The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Aline Frossard - One of the best experts on this subject based on the ideXlab platform.

  • disconnect of Microbial structure and function Enzyme activities and bacterial communities in nascent stream corridors
    The ISME Journal, 2012
    Co-Authors: Aline Frossard, Linda Gerull, Michael Mutz, Mark O Gessner
    Abstract:

    A fundamental issue in Microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential Microbial Enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different Enzymes as specific measures of ecosystem function. Potential Enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the Enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential Enzyme activities indicates high functional redundancy within Microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

  • disconnect of Microbial structure and function Enzyme activities and bacterial communities in nascent stream corridors
    The ISME Journal, 2012
    Co-Authors: Aline Frossard, Linda Gerull, Michael Mutz, Mark O Gessner
    Abstract:

    A fundamental issue in Microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential Microbial Enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different Enzymes as specific measures of ecosystem function. Potential Enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the Enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential Enzyme activities indicates high functional redundancy within Microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

Arnosti Carol - One of the best experts on this subject based on the ideXlab platform.

Catherine L. Drennan - One of the best experts on this subject based on the ideXlab platform.

  • binding site for coEnzyme a revealed in the structure of pyruvate ferredoxin oxidoreductase from moorella thermoacetica
    Proceedings of the National Academy of Sciences of the United States of America, 2018
    Co-Authors: Percival Yangting Chen, Catherine L. Drennan, Heather Aman, Stephen W Ragsdale
    Abstract:

    Pyruvate:ferredoxin oxidoreductase (PFOR) is a Microbial Enzyme that uses thiamine pyrophosphate (TPP), three [4Fe-4S] clusters, and coEnzyme A (CoA) in the reversible oxidation of pyruvate to generate acetyl-CoA and carbon dioxide. The two electrons that are generated as a result of pyruvate decarboxylation are used in the reduction of low potential ferredoxins, which provide reducing equivalents for central metabolism, including the Wood–Ljungdahl pathway. PFOR is a member of the 2-oxoacid:ferredoxin oxidoreductase (OFOR) superfamily, which plays major roles in both Microbial redox reactions and carbon dioxide fixation. Here, we present a set of crystallographic snapshots of the best-studied member of this superfamily, the PFOR from Moorella thermoacetica ( Mt PFOR). These snapshots include the native structure, those of lactyl-TPP and acetyl-TPP reaction intermediates, and the first of an OFOR with CoA bound. These structural data reveal the binding site of CoA as domain III, the function of which in OFORs was previously unknown, and establish sequence motifs for CoA binding in the OFOR superfamily. Mt PFOR structures further show that domain III undergoes a conformational change upon CoA binding that seals off the active site and positions the thiolate of CoA directly adjacent to the TPP cofactor. These structural findings provide a molecular basis for the experimental observation that CoA binding accelerates catalysis by 10 5 -fold.

  • Structure-Guided Identification of a Small Molecule That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria
    2018
    Co-Authors: Marina Orman, Smaranda Bodea, Michael A. Funk, Ana Martínez-del Campo, Maud Bollenbach, Catherine L. Drennan, Emily P. Balskus
    Abstract:

    The anaerobic gut Microbial pathway that converts choline into trimethylamine (TMA) is broadly linked to human disease. Here, we describe the discovery that betaine aldehyde inhibits TMA production from choline by human gut bacterial isolates and a complex gut community. In vitro assays and a crystal structure suggest betaine aldehyde targets the gut Microbial Enzyme choline TMA-lyase (CutC). In our system, we do not observe activity for the previously reported CutC inhibitor 3,3-dimethylbutanol (DMB). The workflow we establish for identifying and characterizing betaine aldehyde provides a framework for developing additional inhibitors of gut Microbial choline metabolism, including therapeutic candidates

Mary K Firestone - One of the best experts on this subject based on the ideXlab platform.

  • changes in Microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests
    Ecology, 2011
    Co-Authors: Daniela F Cusack, Mary K Firestone, Whendee L Silver, Margaret S Torn, Sarah D Burton
    Abstract:

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

  • response of Microbial community composition and function to soil climate change
    Microbial Ecology, 2006
    Co-Authors: M P Waldrop, Mary K Firestone
    Abstract:

    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.

  • seasonal dynamics of Microbial community composition and function in oak canopy and open grassland soils
    Microbial Ecology, 2006
    Co-Authors: M P Waldrop, Mary K Firestone
    Abstract:

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

Mark O Gessner - One of the best experts on this subject based on the ideXlab platform.

  • disconnect of Microbial structure and function Enzyme activities and bacterial communities in nascent stream corridors
    The ISME Journal, 2012
    Co-Authors: Aline Frossard, Linda Gerull, Michael Mutz, Mark O Gessner
    Abstract:

    A fundamental issue in Microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential Microbial Enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different Enzymes as specific measures of ecosystem function. Potential Enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the Enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential Enzyme activities indicates high functional redundancy within Microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

  • disconnect of Microbial structure and function Enzyme activities and bacterial communities in nascent stream corridors
    The ISME Journal, 2012
    Co-Authors: Aline Frossard, Linda Gerull, Michael Mutz, Mark O Gessner
    Abstract:

    A fundamental issue in Microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential Microbial Enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different Enzymes as specific measures of ecosystem function. Potential Enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the Enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential Enzyme activities indicates high functional redundancy within Microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.