Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-11-17

AUTHORS

Meng Li, Brett J. Baker, Karthik Anantharaman, Sunit Jain, John A. Breier, Gregory J. Dick

ABSTRACT

Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling. More... »

PAGES

8933

References to SciGraph publications

  • 2013-08-29. Microbial control of the dark end of the biological pump in NATURE GEOSCIENCE
  • 2009-08-21. Community-wide analysis of microbial genome sequence signatures in GENOME BIOLOGY
  • 2002-11. Respiration in the open ocean in NATURE
  • 2006-02. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea in NATURE
  • 2010-07-05. Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean in NATURE REVIEWS MICROBIOLOGY
  • 2011-09-29. SignalP 4.0: discriminating signal peptides from transmembrane regions in NATURE METHODS
  • 2005-09. Isolation of an autotrophic ammonia-oxidizing marine archaeon in NATURE
  • 2008-05-08. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2014-12-23. A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2015-06-05. Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2015-02-03. Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2015-01-23. Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2012-06-14. Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2014-02-05. Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents in NATURE COMMUNICATIONS
  • 2013-07-14. Insights into the phylogeny and coding potential of microbial dark matter in NATURE
  • 2012-06-14. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2005-06. Genomic studies of uncultivated archaea in NATURE REVIEWS MICROBIOLOGY
  • 1992-03. Novel major archaebacterial group from marine plankton in NATURE
  • 2001-01. Archaeal dominance in the mesopelagic zone of the Pacific Ocean in NATURE
  • 2015-02-06. Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2014-12-09. Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ncomms9933

    DOI

    http://dx.doi.org/10.1038/ncomms9933

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1010303711

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26573375


    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/2008/04", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Earth Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "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/2008/0402", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Geochemistry", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0405", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Oceanography", 
            "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": "Archaea", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Carbohydrate Metabolism", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Carbohydrates", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Carbon", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Carbon Cycle", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Caribbean Region", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Fatty Acids", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Profiling", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Hydrothermal Vents", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Lipid Metabolism", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Lipids", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Oceans and Seas", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Seawater", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China", 
              "id": "http://www.grid.ac/institutes/grid.263488.3", 
              "name": [
                "Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA", 
                "Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Li", 
            "givenName": "Meng", 
            "id": "sg:person.0715634401.25", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0715634401.25"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Marine Science, University of Texas Austin, Marine Science Institute, 750 Channel View Drive, 78373, Port Aransas, Texas, USA", 
              "id": "http://www.grid.ac/institutes/grid.89336.37", 
              "name": [
                "Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA", 
                "Department of Marine Science, University of Texas Austin, Marine Science Institute, 750 Channel View Drive, 78373, Port Aransas, Texas, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Baker", 
            "givenName": "Brett J.", 
            "id": "sg:person.0651757375.15", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0651757375.15"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA", 
              "id": "http://www.grid.ac/institutes/grid.214458.e", 
              "name": [
                "Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Anantharaman", 
            "givenName": "Karthik", 
            "id": "sg:person.0714252516.09", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714252516.09"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA", 
              "id": "http://www.grid.ac/institutes/grid.214458.e", 
              "name": [
                "Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Jain", 
            "givenName": "Sunit", 
            "id": "sg:person.0646137316.29", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0646137316.29"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Texas Rio Grande Valley, 78520, Brownsville, Texas, USA", 
              "id": "http://www.grid.ac/institutes/grid.449717.8", 
              "name": [
                "Woods Hole Oceanographic Institution, 02543, Woods Hole, Massachusetts, USA", 
                "University of Texas Rio Grande Valley, 78520, Brownsville, Texas, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Breier", 
            "givenName": "John A.", 
            "id": "sg:person.0717100154.32", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717100154.32"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Center of Computational Medicine and Bioinformatics, University of Michigan, 48109, Ann Arbor, Michigan, USA", 
              "id": "http://www.grid.ac/institutes/grid.214458.e", 
              "name": [
                "Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA", 
                "Department of Ecology and Evolutionary Biology, University of Michigan, 48109, Ann Arbor, Michigan, USA", 
                "Center of Computational Medicine and Bioinformatics, University of Michigan, 48109, Ann Arbor, Michigan, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Dick", 
            "givenName": "Gregory J.", 
            "id": "sg:person.01030501116.39", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030501116.39"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/nature03911", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049439003", 
              "https://doi.org/10.1038/nature03911"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro1159", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013185112", 
              "https://doi.org/10.1038/nrmicro1159"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/356148a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035920601", 
              "https://doi.org/10.1038/356148a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2014.260", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050721755", 
              "https://doi.org/10.1038/ismej.2014.260"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature12352", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019299949", 
              "https://doi.org/10.1038/nature12352"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1701", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049894869", 
              "https://doi.org/10.1038/nmeth.1701"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2015.8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031291647", 
              "https://doi.org/10.1038/ismej.2015.8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2015.4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008236051", 
              "https://doi.org/10.1038/ismej.2015.4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2014.249", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021352867", 
              "https://doi.org/10.1038/ismej.2014.249"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2012.63", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035843725", 
              "https://doi.org/10.1038/ismej.2012.63"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35054051", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000389432", 
              "https://doi.org/10.1038/35054051"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2012.64", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013864277", 
              "https://doi.org/10.1038/ismej.2012.64"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro2386", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024546834", 
              "https://doi.org/10.1038/nrmicro2386"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2008.40", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018243775", 
              "https://doi.org/10.1038/ismej.2008.40"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms4192", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050322991", 
              "https://doi.org/10.1038/ncomms4192"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2015.81", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023964718", 
              "https://doi.org/10.1038/ismej.2015.81"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature04435", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000290333", 
              "https://doi.org/10.1038/nature04435"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2014.228", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030711964", 
              "https://doi.org/10.1038/ismej.2014.228"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature01165", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008007474", 
              "https://doi.org/10.1038/nature01165"
            ], 
            "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.10.1038/ngeo1921", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036802340", 
              "https://doi.org/10.1038/ngeo1921"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2015-11-17", 
        "datePublishedReg": "2015-11-17", 
        "description": "Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950\u2009m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/ncomms9933", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.3118884", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3118871", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1043282", 
            "issn": [
              "2041-1723"
            ], 
            "name": "Nature Communications", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "6"
          }
        ], 
        "keywords": [
          "deep ocean", 
          "marine archaea", 
          "different ocean basins", 
          "transcriptomic evidence", 
          "hydrothermal vent plume", 
          "global carbon cycle", 
          "global carbon cycling", 
          "deep-sea archaea", 
          "ocean basins", 
          "background seawater", 
          "ocean surface", 
          "gene expression patterns", 
          "vent plumes", 
          "carbon cycle", 
          "carbon cycling", 
          "organic carbon", 
          "organic matter", 
          "archaeal groups", 
          "metabolic reconstruction", 
          "source of carbon", 
          "metabolic strategies", 
          "Ocean", 
          "expression patterns", 
          "archaea", 
          "microbial activity", 
          "important process", 
          "extensive mechanisms", 
          "organic compounds", 
          "physiological properties", 
          "critical role", 
          "diverse organic compounds", 
          "carbon", 
          "fatty acids", 
          "seafloor", 
          "basin", 
          "plume", 
          "seawater", 
          "depth", 
          "genome", 
          "flux", 
          "heterotrophs", 
          "protein", 
          "cycling", 
          "microorganisms", 
          "key step", 
          "matter", 
          "reconstruction", 
          "source", 
          "lipids", 
          "cycle", 
          "carbohydrates", 
          "evidence", 
          "surface", 
          "acid", 
          "patterns", 
          "mechanism", 
          "role", 
          "activity", 
          "process", 
          "compounds", 
          "light", 
          "step", 
          "strategies", 
          "results", 
          "energy", 
          "properties", 
          "group"
        ], 
        "name": "Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea", 
        "pagination": "8933", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1010303711"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/ncomms9933"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "26573375"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/ncomms9933", 
          "https://app.dimensions.ai/details/publication/pub.1010303711"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-05-20T07:31", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220519/entities/gbq_results/article/article_678.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/ncomms9933"
      }
    ]
     

    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.10.1038/ncomms9933'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/ncomms9933'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/ncomms9933'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/ncomms9933'


     

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

    338 TRIPLES      22 PREDICATES      132 URIs      100 LITERALS      22 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/ncomms9933 schema:about N19872274cfbf40a2a5dc2fe890796563
    2 N3e993f43dc144bada720bf32eac12167
    3 N42d3e32388584c56a4aa605acbcaf7d7
    4 N68e69cefc61f41e99106b1ce136dcb2c
    5 N71f9f4a602e6489ca0ec1ac10b17517c
    6 N7cf3ce9acae344358fcc884fe095aff1
    7 N85cb90b8fb804575be4a39341223fff9
    8 N94c6f160ec3645719391ecbccb51a425
    9 Nb414c81c5d9a47299f756506120a6e3c
    10 Nc30485ac1f7a4a2c96ffc24478dac4a1
    11 Ncd9562ed62454fccbd53908974376e82
    12 Nef975ab88a0449308ff86937cd5f04b7
    13 Nf0ed1e308c344249ad12ded644bec53d
    14 Nf4df914562f141aaaa136ebd36bb7ac6
    15 Nf5d91d0933624d23b1c588ea04a24389
    16 anzsrc-for:04
    17 anzsrc-for:0402
    18 anzsrc-for:0405
    19 anzsrc-for:06
    20 anzsrc-for:0605
    21 schema:author Nb2a0249c458e43c4bc45e53514ce88fe
    22 schema:citation sg:pub.10.1038/35054051
    23 sg:pub.10.1038/356148a0
    24 sg:pub.10.1038/ismej.2008.40
    25 sg:pub.10.1038/ismej.2012.63
    26 sg:pub.10.1038/ismej.2012.64
    27 sg:pub.10.1038/ismej.2014.228
    28 sg:pub.10.1038/ismej.2014.249
    29 sg:pub.10.1038/ismej.2014.260
    30 sg:pub.10.1038/ismej.2015.4
    31 sg:pub.10.1038/ismej.2015.8
    32 sg:pub.10.1038/ismej.2015.81
    33 sg:pub.10.1038/nature01165
    34 sg:pub.10.1038/nature03911
    35 sg:pub.10.1038/nature04435
    36 sg:pub.10.1038/nature12352
    37 sg:pub.10.1038/ncomms4192
    38 sg:pub.10.1038/ngeo1921
    39 sg:pub.10.1038/nmeth.1701
    40 sg:pub.10.1038/nrmicro1159
    41 sg:pub.10.1038/nrmicro2386
    42 sg:pub.10.1186/gb-2009-10-8-r85
    43 schema:datePublished 2015-11-17
    44 schema:datePublishedReg 2015-11-17
    45 schema:description Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.
    46 schema:genre article
    47 schema:inLanguage en
    48 schema:isAccessibleForFree true
    49 schema:isPartOf N38b193f1018f411eab685e2166076f22
    50 N79848fd6f47c4962a030fcf4072ea27a
    51 sg:journal.1043282
    52 schema:keywords Ocean
    53 acid
    54 activity
    55 archaea
    56 archaeal groups
    57 background seawater
    58 basin
    59 carbohydrates
    60 carbon
    61 carbon cycle
    62 carbon cycling
    63 compounds
    64 critical role
    65 cycle
    66 cycling
    67 deep ocean
    68 deep-sea archaea
    69 depth
    70 different ocean basins
    71 diverse organic compounds
    72 energy
    73 evidence
    74 expression patterns
    75 extensive mechanisms
    76 fatty acids
    77 flux
    78 gene expression patterns
    79 genome
    80 global carbon cycle
    81 global carbon cycling
    82 group
    83 heterotrophs
    84 hydrothermal vent plume
    85 important process
    86 key step
    87 light
    88 lipids
    89 marine archaea
    90 matter
    91 mechanism
    92 metabolic reconstruction
    93 metabolic strategies
    94 microbial activity
    95 microorganisms
    96 ocean basins
    97 ocean surface
    98 organic carbon
    99 organic compounds
    100 organic matter
    101 patterns
    102 physiological properties
    103 plume
    104 process
    105 properties
    106 protein
    107 reconstruction
    108 results
    109 role
    110 seafloor
    111 seawater
    112 source
    113 source of carbon
    114 step
    115 strategies
    116 surface
    117 transcriptomic evidence
    118 vent plumes
    119 schema:name Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea
    120 schema:pagination 8933
    121 schema:productId N1143171d98e94e138326874aba6af0be
    122 Na0947484de7e4d9495a83a75f1d039ed
    123 Nfc4d67893fd84001a570d2b1afab7bb0
    124 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010303711
    125 https://doi.org/10.1038/ncomms9933
    126 schema:sdDatePublished 2022-05-20T07:31
    127 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    128 schema:sdPublisher N96a7c3bfc0ee4eda8759e51f2ab51462
    129 schema:url https://doi.org/10.1038/ncomms9933
    130 sgo:license sg:explorer/license/
    131 sgo:sdDataset articles
    132 rdf:type schema:ScholarlyArticle
    133 N1143171d98e94e138326874aba6af0be schema:name doi
    134 schema:value 10.1038/ncomms9933
    135 rdf:type schema:PropertyValue
    136 N19872274cfbf40a2a5dc2fe890796563 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    137 schema:name Archaea
    138 rdf:type schema:DefinedTerm
    139 N38b193f1018f411eab685e2166076f22 schema:issueNumber 1
    140 rdf:type schema:PublicationIssue
    141 N3e993f43dc144bada720bf32eac12167 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    142 schema:name Carbohydrate Metabolism
    143 rdf:type schema:DefinedTerm
    144 N3f7a6873aeb64f0a8fbd6eda6e7c3b58 rdf:first sg:person.0651757375.15
    145 rdf:rest Ne923fed730bb4632b2208498d7284cc3
    146 N42d3e32388584c56a4aa605acbcaf7d7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    147 schema:name Lipid Metabolism
    148 rdf:type schema:DefinedTerm
    149 N68e69cefc61f41e99106b1ce136dcb2c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    150 schema:name Lipids
    151 rdf:type schema:DefinedTerm
    152 N71f9f4a602e6489ca0ec1ac10b17517c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    153 schema:name Carbon Cycle
    154 rdf:type schema:DefinedTerm
    155 N79848fd6f47c4962a030fcf4072ea27a schema:volumeNumber 6
    156 rdf:type schema:PublicationVolume
    157 N79ace53067ef4a4690806f2b776dd5a1 rdf:first sg:person.0646137316.29
    158 rdf:rest Ncd2ce0dfa70a4c7d8bb54e15346c64e8
    159 N7cf3ce9acae344358fcc884fe095aff1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    160 schema:name Carbohydrates
    161 rdf:type schema:DefinedTerm
    162 N85cb90b8fb804575be4a39341223fff9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    163 schema:name Oceans and Seas
    164 rdf:type schema:DefinedTerm
    165 N94c6f160ec3645719391ecbccb51a425 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    166 schema:name Gene Expression Profiling
    167 rdf:type schema:DefinedTerm
    168 N96a7c3bfc0ee4eda8759e51f2ab51462 schema:name Springer Nature - SN SciGraph project
    169 rdf:type schema:Organization
    170 Na0947484de7e4d9495a83a75f1d039ed schema:name pubmed_id
    171 schema:value 26573375
    172 rdf:type schema:PropertyValue
    173 Nb2a0249c458e43c4bc45e53514ce88fe rdf:first sg:person.0715634401.25
    174 rdf:rest N3f7a6873aeb64f0a8fbd6eda6e7c3b58
    175 Nb414c81c5d9a47299f756506120a6e3c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    176 schema:name Proteins
    177 rdf:type schema:DefinedTerm
    178 Nc30485ac1f7a4a2c96ffc24478dac4a1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    179 schema:name Seawater
    180 rdf:type schema:DefinedTerm
    181 Ncd2ce0dfa70a4c7d8bb54e15346c64e8 rdf:first sg:person.0717100154.32
    182 rdf:rest Nda97ca8b4df64f09bc7f337cf156ad1c
    183 Ncd9562ed62454fccbd53908974376e82 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    184 schema:name Genomics
    185 rdf:type schema:DefinedTerm
    186 Nda97ca8b4df64f09bc7f337cf156ad1c rdf:first sg:person.01030501116.39
    187 rdf:rest rdf:nil
    188 Ne923fed730bb4632b2208498d7284cc3 rdf:first sg:person.0714252516.09
    189 rdf:rest N79ace53067ef4a4690806f2b776dd5a1
    190 Nef975ab88a0449308ff86937cd5f04b7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    191 schema:name Hydrothermal Vents
    192 rdf:type schema:DefinedTerm
    193 Nf0ed1e308c344249ad12ded644bec53d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    194 schema:name Caribbean Region
    195 rdf:type schema:DefinedTerm
    196 Nf4df914562f141aaaa136ebd36bb7ac6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    197 schema:name Fatty Acids
    198 rdf:type schema:DefinedTerm
    199 Nf5d91d0933624d23b1c588ea04a24389 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    200 schema:name Carbon
    201 rdf:type schema:DefinedTerm
    202 Nfc4d67893fd84001a570d2b1afab7bb0 schema:name dimensions_id
    203 schema:value pub.1010303711
    204 rdf:type schema:PropertyValue
    205 anzsrc-for:04 schema:inDefinedTermSet anzsrc-for:
    206 schema:name Earth Sciences
    207 rdf:type schema:DefinedTerm
    208 anzsrc-for:0402 schema:inDefinedTermSet anzsrc-for:
    209 schema:name Geochemistry
    210 rdf:type schema:DefinedTerm
    211 anzsrc-for:0405 schema:inDefinedTermSet anzsrc-for:
    212 schema:name Oceanography
    213 rdf:type schema:DefinedTerm
    214 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    215 schema:name Biological Sciences
    216 rdf:type schema:DefinedTerm
    217 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
    218 schema:name Microbiology
    219 rdf:type schema:DefinedTerm
    220 sg:grant.3118871 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms9933
    221 rdf:type schema:MonetaryGrant
    222 sg:grant.3118884 http://pending.schema.org/fundedItem sg:pub.10.1038/ncomms9933
    223 rdf:type schema:MonetaryGrant
    224 sg:journal.1043282 schema:issn 2041-1723
    225 schema:name Nature Communications
    226 schema:publisher Springer Nature
    227 rdf:type schema:Periodical
    228 sg:person.01030501116.39 schema:affiliation grid-institutes:grid.214458.e
    229 schema:familyName Dick
    230 schema:givenName Gregory J.
    231 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030501116.39
    232 rdf:type schema:Person
    233 sg:person.0646137316.29 schema:affiliation grid-institutes:grid.214458.e
    234 schema:familyName Jain
    235 schema:givenName Sunit
    236 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0646137316.29
    237 rdf:type schema:Person
    238 sg:person.0651757375.15 schema:affiliation grid-institutes:grid.89336.37
    239 schema:familyName Baker
    240 schema:givenName Brett J.
    241 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0651757375.15
    242 rdf:type schema:Person
    243 sg:person.0714252516.09 schema:affiliation grid-institutes:grid.214458.e
    244 schema:familyName Anantharaman
    245 schema:givenName Karthik
    246 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714252516.09
    247 rdf:type schema:Person
    248 sg:person.0715634401.25 schema:affiliation grid-institutes:grid.263488.3
    249 schema:familyName Li
    250 schema:givenName Meng
    251 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0715634401.25
    252 rdf:type schema:Person
    253 sg:person.0717100154.32 schema:affiliation grid-institutes:grid.449717.8
    254 schema:familyName Breier
    255 schema:givenName John A.
    256 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717100154.32
    257 rdf:type schema:Person
    258 sg:pub.10.1038/35054051 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000389432
    259 https://doi.org/10.1038/35054051
    260 rdf:type schema:CreativeWork
    261 sg:pub.10.1038/356148a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035920601
    262 https://doi.org/10.1038/356148a0
    263 rdf:type schema:CreativeWork
    264 sg:pub.10.1038/ismej.2008.40 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018243775
    265 https://doi.org/10.1038/ismej.2008.40
    266 rdf:type schema:CreativeWork
    267 sg:pub.10.1038/ismej.2012.63 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035843725
    268 https://doi.org/10.1038/ismej.2012.63
    269 rdf:type schema:CreativeWork
    270 sg:pub.10.1038/ismej.2012.64 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013864277
    271 https://doi.org/10.1038/ismej.2012.64
    272 rdf:type schema:CreativeWork
    273 sg:pub.10.1038/ismej.2014.228 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030711964
    274 https://doi.org/10.1038/ismej.2014.228
    275 rdf:type schema:CreativeWork
    276 sg:pub.10.1038/ismej.2014.249 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021352867
    277 https://doi.org/10.1038/ismej.2014.249
    278 rdf:type schema:CreativeWork
    279 sg:pub.10.1038/ismej.2014.260 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050721755
    280 https://doi.org/10.1038/ismej.2014.260
    281 rdf:type schema:CreativeWork
    282 sg:pub.10.1038/ismej.2015.4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008236051
    283 https://doi.org/10.1038/ismej.2015.4
    284 rdf:type schema:CreativeWork
    285 sg:pub.10.1038/ismej.2015.8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031291647
    286 https://doi.org/10.1038/ismej.2015.8
    287 rdf:type schema:CreativeWork
    288 sg:pub.10.1038/ismej.2015.81 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023964718
    289 https://doi.org/10.1038/ismej.2015.81
    290 rdf:type schema:CreativeWork
    291 sg:pub.10.1038/nature01165 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008007474
    292 https://doi.org/10.1038/nature01165
    293 rdf:type schema:CreativeWork
    294 sg:pub.10.1038/nature03911 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049439003
    295 https://doi.org/10.1038/nature03911
    296 rdf:type schema:CreativeWork
    297 sg:pub.10.1038/nature04435 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000290333
    298 https://doi.org/10.1038/nature04435
    299 rdf:type schema:CreativeWork
    300 sg:pub.10.1038/nature12352 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019299949
    301 https://doi.org/10.1038/nature12352
    302 rdf:type schema:CreativeWork
    303 sg:pub.10.1038/ncomms4192 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050322991
    304 https://doi.org/10.1038/ncomms4192
    305 rdf:type schema:CreativeWork
    306 sg:pub.10.1038/ngeo1921 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036802340
    307 https://doi.org/10.1038/ngeo1921
    308 rdf:type schema:CreativeWork
    309 sg:pub.10.1038/nmeth.1701 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049894869
    310 https://doi.org/10.1038/nmeth.1701
    311 rdf:type schema:CreativeWork
    312 sg:pub.10.1038/nrmicro1159 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013185112
    313 https://doi.org/10.1038/nrmicro1159
    314 rdf:type schema:CreativeWork
    315 sg:pub.10.1038/nrmicro2386 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024546834
    316 https://doi.org/10.1038/nrmicro2386
    317 rdf:type schema:CreativeWork
    318 sg:pub.10.1186/gb-2009-10-8-r85 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014147708
    319 https://doi.org/10.1186/gb-2009-10-8-r85
    320 rdf:type schema:CreativeWork
    321 grid-institutes:grid.214458.e schema:alternateName Center of Computational Medicine and Bioinformatics, University of Michigan, 48109, Ann Arbor, Michigan, USA
    322 Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA
    323 schema:name Center of Computational Medicine and Bioinformatics, University of Michigan, 48109, Ann Arbor, Michigan, USA
    324 Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA
    325 Department of Ecology and Evolutionary Biology, University of Michigan, 48109, Ann Arbor, Michigan, USA
    326 rdf:type schema:Organization
    327 grid-institutes:grid.263488.3 schema:alternateName Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
    328 schema:name Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA
    329 Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
    330 rdf:type schema:Organization
    331 grid-institutes:grid.449717.8 schema:alternateName University of Texas Rio Grande Valley, 78520, Brownsville, Texas, USA
    332 schema:name University of Texas Rio Grande Valley, 78520, Brownsville, Texas, USA
    333 Woods Hole Oceanographic Institution, 02543, Woods Hole, Massachusetts, USA
    334 rdf:type schema:Organization
    335 grid-institutes:grid.89336.37 schema:alternateName Department of Marine Science, University of Texas Austin, Marine Science Institute, 750 Channel View Drive, 78373, Port Aransas, Texas, USA
    336 schema:name Department of Earth and Environmental Sciences, University of Michigan, 48109, Ann Arbor, Michigan, USA
    337 Department of Marine Science, University of Texas Austin, Marine Science Institute, 750 Channel View Drive, 78373, Port Aransas, Texas, USA
    338 rdf:type schema:Organization
     




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


    ...