Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-07-17

AUTHORS

Alexis P Yelton, Luis R Comolli, Nicholas B Justice, Cindy Castelle, Vincent J Denef, Brian C Thomas, Jillian F Banfield

ABSTRACT

BACKGROUND: Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. RESULTS: We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. CONCLUSION: The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities. More... »

PAGES

485-485

References to SciGraph publications

  • 2004-09-09. Functionally specified protein signatures distinctive for each of the different blue copper proteins in BMC BIOINFORMATICS
  • 1993-01. Acetyl-CoA synthetase (ADP forming) in archaea, a novel enzyme involved in acetate formation and ATP synthesis in ARCHIVES OF MICROBIOLOGY
  • 2001-06-01. Insertional inactivation of the flaH gene in the archaeon Methanococcus voltae results in non-flagellated cells in MOLECULAR GENETICS AND GENOMICS
  • 2010-09. Formate-driven growth coupled with H2 production in NATURE
  • 1994-02. Plastocyanin: Structural and functional analysis in JOURNAL OF BIOENERGETICS AND BIOMEMBRANES
  • 2000-09. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum in NATURE
  • 2007. Genetic and Bioinformatic Insights into Iron and Sulfur Oxidation Mechanisms of Bioleaching Organisms in BIOMINING
  • 2004-02-01. Community structure and metabolism through reconstruction of microbial genomes from the environment in NATURE
  • 2008-07-30. The rus Operon Genes Are Differentially Regulated When Acidithiobacillus ferrooxidans LR is Kept in Contact with Metal Sulfides in CURRENT MICROBIOLOGY
  • 2005-05-06. Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates in MICROBIAL CELL FACTORIES
  • 2008-10-09. Natural acidophilic biofilm communities reflect distinct organismal and functional organization in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2006-05-24. Ferroplasma cupricumulans sp. nov., a novel moderately thermophilic, acidophilic archaeon isolated from an industrial-scale chalcocite bioleach heap in EXTREMOPHILES
  • 2004-08-31. Unusual ADP-forming acetyl-coenzyme A synthetases from the mesophilic halophilic euryarchaeon Haloarcula marismortui and from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum in ARCHIVES OF MICROBIOLOGY
  • 2005-01-04. Soluble expression of recombinant proteins in the cytoplasm of Escherichia coli in MICROBIAL CELL FACTORIES
  • 2009-08-21. Community-wide analysis of microbial genome sequence signatures in GENOME BIOLOGY
  • 2011-06-30. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2003-01-16. Arsenic resistance in the archaeon "Ferroplasma acidarmanus": new insights into the structure and evolution of the ars genes in EXTREMOPHILES
  • 2012-04-18. Involvement of alkylhydroxybenzenes in the Escherichia coli response to the lethal effect of UV irradiation in MICROBIOLOGY
  • 2006-10-18. Towards determining details of anaerobic growth coupled to ferric iron reduction by the acidophilic archaeon ‘Ferroplasma acidarmanus’ Fer1 in EXTREMOPHILES
  • 2003-08-29. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ in GENOME BIOLOGY
  • 2007-01-15. Prediction of effective genome size in metagenomic samples in GENOME BIOLOGY
  • 2010-11-11. Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2006. Thermoplasmatales in THE PROKARYOTES
  • 2007-10-04. Production of methanethiol and volatile sulfur compounds by the archaeon “Ferroplasma acidarmanus” in EXTREMOPHILES
  • 2011-06-30. Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2013-01-05. Ferrous iron oxidation by sulfur-oxidizing Acidithiobacillus ferrooxidans and analysis of the process at the levels of transcription and protein synthesis in ANTONIE VAN LEEUWENHOEK
  • 2009-07-29. Acyl-CoA Dehydrogenases: Dynamic History of Protein Family Evolution in JOURNAL OF MOLECULAR EVOLUTION
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-14-485

    DOI

    http://dx.doi.org/10.1186/1471-2164-14-485

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1002051529

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23865623


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Microbiology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Aerobiosis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Aldehyde Oxidoreductases", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Amino Acids", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Biofilms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Cell Wall", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Drug Resistance", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Electron Transport", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Energy Metabolism", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Fermentation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genes, Archaeal", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genomic Islands", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Glyoxylates", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Hydrogen-Ion Concentration", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Iron", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Metals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mining", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Molecular Imaging", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Molecular Sequence Annotation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Multienzyme Complexes", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Thermoplasmales", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Trehalose", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Current address: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA", 
              "id": "http://www.grid.ac/institutes/grid.116068.8", 
              "name": [
                "Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA", 
                "Current address: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yelton", 
            "givenName": "Alexis P", 
            "id": "sg:person.0773144006.96", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773144006.96"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.184769.5", 
              "name": [
                "Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Comolli", 
            "givenName": "Luis R", 
            "id": "sg:person.01315502051.02", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315502051.02"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA", 
              "id": "http://www.grid.ac/institutes/grid.47840.3f", 
              "name": [
                "Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Justice", 
            "givenName": "Nicholas B", 
            "id": "sg:person.01073026722.17", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01073026722.17"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.184769.5", 
              "name": [
                "Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Castelle", 
            "givenName": "Cindy", 
            "id": "sg:person.0735524175.28", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0735524175.28"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Current address: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA", 
              "id": "http://www.grid.ac/institutes/grid.214458.e", 
              "name": [
                "Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA", 
                "Current address: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Denef", 
            "givenName": "Vincent J", 
            "id": "sg:person.01147101101.38", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01147101101.38"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA", 
              "id": "http://www.grid.ac/institutes/grid.47840.3f", 
              "name": [
                "Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Thomas", 
            "givenName": "Brian C", 
            "id": "sg:person.0732742066.21", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0732742066.21"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA", 
              "id": "http://www.grid.ac/institutes/grid.47840.3f", 
              "name": [
                "Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA", 
                "Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Banfield", 
            "givenName": "Jillian F", 
            "id": "sg:person.01350542775.47", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01350542775.47"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1186/1475-2859-4-13", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050884074", 
              "https://doi.org/10.1186/1475-2859-4-13"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00792-007-0108-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038703426", 
              "https://doi.org/10.1007/s00792-007-0108-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35035069", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019679930", 
              "https://doi.org/10.1038/35035069"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2009-10-8-r85", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014147708", 
              "https://doi.org/10.1186/gb-2009-10-8-r85"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/0-387-30743-5_7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040882595", 
              "https://doi.org/10.1007/0-387-30743-5_7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-3-540-34911-2_14", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035714652", 
              "https://doi.org/10.1007/978-3-540-34911-2_14"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00239-009-9263-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032388075", 
              "https://doi.org/10.1007/s00239-009-9263-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02340", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023089166", 
              "https://doi.org/10.1038/nature02340"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2011.75", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029730701", 
              "https://doi.org/10.1038/ismej.2011.75"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature09375", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015326716", 
              "https://doi.org/10.1038/nature09375"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2011.78", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019104224", 
              "https://doi.org/10.1038/ismej.2011.78"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10482-012-9872-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045576362", 
              "https://doi.org/10.1007/s10482-012-9872-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1134/s0026261712010043", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023930793", 
              "https://doi.org/10.1134/s0026261712010043"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00792-006-0527-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027279496", 
              "https://doi.org/10.1007/s00792-006-0527-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00792-006-0029-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006128997", 
              "https://doi.org/10.1007/s00792-006-0029-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-5-127", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051350576", 
              "https://doi.org/10.1186/1471-2105-5-127"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s004380100451", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029946056", 
              "https://doi.org/10.1007/s004380100451"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00792-002-0303-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1075259975", 
              "https://doi.org/10.1007/s00792-002-0303-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00763219", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013429077", 
              "https://doi.org/10.1007/bf00763219"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1475-2859-4-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048360411", 
              "https://doi.org/10.1186/1475-2859-4-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2010.170", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031676008", 
              "https://doi.org/10.1038/ismej.2010.170"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00244267", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052180236", 
              "https://doi.org/10.1007/bf00244267"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2008.90", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011791054", 
              "https://doi.org/10.1038/ismej.2008.90"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00284-008-9208-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024411738", 
              "https://doi.org/10.1007/s00284-008-9208-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00203-004-0702-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038992778", 
              "https://doi.org/10.1007/s00203-004-0702-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2003-4-9-r55", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041778603", 
              "https://doi.org/10.1186/gb-2003-4-9-r55"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2007-8-1-r10", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044994861", 
              "https://doi.org/10.1186/gb-2007-8-1-r10"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2013-07-17", 
        "datePublishedReg": "2013-07-17", 
        "description": "BACKGROUND: Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order.\nRESULTS: We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis.\nCONCLUSION: The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/1471-2164-14-485", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.8695213", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1023790", 
            "issn": [
              "1471-2164"
            ], 
            "name": "BMC Genomics", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "14"
          }
        ], 
        "keywords": [
          "biofilm communities", 
          "microbial biofilm communities", 
          "same carbon substrates", 
          "toxic metal resistance", 
          "features of organisms", 
          "cryogenic electron microscopy", 
          "uncultivated organisms", 
          "niche differentiation", 
          "comparative genomics", 
          "flagellar genes", 
          "gene content", 
          "archaeal order", 
          "most genes", 
          "AMD community", 
          "novel organisms", 
          "important genomic differences", 
          "genomic information", 
          "complete genome", 
          "genomic analysis", 
          "histidine synthesis", 
          "cultivation efforts", 
          "metabolic capabilities", 
          "genetic capability", 
          "genomic differences", 
          "archaea", 
          "gene expression", 
          "oxidation genes", 
          "metal resistance", 
          "aerobic heterotrophs", 
          "sulfide mineral dissolution", 
          "surface layer production", 
          "genes", 
          "pili production", 
          "organisms", 
          "Aplasma", 
          "spp", 
          "unknown differences", 
          "new insights", 
          "structural differentiation", 
          "differentiation", 
          "carbon substrates", 
          "iron oxidation", 
          "notable variety", 
          "Euryarchaea", 
          "full suite", 
          "Thermoplasmatales", 
          "genome", 
          "metagenomics", 
          "genomics", 
          "lineages", 
          "biosynthesis", 
          "heterotrophs", 
          "type I", 
          "most life", 
          "members", 
          "mine drainage formation", 
          "bacteria", 
          "acid mine drainage formation", 
          "community", 
          "iPlasma", 
          "motility", 
          "production", 
          "expression", 
          "valine", 
          "large number", 
          "dominance", 
          "small number", 
          "cobalamin", 
          "insights", 
          "substrate", 
          "analysis", 
          "variation", 
          "number", 
          "resistance", 
          "formation", 
          "variety", 
          "bioleaching", 
          "ability", 
          "suite", 
          "microscopy", 
          "synthesis", 
          "differences", 
          "environment", 
          "content", 
          "oxidation", 
          "functioning", 
          "results", 
          "study", 
          "efforts", 
          "features", 
          "information", 
          "order", 
          "prediction", 
          "capability", 
          "life", 
          "coexisting", 
          "mineral dissolution", 
          "reasons", 
          "methanol", 
          "dissolution", 
          "tomography", 
          "Metal sulfide mineral dissolution", 
          "drainage (AMD) formation", 
          "AMD microbial biofilm communities", 
          "related Euryarchaea", 
          "co-occurring AMD archaea", 
          "AMD archaea", 
          "low abundance organisms A", 
          "abundance organisms A", 
          "organisms A", 
          "Gplasma", 
          "Thermoplasmatales order", 
          "Ferroplasma type I", 
          "facultative aerobic heterotrophs", 
          "genomes share genes", 
          "share genes", 
          "Eplasma", 
          "Ferroplasma spp", 
          "metagenomics-based ultrastructural predictions", 
          "ultrastructural predictions", 
          "iron oxidation genes", 
          "Thermoplasmatales AMD archaea", 
          "characterized Ferroplasma spp", 
          "Thermoplasmatales lineage", 
          "acid mine drainage biofilm communities", 
          "mine drainage biofilm communities", 
          "drainage biofilm communities", 
          "co-occurring archaea"
        ], 
        "name": "Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea", 
        "pagination": "485-485", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1002051529"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/1471-2164-14-485"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "23865623"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/1471-2164-14-485", 
          "https://app.dimensions.ai/details/publication/pub.1002051529"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-01-01T18:31", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220101/entities/gbq_results/article/article_614.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/1471-2164-14-485"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-14-485'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-14-485'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-14-485'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-14-485'


     

    This table displays all metadata directly associated to this object as RDF triples.

    451 TRIPLES      22 PREDICATES      205 URIs      169 LITERALS      30 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/1471-2164-14-485 schema:about N0215dee52c94464cbe979e3b0186c616
    2 N043edbdb8a204eacadcf0d0c463f3d51
    3 N166a5663f1f648f3830f1fbe03cd4adf
    4 N21c5167d430744a5a12ae4b54b6ba134
    5 N3300892a4f354209856b2ea12df82f79
    6 N3fb224bf2d1a4580953b61789a4233cb
    7 N404e33b2b0e5446ba617a3987cc3c6e8
    8 N50a250dcb4ae4ce79c9f1344697529be
    9 N6496907dbfed4fec9d3add6c6d86c435
    10 N6b8081d688be4bdb973600868bc20ecd
    11 N743ea657040a42699d9553d9a05943f9
    12 N7775806537d04d0693a070e551ed5ed4
    13 N7f61cf1c10ad4fb8a193b61620a2c271
    14 N800f2327bae3403e8b02d21e0aff8f73
    15 N827c967aa69c4d809a5c2de915c68936
    16 N82cb7d52f69a4a848e03329e08201e3a
    17 Na6774ac458ec45e18fa40de7820e27af
    18 Nc2e3e2f82cf746d8b1452903146dd2c3
    19 Nc75c57da4695405cb772fb664a033630
    20 Ne3f74cf1e36f4a27950d3892705ac83d
    21 Ne613dbebef3f4731b8334e2735b98561
    22 Ne875e0a9b92c4157b4af5030bdf8c71a
    23 Nfd9061b32ae74cb8b2e7bc4ee4691bb3
    24 anzsrc-for:06
    25 anzsrc-for:0604
    26 anzsrc-for:0605
    27 schema:author N606d624e9d7747688b6d9513b544593f
    28 schema:citation sg:pub.10.1007/0-387-30743-5_7
    29 sg:pub.10.1007/978-3-540-34911-2_14
    30 sg:pub.10.1007/bf00244267
    31 sg:pub.10.1007/bf00763219
    32 sg:pub.10.1007/s00203-004-0702-4
    33 sg:pub.10.1007/s00239-009-9263-0
    34 sg:pub.10.1007/s00284-008-9208-7
    35 sg:pub.10.1007/s004380100451
    36 sg:pub.10.1007/s00792-002-0303-6
    37 sg:pub.10.1007/s00792-006-0029-y
    38 sg:pub.10.1007/s00792-006-0527-y
    39 sg:pub.10.1007/s00792-007-0108-8
    40 sg:pub.10.1007/s10482-012-9872-2
    41 sg:pub.10.1038/35035069
    42 sg:pub.10.1038/ismej.2008.90
    43 sg:pub.10.1038/ismej.2010.170
    44 sg:pub.10.1038/ismej.2011.75
    45 sg:pub.10.1038/ismej.2011.78
    46 sg:pub.10.1038/nature02340
    47 sg:pub.10.1038/nature09375
    48 sg:pub.10.1134/s0026261712010043
    49 sg:pub.10.1186/1471-2105-5-127
    50 sg:pub.10.1186/1475-2859-4-1
    51 sg:pub.10.1186/1475-2859-4-13
    52 sg:pub.10.1186/gb-2003-4-9-r55
    53 sg:pub.10.1186/gb-2007-8-1-r10
    54 sg:pub.10.1186/gb-2009-10-8-r85
    55 schema:datePublished 2013-07-17
    56 schema:datePublishedReg 2013-07-17
    57 schema:description BACKGROUND: Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. RESULTS: We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. CONCLUSION: The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.
    58 schema:genre article
    59 schema:inLanguage en
    60 schema:isAccessibleForFree true
    61 schema:isPartOf N1eaebd7f837346a5a4be3a89ea3c3829
    62 N2c2ad2334f8e44c4b8d2490be4417565
    63 sg:journal.1023790
    64 schema:keywords AMD archaea
    65 AMD community
    66 AMD microbial biofilm communities
    67 Aplasma
    68 Eplasma
    69 Euryarchaea
    70 Ferroplasma spp
    71 Ferroplasma type I
    72 Gplasma
    73 Metal sulfide mineral dissolution
    74 Thermoplasmatales
    75 Thermoplasmatales AMD archaea
    76 Thermoplasmatales lineage
    77 Thermoplasmatales order
    78 ability
    79 abundance organisms A
    80 acid mine drainage biofilm communities
    81 acid mine drainage formation
    82 aerobic heterotrophs
    83 analysis
    84 archaea
    85 archaeal order
    86 bacteria
    87 biofilm communities
    88 bioleaching
    89 biosynthesis
    90 capability
    91 carbon substrates
    92 characterized Ferroplasma spp
    93 co-occurring AMD archaea
    94 co-occurring archaea
    95 cobalamin
    96 coexisting
    97 community
    98 comparative genomics
    99 complete genome
    100 content
    101 cryogenic electron microscopy
    102 cultivation efforts
    103 differences
    104 differentiation
    105 dissolution
    106 dominance
    107 drainage (AMD) formation
    108 drainage biofilm communities
    109 efforts
    110 environment
    111 expression
    112 facultative aerobic heterotrophs
    113 features
    114 features of organisms
    115 flagellar genes
    116 formation
    117 full suite
    118 functioning
    119 gene content
    120 gene expression
    121 genes
    122 genetic capability
    123 genome
    124 genomes share genes
    125 genomic analysis
    126 genomic differences
    127 genomic information
    128 genomics
    129 heterotrophs
    130 histidine synthesis
    131 iPlasma
    132 important genomic differences
    133 information
    134 insights
    135 iron oxidation
    136 iron oxidation genes
    137 large number
    138 life
    139 lineages
    140 low abundance organisms A
    141 members
    142 metabolic capabilities
    143 metagenomics
    144 metagenomics-based ultrastructural predictions
    145 metal resistance
    146 methanol
    147 microbial biofilm communities
    148 microscopy
    149 mine drainage biofilm communities
    150 mine drainage formation
    151 mineral dissolution
    152 most genes
    153 most life
    154 motility
    155 new insights
    156 niche differentiation
    157 notable variety
    158 novel organisms
    159 number
    160 order
    161 organisms
    162 organisms A
    163 oxidation
    164 oxidation genes
    165 pili production
    166 prediction
    167 production
    168 reasons
    169 related Euryarchaea
    170 resistance
    171 results
    172 same carbon substrates
    173 share genes
    174 small number
    175 spp
    176 structural differentiation
    177 study
    178 substrate
    179 suite
    180 sulfide mineral dissolution
    181 surface layer production
    182 synthesis
    183 tomography
    184 toxic metal resistance
    185 type I
    186 ultrastructural predictions
    187 uncultivated organisms
    188 unknown differences
    189 valine
    190 variation
    191 variety
    192 schema:name Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea
    193 schema:pagination 485-485
    194 schema:productId N297e77da7562490596a8a4c0ec3e4031
    195 N66a7e2ef8ea748b9bc58bcd19fdc5e41
    196 Naef9ec7cc76d42a59b747cd36b5f0f88
    197 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002051529
    198 https://doi.org/10.1186/1471-2164-14-485
    199 schema:sdDatePublished 2022-01-01T18:31
    200 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    201 schema:sdPublisher Naa7c6ff16436492fb767cff872ebc0d8
    202 schema:url https://doi.org/10.1186/1471-2164-14-485
    203 sgo:license sg:explorer/license/
    204 sgo:sdDataset articles
    205 rdf:type schema:ScholarlyArticle
    206 N0215dee52c94464cbe979e3b0186c616 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    207 schema:name Hydrogen-Ion Concentration
    208 rdf:type schema:DefinedTerm
    209 N043edbdb8a204eacadcf0d0c463f3d51 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    210 schema:name Electron Transport
    211 rdf:type schema:DefinedTerm
    212 N166a5663f1f648f3830f1fbe03cd4adf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    213 schema:name Energy Metabolism
    214 rdf:type schema:DefinedTerm
    215 N1eaebd7f837346a5a4be3a89ea3c3829 schema:volumeNumber 14
    216 rdf:type schema:PublicationVolume
    217 N21c5167d430744a5a12ae4b54b6ba134 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    218 schema:name Mining
    219 rdf:type schema:DefinedTerm
    220 N297e77da7562490596a8a4c0ec3e4031 schema:name pubmed_id
    221 schema:value 23865623
    222 rdf:type schema:PropertyValue
    223 N2a58dc0bcd4246fca9f2096e2389098d rdf:first sg:person.0732742066.21
    224 rdf:rest N8d09f5d3523147b1b5cf5819e0d8c2b8
    225 N2c2ad2334f8e44c4b8d2490be4417565 schema:issueNumber 1
    226 rdf:type schema:PublicationIssue
    227 N3300892a4f354209856b2ea12df82f79 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    228 schema:name Aldehyde Oxidoreductases
    229 rdf:type schema:DefinedTerm
    230 N3fb224bf2d1a4580953b61789a4233cb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    231 schema:name Trehalose
    232 rdf:type schema:DefinedTerm
    233 N404e33b2b0e5446ba617a3987cc3c6e8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    234 schema:name Fermentation
    235 rdf:type schema:DefinedTerm
    236 N50a250dcb4ae4ce79c9f1344697529be schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    237 schema:name Genomic Islands
    238 rdf:type schema:DefinedTerm
    239 N606d624e9d7747688b6d9513b544593f rdf:first sg:person.0773144006.96
    240 rdf:rest N78dcb73197db4567a9799afc07f0f100
    241 N6496907dbfed4fec9d3add6c6d86c435 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    242 schema:name Iron
    243 rdf:type schema:DefinedTerm
    244 N66a7e2ef8ea748b9bc58bcd19fdc5e41 schema:name doi
    245 schema:value 10.1186/1471-2164-14-485
    246 rdf:type schema:PropertyValue
    247 N6b8081d688be4bdb973600868bc20ecd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    248 schema:name Phylogeny
    249 rdf:type schema:DefinedTerm
    250 N743ea657040a42699d9553d9a05943f9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    251 schema:name Molecular Sequence Annotation
    252 rdf:type schema:DefinedTerm
    253 N7775806537d04d0693a070e551ed5ed4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    254 schema:name Cell Wall
    255 rdf:type schema:DefinedTerm
    256 N78dcb73197db4567a9799afc07f0f100 rdf:first sg:person.01315502051.02
    257 rdf:rest N85a86a6d73a5402fa1af17675f2ac749
    258 N7f61cf1c10ad4fb8a193b61620a2c271 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    259 schema:name Thermoplasmales
    260 rdf:type schema:DefinedTerm
    261 N800f2327bae3403e8b02d21e0aff8f73 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    262 schema:name Molecular Imaging
    263 rdf:type schema:DefinedTerm
    264 N827c967aa69c4d809a5c2de915c68936 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    265 schema:name Aerobiosis
    266 rdf:type schema:DefinedTerm
    267 N82cb7d52f69a4a848e03329e08201e3a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    268 schema:name Biofilms
    269 rdf:type schema:DefinedTerm
    270 N85a86a6d73a5402fa1af17675f2ac749 rdf:first sg:person.01073026722.17
    271 rdf:rest Nbd0578c5b73848b8b138406b6a61c8d3
    272 N8d09f5d3523147b1b5cf5819e0d8c2b8 rdf:first sg:person.01350542775.47
    273 rdf:rest rdf:nil
    274 N9bc0a459e63b4e2a83f9fc222ef78546 rdf:first sg:person.01147101101.38
    275 rdf:rest N2a58dc0bcd4246fca9f2096e2389098d
    276 Na6774ac458ec45e18fa40de7820e27af schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    277 schema:name Glyoxylates
    278 rdf:type schema:DefinedTerm
    279 Naa7c6ff16436492fb767cff872ebc0d8 schema:name Springer Nature - SN SciGraph project
    280 rdf:type schema:Organization
    281 Naef9ec7cc76d42a59b747cd36b5f0f88 schema:name dimensions_id
    282 schema:value pub.1002051529
    283 rdf:type schema:PropertyValue
    284 Nbd0578c5b73848b8b138406b6a61c8d3 rdf:first sg:person.0735524175.28
    285 rdf:rest N9bc0a459e63b4e2a83f9fc222ef78546
    286 Nc2e3e2f82cf746d8b1452903146dd2c3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    287 schema:name Amino Acids
    288 rdf:type schema:DefinedTerm
    289 Nc75c57da4695405cb772fb664a033630 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    290 schema:name Multienzyme Complexes
    291 rdf:type schema:DefinedTerm
    292 Ne3f74cf1e36f4a27950d3892705ac83d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    293 schema:name Genes, Archaeal
    294 rdf:type schema:DefinedTerm
    295 Ne613dbebef3f4731b8334e2735b98561 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    296 schema:name Drug Resistance
    297 rdf:type schema:DefinedTerm
    298 Ne875e0a9b92c4157b4af5030bdf8c71a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    299 schema:name Genomics
    300 rdf:type schema:DefinedTerm
    301 Nfd9061b32ae74cb8b2e7bc4ee4691bb3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    302 schema:name Metals
    303 rdf:type schema:DefinedTerm
    304 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    305 schema:name Biological Sciences
    306 rdf:type schema:DefinedTerm
    307 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    308 schema:name Genetics
    309 rdf:type schema:DefinedTerm
    310 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
    311 schema:name Microbiology
    312 rdf:type schema:DefinedTerm
    313 sg:grant.8695213 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-14-485
    314 rdf:type schema:MonetaryGrant
    315 sg:journal.1023790 schema:issn 1471-2164
    316 schema:name BMC Genomics
    317 schema:publisher Springer Nature
    318 rdf:type schema:Periodical
    319 sg:person.01073026722.17 schema:affiliation grid-institutes:grid.47840.3f
    320 schema:familyName Justice
    321 schema:givenName Nicholas B
    322 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01073026722.17
    323 rdf:type schema:Person
    324 sg:person.01147101101.38 schema:affiliation grid-institutes:grid.214458.e
    325 schema:familyName Denef
    326 schema:givenName Vincent J
    327 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01147101101.38
    328 rdf:type schema:Person
    329 sg:person.01315502051.02 schema:affiliation grid-institutes:grid.184769.5
    330 schema:familyName Comolli
    331 schema:givenName Luis R
    332 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315502051.02
    333 rdf:type schema:Person
    334 sg:person.01350542775.47 schema:affiliation grid-institutes:grid.47840.3f
    335 schema:familyName Banfield
    336 schema:givenName Jillian F
    337 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01350542775.47
    338 rdf:type schema:Person
    339 sg:person.0732742066.21 schema:affiliation grid-institutes:grid.47840.3f
    340 schema:familyName Thomas
    341 schema:givenName Brian C
    342 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0732742066.21
    343 rdf:type schema:Person
    344 sg:person.0735524175.28 schema:affiliation grid-institutes:grid.184769.5
    345 schema:familyName Castelle
    346 schema:givenName Cindy
    347 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0735524175.28
    348 rdf:type schema:Person
    349 sg:person.0773144006.96 schema:affiliation grid-institutes:grid.116068.8
    350 schema:familyName Yelton
    351 schema:givenName Alexis P
    352 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773144006.96
    353 rdf:type schema:Person
    354 sg:pub.10.1007/0-387-30743-5_7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040882595
    355 https://doi.org/10.1007/0-387-30743-5_7
    356 rdf:type schema:CreativeWork
    357 sg:pub.10.1007/978-3-540-34911-2_14 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035714652
    358 https://doi.org/10.1007/978-3-540-34911-2_14
    359 rdf:type schema:CreativeWork
    360 sg:pub.10.1007/bf00244267 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052180236
    361 https://doi.org/10.1007/bf00244267
    362 rdf:type schema:CreativeWork
    363 sg:pub.10.1007/bf00763219 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013429077
    364 https://doi.org/10.1007/bf00763219
    365 rdf:type schema:CreativeWork
    366 sg:pub.10.1007/s00203-004-0702-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038992778
    367 https://doi.org/10.1007/s00203-004-0702-4
    368 rdf:type schema:CreativeWork
    369 sg:pub.10.1007/s00239-009-9263-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032388075
    370 https://doi.org/10.1007/s00239-009-9263-0
    371 rdf:type schema:CreativeWork
    372 sg:pub.10.1007/s00284-008-9208-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024411738
    373 https://doi.org/10.1007/s00284-008-9208-7
    374 rdf:type schema:CreativeWork
    375 sg:pub.10.1007/s004380100451 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029946056
    376 https://doi.org/10.1007/s004380100451
    377 rdf:type schema:CreativeWork
    378 sg:pub.10.1007/s00792-002-0303-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1075259975
    379 https://doi.org/10.1007/s00792-002-0303-6
    380 rdf:type schema:CreativeWork
    381 sg:pub.10.1007/s00792-006-0029-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1006128997
    382 https://doi.org/10.1007/s00792-006-0029-y
    383 rdf:type schema:CreativeWork
    384 sg:pub.10.1007/s00792-006-0527-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1027279496
    385 https://doi.org/10.1007/s00792-006-0527-y
    386 rdf:type schema:CreativeWork
    387 sg:pub.10.1007/s00792-007-0108-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038703426
    388 https://doi.org/10.1007/s00792-007-0108-8
    389 rdf:type schema:CreativeWork
    390 sg:pub.10.1007/s10482-012-9872-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045576362
    391 https://doi.org/10.1007/s10482-012-9872-2
    392 rdf:type schema:CreativeWork
    393 sg:pub.10.1038/35035069 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019679930
    394 https://doi.org/10.1038/35035069
    395 rdf:type schema:CreativeWork
    396 sg:pub.10.1038/ismej.2008.90 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011791054
    397 https://doi.org/10.1038/ismej.2008.90
    398 rdf:type schema:CreativeWork
    399 sg:pub.10.1038/ismej.2010.170 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031676008
    400 https://doi.org/10.1038/ismej.2010.170
    401 rdf:type schema:CreativeWork
    402 sg:pub.10.1038/ismej.2011.75 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029730701
    403 https://doi.org/10.1038/ismej.2011.75
    404 rdf:type schema:CreativeWork
    405 sg:pub.10.1038/ismej.2011.78 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019104224
    406 https://doi.org/10.1038/ismej.2011.78
    407 rdf:type schema:CreativeWork
    408 sg:pub.10.1038/nature02340 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023089166
    409 https://doi.org/10.1038/nature02340
    410 rdf:type schema:CreativeWork
    411 sg:pub.10.1038/nature09375 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015326716
    412 https://doi.org/10.1038/nature09375
    413 rdf:type schema:CreativeWork
    414 sg:pub.10.1134/s0026261712010043 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023930793
    415 https://doi.org/10.1134/s0026261712010043
    416 rdf:type schema:CreativeWork
    417 sg:pub.10.1186/1471-2105-5-127 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051350576
    418 https://doi.org/10.1186/1471-2105-5-127
    419 rdf:type schema:CreativeWork
    420 sg:pub.10.1186/1475-2859-4-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048360411
    421 https://doi.org/10.1186/1475-2859-4-1
    422 rdf:type schema:CreativeWork
    423 sg:pub.10.1186/1475-2859-4-13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050884074
    424 https://doi.org/10.1186/1475-2859-4-13
    425 rdf:type schema:CreativeWork
    426 sg:pub.10.1186/gb-2003-4-9-r55 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041778603
    427 https://doi.org/10.1186/gb-2003-4-9-r55
    428 rdf:type schema:CreativeWork
    429 sg:pub.10.1186/gb-2007-8-1-r10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044994861
    430 https://doi.org/10.1186/gb-2007-8-1-r10
    431 rdf:type schema:CreativeWork
    432 sg:pub.10.1186/gb-2009-10-8-r85 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014147708
    433 https://doi.org/10.1186/gb-2009-10-8-r85
    434 rdf:type schema:CreativeWork
    435 grid-institutes:grid.116068.8 schema:alternateName Current address: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    436 schema:name Current address: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    437 Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    438 rdf:type schema:Organization
    439 grid-institutes:grid.184769.5 schema:alternateName Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    440 schema:name Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    441 rdf:type schema:Organization
    442 grid-institutes:grid.214458.e schema:alternateName Current address: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    443 schema:name Current address: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    444 Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
    445 rdf:type schema:Organization
    446 grid-institutes:grid.47840.3f schema:alternateName Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
    447 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    448 schema:name Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
    449 Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    450 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    451 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...