The Experts below are selected from a list of 8667 Experts worldwide ranked by ideXlab platform

Donald A Bryant - One of the best experts on this subject based on the ideXlab platform.

  • the dark side of the mushroom spring microbial Mat life in the shadow of chlorophototrophs ii metabolic functions of abundant community members predicted from metagenomic analyses
    Frontiers in Microbiology, 2017
    Co-Authors: Vera Thiel, Donald A Bryant, Michael Hugler, David M Ward
    Abstract:

    Abstract. Microbial Mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the Mat, are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the underMat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. We analyzed the assembled metagenome of the orange-colored underMat portion of the community of Mushroom Spring Mats and here discuss the genomic potential and metabolic functions of the major members. This part of the community was found to be a mixture of photo- and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper Mat Layer and Thermodesulfovibrio sp. in the underMat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly by phototrophs. Finally, a variety of underMat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.

  • The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses
    Frontiers Media S.A., 2017
    Co-Authors: Vera Thiel, Donald A Bryant, Michael Hugler, David M Ward
    Abstract:

    Microbial Mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the Mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the underMat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored underMat portion of the community of Mushroom Spring Mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The underMat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper Mat Layer and Thermodesulfovibrio sp. in the underMat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of underMat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns

  • the molecular dimension of microbial species 1 ecological distinctions among and homogeneity within putative ecotypes of synechococcus inhabiting the cyanobacterial Mat of mushroom spring yellowstone national park
    Frontiers in Microbiology, 2015
    Co-Authors: Jason M Wood, Eric D Becraft, Douglas B Rusch, Michael Kuhl, Sheila Ingemann Jensen, Donald A Bryant
    Abstract:

    Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial Mat. Putative ecological species (putative ecotypes), which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick Mat Layer. Importantly, in most cases variants predicted to belong to the same putative ecotype formed unique clusters relative to temperature and depth in the Mat in canonical correspondence analysis, supporting the hypothesis that while the putative ecotypes are ecologically distinct, the members of each ecotype are ecologically homogeneous. Putative ecotypes responded differently to experimental perturbations of temperature and light, but the genetic variation within each putative ecotype was maintained as the relative abundances of putative ecotypes changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to putative ecotypes that predominate deeper within the Mat photic zone, the timing of transcript abundances for selected genes differed for putative ecotypes that predominate in microenvironments closer to upper surface of the Mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring Mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.

Vera Thiel - One of the best experts on this subject based on the ideXlab platform.

  • the dark side of the mushroom spring microbial Mat life in the shadow of chlorophototrophs ii metabolic functions of abundant community members predicted from metagenomic analyses
    Frontiers in Microbiology, 2017
    Co-Authors: Vera Thiel, Donald A Bryant, Michael Hugler, David M Ward
    Abstract:

    Abstract. Microbial Mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the Mat, are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the underMat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. We analyzed the assembled metagenome of the orange-colored underMat portion of the community of Mushroom Spring Mats and here discuss the genomic potential and metabolic functions of the major members. This part of the community was found to be a mixture of photo- and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper Mat Layer and Thermodesulfovibrio sp. in the underMat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly by phototrophs. Finally, a variety of underMat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.

  • The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses
    Frontiers Media S.A., 2017
    Co-Authors: Vera Thiel, Donald A Bryant, Michael Hugler, David M Ward
    Abstract:

    Microbial Mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the Mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the underMat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored underMat portion of the community of Mushroom Spring Mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The underMat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper Mat Layer and Thermodesulfovibrio sp. in the underMat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of underMat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns

Stephanos P. Kilias - One of the best experts on this subject based on the ideXlab platform.

  • MICROBIAL Mat–RELATED STRUCTURES IN THE QUATERNARY CAPE VANI MANGANESE-OXIDE (-BARITE) DEPOSIT, NW MILOS ISLAND, GREECE
    2016
    Co-Authors: Stephanos P. Kilias
    Abstract:

    ABSTRACT: Microbial Mat–related sedimentary structures are present in Lower Pleistocene mixed epiclastic-volcaniclastic sediments that host the Cape Vani manganese-oxide (-barite) deposit on NW Milos Island, Greece. Milos Island is a dormant and recently emergent 2 Ma volcano of the active Southern Aegean volcanic arc. The deposit occurs in a 1-km-long marine rift basin floored by a dacite dome. Basin fill is a.60-m-thick sequence of epiclastic glauconite-bearing sediments sandwiched between lower and upper mixed volcaniclastic sandy tuffs and epiclastic sandstones. Host siliciclastics consist of glass shards, lithic fragments, plagioclase, K-feldspar, biotite, pyroxene, and silica and clay cements, overprinted by a barite– silica–K-feldspar–illite assemblage. Manganese (IV)–oxide minerals include dominantly d-MnO2 (vernadite), hollandite group minerals, pyrolusite, ramsdellite, and nanocrystalline todorokite. Microbially induced structures occur in a specific lithofacies referred to as upper ‘‘ferruginous and white volcaniclastic sandy tuffs/sandstones’ ’ and are characterized by: (1) planar and herringbone cross-bedding, (2) small-scale, vertical fining-upward sequences, (3) flaser, wavy, and lenticular bedding, (4) marine trace fossils similar to Skolithos, and (5) beveling of ripple marks and desiccated silicified mudstone beds. These features, together with the microbially induced structures and the widespread presence of glauconite, reflect a littoral to tidal-flat paleoenvironment. The microbial Mat–related sedimentary structures developed in the Mn-oxide ore forMation are recognized as: (1) Mat-Layer structures, (2) growth bedding structures and nodules, (3) wrinkle structures and exfoliating sand laminae, (4) cracks with upturned and curled margins, (5) roll-up structures, (6) fossil gas domes, (7) Mat fragments and chips, and (8) Mat slump structures, suggesting photoautotrophic, possibly cyanobacterial, Mats. The ubiquitous presence of barite, in the host sediments, in the Mat-related structures, in feeder-vein and bedding conformabl

  • microbial Mat related structures in the quaternary cape vani manganese oxide barite deposit nw milos island greece
    2012
    Co-Authors: Stephanos P. Kilias
    Abstract:

    Microbial Mat–related sedimentary structures are present in Lower Pleistocene mixed epiclastic-volcaniclastic sediments that host the Cape Vani manganese-oxide (-barite) deposit on NW Milos Island, Greece. Milos Island is a dormant and recently emergent 2 Ma volcano of the active Southern Aegean volcanic arc. The deposit occurs in a 1-km-long marine rift basin floored by a dacite dome. Basin fill is a .60-m-thick sequence of epiclastic glauconite-bearing sediments sandwiched between lower and upper mixed volcaniclastic sandy tuffs and epiclastic sandstones. Host siliciclastics consist of glass shards, lithic fragments, plagioclase, K-feldspar, biotite, pyroxene, and silica and clay cements, overprinted by a barite– silica–K-feldspar–illite assemblage. Manganese (IV)–oxide minerals include dominantly d-MnO2 (vernadite), hollandite group minerals, pyrolusite, ramsdellite, and nanocrystalline todorokite. Microbially induced structures occur in a specific lithofacies referred to as upper ‘‘ferruginous and white volcaniclastic sandy tuffs/sandstones’’ and are characterized by: (1) planar and herringbone cross-bedding, (2) small-scale, vertical fining-upward sequences, (3) flaser, wavy, and lenticular bedding, (4) marine trace fossils similar to Skolithos, and (5) beveling of ripple marks and desiccated silicified mudstone beds. These features, together with the microbially induced structures and the widespread presence of glauconite, reflect a littoral to tidal-flat paleoenvironment. The microbial Mat–related sedimentary structures developed in the Mn-oxide ore forMation are recognized as: (1) Mat-Layer structures, (2) growth bedding structures and nodules, (3) wrinkle structures and exfoliating sand laminae, (4) cracks with upturned and curled margins, (5) roll-up structures, (6) fossil gas domes, (7) Mat fragments and chips, and (8) Mat slump structures, suggesting photoautotrophic, possibly cyanobacterial, Mats. The ubiquitous presence of barite, in the host sediments, in the Mat-related structures, in feeder-vein and bedding conformable Layers, and in the gravel unit that caps the Cape Vani sedimentary rocks, suggests that microbial Mats were developed in association with white smokers acting as Mn(II) suppliers, in a sunlit shallow-water or tidal-flat paleogeothermal system. The intiMate relationship of Mn(IV)-oxide ore mineralization with the microbial Mat–related sedimentary structures, coupled with the presence of Mn mineralized microbial fossils in the ore, strongly suggests the possible role of bacterial photosynthesis in Mn(II) bio-oxidation and Mn(IV)-oxide biomineralization at Cape Vani. It is envisaged that most Mn(IV)oxide mineralization was synsedimentary and syngenetic and formed due to an interplay among shallow-marine/tidal-flat sedimentation, hydrothermal seafloor to subaerial hot spring activity, which provided Mn(II), and active, possibly photosynthetic, microbial activity. Chemotrophic influence on Mn(IV)-oxide biomineralization cannot be excluded.

David M Ward - One of the best experts on this subject based on the ideXlab platform.

  • the dark side of the mushroom spring microbial Mat life in the shadow of chlorophototrophs ii metabolic functions of abundant community members predicted from metagenomic analyses
    Frontiers in Microbiology, 2017
    Co-Authors: Vera Thiel, Donald A Bryant, Michael Hugler, David M Ward
    Abstract:

    Abstract. Microbial Mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the Mat, are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the underMat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. We analyzed the assembled metagenome of the orange-colored underMat portion of the community of Mushroom Spring Mats and here discuss the genomic potential and metabolic functions of the major members. This part of the community was found to be a mixture of photo- and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper Mat Layer and Thermodesulfovibrio sp. in the underMat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly by phototrophs. Finally, a variety of underMat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.

  • The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses
    Frontiers Media S.A., 2017
    Co-Authors: Vera Thiel, Donald A Bryant, Michael Hugler, David M Ward
    Abstract:

    Microbial Mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the Mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the underMat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored underMat portion of the community of Mushroom Spring Mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The underMat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper Mat Layer and Thermodesulfovibrio sp. in the underMat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of underMat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns

Michael Hugler - One of the best experts on this subject based on the ideXlab platform.

  • the dark side of the mushroom spring microbial Mat life in the shadow of chlorophototrophs ii metabolic functions of abundant community members predicted from metagenomic analyses
    Frontiers in Microbiology, 2017
    Co-Authors: Vera Thiel, Donald A Bryant, Michael Hugler, David M Ward
    Abstract:

    Abstract. Microbial Mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the Mat, are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the underMat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. We analyzed the assembled metagenome of the orange-colored underMat portion of the community of Mushroom Spring Mats and here discuss the genomic potential and metabolic functions of the major members. This part of the community was found to be a mixture of photo- and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper Mat Layer and Thermodesulfovibrio sp. in the underMat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly by phototrophs. Finally, a variety of underMat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.

  • The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses
    Frontiers Media S.A., 2017
    Co-Authors: Vera Thiel, Donald A Bryant, Michael Hugler, David M Ward
    Abstract:

    Microbial Mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the Mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the underMat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored underMat portion of the community of Mushroom Spring Mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The underMat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper Mat Layer and Thermodesulfovibrio sp. in the underMat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of underMat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns