yamanaka, Toshiro; Toki, Tomohiro; Yamamoto, Masahiro; Furushima, Yasuo; Ueno, Yuichiro; Yamamoto, Hiroyuki; Takai, Ken

2012-01-01

Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments. PMID:22210205

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

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

Firestone, Mary

2015-03-31

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

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.

Use of slow filtration columns to assess oxygen respiration, consumption of dissolved organic carbon, nitrogen transformations, and microbial parameters in hyporheic sediments.

PubMed

Mermillod-Blondin, F; Mauclaire, L; Montuelle, B

2005-05-01

Biogeochemical processes mediated by microorganisms in river sediments (hyporheic sediments) play a key role in river metabolism. Because biogeochemical reactions in the hyporheic zone are often limited to the top few decimetres of sediments below the water-sediment interface, slow filtration columns were used in the present study to quantify biogeochemical processes (uptakes of O2, DOC, and nitrate) and the associated microbial compartment (biomass, respiratory activity, and hydrolytic activity) at a centimetre scale in heterogeneous (gravel and sand) sediments. The results indicated that slow filtration columns recreated properly the aerobic-anaerobic gradient classically observed in the hyporheic zone. O2 and NO3- consumptions (256 +/- 13 microg of O2 per hour and 14.6 +/- 6.1 microg of N-NO3- per hour) measured in columns were in the range of values measured in different river sediments. Slow filtration columns also reproduced the high heterogeneity of the hyporheic zone with the presence of anaerobic pockets in sediments where denitrification and fermentation processes occurred. The respiratory and hydrolytic activities of bacteria were strongly linked with the O2 consumption in the experimental system, highlighting the dominance of aerobic processes in our river sediments. In comparison with these activities, the bacterial biomass (protein content) integrated both aerobic and anaerobic processes and could be used as a global microbial indicator in our system. Finally, slow filtration columns are an appropriate tool to quantify in situ rates of biogeochemical processes and to determine the relationship between the microbial compartment and the physico-chemical environment in coarse river sediments.

Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota

PubMed Central

Warren, Melissa J.; Lin, Xueju; Gaby, John C.; Kretz, Cecilia B.; Kolton, Max; Morton, Peter L.; Pett-Ridge, Jennifer; Weston, David J.; Schadt, Christopher W.; Kostka, Joel E.

2017-01-01

ABSTRACT Microbial N2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, and CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and 15N2 incorporation. A molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (Bradyrhizobiaceae and Beijerinckiaceae). Despite higher concentrations of dissolved vanadium ([V] 11 nM) than molybdenum ([Mo] 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing, and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water contents. Incorporation of 15N2 was suppressed 90% by O2 and 55% by C2H2 and was unaffected by CH4 and CO2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2-sensitive and C2H2-insensitive microbes that are more active at low concentrations of O2 and show similar activity at high and low concentrations of CH4. IMPORTANCE Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme. PMID:28667112

Molybdenum-based diazotrophy in a Sphagnum peatland in northern Minnesota.

PubMed

Warren, Melissa J; Lin, Xueju; Gaby, John C; Kretz, Cecilia B; Kolton, Max; Morton, Peter L; Pett-Ridge, Jennifer; Weston, David J; Schadt, Christopher W; Kostka, Joel E; Glass, Jennifer B

2017-06-30

Microbial N 2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO 2 and susceptible to changing climate. The objectives of this study were: (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in a ombrotrophic Sphagnum -dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O 2 , CO 2 , CH 4 ) on potential rates of diazotrophy measured by acetylene (C 2 H 2 ) reduction and 15 N 2 incorporation. Molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria ( Bradyrhizobiaceae and Beijerinckiaceae ). Despite higher dissolved vanadium (V; 11 nM) than molybdenum (Mo; 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water content. Incorporation of 15 N 2 was suppressed 90% by O 2 and 55% by C 2 H 2 , and was unaffected by CH 4 and CO 2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C 2 H 2 -sensitive and C 2 H 2 -insensitive microbes that are more active at low O 2 and show similar activity at high and low CH 4 Importance Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum -dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy, and that members of the Alphaproteobacteria ( Rhizobiales ) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme. Copyright © 2017 American Society for Microbiology.

Soil Biogeochemical and Microbial Feedbacks along a Snowmelt-Dominated Hillslope-to-Floodplain Transect in Colorado.

NASA Astrophysics Data System (ADS)

Sorensen, P.; Beller, H. R.; Bill, M.; Bouskill, N.; Brodie, E.; Chakraborty, R.; Conrad, M. E.; Karaoz, U.; Polussa, A.; Steltzer, H.; Wang, S.; Williams, K. H.; Wilmer, C.; Wu, Y.

2017-12-01

Nitrogen export from mountainous watersheds is a product of multiple interactions among hydrological processes and soil-microbial-plant feedbacks along the continuum from terrestrial to aquatic environments. In snow-dominated systems, like the East River Watershed (CO), seasonal processes such as snowmelt exert significant influence on the annual hydrologic cycle and may also link spatially distinct catchment subsystems, such as hillslope and adjoining riparian floodplains. Further, snowmelt is occurring earlier each year and this is predicted to result in a temporal asynchrony between historically coupled microbial nutrient release and plant nutrient demand in spring, with the potential to increase N export from the East River Watershed. Here we summarize biogeochemical data collected along a hillslope-to-riparian floodplain transect at the East River site. Starting in Fall 2016, we sampled soils at 3 depths and measured dissolved pools of soil nutrients (e.g., NH4+, NO3-, DOC, P), microbial biomass CN, and microbial community composition over a seasonal time course, through periods of snow accumulation, snowmelt, and plant senescence. Soil moisture content in the top 5 cm of floodplain soils was nearly 4X greater across sampling dates, coinciding with 2X greater microbial biomass C, larger extractable pools of NH4+, and smaller pools of NO3- in floodplain vs. hillslope soils. These results suggest that microbially mediated redox processes played an important role in N cycling along the transect. Hillslope vs. floodplain location also appeared to be a key factor that differentiated soil microbial communities (e.g., a more important factor than seasonality or soil depth or type). Snow accumulation and snowmelt exerted substantial influence on soil biogeochemistry. For example, microbial biomass accumulation increased about 2X beneath the winter snowpack. Snowmelt resulted in a precipitous crash in the microbial population, with 2.5X reductions in floodplain and 2X reductions in hillslope soils. Immediately following snowmelt, NO3- concentrations in soil porewater and soil extracts increased dramatically. Overall, these results suggest that N export is strongly influenced by distinct soil biogeochemical and microbiological patterns along hillslope-to-floodplain transects at East River.

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.

Leaf Litter Mixtures Alter Microbial Community Development: Mechanisms for Non-Additive Effects in Litter Decomposition

PubMed Central

Chapman, Samantha K.; Newman, Gregory S.; Hart, Stephen C.; Schweitzer, Jennifer A.; Koch, George W.

2013-01-01

To what extent microbial community composition can explain variability in ecosystem processes remains an open question in ecology. Microbial decomposer communities can change during litter decomposition due to biotic interactions and shifting substrate availability. Though relative abundance of decomposers may change due to mixing leaf litter, linking these shifts to the non-additive patterns often recorded in mixed species litter decomposition rates has been elusive, and links community composition to ecosystem function. We extracted phospholipid fatty acids (PLFAs) from single species and mixed species leaf litterbags after 10 and 27 months of decomposition in a mixed conifer forest. Total PLFA concentrations were 70% higher on litter mixtures than single litter types after 10 months, but were only 20% higher after 27 months. Similarly, fungal-to-bacterial ratios differed between mixed and single litter types after 10 months of decomposition, but equalized over time. Microbial community composition, as indicated by principal components analyses, differed due to both litter mixing and stage of litter decomposition. PLFA biomarkers a15∶0 and cy17∶0, which indicate gram-positive and gram-negative bacteria respectively, in particular drove these shifts. Total PLFA correlated significantly with single litter mass loss early in decomposition but not at later stages. We conclude that litter mixing alters microbial community development, which can contribute to synergisms in litter decomposition. These findings advance our understanding of how changing forest biodiversity can alter microbial communities and the ecosystem processes they mediate. PMID:23658639

Extracellular Electron Uptake: Among Autotrophs and Mediated by Surfaces.

PubMed

Tremblay, Pier-Luc; Angenent, Largus T; Zhang, Tian

2017-04-01

Autotrophic microbes can acquire electrons from solid donors such as steel, other microbial cells, or electrodes. Based on this feature, bioprocesses are being developed for the microbial electrosynthesis (MES) of useful products from the greenhouse gas CO 2 . Extracellular electron-transfer mechanisms involved in the acquisition of electrons from metals by electrical microbially influenced corrosion (EMIC), from other living cells by interspecies electron transfer (IET), or from an electrode during MES rely on: (i) mediators such as H 2 ; (ii) physical contact through electron-transfer proteins; or (iii) mediator-generating enzymes detached from cells. This review explores the interactions of autotrophs with solid electron donors and their importance in nature and for biosustainable technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

In Situ Biomineralization and Particle Deposition Distinctively Mediate Biofilm Susceptibility to Chlorine

PubMed Central

Li, Xiaobao; Chopp, David L.; Russin, William A.; Brannon, Paul T.; Parsek, Matthew R.

2016-01-01

Microbial biofilms and mineral precipitation commonly co-occur in engineered water systems, such as cooling towers and water purification systems, and both decrease process performance. Microbial biofilms are extremely challenging to control and eradicate. We previously showed that in situ biomineralization and the precipitation and deposition of abiotic particles occur simultaneously in biofilms under oversaturated conditions. Both processes could potentially alter the essential properties of biofilms, including susceptibility to biocides. However, the specific interactions between mineral formation and biofilm processes remain poorly understood. Here we show that the susceptibility of biofilms to chlorination depends specifically on internal transport processes mediated by biomineralization and the accumulation of abiotic mineral deposits. Using injections of the fluorescent tracer Cy5, we show that Pseudomonas aeruginosa biofilms are more permeable to solutes after in situ calcite biomineralization and are less permeable after the deposition of abiotically precipitated calcite particles. We further show that biofilms are more susceptible to chlorine killing after biomineralization and less susceptible after particle deposition. Based on these observations, we found a strong correlation between enhanced solute transport and chlorine killing in biofilms, indicating that biomineralization and particle deposition regulate biofilm susceptibility by altering biocide penetration into the biofilm. The distinct effects of in situ biomineralization and particle deposition on biocide killing highlight the importance of understanding the mechanisms and patterns of biomineralization and scale formation to achieve successful biofilm control. PMID:26944848

Information transmission in microbial and fungal communication: from classical to quantum.

PubMed

Majumdar, Sarangam; Pal, Sukla

2018-06-01

Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.

Bioremediation of PAHs and VOCs: Advances in clay mineral-microbial interaction.

PubMed

Biswas, Bhabananda; Sarkar, Binoy; Rusmin, Ruhaida; Naidu, Ravi

2015-12-01

Bioremediation is an effective strategy for cleaning up organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs). Advanced bioremediation implies that biotic agents are more efficient in degrading the contaminants completely. Bioremediation by microbial degradation is often employed and to make this process efficient, natural and cost-effective materials can serve as supportive matrices. Clay/modified clay minerals are effective adsorbents of PAHs/VOCs, and readily available substrate and habitat for microorganisms in the natural soil and sediment. However, the mechanism underpinning clay-mediated biodegradation of organic compounds is often unclear, and this requires critical investigation. This review describes the role of clay/modified clay minerals in hydrocarbon bioremediation through interaction with microbial agents in specific scenarios. The vision is on a faster, more efficient and cost-effective bioremediation technique using clay-based products. This review also proposes future research directions in the field of clay modulated microbial degradation of hydrocarbons. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbially mediated clinoptilolite regeneration in a multifunctional permeable reactive barrier used to remove ammonium from landfill leachate contamination: laboratory column evaluation.

PubMed

Nooten, Thomas Van; Diels, Ludo; Bastiaens, Leen

2010-05-01

This study focuses on multifunctional permeable reactive barrier (multibarrier) technology, combining microbial degradation and abiotic ion exchange processes for removal of ammonium from landfill leachate contamination. The sequential multibarrier concept relies on the use of a clinoptilolite-filled buffer compartment to ensure a robust ammonium removal in case of temporary insufficient microbial activities. An innovative strategy was developed to allow in situ clinoptilolite regeneration. Laboratory-scale clinoptilolite-filled columns were first saturated with ammonium, using real landfill leachate as well as synthetic leachates as feed media. Other inorganic metal cations, typically present in landfill leachate, had a detrimental influence on the ammonium removal capacity by competing for clinoptilolite exchange sites. On the other hand, the metals had a highly favorable impact on regeneration of the saturated material. Feeding the columns with leachate deprived from ammonium (e.g., by microbial nitrification in an upgradient compartment), resulted in a complete release of the previously sorbed ammonium from the clinoptilolite, due to exchange with metal cations present in the leachate. The released ammonium is then available for microbial consumption in a downgradient compartment. The regeneration process resulted in a slightly increased ammonium exchange capacity afterward. The described strategy throws a new light on sustainable use of sorption materials for in situ groundwater remediation, by avoiding the need for material replacement and the use of external chemical regenerants.

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.

Something new from something old? Fracking stimulated microbial processes

NASA Astrophysics Data System (ADS)

Wrighton, K. C.; Daly, R. A.; Hoyt, D.; Trexler, R.; McRae, J.; Wilkins, M.; Mouser, P. J.

2015-12-01

Hydraulic fracturing, colloquially known as "fracking", is employed for effective gas and oil recovery in deep shales. This process injects organisms and liquids from the surface into the deep subsurface (~2500 m), exposing microorganisms to high pressures, elevated temperatures, chemical additives, and brine-level salinities. Here we use assembly-based metagenomics to create a metabolic blueprint from an energy-producing Marcellus shale well over a 328-day period. Using this approach we ask the question: What abiotic and biotic factors drive microbial metabolism and thus biogeochemical cycling during natural gas extraction? We found that after 49 days, increased salinity in produced waters corresponded to a shift in the microbial community, with only organisms that encode salinity adaptations detected. We posit that organic compatible solutes, produced by organisms adapting to increased salinity, fuels a methylamine-driven ecosystem in fractured shale. This metabolic network ultimately results in biogenic methane production from members of Methanohalophilus and Methanolobus. Proton NMR validated these genomic hypotheses, with mono-methylamine being highest in the input material, but detected throughout the sampling. Beyond abiotic constraints, our genomic investigations revealed that viruses can be linked to key members of the microbial community, potentially releasing methylamine osmoprotectants and impacting bacterial strain variation. Collectively our results indicate that adaptation to high salinity, metabolism in the absence of oxidized electron acceptors, and viral predation are controlling factors mediating microbial community metabolism during hydraulic fracturing of the deep subsurface.

Genome Sequence of the Moderately Acidophilic Sulfate-Reducing Firmicute Desulfosporosinus acididurans (Strain M1T)

PubMed Central

Petzsch, Patrick; Poehlein, Anja; Johnson, D. Barrie; Daniel, Rolf; Schlömann, Michael

2015-01-01

Microbial dissimilatory sulfate reduction is commonplace in many anaerobic environments, though few acidophilic bacteria are known to mediate this process. We report the 4.64-Mb draft genome of the type strain of the moderate acidophile Desulfosporosinus acididurans, which was isolated from acidic sediment in a river draining the Soufrière volcano, Montserrat. PMID:26251501

Microbial shaping of wrinkle structures in siliciclastic deposits

NASA Astrophysics Data System (ADS)

Bosak, T.; Mariotti, G.; Pruss, S. B.; Perron, J.; O'Grady, M.

2013-12-01

Wrinkle structures are millimeter- to centimeter-scale elongated or reticulate sedimentary structures that resemble symmetric ripples. Sharp-crested and flat-topped wrinkle structures up to 1 cm wide occur on numerous bedding planes in the Neoproterozoic and Cambrian, as well as in some Archean and Phanerozoic siliciclastic deposits. Because similar, but unlithified structures occur in some modern, microbially-colonized sands, wrinkle structures are typically interpreted as microbially induced sedimentary structures. However, it is unclear if physical processes, such as the motion of suspended sand grains, can produce similar features in sand even before microbial colonization. We introduced mat fragments to the surface of silica sand in wave tanks and generated sharp-crested, flat-topped and pitted wrinkle structures. The abrasion of the sandy surface by rolling, low density, millimeter-size fragments of microbial mats produces wrinkle structures at extremely weak orbital velocities that cannot move sand grains in the absence of light particles. Wrinkle structures form in a few hours and can become colonized by microbial mats within weeks. Thus, wrinkle structures are patterns formed by microbially mediated sand motion at low orbital velocities in the absence of bioturbation. Once formed, wrinkle structures can be colonized and stabilized by microbial mats, but the shape of these mats does not dictate the shape of wrinkle structures. These experiments bolster the interpretation of wrinkle structures as morphological signatures of organic particles and early life in Archean and Proterozoic siliciclastic deposits.

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.

Temperature-driven decoupling of key phases of organic matter degradation in marine sediments.

PubMed

Weston, Nathaniel B; Joye, Samantha B

2005-11-22

The long-term burial of organic carbon in sediments results in the net accumulation of oxygen in the atmosphere, thereby mediating the redox state of the Earth's biosphere and atmosphere. Sediment microbial activity plays a major role in determining whether particulate organic carbon is recycled or buried. A diverse consortium of microorganisms that hydrolyze, ferment, and terminally oxidize organic compounds mediates anaerobic organic matter mineralization in anoxic sediments. Variable temperature regulation of the sequential processes, leading from the breakdown of complex particulate organic carbon to the production and subsequent consumption of labile, low-molecular weight, dissolved intermediates, could play a key role in controlling rates of overall organic carbon mineralization. We examined sediment organic carbon cycling in a sediment slurry and in flow through bioreactor experiments. The data show a variable temperature response of the microbial functional groups mediating organic matter mineralization in anoxic marine sediments, resulting in the temperature-driven decoupling of the production and consumption of organic intermediates. This temperature-driven decoupling leads to the accumulation of labile, low-molecular weight, dissolved organic carbon at low temperatures and low-molecular weight dissolved organic carbon limitation of terminal metabolism at higher temperatures.

Effect of long-term fertilization on humic redox mediators in multiple microbial redox reactions.

PubMed

Guo, Peng; Zhang, Chunfang; Wang, Yi; Yu, Xinwei; Zhang, Zhichao; Zhang, Dongdong

2018-03-01

This study investigated the effects of different long-term fertilizations on humic substances (HSs), humic acids (HAs) and humins, functioning as redox mediators for various microbial redox biotransformations, including 2,2',4,4',5,5'- hexachlorobiphenyl (PCB 153 ) dechlorination, dissimilatory iron reduction, and nitrate reduction, and their electron-mediating natures. The redox activity of HSs for various microbial redox metabolisms was substantially enhanced by long-term application of organic fertilizer (pig manure). As a redox mediator, only humin extracted from soils with organic fertilizer amendment (OF-HM) maintained microbial PCB 153 dechlorination activity (1.03 μM PCB 153 removal), and corresponding HA (OF-HA) most effectively enhanced iron reduction and nitrate reduction by Shewanella putrefaciens. Electrochemical analysis confirmed the enhancement of their electron transfer capacity and redox properties. Fourier transform infrared analysis showed that C=C and C=O bonds, and carboxylic or phenolic groups in HSs might be the redox functional groups affected by fertilization. This research enhances our understanding of the influence of anthropogenic fertility on the biogeochemical cycling of elements and in situ remediation ability in agroecosystems through microorganisms' metabolisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

MICROBIAL ENZYME ACTIVITY FOR CHARACTERIZING NUTRIENT LOADING TO GREAT LAKES COASTAL WETLANDS

EPA Science Inventory

Energy and material flows in aquatic ecosystems are mediated by microbial carbon and nutrient cycling. Extracellular enzymes produced by the microbial community aid in the degradation of organic matter and the resultant acquisition of limiting nutrients. Organic carbon sequestrat...

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.

PubMed

Dini-Andreote, Francisco; Stegen, James C; van Elsas, Jan Dirk; Salles, Joana Falcão

2015-03-17

Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages--which provide a larger spatiotemporal scale relative to within stage analyses--revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended--and experimentally testable--conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

PubMed Central

Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan Dirk; Salles, Joana Falcão

2015-01-01

Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages—which provide a larger spatiotemporal scale relative to within stage analyses—revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended—and experimentally testable—conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems. PMID:25733885

Life cycle of soil sggregates: from root residue to microbial and physical hotspots

NASA Astrophysics Data System (ADS)

Ghezzehei, T. A.; Or, D.

2017-12-01

Soil aggregation is a physical state of soil in which clumps of primary soil particles are held together by biological and/or chemical cementing agents. Aggregations plays important role in storage and movement of water and essential gases, nutrient cycling, and ultimately supporting microbial and plant life. It is also one of the most dynamic and sensitive soil qualities, which readily responds to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against erosion.

Sweating the small stuff: Glycoproteins in human sweat and their unexplored potential for microbial adhesion.

PubMed

Peterson, Robyn A; Gueniche, Audrey; Adam de Beaumais, Ségolène; Breton, Lionel; Dalko-Csiba, Maria; Packer, Nicolle H

2016-03-01

There is increasing evidence that secretory fluids such as tears, saliva and milk play an important role in protecting the human body from infection via a washing mechanism involving glycan-mediated adhesion of potential pathogens to secretory glycoproteins. Interaction of sweat with bacteria is well established as the cause of sweat-associated malodor. However, the role of sweat glycoproteins in microbial attachment has received little, if any, research interest in the past. In this review, we demonstrate how recent published studies involving high-throughput proteomic analysis have inadvertently, and fortuitously, exposed an abundance of glycoproteins in sweat, many of which have also been identified in other secretory fluids. We bring together research demonstrating microbial adhesion to these secretory glycoproteins in tears, saliva and milk and suggest a similar role of the sweat glycoproteins in mediating microbial attachment to sweat and/or skin. The contribution of glycan-mediated microbial adhesion to sweat glycoproteins, and the associated impact on sweat derived malodor and pathogenic skin infections are unchartered new research areas that we are beginning to explore. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A microbial factory for lactate-based polyesters using a lactate-polymerizing enzyme

PubMed Central

Taguchi, Seiichi; Yamada, Miwa; Matsumoto, Ken'ichiro; Tajima, Kenji; Satoh, Yasuharu; Munekata, Masanobu; Ohno, Katsuhiro; Kohda, Katsunori; Shimamura, Takashi; Kambe, Hiromi; Obata, Shusei

2008-01-01

Polylactate (PLA) is synthesized as a representative bio-based polyester by the chemo-bio process on the basis of metal catalyst-mediated chemical polymerization of lactate (LA) supplied by microbial fermentation. To establish the one-step microbial process for synthesis of LA-based polyesters, we explored whether polyhydroxyalkanoate (PHA) synthase would exhibit polymerizing activity toward a LA-coenzyme A (CoA), based on the fact that PHA monomeric constituents, especially 3-hydroxybutyrate (3HB), are structurally analogous to LA. An engineered PHA synthase was discovered as a candidate by a two-phase in vitro polymerization system previously developed. An LA-CoA producing Escherichia coli strain with a CoA transferase gene was constructed, and the generation of LA-CoA was demonstrated by capillary electrophoresis/MS analysis. Next, when the engineered PHA synthase gene was introduced into the resultant recombinant strain, we confirmed the one-step biosynthesis of the LA-incorporated copolyester, P(6 mol% LA-co-94 mol% 3HB), with a number-average molecular weight of 1.9 × 105, as revealed by gel permeation chromatography, gas chromatography/MS, and NMR. PMID:18978031

Natural attenuation process via microbial oxidation of arsenic in a high Andean watershed.

PubMed

Leiva, Eduardo D; Rámila, Consuelo d P; Vargas, Ignacio T; Escauriaza, Cristian R; Bonilla, Carlos A; Pizarro, Gonzalo E; Regan, John M; Pasten, Pablo A

2014-01-01

Rivers in northern Chile have arsenic (As) concentrations at levels that are toxic for humans and other organisms. Microorganism-mediated redox reactions have a crucial role in the As cycle; the microbial oxidation of As (As(III) to As(V)) is a critical transformation because it favors the immobilization of As in the solid phase. We studied the role of microbial As oxidation for controlling the mobility of As in the extreme environment found in the Chilean Altiplano (i.e., > 4000 meters above sea level (masl) and < 310 mm annual rainfall), which are conditions that have rarely been studied. Our model system was the upper Azufre River sub-basin, where the natural attenuation of As from hydrothermal discharge (pH 4-6) was observed. As(III) was actively oxidized by a microbial consortium, leading to a significant decrease in the dissolved As concentrations and a corresponding increase in the sediment's As concentration downstream of the hydrothermal source. In-situ oxidation experiments demonstrated that the As oxidation required biological activity, and microbiological molecular analysis confirmed the presence of As(III)-oxidizing groups (aroA-like genes) in the system. In addition, the pH measurements and solid phase analysis strongly suggested that the As removal mechanism involved adsorption or coprecipitation with Fe-oxyhydroxides. Taken together, these results indicate that the microorganism-mediated As oxidation contributed to the attenuation of As concentrations and the stabilization of As in the solid phase, therefore controlling the amount of As transported downstream. This study is the first to demonstrate the microbial oxidation of As in Altiplano basins and its relevance in the immobilization of As. © 2013.

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.

Applicability of anaerobic nitrate-dependent Fe(II) oxidation to microbial enhanced oil recovery (MEOR).

PubMed

Zhu, Hongbo; Carlson, Han K; Coates, John D

2013-08-06

Microbial processes that produce solid-phase minerals could be judiciously applied to modify rock porosity with subsequent alteration and improvement of floodwater sweep in petroleum reservoirs. However, there has been little investigation of the application of this to enhanced oil recovery (EOR). Here, we investigate a unique approach of altering reservoir petrology through the biogenesis of authigenic rock minerals. This process is mediated by anaerobic chemolithotrophic nitrate-dependent Fe(II)-oxidizing microorganisms that precipitate iron minerals from the metabolism of soluble ferrous iron (Fe(2+)) coupled to the reduction of nitrate. This mineral biogenesis can result in pore restriction and reduced pore throat diameter. Advantageously and unlike biomass plugs, these biominerals are not susceptible to pressure or thermal degradation. Furthermore, they do not require continual substrate addition for maintenance. Our studies demonstrate that the biogenesis of insoluble iron minerals in packed-bed columns results in effective hydrology alteration and homogenization of heterogeneous flowpaths upon stimulated microbial Fe(2+) biooxidation. We also demonstrate almost 100% improvement in oil recovery from hydrocarbon-saturated packed-bed columns as a result of this metabolism. These studies represent a novel departure from traditional microbial EOR approaches and indicate the potential for nitrate-dependent Fe(2+) biooxidation to improve volumetric sweep efficiency and enhance both the quality and quantity of oil recovered.

From birth to ‘immuno-health’, allergies and enterocolitis

PubMed Central

Houghteling, Pearl D.; Walker, W. Allan

2015-01-01

Microbial signals stimulate development and maintenance of the neonatal immune system. The process begins in utero, with limited exposure to microbes in the intrauterine environment, as well as maternal immune signals priming the developing immune system. After birth and initial colonization, the immune system must be able to activate against pathogens, but also achieve oral tolerance of food and resident gut microbes. Through microbial signals and appropriate nutrition, the immune system is able to achieve homeostasis. Major challenges to successful colonization and immune system regulation include abnormal microbial inoculi (cesarean section, hygiene) and antibiotics. When normal colonization is interrupted, dysbiosis occurs. This imbalance of microbes and subsequently of the immune system can result in allergic diseases, asthma or necrotizing enterocolitis. Probiotics and probiotic-derived therapies represent an exciting avenue to replete the population of commensal microbes and to prevent the immune-mediated sequelae of dysbiosis. PMID:26447970

How to access and exploit natural resources sustainably: petroleum biotechnology.

PubMed

Sherry, Angela; Andrade, Luiza; Velenturf, Anne; Christgen, Beate; Gray, Neil D; Head, Ian M

2017-09-01

As we transition from fossil fuel reliance to a new energy future, innovative microbial biotechnologies may offer new routes to maximize recovery from conventional and unconventional energy assets; as well as contributing to reduced emission pathways and new technologies for carbon capture and utilization. Here we discuss the role of microbiology in petroleum biotechnologies in relation to addressing UN Sustainable Development Goal 12 (ensure sustainable consumption and production patterns), with a focus on microbially-mediated energy recovery from unconventionals (heavy oil to methane), shale gas and fracking, bioelectrochemical systems for the production of electricity from fossil fuel resources, and innovations in synthetic biology. Furthermore, using wastes to support a more sustainable approach to fossil fuel extraction processes is considered as we undertake the move towards a more circular global economy. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Evidence for iron-sulfate coupling in salt marsh sediments

NASA Astrophysics Data System (ADS)

Mills, Jennifer; Antler, Gilad; Turchyn, Alexandra

2014-05-01

Organic carbon burial in shallow marine sediments represents an important net sink in the global carbon cycle. Microbially mediated oxidation of organic matter in oxic, suboxic, and anoxic sediments however, prevents the ultimate burial of organic carbon and its removal from the surface of the planet. Although the subsurface transformations of organic carbon have been studied extensively, an enigmatic question remains: when organic matter is deposited, what determines whether it will be buried, reoxidized, or undergo methanogenesis? One hypothesis is that the sulfur cycle, due to the abundance of sulfate in many surface environments, dominates the subsurface oxidation or other fate of organic carbon. However, it has also been suggested that iron may in turn play a key role in determining the behavior of the sulfur cycle. To better understand the controls on these processes, we are using stable isotope and geochemical techniques to explore the microbially mediated oxidation of organic carbon in salt marsh sediments in North Norfolk, UK. In these sediments there is a high supply of organic carbon, iron, and sulfate (from diurnal tidal cycles). Thus these environments may provide insight into the nature of interactions between the carbon, iron, and sulfur cycles. A series of sampling missions was undertaken in the autumn and winter of 2013-2014. In subsurface fluid samples we observe very high ferrous iron concentrations (>1mM), indicative of extended regions of iron reduction (to over 30cm depth). Within these zones of iron reduction we would predict no sulfate reduction, and as expected δ34Ssulfate remains unchanged with depth. However, δ18Osulfate exhibits significant enrichments of up to 5 permil. This decoupling in the sulfur and oxygen isotopes of sulfate is suggestive of a sulfate recycling process in which sulfate is reduced to an intermediate sulfur species and subsequently reoxidized to sulfate. Taken together, these data suggest that microbial assemblages in these salt marsh sediments facilitate a cryptic cycling of sulfur, potentially mediated by iron species in the zone of iron reduction.

Genome Sequence of the Moderately Acidophilic Sulfate-Reducing Firmicute Desulfosporosinus acididurans (Strain M1T).

PubMed

Petzsch, Patrick; Poehlein, Anja; Johnson, D Barrie; Daniel, Rolf; Schlömann, Michael; Mühling, Martin

2015-08-06

Microbial dissimilatory sulfate reduction is commonplace in many anaerobic environments, though few acidophilic bacteria are known to mediate this process. We report the 4.64-Mb draft genome of the type strain of the moderate acidophile Desulfosporosinus acididurans, which was isolated from acidic sediment in a river draining the Soufrière volcano, Montserrat. Copyright © 2015 Petzsch et al.

Microbial processes at the beds of glaciers and ice sheets: a look at life below the Whillans Ice Stream

NASA Astrophysics Data System (ADS)

Mikucki, J.; Campen, R.; Vancleave, S.; Scherer, R. P.; Coenen, J. J.; Powell, R. D.; Tulaczyk, S. M.

2017-12-01

Groundwater, saturated sediments and hundreds of subglacial lakes exist below the ice sheets of Antarctica. The few Antarctic subglacial environments sampled to date all contain viable microorganisms. This is a significant finding because microbes are known to be key in mediating biogeochemical cycles. In sediments, microbial metabolic activity can also result in byproducts or direct interactions with sediment particles that influence the physical and geochemical characteristics of the matrix they inhabit. Subglacial Lake Whillans (SLW), a fresh water lake under the Whillans Ice Stream that drains into the Ross Sea at its grounding zone, was recently sampled as part of the NSF-funded Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project. Sediments from both SLW and its grounding zone contain microbial taxa related to iron, sulfur, nitrogen and methane oxidizers. In addition to molecular data, biogeochemical measurements and culture based experiments on Whillans sediments support the notion that the system is chemosynthetic with energy derived in part by cycling inorganic compounds. Etch pitting and mineral precipitates on fossil sponge spicules suggest that spicules may also provide microbial nutrients in these environments. Perhaps the most widespread microbial process that affects sediment structure and mineral weathering is the production of extra polymeric substances (EPS). Several phylogenetic groups detected in Whillans sediments are known to produce EPS and we have observed its production in pure cultures enriched directly from these sediments. Our data sheds light on how microbial life persists below the Antarctic Ice Sheet despite extended isolation in icy darkness, and how these microbes may be shaping their environment.

Processes of carbonate precipitation in modern microbial mats

NASA Astrophysics Data System (ADS)

Dupraz, Christophe; Reid, R. Pamela; Braissant, Olivier; Decho, Alan W.; Norman, R. Sean; Visscher, Pieter T.

2009-10-01

Microbial mats are ecosystems that arguably greatly affected the conditions of the biosphere on Earth through geological time. These laminated organosedimentary systems, which date back to > 3.4 Ga bp, are characterized by high metabolic rates, and coupled to this, rapid cycling of major elements on very small (mm-µm) scales. The activity of the mat communities has changed Earth's redox conditions (i.e. oxidation state) through oxygen and hydrogen production. Interpretation of fossil microbial mats and their potential role in alteration of the Earth's geochemical environment is challenging because these mats are generally not well preserved. Preservation of microbial mats in the fossil record can be enhanced through carbonate precipitation, resulting in the formation of lithified mats, or microbialites. Several types of microbially-mediated mineralization can be distinguished, including biologically-induced and biologically influenced mineralization. Biologically-induced mineralization results from the interaction between biological activity and the environment. Biologically-influenced mineralization is defined as passive mineralization of organic matter (biogenic or abiogenic in origin), whose properties influence crystal morphology and composition. We propose to use the term organomineralization sensu lato as an umbrella term encompassing biologically influenced and biologically induced mineralization. Key components of organomineralization sensu lato are the "alkalinity" engine (microbial metabolism and environmental conditions impacting the calcium carbonate saturation index) and an organic matrix comprised of extracellular polymeric substances (EPS), which may provide a template for carbonate nucleation. Here we review the specific role of microbes and the EPS matrix in various mineralization processes and discuss examples of modern aquatic (freshwater, marine and hypersaline) and terrestrial microbialites.

Microbial biofilms in intertidal systems: an overview

NASA Astrophysics Data System (ADS)

Decho, Alan W.

2000-07-01

Intertidal marine systems are highly dynamic systems which are characterized by periodic fluctuations in environmental parameters. Microbial processes play critical roles in the remineralization of nutrients and primary production in intertidal systems. Many of the geochemical and biological processes which are mediated by microorganisms occur within microenvironments which can be measured over micrometer spatial scales. These processes are localized by cells within a matrix of extracellular polymeric secretions (EPS), collectively called a "microbial biofilm". Recent examinations of intertidal systems by a range of investigators using new approaches show an abundance of biofilm communities. The purpose of this overview is to examine recent information concerning the roles of microbial biofilms in intertidal systems. The microbial biofilm is a common adaptation of natural bacteria and other microorganisms. In the fluctuating environments of intertidal systems, biofilms form protective microenvironments and may structure a range of microbial processes. The EPS matrix of biofilm forms sticky coatings on individual sediment particles and detrital surfaces, which act as a stabilizing anchor to buffer cells and their extracellular processes during the frequent physical stresses (e.g., changes in salinity and temperature, UV irradiation, dessication). EPS is an operational definition designed to encompass a range of large microbially-secreted molecules having widely varying physical and chemical properties, and a range of biological roles. Examinations of EPS using Raman and Fourier-transform infared spectroscopy, and atomic-force microscopy suggest that some EPS gels possess physical and chemical properties which may hasten the development of sharp geochemical gradients, and contribute a protective effect to cells. Biofilm polymers act as a sorptive sponge which binds and concentrates organic molecules and ions close to cells. Concurrently, the EPS appear to localize extracellular enzyme activities of bacteria, and hence contribute to the efficient biomineralization of organics. At larger spatial scales, the copious secretion of specific types of EPS by diatoms on the surfaces of intertidal mudflats may stabilize sediments against resuspension. Biofilms exert important roles in environmental- and public health processes occurring within intertidal systems. The sorptive properties of EPS effectively chelate toxic metals and other contaminants, which then act as an efficient trophic-transfer vehicle for the entry of contaminants into food webs. In the water column, biofilm microenvironments in suspended flocs may form a stabilizing refugia that enhances the survival and propagation of pathogenic (i.e., disease-causing) bacteria entering coastal waters from terrestrial and freshwater sources. The EPS matrix affords microbial cells a tremendous potential for resiliency during periods of stress, and may enhance the overall physiological activities of bacteria. It is emphasized here that the influences of small-scale microbial biofilms must be addressed in understanding larger-scale processes within intertidal systems.

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone

PubMed Central

Hawley, Alyse K.; Katsev, Sergei; Torres-Beltran, Monica; Bhatia, Maya P.; Kheirandish, Sam; Michiels, Céline C.; Capelle, David; Lavik, Gaute; Doebeli, Michael; Crowe, Sean A.; Hallam, Steven J.

2016-01-01

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet—a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite “leakage” during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales. PMID:27655888

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.

PubMed

Louca, Stilianos; Hawley, Alyse K; Katsev, Sergei; Torres-Beltran, Monica; Bhatia, Maya P; Kheirandish, Sam; Michiels, Céline C; Capelle, David; Lavik, Gaute; Doebeli, Michael; Crowe, Sean A; Hallam, Steven J

2016-10-04

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite "leakage" during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.

Microbial activity in the marine deep biosphere: progress and prospects.

PubMed

Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

Microbial activity in the marine deep biosphere: progress and prospects

PubMed Central

Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

PubMed

Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

2017-10-15

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

The response of soil carbon storage and microbially mediated carbon turnover to simulated climatic disturbance in a northern peatland forest. Revisiting the concept of soil organic matter recalcitrance

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

Kostka, Joel

The goal of this project was to investigate changes in the structure of dissolved and solid phase organic matter, the production of CO 2 and CH 4, and the composition of decomposer microbial communities in response to the climatic forcing of environmental processes that determine the balance between carbon gas production versus storage and sequestration in peatlands. Cutting-edge analytical chemistry and next generation sequencing of microbial genes were been applied to habitats at the Marcell Experimental Forest (MEF), where the US DOE’s Oak Ridge National Laboratory and the USDA Forest Service are constructing a large-scale ecosystem study entitled, “Spruce andmore » Peatland Responses Under Climatic and Environmental Change”(SPRUCE). Our study represented a comprehensive characterization of the sources, transformation, and decomposition of organic matter in the S1 bog at MEF. Multiple lines of evidence point to distinct, vertical zones of organic matter transformation: 1) the acrotelm consisting of living mosses, root material, and newly formed litter (0-30 cm), 2) the mesotelm, a mid-depth transition zone (30-75 cm) characterized by labile organic C compounds and intense decomposition, and 3) the underlying catotelm (below 75cm) characterized by refractory organic compounds as well as relatively low decomposition rates. These zones are in part defined by physical changes in hydraulic conductivity and water table depth. O-alkyl-C, which represents the carbohydrate fraction in the peat, was shown to be an excellent proxy for soil decomposition rates. The carbon cycle in deep peat was shown to be fueled by modern carbon sources further indicating that hydrology and surface vegetation play a role in belowground carbon cycling. We provide the first metagenomic study of an ombrotrophic peat bog, with novel insights into microbial specialization and functions in this unique terrestrial ecosystem. Vertical structuring of microbial communities closely paralleled the chemical evolution of peat, with large shifts in microbial populations occurring in the biogeochemical hotspot, the mesotelm, where the highest rates of decomposition were detected. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens dominated in the deeper catotelm. Evidence pointed to the availability of phosphorus as well as nitrogen limiting the microbially-mediated turnover of organic carbon at MEF. Prior to initiation of the experimental treatments, our study provided key baseline data for the SPRUCE site on the vertical stratification of peat decomposition, key enzymatic pathways, and microbial taxa containing these pathways. The sensitivity of soil carbon turnover to climate change is strongly linked to recalcitrant carbon stocks and the temperature sensitivity of decomposition is thought to increase with increasing molecular complexity of carbon substrates. This project delivered results on how climate change perturbations impact the microbially-mediated turnover of recalcitrant organic matter in peatland forest soils, both under controlled conditions in the laboratory and at the ecosystem-scale in the field. This project revisited the concept of “recalcitrance” in the regulation of soil carbon turnover using a combination of natural abundance radiocarbon and optical spectroscopic measurements on bulk DOM, and high resolution molecular characterization of DOM. The project elucidated how organic matter reactivity and decomposition will respond to climate change in a both a qualitative (organic matter lability) and quantitiative (increased rates) manner. An Aromaticity Index was developed to represent a more direct and accurate parameter for modeling of DOM reactivity in peatlands. The abundance and community composition of soil microorganisms that mediate C cycling were interrogated with depth in the peat, with season, and in manipulated climate enclosures at unprecedented resolution. Therefore this project delivered strategic new insights on the functioning of peatland ecosystems that collectively store approximately one-third of the world's soil carbon. Furthermore, results from the detailed characterization of DOM lability and microbial community structure/ function will be employed to further develop biogeochemical models to include microbial respiration pathways as well as to track carbon flow with a term that incorporates relative reactivity based on aromaticity index. As it stands now, detailed soil organic matter structure and microbial parameters are not included in Earth system models.« 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.

The development of stromatolitic features from laminated microbial mats in the coastal sabkha of Abu Dhabi (UAE)

NASA Astrophysics Data System (ADS)

Paul, Andreas; Lessa Andrade, Luiza; Dutton, Kirsten E.; Sherry, Angela; Court, Wesley M.; Van der Land, Cees; Lokier, Stephen W.; Head, Ian M.

2017-04-01

Stromatolitic features are documented from both marine and terrestrial environments worldwide. These features form through a combination of trapping and binding of allochthonous grains, and through microbially mediated and/or controlled precipitation of carbonate minerals. The combined effects of these processes result in the continuous vertical and lateral growth of stromatolites. While the Abu Dhabi coastal sabkha is well known for a vast microbial mat belt that is dominated by continuous polygonal and internally-laminated microbial mats, no stromatolitic features have been reported from this area so far. In this study, we report evidence for stromatolitic features from the coastal sabkha of Abu Dhabi, based on observations in an intertidal but permanently submerged pool. This pool lies embedded within the laminated microbial mat zone, and is marked by the development of true laminated stromatolite at its margins and microbial build-ups at its centre. In order to characterise processes that lead to the formation of these stromatolitic features, and to develop a conceptual model that describes their development in the context of variations in sea level, tidal energy and other environmental factors, we employ a multitude of environmental, sedimentological, mineralogical and geochemical methods. These methods include the analysis of water data in terms of temporal variations in temperature, salinity, dissolved oxygen and water level, the analysis of petrographic thin sections of both lithified and unlithified features as well as an analysis of the stromatolites' mineralogical composition, and the amounts of incorporated organic carbon and calcium carbonate. Initial results suggest that the development of the observed stromatolitic features in the coastal sabkha of Abu Dhabi is the result of a complex interplay between simultaneous erosion of laminated microbial mat, and biotic/abiotic lithification processes. Initially, the location of this pool was characterised by a continuous laminated microbial mat. Through Recent changes in sea level and/or of the associated environmental conditions, this microbial mat was removed. At the same time as this erosion occurred, lithification processes set-in that continuously stabilised the extending pool margin. Through this extension, selected areas of the newly lithified mat were left behind, and formed the build-ups in the pool's centre that are observed today. This lithification might have been controlled by a change in the associated microbial mat communities from non-lithifying to lithifying, due to the permanent exposure to seawater by which this pool is characterised.

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

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

Interspecies Interactions Determine the Impact of the Gut Microbiota on Nutrient Allocation in Drosophila melanogaster

PubMed Central

Douglas, Angela E.

2014-01-01

The animal gut is perpetually exposed to microorganisms, and this microbiota affects development, nutrient allocation, and immune homeostasis. A major challenge is to understand the contribution of individual microbial species and interactions among species in shaping these microbe-dependent traits. Using the Drosophila melanogaster gut microbiota, we tested whether microbe-dependent performance and nutritional traits of Drosophila are functionally modular, i.e., whether the impact of each microbial taxon on host traits is independent of the presence of other microbial taxa. Gnotobiotic flies were constructed with one or a set of five of the Acetobacter and Lactobacillus species which dominate the gut microbiota of conventional flies (Drosophila with untreated microbiota). Axenic (microbiota-free) flies exhibited prolonged development time and elevated glucose and triglyceride contents. The low glucose content of conventional flies was recapitulated in gnotobiotic Drosophila flies colonized with any of the 5 bacterial taxa tested. In contrast, the development rates and triglyceride levels in monocolonized flies varied depending on the taxon present: Acetobacter species supported the largest reductions, while most Lactobacillus species had no effect. Only flies with both Acetobacter and Lactobacillus had triglyceride contents restored to the level in conventional flies. This could be attributed to two processes: Lactobacillus-mediated promotion of Acetobacter abundance in the fly and a significant negative correlation between fly triglyceride content and Acetobacter abundance. We conclude that the microbial basis of host traits varies in both specificity and modularity; microbe-mediated reduction in glucose is relatively nonspecific and modular, while triglyceride content is influenced by interactions among microbes. PMID:24242251

Lipidomic analysis of patients with microbial invasion of the amniotic cavity reveals up-regulation of leukotriene B4

PubMed Central

Maddipati, Krishna Rao; Romero, Roberto; Chaiworapongsa, Tinnakorn; Chaemsaithong, Piya; Zhou, Sen-Lin; Xu, Zhonghui; Tarca, Adi L.; Kusanovic, Juan Pedro; Gomez, Ricardo; Chaiyasit, Noppadol; Honn, Kenneth V.

2016-01-01

Bioactive lipids derived from the metabolism of polyunsaturated fatty acids are important mediators of the inflammatory response. Labor per se is considered a sterile inflammatory process. Intra-amniotic inflammation (IAI) due to microorganisms (i.e., intra-amniotic infection) or danger signals (i.e., sterile IAI) has been implicated in the pathogenesis of preterm labor and clinical chorioamnionitis at term. Early and accurate diagnosis of microbial invasion of the amniotic cavity (MIAC) requires analysis of amniotic fluid (AF). It is possible that IAI caused by microorganisms is associated with a stereotypic lipidomic profile, and that analysis of AF may help in the identification of patients with this condition. To test this hypothesis, we analyzed the fatty acyl lipidome of AF by liquid chromatography—mass spectrometry from patients in spontaneous labor at term and preterm gestations. We report that the AF concentrations of proinflammatory lipid mediators of the 5-lipoxygenase pathway are significantly higher in MIAC than in cases of sterile IAI. These results suggest that the concentrations of 5-lipoxygenase metabolites of arachidonic acid, 5-hydroxyeicosatetraenoic acid, and leukotriene B4 in particular could serve as potential biomarkers of MIAC. This finding could have important implications for the rapid identification of patients who may benefit from anti-microbial treatment.—Maddipati, K. R., Romero, R., Chaiworapongsa ,T., Chaemsaithong, P., Zhou, S.-L., Xu, Z., Tarca, A. L., Kusanovic, J. P., Gomez, R., Chaiyasit, N., Honn, K. V. Lipidomic analysis of patients with microbial invasion of the amniotic cavity reveals up-regulation of leukotriene B4. PMID:27312808

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

PubMed

Long, Philip E; Williams, Kenneth H; Hubbard, Susan S; Banfield, Jillian F

2016-08-01

Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O. Copyright © 2016 Elsevier Ltd. All rights reserved.

Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

NASA Astrophysics Data System (ADS)

Upton, R.; Bach, E.; Hofmockel, K. S.

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system provides increased C cycling activity. Our results showed that diverse cropping systems still benefit from N fertilization to confer resiliency to abiotic stress factors. Long-term studies for microbial mediation of soil C are necessary for modeling the impacts of restoration on SOC to assure inclusion of sustainability and resiliency.

Geophysical methods for monitoring soil stabilization processes

NASA Astrophysics Data System (ADS)

Saneiyan, Sina; Ntarlagiannis, Dimitrios; Werkema, D. Dale; Ustra, Andréa

2018-01-01

Soil stabilization involves methods used to turn unconsolidated and unstable soil into a stiffer, consolidated medium that could support engineered structures, alter permeability, change subsurface flow, or immobilize contamination through mineral precipitation. Among the variety of available methods carbonate precipitation is a very promising one, especially when it is being induced through common soil borne microbes (MICP - microbial induced carbonate precipitation). Such microbial mediated precipitation has the added benefit of not harming the environment as other methods can be environmentally detrimental. Carbonate precipitation, typically in the form of calcite, is a naturally occurring process that can be manipulated to deliver the expected soil strengthening results or permeability changes. This study investigates the ability of spectral induced polarization and shear-wave velocity for monitoring calcite driven soil strengthening processes. The results support the use of these geophysical methods as soil strengthening characterization and long term monitoring tools, which is a requirement for viable soil stabilization projects. Both tested methods are sensitive to calcite precipitation, with SIP offering additional information related to long term stability of precipitated carbonate. Carbonate precipitation has been confirmed with direct methods, such as direct sampling and scanning electron microscopy (SEM). This study advances our understanding of soil strengthening processes and permeability alterations, and is a crucial step for the use of geophysical methods as monitoring tools in microbial induced soil alterations through carbonate precipitation.

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.

Evaluation of Kefir as a New Anodic Biocatalyst Consortium for Microbial Fuel Cell.

PubMed

Silveira, Gustavo; Schneedorf, José Maurício

2018-02-21

Kefir, a combined consortium of bacteria and yeast encapsulated by a polymeric matrix of exopolysaccharides, was used as anodic biocatalyst in a two-chamber microbial fuel cell (MFC). Fermentation was followed during 72 h and polarization curves were obtained from linear sweep voltammetry. The effect of methylene blue as charge-transfer mediator in the kefir metabolism was evaluated. UV/Vis spectrophotometry and cyclic voltammetry were applied to evaluate the redox state of the mediator and to characterize the electrochemical activity, whereas current interruption was used for internal resistance determination. Aiming to establish a relationship between the microbial development inside the anodic chamber with the generated power in the MFC, total titratable acidity, pH, viscosity, carbohydrate assimilation, and microbial counting were assayed. The kefir-based MFC demonstrated a maximum power density of 54 mW m -2 after 24 h fermentation, revealing the potential use of kefir as a biocatalyst for microbial fuel cells.

Outlook for benefits of sediment microbial fuel cells with two bio‐electrodes

PubMed Central

De Schamphelaire, Liesje; Rabaey, Korneel; Boeckx, Pascal; Boon, Nico; Verstraete, Willy

2008-01-01

Summary The benefits of sediment microbial fuel cells (SMFCs) go beyond energy generation for low‐power applications. Aside from producing electrical energy, SMFCs can enhance the oxidation of reduced compounds at the anode, thus bringing about the removal of excessive or unwanted reducing equivalents from submerged soils. Moreover, an SMFC could be applied to control redox‐dependent processes in sediment layers. Several cathodic reactions that may drive these sediment oxidation reactions are examined. Special attention is given to two biologically mediated cathodic reactions, respectively employing an oxygen reduction and a manganese cycle. Both reactions imply a low cost and a high electrode potential and are of interest for reactor‐type MFCs as well as for SMFCs. PMID:21261866

Performance Indicators for Uranium Bioremediation in the Subsurface: Basis and Assessment

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

Long, Philip E.; Yabusaki, Steven B.

2006-12-29

The purpose of this letter report is to identify performance indicators for in situ engineered bioremediation of subsurface uranium (U) contamination. This report focuses on in situ treatment of groundwater by biostimulation of extant in situ microbial populations (see http://128.3.7.51/NABIR/generalinfo/primers_guides/03_NABIR_primer.pdf for background information on bioremediation of metals and radionuclides). The treatment process involves amendment of the subsurface with an electron donor such as acetate, lactate, ethanol or other organic compound such that in situ microorganisms mediate the reduction of U(VI) to U(IV). U(VI) precipitates as uraninite or other insoluble U phase. Uranium is thus immobilized in place by such processesmore » and is subject to reoxidation that may remobilize the reduced uranium. Related processes include augmenting the extant subsurface microbial populations, addition of electron acceptors, and introduction of chemically reducing materials such as zero-valent Fe. While metrics for such processes may be similar to those for in situ biostimulation, these related processes are not directly in the scope of this letter report.« less

An Overview of Electron Acceptors in Microbial Fuel Cells

PubMed Central

Ucar, Deniz; Zhang, Yifeng; Angelidaki, Irini

2017-01-01

Microbial fuel cells (MFC) have recently received increasing attention due to their promising potential in sustainable wastewater treatment and contaminant removal. In general, contaminants can be removed either as an electron donor via microbial catalyzed oxidization at the anode or removed at the cathode as electron acceptors through reduction. Some contaminants can also function as electron mediators at the anode or cathode. While previous studies have done a thorough assessment of electron donors, cathodic electron acceptors and mediators have not been as well described. Oxygen is widely used as an electron acceptor due to its high oxidation potential and ready availability. Recent studies, however, have begun to assess the use of different electron acceptors because of the (1) diversity of redox potential, (2) needs of alternative and more efficient cathode reaction, and (3) expanding of MFC based technologies in different areas. The aim of this review was to evaluate the performance and applicability of various electron acceptors and mediators used in MFCs. This review also evaluated the corresponding performance, advantages and disadvantages, and future potential applications of select electron acceptors (e.g., nitrate, iron, copper, perchlorate) and mediators. PMID:28469607

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.

Predicting Biological Information Flow in a Model Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Louca, S.; Hawley, A. K.; Katsev, S.; Beltran, M. T.; Bhatia, M. P.; Michiels, C.; Capelle, D.; Lavik, G.; Doebeli, M.; Crowe, S.; Hallam, S. J.

2016-02-01

Microbial activity drives marine biochemical fluxes and nutrient cycling at global scales. Geochemical measurements as well as molecular techniques such as metagenomics, metatranscriptomics and metaproteomics provide great insight into microbial activity. However, an integration of molecular and geochemical data into mechanistic biogeochemical models is still lacking. Recent work suggests that microbial metabolic pathways are, at the ecosystem level, strongly shaped by stoichiometric and energetic constraints. Hence, models rooted in fluxes of matter and energy may yield a holistic understanding of biogeochemistry. Furthermore, such pathway-centric models would allow a direct consolidation with meta'omic data. Here we present a pathway-centric biogeochemical model for the seasonal oxygen minimum zone in Saanich Inlet, a fjord off the coast of Vancouver Island. The model considers key dissimilatory nitrogen and sulfur fluxes, as well as the population dynamics of the genes that mediate them. By assuming a direct translation of biocatalyzed energy fluxes to biosynthesis rates, we make predictions about the distribution and activity of the corresponding genes. A comparison of the model to molecular measurements indicates that the model explains observed DNA, RNA, protein and cell depth profiles. This suggests that microbial activity in marine ecosystems such as oxygen minimum zones is well described by DNA abundance, which, in conjunction with geochemical constraints, determines pathway expression and process rates. Our work further demonstrates how meta'omic data can be mechanistically linked to environmental redox conditions and biogeochemical processes.

Manganese(II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes.

PubMed

Dick, Gregory J; Lee, Yifan E; Tebo, Bradley M

2006-05-01

Microbial oxidation and precipitation of manganese at deep-sea hydrothermal vents are important oceanic biogeochemical processes, yet nothing is known about the types of microorganisms or mechanisms involved. Here we report isolation of a number of diverse spore-forming Mn(II)-oxidizing Bacillus species from Guaymas Basin, a deep-sea hydrothermal vent environment in the Gulf of California, where rapid microbially mediated Mn(II) oxidation was previously observed. mnxG multicopper oxidase genes involved in Mn(II) oxidation were amplified from all Mn(II)-oxidizing Bacillus spores isolated, suggesting that a copper-mediated mechanism of Mn(II) oxidation could be important at deep-sea hydrothermal vents. Phylogenetic analysis of 16S rRNA and mnxG genes revealed that while many of the deep-sea Mn(II)-oxidizing Bacillus species are very closely related to previously recognized isolates from coastal sediments, other organisms represent novel strains and clusters. The growth and Mn(II) oxidation properties of these Bacillus species suggest that in hydrothermal sediments they are likely present as spores that are active in oxidizing Mn(II) as it emerges from the seafloor.

Chromite oxidation by manganese oxides in subseafloor basalts and the presence of putative fossilized microorganisms.

PubMed

Ivarsson, Magnus; Broman, Curt; Holm, Nils G

2011-06-03

Chromite is a mineral with low solubility and is thus resistant to dissolution. The exception is when manganese oxides are available, since they are the only known naturally occurring oxidants for chromite. In the presence of Mn(IV) oxides, Cr(III) will oxidise to Cr(VI), which is more soluble than Cr(III), and thus easier to be removed. Here we report of chromite phenocrysts that are replaced by rhodochrosite (Mn(II) carbonate) in subseafloor basalts from the Koko Seamount, Pacific Ocean, that were drilled and collected during the Ocean Drilling Program (ODP) Leg 197. The mineral succession chromite-rhodochrosite-saponite in the phenocrysts is interpreted as the result of chromite oxidation by manganese oxides. Putative fossilized microorganisms are abundant in the rhodochrosite and we suggest that the oxidation of chromite has been mediated by microbial activity. It has previously been shown in soils and in laboratory experiments that chromium oxidation is indirectly mediated by microbial formation of manganese oxides. Here we suggest a similar process in subseafloor basalts.

Chromite oxidation by manganese oxides in subseafloor basalts and the presence of putative fossilized microorganisms

PubMed Central

2011-01-01

Chromite is a mineral with low solubility and is thus resistant to dissolution. The exception is when manganese oxides are available, since they are the only known naturally occurring oxidants for chromite. In the presence of Mn(IV) oxides, Cr(III) will oxidise to Cr(VI), which is more soluble than Cr(III), and thus easier to be removed. Here we report of chromite phenocrysts that are replaced by rhodochrosite (Mn(II) carbonate) in subseafloor basalts from the Koko Seamount, Pacific Ocean, that were drilled and collected during the Ocean Drilling Program (ODP) Leg 197. The mineral succession chromite-rhodochrosite-saponite in the phenocrysts is interpreted as the result of chromite oxidation by manganese oxides. Putative fossilized microorganisms are abundant in the rhodochrosite and we suggest that the oxidation of chromite has been mediated by microbial activity. It has previously been shown in soils and in laboratory experiments that chromium oxidation is indirectly mediated by microbial formation of manganese oxides. Here we suggest a similar process in subseafloor basalts. PMID:21639896

Postmortem succession of gut microbial communities in deceased human subjects

PubMed Central

Hauther, Kathleen A.

2017-01-01

The human microbiome has demonstrated an importance for the health and functioning in living individuals. However, the fate of the microbiome after death is less understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs =  − 0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) significantly declined while Clostridiales (Clostridium, Anaerosphaera) and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes. PMID:28626612

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities.

PubMed

Davison, John; Moora, Mari; Öpik, Maarja; Ainsaar, Leho; Ducousso, Marc; Hiiesalu, Inga; Jairus, Teele; Johnson, Nancy; Jourand, Philippe; Kalamees, Rein; Koorem, Kadri; Meyer, Jean-Yves; Püssa, Kersti; Reier, Ülle; Pärtel, Meelis; Semchenko, Marina; Traveset, Anna; Vasar, Martti; Zobel, Martin

2018-06-08

Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored taxa, indicating that dispersal may be human-mediated or require tolerance of significant environmental stress, such as exposure to sunlight or high salinity. The processes driving large-scale patterns of microbial diversity are a key consideration for attempts to conserve and restore functioning ecosystems in this era of rapid global change.

Sulfur-Mediated Electron Shuttling Sustains Microbial Long-Distance Extracellular Electron Transfer with the Aid of Metallic Iron Sulfides.

PubMed

Kondo, Katsuhito; Okamoto, Akihiro; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-07-07

In addition to serving as an energy source for microbial growth, iron sulfides are proposed to act as naturally occurring electrical wires that mediate long-distance extracellular electron transfer (EET) and bridge spatially discrete redox environments. These hypothetical EET reactions stand on the abilities of microbes to use the interfacial electrochemistry of metallic/semiconductive iron sulfides to maintain metabolisms; however, the mechanisms of these phenomena remain unexplored. To obtain insight into EET to iron sulfides, we monitored EET at the interface between Shewanella oneidensis MR-1 cells and biomineralized iron sulfides in an electrochemical cell. Respiratory current steeply increased with the concomitant formation of poorly crystalline mackinawite (FeS) minerals, indicating that S. oneidensis has the ability to exploit extracellularly formed metallic FeS for long-distance EET. Deletion of major proteins of the metal-reduction (Mtr) pathway (OmcA, MtrC, CymA, and PilD) caused only subtle effects on the EET efficiency, a finding that sharply contrasts the majority of studies that report that the Mtr pathway is indispensable for the reduction of metal oxides and electrodes. The gene expression analyses of polysulfide and thiosulfate reductase suggest the existence of a sulfur-mediated electron-shuttling mechanism by which HS(-) ions and water-soluble polysulfides (HS(n)(-), where n ≥ 2) generated in the periplasmic space deliver electrons from cellular metabolic processes to cell surface-associated FeS. The finding of this Mtr-independent pathway indicates that polysulfide reductases complement the function of outer-membrane cytochromes in EET reactions and, thus, significantly expand the number of microbial species potentially capable of long-distance EET in sulfur-rich anoxic environments.

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.

Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition

PubMed Central

Freedman, Zachary; Zak, Donald R.; Xue, Kai; He, Zhili; Zhou, Jizhong

2013-01-01

Future rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems. PMID:23220961

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

PubMed Central

Levine, Jonathan M.; HilleRisLambers, Janneke

2014-01-01

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

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

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

NASA Astrophysics Data System (ADS)

Tully, B. J.; Wheat, C. G.; Glazer, B. T.; Huber, J. A.

2017-12-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized genomic reconstruction of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement. Twenty-one samples were collected during a two-year period at three different depths and two locations with the basaltic aquifer to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the two years, yet a dynamic microbial community was present in the crustal fluids that underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the dataset and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in a diverse group of microorganisms. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes and alternative electron acceptors. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles.

Siderophores mediate reduced and increased uptake of cadmium by Streptomyces tendae F4 and sunflower (Helianthus annuus), respectively.

PubMed

Dimkpa, C O; Merten, D; Svatos, A; Büchel, G; Kothe, E

2009-11-01

As a toxic metal, cadmium (Cd) affects microbial and plant metabolic processes, thereby potentially reducing the efficiency of microbe or plant-mediated remediation of Cd-polluted soil. The role of siderophores produced by Streptomyces tendae F4 in the uptake of Cd by bacteria and plant was investigated to gain insight into the influence of siderophores on Cd availability to micro-organisms and plants. The bacterium was cultured under siderophore-inducing conditions in the presence of Cd. The kinetics of siderophore production and identification of the siderophores and their metal-bound forms were performed using electrospray ionization mass spectrometry. Inductively coupled plasma spectroscopy was used to measure iron (Fe) and Cd contents in the bacterium and in sunflower plant grown in Cd-amended soil. Siderophores significantly reduced the Cd uptake by the bacterium, while supplying it with iron. Bacterial culture filtrates containing three hydroxamate siderophores secreted by S. tendae F4 significantly promoted plant growth and enhanced uptake of Cd and Fe by the plant, relative to the control. Furthermore, application of siderophores caused slightly more Cd, but similar Fe uptake, compared with EDTA. Bioinoculation with Streptomyces caused a dramatic increase in plant Fe content, but resulted only in slight increase in plant Cd content. It is concluded that siderophores can help reduce toxic metal uptake in bacteria, while simultaneously facilitating the uptake of such metals by plants. Also, EDTA is not superior to hydroxamate siderophores in terms of metal solubilization for plant uptake. The study showed that microbial processes could indirectly influence the availability and amount of toxic metals taken up from the rhizosphere of plants. Furthermore, although EDTA is used for chelator-enhanced phytoremediation, microbial siderophores would be ideal for this purpose.

Temporal changes in soil bacterial diversity and humic substances degradation in subarctic tundra soil.

PubMed

Park, Ha Ju; Chae, Namyi; Sul, Woo Jun; Lee, Bang Yong; Lee, Yoo Kyung; Kim, Dockyu

2015-04-01

Humic substances (HS), primarily humic acids (HA) and fulvic acids (FA), are the largest constituent of soil organic matter. In microcosm systems with subarctic HS-rich tundra soil (site AK 1-75; approximately 5.6 °C during the thawing period) from Council, Alaska, the HA content significantly decreased to 48% after a 99-day incubation at 5 °C as part of a biologically mediated process. Accordingly, levels of FA, a putative byproduct of HA degradation, consistently increased to 172% during an identical incubation process. Culture-independent microbial community analysis showed that during the microcosm experiments, the relative abundance of phyla Proteobacteria (bacteria) and Euryarchaeota (archaea) largely increased, indicating their involvement in HS degradation. When the indigenous bacteria in AK 1-75 were enriched in an artificial mineral medium spiked with HA, the changes in relative abundance were most conspicuous in Proteobacteria (from 60.2 to 79.0%), specifically Betaproteobacteria-related bacteria. One hundred twenty-two HA-degrading bacterial strains, primarily from the genera Paenibacillus (phylum Firmicutes) and Pseudomonas (class Gammaproteobacteria), were cultivated from AK 1-75 and nearby sites. Through culture-dependent analysis with these bacterial isolates, we observed increasing HS-degradation rates in parallel with rising temperatures in a range of 0 °C to 20 °C, with the most notable increase occurring at 8 °C compared to 6 °C. Our results indicate that, although microbial-mediated HS degradation occurs at temperature as low as 5 °C in tundra ecosystems, increasing soil temperature caused by global climate change could enhance HS degradation rates. Extending the thawing period could also increase degradation activity, thereby directly affecting nearby microbial communities and rhizosphere environments.

Preliminary assessment of microbial communities and biodegradation of chlorinated volatile organic compounds in wetlands at Cluster 13, Lauderick Creek area, Aberdeen Proving Ground, Maryland

USGS Publications Warehouse

Lorah, Michelle M.; Voytek, Mary A.; Spencer, Tracey A.

2003-01-01

A preliminary assessment of the microbial communities and biodegradation processes for chlorinated volatile organic compounds was con-ducted by the U.S. Geological Survey in wetlands at the Cluster 13, Lauderick Creek area at Aberdeen Proving Ground, Maryland. The U.S. Geological Survey collected wetland sediment samples from 11 sites in the Lauderick Creek area for microbial analyses, and used existing data to evaluate biodegradation processes and rates. The bacterial and methanogen communities in the Lauderick Creek wetland sediments were similar to those observed in a previous U.S. Geological Survey study at the West Branch Canal Creek wet-land area, Aberdeen Proving Ground. Evaluation of the degradation rate of 1,1,2,2-tetrachloroethane and the daughter compounds produced also showed similar results for the two wetlands. How-ever, a vertical profile of contaminant concentra-tions in the wetlands was available at only one site in the Lauderick Creek area, and flow velocities in the wetland sediment are unknown. To better evaluate natural attenuation processes and rates in the wetland sediments at Lauderick Creek, chemi-cal and hydrologic measurements are needed along ground-water flowpaths in the wetland at additional sites and during different seasons. Nat-ural attenuation in the wetlands, enhanced biore-mediation, and constructed wetlands could be feasible remediation methods for the chlorinated volatile organic compounds discharging in the Lauderick Creek area. The similarities in the microbial communities and biodegradation pro-cesses at the Lauderick Creek and West Branch Canal Creek areas indicate that enhanced bioreme-diation techniques currently being developed for the West Branch Canal Creek wetland area would be transferable to this area.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer.

PubMed

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb 3 - and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats.

PubMed

Dick, Gregory J; Anantharaman, Karthik; Baker, Brett J; Li, Meng; Reed, Daniel C; Sheik, Cody S

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales.

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats

PubMed Central

Dick, Gregory J.; Anantharaman, Karthik; Baker, Brett J.; Li, Meng; Reed, Daniel C.; Sheik, Cody S.

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales. PMID:23720658

Adaptation of Aquatic Microbial Communities to Hg2+ Stress †

PubMed Central

Barkay, Tamar

1987-01-01

The mechanism of adaptation to Hg2+ in four aquatic habitats was studied by correlating microbially mediated Hg2+ volatilization with the adaptive state of the exposed communities. Community diversity, heterotrophic activity, and Hg2+ resistance measurements indicated that adaptation of all four communities was stimulated by preexposure to Hg2+. In saline water communities, adaptation was associated with rapid volatilization after an initial lag period. This mechanism, however, did not promote adaptation in a freshwater sample, in which Hg2+ was volatilized slowly, regardless of the resistance level of the microbial community. Distribution of the mer operon among representative colonies of the communities was not related to adaptation to Hg2+. Thus, although volatilization enabled some microbial communities to sustain their functions in Hg2+-stressed environments, it was not mediated by the genes that serve as a model system in molecular studies of bacterial resistance to mercurials. PMID:16347488

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches.

PubMed

Malla, Muneer A; Dubey, Anamika; Yadav, Shweta; Kumar, Ashwani; Hashem, Abeer; Abd Allah, Elsayed Fathi

2018-01-01

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

PubMed Central

Malla, Muneer A.; Dubey, Anamika; Yadav, Shweta; Kumar, Ashwani; Hashem, Abeer; Abd_Allah, Elsayed Fathi

2018-01-01

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches. PMID:29915565

Microbe-surface interactions in biofouling and biocorrosion processes.

PubMed

Beech, Iwona B; Sunner, Jan A; Hiraoka, Kenzo

2005-09-01

The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.

How agricultural management shapes soil microbial communities: patterns emerging from genetic and genomic studies

NASA Astrophysics Data System (ADS)

Daly, Amanda; Grandy, A. Stuart

2016-04-01

Agriculture is a predominant land use and thus a large influence on global carbon (C) and nitrogen (N) balances, climate, and human health. If we are to produce food, fiber, and fuel sustainably we must maximize agricultural yield while minimizing negative environmental consequences, goals towards which we have made great strides through agronomic advances. However, most agronomic strategies have been designed with a view of soil as a black box, largely ignoring the way management is mediated by soil biota. Because soil microbes play a central role in many of the processes that deliver nutrients to crops and support their health and productivity, agricultural management strategies targeted to exploit or support microbial activity should deliver additional benefits. To do this we must determine how microbial community structure and function are shaped by agricultural practices, but until recently our characterizations of soil microbial communities in agricultural soils have been largely limited to broad taxonomic classes due to methodological constraints. With advances in high-throughput genetic and genomic sequencing techniques, better taxonomic resolution now enables us to determine how agricultural management affects specific microbes and, in turn, nutrient cycling outcomes. Here we unite findings from published research that includes genetic or genomic data about microbial community structure (e.g. 454, Illumina, clone libraries, qPCR) in soils under agricultural management regimes that differ in type and extent of tillage, cropping selections and rotations, inclusion of cover crops, organic amendments, and/or synthetic fertilizer application. We delineate patterns linking agricultural management to microbial diversity, biomass, C- and N-content, and abundance of microbial taxa; furthermore, where available, we compare patterns in microbial communities to patterns in soil extracellular enzyme activities, catabolic profiles, inorganic nitrogen pools, and nitrogen transforming processes. Where genetic data are scarce, we further inform our observations with data from phosopholipid fatty acid, ribosomal intergenic spacer, (terminal) restriction fragment length polymorphism, and denaturing gradient gel electrophoresis analyses. By summarizing the most current information about microbial community structure under different agricultural management strategies, we hope to jumpstart a dialogue that could ultimately inspire novel - and sustainable - agronomic approaches that work with and through soil microbes.

Biofilms in Endodontics-Current Status and Future Directions.

PubMed

Neelakantan, Prasanna; Romero, Monica; Vera, Jorge; Daood, Umer; Khan, Asad U; Yan, Aixin; Cheung, Gary Shun Pan

2017-08-11

Microbiota are found in highly organized and complex entities, known as biofilms, the characteristics of which are fundamentally different from microbes in planktonic suspensions. Root canal infections are biofilm mediated. The complexity and variability of the root canal system, together with the multi-species nature of biofilms, make disinfection of this system extremely challenging. Microbial persistence appears to be the most important factor for failure of root canal treatment and this could further have an impact on pain and quality of life. Biofilm removal is accomplished by a chemo-mechanical process, using specific instruments and disinfecting chemicals in the form of irrigants and/or intracanal medicaments. Endodontic research has focused on the characterization of root canal biofilms and the clinical methods to disrupt the biofilms in addition to achieving microbial killing. In this narrative review, we discuss the role of microbial biofilms in endodontics and review the literature on the role of root canal disinfectants and disinfectant-activating methods on biofilm removal.

Biofilms in Endodontics—Current Status and Future Directions

PubMed Central

Neelakantan, Prasanna; Romero, Monica; Vera, Jorge; Daood, Umer; Khan, Asad U.; Yan, Aixin; Cheung, Gary Shun Pan

2017-01-01

Microbiota are found in highly organized and complex entities, known as biofilms, the characteristics of which are fundamentally different from microbes in planktonic suspensions. Root canal infections are biofilm mediated. The complexity and variability of the root canal system, together with the multi-species nature of biofilms, make disinfection of this system extremely challenging. Microbial persistence appears to be the most important factor for failure of root canal treatment and this could further have an impact on pain and quality of life. Biofilm removal is accomplished by a chemo-mechanical process, using specific instruments and disinfecting chemicals in the form of irrigants and/or intracanal medicaments. Endodontic research has focused on the characterization of root canal biofilms and the clinical methods to disrupt the biofilms in addition to achieving microbial killing. In this narrative review, we discuss the role of microbial biofilms in endodontics and review the literature on the role of root canal disinfectants and disinfectant-activating methods on biofilm removal. PMID:28800075

Remote Sensing of Subsurface Microbial Transformations

NASA Astrophysics Data System (ADS)

Williams, K. H.; Ntarlagiannis, D.; Slater, L.; Long, P.; Dohnalkova, A.; Hubbard, S. S.; Banfield, J. F.

2004-12-01

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to detect microbial dynamics in real time with high spatial resolution. Here we have used non-invasive geophysical methods to monitor biomineralization and related processes during biostimulation at both laboratory and field scales. Alterations in saturated sediment characteristics resulting from microbe-mediated transformations were concomitant with changes in complex resistivity, spontaneous potential, and acoustic wave signatures. Variability in complex resistivity and acoustic wave amplitudes appears tied to the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. In contrast, time-varying spontaneous potentials appear primarily sensitive to the electrochemical gradients resulting from metabolic pathways, such as iron- and sulfate-reduction. Furthermore, they enable us to track mobile fronts of active respiration that arise due to microbial chemotaxis. In this way, geophysical data may be used to image the distribution of mineral precipitates, biomass, and biogeochemical fronts evolving over time and suggest the ability to remotely monitor contaminated aquifers undergoing bioremediation.

Gold nanoparticles produced in situ mediate bioelectricity and hydrogen production in a microbial fuel cell by quantized capacitance charging.

PubMed

Kalathil, Shafeer; Lee, Jintae; Cho, Moo Hwan

2013-02-01

Oppan quantized style: By adding a gold precursor at its cathode, a microbial fuel cell (MFC) is demonstrated to form gold nanoparticles that can be used to simultaneously produce bioelectricity and hydrogen. By exploiting the quantized capacitance charging effect, the gold nanoparticles mediate the production of hydrogen without requiring an external power supply, while the MFC produces a stable power density. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Periodontitis: from microbial immune subversion to systemic inflammation

PubMed Central

Hajishengallis, George

2014-01-01

Periodontitis is a dysbiotic inflammatory disease with an adverse impact on systemic health. Recent studies have provided insights into the emergence and persistence of dysbiotic oral microbial communities, which can mediate inflammatory pathology at local as well as distant sites. This Review discusses mechanisms of microbial immune subversion that tip the balance from homeostasis to disease in oral or extraoral sites. PMID:25534621

Formation and Stability of Microbially Derived Soil Organic Matter

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

A chemical arms race at sea mediates algal host-virus interactions.

PubMed

Bidle, Kay D; Vardi, Assaf

2011-08-01

Despite the critical importance of viruses in shaping marine microbial ecosystems and lubricating upper ocean biogeochemical cycles, relatively little is known about the molecular mechanisms mediating phytoplankton host-virus interactions. Recent work in algal host-virus systems has begun to shed novel insight into the elegant strategies of viral infection and subcellular regulation of cell fate, which not only reveal tantalizing aspects of viral replication and host resistance strategies but also provide new diagnostic tools toward elucidating the impact of virus-mediated processes in the ocean. Widespread lateral gene transfer between viruses and their hosts plays a prominent role in host-virus diversification and in the regulation of host-virus infection mechanisms by allowing viruses to manipulate and 'rewire' host metabolic pathways to facilitate infection. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

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.

Diflerent formulations of microbial respiratory losses and microbial efficiency have pronounced short and long term consequences for soil C dynamics and soil respiration

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Billings, S. A.

2016-12-01

Much of the variability in projections of Earth's future C balance derives from uncertainty in how to formulate and parameterize models of biologically mediated transformations of soil organic C (SOC). Over the past decade, models of belowground decomposition have incorporated more realism, namely microbial biomass and exoenzyme pools, but it remains unclear whether microbially mediated decomposition is accurately formulated. Different models and different assumptions about how microbial efficiency, defined in terms of respiratory losses, varies with temperature exert great influence on SOC and CO2 flux projections for the future. Here, we incorporate a physiologically realistic formulation of CO2 loss from microbes, distinct from extant formulations and logically consistent with microbial C uptake and losses, into belowground dynamics and contrast its projections for SOC pools and CO2 flux from soils to those from the phenomenological formulations of efficiency in current models. We quantitatively describe how short and long term SOC dynamics are influenced by different mathematical formulations of efficiency, and that our lack of knowledge regarding loss rates from SOC and microbial biomass pools, specific respiration rate and maximum substrate uptake rate severely constrains our ability to confidently parameterize microbial SOC modules in Earth System Models. Both steady-state SOC and microbial biomass C pools, as well as transient responses to perturbations, can differ substantially depending on how microbial efficiency is derived. In particular, the discrepancy between SOC stocks for different formulations of efficiency varies from negligible to more than two orders of magnitude, depending on the relative values of respiratory versus non-respiratory losses from microbial biomass. Mass-specific respiration and proportional loss rates from soil microbes emerge as key determinants of the consequences of different formulations of efficiency for C flux in soils.

Disequilibrium δ18O values in microbial carbonates as a tracer of metabolic production of dissolved inorganic carbon

NASA Astrophysics Data System (ADS)

Thaler, Caroline; Millo, Christian; Ader, Magali; Chaduteau, Carine; Guyot, François; Ménez, Bénédicte

2017-02-01

Carbon and oxygen stable isotope compositions of carbonates are widely used to retrieve paleoenvironmental information. However, bias may exist in such reconstructions as carbonate precipitation is often associated with biological activity. Several skeleton-forming eukaryotes have been shown to precipitate carbonates with significant offsets from isotopic equilibrium with water. Although poorly understood, the origin of these biologically-induced isotopic shifts in biogenic carbonates, commonly referred to as "vital effects", could be related to metabolic effects that may not be restricted to mineralizing eukaryotes. The aim of our study was to determine whether microbially-mediated carbonate precipitation can also produce offsets from equilibrium for oxygen isotopes. We present here δ18O values of calcium carbonates formed by the activity of Sporosarcina pasteurii, a carbonatogenic bacterium whose ureolytic activity produces ammonia (thus increasing pH) and dissolved inorganic carbon (DIC) that precipitates as solid carbonates in the presence of Ca2+. We show that the 1000 lnαCaCO3-H2O values for these bacterially-precipitated carbonates are up to 24.7‰ smaller than those expected for precipitation at isotopic equilibrium. A similar experiment run in the presence of carbonic anhydrase (an enzyme able to accelerate oxygen isotope equilibration between DIC and water) resulted in δ18O values of microbial carbonates in line with values expected at isotopic equilibrium with water. These results demonstrate for the first time that bacteria can induce calcium carbonate precipitation in strong oxygen isotope disequilibrium with water, similarly to what is observed for eukaryotes. This disequilibrium effect can be unambiguously ascribed to oxygen isotope disequilibrium between DIC and water inherited from the oxygen isotope composition of the ureolytically produced CO2, probably combined with a kinetic isotope effect during CO2 hydration/hydroxylation. The fact that both disequilibrium effects are triggered by the metabolic production of CO2, which is common in many microbially-mediated carbonation processes, leads us to propose that metabolically-induced offsets from isotopic equilibrium in microbial carbonates may be more common than previously considered. Therefore, precaution should be taken when using the oxygen isotope signature of microbial carbonates for diagenetic and paleoenvironmental reconstructions.

Anticorrosive Microbial Polysaccharides: Structure-Function Relationships

USDA-ARS?s Scientific Manuscript database

Water-soluble microbial polysaccharides are often implicated in biofilm formation and are believed to mediate cell-cell aggregation and adhesion to surfaces. Generally, biofilm formation is considered harmful or undesirable, as it leads to increased drag, plugging of pores, dimished heat transfer, ...

Value added phytoremediation of metal stressed soils using phosphate solubilizing microbial consortium.

PubMed

Gupta, Pratishtha; Kumar, Vipin

2017-01-01

The presence of heavy metals in the soil is a matter of growing concern due to their toxic and non-biodegradable nature. Lack of effectiveness of various conventional methods due to economic and technical constraints resulted in the search for an eco-friendly and cost-effective biological techniques for heavy metal removal from the environment. Until now, phytoremediation has emerged as an innovative technique to address the problem. However, the efficiency of phytoremediation process is hindered under the high metal concentration conditions. Hence, phosphate solubilizing microbes (PSM) assisted phytoremediation technique is gaining more insight as it can reduce the contamination load even under elevated metal stressed conditions. These microbes convert heavy metals into soluble and bioavailable forms, which consequently facilitate phytoremediation. Several studies have reported that the use of microbial consortium for remediation is considered more effective as compared to single strain pure culture. Therefore, this review paper focuses on the current trends in research related to PSM mediated uptake of heavy metal by plants. The efficiency of PSM consortia in enhancing the phytoremediation process has also been reviewed. Moreover, the role of phosphatase enzymes in the mineralization of organic forms of phosphate in soil is further discussed. Biosurfactant mediated bioremediation of metal polluted soils is a matter of extensive research nowadays. Hence, the recent advancement of using biosurfactants in enhanced phytoremediation of metal stressed soils is also described.

Modulation of neonatal microbial recognition: TLR-mediated innate immune responses are specifically and differentially modulated by human milk.

PubMed

LeBouder, Emmanuel; Rey-Nores, Julia E; Raby, Anne-Catherine; Affolter, Michael; Vidal, Karine; Thornton, Catherine A; Labéta, Mario O

2006-03-15

The mechanisms controlling innate microbial recognition in the neonatal gut are still to be fully understood. We have sought specific regulatory mechanisms operating in human breast milk relating to TLR-mediated microbial recognition. In this study, we report a specific and differential modulatory effect of early samples (days 1-5) of breast milk on ligand-induced cell stimulation via TLRs. Although a negative modulation was exerted on TLR2 and TLR3-mediated responses, those via TLR4 and TLR5 were enhanced. This effect was observed in human adult and fetal intestinal epithelial cell lines, monocytes, dendritic cells, and PBMC as well as neonatal blood. In the latter case, milk compensated for the low capacity of neonatal plasma to support responses to LPS. Cell stimulation via the IL-1R or TNFR was not modulated by milk. This, together with the differential effect on TLR activation, suggested that the primary effect of milk is exerted upstream of signaling proximal to TLR ligand recognition. The analysis of TLR4-mediated gene expression, used as a model system, showed that milk modulated TLR-related genes differently, including those coding for signal intermediates and regulators. A proteinaceous milk component of > or =80 kDa was found to be responsible for the effect on TLR4. Notably, infant milk formulations did not reproduce the modulatory activity of breast milk. Together, these findings reveal an unrecognized function of human milk, namely, its capacity to influence neonatal microbial recognition by modulating TLR-mediated responses specifically and differentially. This in turn suggests the existence of novel mechanisms regulating TLR activation.

Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe.

PubMed

Purahong, Witoon; Schloter, Michael; Pecyna, Marek J; Kapturska, Danuta; Däumlich, Veronika; Mital, Sanchit; Buscot, François; Hofrichter, Martin; Gutknecht, Jessica L M; Krüger, Dirk

2014-11-12

The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.

Microbial enzyme activities of peatland soils in south central Alaska lowlands

EPA Science Inventory

Microbial enzyme activities related to carbon and nutrient acquisition were measured on Alaskan peatland soils as indicators of nutrient limitation and biochemical sustainability. Peat decomposition is mediated by microorganisms and enzymes that in turn are limited by various ph...

MICROBIAL TRANSFORMATION RATE CONSTANTS OF STRUCTURALLY DIVERSE MAN-MADE CHEMICALS

EPA Science Inventory

To assist in estimating microbially mediated transformation rates of man-made chemicals from their chemical structures, all second order rate constants that have been measured under conditions that make the values comparable have been extracted from the literature and combined wi...

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

PubMed Central

Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y.-H.; Thompson, Janelle R.

2015-01-01

Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools. PMID:26441948

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.

Development of lower Triassic wrinkle structures: implications for the search for life on other planets.

PubMed

Mata, Scott A; Bottjer, David J

2009-11-01

Wrinkle structures are microbially mediated sedimentary structures that are a common feature of Proterozoic and earliest Phanerozoic siliciclastic seafloors on Earth and occur only rarely in post-Cambrian strata. These macroscopic microbially induced sedimentary structures are readily identifiable at the outcrop scale, and their recognition on other planetary bodies by landed missions may suggest the presence of past microbial life. Wrinkle structures of the Lower Triassic (Spathian) Virgin Limestone Member of the Moenkopi Formation in the western United States record an occurrence of widespread microbialite formation in the wake of the end-Permian mass extinction, the largest biotic crisis of the Phanerozoic. Wrinkle structures occur on proximal sandy tempestites deposited within the offshore transition. Storm layers appear to have been rapidly colonized by microbial mats and were subsequently buried by mud during fair-weather conditions. Wrinkle structures exhibit flat-topped crests and sinuous troughs, with associated mica grains oriented parallel to bedding, suggestive of trapping and binding activity. Although Lower Triassic wrinkle structures postdate the widespread occurrence of these features during the Proterozoic and Cambrian, they exhibit many of the same characteristics and environmental trends, which suggests a conservation of microbial formational and preservational processes in subtidal siliciclastic settings on Earth from the Precambrian into the Phanerozoic. In the search for extraterrestrial life, it may be these conservative characteristics that prove to be the most useful and robust for recognizing microbial features on other planetary bodies, and may add to an ever-growing foundation of knowledge for directing future explorations aimed at seeking out macroscopic microbial signatures.

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

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

PubMed Central

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer. PMID:29099490

Microbial life in a liquid asphalt desert.

PubMed

Schulze-Makuch, Dirk; Haque, Shirin; de Sousa Antonio, Marina Resendes; Ali, Denzil; Hosein, Riad; Song, Young C; Yang, Jinshu; Zaikova, Elena; Beckles, Denise M; Guinan, Edward; Lehto, Harry J; Hallam, Steven J

2011-04-01

Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 10(7) cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.

Microbial Life in a Liquid Asphalt Desert

NASA Astrophysics Data System (ADS)

Schulze-Makuch, Dirk; Haque, Shirin; de Sousa Antonio, Marina Resendes; Ali, Denzil; Hosein, Riad; Song, Young C.; Yang, Jinshu; Zaikova, Elena; Beckles, Denise M.; Guinan, Edward; Lehto, Harry J.; Hallam, Steven J.

2011-04-01

Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 107 cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

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

Extracellular Saccharide-Mediated Reduction of Au3+ to Gold Nanoparticles: New Insights for Heavy Metals Biomineralization on Microbial Surfaces.

PubMed

Kang, Fuxing; Qu, Xiaolei; Alvarez, Pedro J J; Zhu, Dongqiang

2017-03-07

Biomineralization is a critical process controlling the biogeochemical cycling, fate, and potential environmental impacts of heavy metals. Despite the indispensability of extracellular polymeric substances (EPS) to microbial life and their ubiquity in soil and aquatic environments, the role played by EPS in the transformation and biomineralization of heavy metals is not well understood. Here, we used gold ion (Au 3+ ) as a model heavy metal ion to quantitatively assess the role of EPS in biomineralization and discern the responsible functional groups. Integrated spectroscopic analyses showed that Au 3+ was readily reduced to zerovalent gold nanoparticles (AuNPs, 2-15 nm in size) in aqueous suspension of Escherichia coli or dissolved EPS extracted from microbes. The majority of AuNPs (95.2%) was formed outside Escherichia coli cells, and the removal of EPS attached to cells pronouncedly suppressed Au 3+ reduction, reflecting the predominance of the extracellular matrix in Au 3+ reduction. XPS, UV-vis, and FTIR analyses corroborated that Au 3+ reduction was mediated by the hemiacetal groups (aldehyde equivalents) of reducing saccharides of EPS. Consistently, the kinetics of AuNP formation obeyed pseudo-second-order reaction kinetics with respect to the concentrations of Au 3+ and the hemiacetal groups in EPS, with minimal dependency on the source of microbial EPS. Our findings indicate a previously overlooked, universally significant contribution of EPS to the reduction, mineralization, and potential detoxification of metal species with high oxidation state.

Phreatophyte influence on reductive dechlorination in a shallow aquifer contaminated with trichloroethene (TCE)

USGS Publications Warehouse

Lee, R.W.; Jones, S.A.; Kuniansky, E.L.; Harvey, G.; Lollar, B.S.; Slater, G.F.

2000-01-01

Phytoremediation uses the natural ability of plants to degrade contaminants in groundwater. A field demonstration designed to remediate aerobic shallow groundwater contaminated with trichloroethene began in April 1996 with the planting of cottonwood trees, a short-rotation woody crop, over an approximately 0.2-ha area at the Naval Air Station, Fort Worth, Texas. The project was developed to demonstrate capture of contaminated groundwater and degradation of contaminants by phreatophytes. Analyses from samples of groundwater collected from July 1997 to June 1998 indicate that tree roots have the potential to create anaerobic conditions in the groundwater that will facilitate degradation of trichloroethene by microbially mediated reductive dechlorination. Organic matter from root exudates and decay of tree roots probably stimulate microbial activity, consuming dissolved oxygen. Dissolved oxygen concentrations, which varied across the site, were smallest near a mature cottonwood tree (about 20 years of age and 60 meters southwest of the cottonwood plantings) where degradation products of trichloroethene were measured. Oxidation of organic matter is the primary microbially mediated reaction occurring in the groundwater beneath the planted trees whereas near the mature cottonwood tree, data indicate that methanogenesis is the most probable reaction occurring. Reductive dechlorination in groundwater either is not occurring or is not a primary process away from the mature tree. Carbon-13 isotope values for trichloroethene are nearly identical at locations away from the mature tree, further confirming that dechlorination is not occurring at the site.

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.

Conservation and variability in the structure and function of the Cas5d endoribonuclease in the CRISPR-mediated microbial immune system.

PubMed

Koo, Yoon; Ka, Donghyun; Kim, Eun-Jin; Suh, Nayoung; Bae, Euiyoung

2013-10-23

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form an RNA-mediated microbial immune system against invading foreign genetic elements. Cas5 proteins constitute one of the most prevalent Cas protein families in CRISPR-Cas systems and are predicted to have RNA recognition motif (RRM) domains. Cas5d is a subtype I-C-specific Cas5 protein that can be divided into two distinct subgroups, one of which has extra C-terminal residues while the other contains a longer insertion in the middle of its N-terminal RRM domain. Here, we report crystal structures of Cas5d from Streptococcus pyogenes and Xanthomonas oryzae, which respectively represent the two Cas5d subgroups. Despite a common domain architecture consisting of an N-terminal RRM domain and a C-terminal β-sheet domain, the structural differences between the two Cas5d proteins are highlighted by the presence of a unique extended helical region protruding from the N-terminal RRM domain of X. oryzae Cas5d. We also demonstrate that Cas5d proteins possess not only specific endoribonuclease activity for CRISPR RNAs but also nonspecific double-stranded DNA binding affinity. These findings suggest that Cas5d may play multiple roles in CRISPR-mediated immunity. Furthermore, the specific RNA processing was also observed between S. pyogenes Cas5d protein and X. oryzae CRISPR RNA and vice versa. This cross-species activity of Cas5d provides a special opportunity for elucidating conserved features of the CRISPR RNA processing event. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2014-01-01

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

The role of microbial communities in phosphorus cycling during litter decomposition in a tropical forest

NASA Astrophysics Data System (ADS)

Lloret Sevilla, E.; Brodie, E.; Bouskill, N.; Hao, Z.

2016-12-01

Phosphorus is an essential nutrient with a reduced availability in tropical forests. In these ecosystems, P is recycled highly efficiently through resorption and mineralization and P immobilization in the microbial biomass prevents its loss through occlusion in the soil mineral fraction. To improve models of ecosystem response to global change, further studies of the above and belowground plant and microbial traits related to P availability and uptake, are required. In tropical forests, high temperature and rainfall lead to some of the highest rates of litter decomposition on earth. Litter decomposition is a complex process mediated by a range of trophic groups: meso and microfauna initiate litter turnover through litter fragmentation facilitating colonization by fungi, and bacteria mediate the mineralization of organic matter and release of nutrients. To determine the important functional traits of these players in the efficient cycling of P in soils with low P availability, we are performing a leaf litter decomposition experiment in a humid tropical forest in Puerto Rico. Nylon litterbags with three mesh sizes (2mm, 20 μm and 0.45 μm) containing litter with different chemistry (tabonuco and palm) will be deployed on soil surface and sampled 6 times throughout 12 months. The use of different mesh sizes will allow us to identify the leading roles in litter turnover by physical allowance and/or exclusion of the decomposers. The 2 mm bags allow meso and microfauna, roots, fungi and bacteria. 20 μm bags will exclude fauna and roots and 0.45 μm only allow some bacteria. We hypothesize that fungi will dominate over bacteria in earlier stages of the decomposition with a higher production of extracellular hydrolytic enzymes. On the other hand, bacterial biomass is expected to increase with time. Qualitative changes in both fungal and bacterial communities along the decomposition process are also expected leading to changes in enzyme activity. We also postulate an enhanced microbial communities abundance and activity in litter with higher nutrient content. Regarding the microarthropods, we hypothesize that their diversity and abundance will be inversely related to mass loss.

Some Ecological Mechanisms to Generate Habitability in Planetary Subsurface Areas by Chemolithotrophic Communities: The Ro Tinto Subsurface Ecosystem as a Model System

NASA Astrophysics Data System (ADS)

Fernández-Remolar, David C.; Gómez, Felipe; Prieto-Ballesteros, Olga; Schelble, Rachel T.; Rodríguez, Nuria; Amiols, Ricardo

2008-02-01

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Ro Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Ro Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.

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.

Some ecological mechanisms to generate habitability in planetary subsurface areas by chemolithotrophic communities: the Río Tinto subsurface ecosystem as a model system.

PubMed

Fernández-Remolar, David C; Gómez, Felipe; Prieto-Ballesteros, Olga; Schelble, Rachel T; Rodríguez, Nuria; Amils, Ricardo

2008-02-01

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Río Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Río Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.

Trends, application and future prospectives of microbial carbonic anhydrase mediated carbonation process for CCUS.

PubMed

Bhagat, C; Dudhagara, P; Tank, S

2018-02-01

Growing industrialization and the desire for a better economy in countries has accelerated the emission of greenhouse gases (GHGs), by more than the buffering capacity of the earth's atmosphere. Among the various GHGs, carbon dioxide occupies the first position in the anthroposphere and has detrimental effects on the ecosystem. For decarbonization, several non-biological methods of carbon capture, utilization and storage (CCUS) have been in use for the past few decades, but they are suffering from narrow applicability. Recently, CO 2 emission and its disposal related problems have encouraged the implementation of bioprocessing to achieve a zero waste economy for a sustainable environment. Microbial carbonic anhydrase (CA) catalyses reversible CO 2 hydration and forms metal carbonates that mimic the natural phenomenon of weathering/carbonation and is gaining merit for CCUS. Thus, the diversity and specificity of CAs from different micro-organisms could be explored for CCUS. In the literature, more than 50 different microbial CAs have been explored for mineral carbonation. Further, microbial CAs can be engineered for the mineral carbonation process to develop new technology. CA driven carbonation is encouraging due to its large storage capacity and favourable chemistry, allowing site-specific sequestration and reusable product formation for other industries. Moreover, carbonation based CCUS holds five-fold more sequestration capacity over the next 100 years. Thus, it is an eco-friendly, feasible, viable option and believed to be the impending technology for CCUS. Here, we attempt to examine the distribution of various types of microbial CAs with their potential applications and future direction for carbon capture. Although there are few key challenges in bio-based technology, they need to be addressed in order to commercialize the technology. © 2017 The Society for Applied Microbiology.

Diversity of microbial communities correlated to physiochemical parameters in a digestion basin of a zero-discharge mariculture system.

PubMed

Cytryn, Eddie; Gelfand, Ilya; Barak, Yoram; van Rijn, Jaap; Minz, Dror

2003-01-01

Bacterial community structure and physiochemical parameters were examined in a sedimentation basin of a zero-discharge mariculture system. The system consisted of an intensively stocked fish basin from which water was recirculated through two separate treatment loops. Surface water from the basin was pumped over a trickling filter in one loop while bottom-water was recirculated through a sedimentation basin followed by a fluidized bed reactor in the other. Ammonia oxidation to nitrate in the trickling filter and organic matter digestion together with nitrate reduction in the sedimentation basin and fluidized bed reactor, allowed zero-discharge operation of the system. Relatively high concentrations of oxygen, nitrate, sulphate and organic matter detected simultaneously in the digestion basin suggested the potential for a wide range of microbially-mediated transformation processes. In this study, physiochemical parameters were correlated to bacterial diversity and distribution in horizontal and vertical profiles within this basin in an effort to obtain a basic understanding of the chemical and microbial processes in this system. Chemical activity and microbial diversity, the latter measured by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR) amplified 16S rDNA fragments, were higher in the sludge layer than in the overlying aqueous layer of the basin. Chemical parameters in sludge samples close to the basin inlet suggested enhanced microbial activity relative to other sampling areas with evidence of both nitrate and sulphate reduction. Four of the nine DGGE bands identified in this zone were affiliated with the Bacteroidetes phylum. Detected sequences closely related to sequences of organisms involved in the sulphur cycle included Desulfovibrio, Dethiosulfovibrio and apparent sulphur oxidizers from the gamma-proteobacteria. In addition, a number of sequences from the beta and alpha-proteobacteria were identified.

Final Report for Project "A high-throughput pipeline for mapping inter-species interactions and metabolic synergy relevant to next-generation biofuel production"

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

Segre, Daniel; Marx, Christopher J.; Northen, Trent

The goal of our project was to implement a pipeline for the systematic, computationally-driven study and optimization of microbial interactions and their effect on lignocellulose degradation and biofuel production. We specifically sought to design and construct artificial microbial consortia that could collectively degrade lignocellulose from plant biomass, and produce precursors of energy-rich biofuels. This project fits into the bigger picture goal of helping identify a sustainable strategy for the production of energy-rich biofuels that would satisfy the existing energy constraints and demand of our society. Based on the observation that complex natural microbial communities tend to be metabolically efficient andmore » ecologically robust, we pursued the study of a microbial system in which the desired engineering function is achieved through division of labor across multiple microbial species. Our approach was aimed at bypassing the complexity of natural communities by establishing a rational approach to design small synthetic microbial consortia. Towards this goal, we combined multiple approaches, including computer modeling of ecosystem-level microbial metabolism, mass spectrometry of metabolites, genetic engineering, and experimental evolution. The microbial production of biofuels from lignocellulose is a complex, multi-step process. Microbial consortia are an ideal approach to consolidated bioprocessing: a community of microorganisms performs a wide variety of functions more efficiently and is more resilient to environmental perturbations than a microbial monoculture. Each organism we chose for this project addresses a specific challenge: lignin degradation (Pseudomonas putida); (hemi)cellulose degradation (Cellulomonas fimi); lignin degradation product demethoxylation (Methylobacterium spp); generation of biofuel lipid precursors (Yarrowia lipolytica). These organisms are genetically tractable, aerobic, and have been used in biotechnological applications. Throughout the project, we have used mass spectrometry to characterize and measure the metabolic inputs and outputs of each of these consortium members, providing valuable information for model refinement, and enabling the establishment of metabolism-mediated interactions. In addition to lignocellulose degradation, we have started addressing the challenge of removing metabolites (e.g. formaldehyde) produced by the demethoxylation of lignin monomers, which can otherwise inhibit microbial growth due to their toxicity. On the computational side, we have implemented genome-scale models for all consortium members, based on KBase reconstructions and literature curation, and we studied small consortia and their properties. Overall, our project has identified a complex landscape of interactions types and metabolic processes relevant to community-level functions, illustrating the challenges and opportunities of microbial community engineering for the transformation of biomass into bioproducts.« less

Electricity generation from acetate and glucose by sedimentary bacterium attached to electrode in microbial-anode fuel cells

NASA Astrophysics Data System (ADS)

Zhang, Enren; Xu, Wei; Diao, Guowang; Shuang, Chendong

Microbial-anode fuel cells (MAFCs) with high electron recovery (>50%) from acetate and glucose have been constructed in this study. By inoculating fresh sedimentary microorganisms into anaerobic anode compartments, a stable current (∼0.42 mA for acetate-fed MAFCs; ∼0.35 mA for glucose-fed MAFCs) is generated from the oxidation of the added organic matter until its concentration decreases to a low level. SEM micrographs indicate that thick biofilms of microbial communities (coccoid cells with a diameter of ∼0.5 μm in acetate-fed MAFCs; rod-shaped cells with a length of 2.0-4.0 μm and a width of 0.5-0.7 μm in glucose-fed MAFCs) completely cover the anode electrodes. These anodophillic biofilms are thought to be responsible for the current generation, and make these microbial-anode fuel cells exhibit good performance even when the growth medium is replaced by a salt buffer without any growth factor. In comparison with those microbial fuel cells that require the addition of artificial electron transfer-mediating compounds, the findings in this study imply a potential way to develop excellent mediator-less MAFCs for electricity generation from organic matter by using substrate-induced anodophillic microbial species.

Microbial mediated iron redox cycling in Fe (hydr)oxides for nitrite removal.

PubMed

Lu, Yongsheng; Xu, Lu; Shu, Weikang; Zhou, Jizhi; Chen, Xueping; Xu, Yunfeng; Qian, Guangren

2017-01-01

Nitrite, at an environmentally relevant concentration, was significantly reduced with iron (hydr)oxides mediated by Shewanella oneidensis MR-1. The average nitrite removal rates of 1.28±0.08 and 0.65±0.02(mgL -1 )h -1 were achieved with ferrihydrite and magnetite, respectively. The results showed that nitrite removal was able to undergo multiple redox cycles with iron (hydr)oxides mediated by Shewanella oneidensis MR-1. During the bioreduction of the following cycles, biogenic Fe(II) was subsequently chemically oxidized to Fe(III), which is associated with nitrite reduction. There was 11.18±1.26mgL -1 of NH 4 + -N generated in the process of redox cycling of ferrihydrite. Additionally, results obtained by using X-ray diffraction showed that ferrihydrite and magnetite remained mainly stable in the system. This study indicated that redox cycling of Fe in iron (hydr)oxides was a potential process associated with NO 2 - -N removal from solution, and reduced most nitrite abiotically to gaseous nitrogen species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Richness, biomass, and nutrient content of a wetland macrophyte community affect soil nitrogen cycling in a diversity-ecosystem functioning experiment

USGS Publications Warehouse

Korol, Alicia R.; Ahn, Changwoo; Noe, Gregory

2016-01-01

The development of soil nitrogen (N) cycling in created wetlands promotes the maturation of multiple biogeochemical cycles necessary for ecosystem functioning. This development proceeds from gradual changes in soil physicochemical properties and influential characteristics of the plant community, such as competitive behavior, phenology, productivity, and nutrient composition. In the context of a 2-year diversity experiment in freshwater mesocosms (0, 1, 2, 3, or 4 richness levels), we assessed the direct and indirect impacts of three plant community characteristics – species richness, total biomass, and tissue N concentration – on three processes in the soil N cycle – soil net ammonification, net nitrification, and denitrification potentials. Species richness had a positive effect on net ammonification potential (NAP) through higher redox potentials and likely faster microbial respiration. All NAP rates were negative, however, due to immobilization and high rates of ammonium removal. Net nitrification was inhibited at higher species richness without mediation from the measured soil properties. Higher species richness also inhibited denitrification potential through increased redox potential and decreased nitrification. Both lower biomass and/or higher tissue ratios of carbon to nitrogen, characteristics indicative of the two annual plants, were shown to have stimulatory effects on all three soil N processes. The two mediating physicochemical links between the young macrophyte community and microbial N processes were soil redox potential and temperature. Our results suggest that early-successional annual plant communities play an important role in the development of ecosystem N multifunctionality in newly created wetland soils.

A molecular dawn for biogeochemistry

USGS Publications Warehouse

Zak, D.R.; Blackwood, C.B.; Waldrop, M.P.

2006-01-01

Biogeochemistry is at the dawn of an era in which molecular advances enable the discovery of novel microorganisms having unforeseen metabolic capabilities, revealing new insight into the underlying processes regulating elemental cycles at local to global scales. Traditionally, biogeochemical inquiry began by studying a process of interest, and then focusing downward to uncover the microorganisms and metabolic pathways mediating that process. With the ability to sequence functional genes from the environment, molecular approaches now enable the flow of inquiry in the opposite direction. Here, we argue that a focus on functional genes, the microorganisms in which they reside, and the interaction of those organisms with the broader microbial community could transform our understanding of many globally important biogeochemical processes. ?? 2006 Elsevier Ltd. All rights reserved.

Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

NASA Astrophysics Data System (ADS)

Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

2015-12-01

Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined with genome-enabled reactive flow and transport we simulated the importance of pore network properties including connectivity in regulating metabolic interdependencies between microbial functional guilds.

Early microbial contact, the breast milk microbiome and child health.

PubMed

Rautava, S

2016-02-01

The significance of contact with microbes in early life for subsequent health has been the subject of intense research during the last 2 decades. Disturbances in the establishment of the indigenous intestinal microbiome caused by cesarean section delivery or antibiotic exposure in early life have been linked to the risk of immune-mediated and inflammatory conditions such as atopic disorders, inflammatory bowel disease and obesity later in life. Distinct microbial populations have recently been discovered at maternal sites including the amniotic cavity and breast milk, as well as meconium, which have previously been thought to be sterile. Our understanding of the impact of fetal microbial contact on health outcomes is still rudimentary. Breast milk is known to modulate immune and metabolic programming. The breast milk microbiome is hypothesized to guide infant gut colonization and is affected by maternal health status and mode of delivery. Immunomodulatory factors in breast milk interact with the maternal and infant gut microbiome and may mediate some of the health benefits associated with breastfeeding. The intimate connection between the mother and the fetus or the infant is a potential target for microbial therapeutic interventions aiming to support healthy microbial contact and protect against disease.

Development of mediated BOD biosensor system of flow injection mode for shochu distillery wastewater.

PubMed

Oota, Shinichi; Hatae, Yuta; Amada, Kei; Koya, Hidekazu; Kawakami, Mitsuyasu

2010-09-15

Although microbial biochemical oxygen demand (BOD) sensors utilizing redox mediators have attracted much attention as a rapid BOD measurement method, little attempts have been made to apply the mediated BOD biosensors to the flow injection analysis system. In this work, a mediated BOD sensor system of flow injection mode, constructed by combining an immobilized microbial reactor with an electrochemical flow cell of three electrodes configuration, has been developed to estimate BOD of shochu distillery wastewater (SDW). It was demonstrated consequently that the mediated sensing was realized by employing phosphate buffer containing potassium hexacyanoferrate as the carrier. The output current was found to yield a peak with a sample injection, and to result from reoxidation of reduced mediator at the electrode. By employing the peak area as the sensor response, the effects of flow rate and pH of the carrier on the sensitivity were investigated. The sensor system using a microorganism of high SDW-assimilation capacity showed good performance and proved to be available for estimation of BOD of SDW. Copyright 2010 Elsevier B.V. All rights reserved.

Material-mediated pyrogens in medical devices: Applicability of the in vitro Monocyte Activation Test.

PubMed

Borton, Lindsey K; Coleman, Kelly P

2018-06-14

Pyrogenicity presents a challenge to clinicians, medical device manufactures, and regulators. A febrile response may be caused by endotoxin contamination, microbial components other than endotoxin, or chemical agents that generate a material-mediated pyrogenic response. While test methods for the assessment of endotoxin contamination and some microbial components other than endotoxin are well-established, material-mediated pyrogens remain elusively undefined. This review presents the findings of literature searches conducted to identify material-mediated pyrogens associated with medical devices. The in vivo rabbit pyrogen test (RPT) is considered to be the "gold standard" for medical device pyrogenicity testing, despite the fact that few medical device-derived material-mediated pyrogens are known. In line with global efforts to reduce the use of research animals, an in vitro monocyte activation test (MAT) has the potential to replace the RPT. The MAT is used to detect substances that activate human monocytes to release cytokines. This review will also describe the potential opportunities and challenges associated with MAT adoption for the detection of material-mediated pyrogens in medical device testing.

Gut-kidney crosstalk in septic acute kidney injury.

PubMed

Zhang, Jingxiao; Ankawi, Ghada; Sun, Jian; Digvijay, Kumar; Yin, Yongjie; Rosner, Mitchell H; Ronco, Claudio

2018-05-03

Sepsis is the leading cause of acute kidney injury (AKI) in the intensive care unit (ICU). Septic AKI is a complex and multifactorial process that is incompletely understood. During sepsis, the disruption of the mucus membrane barrier, a shift in intestinal microbial flora, and microbial translocation may lead to systemic inflammation, which further alters host immune and metabolic homeostasis. This altered homeostasis may promote and potentiate the development of AKI. As part of this vicious cycle, when AKI develops, the clearance of inflammatory mediators and metabolic products is decreased. This will lead to further gut injury and breakdown in mucous membrane barriers. Thus, changes in the gut during sepsis can initiate and propagate septic AKI. This deleterious gut-kidney crosstalk may be a potential target for therapeutic maneuvers. This review analyses the underlying mechanisms in gut-kidney crosstalk in septic AKI.

Modulation of surgical fibrosis by microbial zwitterionic polysaccharides

NASA Astrophysics Data System (ADS)

Ruiz-Perez, Begonia; Chung, Doo R.; Sharpe, Arlene H.; Yagita, Hideo; Kalka-Moll, Wiltrud M.; Sayegh, Mohamed H.; Kasper, Dennis L.; Tzianabos, Arthur O.

2005-11-01

Bacterial carbohydrates have long been considered T cell-independent antigens that primarily induce humoral immune responses. Recently, it has been demonstrated that bacterial capsules that possess a zwitterionic charge motif can activate CD4+ T cells after processing and presentation by antigen-presenting cells. Here we show that these zwitterionic polysaccharides can prevent T helper 1-mediated fibrosis by signaling for the release of IL-10 from CD4+ T cells in vivo. IL-10 production by these T cells and their ability to prevent fibrosis is controlled by the inducible costimulator (ICOS)-ICOS ligand pathway. These data demonstrate that the interaction of the zwitterionic polysaccharides with T cells results in modulation of surgical fibrosis in vivo and suggest a previously undescribed approach to "harnessing" T cell function to prevent inflammatory tissue disorders in humans. IL-10 | microbial polysaccharides | inducible costimulator

Microbial colonization and controls in dryland systems

USGS Publications Warehouse

Pointing, Stephen B.; Belnap, Jayne

2012-01-01

Drylands constitute the most extensive terrestrial biome, covering more than one-third of the Earth's continental surface. In these environments, stress limits animal and plant life, so life forms that can survive desiccation and then resume growth following subsequent wetting assume the foremost role in ecosystem processes. In this Review, we describe how these organisms assemble in unique soil- and rock-surface communities to form a thin veneer of mostly microbial biomass across hot and cold deserts. These communities mediate inputs and outputs of gases, nutrients and water from desert surfaces, as well as regulating weathering, soil stability, and hydrological and nutrient cycles. The magnitude of regional and global desert-related environmental impacts is affected by these surface communities; here, we also discuss the challenges for incorporating the consideration of these communities and their effects into the management of dryland resources.

What do we really know about the role of microorganisms in iron sulfide mineral formation?

USGS Publications Warehouse

Picard, Aude A.; Gartman, Amy; Girguis, Peter R.

2016-01-01

Iron sulfide mineralization in low-temperature systems is a result of biotic and abiotic processes, though the delineation between these two modes of formation is not always straightforward. Here we review the role of microorganisms in the precipitation of extracellular iron sulfide minerals. We summarize the evidence that links sulfur-metabolizing microorganisms and sulfide minerals in nature and we present a critical overview of laboratory-based studies of the nucleation and growth of iron sulfide minerals in microbial cultures. We discuss whether biologically derived minerals are distinguishable from abiotic minerals, possessing attributes that are uniquely diagnostic of biomineralization. These inquiries have revealed the need for additional thorough, mechanistic and high-resolution studies to understand microbially mediated formation of a variety of sulfide minerals across a range of natural environments.

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

Hydrology, microbiology and carbon cycling at a high Arctic polythermal glacier, (John Evans Glacier, Ellesmere Island, Canada)

NASA Astrophysics Data System (ADS)

Skidmore, Mark Leslie

Analysis of the hydrology, hydrochemistry and microbiology at polythermal John Evans Glacier and geochemical and isotopic data from Haut Glacier d'Arolla demonstrates that certain subglacial chemical weathering processes are microbially mediated. Subglacial drainage is likely an annual occurrence beneath John Evans Glacier and solute rich subglacial waters indicate over winter storage at the glacier bed. Subglacial microbial populations are also present, and are viable under simulated near in situ conditions at 0.3°C. This suggests that temperate subglacial environments at a polythermal glacier, which are isolated by cold ice above and around them, provide a viable habitat for life where basal water and organic carbon are present throughout the year. Thus, a subglacial microbial ecosystem based upon legacy carbon, (from old soils or surface inputs) rather than primary production may exist, where redox processes are a key component, and seasonal anoxia may occur. The existence of anoxic environments is supported by the presence of strictly anaerobic bacteria (sulphate reducing bacteria and methanogens) in the basal sediments---which are viable in culture at 4°C---and also argues that these bacteria are not washed in with oxygenated surface meltwaters, but are present in the subglacial environment. During the summer meltseason there is a large input of surficial waters to the subglacial system and water residence times are drastically reduced. Hence, kinetic weathering processes dominate, resulting in light delta 13C-DIC (dissolved inorganic carbon) in glacial runoff, as verified by experimental work on CaCO3 and John Evans Glacier sediments. The experiments demonstrate kinetic bedrock fractionation (KBF) during carbonate hydrolysis and that kinetic fractionation of CO2 (KFC) is proportional to the rate of CO2 draw down during the carbonation of carbonates. This results in significantly depleted delta13C-DIC values (≤-16 ‰) relative to the bedrock carbonate. Incorporating KBF and KFC processes into geochemical weathering models makes it possible to distinguish between kinetic effects and microbial CO2 as causes of light delta13C-DIC in glacial runoff. However, where kinetically produced DIC dominates, this can potentially mask small microbial respiration signatures. Only in the distributed system waters at Haut Glacier d'Arolla is light delta13C-DIC clearly due to microbial respiration.

Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer

PubMed Central

Rabaey, Korneel; Boon, Nico; Siciliano, Steven D.; Verhaege, Marc; Verstraete, Willy

2004-01-01

Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m−2 of electrode surface to a maximal level of 4.31 W m−2 (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter−1 day−1 and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components. PMID:15345423

Biogeochemistry of three small Eutrophic Lakes Differentially Influenced by Marine Waters from Bayou Chico Bay, Pensacola, Florida

EPA Science Inventory

Biogeochemical models predict microbial mediated pathways but generally do not account for microorganisms. This study was undertaken to better understand relationships among microbial communities and N, S, Fe and C cycling in three lakes. Jackson Lakes formed from abandoned sand...

Synthetic control of a fitness tradeoff in yeast nitrogen metabolism

PubMed Central

Bayer, Travis S; Hoff, Kevin G; Beisel, Chase L; Lee, Jack J; Smolke, Christina D

2009-01-01

Background Microbial communities are involved in many processes relevant to industrial and medical biotechnology, such as the formation of biofilms, lignocellulosic degradation, and hydrogen production. The manipulation of synthetic and natural microbial communities and their underlying ecological parameters, such as fitness, evolvability, and variation, is an increasingly important area of research for synthetic biology. Results Here, we explored how synthetic control of an endogenous circuit can be used to regulate a tradeoff between fitness in resource abundant and resource limited environments in a population of Saccharomyces cerevisiae. We found that noise in the expression of a key enzyme in ammonia assimilation, Gdh1p, mediated a tradeoff between growth in low nitrogen environments and stress resistance in high ammonia environments. We implemented synthetic control of an endogenous Gdh1p regulatory network to construct an engineered strain in which the fitness of the population was tunable in response to an exogenously-added small molecule across a range of ammonia environments. Conclusion The ability to tune fitness and biological tradeoffs will be important components of future efforts to engineer microbial communities. PMID:19118500

Microbial ecology and host-microbiota interactions during early life stages

PubMed Central

Collado, Maria Carmen; Cernada, Maria; Baüerl, Christine; Vento, Máximo; Pérez-Martínez, Gaspar

2012-01-01

The role of human microbiota has been redefined during recent years and its physiological role is now much more important than earlier understood. Intestinal microbial colonization is essential for the maturation of immune system and for the developmental regulation of the intestinal physiology. Alterations in this process of colonization have been shown to predispose and increase the risk to disease later in life. The first contact of neonates with microbes is provided by the maternal microbiota. Moreover, mode of delivery, type of infant feeding and other perinatal factors can influence the establishment of the infant microbiota. Taken into consideration all the available information it could be concluded that the exposure to the adequate microbes early in gestation and neonatal period seems to have a relevant role in health. Maternal microbial environment affects maternal and fetal immune physiology and, of relevance, this interaction with microbes at the fetal-maternal interface could be modulated by specific microbes administered to the pregnant mother. Indeed, probiotic interventions aiming to reduce the risk of immune-mediated diseases may appear effective during early life. PMID:22743759

Utilization of microbial iron assimilation processes for the development of new antibiotics and inspiration for the design of new anticancer agents.

PubMed

Miller, Marvin J; Zhu, Helen; Xu, Yanping; Wu, Chunrui; Walz, Andrew J; Vergne, Anne; Roosenberg, John M; Moraski, Garrett; Minnick, Albert A; McKee-Dolence, Julia; Hu, Jingdan; Fennell, Kelley; Kurt Dolence, E; Dong, Li; Franzblau, Scott; Malouin, Francois; Möllmann, Ute

2009-02-01

Pathogenic microbes rapidly develop resistance to antibiotics. To keep ahead in the "microbial war", extensive interdisciplinary research is needed. A primary cause of drug resistance is the overuse of antibiotics that can result in alteration of microbial permeability, alteration of drug target binding sites, induction of enzymes that destroy antibiotics (ie., beta-lactamase) and even induction of efflux mechanisms. A combination of chemical syntheses, microbiological and biochemical studies demonstrate that the known critical dependence of iron assimilation by microbes for growth and virulence can be exploited for the development of new approaches to antibiotic therapy. Iron recognition and active transport relies on the biosyntheses and use of microbe-selective iron-chelating compounds called siderophores. Our studies, and those of others, demonstrate that siderophores and analogs can be used for iron transport-mediated drug delivery ("Trojan Horse" antibiotics) and induction of iron limitation/starvation (Development of new agents to block iron assimilation). Recent extensions of the use of siderophores for the development of novel potent and selective anticancer agents are also described.

Utilization of microbial iron assimilation processes for the development of new antibiotics and inspiration for the design of new anticancer agents

PubMed Central

Zhu, Helen; Xu, Yanping; Wu, Chunrui; Walz, Andrew J.; Vergne, Anne; Roosenberg, John M.; Moraski, Garrett; Minnick, Albert A.; McKee-Dolence, Julia; Hu, Jingdan; Fennell, Kelley; Dolence, E. Kurt; Dong, Li; Franzblau, Scott; Malouin, Francois; Möllmann, Ute

2014-01-01

Pathogenic microbes rapidly develop resistance to antibiotics. To keep ahead in the “microbial war”, extensive interdisciplinary research is needed. A primary cause of drug resistance is the overuse of antibiotics that can result in alteration of microbial permeability, alteration of drug target binding sites, induction of enzymes that destroy antibiotics (ie., beta-lactamase) and even induction of efflux mechanisms. A combination of chemical syntheses, microbiological and biochemical studies demonstrate that the known critical dependence of iron assimilation by microbes for growth and virulence can be exploited for the development of new approaches to antibiotic therapy. Iron recognition and active transport relies on the biosyntheses and use of microbe-selective iron-chelating compounds called siderophores. Our studies, and those of others, demonstrate that siderophores and analogs can be used for iron transport-mediated drug delivery (“Trojan Horse” antibiotics) and induction of iron limitation/starvation (Development of new agents to block iron assimilation). Recent extensions of the use of siderophores for the development of novel potent and selective anticancer agents are also described. PMID:19130268

A hermetic self-sustained microbial solar cell based on Chlorella vulgaris and a versatile charge transfer chain

NASA Astrophysics Data System (ADS)

Pan, Keliang; Zhou, Peijiang

2015-10-01

A hermetic noble-metal-free membrane-less microbial solar cell (MSC) is established. The substances decomposition and regeneration in this MSC are carried out only by Chlorella vulgaris simultaneously. The conversion of metabolism types of C. vulgaris is controlled only by illumination. By using a pleiotropic redox mediator and a cupric hexacyanoferrate modified cathode, a two-phase three-stage charge transfer chain is formed. Through this pathway, the one microorganism self-sustained system gets a long-term power output up to 0.04773 mW/cm2 at 0.423 V without any material exchange with external, which is 50 times higher than that obtained from the original system. Benefiting from this electron buffer system, the battery will achieve an electricity generation in both light and dark conditions. There is almost no consumption of any substrates throughout the stabilized process, and no more additions are required. This maintenance-free and extremely inexpensive reactor with a simple structure and a long service life demonstrates the possibility of combining the microbial, chemical and photo cells.

Extracellular enzyme kinetics scale with resource availability

EPA Science Inventory

Microbial community metabolism relies on external digestion, mediated by extracellular enzymes that break down complex organic matter into molecules small enough for cells to assimilate. We analyzed the kinetics of 40 extracellular enzymes that mediate the degradation and assimi...

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

PubMed

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

2016-08-15

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

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.

Environmental Genomic Analysis of Stratified Microbial Communities and Climate Active Gases in the Subarctic Pacific Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Wright, J.; Hallam, S.; Merzouk, A.; Tortell, P.

2008-12-01

Oxygen minimum zones (OMZs) are areas of low dissolved oxygen concentrations that play a major role in biogeochemical cycling within the world's oceans. They are major sinks for nitrogen and sources for the greenhouse gases carbon dioxide and nitrous oxide. Therefore, microbial mediated biological activity associated with these systems directly impacts ocean productivity and global climate balance. There is increasing evidence that ocean warming trends will decrease dissolved oxygen concentrations within the coastal and interior regions of the subarctic Pacific, causing an expansion of the hypoxic boundary layer. This expansion will have a direct effect on coastal benthic ecosystems and the productivity of marine fisheries due to habitat loss and changes in nutrient cycling. In order to understand the potential implications of these transitions, we are performing environmental genomic analyses of indigenous microbial communities found in coastal and open ocean OMZs in the subarctic Pacific Ocean in relation to dissolved gas and nutrient concentrations. In addition to identifying and describing the key microbial players and biochemical pathways contributing to carbon, nitrogen and sulfur metabolism within the subarctic Pacific Ocean, this work provides a solid comparative genomic foundation for understanding the biogeochemical processes at work in marine OMZs around the globe.

Formation of Kinneyia via shear-induced instabilities in microbial mats.

PubMed

Thomas, Katherine; Herminghaus, Stephan; Porada, Hubertus; Goehring, Lucas

2013-01-01

Kinneyia are a class of microbially mediated sedimentary fossils. Characterized by clearly defined ripple structures, Kinneyia are generally found in areas that were formally littoral habitats and covered by microbial mats. To date, there has been no conclusive explanation of the processes involved in the formation of these fossils. Microbial mats behave like viscoelastic fluids. We propose that the key mechanism involved in the formation of Kinneyia is a Kelvin-Helmholtz-type instability induced in a viscoelastic film under flowing water. A ripple corrugation is spontaneously induced in the film and grows in amplitude over time. Theoretical predictions show that the ripple instability has a wavelength proportional to the thickness of the film. Experiments carried out using viscoelastic films confirm this prediction. The ripple pattern that forms has a wavelength roughly three times the thickness of the film. This behaviour is independent of the viscosity of the film and the flow conditions. Laboratory-analogue Kinneyia were formed via the sedimentation of glass beads, which preferentially deposit in the troughs of the ripples. Well-ordered patterns form, with both honeycomb-like and parallel ridges being observed, depending on the flow speed. These patterns correspond well with those found in Kinneyia, with similar morphologies, wavelengths and amplitudes being observed.

Formation of Kinneyia via shear-induced instabilities in microbial mats.

PubMed

Thomas, Katherine; Herminghaus, Stephan; Porada, Hubertus; Goehring, Lucas

2013-12-13

Kinneyia are a class of microbially mediated sedimentary fossils. Characterized by clearly defined ripple structures, Kinneyia are generally found in areas that were formally littoral habitats and covered by microbial mats. To date, there has been no conclusive explanation of the processes involved in the formation of these fossils. Microbial mats behave like viscoelastic fluids. We propose that the key mechanism involved in the formation of Kinneyia is a Kelvin-Helmholtz-type instability induced in a viscoelastic film under flowing water. A ripple corrugation is spontaneously induced in the film and grows in amplitude over time. Theoretical predictions show that the ripple instability has a wavelength proportional to the thickness of the film. Experiments carried out using viscoelastic films confirm this prediction. The ripple pattern that forms has a wavelength roughly three times the thickness of the film. This behaviour is independent of the viscosity of the film and the flow conditions. Laboratory-analogue Kinneyia were formed via the sedimentation of glass beads, which preferentially deposit in the troughs of the ripples. Well-ordered patterns form, with both honeycomb-like and parallel ridges being observed, depending on the flow speed. These patterns correspond well with those found in Kinneyia, with similar morphologies, wavelengths and amplitudes being observed.

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust

PubMed Central

Robador, Alberto; Jungbluth, Sean P.; LaRowe, Douglas E.; Bowers, Robert M.; Rappé, Michael S.; Amend, Jan P.; Cowen, James P.

2015-01-01

The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with 35S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling. PMID:25642212

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

The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

NASA Astrophysics Data System (ADS)

Cardarelli, E.; Francis, C. A.

2014-12-01

Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors influence N cycling related gene expression and rates of nitrate reduction.

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume.

PubMed

Dick, Gregory J; Tebo, Bradley M

2010-05-01

Hydrothermal plumes are hot spots of microbial biogeochemistry in the deep ocean, yet little is known about the diversity or ecology of microorganisms inhabiting plumes. Recent biogeochemical evidence shows that Mn(II) oxidation in the Guaymas Basin (GB) hydrothermal plume is microbially mediated and suggests that the plume microbial community is distinct from deep-sea communities. Here we use a molecular approach to compare microbial diversity in the GB plume and in background deep seawater communities, and cultivation to identify Mn(II)-oxidizing bacteria from plumes and sediments. Despite dramatic differences in Mn(II) oxidation rates between plumes and background seawater, microbial diversity and membership were remarkably similar. All bacterial clone libraries were dominated by Gammaproteobacteria and archaeal clone libraries were dominated by Crenarchaeota. Two lineages, both phylogenetically related to methanotrophs and/or methylotrophs, were consistently over-represented in the plume. Eight Mn(II)-oxidizing bacteria were isolated, but none of these or previously identified Mn(II) oxidizers were abundant in clone libraries. Taken together with Mn(II) oxidation rates measured in laboratory cultures and in the field, these results suggest that Mn(II) oxidation in the GB hydrothermal plume is mediated by genome-level dynamics (gene content and/or expression) of microorganisms that are indigenous and abundant in the deep sea but have yet to be unidentified as Mn(II) oxidizers.

Post-Fire Spatial Patterns of Soil Nitrogen Mineralization and Microbial Abundance

PubMed Central

Smithwick, Erica A. H.; Naithani, Kusum J.; Balser, Teri C.; Romme, William H.; Turner, Monica G.

2012-01-01

Stand-replacing fires influence soil nitrogen availability and microbial community composition, which may in turn mediate post-fire successional dynamics and nutrient cycling. However, fires create patchiness at both local and landscape scales and do not result in consistent patterns of ecological dynamics. The objectives of this study were to (1) quantify the spatial structure of microbial communities in forest stands recently affected by stand-replacing fire and (2) determine whether microbial variables aid predictions of in situ net nitrogen mineralization rates in recently burned stands. The study was conducted in lodgepole pine (Pinus contorta var. latifolia) and Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa) forest stands that burned during summer 2000 in Greater Yellowstone (Wyoming, USA). Using a fully probabilistic spatial process model and Bayesian kriging, the spatial structure of microbial lipid abundance and fungi-to-bacteria ratios were found to be spatially structured within plots two years following fire (for most plots, autocorrelation range varied from 1.5 to 10.5 m). Congruence of spatial patterns among microbial variables, in situ net N mineralization, and cover variables was evident. Stepwise regression resulted in significant models of in situ net N mineralization and included variables describing fungal and bacterial abundance, although explained variance was low (R2<0.29). Unraveling complex spatial patterns of nutrient cycling and the biotic factors that regulate it remains challenging but is critical for explaining post-fire ecosystem function, especially in Greater Yellowstone, which is projected to experience increased fire frequencies by mid 21st Century. PMID:23226324

Effects of cadmium and resource quality on freshwater detritus processing chains: a microcosm approach with two insect species.

PubMed

Campos, Diana; Alves, Artur; Lemos, Marco F L; Correia, António; Soares, Amadeu M V M; Pestana, João L T

2014-07-01

Detritus processing is vital for freshwater ecosystems that depend on the leaf litter from riparian vegetation and is mediated by microorganisms and aquatic invertebrates. Shredder invertebrates transform coarse particulate organic matter into fine particulate organic matter used as food by collector species. Direct and indirect effects of contaminants can impair detritus processing and thus affect the functioning of these ecosystems. Here, we assessed the combined effects of a toxic metal (cadmium) and resource quality (leaf species) on detritus processing and shredder-collector interactions. We considered two types of leaves, alder and eucalyptus that were microbially conditioned under different Cd concentrations in the laboratory. The microbial communities present on leaves were analyzed by Denaturing Gradient Gel Electrophoresis (DGGE), and we also measured microbial respiration rates. Sericostoma vittatum (a caddisfly shredder) and Chironomus riparius (a midge collector) were also exposed to Cd and allowed to consume the corresponding alder or eucalyptus leaves. We evaluated C. riparius growth and leaf mass loss in multispecies microcosms. Cadmium exposure affected leaf conditioning and fungal diversity on both leaf species, as assessed by DGGE. Cadmium exposure also affected the mass loss of alder leaves by reductions in detritivore feeding, and impaired C. riparius growth. Chironomus riparius consumed alder leaf discs in the absence of shredders, but S. vittatum appear to promote C. riparius growth in treatments containing eucalyptus. These results show that indirect effects of contaminants along detritus-processing chains can occur through effects on shredder-collector interactions such as facilitation but they also depend on the nutritional quality of detritus and on sensitivity and feeding plasticity of detritivore species.

Microbial mediated retention/transformation of organic and inorganic materials in freshwater and marine ecosystems

EPA Science Inventory

Aquatic ecosystems are globally connected by hydrological and biogeochemical cycles. Microorganisms inhabiting aquatic ecosystems form the basis of food webs, mediate essential element cycles, decompose natural organic matter, transform inorganic nutrients and metals, and degrad...

Final Technical Report: Viral Infection of Subsurface Microorganisms and Metal/Radionuclide Transport

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

Weber, Karrie A.; Bender, Kelly S.; Li, Yusong

Microbially mediated metabolisms have been identified as a significant factor either directly or indirectly impacting the fate and transport of heavy metal/radionuclide contaminants. To date microorganisms have been isolated from contaminated environments. Examination of annotated finished genome sequences of many of these subsurface isolates from DOE sites, revealed evidence of prior viral infection. To date the role that viruses play influencing microbial mortality and the resulting community structure which directly influences biogeochemical cycling in soils and sedimentary environments remains poorly understood. The objective of this exploratory study was to investigate the role of viral infection of subsurface bacteria and themore » formation of contaminant-bearing viral particles. This objective was approached by examining the following working hypotheses: (i) subsurface microorganisms are susceptible to viral infections by the indigenous subsurface viral community, and (ii) viral surfaces will adsorb heavy metals and radionuclides. Our results have addressed basic research needed to accomplish the BER Long Term Measure to provide sufficient scientific understanding such that DOE sites would be able to incorporate coupled physical, chemical and biological processes into decision making for environmental remediation or natural attenuation and long-term stewardship by establishing viral-microbial relationships on the subsequent fate and transport of heavy metals and radionuclides. Here we demonstrated that viruses play a significant role in microbial mortality and community structure in terrestrial subsurface sedimentary systems. The production of viral-like particles within subsurface sediments in response to biostimulation with dissolved organic carbon and a terminal electron acceptor resulted in the production of viral-like particles. Organic carbon alone did not result in significant viral production and required the addition of a terminal electron acceptor (nitrate), indicating that nutrients are not limiting viral production, but rather substrates that can be converted into energy for host metabolism. Our results also revealed that cell abundance was not correlated to the mineralization of organic carbon, but rather viruses were positively correlated with carbon mineralization. This is a result of viral-mediated cell lysis and demonstrates that viruses are sensitive indicators of microbial activity. Viruses as an indicator of microbial activity was not unique to batch culture studies as results obtained from an in situ field experiment conducted at the DOE Old Rifle Field site. This study revealed that viral abundance increased in response to the injection of oxygenated groundwater and influx of dissolved organic carbon whereas cell abundance changes were minimal. However, the extent to which viral-mediated cell lysis alters organic matter pools subsequently influencing microbial community structure and biogeochemical function remains a critical question in subsurface biogeochemical cycling. The production of significant numbers of viruses in groundwater has implications for nanoparticulate metal as well as carbon transport in groundwater. We have demonstrated that the virus surface is reactive and will adsorb heavy metals. Thus viruses can promote colloidal contaminant mobility. Interestingly, the presence of heavy metals has a positive effect on infectivity of the phage, increasing phage infection which could lead to further production of viruses. Together, the results indicate that the sorption of metals to the surface of viruses could not only contribute to nanoparticulate metal as well as carbon transport but could also enhance infectivity further contributing to cell lysis which could subsequently influence biogeochemical cycling. As more viruses infect host microbial populations the high concentration of metals would enhance infection, resulting in cell lysis, and decreasing the metabolically active host population while yielding greater numbers of viruses capable of transporting contaminats. Additional studies will be necessary to further establish the potential relationship(s) between viruses, cells, carbon, and metals/radionuclides to provide sufficient scientific understanding to incorporate coupled physical, chemical, and biological processes into agent based and reactive transport models.« less

Molecular characterization of biochars and their influence on microbiological properties of soil.

PubMed

Chintala, Rajesh; Schumacher, Thomas E; Kumar, Sandeep; Malo, Douglas D; Rice, James A; Bleakley, Bruce; Chilom, Gabriela; Clay, David E; Julson, James L; Papiernik, Sharon K; Gu, Zheng Rong

2014-08-30

The tentative connection between the biochar surface chemical properties and their influence on microbially mediated mineralization of C, N, and S with the help of enzymes is not well established. This study was designed to investigate the effect of different biomass conversion processes (microwave pyrolysis, carbon optimized gasification, and fast pyrolysis using electricity) on the composition and surface chemistry of biochar materials produced from corn stover (Zea mays L.), switchgrass (Panicum virgatum L.), and Ponderosa pine wood residue (Pinus ponderosa Lawson and C. Lawson) and determine the effect of biochars on mineralization of C, N, and S and associated soil enzymatic activities including esterase (fluorescein diacetate hydrolase, FDA), dehydrogenase (DHA), β-glucosidase (GLU), protease (PROT), and aryl sulfatase (ARSUL) in two different soils collected from footslope (Brookings) and crest (Maddock) positions of a landscape. Chemical properties of biochar materials produced from different batches of gasification process were fairly consistent. Biochar materials were found to be highly hydrophobic (low H/C values) with high aromaticity, irrespective of biomass feedstock and pyrolytic process. The short term incubation study showed that biochar had negative effects on microbial activity (FDA and DHA) and some enzymes including β-glucosidase and protease. Published by Elsevier B.V.

Impedance Spectroscopy as a Tool for Non-Intrusive Detection of Extracellular Mediators in Microbial Fuel Cells

DTIC Science & Technology

2009-12-01

bioseparation. Hoboken, NJ: John Wiley & Sons, p. 267. HernandezME, Kappler A, Newman DK. 2004. Phenazines and other redox active antibiotics promote...Verstraete W. 2005. Microbial phenazine production enhances electron transfer in biofuel cells. Environ Sci Technol 39:3401. Ramasamy RP, Ren Z, Mench MM

Influence of redox mediators and salinity level on the (bio)transformation of Direct Blue 71: kinetics aspects.

PubMed

Alvarez, Luis H; Meza-Escalante, Edna R; Gortáres-Moroyoqui, Pablo; Morales, Luz; Rosas, Krystal; García-Reyes, Bernardo; García-González, Alicone

2016-12-01

The rate-limiting step of azo dye decolorization was elucidated by exploring the microbial reduction of a model quinone and the chemical decolorization by previously reduced quinone at different salinity conditions (2-8%). Microbial experiments were performed in batch with a marine consortium. The decolorization of Direct Blue 71 (DB71) by the marine consortium at 2% salinity, mediated with anthraquinone-2,6-disulfonate (AQDS), showed the highest rate of decolorization as compared with those obtained with riboflavin, and two samples of humic acids. Moreover, the incubations at different salinity conditions (0-8%) performed with AQDS showed that the highest rate of decolorization of DB71 by the marine consortium occurred at 2% and 4% salinity. In addition, the highest microbial reduction rate of AQDS occurred in incubations at 0%, 2%, and 4% of salinity. The chemical reduction of DB71 by reduced AQDS occurred in two stages and proceeded faster at 4% and 6% salinity. The results indicate that the rate-limiting step during azo decolorization was the microbial reduction of AQDS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Kinetics during the redox biotransformation of pollutants mediated by immobilized and soluble humic acids.

PubMed

Cervantes, Francisco J; Martínez, Claudia M; Gonzalez-Estrella, Jorge; Márquez, Arturo; Arriaga, Sonia

2013-03-01

The aim of this study was to elucidate the kinetic constraints during the redox biotransformation of the azo dye, Reactive Red 2 (RR2), and carbon tetrachloride (CT) mediated by soluble humic acids (HAs) and immobilized humic acids (HAi), as well as by the quinoid model compounds, anthraquinone-2,6-disulfonate (AQDS) and 1,2-naphthoquinone-4-sulfonate (NQS). The microbial reduction of both HAs and HAi by anaerobic granular sludge (AGS) was the rate-limiting step during decolorization of RR2 since the reduction of RR2 by reduced HAi proceeded at more than three orders of magnitute faster than the electron-transferring rate observed during the microbial reduction of HAi by AGS. Similarly, the reduction of RR2 by reduced AQDS proceeded 1.6- and 1.9-fold faster than the microbial reduction of AQDS by AGS when this redox mediator (RM) was supplied in soluble and immobilized form, respectively. In contrast, the reduction of NQS by AGS occurred 1.6- and 19.2-fold faster than the chemical reduction of RR2 by reduced NQS when this RM was supplied in soluble and immobilized form, respectively. The microbial reduction of HAs and HAi by a humus-reducing consortium proceeded 1,400- and 790-fold faster than the transfer of electrons from reduced HAs and HAi, respectively, to achieve the reductive dechlorination of CT to chloroform. Overall, the present study provides elucidation on the rate-limiting steps involved in the redox biotransformation of priority pollutants mediated by both HAs and HAi and offers technical suggestions to overcome the kinetic restrictions identified in the redox reactions evaluated.

Functional resilience of microbial ecosystems in soil: How important is a spatial analysis?

NASA Astrophysics Data System (ADS)

König, Sara; Banitz, Thomas; Centler, Florian; Frank, Karin; Thullner, Martin

2015-04-01

Microbial life in soil is exposed to fluctuating environmental conditions influencing the performance of microbially mediated ecosystem services such as biodegradation of contaminants. However, as this environment is typically very heterogeneous, spatial aspects can be expected to play a major role for the ability to recover from a stress event. To determine key processes for functional resilience, simple scenarios with varying stress intensities were simulated within a microbial simulation model and the biodegradation rate in the recovery phase monitored. Parameters including microbial growth and dispersal rates were varied over a typical range to consider microorganisms with varying properties. Besides an aggregated temporal monitoring, the explicit observation of the spatio-temporal dynamics proved essential to understand the recovery process. For a mechanistic understanding of the model system, scenarios were also simulated with selected processes being switched-off. Results of the mechanistic and the spatial view show that the key factors for functional recovery with respect to biodegradation after a simple stress event depend on the location of the observed habitats. The limiting factors near unstressed areas are spatial processes - the mobility of the bacteria as well as substrate diffusion - the longer the distance to the unstressed region the more important becomes the process growth. Furthermore, recovery depends on the stress intensity - after a low stress event the spatial configuration has no influence on the key factors for functional resilience. To confirm these results, we repeated the stress scenarios but this time including an additional dispersal network representing a fungal network in soil. The system benefits from an increased spatial performance due to the higher mobility of the degrading microorganisms. However, this effect appears only in scenarios where the spatial distribution of the stressed area plays a role. With these simulations we show that spatial aspects play a main role for recovering after a severe stress event in a highly heterogeneous environment such as soil, and thus the relevance of the exact distribution of the stressed area. In consequence a spatial-mechanistic view is necessary for examining the functional resilience as the aggregated temporal view alone could not have led to these conclusions. Further research should explore the importance of a spatial view for quantifying the recovery of the ecosystem service also after more complex stress regimes.

High power density yeast catalyzed microbial fuel cells

NASA Astrophysics Data System (ADS)

Ganguli, Rahul

Microbial fuel cells leverage whole cell biocatalysis to convert the energy stored in energy-rich renewable biomolecules such as sugar, directly to electrical energy at high efficiencies. Advantages of the process include ambient temperature operation, operation in natural streams such as wastewater without the need to clean electrodes, minimal balance-of-plant requirements compared to conventional fuel cells, and environmentally friendly operation. These make the technology very attractive as portable power sources and waste-to-energy converters. The principal problem facing the technology is the low power densities compared to other conventional portable power sources such as batteries and traditional fuel cells. In this work we examined the yeast catalyzed microbial fuel cell and developed methods to increase the power density from such fuel cells. A combination of cyclic voltammetry and optical absorption measurements were used to establish significant adsorption of electron mediators by the microbes. Mediator adsorption was demonstrated to be an important limitation in achieving high power densities in yeast-catalyzed microbial fuel cells. Specifically, the power densities are low for the length of time mediator adsorption continues to occur. Once the mediator adsorption stops, the power densities increase. Rotating disk chronoamperometry was used to extract reaction rate information, and a simple kinetic expression was developed for the current observed in the anodic half-cell. Since the rate expression showed that the current was directly related to microbe concentration close to the electrode, methods to increase cell mass attached to the anode was investigated. Electrically biased electrodes were demonstrated to develop biofilm-like layers of the Baker's yeast with a high concentration of cells directly connected to the electrode. The increased cell mass did increase the power density 2 times compared to a non biofilm fuel cell, but the power density increase was shown to quickly saturate with cell mass attached on the electrode. Based on recent modelling data that suggested that the electrode currents might be limited by the poor electrical conductivity of the anode, the power density versus electrical conductivity of a yeast-immobilized anode was investigated. Introduction of high aspect ratio carbon fiber filaments to the immobilization matrix increased the electrical conductivity of the anode. Although a higher electrical conductivity clearly led to an increase in power densities, it was shown that the principal limitation to power density increase was coming from proton transfer limitations in the immobilized anode. Partial overcoming of the gradients lead a power density of ca. 250 microW cm-2, which is the highest reported for yeast powered MFCs. A yeast-catalyzed microbial fuel cell was investigated as a power source for low power sensors using raw tree sap. It was shown that yeast can efficiently utilize the sucrose present in the raw tree sap to produce electricity when excess salt is added to the medium. Therefore the salinity of a potential energy source is an important consideration when MFCs are being considered for energy harvesting from natural sources.

Microbial Biotechnology 2020; microbiology of fossil fuel resources.

PubMed

Head, Ian M; Gray, Neil D

2016-09-01

This roadmap examines the future of microbiology research and technology in fossil fuel energy recovery. Globally, the human population will be reliant on fossil fuels for energy and chemical feedstocks for at least the medium term. Microbiology is already important in many areas relevant to both upstream and downstream activities in the oil industry. However, the discipline has struggled for recognition in a world dominated by geophysicists and engineers despite widely known but still poorly understood microbially mediated processes e.g. reservoir biodegradation, reservoir souring and control, microbial enhanced oil recovery. The role of microbiology is even less understood in developing industries such as shale gas recovery by fracking or carbon capture by geological storage. In the future, innovative biotechnologies may offer new routes to reduced emissions pathways especially when applied to the vast unconventional heavy oil resources formed, paradoxically, from microbial activities in the geological past. However, despite this potential, recent low oil prices may make industry funding hard to come by and recruitment of microbiologists by the oil and gas industry may not be a high priority. With regards to public funded research and the imperative for cheap secure energy for economic growth in a growing world population, there are signs of inherent conflicts between policies aimed at a low carbon future using renewable technologies and policies which encourage technologies which maximize recovery from our conventional and unconventional fossil fuel assets. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Microalgae-mediated simultaneous treatment of toxic thiocyanate and production of biodiesel.

PubMed

Ryu, Byung-Gon; Kim, Jungmin; Yoo, Gursong; Lim, Jun-Taek; Kim, Woong; Han, Jong-In; Yang, Ji-Won

2014-04-01

In this work, a method for simultaneously degrading the toxic pollutant, thiocyanate, and producing microalgal lipids using mixed microbial communities was developed. Aerobic activated sludge was used as the seed culture and thiocyanate was used as the sole nitrogen source. Two cultivation methods were sequentially employed: a lithoautotrophic mode and a photoautotrophic mode. Thiocyanate hydrolysis and a nitrification was found to occur under the first (lithoautotrophic) condition, while the oxidized forms of nitrogen were assimilated by the photoautotrophic consortium and lipids were produced under the second condition. The final culture exhibited good settling efficiency (∼ 70% settling over 10 min), which can benefit downstream processing. The highest CO2 fixation rate and lipid productivity were observed with 2.5% and 5% CO2, respectively. The proposed integrated algal-bacterial system appears to be a feasible and even beneficial option for thiocyanate treatment and production of microbial lipids. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial oxidation of lithospheric organic carbon in rapidly eroding tropical mountain soils

NASA Astrophysics Data System (ADS)

Hemingway, Jordon D.; Hilton, Robert G.; Hovius, Niels; Eglinton, Timothy I.; Haghipour, Negar; Wacker, Lukas; Chen, Meng-Chiang; Galy, Valier V.

2018-04-01

Lithospheric organic carbon (“petrogenic”; OCpetro) is oxidized during exhumation and subsequent erosion of mountain ranges. This process is a considerable source of carbon dioxide (CO2) to the atmosphere over geologic time scales, but the mechanisms that govern oxidation rates in mountain landscapes are poorly constrained. We demonstrate that, on average, 67 ± 11% of the OCpetro initially present in bedrock exhumed from the tropical, rapidly eroding Central Range of Taiwan is oxidized in soils, leading to CO2 emissions of 6.1 to 18.6 metric tons of carbon per square kilometer per year. The molecular and isotopic evolution of bulk OC and lipid biomarkers during soil formation reveals that OCpetro remineralization is microbially mediated. Rapid oxidation in mountain soils drives CO2 emission fluxes that increase with erosion rate, thereby counteracting CO2 drawdown by silicate weathering and biospheric OC burial.

A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients.

PubMed

Sibley, Christopher D; Parkins, Michael D; Rabin, Harvey R; Duan, Kangmin; Norgaard, Jens C; Surette, Michael G

2008-09-30

Lung disease is the leading cause of morbidity and mortality in cystic fibrosis (CF) patients. A modest number of bacterial pathogens have been correlated with pulmonary function decline; however, microbiological and molecular evidence suggests that CF airway infection is polymicrobial. To obtain a more complete assessment of the microbial community composition and dynamics, we undertook a longitudinal study by using culture-independent and microbiological approaches. In the process, we demonstrated that within complex and dynamic communities, the Streptococcus milleri group (SMG) can establish chronic pulmonary infections and at the onset of 39% of acute pulmonary exacerbations, SMG is the numerically dominant pathogen. We report the comprehensive polymicrobial community dynamics of a CF lung infection in a clinically relevant context. If a given organism, such as Pseudomonas aeruginosa, becomes resistant to antibiotic therapy, an alternative treatment avenue may mediate the desired clinical response by effectively managing the composition of the microbial community.

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges

PubMed Central

Bruder, Katherine; Malki, Kema; Cooper, Alexandria; Sible, Emily; Shapiro, Jason W.; Watkins, Siobhan C.; Putonti, Catherine

2016-01-01

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations. PMID:27375355

Founder takes all: density-dependent processes structure biodiversity.

PubMed

Waters, Jonathan M; Fraser, Ceridwen I; Hewitt, Godfrey M

2013-02-01

Density-dependent processes play a key role in the spatial structuring of biodiversity. Specifically, interrelated demographic processes, such as gene surfing, high-density blocking, and competitive exclusion, can generate striking geographic contrasts in the distributions of genes and species. Here, we propose that well-studied evolutionary and ecological biogeographic patterns of postglacial recolonization, progressive island colonization, microbial sectoring, and even the 'Out of Africa' pattern of human expansion, are fundamentally similar, underpinned by a 'founder takes all' density-dependent principle. Additionally, we hypothesize that older historic constraints of density-dependent processes are seen today in the dramatic biogeographic shifts that occur in response to human-mediated extinction events, whereby surviving lineages rapidly expand their ranges to replace extinct sister taxa. Copyright © 2012 Elsevier Ltd. All rights reserved.

Incorporating the soil environment and microbial community into plant competition theory

PubMed Central

Ke, Po-Ju; Miki, Takeshi

2015-01-01

Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF). PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach. PMID:26500621

Bioelectricity generation using two chamber microbial fuel cell treating wastewater from food processing.

PubMed

Mansoorian, Hossein Jafari; Mahvi, Amir Hossein; Jafari, Ahmad Jonidi; Amin, Mohammad Mehdi; Rajabizadeh, Ahmad; Khanjani, Narges

2013-05-10

Electricity generation from microbial fuel cells which treat food processing wastewater was investigated in this study. Anaerobic anode and aerobic cathode chambers were separated by a proton exchange membrane in a two-compartment MFC reactor. Buffer solutions and food industry wastewater were used as electrolytes in the anode and cathode chambers, respectively. The produced voltage and current intensity were measured using a digital multimeter. Effluents from the anode compartment were tested for COD, BOD5, NH3, P, TSS, VSS, SO4 and alkalinity. The maximum current density and power production were measured 527mA/m(2) and 230mW/m(2) in the anode area, respectively, at operation organic loading (OLR) of 0.364g COD/l.d. At OLR of 0.182g COD/l.d, maximum voltage and columbic efficiency production were recorded 0.475V and 21%, respectively. Maximum removal efficiency of COD, BOD5, NH3, P, TSS, VSS, SO4 and alkalinity were 86, 79, 73, 18, 68, 62, 30 and 58%, respectively. The results indicated that catalysts and mediator-less microbial fuel cells (CAML-MFC) can be considered as a better choice for simple and complete energy conversion from the wastewater of such industries and also this could be considered as a new method to offset wastewater treatment plant operating costs. Copyright © 2013 Elsevier Inc. All rights reserved.

The Oxidative Metabolism of Fossil Hydrocarbons and Sulfide Minerals by the Lithobiontic Microbial Community Inhabiting Deep Subterrestrial Kupferschiefer Black Shale.

PubMed

Włodarczyk, Agnieszka; Lirski, Maciej; Fogtman, Anna; Koblowska, Marta; Bidziński, Grzegorz; Matlakowska, Renata

2018-01-01

Black shales are one of the largest reservoirs of fossil organic carbon and inorganic reduced sulfur on Earth. It is assumed that microorganisms play an important role in the transformations of these sedimentary rocks and contribute to the return of organic carbon and inorganic sulfur to the global geochemical cycles. An outcrop of deep subterrestrial ~256-million-year-old Kupferschiefer black shale was studied to define the metabolic processes of the deep biosphere important in transformations of organic carbon and inorganic reduced sulfur compounds. This outcrop was created during mining activity 12 years ago and since then it has been exposed to the activity of oxygen and microorganisms. The microbial processes were described based on metagenome and metaproteome studies as well as on the geochemistry of the rock. The microorganisms inhabiting the subterrestrial black shale were dominated by bacterial genera such as Pseudomonas, Limnobacter, Yonghaparkia, Thiobacillus, Bradyrhizobium , and Sulfuricaulis . This study on black shale was the first to detect archaea and fungi, represented by Nitrososphaera and Aspergillus genera, respectively. The enzymatic oxidation of fossil aliphatic and aromatic hydrocarbons was mediated mostly by chemoorganotrophic bacteria, but also by archaea and fungi. The dissimilative enzymatic oxidation of primary reduced sulfur compounds was performed by chemolithotrophic bacteria. The geochemical consequences of microbial activity were the oxidation and dehydrogenation of kerogen, as well as oxidation of sulfide minerals.

Microbial fuel cells coupling with the three-dimensional electro-Fenton technique enhances the degradation of methyl orange in the wastewater.

PubMed

Huang, Tao; Liu, Longfei; Tao, Junjun; Zhou, Lulu; Zhang, Shuwen

2018-04-23

The emission of the source effluent of azo dyes has resulted in a serial of environmental problems including of the direct damage of the natural esthetics, the inhibition of the oxygen exchange, the shortage of the photosynthesis, and the reduction of the aquatic flora and fauna. A bioelectrochemical platform (3D-EF-MFCs) combining two-chamber microbial fuel cells and three dimensional electro-Fenton technique were delicately designed and assembled to explore the decolorization, bio-genericity performance of the methyl orange, and the possible biotic-abiotic degradation mechanisms. The 3D-EF-MFCs processes showed higher decolorization efficiencies, COD removals, and better bioelectricity performance than the pure electro-Fenton-microbial fuel cell (EF-MFC) systems. The two-chamber experiments filling with the granular activated carbons were better than the single-chamber packing system on the whole. The moderate increase of Fe 2+ ions dosing in the cathode chamber accelerated the formation of •OH, which further enhanced the degradation of the methyl orange (MO). The cathode-decolorization and COD removals were decreased with the increase of MO concentration. However, the degradation performance of MO was indirectly improved in the anode compartment at the same conditions. The bed electrodes played a mediator role in the anode and cathode chambers, certainly elevated the voltage output and the power density, and lowered the internal impedance of EF-MFC process.

Succession of bacterial and fungal communities during a traditional pot fermentation of rice vinegar assessed by PCR-mediated denaturing gradient gel electrophoresis.

PubMed

Haruta, Shin; Ueno, Shintaro; Egawa, Isao; Hashiguchi, Kazunori; Fujii, Akira; Nagano, Masanobu; Ishii, Masaharu; Igarashi, Yasuo

2006-05-25

Denaturing gradient gel electrophoresis (DGGE) based on small subunit rRNA gene was applied to a traditional rice vinegar fermentation process in which the conversion of rice starch into acetic acid proceeded in a pot. The fungal DGGE profile indicated that the transition from Aspergillus oryzae to Saccharomyces sp. took place at the initial stage at which alcohol production was observed. The early stage was characterized by the coexistence of Saccharomyces sp. and lactic acid bacteria. Almost all of the bacterial DGGE bands related to lactic acid bacteria were replaced by bands derived from Lactobacillus acetotolerance and Acetobacter pasteurianus at the stage at which acetic acid started to accumulate. The microbial succession, tested in three different pots, was found to be essentially identical. Among the bacteria isolated at the early stage, some species differed from those detected by DGGE. This is the first report to reveal the microbial community succession that occurs during a unique vinegar fermentation process, as determined by a culture-independent method.

Microbial mercury methylation in Antarctic sea ice.

PubMed

Gionfriddo, Caitlin M; Tate, Michael T; Wick, Ryan R; Schultz, Mark B; Zemla, Adam; Thelen, Michael P; Schofield, Robyn; Krabbenhoft, David P; Holt, Kathryn E; Moreau, John W

2016-08-01

Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.

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.

Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

PubMed Central

Hu, Ziye; Meng, Han; Shi, Jin-Huan; Bu, Nai-Shun; Fang, Chang-Ming; Quan, Zhe-Xue

2014-01-01

Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA) are much higher than that of ammonia oxidizing bacteria (AOB). The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition. PMID:25101072

Effect of microbially mediated iron mineral transformation on temporal variation of arsenic in the Pleistocene aquifers of the central Yangtze River basin.

PubMed

Deng, Yamin; Zheng, Tianliang; Wang, Yanxin; Liu, Lun; Jiang, Hongchen; Ma, Teng

2018-04-01

Significant seasonal variation of groundwater arsenic (As) concentrations in shallow aquifers of the Jianghan Plain, central Yangtze River Basin has been reported recently, but the underlying mechanisms remain not well understood. To elaborate biogeochemical processes responsible for the observed As concentration variation, 42-day incubation experiments were done using sediment samples collected respectively from the depth of 26, 36 and 60m of the As-affected aquifer which were labeled respectively as JH26, JH36, JH60. Where JH denotes Jianghan Plain, and the number indicates the depth of the sediment sample. The results indicated that As could be mobilized from the sediments of 26m and 36m depth under the stimulation of exogenous organic carbon, with the maximum As release amount of 1.60 and 1.03mgkg -1 , respectively, while the sediments at 60m depth did not show As mobilization. The microbially mediated reductive dissolution of amorphous iron oxides and reduction of As(V) to As(III) could account for the observed As mobilization. The 16S rRNA high-throughput sequencing results indicated that the variation of microbial community correlated with the released As concentration (R=0.7, P<0.05) and the iron-reducing bacteria, including Pseudomonas, Clostridium and Geobacter, were the main drivers for the As mobilization from the sediments at 26m and 36m depth. The increase of arsC gene abundance (up to 1.4×10 5 copies g -1 ) during As release suggested that As reduction was mediated by the resistant reduction mechanism. By contrast, in the 60m sediments where the Fe and As release was absent, the iron-reducing bacteria accounted for a very minor proportion and sulfate-reducing bacteria were predominant in the microbial community. In addition, after 30days of incubation, the released As in the 26m sediments was immobilized via co-precipitation with or adsorption onto the Fe-sulfide mineral newly-formed by the bacterial sulfate reduction. These results are consistent with the results of our previous field monitoring, indicating that the bacterial sulfate reduction could lead to the temporal decrease in groundwater As concentrations. This study provides insights into the mechanism for As mobilization and seasonal As concentration variation in the Pleistocene aquifers from alluvial plains. Copyright © 2017 Elsevier B.V. All rights reserved.

New developments in microbial interspecies signaling.

PubMed

Shank, Elizabeth Anne; Kolter, Roberto

2009-04-01

There is a growing appreciation that in addition to well-documented intraspecies quorum sensing systems, small molecules act as signals between microbes of different species. This review will focus on how bacterial small molecules modulate these interspecies interactions. We will particularly emphasize complex relationships such as those between microbes and insects, interactions resulting in non-antagonistic outcomes (i.e. developmental and morphological processes), how co-culture can lead to the discovery of new small molecules, and the use of known compounds to evoke unexpected responses and mediate crosstalk between microbes.

Effects of plant diversity on microbial nitrogen and phosphorus dynamics in soil

NASA Astrophysics Data System (ADS)

Prommer, Judith; Braun, Judith; Daly, Amanda; Gorka, Stefan; Hu, Yuntao; Kaiser, Christina; Martin, Victoria; Meyerhofer, Werner; Walker, Tom W. N.; Wanek, Wolfgang; Wasner, Daniel; Wiesenbauer, Julia; Zezula, David; Zheng, Qing; Richter, Andreas

2017-04-01

There is a general consensus that plant diversity affects many ecosystem functions. One example of such an effect is the enhanced aboveground and belowground plant biomass production with increasing species richness, with implications for carbon and nutrient distribution in soil. The Jena Experiment (http://www.the-jena-experiment.de/), a grassland biodiversity experiment established in 2002 in Germany, comprises different levels of plant species richness and different numbers of plant functional groups. It provides the opportunity to examine how changes in biodiversity impact on microbially-mediated nutrient cycling processes. We here report on plant diversity and plant functional composition effects on growth and nitrogen and phosphorus transformation rates, including nitrogen use efficiency, of microbial communities. Microbial growth rates and microbial biomass were positively affected by increasing plant species richness. Amino acid and ammonium concentrations in soil were also positively affected by plant species richness, while phosphate concentrations in contrast were negatively affected. The cycling of organic N in soils (estimated as gross protein depolymerization rates) increased about threefold with plant diversity, while gross N and P mineralization were not significantly affected by either species or functional richness. Microbial nitrogen use efficiency did not respond to different levels of plant diversity but was very high (0.96 and 0.98) across all levels of plant species richness, demonstrating a low N availability for microbes. Taken together this indicates that soil microbial communities were able to meet the well-documented increase in plant N content with species richness, and also the higher N demand of the microbial community by increasing the recycling of organic N such as proteins. In fact, the microbial community even overcompensated the increased plant and microbial N demand, as evidenced by increased levels of free amino acids and ammonium in the soil solution at higher species richness. A possible explanation for increased organic nitrogen transformation rates is the increased microbial biomass, which has previously been related to higher quantity and variety of plant derived compounds that are available to the microbial communities at higher plant diversity. Given that this explanation is right, it is interesting to note that the additional (plant-derived) microbial biomass at higher species richness, did not translate in higher soil P mineralization rates or phosphate availability.

Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases.

PubMed

Welch, David; Buonanno, Manuela; Grilj, Veljko; Shuryak, Igor; Crickmore, Connor; Bigelow, Alan W; Randers-Pehrson, Gerhard; Johnson, Gary W; Brenner, David J

2018-02-09

Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207-222 nm) efficiently inactivates bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently inactivates airborne aerosolized viruses, with a very low dose of 2 mJ/cm 2 of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases.

Diatom Derived Polyunsaturated Aldehydes Do Not Structure the Planktonic Microbial Community in a Mesocosm Study

PubMed Central

Paul, Carsten; Reunamo, Anna; Lindehoff, Elin; Bergkvist, Johanna; Mausz, Michaela A.; Larsson, Henrik; Richter, Hannes; Wängberg, Sten-Åke; Leskinen, Piia; Båmstedt, Ulf; Pohnert, Georg

2012-01-01

Several marine and freshwater diatoms produce polyunsaturated aldehydes (PUA) in wound-activated processes. These metabolites are also released by intact diatom cells during algal blooms. Due to their activity in laboratory experiments, PUA are considered as potential mediators of diatom-bacteria interactions. Here, we tested the hypothesis that PUA mediate such processes in a close-to-field mesocosm experiment. Natural plankton communities enriched with Skeletonema marinoi strains that differ in their PUA production, a plankton control, and a plankton control supplemented with PUA at natural and elevated concentrations were observed. We monitored bacterial and viral abundance as well as bacterial community composition and did not observe any influence of PUA on these parameters even at elevated concentrations. We rather detected an alternation of the bacterial diversity over time and differences between the two S. marinoi strains, indicating unique dynamic bacterial communities in these algal blooms. These results suggest that factors other than PUA are of significance for interactions between diatoms and bacteria. PMID:22690143

Microbial dynamics and enzyme activities in tropical Andosols depending on land use and nutrient inputs

NASA Astrophysics Data System (ADS)

Mganga, Kevin; Razavi, Bahar; Kuzyakov, Yakov

2015-04-01

Microbial decomposition of soil organic matter is mediated by enzymes and is a key source of terrestrial CO2 emissions. Microbial and enzyme activities are necessary to understand soil biochemical functioning and identify changes in soil quality. However, little is known about land use and nutrients availability effects on enzyme activities and microbial processes, especially in tropical soils of Africa. This study was conducted to examine how microbial and enzyme activities differ between different land uses and nutrient availability. As Andosols of Mt. Kilimanjaro are limited by nutrient concentrations, we hypothesize that N and P additions will stimulate enzyme activity. N and P were added to soil samples (0-20 cm) representing common land use types in East Africa: (1) savannah, (2) maize fields, (3) lower montane forest, (4) coffee plantation, (5) grasslands and (6) traditional Chagga homegardens. Total CO2 efflux from soil, microbial biomass and activities of β-glucosidase, cellobiohydrolase, chitinase and phosphatase involved in C, N and P cycling, respectively was monitored for 60 days. Total CO2 production, microbial biomass and enzyme activities varied in the order forest soils > grassland soils > arable soils. Increased β-glucosidase and cellobiohydrolase activities after N addition of grassland soils suggest that microorganisms increased N uptake and utilization to produce C-acquiring enzymes. Low N concentration in all soils inhibited chitinase activity. Depending on land use, N and P addition had an inhibitory or neutral effect on phosphatase activity. We attribute this to the high P retention of Andosols and low impact of N and P on the labile P fractions. Enhanced CO2 production after P addition suggests that increased P availability could stimulate soil organic matter biodegradation in Andosols. In conclusion, land use and nutrients influenced soil enzyme activities and microbial dynamics and demonstrated the decline in soil quality after landuse change. Key words: Andosols, β-glucosidase, Cellobiohydrolase, Chitinase, Phosphatase, Mt. Kilimanjaro

Biodegradation and attenuation of steroidal hormones and alkylphenols by stream biofilms and sediments

USGS Publications Warehouse

Writer, Jeffrey; Barber, Larry B.; Ryan, Joseph N.; Bradley, Paul M.

2011-01-01

Biodegradation of select endocrine-disrupting compounds (17β-estradiol, estrone, 17α-ethynylestradiol, 4-nonylphenol, 4-nonylphenolmonoexthoylate, and 4-nonylphenoldiethoxylate) was evaluated in stream biofilm, sediment, and water matrices collected from locations upstream and downstream from a wastewater treatment plant effluent discharge. Both biologically mediated transformation to intermediate metabolites and biologically mediated mineralization were evaluated in separate time interval experiments. Initial time intervals (0–7 d) evaluated biodegradation by the microbial community dominant at the time of sampling. Later time intervals (70 and 185 d) evaluated the biodegradation potential as the microbial community adapted to the absence of outside energy sources. The sediment matrix was more effective than the biofilm and water matrices at biodegrading 4-nonylphenol and 17β-estradiol. Biodegradation by the sediment matrix of 17α-ethynylestradiol occurred at later time intervals (70 and 185 d) and was not observed in the biofilm or water matrices. Stream biofilms play an important role in the attenuation of endocrine-disrupting compounds in surface waters due to both biodegradation and sorption processes. Because sorption to stream biofilms and bed sediments occurs on a faster temporal scale (<1 h) than the potential to biodegrade the target compounds (50% mineralization at >185 d), these compounds can accumulate in stream biofilms and sediments.

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling.

PubMed

Piao, Hailan; Lachman, Medora; Malfatti, Stephanie; Sczyrba, Alexander; Knierim, Bernhard; Auer, Manfred; Tringe, Susannah G; Mackie, Roderick I; Yeoman, Carl J; Hess, Matthias

2014-01-01

The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome-both microbially facilitated processes with global significance.

Assessing the Relative Effects of Geographic Location and Soil Type on Microbial Communities Associated with Straw Decomposition

PubMed Central

Wang, Xiaoyue; Wang, Feng; Jiang, Yuji

2013-01-01

Decomposition of plant residues is largely mediated by soil-dwelling microorganisms whose activities are influenced by both climate conditions and properties of the soil. However, a comprehensive understanding of their relative importance remains elusive, mainly because traditional methods, such as soil incubation and environmental surveys, have a limited ability to differentiate between the combined effects of climate and soil. Here, we performed a large-scale reciprocal soil transplantation experiment, whereby microbial communities associated with straw decomposition were examined in three initially identical soils placed in parallel in three climate regions of China (red soil, Chao soil, and black soil, located in midsubtropical, warm-temperate, and cold-temperate zones). Maize straws buried in mesh bags were sampled at 0.5, 1, and 2 years after the burial and subjected to chemical, physical, and microbiological analyses, e.g., phospholipid fatty acid analysis for microbial abundance, community-level physiological profiling, and 16S rRNA gene denaturing gradient gel electrophoresis, respectively, for functional and phylogenic diversity. Results of aggregated boosted tree analysis show that location rather soil is the primary determining factor for the rate of straw decomposition and structures of the associated microbial communities. Principal component analysis indicates that the straw communities are primarily grouped by location at any of the three time points. In contrast, microbial communities in bulk soil remained closely related to one another for each soil. Together, our data suggest that climate (specifically, geographic location) has stronger effects than soil on straw decomposition; moreover, the successive process of microbial communities in soils is slower than those in straw residues in response to climate changes. PMID:23524671

Microbial Communities Associated with Phosphorite-bearing Sediments

NASA Astrophysics Data System (ADS)

Zoss, R.; Bailey, J.; Flood, B.; Jones, D. S.

2016-12-01

Phosphorus is a limiting nutrient in the environment and is an important component of many biological molecules. Calcium phosphate mineral deposits known as phosphorites, are also the primary source of P for agriculture. Understanding phosphorite formation may improve management of P resources. However, the processes that mediate calcium phosphate mineral precipitation in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating giant sulfur bacteria (GSB). These bacteria may concentrate phosphate in sediment pore waters - creating supersaturated conditions with respect to apatite. However, the relationship between microbes and phosphogenesis is not fully resolved. To further study this relationship, we examined microbial communities from two sources: sediment cores recovered from the shelf of the Benguela region, and DNA extracted from washed phosphorites recovered from those same sediments. We used itag and clone library sequencing of the 16S rRNA gene to examine the microbial communities and their relationship with the environment. We found that many of our sediments shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfur-reducing bacteria and sulfur-oxidizing bacteria were abundant in our datasets. Phylotypes that are known to carry out nitrification and/or anammox (anaerobic ammonia oxidation) were also well-represented. Our phosphorite extraction, however, contained a distinct microbial community from those observed in the modern sediments. We observed both an enrichment of certain common microbial classes and a complete absence of others. These results could represent an ancient microbial assemblage that was present when the apatite precipitated. While these taxa may or may not have contributed to apatite precipitation, several groups represented in the phosphorite dataset have the genetic potential, as determined through the analysis of published genomes, to synthesize, and perhaps accumulate, polyphosphate.

Genome-resolved metagenomics reveals that sulfur metabolism dominates the microbial ecology of rising hydrothermal plumes

NASA Astrophysics Data System (ADS)

Anantharaman, K.; Breier, J. A., Jr.; Jain, S.; Reed, D. C.; Dick, G.

2015-12-01

Deep-sea hydrothermal plumes occur when hot fluids from hydrothermal vents replete with chemically reduced elements and compounds like sulfide, methane, hydrogen, ammonia, iron and manganese mix with cold, oxic seawater. Chemosynthetic microbes use these reduced chemicals to power primary production and are pervasive throughout the deep sea, even at sites far removed from hydrothermal vents. Although neutrally-buoyant hydrothermal plumes have been well-studied, rising hydrothermal plumes have received little attention even though they represent an important interface in the deep-sea where microbial metabolism and particle formation processes control the transformation of important elements and impact global biogeochemical cycles. In this study, we used genome-resolved metagenomic analyses and thermodynamic-bioenergetic modeling to study the microbial ecology of rising hydrothermal plumes at five different hydrothermal vents spanning a range of geochemical gradients at the Eastern Lau Spreading Center (ELSC) in the Western Pacific Ocean. Our analyses show that differences in the geochemistry of hydrothermal vents do not manifest in microbial diversity and community composition, both of which display only minor variance across ELSC hydrothermal plumes. Microbial metabolism is dominated by oxidation of reduced sulfur species and supports a diversity of bacteria, archaea and viruses that provide intriguing insights into metabolic plasticity and virus-mediated horizontal gene transfer in the microbial community. The manifestation of sulfur oxidation genes in hydrogen and methane oxidizing organisms hints at metabolic opportunism in deep-sea microbes that would enable them to respond to varying redox conditions in hydrothermal plumes. Finally, we infer that the abundance, diversity and metabolic versatility of microbes associated with sulfur oxidation impart functional redundancy that could allow it to persist in the dynamic settings of hydrothermal plumes.

Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems

PubMed Central

Kracke, Frauke; Vassilev, Igor; Krömer, Jens O.

2015-01-01

Microbial electrochemical techniques describe a variety of emerging technologies that use electrode–bacteria interactions for biotechnology applications including the production of electricity, waste and wastewater treatment, bioremediation and the production of valuable products. Central in each application is the ability of the microbial catalyst to interact with external electron acceptors and/or donors and its metabolic properties that enable the combination of electron transport and carbon metabolism. And here also lies the key challenge. A wide range of microbes has been discovered to be able to exchange electrons with solid surfaces or mediators but only a few have been studied in depth. Especially electron transfer mechanisms from cathodes towards the microbial organism are poorly understood but are essential for many applications such as microbial electrosynthesis. We analyze the different electron transport chains that nature offers for organisms such as metal respiring bacteria and acetogens, but also standard biotechnological organisms currently used in bio-production. Special focus lies on the essential connection of redox and energy metabolism, which is often ignored when studying bioelectrochemical systems. The possibility of extracellular electron exchange at different points in each organism is discussed regarding required redox potentials and effect on cellular redox and energy levels. Key compounds such as electron carriers (e.g., cytochromes, ferredoxin, quinones, flavins) are identified and analyzed regarding their possible role in electrode–microbe interactions. This work summarizes our current knowledge on electron transport processes and uses a theoretical approach to predict the impact of different modes of transfer on the energy metabolism. As such it adds an important piece of fundamental understanding of microbial electron transport possibilities to the research community and will help to optimize and advance bioelectrochemical techniques. PMID:26124754

Linking microbial assemblages to paleoenvironmental conditions from the Holocene and Last Glacial Maximum times in Laguna Potrok Aike sediments, Argentina

NASA Astrophysics Data System (ADS)

Vuillemin, Aurele; Ariztegui, Daniel; Leavitt, Peter R.; Bunting, Lynda

2014-05-01

Laguna Potrok Aike is a closed basin located in the southern hemisphere's mid-latitudes (52°S) where paleoenvironmental conditions were recorded as temporal sedimentary sequences resulting from variations in the regional hydrological regime and geology of the catchment. The interpretation of the limnogeological multiproxy record developed during the ICDP-PASADO project allowed the identification of contrasting time windows associated with the fluctuations of Southern Westerly Winds. In the framework of this project, a 100-m-long core was also dedicated to a detailed geomicrobiological study which aimed at a thorough investigation of the lacustrine subsurface biosphere. Indeed, aquatic sediments do not only record past climatic conditions, but also provide a wide range of ecological niches for microbes. In this context, the influence of environmental features upon microbial development and survival remained still unexplored for the deep lacustrine realm. Therefore, we investigated living microbes throughout the sedimentary sequence using in situ ATP assays and DAPI cell count. These results, compiled with pore water analysis, SEM microscopy of authigenic concretions and methane and fatty acid biogeochemistry, provided evidence for a sustained microbial activity in deep sediments and pinpointed the substantial role of microbial processes in modifying initial organic and mineral fractions. Finally, because the genetic material associated with microorganisms can be preserved in sediments over millennia, we extracted environmental DNA from Laguna Potrok Aike sediments and established 16S rRNA bacterial and archaeal clone libraries to better define the use of DNA-based techniques in reconstructing past environments. We focused on two sedimentary horizons both displaying in situ microbial activity, respectively corresponding to the Holocene and Last Glacial Maximum periods. Sequences recovered from the productive Holocene record revealed a microbial community adapted to subsaline conditions producing methane with a high potential of organic matter degradation. In contrast, sediments rich in volcanic detritus from the Last Glacial Maximum showed a substantial presence of lithotrophic microorganisms and sulphate-reducing bacteria mediating authigenic minerals. Together, these features suggested that microbial communities developed in response to climatic control of lake and catchment productivity at the time of sediment deposition. Prevailing climatic conditions exerted a hierarchical control on the microbial composition of lake sediments by regulating the influx of organic and inorganic material to the lake basin, which in turn determined water column chemistry, production and sedimentation of particulate material, resulting in the different niches sheltering these microbial assemblages. Moreover, it demonstrated that environmental DNA can constitute sedimentary archives of phylogenetic diversity and diagenetic processes over tens of millennia.

Strategies Influencing Spatial Heterogeneity of Microbial Life in a Soil Lysimeter

NASA Astrophysics Data System (ADS)

Sengupta, A.; Neilson, J. W.; Meira, A.; Wang, Y.; Meza, M.; Chorover, J.; Maier, R. M.; Troch, P. A. A.

2016-12-01

Soil microorganisms are critical drivers of biogeochemical processes. These microbes, in conjunction with their physical and chemical environment, contribute to ecosystem functioning and services of the landscape, have a profound impact on soil formation, and are of particular importance in oligotrophic environments; ecosystems that are characterized by low biotic diversity due to extremely low nutrient levels. Here, we present a study of microbial heterogeneity in a soil lysimeter under incipient conditions. The key questions asked were: 1) what is the spatial heterogeneity of microbes over a new and evolving landscape with inherent oligotrophic conditions, and 2) can patterns in diversity translate to patterns in microbe-mediated weathering processes and soil formation? We hypothesized that stratification of environmental conditions, brought about by varying water potential, flow paths, and redox conditions, will drive the heterogeneity of microbial life in a sub-meter scale. A suite of traditional and current microbiological tools were employed to study community characteristics. These included isolation on R2A media, quantitative polymerase chain reactions targeted at 16S rRNA bacterial and archaeal genes, and 18S fungal genes, and iTAG phylogenetic gene amplification. Illumina Mi-Seq platform generated sequences were analyzed using various bioinformatics pipelines to identify community patterns, classify microbial metabolic functions, and identify variables affecting the community dynamics. Numerous phyla (Verrucomicrobia, Actinobacteria, Planctomycetes, Proteobacteria, and Euryarchaeota) were identified. The surface layer had distinctly different distribution of communities compared to the other layers. Metabolically heterogeneous groups were found with respect to depth, with metabolic functions further confirmed by predictive functional profiling of the microbial communities. Therefore, despite being highly oligotrophic, the system was rich in species and functional diversity. Alongside physical and chemical data, the patterns observed in spatial and functional heterogeneity of microbes under incipient conditions is unique, and allows us to predict strategies undertaken by these microbes to survive in, and influence their oligotrophic environments.

Initial association of fresh microbial products to soil particles: a joint density fractionation and NanoSIMS study

NASA Astrophysics Data System (ADS)

Hatton, Pierre-Joseph; Remusat, Laurent; Brewer, Elizabeth; Derrien, Delphine

2014-05-01

While soil microorganisms are increasingly seen as shaping stable soil organic matter (OM) formation, the mechanisms controlling the attachment of microbial metabolites to soil particles are not fully understood yet. We investigate the spatial distribution of freshly produced microbial products among density-isolated fractions of soil using stable C and N isotopes and Nano-scale secondary ion mass spectrometry (NanoSIMS). A surface forest soil was amended with uniformly 13C/15N labeled glycine and incubated for 8 hours in gamma-irradiated and non-sterile soils. Sequential density fractionation was then performed to isolate various classes of aggregates and of single mineral particles. Eight hours after the labeled glycine addition, 7 % of the 13C and 15N was tightly bound to soil assemblages. Comparison of sterile and non-sterile treatments revealed that microbial activity was almost completely responsible for this rapid association (>85 %). The distributions of glycine-derived 13C and 15N, considered as markers of new microbial products, were mapped on particles of the non-sterile treatment using NanoSIMS. New microbial products were heterogeneously distributed and spatially decoupled at the surface of on soil particles. 13C microbial products were scarce and presumably within or in the vicinity of microbial cells. In contrast, 15N microbial products seemed evenly spread at the surface of soil particles, likely as soluble exoenzymes diffusing away from their parent cell. Macroscopic measurements among density fractions suggested that the diffusion of such 15N microbial products was spatially limited yet, because of pore space architecture. NanoSIMS images further allowed gaining insight into the attachment of the new microbial products on particle surfaces already covered by OM, in a multilayer fashion. Using an internal calibration method to determine C/N ratios of NanoSIMS images, we showed the preferential attachment of soluble microbial N-metabolites to N-rich mineral-attached OM (C/N ratios mostly < 16). Exceptions were found in dense particles, supposed to contained aluminium and iron (hydr)oxides, with the microbial N-metabolites apparently preferentially attached to C-rich mineral-attached OM (C/N ratios > 80). This work provided visual evidences that the attachment of new microbial products to the soil matrix is mediated by distinct processes for N-rich and C-rich metabolites. It also demonstrated that the pore space architecture has impact on the formation of stable OM by limiting the diffusion of soluble microbial metabolites and their access to reactive and stabilising surfaces.

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community.

PubMed

Gómez-Consarnau, Laura; Sachdeva, Rohan; Gifford, Scott M; Cutter, Lynda S; Fuhrman, Jed A; Sañudo-Wilhelmy, Sergio A; Moran, Mary Ann

2018-04-16

Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B 12 synthesis, but not of vitamin-B 7 , whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B 1 synthesis transcripts. Furthermore, ambient vitamin-B 1 concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Changes in optical characteristics of surface microlayers in the Peruvian upwelling region hint to photochemically and microbially-mediated DOM turnover

NASA Astrophysics Data System (ADS)

Engel, A.; Galgani, L.

2016-02-01

The coastal upwelling system off Peru is characterized by high biological activity and associated subsurface oxygen minimum zone, leading to an enhanced emission of atmospheric trace gases. High biological productivity in the water column may promote the establishment of enriched organic surface films, key environments for processes regulating gas fluxes across the water-air interface. During M91 cruise to the Peruvian upwelling, we focused our attention on 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 in 38 stations determining DOC concentrations, amino acids composition, marine gels, CDOM and bacterial abundance as indicators of photochemical and microbial alteration processes. CDOM composition was characterized by spectral slopes (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. Profound changes in spectral slope properties were observed suggesting smaller MW CDOM in the SML compared to underlying water. Microbial and photochemical degradation are likely the main drivers for organic matter cycling in the top layer of the ocean. Consequences on the formation of inorganic and organic species highly relevant for air-sea gas exchange and for climate dynamics will be discussed.

An investigation of anaerobic methane oxidation by consortia of methanotrophic archaea and bacterial partners using nanoSIMS and process-based modeling

NASA Astrophysics Data System (ADS)

Shi, Y.; Kempes, C.; Chadwick, G.; McGlynn, S.; He, X.; Orphan, V. J.; Meile, C. D.

2016-02-01

The anaerobic oxidation of methane in marine sediments plays an important role in the global methane cycle. Mediated by a microbial consortium consisting of archaea and bacteria, it is estimated that almost 80% of all the methane that arises from marine sediments is oxidized anaerobically by this process (Reeburgh 2007, Chemical Reviews 107, 486-513). We used reactive transport modeling to compare and contrast potential mechanisms of methane oxidation. This included acetate, hydrogen, formate, and disulfide acting as intermediates that are exchanged between archaea and bacteria. Moreover, we investigated electron transport through nanowires, facilitating the electron exchange between the microbial partners. It was shown that reaction kinetics, transport intensities, and energetic considerations all could decisively impact the overall rate of methane consumption. Informed by observed microbial cell distribution, we applied the model to a range of spatial distribution patterns of archaea and bacteria. We found that a consortium with evenly distributed archaeal and bacterial cells has the potential to more efficiently oxidize methane, because the vicinity of bacteria and archaea counteracts the build up of products and therefore prevents the thermodynamic shutdown of microbial metabolism. Single cell stable isotope enrichment in archaeal-bacterial consortia observed by nanoSIMS revealed rather uniform levels of anabolic activity within consortia with different spatial distribution patterns. Comparison to model simulation illustrates that efficient exchange is necessary to reproduce such observations and prevent conditions that are energetically unfavorable for methane oxidation to take place. Model simulations indicate that a recently described mechanism of direct interspecies electron transport between the methanotrophic archaea and its bacterial partner through a conductive matrix (McGlynn et al. 2015, Nature, 10.1038/nature15512) is consistent with observations.

Evolution of Mudstone Porosity, Permeability, and Microstructure in the Presence of Microorganisms During Vertical Compression

NASA Astrophysics Data System (ADS)

Mills, T.; Reece, J. S.

2016-12-01

Here we investigate the influence of microbial activity on the mechanical and transport properties of mudstones during early diagenesis. Despite the proven presence of microbial communities in marine sediments to depths of >500 meters below sea floor (mbsf), little is known about the interactions between microorganisms and sediments, especially during the early stages of burial and compression. To characterize and quantify the impact of microbial activity on mudstone properties, we compare natural mudstone samples treated with iron reducing bacteria Shewanella Oneidensis MR-1 and those without bacteria. Two bulk mudstones are experimentally prepared using sediments from Integrated Ocean Drilling Program Sites U1319 and U1324 in the Gulf of Mexico. The sediments originated from 4-13 mbsf in the Brazos-Trinity Basin and from three depth intervals (3-14 mbsf, 23-32 mbsf, and 493-502 mbsf) in the Ursa Basin. The sediments are dried and ground to clay- and silt-sized particles and homogenized into two natural mudstone powders. These powders are then used to make reproducible mudstone samples through a process called resedimentation, which replicates natural deposition and burial. Changes in microstructure, porosity, compressibility, and permeability are measured while the biotic (with bacteria) and abiotic (without bacteria) mudstones are being uniaxially compressed over several weeks to a maximum stress of 100 kPa. We anticipate that biofilm growth in pore spaces will decrease porosity, compressibility, and permeability, and the resultant microstructural changes created by microorganisms will be evident in high-resolution scanning electron microscope (SEM) images. Recognition of the micro-scale processes that take place during the early stages of mudstone diagenesis, especially those mediated by microbial activity, and their long-term effects on mudstone properties can lead to better identification and more effective production of unconventional hydrocarbon reservoirs.

Carbonic anhydrase distribution across organisms and environments: genomic predictors for soil enzymatic fluxes of carbon cycle tracers δ18O and COS

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Singer, E.

2016-12-01

Carbonyl sulfide (COS) and the oxygen isotope composition (δ18O) of CO2 are potential tools for differentiating the contributions of photosynthesis and respiration to the balance of global carbon cycling. These processes are coupled at the leaf level via the enzyme carbonic anhydrase (CA), which hydrolyzes CO2 in the first biochemical step of the photosynthetic pathway (CO2 + H2O ⇌ HCO3- + H+) and correspondingly structural analogue COS (COS + H2O → CO2 + H2S). CA also accelerates the exchange of oxygen isotopes between CO2 and H2O leading to a distinct isotopic imprint. The biogeochemical cycles of these tracers include significant, yet poorly characterized soil processes that challenge their utility for probing the carbon cycle. In soils, microbial CA also hydrolyze COS and accelerate O isotope exchange between CO2 and soil water. Genomic predictors of microbial CA activity may help account and predict for these soil fluxes. Using a bioinformatics approach, we assess the distribution of the six known CA classes (α, β, γ, δ, η, ζ) in organisms ranging from fungi and plants to archaea and bacteria, and ask whether CA diversity is linked to soil microbial diversity. We survey the diversity and relative abundance of CA in a wide variety of environments and estimate the sensitivity of CA to biome and land use. Finally, we compare the CA distribution in soils to measurements (oxygen isotope and COS fluxes) and models of CA activity to develop genomic predictors for CA activity. This work provides the first survey of CA in soils, a step towards understanding the significant role of CA in microbial ecology and microbe-mediated biogeochemical cycles.

Interaction of abiotic and microbial processes in hexachloroethane reduction in groundwater

USGS Publications Warehouse

Roberts, A. Lynn; Gschwend, Philip M.

1994-01-01

In order to gain insight into mechanisms of hexachloroethane reduction, hexa- and pentachloroethane transformation rates were measured in anaerobic groundwater samples. For samples spiked with pentachloroethane, disappearance of pentachloroethane was accompanied by tetrachloroethylene production. Transformation rates were similar in unpoisoned and in HgCl2-poisoned samples, and rates were within ±20% of predictions based on measured pH and second-order dehydrochlorination rate constants determined in clean laboratory systems, indicating that the fate of pentachloroethane in this system is dominated by abiotic reactions. No hexachloroethane transformation was observed in HgCl2-poisoned samples, whereas in unpoisoned samples, hexachloroethane disappearance was accompanied by production of tetrachloroethylene as well as traces of pentachloroethane. Although only minor amounts of pentachloroethane accumulated, as much as 30% of the hexachloroethane transformation pathway proceeds via a pentachloroethane intermediate. This suggests that the microbial reduction of hexachloroethane proceeds at least in part through a free-radical mechanism. To the extent that hexachloroethane reduction to tetrachloroethylene occurs through a pentachloroethane intermediate, the first step in the sequence, the microbially-mediated step, is the slow step; the subsequent abiotic dehydrohalogenation step occurs much more rapidly.

The Intestinal Microbiome in Early Life: Health and Disease

PubMed Central

Arrieta, Marie-Claire; Stiemsma, Leah T.; Amenyogbe, Nelly; Brown, Eric M.; Finlay, Brett

2014-01-01

Human microbial colonization begins at birth and continues to develop and modulate in species abundance for about 3 years, until the microbiota becomes adult-like. During the same time period, children experience significant developmental changes that influence their health status as well as their immune system. An ever-expanding number of articles associate several diseases with early-life imbalances of the gut microbiota, also referred to as gut microbial dysbiosis. Whether early-life dysbiosis precedes and plays a role in disease pathogenesis, or simply originates from the disease process itself is a question that is beginning to be answered in a few diseases, including IBD, obesity, and asthma. This review describes the gut microbiome structure and function during the formative first years of life, as well as the environmental factors that determine its composition. It also aims to discuss the recent advances in understanding the role of the early-life gut microbiota in the development of immune-mediated, metabolic, and neurological diseases. A greater understanding of how the early-life gut microbiota impacts our immune development could potentially lead to novel microbial-derived therapies that target disease prevention at an early age. PMID:25250028

Development of interactive graphic user interfaces for modeling reaction-based biogeochemical processes in batch systems with BIOGEOCHEM

NASA Astrophysics Data System (ADS)

Chang, C.; Li, M.; Yeh, G.

2010-12-01

The BIOGEOCHEM numerical model (Yeh and Fang, 2002; Fang et al., 2003) was developed with FORTRAN for simulating reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions in batch systems. A complete suite of reactions including aqueous complexation, adsorption/desorption, ion-exchange, redox, precipitation/dissolution, acid-base reactions, and microbial mediated reactions were embodied in this unique modeling tool. Any reaction can be treated as fast/equilibrium or slow/kinetic reaction. An equilibrium reaction is modeled with an implicit finite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. A kinetic reaction is modeled with an explicit finite rate with an elementary rate, microbial mediated enzymatic kinetics, or a user-specified rate equation. None of the existing models has encompassed this wide array of scopes. To ease the input/output learning curve using the unique feature of BIOGEOCHEM, an interactive graphic user interface was developed with the Microsoft Visual Studio and .Net tools. Several user-friendly features, such as pop-up help windows, typo warning messages, and on-screen input hints, were implemented, which are robust. All input data can be real-time viewed and automated to conform with the input file format of BIOGEOCHEM. A post-processor for graphic visualizations of simulated results was also embedded for immediate demonstrations. By following data input windows step by step, errorless BIOGEOCHEM input files can be created even if users have little prior experiences in FORTRAN. With this user-friendly interface, the time effort to conduct simulations with BIOGEOCHEM can be greatly reduced.

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

PubMed Central

Weitz, Joshua S; Stock, Charles A; Wilhelm, Steven W; Bourouiba, Lydia; Coleman, Maureen L; Buchan, Alison; Follows, Michael J; Fuhrman, Jed A; Jover, Luis F; Lennon, Jay T; Middelboe, Mathias; Sonderegger, Derek L; Suttle, Curtis A; Taylor, Bradford P; Frede Thingstad, T; Wilson, William H; Eric Wommack, K

2015-01-01

Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles. PMID:25635642

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes.

PubMed

Weitz, Joshua S; Stock, Charles A; Wilhelm, Steven W; Bourouiba, Lydia; Coleman, Maureen L; Buchan, Alison; Follows, Michael J; Fuhrman, Jed A; Jover, Luis F; Lennon, Jay T; Middelboe, Mathias; Sonderegger, Derek L; Suttle, Curtis A; Taylor, Bradford P; Frede Thingstad, T; Wilson, William H; Eric Wommack, K

2015-06-01

Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.

The Use of Boron-doped Diamond Electrode on Yeast-based Microbial Fuel Cell for Electricity Production

NASA Astrophysics Data System (ADS)

Hanzhola, G.; Tribidasari, A. I.; Endang, S.

2018-01-01

The dependency of fossil energy in Indonesia caused the crude oil production to be drastically decreased since 2001, while energy consumption increased. In addition, The use of fossil energy can cause several environmental problems. Therefore, we need an alternative environment-friendly energy as solution for these problems. A microbial fuel cell is one of the prospective alternative source of an environment-friendly energy source to be developed. In this study, Boron-doped diamond electrode was used as working electrode and Candida fukuyamaensis as biocatalyst in microbial fuel cell. Different pH of anode compartment (pH 6.5-7.5) and mediator concentration (10-100 μM) was used to produce an optimal electricity. MFC was operated for 3 hours. During operation, the current and voltage density was measured with potensiostat. The maximum power and current density are 425,82 mW/m2 and 440 mA/m2, respectively, for MFC using pH 7.5 at anode compartment without addition of methylene blue. The addition of redox mediator is lowering the produced electricity because of its anti microbial properties that can kill the microbe.

Concurrent Phosphorus Recovery and Energy Generation in Mediator-Less Dual Chamber Microbial Fuel Cells: Mechanisms and Influencing Factors

PubMed Central

Almatouq, Abdullah; Babatunde, Akintunde O.

2016-01-01

This study investigated the mechanism and key factors influencing concurrent phosphorus (P) recovery and energy generation in microbial fuel cells (MFC) during wastewater treatment. Using a mediator-less dual chamber microbial fuel cell operated for 120 days; P was shown to precipitate as struvite when ammonium and magnesium chloride solutions were added to the cathode chamber. Monitoring data for chemical oxygen demand (COD), pH, oxidation reduction potential (ORP) and aeration flow rate showed that a maximum 38% P recovery was achieved; and this corresponds to 1.5 g/L, pH > 8, −550 ± 10 mV and 50 mL/min respectively, for COD, pHcathode, ORP and cathode aeration flow rate. More importantly, COD and aeration flow rate were shown to be the key influencing factors for the P recovery and energy generation. Results further show that the maximum P recovery corresponds to 72 mW/m2 power density. However, the energy generated at maximum P recovery was not the optimum; this shows that whilst P recovery and energy generation can be concurrently achieved in a microbial fuel cell, neither can be at the optimal value. PMID:27043584

Concurrent Phosphorus Recovery and Energy Generation in Mediator-Less Dual Chamber Microbial Fuel Cells: Mechanisms and Influencing Factors.

PubMed

Almatouq, Abdullah; Babatunde, Akintunde O

2016-03-29

This study investigated the mechanism and key factors influencing concurrent phosphorus (P) recovery and energy generation in microbial fuel cells (MFC) during wastewater treatment. Using a mediator-less dual chamber microbial fuel cell operated for 120 days; P was shown to precipitate as struvite when ammonium and magnesium chloride solutions were added to the cathode chamber. Monitoring data for chemical oxygen demand (COD), pH, oxidation reduction potential (ORP) and aeration flow rate showed that a maximum 38% P recovery was achieved; and this corresponds to 1.5 g/L, pH > 8, -550 ± 10 mV and 50 mL/min respectively, for COD, pH(cathode), ORP and cathode aeration flow rate. More importantly, COD and aeration flow rate were shown to be the key influencing factors for the P recovery and energy generation. Results further show that the maximum P recovery corresponds to 72 mW/m² power density. However, the energy generated at maximum P recovery was not the optimum; this shows that whilst P recovery and energy generation can be concurrently achieved in a microbial fuel cell, neither can be at the optimal value.

Stimulation of Microbially Mediated Arsenic Release in Bangladesh Aquifers by Young Carbon Indicated by Radiocarbon Analysis of Sedimentary Bacterial Lipids.

PubMed

Whaley-Martin, K J; Mailloux, B J; van Geen, A; Bostick, B C; Silvern, R F; Kim, C; Ahmed, K M; Choudhury, I; Slater, G F

2016-07-19

The sources of reduced carbon driving the microbially mediated release of arsenic to shallow groundwater in Bangladesh remain poorly understood. Using radiocarbon analysis of phospholipid fatty acids (PLFAs) and potential carbon pools, the abundance and carbon sources of the active, sediment-associated, in situ bacterial communities inhabiting shallow aquifers (<30 m) at two sites in Araihazar, Bangladesh, were investigated. At both sites, sedimentary organic carbon (SOC) Δ(14)C signatures of -631 ± 54‰ (n = 12) were significantly depleted relative to dissolved inorganic carbon (DIC) of +24 ± 30‰ and dissolved organic carbon (DOC) of -230 ± 100‰. Sediment-associated PLFA Δ(14)C signatures (n = 10) at Site F (-167‰ to +20‰) and Site B (-163‰ to +21‰) were highly consistent and indicated utilization of carbon sources younger than the SOC, likely from the DOC pool. Sediment-associated PLFA Δ(14)C signatures were consistent with previously determined Δ(14)C signatures of microbial DNA sampled from groundwater at Site F indicating that the carbon source for these two components of the subsurface microbial community is consistent and is temporally stable over the two years between studies. These results demonstrate that the utilization of relatively young carbon sources by the subsurface microbial community occurs at sites with varying hydrology. Further they indicate that these young carbon sources drive the metabolism of the more abundant sediment-associated microbial communities that are presumably more capable of Fe reduction and associated release of As. This implies that an introduction of younger carbon to as of yet unaffected sediments (such as those comprising the deeper Pleistocene aquifer) could stimulate microbial communities and result in arsenic release.

Abundance and activity of soil microorganisms in Cedrus atlantica forests are more related to land use than to altitude or latitude

NASA Astrophysics Data System (ADS)

Ramírez Rojas, Irene; Perez Fernandez, María; Moreno Gallardo, Laura; Lechuga Ordoñez, Victor; Linares, Juan Carlos

2016-04-01

Several environmental traits might change the abundance and the function of soil microorganisms in forest soils by plant-mediated reactions. Few studies have related the landscape-scale forest structural diversity with the micro-scale distribution of microorganism and their activities. High mountain environments harbor ecosystems that are very sensitive to global change and hence highly vulnerable, as those of Atlantic cedar. Altitudinal gradients in mountains are orrelated with changes in vegetation. We propose that altitudinal gradients drive shifts in microbial communities and are correlated with land uses. Thus, the latitudinal and longitudinal pattern of abundance and activity of soil micro-organisms was studied in an intercontinental comparison. We investigate soil extractable organic carbon (EOC) and nitrogen and carbon, microbial biomass and microbial metabolic activities at eight different sites along the latitudinal range of Cedrus atlantica, covering different altitudes and soils characteristics both in Southern Spain and Northern Morocco. Analyses of the abundances of total bacteria, (16S rRNA gene), was conducted using the Ilumina metagenomics technique. Results show that the stands at the highest altitudes had distinct microbial and biochemical characteristics compared with other areas. Overall, microbial activity, as measured by soil respiration, is higher in forests subjected to lower human pressure than in stands highly degraded, probably reflecting the quality of litter input that results of the influence of local assemblage of different tree, shrub and annual species, though changes in the soil N and C contents. Indeed, total soil C and N contents explained the microbial properties at every scale. Our results suggest that in contrast to the observed pronounced altitudinal changes, the kind of human-mediate land management has a stronger role in defining changes in microbial composition and activities in the investigated forest systems.

Arsenic Mobilization Through Microbial Bioreduction of Ferrihydrite Nanoparticles

NASA Astrophysics Data System (ADS)

Tadanier, C. J.; Roller, J.; Schreiber, M. E.

2004-12-01

Under anaerobic conditions Fe(III)-reducing microorganisms can couple the reduction of solid phase Fe(III) (hydr)oxides with the oxidation of organic carbon. Nutrients and trace metals, such as arsenic, associated with Fe(III) hydroxides may be mobilized through microbially-mediated surface reduction. Although arsenic mobilization has been attributed to mineral surface reduction in a variety of pristine and contaminated environments, minimal information exists on the mechanisms causing this arsenic mobilization. Understanding of the fundamental biochemical and physicochemical processes involved in these mobilization mechanisms is still limited, and has been complicated by the often contradictory and interchangeable terminology used in the literature to describe them. We studied arsenic mobilization mechanisms using a series of controlled microcosm experiments containing aggregated arsenic-bearing ferrihydrite nanoparticles and an Fe(III)-reducing microorganism, Geobacter metallireducens. The phase distribution of iron and arsenic was determined through filtration and ultracentrifugation techniques. Experimental results showed that in the biotic trials, approximately 10 percent of the Fe(III) was reduced to Fe(II) by microbial activity, which remained associated with ferrihydrite surfaces. Biotic activity resulted in changes in nanoparticle surface potential and caused deflocculation of nanoparticle aggregates. Deflocculated nanoparticles were able to pass through a 0.2 micron filter and could only be removed from solution by ultracentrifugation. Arsenic mobilized over time in the biotic trials was found to be exclusively associated with the nanoparticles; 98 percent of arsenic that passed through a 0.2 micron filter was removed from solution by ultracentrifugation. None of these changes were observed in abiotic controls. Because arsenic contamination of natural waters due to mobilization from mineral surfaces is a significant route of human arsenic exposure worldwide, improved understanding of the biologically-mediated mechanisms that partition arsenic between solid and solution phases is required for development of effective treatment and remediation strategies.

Large-Scale Experiments in Microbially Induced Calcite Precipitation (MICP): Reactive Transport Model Development and Prediction

NASA Astrophysics Data System (ADS)

Nassar, Mohamed K.; Gurung, Deviyani; Bastani, Mehrdad; Ginn, Timothy R.; Shafei, Babak; Gomez, Michael G.; Graddy, Charles M. R.; Nelson, Doug C.; DeJong, Jason T.

2018-01-01

Design of in situ microbially induced calcite precipitation (MICP) strategies relies on a predictive capability. To date much of the mathematical modeling of MICP has focused on small-scale experiments and/or one-dimensional flow in porous media, and successful parameterizations of models in these settings may not pertain to larger scales or to nonuniform, transient flows. Our objective in this article is to report on modeling to test our ability to predict behavior of MICP under controlled conditions in a meter-scale tank experiment with transient nonuniform transport in a natural soil, using independently determined parameters. Flow in the tank was controlled by three wells, via a complex cycle of injection/withdrawals followed by no-flow intervals. Different injection solution recipes were used in sequence for transport characterization, biostimulation, cementation, and groundwater rinse phases of the 17 day experiment. Reaction kinetics were calibrated using separate column experiments designed with a similar sequence of phases. This allowed for a parsimonious modeling approach with zero fitting parameters for the tank experiment. These experiments and data were simulated using PHT3-D, involving transient nonuniform flow, alternating low and high Damköhler reactive transport, and combined equilibrium and kinetically controlled biogeochemical reactions. The assumption that microbes mediating the reaction were exclusively sessile, and with constant activity, in conjunction with the foregoing treatment of the reaction network, provided for efficient and accurate modeling of the entire process leading to nonuniform calcite precipitation. This analysis suggests that under the biostimulation conditions applied here the assumption of steady state sessile biocatalyst suffices to describe the microbially mediated calcite precipitation.

High salinity facilitates dolomite precipitation mediated by Haloferax volcanii DS52

NASA Astrophysics Data System (ADS)

Qiu, Xuan; Wang, Hongmei; Yao, Yanchen; Duan, Yong

2017-08-01

Although most modern dolomites occur in hypersaline environments, the effects of elevated salinity on the microbial mediation of dolomite precipitation have not been fully evaluated. Here we report results of dolomite precipitation in association with a batch culture of Haloferax volcanii DS52, a halophilic archaeon, under various salinities (from 120‰ to 360‰) and the impact of salinity on microbe-mediated dolomite formation. The mineral phases, morphology and atomic arrangement of the precipitates were analyzed by XRD, SEM and TEM, respectively. The amount of amino acids on the archaeal cell surface was quantified by HPLC/MS. The XRD analysis indicated that disordered dolomite formed successfully with the facilitation of cells harvested from cultures with relatively high salinities (200‰ and 280‰) but was not observed in association with cells harvested from cultures with lower salinity (120‰) or the lysates of cells harvested from extremely high salinity (360‰). The TEM analysis demonstrated that the crystals from cultures with a salinity of 200‰ closely matched that of dolomite. Importantly, we found that more carboxyl groups were presented on the cell surface under high salinity conditions to resist the high osmotic pressure, which may result in the subsequent promotion of dolomite formation. Our finding suggests a link between variations in the hydro-chemical conditions and the formation of dolomite via microbial metabolic activity and enhances our understanding about the mechanism of microbially mediated dolomite formation under high salinity conditions.

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.

Rain Basin Design Implications for Soil Microbial Activity and N-mineralization in a Semi-arid Environment

NASA Astrophysics Data System (ADS)

Stern, C.; Pavao-Zuckerman, M.

2014-12-01

Rain basins have been an increasingly popular Green Infrastructure (GI) solution to the redistribution of water flow caused by urbanization. This study was conducted to examine how different approaches to basin design, specifically mulching (gravel vs. compost and gravel), influence the water availability of rain basins and the effects this has on the soil microbial activity of the basins. Soil microbes are a driving force of biogeochemical process and may impact the carbon and nitrogen dynamics of rain basin GI. In this study we sampled 12 different residential-scale rain basins, differing in design established at Biosphere 2, Arizona in 2013. Soil samples and measurements were collected before and after the onset of the monsoon season in 2014 to determine how the design of basins mediates the transition from dry to wet conditions. Soil abiotic factors were measured, such as moisture content, soil organic matter (SOM) content, texture and pH, and were related to the microbial biomass size within the basins. Field and lab potential N-mineralization and soil respiration were measured to determine how basin design influences microbial activity and N dynamics. We found that pre-monsoon basins with compost had higher moisture contents and that there was a positive correlation between the moisture content and the soil microbial biomass size of the basins. Pre-monsoon data also suggests that N-mineralization rates for basins with compost were higher than those with only gravel. These design influences on basin-scale biogeochemical dynamics and nitrogen retention may have important implications for urban biogeochemistry at neighborhood and watershed scales.

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

PubMed

Baldrian, Petr; Kolařík, Miroslav; Stursová, Martina; Kopecký, Jan; Valášková, Vendula; Větrovský, Tomáš; Zifčáková, Lucia; Snajdr, Jaroslav; Rídl, Jakub; Vlček, Cestmír; Voříšková, Jana

2012-02-01

Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.

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.

Phytoremediation using microbially mediated metal accumulation in Sorghum bicolor.

PubMed

Phieler, René; Merten, Dirk; Roth, Martin; Büchel, Georg; Kothe, Erika

2015-12-01

Reclaiming land that has been anthropogenically contaminated with multiple heavy metal elements, e.g., during mining operations, is a growing challenge worldwide. The use of phytoremediation has been discussed with varying success. Here, we show that a careful examination of options of microbial determination of plant performance is a key element in providing a multielement remediation option for such landscapes. We used both (a) mycorrhiza with Rhizophagus irregularis and (b) bacterial amendments with Streptomyces acidiscabies E13 and Streptomyces tendae F4 to mediate plant-promoting and metal-accumulating properties to Sorghum bicolor. In pot experiments, the effects on plant growth and metal uptake were scored, and in a field trial at a former uranium leaching heap site near Ronneburg, Germany, we could show the efficacy under field conditions. Different metals could be extracted at the same time, with varying microbial inoculation and soil amendment scenarios possible when a certain metal is the focus of interest. Especially, manganese was extracted at very high levels which might be useful even for phytomining approaches.

Protective and destructive immunity in the periodontium: Part 1--innate and humoral immunity and the periodontium.

PubMed

Teng, Y-T A

2006-03-01

Based on the results of recent research in the field, the present paper will discuss the protective and destructive aspects of the innate vs. adaptive (humoral and cell-mediated) immunity associated with the bacterial virulent factors or antigenic determinants during periodontal pathogenesis. Attention will be focused on: (i) the Toll-like receptors (TLR), the innate immune repertoire for recognizing the unique molecular patterns of microbial components that trigger innate and adaptive immunity for effective host defenses, in some general non-oral vs. periodontal microbial infections; (ii) T-cell-mediated immunity, Th-cytokines, and osteoclastogenesis in periodontal disease progression; and (iii) some molecular techniques developed and used to identify critical microbial virulence factors or antigens associated with host immunity (using Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis as the model species). Therefore, further understanding of the molecular interactions and mechanisms associated with the host's innate and adaptive immune responses will facilitate the development of new and innovative therapeutics for future periodontal treatments.

Microbial Biogeography on the Legacies of Historical Events in the Arctic Subsurface Sediments

NASA Astrophysics Data System (ADS)

Han, Dukki; Nam, Seung-Il; Hur, Hor-Gil

2017-04-01

The Arctic marine environment consists of various microbial habitats. The niche preference of microbial assemblages in the Arctic Ocean has been surveyed with the modern environmental change by oceanographic traits such as sea-ice dynamics, current circulation, and sedimentation. The North Pacific inflow from the shallow and narrow Bering Strait is highly susceptible to sea-level fluctuations, and thus the water mass exchange mediated by the history of sea-ice between the North Pacific and the Chukchi Sea in the Arctic Ocean. Over geological timescale, the climate change may provide putative evidences for ecological niche for the Arctic microbial assemblages as well as geological records in response to the paleoclimate change. In the present study, the multidisciplinary approach, based on microbiology, geology, and geochemistry, was applied to survey the microbial assemblages in the Arctic subsurface sediments and help further integrate the microbial biogeography and biogeochemical patterns in the Arctic subsurface biosphere. Our results describe microbial assemblages with high-resolution paleoceanographic records in the Chukchi Sea sediment core (ARA02B/01A-GC; 5.4 mbsf) to show the processes that drive microbial biogeographic patterns in the Arctic subsurface sediments. We found microbial habitat preferences closely linked to Holocene paleoclimate records as well as geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. Especially, the vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota in the ARA02B/01A-GC consistent with the patterns of the known global SMTZs and Holocene sedimentary records, suggesting that in-depth microbiological profiles integrated with geological records may be indirectly useful for reconstructing Arctic paleoclimate changes. In the earliest phase of Mid Holocene in the ARA02B/01A-GC with concentrated crenarchaeol (a unique biomarker for Marine Group I Thaumarchaea), the most abundant archaeal population was Marine Group II Euryarchaeota rather than Marine Group I Thaumarchaea, suggesting that the interpretation of archaeal tetraether lipids in subsurface sediments needs careful consideration for paleoceanography. In conclusion, our findings have important implications for the availability of microbial biogeography in the sedimentary record. The present study offers a deeper understanding of the legacies of historical events during the Holocene and implies that the survey of microbial biogeography may be an appropriate tool to monitor potential effects from the climate change in the Arctic Ocean.

Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System.

PubMed

Schiessl, Konstanze T; Janssen, Elisabeth M-L; Kraemer, Stephan M; McNeill, Kristopher; Ackermann, Martin

2017-01-01

A central question in microbial ecology is whether microbial interactions are predominantly cooperative or competitive. The secretion of siderophores, microbial iron chelators, is a model system for cooperative interactions. However, siderophores have also been shown to mediate competition by sequestering available iron and making it unavailable to competitors. The details of how siderophores mediate competition are not well understood, especially considering the complex distribution of iron phases in the environment. One pertinent question is whether sequestering iron through siderophores can indeed be effective in natural conditions; many natural environments are characterized by large pools of precipitated iron, and it is conceivable that any soluble iron that is sequestered by siderophores is replenished by the dissolution of these precipitated iron sources. Our goal here was to address this issue, and investigate the magnitude and mechanism of siderophore-mediated competition in the presence of precipitated iron. We combined experimental work with thermodynamic modeling, using Pseudomonas aeruginosa as a model system and ferrihydrite precipitates as the iron source with low solubility. Our experiments show that competitive growth inhibition by the siderophore pyochelin is indeed efficient, and that inhibition of a competitor can even have a stronger growth-promoting effect than solubilization of precipitated iron. Based on the results of our thermodynamic models we conclude that the observed inhibition of a competitor is effective because sequestered iron is only very slowly replenished by the dissolution of precipitated iron. Our research highlights the importance of competitive benefits mediated by siderophores, and underlines that the dynamics of siderophore production and uptake in environmental communities could be a signature of competitive, not just cooperative, dynamics.

Dietary and Lifestyle Factors Associated with Colorectal Cancer Risk and Interactions with Microbiota: Fiber, Red or Processed Meat and Alcoholic Drinks

PubMed Central

Tuan, Juan; Chen, Ying-Xuan

2016-01-01

Background Diets and lifestyles have been strongly associated with colorectal cancer (CRC). In the past several decades, emerging evidence has suggested that the gut microbiota may have a role in the development of CRC. Its interaction with diets and lifestyles could affect the carcinogenesis of CRC. Summary This review presents the most recent epidemiologic and experimental evidence of three factors that may convincingly have a role in CRC, including fiber, red or processed meat, and alcohol, focusing on potential mechanisms and their interactions with the gut microbiota. Key Message High consumption of fiber, low consumption of red or processed red meat as well as minimizing alcohol intake have been associated with a lower risk of CRC. Many microbial metabolites formed from those three substances may mediate the microbial diversity and the composition and abundance of the gut microbiota, which eventually affects the balance between health and disease, including CRC. Practical Implications Based on our synthetic review, clinicians may probably offer some recommendations and explanations to their patients who may want to modulate their diet and lifestyle to prevent CRC. As an easily modifiable environmental factor, it may be possible that applying dietary or lifestyle intervention could effectively protect against the development of CRC in the future. PMID:27722153

The Microbiome and Complement Activation: A Mechanistic Model for Preterm Birth

PubMed Central

Dunn, Alexis B.; Dunlop, Anne L.; Hogue, Carol J.; Miller, Andrew; Corwin, Elizabeth J.

2018-01-01

Preterm Birth (PTB, < 37 completed weeks' gestation) is one of the leading obstetrical problems in the United States affecting approximately 1 of every 9 births. Even more concerning are the persistent racial disparities in PTB with particularly high rates in African Americans. There are several recognized pathophysiologic pathways to PTB, including infection and/or exaggerated systemic or local inflammation. Intrauterine infection is a causal factor linked to PTB, thought to result most commonly from inflammatory processes triggered by microbial invasion of bacteria ascending from the vaginal microbiome. Trials to treat various infections have shown limited efficacy in reducing PTB risk, suggesting that other complex mechanisms, including those associated with inflammation, may be involved in the relationship between microbes, infection, and PTB. A key mediator of the inflammatory response, and recently shown to be associated with PTB, is the complement system, an innate defense mechanism involved in both normal physiologic processes that occur during pregnancy implantation, as well as processes that promote the elimination of pathogenic microbes. The purpose of this paper is to present a mechanistic model of inflammation-associated PTB, which hypothesizes a relationship between the microbiome and dysregulation of the complement system. Exploring the relationships between the microbial environment and complement biomarkers may elucidate a potentially modifiable biological pathway to preterm birth. PMID:28073296

Dietary and Lifestyle Factors Associated with Colorectal Cancer Risk and Interactions with Microbiota: Fiber, Red or Processed Meat and Alcoholic Drinks.

PubMed

Tuan, Juan; Chen, Ying-Xuan

2016-09-01

Diets and lifestyles have been strongly associated with colorectal cancer (CRC). In the past several decades, emerging evidence has suggested that the gut microbiota may have a role in the development of CRC. Its interaction with diets and lifestyles could affect the carcinogenesis of CRC. This review presents the most recent epidemiologic and experimental evidence of three factors that may convincingly have a role in CRC, including fiber, red or processed meat, and alcohol, focusing on potential mechanisms and their interactions with the gut microbiota. High consumption of fiber, low consumption of red or processed red meat as well as minimizing alcohol intake have been associated with a lower risk of CRC. Many microbial metabolites formed from those three substances may mediate the microbial diversity and the composition and abundance of the gut microbiota, which eventually affects the balance between health and disease, including CRC. Based on our synthetic review, clinicians may probably offer some recommendations and explanations to their patients who may want to modulate their diet and lifestyle to prevent CRC. As an easily modifiable environmental factor, it may be possible that applying dietary or lifestyle intervention could effectively protect against the development of CRC in the future.

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

PubMed Central

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

2013-01-01

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

Methanogenesis-induced pH–Eh shifts drives aqueous metal(loid) mobility in sulfide mineral systems under CO2 enriched conditions

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

Harvey, Omar R.; Qafoku, Nikolla; Cantrell, Kirk J.

2016-01-15

Accounting for microbially-mediated CO2 transformation is pivotal to assessing geochemical implications for elevated CO2 in subsurface environments. A series of batch-reactor experiments were conducted to decipher links between autotrophic methanogenesis, CO2 dynamics and aqueous Fe, As and Pb concentrations in the presence of sulfide minerals. Microbially-mediated solubility-trapping followed by pseudo-first order reduction of HCO3- to CH4 (k’ = 0.28-0.59 d-1) accounted for 95% of the CO2 loss from methanogenic experiments. Bicarbonate-to-methane reduction was pivotal in the mitigation of CO2-induced acidity (~1 pH unit) and enhancement of reducing conditions (Eh change from -0.215 to -0.332V ). Methanogenesis-associated shifts in pH-Eh valuesmore » showed no significant effect on aqueous Pb but favored, 1) increased aqueous As as a result of microbially-mediated dissolution of arsenopyrite and 2) decreased aqueous Fe due to mineral-trapping of CO2-mobilized Fe as Fe-carbonate. Its order of occurrence (and magnitude), relative to solubility- and mineral-trapping, highlighted the potential for autotrophic methanogenesis to modulate both carbon sequestration and contaminant mobility in CO2-impacted subsurface environments.« less

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

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-11-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

Solar radiation uncorks the lignin bottleneck on plant litter decomposition in terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Austin, A.; Ballare, C. L.; Méndez, M. S.

2015-12-01

Plant litter decomposition is an essential process in the first stages of carbon and nutrient turnover in terrestrial ecosystems, and together with soil microbial biomass, provide the principal inputs of carbon for the formation of soil organic matter. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in low rainfall ecosystems; however, the generality of this process as a control on carbon cycling in terrestrial ecosystems is not known, and the indirect effects of photodegradation on biotic stimulation of carbon turnover have been debated in recent studies. We demonstrate that in a wide range of plant species, previous exposure to solar radiation, and visible light in particular, enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility for microbial enzymes to plant litter carbohydrates due to a reduction in lignin content. Photodegradation of plant litter reduces the structural and chemical bottleneck imposed by lignin in secondary cell walls. In litter from woody plant species, specific interactions with ultraviolet radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized positive effect of solar radiation exposure on subsequent microbial activity is mediated by increased accessibility to cell wall polysaccharides, which suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release and the carbon balance in a broad range of terrestrial ecosystems.

Segregation and Alteration of Phenolic and Aliphatic Components of Root and Leaf Litter by Detritivores and Microbes

NASA Astrophysics Data System (ADS)

Filley, T. R.; Altmann, J.; Szlavecz, K. A.; Kalbitz, K.; Gamblin, D.; Nierop, K.

2012-12-01

The physical and microbial transformation of plant detritus in the litter layer and soil is accompanied by chemical separation of progressively soluble fractions and their movement into the rhizosphere driving subsequent soil processes. We investigated the combined action of specific detritivores, microbial decay, and leaching on the chemical separation of plant aromatic and aliphatic components from root, wood, and leaf tissue using 13C-TMAH thermochemolysis. This method enabled the simultaneous analysis of hydrolyzable tannin and lignin fragments, substituted fatty acids, and condensed tannin composition and revealed process-specific chemical transformations to plant secondary compounds. Long-term incubation and field sampling demonstrated how plant residues are progressively leached of the water soluble, oxidized fragments generated through decay. The residues appeared only slightly altered, in the case of brown rot wood, or enriched in aliphatic fragments, in the case of leaf and root tissue. Water extractable fractions were always selectively dominated by polyphenolics, either as demethylated lignin or tannins, and nearly devoid of aliphatic materials, despite high concentrations in the starting materials. Additionally, for plant materials with high tannin contents, such as pine needles, consumption and passage through some arthropod guts revealed what appeared to be microbially-mediated methylation of phenols, and a loss of tannins in leachates. These findings are indications for an in-situ phenol detoxification mechanism. This research provides important information regarding the links between biochemical decay and the chemical nature of organic matter removed and remaining in the soil profile.

Electrochemically Active Soluble Mediators from Shewanella oneidensis: Relevance to Microbial Fuel Cells and Extracellular Electron Transfer

DTIC Science & Technology

2008-05-01

A second approach is the use of soluble mediators such as, quinones, phenazines , and riboflavin, which are able to shuttle electrons from the cell...done using the equivalent graphite felt or graphite felt coated with platinum nanoparticles . Fuel cell chambers were separated using a gas-permeable

A novel photo-biological engineering method for Salvia miltiorrhiza-mediated fabrication of silver nanoparticles using LED lights sources and its effectiveness against Aedes aegypti mosquito larvae and microbial pathogens

USDA-ARS?s Scientific Manuscript database

In this study, Salvia miltiorrhiza-synthesized Ag nanoparticles (AgNPs) fabricated using sunlight or various LED lights were studied for their biophysical features and evaluated as larvicides against Aedes aegypti mosquitoes and growth inhibitors on different species of microbial pathogens. AgNPs pr...

Unlocking Ft: Modeling thermodynamic controls and isotope fractionation factors in nutrient limited environments

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Giannetta, M.; Sanford, R. A.

2017-12-01

In recent years, reactive transport principles have expanded from early applications, largely based in contaminant hydrology, to a wide range of biologically mediated redox environments including marine sedimentary diagenesis, terrestrial metal ore deposits, soils, and critical zone weathering profiles. A common observation across this diversity of systems is that they often function under energetically limited conditions in comparison to those typical of contaminated aquifers subject to engineered remediation techniques. As a result, the kinetic rate expressions traditionally employed within reactive transport frameworks to simulate microbially mediated redox transformations have required modification. This was recognized in a series of seminal papers by Jin and Bethke (2005, 2007) in which the authors expanded upon a Monod rate law to include a thermodynamic potential factor `Ft' which exerts a limitation on the overall rate based on the thermodynamic driving force of the electron transfer reaction. This new rate expression is now commonly implemented within many of the major reactive transport software packages, though appropriate application has yet to be thoroughly demonstrated. Notably, the characteristically large partitioning of stable isotopes during microbially mediated reactions, which is extensively utilized to identify and quantify these redox transformations, has yet to be simulated under conditions in which the Ft term may be expected to exert a significant mass dependent influence. Here, we develop a series of simplified simulations for the microbially mediated reduction of sulfate based on the datasets reported by Jin and Bethke, and apply appropriate mass-bias within the Ft term to consider the extent to which the resulting isotopic fractionation is consistent with that observed in energetically limited systems. We show that the Ft term can exert a significant influence on the observed fractionation factor under common environmental conditions, resulting in model behavior which is, in effect, a microbial redox analog to the variable observed fractionation factor resulting from a transition state theory rate law as derived by DePaolo (2011).

Antimicrobial Peptides and Wound Healing: Biological and Therapeutic Considerations

PubMed Central

Mangoni, Maria Luisa; McDermott, Alison M.; Zasloff, Michael

2016-01-01

Repair of tissue wounds is a fundamental process to re-establish tissue integrity and regular function. Importantly, infection is a major factor that hinders wound healing. Multicellular organisms have evolved an arsenal of host-defence molecules, including antimicrobial peptides (AMPs), aimed at controlling microbial proliferation and at modulating the host's immune response to a variety of biological or physical insults. In this brief review we provide the evidence for a role of AMPs as endogenous mediators of wound healing and their promising therapeutic potential for treatment of non-life threatening skin and other epithelial injuries. PMID:26738772

Seasonality in ocean microbial communities.

PubMed

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

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.

Impact of Gut Microbiota-Mediated Bile Acid Metabolism on the Solubilization Capacity of Bile Salt Micelles and Drug Solubility.

PubMed

Enright, Elaine F; Joyce, Susan A; Gahan, Cormac G M; Griffin, Brendan T

2017-04-03

In recent years, the gut microbiome has gained increasing appreciation as a determinant of the health status of the human host. Bile salts that are secreted into the intestine may be biotransformed by enzymes produced by the gut bacteria. To date, bile acid research at the host-microbe interface has primarily been directed toward effects on host metabolism. The aim of this work was to investigate the effect of changes in gut microbial bile acid metabolism on the solubilization capacity of bile salt micelles and consequently intraluminal drug solubility. First, the impact of bile acid metabolism, mediated in vivo by the microbial enzymes bile salt hydrolase (BSH) and 7α-dehydroxylase, on drug solubility was assessed by comparing the solubilization capacity of (a) conjugated vs deconjugated and (b) primary vs secondary bile salts. A series of poorly water-soluble drugs (PWSDs) were selected as model solutes on the basis of an increased tendency to associate with bile micelles. Subsequently, PWSD solubility and dissolution was evaluated in conventional biorelevant simulated intestinal fluid containing host-derived bile acids, as well as in media modified to contain microbial bile acid metabolites. The findings suggest that deconjugation of the bile acid steroidal core, as dictated by BSH activity, influences micellar solubilization capacity for some PWSDs; however, these differences appear to be relatively minor. In contrast, the extent of bile acid hydroxylation, regulated by microbial 7α-dehydroxylase, was found to significantly affect the solubilization capacity of bile salt micelles for all nine drugs studied (p < 0.05). Subsequent investigations in biorelevant media containing either the trihydroxy bile salt sodium taurocholate (TCA) or the dihydroxy bile salt sodium taurodeoxycholate (TDCA) revealed altered drug solubility and dissolution. Observed differences in biorelevant media appeared to be both drug- and amphiphile (bile salt/lecithin) concentration-dependent. Our studies herein indicate that bile acid modifications occurring at the host-microbe interface could lead to alterations in the capacity of intestinal bile salt micelles to solubilize drugs, providing impetus to consider the gut microbiota in the drug absorption process. In the clinical setting, disruption of the gut microbial ecosystem, through disease or antibiotic treatment, could transform the bile acid pool with potential implications for drug absorption and bioavailability.

Bioactive Molecules in Soil Ecosystems: Masters of the Underground

PubMed Central

Zhuang, Xuliang; Gao, Jie; Ma, Anzhou; Fu, Shenglei; Zhuang, Guoqiang

2013-01-01

Complex biological and ecological processes occur in the rhizosphere through ecosystem-level interactions between roots, microorganisms and soil fauna. Over the past decade, studies of the rhizosphere have revealed that when roots, microorganisms and soil fauna physically contact one another, bioactive molecular exchanges often mediate these interactions as intercellular signal, which prepare the partners for successful interactions. Despite the importance of bioactive molecules in sustainable agriculture, little is known of their numerous functions, and improving plant health and productivity by altering ecological processes remains difficult. In this review, we describe the major bioactive molecules present in below-ground ecosystems (i.e., flavonoids, exopolysaccharides, antibiotics and quorum-sensing signals), and we discuss how these molecules affect microbial communities, nutrient availability and plant defense responses. PMID:23615474

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long-term chronosequence.

PubMed

Freedman, Zachary; Zak, Donald R

2015-09-01

Soil microbial communities are abundant, hyper-diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper-diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long-term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance-based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long-term temporal scales. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

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.

Mechanisms of Soil Aggregation: a biophysical modeling framework

NASA Astrophysics Data System (ADS)

Ghezzehei, T. A.; Or, D.

2016-12-01

Soil aggregation is one of the main crosscutting concepts in all sub-disciplines and applications of soil science from agriculture to climate regulation. The concept generally refers to adhesion of primary soil particles into distinct units that remain stable when subjected to disruptive forces. It is one of the most sensitive soil qualities that readily respond to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. These changes are commonly quantified and incorporated in soil models indirectly as alterations in carbon content and type, bulk density, aeration, permeability, as well as water retention characteristics. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against erosion.

Disentangling Mechanisms That Mediate the Balance Between Stochastic and Deterministic Processes in Microbial Succession

DOE PAGES

Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan D.; ...

2015-03-17

Despite growing recognition that deterministic and stochastic factors simultaneously influence bacterial communities, little is known about mechanisms shifting their relative importance. To better understand underlying mechanisms, we developed a conceptual model linking ecosystem development during primary succession to shifts in the stochastic/deterministic balance. To evaluate the conceptual model we coupled spatiotemporal data on soil bacterial communities with environmental conditions spanning 105 years of salt marsh development. At the local scale there was a progression from stochasticity to determinism due to Na accumulation with increasing ecosystem age, supporting a main element of the conceptual model. At the regional-scale, soil organic mattermore » (SOM) governed the relative influence of stochasticity and the type of deterministic ecological selection, suggesting scale-dependency in how deterministic ecological selection is imposed. Analysis of a new ecological simulation model supported these conceptual inferences. Looking forward, we propose an extended conceptual model that integrates primary and secondary succession in microbial systems.« less

Microbial oxidation of lithospheric organic carbon in rapidly eroding tropical mountain soils.

PubMed

Hemingway, Jordon D; Hilton, Robert G; Hovius, Niels; Eglinton, Timothy I; Haghipour, Negar; Wacker, Lukas; Chen, Meng-Chiang; Galy, Valier V

2018-04-13

Lithospheric organic carbon ("petrogenic"; OC petro ) is oxidized during exhumation and subsequent erosion of mountain ranges. This process is a considerable source of carbon dioxide (CO 2 ) to the atmosphere over geologic time scales, but the mechanisms that govern oxidation rates in mountain landscapes are poorly constrained. We demonstrate that, on average, 67 ± 11% of the OC petro initially present in bedrock exhumed from the tropical, rapidly eroding Central Range of Taiwan is oxidized in soils, leading to CO 2 emissions of 6.1 to 18.6 metric tons of carbon per square kilometer per year. The molecular and isotopic evolution of bulk OC and lipid biomarkers during soil formation reveals that OC petro remineralization is microbially mediated. Rapid oxidation in mountain soils drives CO 2 emission fluxes that increase with erosion rate, thereby counteracting CO 2 drawdown by silicate weathering and biospheric OC burial. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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.

Bioavailability of phenanthrene in the presence of birnessite-mediated catechol polymers.

PubMed

Russo, Fabio; Rao, Maria A; Gianfreda, Liliana

2005-07-01

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental contaminants and contribute to the pollution of aquatic and terrestrial environments. In soil, their fate may be affected by interactions with the soil biological community and soil colloids. This study was conducted to investigate the fate of phenanthrene (Phe), selected as a representative PAH, in simplified model systems, which simulate processes naturally occurring in soil. Phe was interacted with catechol (Cat), an orthodiphenol, and common intermediate in the microbial degradation of PAHs, and birnessite (Bir), an abiotic strong oxidative catalyst abundant in soil. Two experimental conditions were investigated: Cat (5 mM)+Bir (1 mg ml(-1))+Phe (0.05 mg ml(-1)) mixed at the same time and incubated for 24 h at 25 degrees C (Cat-Bir-Phe) and Cat+Bir incubated for 24 h at 25 degrees C before Phe addition and then incubated for a further 24 h (Cat-Bir+Phe). After incubation, the systems were analysed for residual Cat and Phe, supplied with a selected Phe-degrading mixed bacterial culture, and then the microbial degradation of Phe and the growth of cells were monitored. Complex phenomena simultaneously occurred. Cat was completely removed after a 24-h incubation with Bir, and no interference by Phe in the Bir-mediated transformation of Cat was observed. Elemental analysis and UV-Vis and Fourier transfer infrared spectra showed that Cat transformation by Bir produced soluble and insoluble polymeric aggregates involving Phe. The hydrocarbon also interacted with the surfaces of Bir either previously coated (Cat-Bir+Phe sample) or not by Cat polymers. When a Phe-degrading bacterial culture was added to the systems after Bir-mediated Cat polymerisation, a different behaviour was observed in terms of Phe consumption and bacterial growth, thus suggesting differentiated availability of Phe to the microbial cells. The hydrocarbon was completely transformed in the presence of Bir and/or Bir covered by Cat polymers. By contrast a reduced degradation was measured when the Phe was involved in the polymerisation of Cat and entrapped in the Cat polymers (Cat-Bir-Phe). Although Cat showed a toxic, lethal effect on the bacterial cells, microbial growth was observed in the presence of Cat and Cat polymers, as the only C source. The mechanism leading to the different availability of Phe in the presence of Cat and Bir is still not clear. Further investigations are requested to provide more insight into such a complex phenomenon.

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities.

PubMed

Patin, Nastassia V; Schorn, Michelle; Aguinaldo, Kristen; Lincecum, Tommie; Moore, Bradley S; Jensen, Paul R

2017-02-15

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments. Copyright © 2017 American Society for Microbiology.

Zero-valent sulphur is a key intermediate in marine methane oxidation.

PubMed

Milucka, Jana; Ferdelman, Timothy G; Polerecky, Lubos; Franzke, Daniela; Wegener, Gunter; Schmid, Markus; Lieberwirth, Ingo; Wagner, Michael; Widdel, Friedrich; Kuypers, Marcel M M

2012-11-22

Emissions of methane, a potent greenhouse gas, from marine sediments are controlled by anaerobic oxidation of methane coupled primarily to sulphate reduction (AOM). Sulphate-coupled AOM is believed to be mediated by a consortium of methanotrophic archaea (ANME) and sulphate-reducing Deltaproteobacteria but the underlying mechanism has not yet been resolved. Here we show that zero-valent sulphur compounds (S(0)) are formed during AOM through a new pathway for dissimilatory sulphate reduction performed by the methanotrophic archaea. Hence, AOM might not be an obligate syntrophic process but may be carried out by the ANME alone. Furthermore, we show that the produced S(0)--in the form of disulphide--is disproportionated by the Deltaproteobacteria associated with the ANME. Our observations expand the diversity of known microbially mediated sulphur transformations and have significant implications for our understanding of the biogeochemical carbon and sulphur cycles.

The double life of antibiotics.

PubMed

Yap, Mee-Ngan F

2013-01-01

Antibiotic resistance is a persistent health care problem worldwide. Evidence for the negative consequences of subtherapeutic feeding in livestock production has been mounting while the antibiotic pipeline is drying up. In recent years, there has been a paradigm shift in our perception of antibiotics. Apart from its roles in self-defense, antibiotics also serve as inter-microbial signaling molecules, regulators of gene expression, microbial food sources, and as mediators of host immune response.

A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease

PubMed Central

Bacci, Giovanni; Fiscarelli, Ersilia; Taccetti, Giovanni; Dolce, Daniela; Paganin, Patrizia; Morelli, Patrizia; Tuccio, Vanessa; De Alessandri, Alessandra; Lucidi, Vincenzina

2017-01-01

In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease. PMID:28758937

Volatile Compounds Emitted by Pseudomonas aeruginosa Stimulate Growth of the Fungal Pathogen Aspergillus fumigatus.

PubMed

Briard, Benoit; Heddergott, Christoph; Latgé, Jean-Paul

2016-03-15

Chronic lung infections with opportunistic bacterial and fungal pathogens are a major cause of morbidity and mortality especially in patients with cystic fibrosis. Pseudomonas aeruginosa is the most frequently colonizing bacterium in these patients, and it is often found in association with the filamentous fungus Aspergillus fumigatus. P. aeruginosa is known to inhibit the growth of A. fumigatus in situations of direct contact, suggesting the existence of interspecies communication that may influence disease outcome. Our study shows that the lung pathogens P. aeruginosa and A. fumigatus can interact at a distance via volatile-mediated communication and expands our understanding of interspecific signaling in microbial communities. Microbiota studies have shown that pathogens cannot be studied individually anymore and that the establishment and progression of a specific disease are due not to a single microbial species but are the result of the activity of many species living together. To date, the interaction between members of the human microbiota has been analyzed in situations of direct contact or liquid-mediated contact between organisms. This study showed unexpectedly that human opportunistic pathogens can interact at a distance after sensing volatiles emitted by another microbial species. This finding will open a new research avenue for the understanding of microbial communities. Copyright © 2016 Briard et al.

Microbial reduction of iodate

USGS Publications Warehouse

Councell, T.B.; Landa, E.R.; Lovley, D.R.

1997-01-01

The different oxidation species of iodine have markedly different sorption properties. Hence, changes in iodine redox states can greatly affect the mobility of iodine in the environment. Although a major microbial role has been suggested in the past to account for these redox changes, little has been done to elucidate the responsible microorganisms or the mechanisms involved. In the work presented here, direct microbial reduction of iodate was demonstrated with anaerobic cell suspensions of the sulfate reducing bacterium Desulfovibrio desulfuricans which reduced 96% of an initial 100 ??M iodate to iodide at pH 7 in 30 mM NaHCO3 buffer, whereas anaerobic cell suspensions of the dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens were unable to reduce iodate in 30 mM NaHCO3 buffer (pH 7). Both D. desulfuricans and S. putrefaciens were able to reduce iodate at pH 7 in 10 mM HEPES buffer. Both soluble ferrous iron and sulfide, as well as iron monosulfide (FeS) were shown to abiologically reduce iodate to iodide. These results indicate that ferric iron and/or sulfate reducing bacteria are capable of mediating both direct, enzymatic, as well as abiotic reduction of iodate in natural anaerobic environments. These microbially mediated reactions may be important factors in the fate and transport of 129I in natural systems.

Microbes mediate carbon and nitrogen retention in shallow photic sediments

NASA Astrophysics Data System (ADS)

Hardison, A.; Anderson, I.; Canuel, E. A.; Tobias, C.; Veuger, B.

2009-12-01

Sediments in shallow coastal bays are sites of intense biogeochemical cycling facilitated by a complex microbial consortium. Unlike deeper coastal environments, much of the benthos is illuminated by sunlight in these bays. As a result, benthic autotrophs such as benthic microalgae (BMA) and macroalgae play an integral role in nutrient cycling. Investigating pathways of carbon (C) and nitrogen (N) flow through individual compartments within the sediment microbial community has previously proved challenging due to methodological difficulties. However, it is now possible using stable isotopes and microbial biomarkers such as fatty acids and amino acids to track C and N flow through individual microbial pools. We investigated the uptake and retention of C and N by bacteria and BMA in a shallow subtidal system. Using bulk and compound specific isotopic analysis, we traced the pathways of dissolved inorganic 13C and 15N under various treatments: 1) in ambient light or dark, 2) from porewater or water column sources, and 3) in the presence or absence of bloom forming nuisance macroalgae. Excess 13C and 15N in THAAs and excess 13C in total PLFAs showed a strong dependence on light. Enrichment of these pools represents uptake by the microbial community, which can include both autotrophic and heterotrophic components. Higher excess 13C in benthic microalgal fatty acids (C20, C22 PUFAs) provides evidence that benthic microalgae were fixing 13C. Aditionally, the ratio of excess 13C in branched fatty acids to microbial fatty acids (BAR) and excess 13C and 15N in D-Ala to L-Ala (D/L-Ala) were low, suggesting dominance by benthic microalgae over bacteria to total label incorporation. Our results support uptake and retention of C and N by the sediment microbial community and indicate a tight coupling between BMA and bacteria in shallow illuminated systems. This uptake is diminished in the presence of macroalgae, likely due to shading and/or nutrient competition. Therefore, macroalgae reduce the retention of C and N within surface sediments, diminishing the role of the microbial community in nutrient cycling processes.

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

PubMed Central

Heidelberg, John F.

2016-01-01

ABSTRACT The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. IMPORTANCE This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. PMID:27208118

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments.

PubMed

Tully, Benjamin J; Heidelberg, John F

2016-07-15

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. Copyright © 2016 Tully and Heidelberg.

Microbial Metabolic Response to Carbon Sources in a Uranium Contaminated Floodplain

NASA Astrophysics Data System (ADS)

Barragan, L.; Boye, K.; Bargar, J.; Fendorf, S. E.

2016-12-01

In Riverton, Wyoming, uranium (U) from a former ore processing plant, contaminated the groundwater and accumulated in Naturally Reduced Zones (NRZs). The NRZs have now become a secondary source of U and are releasing U into the ground water due to seasonal water table fluctuations. Microorganisms that mediate the mobilization and retention of U are likely to reside in these zones enriched with organic matter that comprises their energy source of carbon (C) for respiration. In this study, we are measuring microbial respiration (basal and substrate induced) by the MicroRespTM system, which is a quick screening method for respiratory activity in natural samples. This can provide information about the microbial community composition at certain depths and insight into their metabolic pathways which may explain U behavior in the ground water. In addition, we are determining elemental composition in the sediments by X-ray fluorescence spectroscopy (XRF) and elemental analysis (EA). Water soluble cations, anions and organic C is determined by inductively coupled plasma (ICP), mass spectrometry, ion chromatography (IC) and non-purgeable organic carbon (NPOC) analyses, respectively. If the behavior of the microbial community in the NRZ environment (enriched in both U and C) differs from that in unsaturated sediments, this can provide crucial clues to understand what causes U to be retained or released from the NRZs. This information will be used to develop and improve models aimed at predicting U mobility in the floodplain groundwater systems.

Microbial respiration and dissolution precipitation reactions of minerals: thermo-kinetics and reactive transport modelling

NASA Astrophysics Data System (ADS)

Azaroual, M. M.; Parmentier, M.; Andre, L.; Croiset, N.; Pettenati, M.; Kremer, S.

2010-12-01

Microbial processes interact closely with abiotic geochemical reactions and mineralogical transformations in several hydrogeochemical systems. Reactive transport models are aimed to analyze these complex mechanisms integrating as well as the degradation of organic matter as the redox reactions involving successive terminal electron acceptors (TEAPs) mediated by microbes through the continuum of unsaturated zone (soil) - saturated zone (aquifer). The involvement of microbial processes in reactive transport in soil and subsurface geologic greatly complicates the mastery of the major mechanisms and the numerical modelling of these systems. The introduction of kinetic constraints of redox reactions in aqueous phase requires the decoupling of equilibrium reactions and the redefinition of mass balance of chemical elements including the concept of basis species and secondary species of thermodynamic databases used in geochemical modelling tools. An integrated methodology for modelling the reactive transport has been developed and implemented to simulate the transfer of arsenic, denitrification processes and the role of metastable aqueous sulfur species with pyrite and organic matter as electron donors entities. A mechanistic rate law of microbial respiration in various geochemical environments was used to simulate reactive transport of arsenic, nitrate and organic matter combined to the generalized rate law of mineral dissolution - precipitation reactions derived from the transition state theory was used for dissolution - precipitation of silica, aluminosilicate, carbonate, oxyhydroxide, and sulphide minerals. The kinetic parameters are compiled from the literature measurements based on laboratory constrained experiments and field observations. Numerical simulations, using the geochemical software PHREEQC, were performed aiming to identify the key reactions mediated by microbes in the framework of in the first hand the concept of the unsaturated - saturated zones of an artificial recharge of deep aquifers system and in a second hand an acid mine drainage system. A large amount of data is available on the old mine site of Cheni (France). This field data on acid mine drainage are compared to a thermokinetic model including biological kinetics, precipitation-dissolution kinetics and surface complexation on ferrihydrite. The kinetic parameters are from literature and from a fitting on batch biological experiments. The integrated approach combining reaction kinetics and biogeochemical thermodynamic constraints is successfully applied to denitrification experiments in the presence of acetate and pyrite conducted in the laboratory for batch and column systems. The powerful of this coupled approach allows a fine description of the different transition species from nitrate to nitrogen. The fitted kinetic parameters established for modelling these laboratory results are thus extended to simulate the denitrification processes in a field case where organic matter and pyrite FeS2 are the electron donors and O2, NO3, Fe(OH)3, SO4 are the electron acceptors in the framework of a continuum UZ - SZ aiming to identify the stabilized redox zones of acid mine drainage. The detailed results obtained on two actual case studies will be presented.

Leaching of vanadium from waste V2O5-WO3/TiO2 catalyst catalyzed by functional microorganisms.

PubMed

Wang, Shuhua; Xie, Yaling; Yan, Weifu; Wu, Xuee; Wang, Chin-Tsan; Zhao, Feng

2018-05-22

Solid wastes are currently produced in large amounts. Although bioleaching of metals from solid wastes is an economical and sustainable technology, it has seldom been used to recycle metals from abandoned catalyst. In this study, the bioleaching of vanadium from V 2 O 5 -WO 3 /TiO 2 catalyst were comprehensively investigated through five methods: Oligotrophic way, Eutrophic way, S-mediated way, Fe-mediated way and Mixed way of S-mediated and Fe-mediated. The observed vanadium bioleaching effectiveness of the assayed methods was follows: S-mediated > Mixed > Oligotrophic > Eutrophic > Fe-mediated, which yielded the maximum bioleaching efficiencies of approximately 90%, 35%, 33%, 20% and 7%, respectively. The microbial community analysis suggested that the predominant genera Acidithiobacillus and Sulfobacillus from the S-mediated bioleaching way effectively catalyzed the vanadium leaching, which could have occurred through the indirect mechanism from the microbial oxidation of S 0 . In addition, the direct mechanism, involving direct electron transfer between the catalyst and the microorganisms that attached to the catalyst surface, should also help the vanadium to be leached more effectively. Therefore, this work provides guidance for future research and practical application on the treatment of waste V 2 O 5 -WO 3 /TiO 2 catalyst. Copyright © 2018 Elsevier B.V. All rights reserved.

Rate dependent fractionation of sulfur isotopes in through-flowing systems

NASA Astrophysics Data System (ADS)

Giannetta, M.; Sanford, R. A.; Druhan, J. L.

2017-12-01

The fidelity of reactive transport models in quantifying microbial activity in the subsurface is often improved through the use stable isotopes. However, the accuracy of current predictions for microbially mediated isotope fractionations within open through-flowing systems typically depends on nutrient availability. This disparity arises from the common application of a single `effective' fractionation factor assigned to a given system, despite extensive evidence for variability in the fractionation factor between eutrophic environments and many naturally occurring, nutrient-limited environments. Here, we demonstrate a reactive transport model with the capacity to simulate a variable fractionation factor over a range of microbially mediated reduction rates and constrain the model with experimental data for nutrient limited conditions. Two coupled isotope-specific Monod rate laws for 32S and 34S, constructed to quantify microbial sulfate reduction and predict associated S isotope partitioning, were parameterized using a series of batch reactor experiments designed to minimize microbial growth. In the current study, we implement these parameterized isotope-specific rate laws within an open, through-flowing system to predict variable fractionation with distance as a function of sulfate reduction rate. These predictions are tested through a supporting laboratory experiment consisting of a flow-through column packed with homogenous porous media inoculated with the same species of sulfate reducing bacteria used in the previous batch reactors, Desulfovibrio vulgaris. The collective results of batch reactor and flow-through column experiments support a significant improvement for S isotope predictions in isotope-sensitive multi-component reactive transport models through treatment of rate-dependent fractionation. Such an update to the model will better equip reactive transport software for isotope informed characterization of microbial activity within energy and nutrient limited environments.

Application of a weak magnetic field to improve microbial fuel cell performance.

PubMed

Tong, Zhong-Hua; Yu, Han-Qing; Li, Wen-Wei; Wang, Yun-Kun; Sun, Min; Liu, Xian-Wei; Sheng, Guo-Ping

2015-12-01

Microbial fuel cells (MFCs) have emerged as a promising technology for wastewater treatment with concomitant energy production but the performance is usually limited by low microbial activities. This has spurred intensive research interest for microbial enhancement. This study demonstrated an interesting stimulation effect of a static magnetic field (MF) on sludge-inoculated MFCs and explored into the mechanisms. The implementation of a 100-mT MF accelerated the reactor startup and led to increased electricity generation. Under the MF exposure, the activation loss of the MFC was decreased, but there was no increased secretion of redox mediators. Thus, the MF effect was mainly due to enhanced bioelectrochemical activities of anodic microorganisms, which are likely attributed to the oxidative stress and magnetohydrodynamic effects under an MF exposure. This work implies that weak MF may be applied as a simple and effective approach to stimulate microbial activities for various bioelectrochemical energy production and decontamination applications.

Contribution of eukaryotic microbial communities to the formation of Fe-rich accretions in an extreme acidic environment

NASA Astrophysics Data System (ADS)

Rodrigues, L.; Valente, T.; Correia, A.; Alves, A.; Foing, B.; Davies, G. R.

2012-04-01

In the acid mine drainage of Valdarcas, northern Portugal, Fe-rich tubular and spherical macroaccretions are directly associated with the presence of eukaryotic microorganisms. This raises the question whether they are biogenically-derived or the result of an abiotic process mediated by microeukaryotic phototrophs. The drainage water at Valdarcas is characterized by very low pH values (pH<3.5), high metal solubility and presence of iron colloids. Mineralogical analysis (XRD and SEM) of the precipitates indicates a mixture of goethite, schwertmannite and jarosite. Euglenophyta and Chlorophyta acidophilic algal were previously identified in this site. The spatial distribution of Euglena mutabilis indicated that it has a preference to grow up on schwertmannite-rich precipitates. Field observations demonstrate the existence of oxygenated microenvironments created by algal activity suggesting that algae influence iron minerals precipitation, especially schwertmannite. The mineral-microorganism interactions are relevant to understanding this unique and extreme environment. Further investigations regarding the mineralogical and chemical characterization of these deposits, and the identification of microorganisms involved in the process could be helpful to enhance our knowledge of past Fe formations throughout Earth's primordial environment. It is expectable that this information will contribute to establish a framework for recognition of biosignatures on other planets and extraterrestrial bodies. In this study, results on the chemical and mineralogical composition of the structures are presented. The biological context is characterised based on observations made by optical microscopy complemented with molecular data on the microbial communities obtained by culture independent methods. The results are discussed within the context of two models: the studied Fe-rich stromatolites are microeukaryotic-mediated as described by previous workers from similar environments or are the consequence of inorganic precipitation of reduced iron species (Fe(III)) due to the oxygen generated by the photosynthesis?

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

Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling

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

Deng, Jia; McCalley, Carmody K.; Frolking, Steve

Climate change is expected to have significant and uncertain impacts on methane (CH 4) emissions from northern peatlands. Biogeochemical models can extrapolate site-specific CH 4 measurements to larger scales and predict responses of CH 4 emissions to environmental changes. However, these models include considerable uncertainties and limitations in representing CH4 production, consumption, and transport processes. To improve predictions of CH 4 transformations, we incorporated acetate and stable carbon (C) isotopic dynamics associated with CH 4 cycling into a biogeochemistry model, DNDC. By including these new features, DNDC explicitly simulates acetate dynamics and the relative contribution of acetotrophic and hydrogenotrophic methanogenesismore » (AM and HM) to CH 4 production, and predicts the C isotopic signature (δ 13C) in soil C pools and emitted gases. When tested against biogeochemical and microbial community observations at two sites in a zone of thawing permafrost in a subarctic peatland in Sweden, the new formulation substantially improved agreement with CH 4 production pathways and δ 13C in emitted CH 4 (δ 13C-CH 4), a measure of the integrated effects of microbial production and consumption, and of physical transport. We also investigated the sensitivity of simulated δ 13C-CH 4 to C isotopic composition of substrates and, to fractionation factors for CH4 production (α AM and α HM), CH 4 oxidation (α MO), and plant-mediated CH 4 transport (α TP). The sensitivity analysis indicated that the δ13C-CH 4 is highly sensitive to the factors associated with microbial metabolism (α AM, α HM, and α MO). The model framework simulating stable C isotopic dynamics provides a robust basis for better constraining and testing microbial mechanisms in predicting CH 4 cycling in peatlands.« less

Remote Sensing between Liver and Intestine: Importance of Microbial Metabolites

PubMed Central

Fu, Zidong Donna; Cui, Julia Yue

2017-01-01

Recent technological advancements including metagenomics sequencing and metabolomics have allowed the discovery of critical functions of gut microbiota in obesity, malnutrition, neurological disorders, asthma, and xenobiotic metabolism. Classification of the human gut microbiome into distinct “enterotypes” has been proposed to serve as a new paradigm for understanding the interplay between microbial variation and human disease phenotypes, as many organs are affected by gut microbiota modifications during the pathogenesis of diseases. Gut microbiota remotely interacts with liver and other metabolic organs of the host through various microbial metabolites that are absorbed into the systemic circulation. Purpose of review The present review summarizes recent literature regarding the importance of gut microbiota in modulating the physiological and pathological responses of various host organs, and describes the functions of the known microbial metabolites that are involved in this remote sensing process, with a primary focus on the gut microbiota-liver axis. Recent findings Under physiological conditions, gut microbiota modulates the hepatic transcriptome, proteome, and metabolome, most notably down-regulating cytochrome P450 3a mediated xenobiotic metabolism. Gut microbiome also modulates the rhythmicity in liver gene expression, likely through microbial metabolites, such as butyrate and propionate that serve as epigenetic modifiers. Additionally, the production of host hormones such as primary bile acids and glucagon like peptide 1 is altered by gut microbiota to modify intermediary metabolism of the host. Summary Dysregulation of gut microbiota is implicated in various liver diseases such as alcoholic liver disease, non-alcoholic steatohepatitis, liver cirrhosis, cholangitis, and liver cancer. Gut microbiota modifiers such as probiotics and prebiotics are increasingly recognized as novel therapeutic modalities for liver and other types of human diseases. PMID:28983453

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

PubMed Central

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

2013-01-01

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

Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling

DOE PAGES

Deng, Jia; McCalley, Carmody K.; Frolking, Steve; ...

2017-06-13

Climate change is expected to have significant and uncertain impacts on methane (CH 4) emissions from northern peatlands. Biogeochemical models can extrapolate site-specific CH 4 measurements to larger scales and predict responses of CH 4 emissions to environmental changes. However, these models include considerable uncertainties and limitations in representing CH4 production, consumption, and transport processes. To improve predictions of CH 4 transformations, we incorporated acetate and stable carbon (C) isotopic dynamics associated with CH 4 cycling into a biogeochemistry model, DNDC. By including these new features, DNDC explicitly simulates acetate dynamics and the relative contribution of acetotrophic and hydrogenotrophic methanogenesismore » (AM and HM) to CH 4 production, and predicts the C isotopic signature (δ 13C) in soil C pools and emitted gases. When tested against biogeochemical and microbial community observations at two sites in a zone of thawing permafrost in a subarctic peatland in Sweden, the new formulation substantially improved agreement with CH 4 production pathways and δ 13C in emitted CH 4 (δ 13C-CH 4), a measure of the integrated effects of microbial production and consumption, and of physical transport. We also investigated the sensitivity of simulated δ 13C-CH 4 to C isotopic composition of substrates and, to fractionation factors for CH4 production (α AM and α HM), CH 4 oxidation (α MO), and plant-mediated CH 4 transport (α TP). The sensitivity analysis indicated that the δ13C-CH 4 is highly sensitive to the factors associated with microbial metabolism (α AM, α HM, and α MO). The model framework simulating stable C isotopic dynamics provides a robust basis for better constraining and testing microbial mechanisms in predicting CH 4 cycling in peatlands.« less

Removal Mechanisms of Para-nitrophenol in Reclaimed Water using SAT and its Bio-enhancement

NASA Astrophysics Data System (ADS)

Wen, Y. L.; Yang, Y.; Zhang, H.; Lou, B.

2017-12-01

Nowadays, we were facing with water resource shortage along with water pollution. It was important to undertake the cost effective technology to treat polluted water whilst encourage water reuse. Soil aquifer treatment (SAT) was an efficient technology, using the infiltration process of mediation, adsorption and biodegradation on the pollutants in the environment to achieve the goal of recycling water. For a better understanding of the transport and attenuation of para-nitrophenol (P-NP) and the change of microbial community at the stress of p-nitrophenol in soil aquifer treatment system, two column experiments were operated to investigate the physical, chemical, and microbial dynamics. At the same time, the bio-augment method was used to enhance the SAT biodegradation system. The SAT column experiment was operated about 38 days, which demonstrated that two reduction zones were revealed at the middle of the column and the biodiversity of the microbial community could be destroyed under the P-NP stress. Absorption was the main removal mechanism according to the obtained experimental data. By using the displacement method, the BIO-SAT system was operated about 36 days, which showed perfect outcome for the P-NP removal at a higher concentration. From the PCR-DGGE and high throughput sequencing study, enhanced bacteria could form a stable biological community with indigenous communities. Through the Canonical Correspondence Analysis (CCA) microbial degradation and environmental factors, the results showed that the pH was a very important parameter affects the degradation of nitrophenol degradation bacteria. The metal ions under the condition of low concentration can promote the growth of microbial degradation. This study provide valuable result on the attenuation potential of for the bio-enhanced SAT system (BIO-SAT). (No Image Selected)

Arsenic release from shallow aquifers of the Hetao basin, Inner Mongolia: evidence from bacterial community in aquifer sediments and groundwater.

PubMed

Li, Yuan; Guo, Huaming; Hao, Chunbo

2014-12-01

Indigenous microbes play crucial roles in arsenic mobilization in high arsenic groundwater systems. Databases concerning the presence and the activity of microbial communities are very useful in evaluating the potential of microbe-mediated arsenic mobilization in shallow aquifers hosting high arsenic groundwater. This study characterized microbial communities in groundwaters at different depths with different arsenic concentrations by DGGE and one sediment by 16S rRNA gene clone library, and evaluated arsenic mobilization in microcosm batches with the presence of indigenous bacteria. DGGE fingerprints revealed that the community structure changed substantially with depth at the same location. It indicated that a relatively higher bacterial diversity was present in the groundwater sample with lower arsenic concentration. Sequence analysis of 16S rRNA gene demonstrated that the sediment bacteria mainly belonged to Pseudomonas, Dietzia and Rhodococcus, which have been widely found in aquifer systems. Additionally, NO3(-)-reducing bacteria Pseudomonas sp. was the largest group, followed by Fe(III)-reducing, SO4(2-)-reducing and As(V)-reducing bacteria in the sediment sample. These anaerobic bacteria used the specific oxyanions as electron acceptor and played a significant role in reductive dissolution of Fe oxide minerals, reduction of As(V), and release of arsenic from sediments into groundwater. Microcosm experiments, using intact aquifer sediments, showed that arsenic release and Fe(III) reduction were microbially mediated in the presence of indigenous bacteria. High arsenic concentration was also observed in the batch without amendment of organic carbon, demonstrating that the natural organic matter in sediments was the potential electron donor for microbially mediated arsenic release from these aquifer sediments.

The role microbial sulfate reduction in the direct mediation of sedimentary authigenic carbonate precipitation

NASA Astrophysics Data System (ADS)

Turchyn, A. V.; Walker, K.; Sun, X.

2016-12-01

The majority of modern deep marine sediments are bathed in water that is undersaturated with respect to calcium carbonate. However, within marine sediments changing chemical conditions, driven largely by the microbial oxidation of organic carbon in the absence of oxygen, lead to supersaturated conditions and drive calcium carbonate precipitation. This sedimentary calcium carbonate is often called `authigenic carbonate', and is found in the form of cements and disseminated crystals within the marine sedimentary pile. As this precipitation of this calcium carbonate is microbially mediated, identifying authigenic carbonate within the geological record and understanding what information its geochemical and/or isotopic signature may hold is key for understanding its importance and what information it may contain past life. However, the modern controls on authigenic carbonate precipitation remain enigmatic because the myriad of microbially mediated reactions occurring within sediments both directly and indirectly impact the proton balance. In this submission we present data from 25 ocean sediment cores spanning the globe where we explore the deviation from the stoichiometrically predicted relationships among alkalinity, calcium and sulfate concentrations. In theory for every mol of organic carbon reduced by sulfate, two mol of alkalinity is produced, and to precipitate subsurface calcium carbonate one mol of calcium is used to consume two mol of alkalinity. We use this data with a model to explore changes in carbonate saturation state with depth below the seafloor. Alkalinity changes in the subsurface are poorly correlated with changes in calcium concentrations, however calcium concentrations are directly and tightly coupled to changes in sulfate concentrations in all studied sites. This suggests a direct role for sulfate reducing bacteria in the precipitation of subsurface carbonate cements.

Single-cell force spectroscopy of pili-mediated adhesion

NASA Astrophysics Data System (ADS)

Sullan, Ruby May A.; Beaussart, Audrey; Tripathi, Prachi; Derclaye, Sylvie; El-Kirat-Chatel, Sofiane; Li, James K.; Schneider, Yves-Jacques; Vanderleyden, Jos; Lebeer, Sarah; Dufrêne, Yves F.

2013-12-01

Although bacterial pili are known to mediate cell adhesion to a variety of substrates, the molecular interactions behind this process are poorly understood. We report the direct measurement of the forces guiding pili-mediated adhesion, focusing on the medically important probiotic bacterium Lactobacillus rhamnosus GG (LGG). Using non-invasive single-cell force spectroscopy (SCFS), we quantify the adhesion forces between individual bacteria and biotic (mucin, intestinal cells) or abiotic (hydrophobic monolayers) surfaces. On hydrophobic surfaces, bacterial pili strengthen adhesion through remarkable nanospring properties, which - presumably - enable the bacteria to resist high shear forces under physiological conditions. On mucin, nanosprings are more frequent and adhesion forces larger, reflecting the influence of specific pili-mucin bonds. Interestingly, these mechanical responses are no longer observed on human intestinal Caco-2 cells. Rather, force curves exhibit constant force plateaus with extended ruptures reflecting the extraction of membrane nanotethers. These single-cell analyses provide novel insights into the molecular mechanisms by which piliated bacteria colonize surfaces (nanosprings, nanotethers), and offer exciting avenues in nanomedicine for understanding and controlling the adhesion of microbial cells (probiotics, pathogens).

Neurotoxicity of fungal volatile organic compounds in Drosophila melanogaster.

PubMed

Inamdar, Arati A; Masurekar, Prakash; Bennett, Joan Wennstrom

2010-10-01

Many volatile organic compounds (VOCs) are found in indoor environment as products of microbial metabolism. In damp indoor environments, fungi are associated with poor air quality. Some epidemiological studies have suggested that microbial VOCs have a negative impact on human health. Our study was designed to provide a reductionist approach toward studying fungal VOC-mediated toxicity using the inexpensive model organism, Drosophila melanogaster, and pure chemical standards of several important fungal VOCs. Low concentrations of the following known fungal VOCs, 0.1% of 1-octen-3-ol and 0.5% of 2-octanone; 2,5 dimethylfuran; 3-octanol; and trans-2-octenal, caused locomotory defects and changes in green fluorescent protein (GFP)- and antigen-labeled dopaminergic neurons in adult D. melanogaster. Locomotory defects could be partially rescued with L-DOPA. Ingestion of the antioxidant, vitamin E, improved the survival span and delayed the VOC-mediated changes in dopaminergic neurons, indicating that the VOC-mediated toxicity was due, in part, to generation of reactive oxygen species.

Phosphate-Mediated Remediation of Metals and Radionuclides

DOE PAGES

Martinez, Robert J.; Beazley, Melanie J.; Sobecky, Patricia A.

2014-01-01

Worldwide industrialization activities create vast amounts of organic and inorganic waste streams that frequently result in significant soil and groundwater contamination. Metals and radionuclides are of particular concern due to their mobility and long-term persistence in aquatic and terrestrial environments. As the global population increases, the demand for safe, contaminant-free soil and groundwater will increase as will the need for effective and inexpensive remediation strategies. Remediation strategies that include physical and chemical methods (i.e., abiotic) or biological activities have been shown to impede the migration of radionuclide and metal contaminants within soil and groundwater. However, abiotic remediation methods are oftenmore » too costly owing to the quantities and volumes of soils and/or groundwater requiring treatment. The in situ sequestration of metals and radionuclides mediated by biological activities associated with microbial phosphorus metabolism is a promising and less costly addition to our existing remediation methods. This review highlights the current strategies for abiotic and microbial phosphate-mediated techniques for uranium and metal remediation.« 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.

Fate of Eight Different Polymers under Uncontrolled Composting Conditions: Relationships Between Deterioration, Biofilm Formation, and the Material Surface Properties.

PubMed

Mercier, Anne; Gravouil, Kevin; Aucher, Willy; Brosset-Vincent, Sandra; Kadri, Linette; Colas, Jenny; Bouchon, Didier; Ferreira, Thierry

2017-02-21

With the ever-increasing volume of polymer wastes and their associated detrimental impacts on the environment, the plastic life cycle has drawn increasing attention. Here, eight commercial polymers selected from biodegradable to environmentally persistent materials, all formulated under a credit card format, were incubated in an outdoor compost to evaluate their fate over time and to profile the microbial communities colonizing their surfaces. After 450 days in compost, the samples were all colonized by multispecies biofilms, these latest displaying different amounts of adhered microbial biomass and significantly distinct bacterial and fungal community compositions depending on the substrate. Interestingly, colonization experiments on the eight polymers revealed a large core of shared microbial taxa, predominantly composed of microorganisms previously reported from environments contaminated with petroleum hydrocarbons or plastics debris. These observations suggest that biofilms may contribute to the alteration process of all the polymers studied. Actually, four substrates, independently of their assignment to a polymer group, displayed a significant deterioration, which might be attributed to biologically mediated mechanisms. Relevantly, the deterioration appears strongly associated with the formation of a high-cell density biofilm onto the polymer surfaces. The analysis of various surface properties revealed that roughness and hydrophilicity are likely prominent parameters for driving the biological interactions with the polymers.

Microbial involvement in the formation of Cambrian sea-floor silica-iron oxide deposits, Australia

NASA Astrophysics Data System (ADS)

Duhig, Nathan C.; Davidson, Garry J.; Stolz, Joe

1992-06-01

The Cambrian-Ordovician Mount Windsor volcanic belt in northern Australia is host to stratiform lenses of massive ferruginous chert that are spatially associated with volcanogenic massive sulfide occurrences, in particular the Thalanga zinc-lead-copper-silver deposit. The rocks are composed principally of Fe2O3 and SiO2, with very low concentrations of alkalic elements, and lithogenous elements such as Al, Zr, and Ti; they are interpreted as nearly pure chemical sediments. Textural evidence is documented of the integral role of filamentous bacteria (and/or fungi) in depositing iron from hydrothermal fluids, and of the inorganic precipitation of silica-iron-oxyhydroxide gels that subsequently matured to subcrystalline and crystalline silica forms. At least three distinct iron-accumulating microbial forms are distinguished: networks of septate filaments, nonseptate filament networks, and extremely coarse branching filaments that do not reconnect. Values for δ34S in disseminated pyrite are up to 50‰ lighter than those of contemporaneous Cambrian seawater, suggesting postdepositional colonization of some ironstones by sulfur-reducing bacteria. The site not only preserves the textural interplay of biological and inorganic depositional processes in exhalites, but also extends the oldest known instance of microbial mediation in vent-proximal hydrothermal iron precipitation to at least 500 Ma.

Biofilm formation and potential for iron cycling in serpentinization-influenced groundwater of the Zambales and Coast Range ophiolites.

PubMed

Meyer-Dombard, D'Arcy R; Casar, Caitlin P; Simon, Alexander G; Cardace, Dawn; Schrenk, Matthew O; Arcilla, Carlo A

2018-05-01

Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems. Biofilms formed on rock cores from the Zambales ophiolite on surface and in-pit associations, confirming that organisms from serpentinizing systems can form biofilms in subsurface environments. Analysis by XPS and FTIR confirmed that enrichment culturing utilizing ferric iron growth substrates produced reduced, magnetic solids containing siderite, spinels, and FeO minerals. Microcosms and enrichment cultures supported organisms whose near relatives participate in iron redox transformations. Further, a potential 'principal' microbial community common to solid samples in serpentinizing systems was identified. These results indicate collectively that iron redox transformations should be more thoroughly and universally considered when assessing the function of terrestrial subsurface ecosystems driven by serpentinization.

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.

PubMed

Zhang, Zhimin; Li, Dapeng

2018-05-31

Adoption of thermal processing of the diet drives human evolution and gut microbiota diversity changes in a dietary habit-dependent manner. However, whether thermal processing of food triggers gut microbial variation remains unknown. Herein, we compared the microbiota of non-thermally processed and thermally processed food (NF and TF) and investigated gut microbiota associated with NF and TF in catfish Silurus meridionalis and C57BL/6 mice to assess effects of thermal processing of food on gut microbiota and to further identify the differences in host responses. We found no differences in overall microbial composition and structure in the pairwise NF and TF, but identified differential microbial communities between food and gut. Both fish and mice fed TF had significantly lower gut microbial diversity than those fed NF. Moreover, thermal processing of food triggered the changes in their microbial communities. Comparative host studies further indicated host species determined gut microbial assemblies, even if fed with the same food. Fusobacteria was the most abundant phylum in the fish, and Bacteroidetes and Firmicutes dominated in the mice. Besides the consistent reduction of Bacteroidetes and the balanced Protebacteria, the response of other dominated gut microbiota in the fish and mice to TF was taxonomically opposite at the phylum level, and those further found at the genus level. Our results reveal that thermal processing of food strongly contributes to the reduction of gut microbial diversity and differentially drives microbial alterations in a host-dependent manner, suggesting specific adaptations of host-gut microbiota in vertebrates responding to thermal processing of food. These findings open a window of opportunity to understand the decline in gut microbial diversity and the community variation in human evolution and provide new insights into the host-specific microbial assemblages associated with the use of processing techniques in food preparation in humans and domesticated animals.

Linking microbial community structure and microbial processes: An empirical and conceptual overview

USGS Publications Warehouse

Bier, R.L.; Bernhardt, Emily S.; Boot, Claudia M.; Graham, Emily B.; Hall, Edward K.; Lennon, Jay T.; Nemergut, Diana R.; Osborne, Brooke B.; Ruiz-Gonzalez, Clara; Schimel, Joshua P.; Waldrop, Mark P.; Wallenstein, Matthew D.

2015-01-01

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

PubMed

Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

2017-05-01

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Sulfur Cycling Mediates Calcium Carbonate Geochemistry in Modern Marine Stromatolites

NASA Technical Reports Server (NTRS)

Visscher, P. T.; Hoeft, S. E.; Bebout, B. M.; Reid, R. P.

2004-01-01

Modem marine stromatolites forming in Highborne Cay, Exumas (Bahamas), contain microbial mats dominated by Schizothrix. Although saturating concentrations of Ca2+ and CO32- exist, microbes mediate CaCO3 precipitation. Cyanobacterial photosynthesis in these stromatolites aids calcium carbonate precipitation by removal of HS+ through CO2 use. Photorespiration and exopolymer production predominantly by oxygenic phototrophs fuel heterotrophic activity: aerobic respiration (approximately 60 umol/sq cm.h) and sulfate reduction (SR; 1.2 umol SO42-/sq cm.h) are the dominant C- consuming processes. Aerobic microbial respiration and the combination of SR and H2S oxidation both facilitate CaCO3 dissolution through H+ production. Aerobic respiration consumes much more C on an hourly basis, but duel fluctuating O2 and H2 depth profiles indicate that overall, SR consumes only slightly less (0.2-0.5) of the primary production. Moreover, due to low O2 concentrations when SR rates are peaking, reoxidation of the H2S formed is incomplete: both thiosulfate and polythionates are formed. The process of complete H2S oxidation yields H+. However, due to a low O2 concentration late in the day and relatively high O2 concentrations early in the following morning, a two-stage oxidation takes place: first, polythionates are formed from H2S, creating alkalinity which coincides with CaCO3 precipitation; secondly, oxidation of polythionates to sulfate yields acidity, resulting in dissolution, etc. Vertical profiles confirmed that the pH peaked late in the afternoon (greater than 8.8) and had the lowest values (less than 7.4) early in the morning. Thus, the effect of this S-cycling through alkalinity production, followed by acidification during H2S oxidation, results in a six times stronger fluctuation in acidity than photosynthesis plus aerobic respiration accomplish. This implies that anaerobic processes play a pivotal role in stromatolite formation.

The clinical and cellular basis of contact lens-related corneal infections

PubMed Central

Robertson, Danielle M; Cavanagh, H Dwight

2008-01-01

Microbial keratitis (MK) is the most visually devastating complication associated with contact lens wear. Pseudomonas aeruginosa (PA) is highly invasive in the corneal epithelium and is responsible for more than half of the reported cases of contact lens-related MK. To protect against Pseudomonas-mediated MK, the corneal epithelium has evolved overlapping defense mechanisms that function to protect the ocular surface from microbial invasion. Research has shown that contact lens wear disrupts these protective mechanisms through breakdown of normal homeostatic surface renewal as well as damaging the corneal surface, exposing underlying cell membrane receptors that bind and internalize PA through the formation of lipid rafts. Human clinical trials have shown that initial adherence of PA with resulting increased risk for microbial infection is mediated in part by contact lens oxygen transmissibility. Recently, chemical preserved multipurpose solutions (MPS) have been implicated in increasing PA adherence to corneal epithelial cells, in addition to inducing significant levels of toxic staining when used in conjunction with specific silicone hydrogel lenses. This review summarizes what is currently known about the relationship between contact lenses, the corneal epithelium, MPS, and infection. PMID:19277209

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease

NASA Astrophysics Data System (ADS)

Baldassano, Steven N.; Bassett, Danielle S.

2016-05-01

The gut microbiome plays a key role in human health, and alterations of the normal gut flora are associated with a variety of distinct disease states. Yet, the natural dependencies between microbes in healthy and diseased individuals remain far from understood. Here we use a network-based approach to characterize microbial co-occurrence in individuals with inflammatory bowel disease (IBD) and healthy (non-IBD control) individuals. We find that microbial networks in patients with IBD differ in both global structure and local connectivity patterns. While a “core” microbiome is preserved, network topology of other densely interconnected microbe modules is distorted, with potent inflammation-mediating organisms assuming roles as integrative and highly connected inter-modular hubs. We show that while both networks display a rich-club organization, in which a small set of microbes commonly co-occur, the healthy network is more easily disrupted by elimination of a small number of key species. Further investigation of network alterations in disease might offer mechanistic insights into the specific pathogens responsible for microbiome-mediated inflammation in IBD.

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.

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

PubMed

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

2017-08-01

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

Physical and Biological Carbon Isotope Fractionation in Methane During Gas-Push-Pull-Tests

NASA Astrophysics Data System (ADS)

Gonzalez-Gil, G.; Schroth, M. H.; Gomez, K.; Zeyer, J.

2005-12-01

Stable isotope analyses have become a common tool to assess microbially-mediated processes in subsurface environments. We investigated if stable carbon isotope analysis can be used as a tool to complement gas push-pull tests (GPPTs), a novel technique that was recently developed and tested for the in-situ quantification of CH4 oxidation in soils. During a GPPT a gas mixture containing CH4, O2 and nonreactive tracer gases is injected into the soil, where CH4 is oxidized by indigenous microorganisms. Thereafter, a blend of injected gas mixture and soil air is extracted from the same location, and CH4 oxidation is quantified from an analysis of extracted CH4 and tracer gases. To assess the magnitude of physical isotope fractionation due to molecular diffusion during GPPTs, we conducted laboratory experiments in the absence of microbial activity in a 1m-high, 1m-diameter tank filled with dry sand. During the GPPTs' extraction phase, the isotopic composition of methane was analyzed. Results indicated strong carbon isotope fractionation (>20 per mil) during GPPTs. To assess the combined effect of physical and biological isotope fractionation, numerical simulations of GPPTs were conducted in which microbial CH4 isotope fractionation was simulated using first-order rate constants and microbial kinetic isotope fractionation factors previously reported for methane oxidation in landfill environments. Results of these simulations indicated that for small CH4 oxidation rates, overall isotope fractionation in CH4 is dominated by physical fractionation. Conversely, for high CH4 oxidation rates, overall fractionation is dominated by biological fractionation. Thus, CH4 isotope fractionation data alone from a single GPPT cannot be used to assess microbial CH4 oxidation. However, biological fractionation may be quantified if physical fractionation due to diffusion is known. This can be achieved by conducting two sequential GPPTs, with microbial activity being inhibited in the second test.

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

PubMed

Kinsman-Costello, L E; Sheik, C S; Sheldon, N D; Allen Burton, G; Costello, D M; Marcus, D; Uyl, P A Den; Dick, G J

2017-03-01

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH communities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling. © 2016 John Wiley & Sons Ltd.

How, with whom and when: an overview of CD147-mediated regulatory networks influencing matrix metalloproteinase activity.

PubMed

Grass, G Daniel; Toole, Bryan P

2015-11-24

Matrix metalloproteinases (MMPs) comprise a family of 23 zinc-dependent enzymes involved in various pathologic and physiologic processes. In cancer, MMPs contribute to processes from tumour initiation to establishment of distant metastases. Complex signalling and protein transport networks regulate MMP synthesis, cell surface presentation and release. Earlier attempts to disrupt MMP activity in patients have proven to be intolerable and with underwhelming clinical efficacy; thus targeting ancillary proteins that regulate MMP activity may be a useful therapeutic approach. Extracellular matrix metalloproteinase inducer (EMMPRIN) was originally characterized as a factor present on lung cancer cells, which stimulated collagenase (MMP-1) production in fibroblasts. Subsequent studies demonstrated that EMMPRIN was identical with several other protein factors, including basigin (Bsg), all of which are now commonly termed CD147. CD147 modulates the synthesis and activity of soluble and membrane-bound [membrane-type MMPs (MT-MMPs)] in various contexts via homophilic/heterophilic cell interactions, vesicular shedding or cell-autonomous processes. CD147 also participates in inflammation, nutrient and drug transporter activity, microbial pathology and developmental processes. Despite the hundreds of manuscripts demonstrating CD147-mediated MMP regulation, the molecular underpinnings governing this process have not been fully elucidated. The present review summarizes our present knowledge of the complex regulatory systems influencing CD147 biology and provides a framework to understand how CD147 may influence MMP activity. © 2016 Authors.

How, with whom and when: an overview of CD147-mediated regulatory networks influencing matrix metalloproteinase activity

PubMed Central

Grass, G. Daniel; Toole, Bryan P.

2015-01-01

Matrix metalloproteinases (MMPs) comprise a family of 23 zinc-dependent enzymes involved in various pathologic and physiologic processes. In cancer, MMPs contribute to processes from tumour initiation to establishment of distant metastases. Complex signalling and protein transport networks regulate MMP synthesis, cell surface presentation and release. Earlier attempts to disrupt MMP activity in patients have proven to be intolerable and with underwhelming clinical efficacy; thus targeting ancillary proteins that regulate MMP activity may be a useful therapeutic approach. Extracellular matrix metalloproteinase inducer (EMMPRIN) was originally characterized as a factor present on lung cancer cells, which stimulated collagenase (MMP-1) production in fibroblasts. Subsequent studies demonstrated that EMMPRIN was identical with several other protein factors, including basigin (Bsg), all of which are now commonly termed CD147. CD147 modulates the synthesis and activity of soluble and membrane-bound [membrane-type MMPs (MT-MMPs)] in various contexts via homophilic/heterophilic cell interactions, vesicular shedding or cell-autonomous processes. CD147 also participates in inflammation, nutrient and drug transporter activity, microbial pathology and developmental processes. Despite the hundreds of manuscripts demonstrating CD147-mediated MMP regulation, the molecular underpinnings governing this process have not been fully elucidated. The present review summarizes our present knowledge of the complex regulatory systems influencing CD147 biology and provides a framework to understand how CD147 may influence MMP activity. PMID:26604323

Microbial-mediated method for metal oxide nanoparticle formation

DOEpatents

Rondinone, Adam J.; Moon, Ji Won; Love, Lonnie J.; Yeary, Lucas W.; Phelps, Tommy J.

2015-09-08

The invention is directed to a method for producing metal oxide nanoparticles, the method comprising: (i) subjecting a combination of reaction components to conditions conducive to microbial-mediated formation of metal oxide nanoparticles, wherein said combination of reaction components comprise: metal-reducing microbes, a culture medium suitable for sustaining said metal-reducing microbes, an effective concentration of one or more surfactants, a reducible metal oxide component containing one or more reducible metal species, and one or more electron donors that provide donatable electrons to said metal-reducing microbes during consumption of the electron donor by said metal-reducing microbes; and (ii) isolating said metal oxide nanoparticles, which contain a reduced form of said reducible metal oxide component. The invention is also directed to metal oxide nanoparticle compositions produced by the inventive method.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-05-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism, substrate affinity and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), neither hydrogen nor formate is exchanged fast enough between the consortia partners to achieve measured rates of metabolic activity, but that acetate exchange might support rates that approach those observed.

High resolution and comprehensive techniques to analyze aerobic methane oxidation in mesocosm experiments

NASA Astrophysics Data System (ADS)

Chan, E. W.; Kessler, J. D.; Redmond, M. C.; Shiller, A. M.; Arrington, E. C.; Valentine, D. L.; Colombo, F.

2015-12-01

Many studies of microbially mediated aerobic methane oxidation in oceanic environments have examined the many different factors that control the rates of oxidation. However, there is debate on how quickly methane is oxidized once a microbial population is established and what factor(s) are limiting in these types of environments. These factors include the availability of CH4, O2, trace metals, nutrients, and the density of cell population. Limits to these factors can also control the temporal aspects of a methane oxidation event. In order to look at this process in its entirety and with higher temporal resolution, a mesocosm incubation system was developed with a Dissolved Gas Analyzer System (DGAS) coupled with a set of analytical tools to monitor aerobic methane oxidation in real time. With the addition of newer laser spectroscopy techniques (cavity ringdown spectroscopy), stable isotope fractionation caused by microbial processes can also be examined on a real time and automated basis. Cell counting, trace metal, nutrient, and DNA community analyses have also been carried out in conjunction with these mesocosm samples to provide a clear understanding of the biology in methane oxidation dynamics. This poster will detail the techniques involved to provide insights into the chemical and isotopic kinetics controlling aerobic methane oxidation. Proof of concept applications will be presented from seep sites in the Hudson Canyon and the Sleeping Dragon seep field, Mississippi Canyon 118 (MC 118). This system was used to conduct mesocosm experiments to examine methane consumption, O2 consumption, nutrient consumption, and biomass production.

Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments.

PubMed

Hansel, Colleen M; Lentini, Chris J; Tang, Yuanzhi; Johnston, David T; Wankel, Scott D; Jardine, Philip M

2015-11-01

A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration--a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder.

Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments

PubMed Central

Hansel, Colleen M; Lentini, Chris J; Tang, Yuanzhi; Johnston, David T; Wankel, Scott D; Jardine, Philip M

2015-01-01

A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration—a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder. PMID:25871933

Chiral chemicals as tracers of atmospheric sources and fate processes in a world of changing climate.

PubMed

F Bidleman, Terry; M Jantunen, Liisa; Binnur Kurt-Karakus, Perihan; Wong, Fiona; Hung, Hayley; Ma, Jianmin; Stern, Gary; Rosenberg, Bruno

2013-01-01

Elimination of persistent organic pollutants (POPs) under national and international regulations reduces "primary" emissions, but "secondary" emissions continue from residues deposited in soil, water, ice and vegetation during former years of usage. In a future, secondary source controlled world, POPs will follow the carbon cycle and biogeochemical processes will determine their transport, accumulation and fate. Climate change is likely to affect mobilisation of POPs through e.g., increased temperature, altered precipitation and wind patterns, flooding, loss of ice cover in polar regions, melting glaciers, and changes in soil and water microbiology which affect degradation and transformation. Chiral compounds offer advantages for following transport and fate pathways because of their ability to distinguish racemic (newly released or protected from microbial attack) and nonracemic (microbially degraded) sources. This paper discusses the rationale for this approach and suggests applications where chiral POPs could aid investigation of climate-mediated exchange and degradation processes. Multiyear measurements of two chiral POPs, trans-chlordane and α-HCH, at a Canadian Arctic air monitoring station show enantiomer compositions which cycle seasonally, suggesting varying source contributions which may be under climatic control. Large-scale shifts in the enantioselective metabolism of chiral POPs in soil and water might influence the enantiomer composition of atmospheric residues, and it would be advantageous to include enantiospecific analysis in POPs monitoring programs.

Guidelines To Validate Control of Cross-Contamination during Washing of Fresh-Cut Leafy Vegetables.

PubMed

Gombas, D; Luo, Y; Brennan, J; Shergill, G; Petran, R; Walsh, R; Hau, H; Khurana, K; Zomorodi, B; Rosen, J; Varley, R; Deng, K

2017-02-01

The U.S. Food and Drug Administration requires food processors to implement and validate processes that will result in significantly minimizing or preventing the occurrence of hazards that are reasonably foreseeable in food production. During production of fresh-cut leafy vegetables, microbial contamination that may be present on the product can spread throughout the production batch when the product is washed, thus increasing the risk of illnesses. The use of antimicrobials in the wash water is a critical step in preventing such water-mediated cross-contamination; however, many factors can affect antimicrobial efficacy in the production of fresh-cut leafy vegetables, and the procedures for validating this key preventive control have not been articulated. Producers may consider three options for validating antimicrobial washing as a preventive control for cross-contamination. Option 1 involves the use of a surrogate for the microbial hazard and the demonstration that cross-contamination is prevented by the antimicrobial wash. Option 2 involves the use of antimicrobial sensors and the demonstration that a critical antimicrobial level is maintained during worst-case operating conditions. Option 3 validates the placement of the sensors in the processing equipment with the demonstration that a critical antimicrobial level is maintained at all locations, regardless of operating conditions. These validation options developed for fresh-cut leafy vegetables may serve as examples for validating processes that prevent cross-contamination during washing of other fresh produce commodities.

Chiral Chemicals as Tracers of Atmospheric Sources and Fate Processes in a World of Changing Climate

PubMed Central

F. Bidleman, Terry; M. Jantunen, Liisa; Binnur Kurt-Karakus, Perihan; Wong, Fiona; Hung, Hayley; Ma, Jianmin; Stern, Gary; Rosenberg, Bruno

2013-01-01

Elimination of persistent organic pollutants (POPs) under national and international regulations reduces “primary” emissions, but “secondary” emissions continue from residues deposited in soil, water, ice and vegetation during former years of usage. In a future, secondary source controlled world, POPs will follow the carbon cycle and biogeochemical processes will determine their transport, accumulation and fate. Climate change is likely to affect mobilisation of POPs through e.g., increased temperature, altered precipitation and wind patterns, flooding, loss of ice cover in polar regions, melting glaciers, and changes in soil and water microbiology which affect degradation and transformation. Chiral compounds offer advantages for following transport and fate pathways because of their ability to distinguish racemic (newly released or protected from microbial attack) and nonracemic (microbially degraded) sources. This paper discusses the rationale for this approach and suggests applications where chiral POPs could aid investigation of climate-mediated exchange and degradation processes. Multiyear measurements of two chiral POPs, trans-chlordane and α-HCH, at a Canadian Arctic air monitoring station show enantiomer compositions which cycle seasonally, suggesting varying source contributions which may be under climatic control. Large-scale shifts in the enantioselective metabolism of chiral POPs in soil and water might influence the enantiomer composition of atmospheric residues, and it would be advantageous to include enantiospecific analysis in POPs monitoring programs. PMID:24349938

Remediation of Groundwater Contaminated by Nuclear Waste

NASA Astrophysics Data System (ADS)

Parker, Jack; Palumbo, Anthony

2008-07-01

A Workshop on Accelerating Development of Practical Field-Scale Bioremediation Models; An Online Meeting, 23 January to 20 February 2008; A Web-based workshop sponsored by the U.S. Department of Energy Environmental Remediation Sciences Program (DOE/ERSP) was organized in early 2008 to assess the state of the science and knowledge gaps associated with the use of computer models to facilitate remediation of groundwater contaminated by wastes from Cold War era nuclear weapons development and production. Microbially mediated biological reactions offer a potentially efficient means to treat these sites, but considerable uncertainty exists in the coupled biological, chemical, and physical processes and their mathematical representation.

Enterobactin: An archetype for microbial iron transport

PubMed Central

Raymond, Kenneth N.; Dertz, Emily A.; Kim, Sanggoo S.

2003-01-01

Bacteria have aggressive acquisition processes for iron, an essential nutrient. Siderophores are small iron chelators that facilitate cellular iron transport. The siderophore enterobactin is a triscatechol derivative of a cyclic triserine lactone. Studies of the chemistry, regulation, synthesis, recognition, and transport of enterobactin make it perhaps the best understood of the siderophore-mediated iron uptake systems, displaying a lot of function packed into this small molecule. However, recent surprises include the isolation of corynebactin, a closely related trithreonine triscatechol derivative lactone first found in Gram-positive bacteria, and the crystal structure of a ferric enterobactin complex of a protein identified as an antibacterial component of the human innate immune system. PMID:12655062

Using a Mechanistic Reactive Transport Model to Represent Soil Organic Matter Dynamics and Climate Sensitivity

NASA Astrophysics Data System (ADS)

Guerry, N.; Riley, W. J.; Maggi, F.; Torn, M. S.; Kleber, M.

2011-12-01

The nature of long term Soil Organic Matter (SOM) dynamics is uncertain and the mechanisms involved are crudely represented in site, regional, and global models. Recent work challenging the paradigm that SOM is stabilized because of its sequential transformations to more intrinsically recalcitrant compounds motivated us to develop a mechanistic modeling framework that can be used to test hypotheses of SOM dynamics. We developed our C cycling model in TOUGHREACT, an established 3-dimensional reactive transport solver that accounts for multiple phases (aqueous, gaseous, sorbed), multiple species, advection and diffusion, and multiple microbial populations. Energy and mass exchange through the soil boundaries are accounted for via ground heat flux, rainfall, C sources (e.g., exudation, woody, leaf, root litter) and C losses (e.g., CO2 emissions and DOC deep percolation). SOM is categorized according to the various types of compounds commonly found in the above mentioned C sources and microbial byproducts, including poly- and monosaccharides, lignin, amino compounds, organic acids, nucleic acids, lipids, and phenols. Each of these compounds is accounted for by one or more representative species in the model. A reaction network was developed to describe the microbially-mediated processes and chemical interactions of these species, including depolymerization, microbial assimilation, respiration and deposition of byproducts, and incorporation of dead biomass into SOM stocks. Enzymatic reactions are characterized by Michaelis-Menten kinetics, with maximum reaction rates determined by the species' O/C ratio. Microbial activity is further regulated by soil moisture content, O2 availability, pH, and temperature. For the initial set of simulations, literature values were used to constrain microbial Monod parameters, Michaelis-Menten parameters, sorption parameters, physical protection, partitioning of microbial byproducts, and partitioning of litter inputs, although there is substantial uncertainty in how these relationships should be represented. We also developed several other model formulations, including one that represents SOM in pools of varying decomposability, but lacking explicit protection mechanisms. We tested the model against several observational and experimental datasets. An important conclusion of our analysis is that although several of the model structural formulations were able to represent the bulk SOM observations, including 14C vertical profiles, the temperature, moisture, and soil chemistry sensitivity of decomposition varied strongly between each formulation. Finally, we applied the model to design observations that would be required to better constrain process representation and improve predictions of changes in SOM under changing climate.

Electrochemical performance and microbial community profiles in microbial fuel cells in relation to electron transfer mechanisms.

PubMed

Uria, Naroa; Ferrera, Isabel; Mas, Jordi

2017-10-18

Microbial fuel cells (MFCs) operating with complex microbial communities have been extensively reported in the past, and are commonly used in applications such as wastewater treatment, bioremediation or in-situ powering of environmental sensors. However, our knowledge on how the composition of the microbial community and the different types of electron transfer to the anode affect the performance of these bioelectrochemical systems is far from complete. To fill this gap of knowledge, we designed a set of three MFCs with different constrains limiting direct and mediated electron transfer to the anode. The results obtained indicate that MFCs with a naked anode on which a biofilm was allowed unrestricted development (MFC-A) had the most diverse archaeal and bacterial community, and offered the best performance. In this MFC both, direct and mediated electron transfer, occurred simultaneously, but direct electron transfer was the predominant mechanism. Microbial fuel cells in which the anode was enclosed in a dialysis membrane and biofilm was not allowed to develop (MFC-D), had a much lower power output (about 60% lower), and a prevalence of dissolved redox species that acted as putative electron shuttles. In the anolyte of this MFC, Arcobacter and Methanosaeta were the prevalent bacteria and archaea respectively. In the third MFC, in which the anode had been covered by a cation selective nafion membrane (MFC-N), power output decreased a further 5% (95% less than MFC-A). In this MFC, conventional organic electron shuttles could not operate and the low power output obtained was presumably attributed to fermentation end-products produced by some of the organisms present in the anolyte, probably Pseudomonas or Methanosaeta. Electron transfer mechanisms have an impact on the development of different microbial communities and in turn on MFC performance. Although a stable current was achieved in all cases, direct electron transfer MFC showed the best performance concluding that biofilms are the major contributors to current production in MFCs. Characterization of the complex microbial assemblages in these systems may help us to unveil new electrogenic microorganisms and improve our understanding on their role to the functioning of MFCs.

Fungicide dissipation and impact on metolachlor aerobic soil degradation and soil microbial dynamics.

PubMed

White, Paul M; Potter, Thomas L; Culbreath, Albert K

2010-02-15

Pesticides are typically applied as mixtures and or sequentially to soil and plants during crop production. A common scenario is herbicide application at planting followed by sequential fungicide applications post-emergence. Fungicides depending on their spectrum of activity may alter and impact soil microbial communities. Thus there is a potential to impact soil processes responsible for herbicide degradation. This may change herbicide efficacy and environmental fate characteristics. Our study objective was to determine the effects of 4 peanut fungicides, chlorothalonil (2,4,5,6-tetrachloro-1,3-benzenedicarbonitrile), tebuconazole (alpha-[2-(4-chlorophenyl)ethyl]-alpha-(1,1-dimethylethyl)-1H-1,2,4-triazole-1-ethanol), flutriafol (alpha-(2-fluorophenyl)-alpha-(4-fluorophenyl)-1H-1,2,4-triazole-1-ethanol), and cyproconazole (alpha-(4-chlorophenyl)-alpha-(1-cyclopropylethyl)-1H-1,2,4-triazole-1-ethanol) on the dissipation kinetics of the herbicide, metolachlor (2-chloro-N-(6-ethyl-o-tolyl)-N-[(1RS)-2-methoxy-1-methylethyl]acetamide), and on the soil microbial community. This was done through laboratory incubation of field treated soil. Chlorothalonil significantly reduced metolachlor soil dissipation as compared to the non-treated control or soil treated with the other fungicides. Metolachlor DT(50) was 99 days for chlorothalonil-treated soil and 56, 45, 53, and 46 days for control, tebuconazole, flutriafol, and cyproconazole-treated soils, respectively. Significant reductions in predominant metolachlor metabolites, metolachlor ethane sulfonic acid (MESA) and metolachlor oxanilic acid (MOA), produced by oxidation of glutathione-metolachlor conjugates were also observed in chlorothalonil-treated soil. This suggested that the fungicide impacted soil glutathione-S-transferase (GST) activity. Fungicide DT(50) was 27-80 days but impacts on the soil microbial community as indicated by lipid biomarker analysis were minimal. Overall study results indicated that chlorothalonil has the potential to substantially increase soil persistence (2-fold) of metolachlor and alter fate and transport processes. GST mediated metabolism is common pesticide detoxification process in soil; thus there are implications for the fate of many active ingredients.

Human iNKT cells induce IL-1β secretion by peripheral blood monocytes via a P2X7-independent pathway

PubMed Central

Felley, Laura E.; Sharma, Akshat; Theisen, Erin; Romero-Masters, James C.; Sauer, John-Demian; Gumperz, Jenny E.

2016-01-01

The cytokine IL-1β plays a central role in inflammatory responses that are initiated by microbial challenges, as well as in those that are due to endogenous processes (often called “sterile” inflammation). IL-1β secretion that occurs independently of microbial stimulation is typically associated with the presence of endogenous alarmins, such as extracellular ATP (an indicator of cytopathic damage). Here we show that IL-2 activated human iNKT cells stimulate the secretion of IL-1β protein by human peripheral blood monocytes in a manner that requires neither the presence of microbial compounds nor signaling through the extracellular ATP receptor P2X7. Monocyte IL-1β production was specifically induced by iNKT cells, since similarly activated polyclonal autologous T cells did not have this effect. Secretion of IL-1β protein occurred rapidly (within 3-4 hours), and required cell contact between the iNKT cells and monocytes. Similar to IL-1β production induced by TLR stimulation, the iNKT-induced pathway appeared to entail a two-step process involving NFκB signaling and IL1B gene transcription, as well as assembly of the NLRP3 inflammasome and activation of caspase 1. However, in contrast to the classical inflammasome-mediated pathway of IL-1β production, activation of monocytes via P2X7 was dispensable for iNKT-induced IL-1β secretion and potassium efflux was not required. Moreover, the iNKT-induced effect involved caspase 8 activity, yet induced little monocyte death. These results suggest that IL-2 activated human iNKT cells induce monocytes to produce IL-1β through a distinctive pathway that does not require the presence of microbial danger signals or alarmins associated with cytopathic damage. PMID:27534556

Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

PubMed

Baker, Nameer R; Khalili, Banafshe; Martiny, Jennifer B H; Allison, Steven D

2018-06-01

Microbial decomposers mediate the return of CO 2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities. © 2018 by the Ecological Society of America.

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

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

2006-01-01

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

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.

Social network community structure and the contact-mediated sharing of commensal E. coli among captive rhesus macaques (Macaca mulatta).

PubMed

Balasubramaniam, Krishna; Beisner, Brianne; Guan, Jiahui; Vandeleest, Jessica; Fushing, Hsieh; Atwill, Edward; McCowan, Brenda

2018-01-01

In group-living animals, heterogeneity in individuals' social connections may mediate the sharing of microbial infectious agents. In this regard, the genetic relatedness of individuals' commensal gut bacterium Escherichia coli may be ideal to assess the potential for pathogen transmission through animal social networks. Here we use microbial phylogenetics and population genetics approaches, as well as host social network reconstruction, to assess evidence for the contact-mediated sharing of E. coli among three groups of captively housed rhesus macaques ( Macaca mulatta ), at multiple organizational scales. For each group, behavioral data on grooming, huddling, and aggressive interactions collected for a six-week period were used to reconstruct social network communities via the Data Cloud Geometry (DCG) clustering algorithm. Further, an E. coli isolate was biochemically confirmed and genotypically fingerprinted from fecal swabs collected from each macaque. Population genetics approaches revealed that Group Membership, in comparison to intrinsic attributes like age, sex, and/or matriline membership of individuals, accounted for the highest proportion of variance in E. coli genotypic similarity. Social network approaches revealed that such sharing was evident at the community-level rather than the dyadic level. Specifically, although we found no links between dyadic E. coli similarity and social contact frequencies, similarity was significantly greater among macaques within the same social network communities compared to those across different communities. Moreover, tests for one of our study-groups confirmed that E. coli isolated from macaque rectal swabs were more genotypically similar to each other than they were to isolates from environmentally deposited feces. In summary, our results suggest that among frequently interacting, spatially constrained macaques with complex social relationships, microbial sharing via fecal-oral, social contact-mediated routes may depend on both individuals' direct connections and on secondary network pathways that define community structure. They lend support to the hypothesis that social network communities may act as bottlenecks to contain the spread of infectious agents, thereby encouraging disease control strategies to focus on multiple organizational scales. Future directions includeincreasing microbial sampling effort per individual to better-detect dyadic transmission events, and assessments of the co-evolutionary links between sociality, infectious agent risk, and host immune function.

NF-kappaB Activity in Macrophages Determines Metastatic Potential of Breast Tumor Cells

DTIC Science & Technology

2011-08-01

Cheng DS, Chodosh LA, Blackwell TS, Yull FE: Activation of nuclear factor kappa B in mammary epithelium promotes milk loss during mammary... microbial products (15, 16). To date, the potential role of macrophages in the fetal lung innate immune response has not been closely examined. Studies...In this model, microbial products initially activate NF-kB in lung macrophages. The release of inflammatory mediators, particularly IL-1b and/or TNF-a

Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils

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

Jeremy Semrau; Sung-Woo Lee; Jeongdae Im

2010-09-30

The overall objective of this project, 'Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils' was to develop effective, efficient, and economic methodologies by which microbial production of nitrous oxide can be minimized while also maximizing microbial consumption of methane in landfill cover soils. A combination of laboratory and field site experiments found that the addition of nitrogen and phenylacetylene stimulated in situ methane oxidation while minimizing nitrous oxide production. Molecular analyses also indicated that methane-oxidizing bacteria may play a significant role in not only removing methane, but in nitrous oxide production as well, although themore » contribution of ammonia-oxidizing archaea to nitrous oxide production can not be excluded at this time. Future efforts to control both methane and nitrous oxide emissions from landfills as well as from other environments (e.g., agricultural soils) should consider these issues. Finally, a methanotrophic biofiltration system was designed and modeled for the promotion of methanotrophic activity in local methane 'hotspots' such as landfills. Model results as well as economic analyses of these biofilters indicate that the use of methanotrophic biofilters for controlling methane emissions is technically feasible, and provided either the costs of biofilter construction and operation are reduced or the value of CO{sub 2} credits is increased, can also be economically attractive.« less

Novel approaches to microbial enhancement of oil recovery.

PubMed

Kryachko, Yuriy

2018-01-20

Microbially enhanced oil recovery (MEOR) was shown to be feasible in a number of laboratory experiments and field trials. However, it has not been widely used in the oil industry because necessary conditions cannot always be easily established in an oil reservoir. Novel approaches to MEOR, which are based on newly discovered biosurfactant-mediated MEOR-mechanisms, are discussed in this review. Particularly, the possibility of combining MEOR with chemical enhancement of oil recovery in heterogeneous oil reservoirs, which involves rock surface wettability shifts and emulsion inversions, is discussed. In wider (centimeter/millimeter-scale) rock pores, the activity of (bio)surfactants and microbial cells attached to oil may allow releasing trapped oil blobs through oil-in-water emulsification. After no more oil can be emulsified, the addition of alkali or surfactants, which turn rock surface oil-wet, may help release oil droplets trapped in narrow (micrometer-scale) pores through coalescence of the droplets and water-in-oil emulsification. Experiments demonstrating the possibility of (bio)surfactant-mediated enhancement of immiscible gas-driven oil recovery are also reviewed. Interestingly, very low (bio)surfactant concentrations were shown to be needed for enhancement of immiscible gas-driven oil recovery. Some possible side effects of MEOR, such as unintended bioplugging and microbially influenced corrosion (MIC), are discussed as well. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Community Assembly Processes of the Microbial Rare Biosphere.

PubMed

Jia, Xiu; Dini-Andreote, Francisco; Falcão Salles, Joana

2018-03-14

Our planet teems with microorganisms that often present a skewed abundance distribution in a local community, with relatively few dominant species coexisting alongside a high number of rare species. Recent studies have demonstrated that these rare taxa serve as limitless reservoirs of genetic diversity, and perform disproportionate types of functions despite their low abundances. However, relatively little is known about the mechanisms controlling rarity and the processes promoting the development of the rare biosphere. Here, we propose the use of multivariate cut-offs to estimate rare species and phylogenetic null models applied to predefined rare taxa to disentangle the relative influences of ecoevolutionary processes mediating the assembly of the rare biosphere. Importantly, the identification of the factors controlling rare species assemblages is critical for understanding the types of rarity, how the rare biosphere is established, and how rare microorganisms fluctuate over spatiotemporal scales, thus enabling prospective predictions of ecosystem responses. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbial Metabolism in Serpentinite Fluids

NASA Astrophysics Data System (ADS)

Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

2013-12-01

Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid chemistry and microbial community composition. These experiments are expected to provide insight into the biogeochemical dynamics of the serpentinite subsurface at CROMO and represent a first step for developing metatranscriptomic and RNA-based Stable Isotope Probing (RNA-SIP) experiments to trace microbial activity at this site. [1] Brazelton et al. (2012) Frontiers in Microbiology 2:268

Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis.

PubMed

Velmurugan, Ganesan; Ramprasath, Tharmarajan; Swaminathan, Krishnan; Mithieux, Gilles; Rajendhran, Jeyaprakash; Dhivakar, Mani; Parthasarathy, Ayothi; Babu, D D Venkatesh; Thumburaj, Leishman John; Freddy, Allen J; Dinakaran, Vasudevan; Puhari, Shanavas Syed Mohamed; Rekha, Balakrishnan; Christy, Yacob Jenifer; Anusha, Sivakumar; Divya, Ganesan; Suganya, Kannan; Meganathan, Boominathan; Kalyanaraman, Narayanan; Vasudevan, Varadaraj; Kamaraj, Raju; Karthik, Maruthan; Jeyakumar, Balakrishnan; Abhishek, Albert; Paul, Eldho; Pushpanathan, Muthuirulan; Rajmohan, Rajamani Koushick; Velayutham, Kumaravel; Lyon, Alexander R; Ramasamy, Subbiah

2017-01-24

Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. The diabetogenic nature of organophosphates was recently reported but the underlying molecular mechanism is unclear. We aimed to understand the role of gut microbiota in organophosphate-induced hyperglycemia and to unravel the molecular mechanism behind this process. Here we demonstrate a high prevalence of diabetes among people directly exposed to organophosphates in rural India (n = 3080). Correlation and linear regression analysis reveal a strong association between plasma organophosphate residues and HbA1c but no association with acetylcholine esterase was noticed. Chronic treatment of mice with organophosphate for 180 days confirms the induction of glucose intolerance with no significant change in acetylcholine esterase. Further fecal transplantation and culture transplantation experiments confirm the involvement of gut microbiota in organophosphate-induced glucose intolerance. Intestinal metatranscriptomic and host metabolomic analyses reveal that gut microbial organophosphate degradation produces short chain fatty acids like acetic acid, which induces gluconeogenesis and thereby accounts for glucose intolerance. Plasma organophosphate residues are positively correlated with fecal esterase activity and acetate level of human diabetes. Collectively, our results implicate gluconeogenesis as the key mechanism behind organophosphate-induced hyperglycemia, mediated by the organophosphate-degrading potential of gut microbiota. This study reveals the gut microbiome-mediated diabetogenic nature of organophosphates and hence that the usage of these insecticides should be reconsidered.

Microbial responses to southward and northward Cambisol soil transplant

DOE PAGES

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

2015-10-26

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

Microbial diversity in restored wetlands of San Francisco Bay

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

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils,more » we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.« less

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

PubMed

Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

2017-09-12

Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

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

Wang, Mengmeng; Liu, Shanshan; Wang, Feng

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

Metabolic interactions and dynamics in microbial communities

NASA Astrophysics Data System (ADS)

Segre', Daniel

Metabolism, in addition to being the engine of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of many isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. We are developing mechanistic computational approaches for studying the interactions between different organisms based on the knowledge of their entire metabolic networks. In particular, we have recently built an open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), which combines metabolic models with convection-diffusion equations to simulate the spatio-temporal dynamics of metabolism in microbial communities. COMETS has been experimentally tested on small artificial communities, and is scalable to hundreds of species in complex environments. I will discuss recent developments and challenges towards the implementation of models for microbiomes and synthetic microbial communities.

Circulating Inflammatory Mediators in Patients with Fever: Predicting Bloodstream Infection

PubMed Central

Groeneveld, A. B. Johan; Bossink, Ailko W. J.; van Mierlo, Gerard J.; Hack, C. Erik

2001-01-01

The systemic host response to microbial infection involves clinical signs and symptoms of infection, including fever and elevated white blood cell (WBC) counts. In addition, inflammatory mediators are released, including activated complement product C3a, interleukin 6 (IL-6), and the acute-phase reactant secretory phospholipase A2 (sPLA2). To compare the value of the latter with the former in predicting (the degree of) microbial infection at the bedside, we determined clinical variables and took blood samples daily for 3 consecutive days in 300 patients with a new fever (>38.0°C rectally or >38.3°C axillary). Microbiological culture results for 7 days after inclusion were collected. Patients were divided into clinical and microbial categories: those without and with a clinical focus of infection and those with negative cultures, with positive local cultures or specific stains for fungal (n = 13) or tuberculous infections (n = 1), and with positive blood cultures, including one patient with malaria parasitemia. The area under the curve (AUC) of the receiver operating characteristic (ROC) for prediction of positive cultures was 0.60 (P < 0.005) for peak temperature and 0.59 (P < 0.01) for peak WBC count, 0.60 (P < 0.005) for peak C3a, 0.63 (P < 0.001) for peak IL-6, and 0.61 (P < 0.001) for peak sPLA2. The AUC under the ROC curve for prediction of positive blood cultures was 0.68 (P < 0.001) for peak temperature and 0.56 for peak WBC count (P < 0.05). The AUC for peak C3a was 0.69, that for peak IL-6 was 0.70, and that for sPLA2 was 0.67 (for all, P < 0.001). The degree of microbial invasion is thus a major determinant of the clinical and inflammatory host response in patients with fever. Moreover, circulating inflammatory mediators such as C3a and IL-6 may help to predict positive blood cultures, together with clinical signs and symptoms of the host response to microbial infection, even before culture results are available. This may help in the designing of entry criteria for therapeutic intervention studies. PMID:11687462

Biological reduction of chlorinated solvents: Batch-scale geochemical modeling

NASA Astrophysics Data System (ADS)

Kouznetsova, Irina; Mao, Xiaomin; Robinson, Clare; Barry, D. A.; Gerhard, Jason I.; McCarty, Perry L.

2010-09-01

Simulation of biodegradation of chlorinated solvents in dense non-aqueous phase liquid (DNAPL) source zones requires a model that accounts for the complexity of processes involved and that is consistent with available laboratory studies. This paper describes such a comprehensive modeling framework that includes microbially mediated degradation processes, microbial population growth and decay, geochemical reactions, as well as interphase mass transfer processes such as DNAPL dissolution, gas formation and mineral precipitation/dissolution. All these processes can be in equilibrium or kinetically controlled. A batch modeling example was presented where the degradation of trichloroethene (TCE) and its byproducts and concomitant reactions (e.g., electron donor fermentation, sulfate reduction, pH buffering by calcite dissolution) were simulated. Local and global sensitivity analysis techniques were applied to delineate the dominant model parameters and processes. Sensitivity analysis indicated that accurate values for parameters related to dichloroethene (DCE) and vinyl chloride (VC) degradation (i.e., DCE and VC maximum utilization rates, yield due to DCE utilization, decay rate for DCE/VC dechlorinators) are important for prediction of the overall dechlorination time. These parameters influence the maximum growth rate of the DCE and VC dechlorinating microorganisms and, thus, the time required for a small initial population to reach a sufficient concentration to significantly affect the overall rate of dechlorination. Self-inhibition of chlorinated ethenes at high concentrations and natural buffering provided by the sediment were also shown to significantly influence the dechlorination time. Furthermore, the analysis indicated that the rates of the competing, nonchlorinated electron-accepting processes relative to the dechlorination kinetics also affect the overall dechlorination time. Results demonstrated that the model developed is a flexible research tool that is able to provide valuable insight into the fundamental processes and their complex interactions during bioremediation of chlorinated ethenes in DNAPL source zones.

Carbonate precipitation under bulk acidic conditions as a potential biosignature for searching life on Mars

NASA Astrophysics Data System (ADS)

Fernández-Remolar, David C.; Preston, Louisa J.; Sánchez-Román, Mónica; Izawa, Matthew R. M.; Huang, L.; Southam, Gordon; Banerjee, Neil R.; Osinski, Gordon R.; Flemming, Roberta; Gómez-Ortíz, David; Prieto Ballesteros, Olga; Rodríguez, Nuria; Amils, Ricardo; Darby Dyar, M.

2012-10-01

Recent observations of carbonate minerals in ancient Martian rocks have been interpreted as evidence for the former presence of circumneutral solutions optimal for carbonate precipitation. Sampling from surface and subsurface regions of the low-pH system of Río Tinto has shown, unexpectedly, that carbonates can form under diverse macroscopic physicochemical conditions ranging from very low to neutral pH (1.5-7.0). A multi-technique approach demonstrates that carbonate minerals are closely associated with microbial activity. Carbonates occur in the form of micron-size carbonate precipitates under bacterial biofilms, mineralization of subsurface colonies, and possible biogenic microstructures including globules, platelets and dumbbell morphologies. We propose that carbonate precipitation in the low-pH environment of Río Tinto is a process enabled by microbially-mediated neutralization driven by the reduction of ferric iron coupled to the oxidation of biomolecules in microbially-maintained circumneutral oases, where the local pH (at the scale of cells or cell colonies) can be much different than in the macroscopic environment. Acidic conditions were likely predominant in vast regions of Mars over the last four billion years of planetary evolution. Ancient Martian microbial life inhabiting low-pH environments could have precipitated carbonates similar to those observed at Río Tinto. Preservation of carbonates at Río Tinto over geologically significant timescales suggests that similarly-formed carbonate minerals could also be preserved on Mars. Such carbonates could soon be observed by the Mars Science Laboratory, and by future missions to the red planet.

Biogeochemical Signals from Deep Microbial Life in Terrestrial Crust

PubMed Central

Fukuda, Akari; Komatsu, Daisuke D.; Hirota, Akinari; Watanabe, Katsuaki; Togo, Yoko; Morikawa, Noritoshi; Hagiwara, Hiroki; Aosai, Daisuke; Iwatsuki, Teruki; Tsunogai, Urumu; Nagao, Seiya; Ito, Kazumasa; Mizuno, Takashi

2014-01-01

In contrast to the deep subseafloor biosphere, a volumetrically vast and stable habitat for microbial life in the terrestrial crust remains poorly explored. For the long-term sustainability of a crustal biome, high-energy fluxes derived from hydrothermal circulation and water radiolysis in uranium-enriched rocks are seemingly essential. However, the crustal habitability depending on a low supply of energy is unknown. We present multi-isotopic evidence of microbially mediated sulfate reduction in a granitic aquifer, a representative of the terrestrial crust habitat. Deep meteoric groundwater was collected from underground boreholes drilled into Cretaceous Toki granite (central Japan). A large sulfur isotopic fractionation of 20–60‰ diagnostic to microbial sulfate reduction is associated with the investigated groundwater containing sulfate below 0.2 mM. In contrast, a small carbon isotopic fractionation (<30‰) is not indicative of methanogenesis. Except for 2011, the concentrations of H2 ranged mostly from 1 to 5 nM, which is also consistent with an aquifer where a terminal electron accepting process is dominantly controlled by ongoing sulfate reduction. High isotopic ratios of mantle-derived 3He relative to radiogenic 4He in groundwater and the flux of H2 along adjacent faults suggest that, in addition to low concentrations of organic matter (<70 µM), H2 from deeper sources might partly fuel metabolic activities. Our results demonstrate that the deep biosphere in the terrestrial crust is metabolically active and playing a crucial role in the formation of reducing groundwater even under low-energy fluxes. PMID:25517230

Biochar and microbial signaling: production conditions determine effects on microbial communication.

PubMed

Masiello, Caroline A; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R; Rudgers, Jennifer A; Wagner, Daniel S; Zygourakis, Kyriacos; Silberg, Jonathan J

2013-10-15

Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700 °C (surface area of 301 m(2)/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300 °C (surface area of 3 m(2)/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops.

Biochar and microbial signaling: production conditions determine effects on microbial communication

PubMed Central

Masiello, Caroline A.; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R.; Rudgers, Jennifer A.; Wagner, Daniel S.; Zygourakis, Kyriacos; Silberg, Jonathan J.

2013-01-01

Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700°C (surface area of 301 m2/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300°C (surface area of 3 m2/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops. PMID:24066613

Microbiome-mediated bile acid modification: Role in intestinal drug absorption and metabolism.

PubMed

Enright, Elaine F; Griffin, Brendan T; Gahan, Cormac G M; Joyce, Susan A

2018-04-13

Once regarded obscure and underappreciated, the gut microbiota (the microbial communities colonizing the gastrointestinal tract) is gaining recognition as an influencer of many aspects of human health. Also increasingly apparent is the breadth of interindividual variation in these co-evolved microbial-gut associations, presenting novel quests to explore implications for disease and therapeutic response. In this respect, the unearthing of the drug-metabolizing capacity of the microbiota has provided impetus for the integration of microbiological and pharmacological research. This review considers a potential mechanism, 'microbial bile acid metabolism', by which the intricate interplay between the host and gut bacteria may influence drug pharmacokinetics. Bile salts traditionally regarded as biological surfactants, synthesized by the host and biotransformed by gut bacteria, are now also recognized as signalling molecules that affect diverse physiological processes. Accumulating data indicate that bile salts are not equivalent with respect to their physicochemical properties, micellar solubilization capacities for poorly water-soluble drugs, crystallization inhibition tendencies nor potencies for bile acid receptor activation. Herein, the origin, physicochemical properties, physiological functions, plasticity and pharmaceutical significance of the human bile acid pool are discussed. Microbial dependant differences in the composition of the human bile acid pool, simulated intestinal media and commonly used preclinical species is highlighted to better understand in vivo performance predictiveness. While the precise impact of an altered gut microbiome, and consequently bile acid pool, in the biopharmaceutical setting remains largely elusive, the objective of this article is to aid knowledge acquisition through a detailed review of the literature. Copyright © 2018 Elsevier Ltd. All rights reserved.

Non-enzymatic palladium recovery on microbial and synthetic surfaces.

PubMed

Rotaru, Amelia-Elena; Jiang, Wei; Finster, Kai; Skrydstrup, Troels; Meyer, Rikke Louise

2012-08-01

The use of microorganisms as support for reduction of dissolved Pd(II) to immobilized Pd(0) nanoparticles is an environmentally friendly approach for Pd recovery from waste. To better understand and engineer Pd(0) nanoparticle synthesis, one has to consider the mechanisms by which Pd(II) is reduced on microbial surfaces. Escherichia coli, Shewanella oneidensis, and Pseudomonas putida were used as model organisms in order to elucidate the role of microbial cells in Pd(II) reduction under acidic conditions. Pd(II) was reduced by formate under acidic conditions, and the process occurred substantially faster in the presence of cells as compared to cell-free controls. We found no difference between native (untreated) and autoclaved cells, and could demonstrate that even a non-enzymatic protein (bovine serum albumin) stimulated Pd(II) reduction as efficiently as bacterial cells. Amine groups readily interact with Pd(II), and to specifically test their role in surface-assisted Pd(II) reduction by formate, we replaced bacterial cells with polystyrene microparticles functionalized with amine or carboxyl groups. Amine-functionalized microparticles had the same effect on Pd(II) reduction as bacterial cells, and the effect could be hampered if the amine groups were blocked by acetylation. The interaction with amine groups was confirmed by infrared spectroscopy on whole cells and amine-functionalized microparticles. In conclusion, bio-supported Pd(II) reduction on microbial surfaces is possibly mediated by a non-enzymatic mechanism. We therefore suggest the use of amine-rich biomaterials rather than intact cells for Pd bio-recovery from waste. Copyright © 2012 Wiley Periodicals, Inc.

Controlling Microbial Byproducts using Model-Based Substrate Monitoring and Control Strategies

NASA Technical Reports Server (NTRS)

Smernoff, David T.; Blackwell, Charles; Mancinelli, Rocco L.; DeVincenzi, Donald (Technical Monitor)

2000-01-01

We have developed a computer-controlled bioreactor system to study various aspects of microbially-mediated nitrogen cycling. The system has been used to investigate methods for controlling microbial denitrification (the dissimilatory reduction of nitrate to N2O and N2) in hydroponic plant growth chambers. Such chambers are key elements of advanced life support systems being designed for use on long duration space missions, but nitrogen use efficiency in them is reduced by denitrification. Control software architecture was designed which permits the heterogeneous control of system hardware using traditional feedback control, and quantitative and qualitative models of various system features. Model-based feed forward control entails prediction of future systems in states and automated regulation of system parameters to achieve desired and avoid undesirable system states. A bacterial growth rate model based on the classic Monod model of saturation kinetics was used to evaluate the response of several individual denitrifying species to varying environmental conditions. The system and models are now being applied to mixed microbial communities harvested from the root zone of a hydroponic growth chamber. The use of a modified Monod organism interaction model was evaluated as a means of achieving more accurate description of the dynamic behavior of the communities. A minimum variance parameter estimation routine was also' used to calibrate the constant parameters in the model by iterative evaluation of substrate (nitrate) uptake and growth kinetics. This representation of processes and interactions aids in the formulation of control laws. The feed forward control strategy being developed will increase system autonomy, reduce crew intervention and limit the accumulation of undesirable waste products (NOx).

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

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

PubMed

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

2015-06-15

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

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.

pH-Dependent Activation of Streptomyces hygroscopicus Transglutaminase Mediated by Intein

PubMed Central

Du, Kun; Liu, Zhongmei; Cui, Wenjing; Zhou, Li; Liu, Yi; Chen, Jian

2014-01-01

Microbial transglutaminase (MTG) from Streptomyces is naturally secreted as a zymogen (pro-MTG), which is then activated by the removal of its N-terminal proregion by additional proteases. Inteins are protein-intervening sequences that catalyze protein splicing without cofactors. In this study, a pH-dependent Synechocystis sp. strain PCC6803 DnaB mini-intein (SDB) was introduced into pro-MTG to simplify its activation process by controlling pH. The recombinant protein (pro-SDB-MTG) was obtained, and the activation process was determined to take 24 h at pH 7 in vitro. To investigate the effect of the first residue in MTG on the activity and the cleavage time, two variants, pro-SDB-MTG(D1S) and pro-SDB-MTG(ΔD1), were expressed, and the activation time was found to be 6 h and 30 h, respectively. The enzymatic property and secondary structure of the recombinant MTG and two variants were similar to those of the wild type, indicating that the insertion of mini-intein did not affect the function of MTG. This insignificant effect was further illustrated by molecular dynamics simulations. This study revealed a controllable and effective strategy to regulate the activation process of pro-MTG mediated by a mini-intein, and it may have great potential for industrial MTG production. PMID:24242235

Changes in optical characteristics of surface microlayers hint to photochemically and microbially mediated DOM turnover in the upwelling region off the coast of Peru

NASA Astrophysics Data System (ADS)

Galgani, Luisa; Engel, Anja

2016-04-01

The coastal upwelling system off the coast of 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. From 3 to 23 December 2012, R/V Meteor (M91) cruise took place in the Peruvian upwelling system between 4.59 and 15.4° S, and 82.0 to 77.5° W. During M91 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. We analyzed SML and underlying water (ULW) samples at 38 stations focusing on CDOM spectral characteristics as indicator of photochemical and microbial alteration processes. CDOM composition was characterized by spectral slope (S) values and excitation-emission matrix fluorescence (EEMs), which allow us to track changes in molecular weight (MW) of DOM, and to determine potential DOM sources and sinks. Spectral slope S varied between 0.012 to 0.043 nm-1 and was quite similar between SML and ULW, with no significant differences between the two compartments. Higher S values were observed in the ULW of the southern stations below 15° S. By EEMs, we identified five fluorescent components (F1-5) of the CDOM pool, of which two had excitation/emission characteristics of amino-acid-like fluorophores (F1, F4) and were highly enriched in the SML, with a median ratio SML : ULW of 1.5 for both fluorophores. In the study region, values for CDOM absorption ranged from 0.07 to 1.47 m-1. CDOM was generally highly concentrated in the SML, with a median enrichment with respect to the ULW of 1.2. CDOM composition and changes in spectral slope properties suggested a local microbial release of DOM directly in the SML as a response to light exposure in this extreme environment. In a conceptual model of the sources and modifications of optically active DOM in the SML and underlying seawater (ULW), we describe processes we think may take place (Fig. 1); the production of CDOM of higher MW by microbial release through growth, exudation and lysis in the euphotic zone, includes the identified fluorophores (F1, F2, F3, F4, F5). Specific amino-acid-like fluorophores (F1, F4) accumulate in the SML with respect to the ULW, as photochemistry may enhance microbial CDOM release by (a) photoprotection mechanisms and (b) cell-lysis processes. Microbial and photochemical degradation are potential sinks of the amino-acid-like fluorophores (F1, F4), and potential sources of reworked and more refractory humic-like components (F2, F3, F5). In the highly productive upwelling region along the Peruvian coast, the interplay of microbial and photochemical processes controls the enrichment of amino-acid-like CDOM in the SML. We discuss potential implications for air-sea gas exchange in this area.

Yeast surface display of dehydrogenases in microbial fuel-cells.

PubMed

Gal, Idan; Schlesinger, Orr; Amir, Liron; Alfonta, Lital

2016-12-01

Two dehydrogenases, cellobiose dehydrogenase from Corynascus thermophilus and pyranose dehydrogenase from Agaricus meleagris, were displayed for the first time on the surface of Saccharomyces cerevisiae using the yeast surface display system. Surface displayed dehydrogenases were used in a microbial fuel cell and generated high power outputs. Surface displayed cellobiose dehydrogenase has demonstrated a midpoint potential of -28mV (vs. Ag/AgCl) at pH=6.5 and was used in a mediator-less anode compartment of a microbial fuel cell producing a power output of 3.3μWcm(-2) using lactose as fuel. Surface-displayed pyranose dehydrogenase was used in a microbial fuel cell and generated high power outputs using different substrates, the highest power output that was achieved was 3.9μWcm(-2) using d-xylose. These results demonstrate that surface displayed cellobiose dehydrogenase and pyranose dehydrogenase may successfully be used in microbial bioelectrochemical systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Ecological feedback in quorum-sensing microbial populations can induce heterogeneous production of autoinducers

PubMed Central

Bauer, Matthias; Knebel, Johannes; Lechner, Matthias; Pickl, Peter; Frey, Erwin

2017-01-01

Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via ‘quorum sensing’. Elucidating the mechanisms that control autoinducer production is, thus, pertinent to understanding collective microbial behavior, such as virulence and bioluminescence. Recent experiments have shown a heterogeneous promoter activity of autoinducer synthase genes, suggesting that some of the isogenic cells in a population might produce autoinducers, whereas others might not. However, the mechanism underlying this phenotypic heterogeneity in quorum-sensing microbial populations has remained elusive. In our theoretical model, cells synthesize and secrete autoinducers into the environment, up-regulate their production in this self-shaped environment, and non-producers replicate faster than producers. We show that the coupling between ecological and population dynamics through quorum sensing can induce phenotypic heterogeneity in microbial populations, suggesting an alternative mechanism to stochastic gene expression in bistable gene regulatory circuits. DOI: http://dx.doi.org/10.7554/eLife.25773.001 PMID:28741470

Using dispersants after oil spills: impacts on the composition and activity of microbial communities.

PubMed

Kleindienst, Sara; Paul, John H; Joye, Samantha B

2015-06-01

Dispersants are globally and routinely applied as an emergency response to oil spills in marine ecosystems with the goal of chemically enhancing the dissolution of oil into water, which is assumed to stimulate microbially mediated oil biodegradation. However, little is known about how dispersants affect the composition of microbial communities or their biodegradation activities. The published findings are controversial, probably owing to variations in laboratory methods, the selected model organisms and the chemistry of different dispersant-oil mixtures. Here, we argue that an in-depth assessment of the impacts of dispersants on microorganisms is needed to evaluate the planning and use of dispersants during future responses to oil spills.

Potential for Mercury Reduction by Microbes in the High Arctic▿

PubMed Central

Poulain, Alexandre J.; Ní Chadhain, Sinéad M.; Ariya, Parisa A.; Amyot, Marc; Garcia, Edenise; Campbell, Peter G. C.; Zylstra, Gerben J.; Barkay, Tamar

2007-01-01

The contamination of polar regions due to the global distribution of anthropogenic pollutants is of great concern because it leads to the bioaccumulation of toxic substances, methylmercury among them, in Arctic food chains. Here we present the first evidence that microbes in the high Arctic possess and express diverse merA genes, which specify the reduction of ionic mercury [Hg(II)] to the volatile elemental form [Hg(0)]. The sampled microbial biomass, collected from microbial mats in a coastal lagoon and from the surface of marine macroalgae, was comprised of bacteria that were most closely related to psychrophiles that had previously been described in polar environments. We used a kinetic redox model, taking into consideration photoredox reactions as well as mer-mediated reduction, to assess if the potential for Hg(II) reduction by Arctic microbes can affect the toxicity and environmental mobility of mercury in the high Arctic. Results suggested that mer-mediated Hg(II) reduction could account for most of the Hg(0) that is produced in high Arctic waters. At the surface, with only 5% metabolically active cells, up to 68% of the mercury pool was resolved by the model as biogenic Hg(0). At a greater depth, because of incident light attenuation, the significance of photoredox transformations declined and merA-mediated activity could account for up to 90% of Hg(0) production. These findings highlight the importance of microbial redox transformations in the biogeochemical cycling, and thus the toxicity and mobility, of mercury in polar regions. PMID:17293515

Characterization of mediators of microbial virulence and innate immunity using the Caenorhabditis elegans host-pathogen model.

PubMed

Alegado, Rosanna A; Campbell, Marianne C; Chen, Will C; Slutz, Sandra S; Tan, Man-Wah

2003-07-01

The soil-borne nematode, Caenorhabditis elegans, is emerging as a versatile model in which to study host-pathogen interactions. The worm model has shown to be particularly effective in elucidating both microbial and animal genes involved in toxin-mediated killing. In addition, recent work on worm infection by a variety of bacterial pathogens has shown that a number of virulence regulatory genes mediate worm susceptibility. Many of these regulatory genes, including the PhoP/Q two-component regulators in Salmonella and LasR in Pseudomonas aeruginosa, have also been implicated in mammalian models suggesting that findings in the worm model will be relevant to other systems. In keeping with this concept, experiments aimed at identifying host innate immunity genes have also implicated pathways that have been suggested to play a role in plants and animals, such as the p38 MAP kinase pathway. Despite rapid forward progress using this model, much work remains to be done including the design of more sensitive methods to find effector molecules and further characterization of the exact interaction between invading pathogens and C. elegans' cellular components.

A microbial fuel cell operating at low pH using an acidophile, Acidiphilium cryptum.

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

Borole, Abhijeet P; Cesar, Scott A; O'Neill, Hugh Michael

2008-01-01

A microbial fuel cell using an acidophilic microorganism, Acidiphilium cryptum, as the anode biocatalyst was investigated. The mode of electron transfer by this organism to the electrode was studied. Electricity production in the presence of a mediator was demonstrated using its natural electron acceptor, iron, as well as phenosafranin as the electron mediating agent. Production of Fe(II), as a result of iron reduction, at a pH of 4.0 or below was found to support electricity production. Accumulation of the oxidized iron, Fe(III) as a result of electron donation to the electrode, however, restricted higher current output. Addition of nitrilotriacetic acidmore » helped resolve the problem by redissolution of deposited Fe(III). Further, use of phenosafranin as a secondary mediator resulted in improvement in power output. At a cell loading equivalent to OD600 of 1.0, a power output of 12.7 mW/m2 was obtained in a two-chamber air-sparged fuel cell. Potential for direct electron transfer was also investigated but not detected under the conditions studied.« less

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.

Effects of Bacillus subtilis endospore surface reactivity on the rate of forsterite dissolution

NASA Astrophysics Data System (ADS)

Harrold, Z.; Gorman-Lewis, D.

2013-12-01

Primary mineral dissolution products, such as silica (Si), calcium (Ca) and magnesium (Mg), play an important role in numerous biologic and geochemical cycles including microbial metabolism, plant growth and secondary mineral precipitation. The flux of these and other dissolution products into the environment is largely controlled by the rate of primary silicate mineral dissolution. Bacteria, a ubiquitous component in water-rock systems, are known to facilitate mineral dissolution and may play a substantial role in determining the overall flux of dissolution products into the environment. Bacterial cell walls are complex and highly reactive organic surfaces that can affect mineral dissolution rates directly through microbe-mineral adsorption or indirectly by complexing dissolution products. The effect of bacterial surface adsorption on chemical weathering rates may even outweigh the influence of active processes in environments where a high proportion of cells are metabolically dormant or cell metabolism is slow. Complications associated with eliminating or accounting for ongoing metabolic processes in long-term dissolution studies have made it challenging to isolate the influence of cell wall interactions on mineral dissolution rates. We utilized Bacillus subtilis endospores, a robust and metabolically dormant cell type, to isolate and quantify the effects of bacterial surface reactivity on forsterite (Mg2SiO4) dissolution rates. We measured the influence of both direct and indirect microbe-mineral interactions on forsterite dissolution. Indirect pathways were isolated using dialysis tubing to prevent mineral-microbe contact while allowing free exchange of dissolved mineral products and endospore-ion adsorption. Homogenous experimental assays allowed both direct microbe-mineral and indirect microbe-ion interactions to affect forsterite dissolution rates. Dissolution rates were calculated based on silica concentrations and zero-order dissolution kinetics. Additional analyses including Mg concentrations, microprobe and BET analyses support mineral dissolution rate calculations and stoichiometry considerations. All experimental assays containing endospores show increased forsterite dissolution rates relative to abiotic controls. Forsterite dissolution rates increased by approximately one order of magnitude in dialysis bound, biotic experiments relative to abiotic assays. Homogenous biotic assays exhibited a more complex dissolution rate profile that changes over time. All microbially mediated forsterite dissolution rates returned to abiotic control rates after 10 to 15 days of incubation. This shift in dissolution rate likely corresponds to maximum endospore surface adsorption capacity. The Bacillus subtilis endospore surface serves as a first-order proxy for studying the effect of metabolizing microbe surfaces on silicate dissolution rates. Comparisons with published abiotic, microbial, and organic acid mediated forsterite dissolution rates will provide insight on the importance of bacterial surfaces in primary mineral dissolution processes.

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...

Dissolution of Calcite in the Twilight Zone: Bacterial Control of Dissolution of Sinking Planktonic Carbonates Is Unlikely

PubMed Central

Bissett, Andrew; Neu, Thomas R.; de Beer, Dirk

2011-01-01

We investigated the ability of bacterial communities to colonize and dissolve two biogenic carbonates (Foraminifera and oyster shells). Bacterial carbonate dissolution in the upper water column is postulated to be driven by metabolic activity of bacteria directly colonising carbonate surfaces and the subsequent development of acidic microenvironments. We employed a combination of microsensor measurements, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM) and image analysis and molecular documentation of colonising bacteria to monitor microbial processes and document changes in shell surface topography. Bacterial communities rapidly colonised shell surfaces, forming dense biofilms with extracellular polymeric substance (EPS) deposits. Despite this, we found no evidence of bacterially mediated carbonate dissolution. Dissolution was not indicated by Ca2+ microprofiles, nor was changes in shell surface structure related to the presence of colonizing bacteria. Given the short time (days) settling carbonate material is actually in the twilight zone (500–1000 m), it is highly unlikely that microbial metabolic activity on directly colonised shells plays a significant role in dissolving settling carbonates in the shallow ocean. PMID:22102861

Dissolution of calcite in the twilight zone: bacterial control of dissolution of sinking planktonic carbonates is unlikely.

PubMed

Bissett, Andrew; Neu, Thomas R; Beer, Dirk de

2011-01-01

We investigated the ability of bacterial communities to colonize and dissolve two biogenic carbonates (Foraminifera and oyster shells). Bacterial carbonate dissolution in the upper water column is postulated to be driven by metabolic activity of bacteria directly colonising carbonate surfaces and the subsequent development of acidic microenvironments. We employed a combination of microsensor measurements, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM) and image analysis and molecular documentation of colonising bacteria to monitor microbial processes and document changes in shell surface topography. Bacterial communities rapidly colonised shell surfaces, forming dense biofilms with extracellular polymeric substance (EPS) deposits. Despite this, we found no evidence of bacterially mediated carbonate dissolution. Dissolution was not indicated by Ca²⁺ microprofiles, nor was changes in shell surface structure related to the presence of colonizing bacteria. Given the short time (days) settling carbonate material is actually in the twilight zone (500-1000 m), it is highly unlikely that microbial metabolic activity on directly colonised shells plays a significant role in dissolving settling carbonates in the shallow ocean.

Self-organization of dissolved organic matter to micelle-like microparticles in river water.

PubMed

Kerner, Martin; Hohenberg, Heinz; Ertl, Siegmund; Reckermann, Marcus; Spitzy, Alejandro

2003-03-13

In aquatic systems, the concept of the 'microbial loop' is invoked to describe the conversion of dissolved organic matter to particulate organic matter by bacteria. This process mediates the transfer of energy and matter from dissolved organic matter to higher trophic levels, and therefore controls (together with primary production) the productivity of aquatic systems. Here we report experiments on laboratory incubations of sterile filtered river water in which we find that up to 25% of the dissolved organic carbon (DOC) aggregates abiotically to particles of diameter 0.4-0.8 micrometres, at rates similar to bacterial growth. Diffusion drives aggregation of low- to high-molecular-mass DOC and further to larger micelle-like microparticles. The chemical composition of these microparticles suggests their potential use as food by planktonic bacterivores. This pathway is apparent from differences in the stable carbon isotope compositions of picoplankton and the microparticles. A large fraction of dissolved organic matter might therefore be channelled through microparticles directly to higher trophic levels--bypassing the microbial loop--suggesting that current concepts of carbon conversion in aquatic systems require revision.

Inflammation and cellular stress: a mechanistic link between immune-mediated and metabolically driven pathologies.

PubMed

Rath, Eva; Haller, Dirk

2011-06-01

Multiple cellular stress responses have been implicated in chronic diseases such as obesity, diabetes, cardiovascular, and inflammatory bowel diseases. Even though phenotypically different, chronic diseases share cellular stress signaling pathways, in particular endoplasmic reticulum (ER) unfolded protein response (UPR). The purpose of the ER UPR is to restore ER homeostasis after challenges of the ER function. Among the triggers of ER UPR are changes in the redox status, elevated protein synthesis, accumulation of unfolded or misfolded proteins, energy deficiency and glucose deprivation, cholesterol depletion, and microbial signals. Numerous mouse models have been used to characterize the contribution of ER UPR to several pathologies, and ER UPR-associated signaling has also been demonstrated to be relevant in humans. Additionally, recent evidence suggests that the ER UPR is interrelated with metabolic and inflammatory pathways, autophagy, apoptosis, and mitochondrial stress signaling. Furthermore, microbial as well as nutrient sensing is integrated into the ER-associated signaling network. The data discussed in the present review highlight the interaction of ER UPR with inflammatory pathways, metabolic processes and mitochondrial function, and their interrelation in the context of chronic diseases.

Degradation of azo dyes by environmental microorganisms and helminths

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

Kingthom Chung; Stevens, S.E. Jr.

1993-11-01

The degradation of azo dyes by environmental microorganisms, fungi, and helminths is reviewed. Azo dyes are used in a wide variety of products and can be found in the effluent of most sewage treatment facilities. Substantial quantities of these dyes have been deposited in the environment, particularly in streams and rivers. Azo dyes were shown to affect microbial activities and microbial population sizes in the sediments and in the water columns of aquatic habitats. Only a few aerobic bacteria have been found to reduce azo dyes under aerobic conditions, and little is known about the process. A substantial number ofmore » anaerobic bacteria capable of azo dye reduction have been reported. The enzyme responsible for azo dye reduction has been partially purified, and characterization of the enzyme is proceeding. The nematode Ascaris lumbricoides and the cestode Moniezia expanza have been reported to reduce azo dyes anaerobically. Recently the fungus Phanerochaete chrysoporium was reported to mineralize azo dyes via a peroxidation-mediated pathway. A possible degradation pathway for the mineralization of azo dye is proposed and future research needs are discussed.« less

Microbially mediated mineral carbonation

NASA Astrophysics Data System (ADS)

Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

2010-12-01

Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily implemented and economically efficient alternative to other technologies currently under development for mineral sequestration. Dismukes GC, Carrieri D, Bennette N, Ananyev GM, Posewitz MC (2008) Aquatic phototrophs: efficient alternatives to land-based crops for biofuels. Current Opinion in Biotechnology, 19, 235-240. Ferris FG, Wiese RG, Fyfe WS (1994) Precipitation of carbonate minerals by microorganisms: Implications of silicate weathering and the global carbon dioxide budget. Geomicrobiology Journal, 12, 1-13. Lackner KS, Wendt CH, Butt DP, Joyce EL, Jr., Sharp DH (1995) Carbon dioxide disposal in carbonate minerals. Energy, 20, 1153-1170. Power IM, Wilson SA, Thom JM, Dipple GM, Gabites JE, Southam G (2009) The hydromagnesite playas of Atlin, British Columbia, Canada: A biogeochemical model for CO2 sequestration. Chemical Geology, 206, 302-316. Thompson JB, Ferris FG (1990) Cyanobacterial precipitation of gypsum, calcite, and magnesite from natural alkaline lake water. Geology, 18, 995-998.

Hematite Reduction Buffers Acid Generation and Enhances Nutrient Uptake by a Fermentative Iron Reducing Bacterium, Orenia metallireducens Strain Z6.

PubMed

Dong, Yiran; Sanford, Robert A; Chang, Yun-Juan; McInerney, Michael J; Fouke, Bruce W

2017-01-03

Fermentative iron-reducing organisms have been identified in a variety of environments. Instead of coupling iron reduction to respiration, they have been consistently observed to use ferric iron minerals as an electron sink for fermentation. In the present study, a fermentative iron reducer, Orenia metallireducens strain Z6, was shown to use iron reduction to enhance fermentation not only by consuming electron equivalents, but also by generating alkalinity that effectively buffers the pH. Fermentation of glucose by this organism in the presence of a ferric oxide mineral, hematite (Fe 2 O 3 ), resulted in enhanced glucose decomposition compared with fermentation in the absence of an iron source. Parallel evidence (i.e., genomic reconstruction, metabolomics, thermodynamic analyses, and calculation of electron transfer) suggested hematite reduction as a proton-consuming reaction effectively consumed acid produced by fermentation. The buffering effect of hematite was further supported by a greater extent of glucose utilization by strain Z6 in media with increasing buffer capacity. Such maintenance of a stable pH through hematite reduction for enhanced glucose fermentation complements the thermodynamic interpretation of interactions between microbial iron reduction and other biogeochemical processes. This newly discovered feature of iron reducer metabolism also has significant implications for groundwater management and contaminant remediation by providing microbially mediated buffering systems for the associated microbial and/or chemical reactions.

Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218 microbial consortia are not correlated to cell surface hydrophobicity.

PubMed

Owsianiak, Mikołaj; Szulc, Alicja; Chrzanowski, Łukasz; Cyplik, Paweł; Bogacki, Mariusz; Olejnik-Schmidt, Agnieszka K; Heipieper, Hermann J

2009-09-01

In this study, we elucidated the role of cell surface hydrophobicity (microbial adhesion to hydrocarbons method, MATH) and the effect of anionic rhamnolipids and nonionic Triton X-100 surfactants on biodegradation of diesel fuel employing 218 microbial consortia isolated from petroleum-contaminated soils. Applied enrichment procedure with floating diesel fuel as a sole carbon source in liquid cultures resulted in consortia of varying biodegradation potential and diametrically different cell surface properties, suggesting that cell surface hydrophobicity is a conserved parameter. Surprisingly, no correlations between cell surface hydrophobicity and biodegradation of diesel fuel were found. Nevertheless, both surfactants altered cell surface hydrophobicity of the consortia in similar manner: increased for the hydrophilic and decreased for the hydrophobic cultures. In addition to this, the surfactants exhibited similar influence on diesel fuel biodegradation: Increase was observed for initially slow-degrading cultures and the opposite for fast degraders. This indicates that in the surfactant-mediated biodegradation, effectiveness of surfactants depends on the specification of microorganisms and not on the type of surfactant. In contrary to what was previously reported for pure strains, cell surface hydrophobicity, as determined by MATH, is not a good descriptor of biodegrading potential for mixed cultures.

The development of Fe-nodules surrounding biological material mediated by microorganisms

NASA Astrophysics Data System (ADS)

Yoshida, Hidekazu; Yamamoto, Koshi; Murakami, Yuki; Katsuta, Nagayoshi; Hayashi, Toru; Naganuma, Takeshi

2008-09-01

Takashikozo is a phenomenon of Quaternary sediments in Japan. They are cylindrical Fe-oxyhydroxide nodules that form as plaques round plant roots, where Fe is preferentially concentrated to develop a solid wall. Structural features suggest that after the roots have decayed, the central space where the roots were situated acts as a flow path for oxidized water. Analysis of microbial 16S rDNA extracted from the nodules identified iron-oxidizing bacteria encrusted round the roots where they are the likely initiators of nodule formation. Direct microscopic observation revealed an accumulation of Fe-oxyhydroxides that fill the pore spaces and is also likely to be linked with the encrusting microbial colonies. Geological history and nanofossil evidence suggest that these Fe-nodules may have been buried at a depth of up to several tens of meters for at least 105 years in reducing Quaternary sediments. Thus Fe-oxyhydroxide nodules that have formed in a geological environment at the interfaces between water and rock by microbial mediation can persist under reducing conditions. If this is the case, the phenomenon is significant as an analogue of post-closure conditions in radioactive waste repositories, since it could influence nuclide migration.

Candida albicans Pathogenesis: Fitting within the Host-Microbe Damage Response Framework

PubMed Central

Kong, Eric F.; Tsui, Christina; Nguyen, M. Hong; Clancy, Cornelius J.; Fidel, Paul L.; Noverr, Mairi

2016-01-01

Historically, the nature and extent of host damage by a microbe were considered highly dependent on virulence attributes of the microbe. However, it has become clear that disease is a complex outcome which can arise because of pathogen-mediated damage, host-mediated damage, or both, with active participation from the host microbiota. This awareness led to the formulation of the damage response framework (DRF), a revolutionary concept that defined microbial virulence as a function of host immunity. The DRF outlines six classifications of host damage outcomes based on the microbe and the strength of the immune response. In this review, we revisit this concept from the perspective of Candida albicans, a microbial pathogen uniquely adapted to its human host. This fungus commonly colonizes various anatomical sites without causing notable damage. However, depending on environmental conditions, a diverse array of diseases may occur, ranging from mucosal to invasive systemic infections resulting in microbe-mediated and/or host-mediated damage. Remarkably, C. albicans infections can fit into all six DRF classifications, depending on the anatomical site and associated host immune response. Here, we highlight some of these diverse and site-specific diseases and how they fit the DRF classifications, and we describe the animal models available to uncover pathogenic mechanisms and related host immune responses. PMID:27430274

[Competition between redox mediator and oxygen in the microbial fuel cell].

PubMed

Alferov, S V; Vozchikova, S V; Arlyapov, V A; Alferov, V A; Reshetilov, A N

2017-01-01

The maximal rates and effective constants of 2,6-dichlorphenolindophenol and oxygen reduction by bacterim Gluconobacter oxydans in bacterial fuel cells under different conditions were evaluated. In an open-circuit mode, the rate of 2,6-dichlorphenolindophenol reduction coupled with ethanol oxidation under oxygen and nirogen atmospheres were 1.0 and 1.1 μM s–1 g–1, respectively. In closed-circuit mode, these values were 0.4 and 0.44 μM s–1 g–1, respectively. The initial rate of mediator reduction with the use of membrane fractions of bacteria in oxygen and nitrogen atmospheres in open-circuit mode were 6.3 and 6.9 μM s–1 g–1, whereas these values in closed-circuit mode comprised 2.2 and 2.4 μM s–1 g–1, respectively. The oxygen reduction rates in the presence and absence of 2,6-dichlorphenolindophenol were 0.31 and 0.32 μM s–1 g–1, respectively. The data obtained in this work demonstrated independent electron transfer from bacterial redox centers to the mediator and the absence of competition between the redox mediator and oxygen. The results can make it possible to reduce costs of microbial fuel cells based on activity of acetic acid bacteria G. oxydans.

Immune indexes of larks from desert and temperate regions show weak associations with life history but stronger links to environmental variation in microbial abundance.

PubMed

Horrocks, Nicholas P C; Hegemann, Arne; Matson, Kevin D; Hine, Kathryn; Jaquier, Sophie; Shobrak, Mohammed; Williams, Joseph B; Tinbergen, Joost M; Tieleman, B Irene

2012-01-01

Immune defense may vary as a result of trade-offs with other life-history traits or in parallel with variation in antigen levels in the environment. We studied lark species (Alaudidae) in the Arabian Desert and temperate Netherlands to test opposing predictions from these two hypotheses. Based on their slower pace of life, the trade-off hypothesis predicts relatively stronger immune defenses in desert larks compared with temperate larks. However, as predicted by the antigen exposure hypothesis, reduced microbial abundances in deserts should result in desert-living larks having relatively weaker immune defenses. We quantified host-independent and host-dependent microbial abundances of culturable microbes in ambient air and from the surfaces of birds. We measured components of immunity by quantifying concentrations of the acute-phase protein haptoglobin, natural antibody-mediated agglutination titers, complement-mediated lysis titers, and the microbicidal ability of whole blood. Desert-living larks were exposed to significantly lower concentrations of airborne microbes than temperate larks, and densities of some bird-associated microbes were also lower in desert species. Haptoglobin concentrations and lysis titers were also significantly lower in desert-living larks, but other immune indexes did not differ. Thus, contrary to the trade-off hypothesis, we found little evidence that a slow pace of life predicted increased immunological investment. In contrast, and in support of the antigen exposure hypothesis, associations between microbial exposure and some immune indexes were apparent. Measures of antigen exposure, including assessment of host-independent and host-dependent microbial assemblages, can provide novel insights into the mechanisms underlying immunological variation.

Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides.

PubMed

Thomson, Pamela; Medina, Daniel A; Ortúzar, Verónica; Gotteland, Martín; Garrido, Daniel

2018-07-01

The gut microbiome has a significant impact on host health, especially at the metabolic level. Dietary compounds arriving at the colon have a large influence on the composition of the gut microbiome. High fiber diets have been associated to health benefits that are mediated in great part by short chain fatty acids (SCFA). Gut microbial interactions are relevant for the utilization of complex carbohydrates in the gut microbiome. In this work we characterized the utilization of two dietary polysaccharides by combinations of representative adult gut microbes, and the impact of their activities on a cellular inflammation model. Paired combinations of Bifidobacterium adolescentis, Bacteroides dorei, Lactobacillus plantarum, Escherichia coli and Clostridium symbiosum were grown in inulin or xylan as carbon source. Their relative abundance, substrate consumption and major SCFAs produced were determined. Higher cell growth was observed during inulin consumption, and B. adolescentis and L. plantarum were dominant in co-cultures. The co-culture of B. dorei and C. symbiosum was dominant in xylan. In several cases the combined bacterial growth was lower in co-cultures than monocultures, with a few exceptions of synergistic growth between microorganisms. Inulin fermentation resulted in larger acetate and lactate concentrations, and several combinations grown in xylan containing C. symbiosum were characterized by high amounts of butyrate. These microbial consortia were scaled to batch bioreactor fermentations reaching high cell densities and similar profiles to co-culture experiments. Interestingly, a microbial combination producing high amounts of butyrate was able to reduce IL-8 expression in HT-29 cells co-incubated with TNFα. In summary, this work shows that microbial interactions during the utilization of dietary polysaccharides are complex and substrate dependent. Moreover, certain combinations deploy potent anti-inflammatory effects, which are independent of individual microbial growth, and could be mediated in part by higher butyrate production. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Effect of a Reduction in Microbial Diversity on Greenhouse Gas Production in Alaskan Tundra Soils.

NASA Astrophysics Data System (ADS)

Wagner, R.; Oechel, W. C.; Lipson, D.

2017-12-01

Atmospheric methane accounts for 20% of the warming potential of all greenhouse gases, has increased by 150% since pre-industrial times, and has the potential to double again over the next century. Microbially mediated CH4 emissions from natural wetlands represent the highest uncertainty in relative contributions to atmospheric CH4 levels of all CH4 sources, with Arctic wetlands currently experiencing twice the rate of warming as the rest of the planet. Notwithstanding the central role that the soil microbial community plays, and the high uncertainty in CH4 emissions from this ecosystem, surprisingly little research has been done to directly connect the microbial community structure to methane production rates. This is especially disconcerting given that most current CH4 emission models completely neglect microbial characteristics, despite the fact that the soil microbial community is predicted to be heavily impacted by a changing climate. Here, the effect of an artificial reduction in soil microbial α-diversity was investigated with regard to methane production and respiration rates. The microbial community was serially diluted followed by re-inoculation of sterilized Arctic soils in a mesocosm experiment. Methane production and respiration rates were measured, metagenomic sequencing was performed to determine microbial community diversity measures, and the effect of the oxidation state of iron was investigated. Preliminary results indicate that microbial communities with reduced α-diversity have lowered respiration rates in these soils. Analyses are ongoing and are expected to provide critical observations linking the role of soil microbial community diversity and greenhouse gas production in Arctic tundra ecosystems.

Fosfomycin enhances phagocyte-mediated killing of Staphylococcus aureus by extracellular traps and reactive oxygen species.

PubMed

Shen, Fengge; Tang, Xudong; Cheng, Wei; Wang, Yang; Wang, Chao; Shi, Xiaochen; An, Yanan; Zhang, Qiaoli; Liu, Mingyuan; Liu, Bo; Yu, Lu

2016-01-18

The successful treatment of bacterial infections is the achievement of a synergy between the host's immune defences and antibiotics. Here, we examined whether fosfomycin (FOM) could improve the bactericidal effect of phagocytes, and investigated the potential mechanisms. FOM enhanced the phagocytosis and extra- or intracellular killing of S. aureus by phagocytes. And FOM enhanced the extracellular killing of S. aureus in macrophage (MФ) and in neutrophils mediated by extracellular traps (ETs). ET production was related to NADPH oxidase-dependent reactive oxygen species (ROS). Additionally, FOM increased the intracellular killing of S. aureus in phagocytes, which was mediated by ROS through the oxidative burst process. Our results also showed that FOM alone induced S. aureus producing hydroxyl radicals in order to kill the bacterial cells in vitro. In a mouse peritonitis model, FOM treatment increased the bactericidal extra- and intracellular activity in vivo, and FOM strengthened ROS and ET production from peritoneal lavage fluid ex vivo. An IVIS imaging system assay further verified the observed in vivo bactericidal effect of the FOM treatment. This work may provide a deeper understanding of the role of the host's immune defences and antibiotic interactions in microbial infections.

Fosfomycin enhances phagocyte-mediated killing of Staphylococcus aureus by extracellular traps and reactive oxygen species

PubMed Central

Shen, Fengge; Tang, Xudong; Cheng, Wei; Wang, Yang; Wang, Chao; Shi, Xiaochen; An, Yanan; Zhang, Qiaoli; Liu, Mingyuan; Liu, Bo; Yu, Lu

2016-01-01

The successful treatment of bacterial infections is the achievement of a synergy between the host’s immune defences and antibiotics. Here, we examined whether fosfomycin (FOM) could improve the bactericidal effect of phagocytes, and investigated the potential mechanisms. FOM enhanced the phagocytosis and extra- or intracellular killing of S. aureus by phagocytes. And FOM enhanced the extracellular killing of S. aureus in macrophage (MФ) and in neutrophils mediated by extracellular traps (ETs). ET production was related to NADPH oxidase-dependent reactive oxygen species (ROS). Additionally, FOM increased the intracellular killing of S. aureus in phagocytes, which was mediated by ROS through the oxidative burst process. Our results also showed that FOM alone induced S. aureus producing hydroxyl radicals in order to kill the bacterial cells in vitro. In a mouse peritonitis model, FOM treatment increased the bactericidal extra- and intracellular activity in vivo, and FOM strengthened ROS and ET production from peritoneal lavage fluid ex vivo. An IVIS imaging system assay further verified the observed in vivo bactericidal effect of the FOM treatment. This work may provide a deeper understanding of the role of the host’s immune defences and antibiotic interactions in microbial infections. PMID:26778774

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.

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

The effects of food web structure on ecosystem function exceeds those of precipitation.

PubMed

Trzcinski, M Kurtis; Srivastava, Diane S; Corbara, Bruno; Dézerald, Olivier; Leroy, Céline; Carrias, Jean-François; Dejean, Alain; Céréghino, Régis

2016-09-01

Ecosystems are being stressed by climate change, but few studies have tested food web responses to changes in precipitation patterns and the consequences to ecosystem function. Fewer still have considered whether results from one geographic region can be applied to other regions, given the degree of community change over large biogeographic gradients. We assembled, in one field site, three types of macroinvertebrate communities within water-filled bromeliads. Two represented food webs containing both a fast filter feeder-microbial and slow detritivore energy channels found in Costa Rica and Puerto Rico, and one represented the structurally simpler food webs in French Guiana, which only contained the fast filter feeder-microbial channel. We manipulated the amount and distribution of rain entering bromeliads and examined how food web structure mediated ecosystem responses to changes in the quantity and temporal distribution of precipitation. Food web structure affected the survival of functional groups in general and ecosystem functions such as decomposition and the production of fine particulate organic matter. Ecosystem processes were more affected by decreased precipitation than were the abundance of micro-organisms and metazoans. In our experiments, the sensitivity of the ecosystem to precipitation change was primarily revealed in the food web dominated by the single filter feeder-microbial channel because other top-down and bottom-up processes were weak or absent. Our results show stronger effects of food web structure than precipitation change per se on the functioning of bromeliad ecosystems. Consequently, we predict that ecosystem function in bromeliads throughout the Americas will be more sensitive to changes in the distribution of species, rather than to the direct effects caused by changes in precipitation. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Galectins as self/non-self recognition receptors in innate and adaptive immunity: an unresolved paradox

PubMed Central

Vasta, Gerardo R.; Ahmed, Hafiz; Nita-Lazar, Mihai; Banerjee, Aditi; Pasek, Marta; Shridhar, Surekha; Guha, Prasun; Fernández-Robledo, José A.

2012-01-01

Galectins are characterized by their binding affinity for β-galactosides, a unique binding site sequence motif, and wide taxonomic distribution and structural conservation in vertebrates, invertebrates, protista, and fungi. Since their initial description, galectins were considered to bind endogenous (“self”) glycans and mediate developmental processes and cancer. In the past few years, however, numerous studies have described the diverse effects of galectins on cells involved in both innate and adaptive immune responses, and the mechanistic aspects of their regulatory roles in immune homeostasis. More recently, however, evidence has accumulated to suggest that galectins also bind exogenous (“non-self”) glycans on the surface of potentially pathogenic microbes, parasites, and fungi, suggesting that galectins can function as pattern recognition receptors (PRRs) in innate immunity. Thus, a perplexing paradox arises by the fact that galectins also recognize lactosamine-containing glycans on the host cell surface during developmental processes and regulation of immune responses. According to the currently accepted model for non-self recognition, PRRs recognize pathogens via highly conserved microbial surface molecules of wide distribution such as LPS or peptidoglycan (pathogen-associated molecular patterns; PAMPs), which are absent in the host. Hence, this would not apply to galectins, which apparently bind similar self/non-self molecular patterns on host and microbial cells. This paradox underscores first, an oversimplification in the use of the PRR/PAMP terminology. Second, and most importantly, it reveals significant gaps in our knowledge about the diversity of the host galectin repertoire, and the subcellular targeting, localization, and secretion. Furthermore, our knowledge about the structural and biophysical aspects of their interactions with the host and microbial carbohydrate moieties is fragmentary, and warrants further investigation. PMID:22811679

Microbial biomass and productivity in seagrass beds

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

Moriarty, P.J.W.; Boon, P.I.; Hansen, J.A.

1985-01-01

Different methods for measuring the rates of processes mediated by bacteria in sediments and the rates of bacterial cell production have been compared. In addition, net production of the seagrass Zostera capricorni and bacterial production have been compared and some interrelationships with the nitrogen cycle discussed. Seagrass productivity was estimated by measuring the plastochrone interval using a leaf stapling technique. The average productivity over four seasons was 1.28 +- 0.28 g C/m/sup 2/ day (meand +- standard deviation, n = 4). Bacterial productivity was measured five times throughout a year using the rate of tritiated thymidine incorporated into DNA. Averagemore » values were 33 +- 12 mg C/m/sup 2/ day for sediment and 23 +- 4 for water column (n = 5). Spatial variability between samples was greater than seasonal variation for both seagrass productivity and bacterial productivity. On one occasion, bacterial productivity was measured using the rate of /sup 32/P incorporated into phospholipid. The values were comparable to those obtained with tritiated thymidine. The rate of sulfate reduction was 10 mmol SO/sub 4//m/sup 2/ day. The rate of methanogenesis was low, being 5.6 mg CH/sub 4/ produced/m/sup 2/ day. A comparison of C flux measured using rates of sulfate reduction and DNA synthesis indicated that anaerobic processes were predominant in these sediments. An analysis of microbial biomass and community structure, using techniques of phospholipid analysis, showed that bacteria were predominant members of the microbial biomass and that of these strictly anaerobic bacteria were the main components. Ammonia concentration in interstitial water varied from 23 to 71 ..mu..M. Estimates of the amount of ammonia required by seagrass showed that the ammonia would turn over about once per day. Rapid recycling of nitrogen by bacteria and bacterial grazers is probably important.« less

Degradation of Potassium Rock by Earthworms and Responses of Bacterial Communities in Its Gut and Surrounding Substrates after Being Fed with Mineral

PubMed Central

Liu, Dianfeng; Lian, Bin; Wang, Bin; Jiang, Guofang

2011-01-01

Background Earthworms are an ecosystem's engineers, contributing to a wide range of nutrient cycling and geochemical processes in the ecosystem. Their activities can increase rates of silicate mineral weathering. Their intestinal microbes usually are thought to be one of the key drivers of mineral degradation mediated by earthworms,but the diversities of the intestinal microorganisms which were relevant with mineral weathering are unclear. Methodology/Principal Findings In this report, we show earthworms' effect on silicate mineral weathering and the responses of bacterial communities in their gut and surrounding substrates after being fed with potassium-bearing rock powder (PBRP). Determination of water-soluble and HNO3-extractable elements indicated some elements such as Al, Fe and Ca were significantly released from mineral upon the digestion of earthworms. The microbial communities in earthworms' gut and the surrounding substrates were investigated by amplified ribosomal DNA restriction analysis (ARDRA) and the results showed a higher bacterial diversity in the guts of the earthworms fed with PBRP and the PBRP after being fed to earthworms. UPGMA dendrogram with unweighted UniFrac analysis, considering only taxa that are present, revealed that earthworms' gut and their surrounding substrate shared similar microbiota. UPGMA dendrogram with weighted UniFrac, considering the relative abundance of microbial lineages, showed the two samples from surrounding substrate and the two samples from earthworms' gut had similarity in microbial community, respectively. Conclusions/Significance Our results indicated earthworms can accelerate degradation of silicate mineral. Earthworms play an important role in ecosystem processe since they not only have some positive effects on soil structure, but also promote nutrient cycling of ecosystem by enhancing the weathering of minerals. PMID:22174903

Microbial biomass and productivity in seagrass beds

NASA Technical Reports Server (NTRS)

Moriarty, D. J.; Boon, P. I.; Hansen, J. A.; Hunt, W. G.; Poiner, I. R.; Pollard, P. C.; Skyring, G. W.; White, D. C.

1985-01-01

Different methods for measuring the rates of processes mediated by bacteria in sediments and the rates of bacterial cell production have been compared. In addition, net production of the seagrass Zostera capricorni and bacterial production have been compared and some interrelationships with the nitrogen cycle discussed. Seagrass productivity was estimated by measuring the plastochrone interval using a leaf stapling technique. The average productivity over four seasons was 1.28 +/- 0.28 g C m-2 day-1 (mean +/- standard deviation, n = 4). Bacterial productivity was measured five times throughout a year using the rate of tritiated thymidine incorporated into DNA. Average values were 33 +/- 12 mg C m-2 day-1 for sediment and 23 +/- 4 for water column (n = 5). Spatial variability between samples was greater than seasonal variation for both seagrass productivity and bacterial productivity. On one occasion, bacterial productivity was measured using the rate of 32P incorporated into phospholipid. The values were comparable to those obtained with tritiated thymidine. The rate of sulfate reduction was 10 mmol SO4(-2) m-2 day-1. The rate of methanogenesis was low, being 5.6 mg CH4 produced m-2 day-1. A comparison of C flux measured using rates of sulfate reduction and DNA synthesis indicated that anaerobic processes were predominant in these sediments. An analysis of microbial biomass and community structure, using techniques of phospholipid analysis, showed that bacteria were predominant members of the microbial biomass and that of these, strictly anaerobic bacteria were the main components. Ammonia concentration in interstitial water varied from 23 to 71 micromoles. Estimates of the amount of ammonia required by seagrass showed that the ammonia would turn over about once per day. Rapid recycling of nitrogen by bacteria and bacterial grazers is probably important.

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.

Comparative Toxicities of Salts on Microbial Processes in Soil

PubMed Central

Maheshwari, Arpita; Bengtson, Per; Rousk, Johannes

2016-01-01

Soil salinization is a growing threat to global agriculture and carbon sequestration, but to date it remains unclear how microbial processes will respond. We studied the acute response to salt exposure of a range of anabolic and catabolic microbial processes, including bacterial (leucine incorporation) and fungal (acetate incorporation into ergosterol) growth rates, respiration, and gross N mineralization and nitrification rates. To distinguish effects of specific ions from those of overall ionic strength, we compared the addition of four salts frequently associated with soil salinization (NaCl, KCl, Na2SO4, and K2SO4) to a nonsaline soil. To compare the tolerance of different microbial processes to salt and to interrelate the toxicity of different salts, concentration-response relationships were established. Growth-based measurements revealed that fungi were more resistant to salt exposure than bacteria. Effects by salt on C and N mineralization were indistinguishable, and in contrast to previous studies, nitrification was not found to be more sensitive to salt exposure than other microbial processes. The ion-specific toxicity of certain salts could be observed only for respiration, which was less inhibited by salts containing SO42− than Cl− salts, in contrast to the microbial growth assessments. This suggested that the inhibition of microbial growth was explained solely by total ionic strength, while ion-specific toxicity also should be considered for effects on microbial decomposition. This difference resulted in an apparent reduction of microbial growth efficiency in response to exposure to SO42− salts but not to Cl− salts; no evidence was found to distinguish K+ and Na+ salts. PMID:26801570

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.

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions.

PubMed

He, Tianliang; Li, Hongyun; Zhang, Xiaobo

2017-07-11

Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions. IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival. Copyright © 2017 He et al.

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.