Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea) View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-01-06

AUTHORS

Michail M Yakimov, Violetta La Cono, Francesco Smedile, Thomas H DeLuca, Silvia Juárez, Sergio Ciordia, Marisol Fernández, Juan Pablo Albar, Manuel Ferrer, Peter N Golyshin, Laura Giuliano

ABSTRACT

Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of ‘deep-sea’ clades distinct from ‘shallow’ representatives. Measured deep-sea dark CO2 fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [14C]HCO3 incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance. More... »

PAGES

945-961

References to SciGraph publications

  • 2008-03. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota in NATURE REVIEWS MICROBIOLOGY
  • 2008-12-10. Metabolism of the deep in NATURE
  • 2007-09-17. Type-2 copper-containing enzymes in CELLULAR AND MOLECULAR LIFE SCIENCES
  • 2008-11-26. Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic in NATURE
  • 2007-10-04. Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic lake L'Atalante, Eastern Mediterranean Sea in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2009-09-30. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria in NATURE
  • 2010-05-10. Autotrophic carbon fixation in archaea in NATURE REVIEWS MICROBIOLOGY
  • 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
  • 2008-01-17. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-08-14. Molecular signatures for the Crenarchaeota and the Thaumarchaeota in ANTONIE VAN LEEUWENHOEK
  • 2007-06-01. Role of nitrite reductase in the ammonia-oxidizing pathway of Nitrosomonas europaea in ARCHIVES OF MICROBIOLOGY
  • 2008-09-25. Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2001-01. Archaeal dominance in the mesopelagic zone of the Pacific Ocean in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ismej.2010.197

    DOI

    http://dx.doi.org/10.1038/ismej.2010.197

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1007955479

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21209665


    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/2008/05", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Environmental 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/2008/10", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Technology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Ammonia", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Autotrophic Processes", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Carbon", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Crenarchaeota", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Hydro-Lyases", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mediterranean Sea", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Molecular Sequence Data", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Nitrogen", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Oxidation-Reduction", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Oxidoreductases", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Messenger", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Seawater", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Urease", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy", 
              "id": "http://www.grid.ac/institutes/grid.5326.2", 
              "name": [
                "Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yakimov", 
            "givenName": "Michail M", 
            "id": "sg:person.01154204633.81", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01154204633.81"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy", 
              "id": "http://www.grid.ac/institutes/grid.5326.2", 
              "name": [
                "Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Cono", 
            "givenName": "Violetta La", 
            "id": "sg:person.01266255136.66", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01266255136.66"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy", 
              "id": "http://www.grid.ac/institutes/grid.5326.2", 
              "name": [
                "Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Smedile", 
            "givenName": "Francesco", 
            "id": "sg:person.0723527633.28", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0723527633.28"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, UK", 
              "id": "http://www.grid.ac/institutes/grid.7362.0", 
              "name": [
                "School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "DeLuca", 
            "givenName": "Thomas H", 
            "id": "sg:person.0631423323.50", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0631423323.50"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Proteomic Facility, Centro Nacional de Biotecnolog\u00eda, CSIC, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.428469.5", 
              "name": [
                "Proteomic Facility, Centro Nacional de Biotecnolog\u00eda, CSIC, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ju\u00e1rez", 
            "givenName": "Silvia", 
            "id": "sg:person.01133004220.53", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01133004220.53"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Proteomic Facility, Centro Nacional de Biotecnolog\u00eda, CSIC, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.428469.5", 
              "name": [
                "Proteomic Facility, Centro Nacional de Biotecnolog\u00eda, CSIC, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ciordia", 
            "givenName": "Sergio", 
            "id": "sg:person.0756375026.78", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756375026.78"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Proteomic Facility, Centro Nacional de Biotecnolog\u00eda, CSIC, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.428469.5", 
              "name": [
                "Proteomic Facility, Centro Nacional de Biotecnolog\u00eda, CSIC, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Fern\u00e1ndez", 
            "givenName": "Marisol", 
            "id": "sg:person.0605571626.58", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0605571626.58"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Proteomic Facility, Centro Nacional de Biotecnolog\u00eda, CSIC, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.428469.5", 
              "name": [
                "Proteomic Facility, Centro Nacional de Biotecnolog\u00eda, CSIC, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Albar", 
            "givenName": "Juan Pablo", 
            "id": "sg:person.01002654241.76", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01002654241.76"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Laboratory of Enzyme Discovery, Institute of Catalysis, CSIC, Madrid, Spain", 
              "id": "http://www.grid.ac/institutes/grid.418900.4", 
              "name": [
                "Laboratory of Enzyme Discovery, Institute of Catalysis, CSIC, Madrid, Spain"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ferrer", 
            "givenName": "Manuel", 
            "id": "sg:person.0623750303.04", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623750303.04"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK", 
              "id": "http://www.grid.ac/institutes/grid.7362.0", 
              "name": [
                "School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Golyshin", 
            "givenName": "Peter N", 
            "id": "sg:person.016136043077.19", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016136043077.19"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Mediterranean Science Commission (CIESM), Monaco", 
              "id": "http://www.grid.ac/institutes/grid.493967.6", 
              "name": [
                "Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy", 
                "Mediterranean Science Commission (CIESM), Monaco"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Giuliano", 
            "givenName": "Laura", 
            "id": "sg:person.01325043110.55", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01325043110.55"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/s00018-007-7310-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008459590", 
              "https://doi.org/10.1007/s00018-007-7310-9"
            ], 
            "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/nrmicro2365", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000545292", 
              "https://doi.org/10.1038/nrmicro2365"
            ], 
            "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/nature07535", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010350008", 
              "https://doi.org/10.1038/nature07535"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "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.10.1038/456712a", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048015971", 
              "https://doi.org/10.1038/456712a"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00203-007-0255-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020689761", 
              "https://doi.org/10.1007/s00203-007-0255-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro1852", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051468230", 
              "https://doi.org/10.1038/nrmicro1852"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08465", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011818868", 
              "https://doi.org/10.1038/nature08465"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2008.94", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021747624", 
              "https://doi.org/10.1038/ismej.2008.94"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10482-010-9488-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030785101", 
              "https://doi.org/10.1007/s10482-010-9488-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2007.83", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032428643", 
              "https://doi.org/10.1038/ismej.2007.83"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ismej.2007.118", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007290897", 
              "https://doi.org/10.1038/ismej.2007.118"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2011-01-06", 
        "datePublishedReg": "2011-01-06", 
        "description": "Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of \u2018deep-sea\u2019 clades distinct from \u2018shallow\u2019 representatives. Measured deep-sea dark CO2 fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [14C]HCO3 incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/ismej.2010.197", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.3770987", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3772495", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1038436", 
            "issn": [
              "1751-7362", 
              "1751-7370"
            ], 
            "name": "The ISME Journal: Multidisciplinary Journal of Microbial Ecology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "6", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "5"
          }
        ], 
        "keywords": [
          "ammonia-oxidizing Crenarchaeota", 
          "shotgun proteomics approach", 
          "different metabolic processes", 
          "autotrophic ammonia oxidizers", 
          "acetyl-CoA carboxylase", 
          "mesophilic Crenarchaeota", 
          "pivotal organisms", 
          "specific functional attributes", 
          "proteomic approach", 
          "molecular data", 
          "photosynthetic biomass production", 
          "ammonia oxidizers", 
          "Crenarchaeota", 
          "marine ecosystems", 
          "metabolic processes", 
          "nitrite reductase", 
          "epipelagic zone", 
          "biomass production", 
          "primary production", 
          "gene ratio", 
          "carbon cycling", 
          "genes", 
          "incorporation experiments", 
          "functional attributes", 
          "predominant group", 
          "Tyrrhenian Sea", 
          "nirK", 
          "C cycle", 
          "protein", 
          "global importance", 
          "ureC", 
          "deep-sea sequences", 
          "southern Tyrrhenian Sea", 
          "autotrophy", 
          "offshore sites", 
          "carboxylase", 
          "organisms", 
          "deep water", 
          "vertical distribution", 
          "ecosystems", 
          "dehydratase", 
          "reductase", 
          "microorganisms", 
          "physiology", 
          "Sea", 
          "sequence", 
          "production", 
          "cells", 
          "urease", 
          "oligopeptides", 
          "cycling", 
          "sites", 
          "nitrogen", 
          "oxidizer", 
          "shallow", 
          "process", 
          "representatives", 
          "cycle", 
          "Tyrrhenian Deep Water", 
          "sink", 
          "presence", 
          "hitherto", 
          "significant contributor", 
          "importance", 
          "ammonia", 
          "affiliation", 
          "significance", 
          "distribution", 
          "analysis", 
          "water", 
          "zone", 
          "contributor", 
          "experiments", 
          "capacity", 
          "clear proof", 
          "study", 
          "contribution", 
          "area", 
          "data", 
          "attributes", 
          "results", 
          "group", 
          "estimates", 
          "approach", 
          "ratio", 
          "values", 
          "proof", 
          "cases", 
          "median value"
        ], 
        "name": "Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)", 
        "pagination": "945-961", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1007955479"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/ismej.2010.197"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "21209665"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/ismej.2010.197", 
          "https://app.dimensions.ai/details/publication/pub.1007955479"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-08-04T16:59", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220804/entities/gbq_results/article/article_539.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/ismej.2010.197"
      }
    ]
     

    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/ismej.2010.197'

    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/ismej.2010.197'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/ismej.2010.197'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/ismej.2010.197'


     

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

    355 TRIPLES      21 PREDICATES      143 URIs      120 LITERALS      21 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/ismej.2010.197 schema:about N0805bc434c634d6b894f2dfe3f2d4cf1
    2 N0a0c18c6b97747749dab2dc171ee2344
    3 N275ef97dfa4b45af8d3117a481f71830
    4 N3171c9cf7b2448398871822d41887d55
    5 N55f32434bbf942b18c74893113ce5ff3
    6 N58557f61529a4fad84dcb016285af442
    7 N5f6e8f9526314fd0973719057080eabb
    8 N662274060457483e8a37bbe036821faf
    9 N8363eca9e5534f229ec1ff47ee275239
    10 N906446e38eae4678962941904d773d84
    11 N9c52779266784ef79cabdae04ea87230
    12 Na1f33c1349924101b3121ae247ddc365
    13 Na8f60a0334f64546a406effe57c7754b
    14 Naa2973fea5f2487780177d1cb0241264
    15 anzsrc-for:05
    16 anzsrc-for:06
    17 anzsrc-for:10
    18 schema:author N24602527710f4c63be4a6bc23df30c0d
    19 schema:citation sg:pub.10.1007/s00018-007-7310-9
    20 sg:pub.10.1007/s00203-007-0255-4
    21 sg:pub.10.1007/s10482-010-9488-3
    22 sg:pub.10.1038/35054051
    23 sg:pub.10.1038/456712a
    24 sg:pub.10.1038/ismej.2007.118
    25 sg:pub.10.1038/ismej.2007.83
    26 sg:pub.10.1038/ismej.2008.40
    27 sg:pub.10.1038/ismej.2008.94
    28 sg:pub.10.1038/nature03911
    29 sg:pub.10.1038/nature07535
    30 sg:pub.10.1038/nature08465
    31 sg:pub.10.1038/nrmicro1852
    32 sg:pub.10.1038/nrmicro2365
    33 schema:datePublished 2011-01-06
    34 schema:datePublishedReg 2011-01-06
    35 schema:description Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of ‘deep-sea’ clades distinct from ‘shallow’ representatives. Measured deep-sea dark CO2 fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [14C]HCO3 incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance.
    36 schema:genre article
    37 schema:isAccessibleForFree true
    38 schema:isPartOf N3ce277f40f4f4a54bf66aca6eba05c28
    39 N55ca59ba43ca49538b9faae2b77c6201
    40 sg:journal.1038436
    41 schema:keywords C cycle
    42 Crenarchaeota
    43 Sea
    44 Tyrrhenian Deep Water
    45 Tyrrhenian Sea
    46 acetyl-CoA carboxylase
    47 affiliation
    48 ammonia
    49 ammonia oxidizers
    50 ammonia-oxidizing Crenarchaeota
    51 analysis
    52 approach
    53 area
    54 attributes
    55 autotrophic ammonia oxidizers
    56 autotrophy
    57 biomass production
    58 capacity
    59 carbon cycling
    60 carboxylase
    61 cases
    62 cells
    63 clear proof
    64 contribution
    65 contributor
    66 cycle
    67 cycling
    68 data
    69 deep water
    70 deep-sea sequences
    71 dehydratase
    72 different metabolic processes
    73 distribution
    74 ecosystems
    75 epipelagic zone
    76 estimates
    77 experiments
    78 functional attributes
    79 gene ratio
    80 genes
    81 global importance
    82 group
    83 hitherto
    84 importance
    85 incorporation experiments
    86 marine ecosystems
    87 median value
    88 mesophilic Crenarchaeota
    89 metabolic processes
    90 microorganisms
    91 molecular data
    92 nirK
    93 nitrite reductase
    94 nitrogen
    95 offshore sites
    96 oligopeptides
    97 organisms
    98 oxidizer
    99 photosynthetic biomass production
    100 physiology
    101 pivotal organisms
    102 predominant group
    103 presence
    104 primary production
    105 process
    106 production
    107 proof
    108 protein
    109 proteomic approach
    110 ratio
    111 reductase
    112 representatives
    113 results
    114 sequence
    115 shallow
    116 shotgun proteomics approach
    117 significance
    118 significant contributor
    119 sink
    120 sites
    121 southern Tyrrhenian Sea
    122 specific functional attributes
    123 study
    124 ureC
    125 urease
    126 values
    127 vertical distribution
    128 water
    129 zone
    130 schema:name Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)
    131 schema:pagination 945-961
    132 schema:productId Na99a0bd430c04d4aa84f89df48321c4f
    133 Nc2bea63f4fd6421f83bf93fb9150297b
    134 Nd41fe96665fb49d7918a80b6ed1a5e80
    135 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007955479
    136 https://doi.org/10.1038/ismej.2010.197
    137 schema:sdDatePublished 2022-08-04T16:59
    138 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    139 schema:sdPublisher Nb60aff07e78c4e1bb395ef8467cf549d
    140 schema:url https://doi.org/10.1038/ismej.2010.197
    141 sgo:license sg:explorer/license/
    142 sgo:sdDataset articles
    143 rdf:type schema:ScholarlyArticle
    144 N0805bc434c634d6b894f2dfe3f2d4cf1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    145 schema:name RNA, Messenger
    146 rdf:type schema:DefinedTerm
    147 N0a0c18c6b97747749dab2dc171ee2344 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    148 schema:name Mediterranean Sea
    149 rdf:type schema:DefinedTerm
    150 N0eaf4bb088ed4cc0bf01f71b1e9cff3c rdf:first sg:person.0623750303.04
    151 rdf:rest N8498e7fbce9446409b7095efa42b5f05
    152 N24602527710f4c63be4a6bc23df30c0d rdf:first sg:person.01154204633.81
    153 rdf:rest N556361560a7244e184cd8d753ba30d16
    154 N275ef97dfa4b45af8d3117a481f71830 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    155 schema:name Autotrophic Processes
    156 rdf:type schema:DefinedTerm
    157 N3171c9cf7b2448398871822d41887d55 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    158 schema:name Phylogeny
    159 rdf:type schema:DefinedTerm
    160 N3ce277f40f4f4a54bf66aca6eba05c28 schema:issueNumber 6
    161 rdf:type schema:PublicationIssue
    162 N48e7ec1d2db9465080553a088c9d868f rdf:first sg:person.01325043110.55
    163 rdf:rest rdf:nil
    164 N556361560a7244e184cd8d753ba30d16 rdf:first sg:person.01266255136.66
    165 rdf:rest N9cfbec2e390c483abf96cf408145cc8f
    166 N55ca59ba43ca49538b9faae2b77c6201 schema:volumeNumber 5
    167 rdf:type schema:PublicationVolume
    168 N55f32434bbf942b18c74893113ce5ff3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    169 schema:name Oxidoreductases
    170 rdf:type schema:DefinedTerm
    171 N58557f61529a4fad84dcb016285af442 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    172 schema:name Carbon
    173 rdf:type schema:DefinedTerm
    174 N5f6e8f9526314fd0973719057080eabb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    175 schema:name Nitrogen
    176 rdf:type schema:DefinedTerm
    177 N662274060457483e8a37bbe036821faf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    178 schema:name Seawater
    179 rdf:type schema:DefinedTerm
    180 N8363eca9e5534f229ec1ff47ee275239 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    181 schema:name Hydro-Lyases
    182 rdf:type schema:DefinedTerm
    183 N8498e7fbce9446409b7095efa42b5f05 rdf:first sg:person.016136043077.19
    184 rdf:rest N48e7ec1d2db9465080553a088c9d868f
    185 N906446e38eae4678962941904d773d84 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    186 schema:name Crenarchaeota
    187 rdf:type schema:DefinedTerm
    188 N9c52779266784ef79cabdae04ea87230 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    189 schema:name Ammonia
    190 rdf:type schema:DefinedTerm
    191 N9cfbec2e390c483abf96cf408145cc8f rdf:first sg:person.0723527633.28
    192 rdf:rest Ned8c44558954449ebaecb8ce3b63a61d
    193 Na1f33c1349924101b3121ae247ddc365 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    194 schema:name Molecular Sequence Data
    195 rdf:type schema:DefinedTerm
    196 Na8f60a0334f64546a406effe57c7754b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    197 schema:name Urease
    198 rdf:type schema:DefinedTerm
    199 Na99a0bd430c04d4aa84f89df48321c4f schema:name doi
    200 schema:value 10.1038/ismej.2010.197
    201 rdf:type schema:PropertyValue
    202 Naa2973fea5f2487780177d1cb0241264 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    203 schema:name Oxidation-Reduction
    204 rdf:type schema:DefinedTerm
    205 Nb4608584284440d1a52df0f5ba7e5331 rdf:first sg:person.0605571626.58
    206 rdf:rest Nfbd75dce4a5c49e0ba710084c650d342
    207 Nb60aff07e78c4e1bb395ef8467cf549d schema:name Springer Nature - SN SciGraph project
    208 rdf:type schema:Organization
    209 Nc2bea63f4fd6421f83bf93fb9150297b schema:name dimensions_id
    210 schema:value pub.1007955479
    211 rdf:type schema:PropertyValue
    212 Nd30e31ec966e42be95f974b9543f6274 rdf:first sg:person.01133004220.53
    213 rdf:rest Nf27d7f678de94db4a89f113ac60a0d56
    214 Nd41fe96665fb49d7918a80b6ed1a5e80 schema:name pubmed_id
    215 schema:value 21209665
    216 rdf:type schema:PropertyValue
    217 Ned8c44558954449ebaecb8ce3b63a61d rdf:first sg:person.0631423323.50
    218 rdf:rest Nd30e31ec966e42be95f974b9543f6274
    219 Nf27d7f678de94db4a89f113ac60a0d56 rdf:first sg:person.0756375026.78
    220 rdf:rest Nb4608584284440d1a52df0f5ba7e5331
    221 Nfbd75dce4a5c49e0ba710084c650d342 rdf:first sg:person.01002654241.76
    222 rdf:rest N0eaf4bb088ed4cc0bf01f71b1e9cff3c
    223 anzsrc-for:05 schema:inDefinedTermSet anzsrc-for:
    224 schema:name Environmental Sciences
    225 rdf:type schema:DefinedTerm
    226 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    227 schema:name Biological Sciences
    228 rdf:type schema:DefinedTerm
    229 anzsrc-for:10 schema:inDefinedTermSet anzsrc-for:
    230 schema:name Technology
    231 rdf:type schema:DefinedTerm
    232 sg:grant.3770987 http://pending.schema.org/fundedItem sg:pub.10.1038/ismej.2010.197
    233 rdf:type schema:MonetaryGrant
    234 sg:grant.3772495 http://pending.schema.org/fundedItem sg:pub.10.1038/ismej.2010.197
    235 rdf:type schema:MonetaryGrant
    236 sg:journal.1038436 schema:issn 1751-7362
    237 1751-7370
    238 schema:name The ISME Journal: Multidisciplinary Journal of Microbial Ecology
    239 schema:publisher Springer Nature
    240 rdf:type schema:Periodical
    241 sg:person.01002654241.76 schema:affiliation grid-institutes:grid.428469.5
    242 schema:familyName Albar
    243 schema:givenName Juan Pablo
    244 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01002654241.76
    245 rdf:type schema:Person
    246 sg:person.01133004220.53 schema:affiliation grid-institutes:grid.428469.5
    247 schema:familyName Juárez
    248 schema:givenName Silvia
    249 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01133004220.53
    250 rdf:type schema:Person
    251 sg:person.01154204633.81 schema:affiliation grid-institutes:grid.5326.2
    252 schema:familyName Yakimov
    253 schema:givenName Michail M
    254 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01154204633.81
    255 rdf:type schema:Person
    256 sg:person.01266255136.66 schema:affiliation grid-institutes:grid.5326.2
    257 schema:familyName Cono
    258 schema:givenName Violetta La
    259 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01266255136.66
    260 rdf:type schema:Person
    261 sg:person.01325043110.55 schema:affiliation grid-institutes:grid.493967.6
    262 schema:familyName Giuliano
    263 schema:givenName Laura
    264 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01325043110.55
    265 rdf:type schema:Person
    266 sg:person.016136043077.19 schema:affiliation grid-institutes:grid.7362.0
    267 schema:familyName Golyshin
    268 schema:givenName Peter N
    269 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016136043077.19
    270 rdf:type schema:Person
    271 sg:person.0605571626.58 schema:affiliation grid-institutes:grid.428469.5
    272 schema:familyName Fernández
    273 schema:givenName Marisol
    274 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0605571626.58
    275 rdf:type schema:Person
    276 sg:person.0623750303.04 schema:affiliation grid-institutes:grid.418900.4
    277 schema:familyName Ferrer
    278 schema:givenName Manuel
    279 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623750303.04
    280 rdf:type schema:Person
    281 sg:person.0631423323.50 schema:affiliation grid-institutes:grid.7362.0
    282 schema:familyName DeLuca
    283 schema:givenName Thomas H
    284 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0631423323.50
    285 rdf:type schema:Person
    286 sg:person.0723527633.28 schema:affiliation grid-institutes:grid.5326.2
    287 schema:familyName Smedile
    288 schema:givenName Francesco
    289 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0723527633.28
    290 rdf:type schema:Person
    291 sg:person.0756375026.78 schema:affiliation grid-institutes:grid.428469.5
    292 schema:familyName Ciordia
    293 schema:givenName Sergio
    294 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756375026.78
    295 rdf:type schema:Person
    296 sg:pub.10.1007/s00018-007-7310-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008459590
    297 https://doi.org/10.1007/s00018-007-7310-9
    298 rdf:type schema:CreativeWork
    299 sg:pub.10.1007/s00203-007-0255-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020689761
    300 https://doi.org/10.1007/s00203-007-0255-4
    301 rdf:type schema:CreativeWork
    302 sg:pub.10.1007/s10482-010-9488-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030785101
    303 https://doi.org/10.1007/s10482-010-9488-3
    304 rdf:type schema:CreativeWork
    305 sg:pub.10.1038/35054051 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000389432
    306 https://doi.org/10.1038/35054051
    307 rdf:type schema:CreativeWork
    308 sg:pub.10.1038/456712a schema:sameAs https://app.dimensions.ai/details/publication/pub.1048015971
    309 https://doi.org/10.1038/456712a
    310 rdf:type schema:CreativeWork
    311 sg:pub.10.1038/ismej.2007.118 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007290897
    312 https://doi.org/10.1038/ismej.2007.118
    313 rdf:type schema:CreativeWork
    314 sg:pub.10.1038/ismej.2007.83 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032428643
    315 https://doi.org/10.1038/ismej.2007.83
    316 rdf:type schema:CreativeWork
    317 sg:pub.10.1038/ismej.2008.40 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018243775
    318 https://doi.org/10.1038/ismej.2008.40
    319 rdf:type schema:CreativeWork
    320 sg:pub.10.1038/ismej.2008.94 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021747624
    321 https://doi.org/10.1038/ismej.2008.94
    322 rdf:type schema:CreativeWork
    323 sg:pub.10.1038/nature03911 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049439003
    324 https://doi.org/10.1038/nature03911
    325 rdf:type schema:CreativeWork
    326 sg:pub.10.1038/nature07535 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010350008
    327 https://doi.org/10.1038/nature07535
    328 rdf:type schema:CreativeWork
    329 sg:pub.10.1038/nature08465 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011818868
    330 https://doi.org/10.1038/nature08465
    331 rdf:type schema:CreativeWork
    332 sg:pub.10.1038/nrmicro1852 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051468230
    333 https://doi.org/10.1038/nrmicro1852
    334 rdf:type schema:CreativeWork
    335 sg:pub.10.1038/nrmicro2365 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000545292
    336 https://doi.org/10.1038/nrmicro2365
    337 rdf:type schema:CreativeWork
    338 grid-institutes:grid.418900.4 schema:alternateName Laboratory of Enzyme Discovery, Institute of Catalysis, CSIC, Madrid, Spain
    339 schema:name Laboratory of Enzyme Discovery, Institute of Catalysis, CSIC, Madrid, Spain
    340 rdf:type schema:Organization
    341 grid-institutes:grid.428469.5 schema:alternateName Proteomic Facility, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
    342 schema:name Proteomic Facility, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
    343 rdf:type schema:Organization
    344 grid-institutes:grid.493967.6 schema:alternateName Mediterranean Science Commission (CIESM), Monaco
    345 schema:name Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy
    346 Mediterranean Science Commission (CIESM), Monaco
    347 rdf:type schema:Organization
    348 grid-institutes:grid.5326.2 schema:alternateName Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy
    349 schema:name Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina, Italy
    350 rdf:type schema:Organization
    351 grid-institutes:grid.7362.0 schema:alternateName School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK
    352 School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, UK
    353 schema:name School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK
    354 School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, UK
    355 rdf:type schema:Organization
     




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


    ...