<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-03365290</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-14T06:02:29+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages</title>
            <author role="aut">
              <persName>
                <forename type="first">Melina</forename>
                <surname>Kerou</surname>
              </persName>
              <idno type="idhal" notation="numeric">786006</idno>
              <idno type="halauthorid" notation="string">1308825-786006</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-1657-3041</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Rafael</forename>
                <surname>Ponce-Toledo</surname>
              </persName>
              <idno type="halauthorid">2299119-0</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Rui</forename>
                <surname>Zhao</surname>
              </persName>
              <idno type="halauthorid">366610-0</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Sophie S.</forename>
                <surname>Abby</surname>
              </persName>
              <email type="md5">d6d32dcd68106145e4984894ef1a7bf2</email>
              <email type="domain">univ-grenoble-alpes.fr</email>
              <idno type="idhal" notation="string">sophie-abby</idno>
              <idno type="idhal" notation="numeric">177950</idno>
              <idno type="halauthorid" notation="string">31469-177950</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/H-4817-2011</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-5231-3346</idno>
              <idno type="GOOGLE SCHOLAR">https://scholar.google.fr/citations?hl=en&amp;user=pJ3h0iMAAAAJ&amp;view_op=list_works</idno>
              <idno type="IDREF">https://www.idref.fr/226323552</idno>
              <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/H-4817-2011</idno>
              <affiliation ref="#struct-1069752"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Miho</forename>
                <surname>Hirai</surname>
              </persName>
              <idno type="halauthorid">798202-0</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Hidetaka</forename>
                <surname>Nomaki</surname>
              </persName>
              <idno type="halauthorid">1982950-0</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Yoshihiro</forename>
                <surname>Takaki</surname>
              </persName>
              <idno type="idhal" notation="numeric">809802</idno>
              <idno type="halauthorid" notation="string">2299120-809802</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-1247-4946</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Takuro</forename>
                <surname>Nunoura</surname>
              </persName>
              <idno type="idhal" notation="numeric">764571</idno>
              <idno type="halauthorid" notation="string">571772-764571</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-2323-0880</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Steffen</forename>
                <surname>Jørgensen</surname>
              </persName>
              <idno type="idhal" notation="numeric">804824</idno>
              <idno type="halauthorid" notation="string">2111648-804824</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-0240-7907</idno>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Christa</forename>
                <surname>Schleper</surname>
              </persName>
              <idno type="idhal" notation="numeric">761568</idno>
              <idno type="halauthorid" notation="string">409489-761568</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-1918-2735</idno>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Sophie</forename>
                <surname>Abby</surname>
              </persName>
              <email type="md5">d6d32dcd68106145e4984894ef1a7bf2</email>
              <email type="domain">univ-grenoble-alpes.fr</email>
            </editor>
            <funder ref="#projanr-38027"/>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2021-11-04 15:51:42</date>
              <date type="whenModified">2025-09-27 18:46:01</date>
              <date type="whenReleased">2021-11-05 13:42:44</date>
              <date type="whenProduced">2021-04-01</date>
              <date type="whenEndEmbargoed">2021-11-04</date>
              <ref type="file" target="https://hal.science/hal-03365290v1/document">
                <date notBefore="2021-11-04"/>
              </ref>
              <ref type="file" subtype="greenPublisher" n="1" target="https://hal.science/hal-03365290v1/file/2021_Kerou_s41396-021-00962-6.pdf" id="file-3414702-2993876">
                <date notBefore="2021-11-04"/>
              </ref>
              <ref type="externalLink" target="https://www.nature.com/articles/s41396-021-00962-6.pdf"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="328884">
                <persName>
                  <forename>Sophie</forename>
                  <surname>Abby</surname>
                </persName>
                <email type="md5">d6d32dcd68106145e4984894ef1a7bf2</email>
                <email type="domain">univ-grenoble-alpes.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-03365290</idno>
            <idno type="halUri">https://hal.science/hal-03365290</idno>
            <idno type="halBibtex">kerou:hal-03365290</idno>
            <idno type="halRefHtml">&lt;i&gt;The International Society of Microbiologial Ecology Journal&lt;/i&gt;, 2021, 15 (9), pp.2792-2808. &lt;a target="_blank" href="https://dx.doi.org/10.1038/s41396-021-00962-6"&gt;&amp;#x27E8;10.1038/s41396-021-00962-6&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">The International Society of Microbiologial Ecology Journal, 2021, 15 (9), pp.2792-2808. &amp;#x27E8;10.1038/s41396-021-00962-6&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-3414702-2993876"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="UGA">HAL Grenoble Alpes</idno>
            <idno type="stamp" n="IMAG">IMAG</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="INPG">Institut polytechnique de Grenoble</idno>
            <idno type="stamp" n="GIP-BE">GIP Bretagne Environnement</idno>
            <idno type="stamp" n="TIMC-IMAG">TIMC</idno>
            <idno type="stamp" n="UNIV-LYON">Université de Lyon</idno>
            <idno type="stamp" n="UGA-EPE">Université Grenoble Alpes [2020-*]</idno>
            <idno type="stamp" n="ANR">ANR</idno>
            <idno type="stamp" n="TIMC-TREE" corresp="TIMC-IMAG">TrEE : Translational microbial Evolution and Engineering</idno>
            <idno type="stamp" n="MICROSCOPE" corresp="CEA">Microbial Genome Annotation &amp; Analysis Platform (MAGE)</idno>
            <idno type="stamp" n="TEST-UGA">TEST-UGA</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Melina</forename>
                    <surname>Kerou</surname>
                  </persName>
                  <idno type="idhal" notation="numeric">786006</idno>
                  <idno type="halauthorid" notation="string">1308825-786006</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-1657-3041</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Rafael</forename>
                    <surname>Ponce-Toledo</surname>
                  </persName>
                  <idno type="halauthorid">2299119-0</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Rui</forename>
                    <surname>Zhao</surname>
                  </persName>
                  <idno type="halauthorid">366610-0</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Sophie S.</forename>
                    <surname>Abby</surname>
                  </persName>
                  <email type="md5">d6d32dcd68106145e4984894ef1a7bf2</email>
                  <email type="domain">univ-grenoble-alpes.fr</email>
                  <idno type="idhal" notation="string">sophie-abby</idno>
                  <idno type="idhal" notation="numeric">177950</idno>
                  <idno type="halauthorid" notation="string">31469-177950</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/H-4817-2011</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-5231-3346</idno>
                  <idno type="GOOGLE SCHOLAR">https://scholar.google.fr/citations?hl=en&amp;user=pJ3h0iMAAAAJ&amp;view_op=list_works</idno>
                  <idno type="IDREF">https://www.idref.fr/226323552</idno>
                  <idno type="RESEARCHERID">http://www.researcherid.com/rid/http://www.researcherid.com/rid/H-4817-2011</idno>
                  <affiliation ref="#struct-1069752"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Miho</forename>
                    <surname>Hirai</surname>
                  </persName>
                  <idno type="halauthorid">798202-0</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Hidetaka</forename>
                    <surname>Nomaki</surname>
                  </persName>
                  <idno type="halauthorid">1982950-0</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Yoshihiro</forename>
                    <surname>Takaki</surname>
                  </persName>
                  <idno type="idhal" notation="numeric">809802</idno>
                  <idno type="halauthorid" notation="string">2299120-809802</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-1247-4946</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Takuro</forename>
                    <surname>Nunoura</surname>
                  </persName>
                  <idno type="idhal" notation="numeric">764571</idno>
                  <idno type="halauthorid" notation="string">571772-764571</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-2323-0880</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Steffen</forename>
                    <surname>Jørgensen</surname>
                  </persName>
                  <idno type="idhal" notation="numeric">804824</idno>
                  <idno type="halauthorid" notation="string">2111648-804824</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-0240-7907</idno>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Christa</forename>
                    <surname>Schleper</surname>
                  </persName>
                  <idno type="idhal" notation="numeric">761568</idno>
                  <idno type="halauthorid" notation="string">409489-761568</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-1918-2735</idno>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">101584</idno>
                <idno type="issn">1751-7362</idno>
                <idno type="eissn">1751-7370</idno>
                <title level="j">The International Society of Microbiologial Ecology Journal</title>
                <imprint>
                  <publisher>Nature Publishing Group</publisher>
                  <biblScope unit="volume">15</biblScope>
                  <biblScope unit="issue">9</biblScope>
                  <biblScope unit="pp">2792-2808</biblScope>
                  <date type="datePub">2021-04-01</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1038/s41396-021-00962-6</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="sdv.bbm.gtp">Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]</classCode>
              <classCode scheme="halDomain" n="sdv.bid.evo">Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]</classCode>
              <classCode scheme="halDomain" n="sdv.bibs">Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]</classCode>
              <classCode scheme="halTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halOldTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halTreeTypology" n="ART">Journal articles</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>Abstract Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales , of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="researchteam" xml:id="struct-1069752" status="VALID">
          <orgName>Translational microbial Evolution and Engineering</orgName>
          <orgName type="acronym">TIMC-TrEE</orgName>
          <date type="start">2021-01-01</date>
          <desc>
            <address>
              <addrLine>Faculté de médecine de Grenoble, bâtiment Jean Roget, 38706 La Tronche</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.timc.fr/TrEE</ref>
          </desc>
          <listRelation>
            <relation active="#struct-1043049" type="direct"/>
            <relation active="#struct-301767" type="indirect"/>
            <relation name="UMR5525" active="#struct-441569" type="indirect"/>
            <relation active="#struct-1042703" type="indirect"/>
            <relation active="#struct-1043329" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-1043049" status="VALID">
          <idno type="IdRef">14728936X</idno>
          <idno type="ISNI">0000 0004 4687 1979</idno>
          <idno type="RNSR">199511969L</idno>
          <idno type="ROR">https://ror.org/03985kf35</idno>
          <orgName>Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525</orgName>
          <orgName type="acronym">TIMC</orgName>
          <date type="start">2021-01-01</date>
          <desc>
            <address>
              <addrLine>Domaine de la Merci, 38706 La Tronche, France</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.timc.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-301767" type="direct"/>
            <relation name="UMR5525" active="#struct-441569" type="direct"/>
            <relation active="#struct-1042703" type="direct"/>
            <relation active="#struct-1043329" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-301767" status="VALID">
          <idno type="ROR">https://ror.org/01c7wz417</idno>
          <orgName>VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement</orgName>
          <orgName type="acronym">VAS</orgName>
          <date type="start">2010-01-01</date>
          <desc>
            <address>
              <addrLine>Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile (campus vétérinaire); Université de Clermont, VetAgro Sup, 63370 Lempdes (campus agronomique)</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.vetagro-sup.fr/</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-1042703" status="VALID">
          <idno type="IdRef">240648315</idno>
          <idno type="ROR">https://ror.org/02rx3b187</idno>
          <orgName>Université Grenoble Alpes</orgName>
          <orgName type="acronym">UGA</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <addrLine>Adresse CS 40700 - 38058 Grenoble cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-grenoble-alpes.fr</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-1043329" status="VALID">
          <idno type="IdRef">026388804</idno>
          <idno type="ROR">https://ror.org/05sbt2524</idno>
          <orgName>Institut polytechnique de Grenoble - Grenoble Institute of Technology</orgName>
          <orgName type="acronym">Grenoble INP</orgName>
          <date type="start">2020-01-01</date>
          <desc>
            <address>
              <addrLine>46 avenue Félix Viallet 38031 Grenoble Cedex 1</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.grenoble-inp.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-1042703" type="direct"/>
          </listRelation>
        </org>
      </listOrg>
      <listOrg type="projects">
        <org type="anrProject" xml:id="projanr-38027" status="VALID">
          <idno type="anr">ANR-11-INBS-0013</idno>
          <idno type="program">Infrastructures</idno>
          <orgName>IFB (ex Renabi-IFB)</orgName>
          <desc>Institut français de bioinformatique</desc>
          <date type="start">2011</date>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>