Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l
Identifieur interne : 000530 ( Pmc/Curation ); précédent : 000529; suivant : 000531Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l
Auteurs : Esther Singer [États-Unis] ; John F. Heidelberg [États-Unis] ; Ashita Dhillon [États-Unis] ; Katrina J. Edwards [États-Unis]Source :
- Frontiers in Microbiology [ 1664-302X ] ; 2013.
Abstract
Url:
DOI: 10.3389/fmicb.2013.00052
PubMed: 23518919
PubMed Central: 3603346
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Metagenomic insights into the dominant Fe(II) oxidizing <italic>Zetaproteobacteria</italic> from an iron mat at Lō´ihi, Hawai´l</title><author><name sortKey="Singer, Esther" sort="Singer, Esther" uniqKey="Singer E" first="Esther" last="Singer">Esther Singer</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Earth Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Heidelberg, John F" sort="Heidelberg, John F" uniqKey="Heidelberg J" first="John F." last="Heidelberg">John F. Heidelberg</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biological Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Dhillon, Ashita" sort="Dhillon, Ashita" uniqKey="Dhillon A" first="Ashita" last="Dhillon">Ashita Dhillon</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Genzyme Corporation</institution><country>Allston, MA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Edwards, Katrina J" sort="Edwards, Katrina J" uniqKey="Edwards K" first="Katrina J." last="Edwards">Katrina J. Edwards</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Earth Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biological Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23518919</idno><idno type="pmc">3603346</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603346</idno><idno type="RBID">PMC:3603346</idno><idno type="doi">10.3389/fmicb.2013.00052</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000530</idno><idno type="wicri:Area/Pmc/Curation">000530</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Metagenomic insights into the dominant Fe(II) oxidizing <italic>Zetaproteobacteria</italic> from an iron mat at Lō´ihi, Hawai´l</title><author><name sortKey="Singer, Esther" sort="Singer, Esther" uniqKey="Singer E" first="Esther" last="Singer">Esther Singer</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Earth Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Heidelberg, John F" sort="Heidelberg, John F" uniqKey="Heidelberg J" first="John F." last="Heidelberg">John F. Heidelberg</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biological Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Dhillon, Ashita" sort="Dhillon, Ashita" uniqKey="Dhillon A" first="Ashita" last="Dhillon">Ashita Dhillon</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Genzyme Corporation</institution><country>Allston, MA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Edwards, Katrina J" sort="Edwards, Katrina J" uniqKey="Edwards K" first="Katrina J." last="Edwards">Katrina J. Edwards</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Earth Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Biological Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Microbiology</title><idno type="eISSN">1664-302X</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Zetaproteobacteria</italic> are among the most prevalent Fe(II)-oxidizing bacteria (FeOB) at deep-sea hydrothermal vents; however, knowledge about their environmental significance is limited. We provide metagenomic insights into an iron mat at the Lō´ihi Seamount, Hawai´l, revealing novel genomic information of locally dominant <italic>Zetaproteobacteria</italic> lineages. These lineages were previously estimated to account for ~13% of all local <italic>Zetaproteobacteria</italic> based on 16S clone library data. Biogeochemically relevant genes include nitrite reductases, which were previously not identified in <italic>Zetaproteobacteria</italic>, sulfide:quinone oxidases, and ribulose-1,5-bisphosphate carboxylase (RuBisCo). Genes assumed to be involved in Fe(II) oxidation correlate in synteny and share 87% amino acid similarity with those previously identified in the related <italic>Zetaproteobacterium</italic><italic>Mariprofundus ferrooxydans</italic> PV-1. Overall, <italic>Zetaproteobacteria</italic> genes appear to originate primarily from within the <italic>Proteobacteria</italic> and the Fe(II)-oxidizing <italic>Leptospirillum</italic> spp. and are predicted to facilitate adaptation to a deep-sea hydrothermal vent environment in addition to microaerophilic Fe(II) and H<sub>2</sub>S oxidation. This dataset represents the first metagenomic study of FeOB from an iron oxide mat at a deep-sea hydrothermal habitat.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Acinas, S G" uniqKey="Acinas S">S. G. Acinas</name></author><author><name sortKey="Sarma Rupavtarm, R" uniqKey="Sarma Rupavtarm R">R. Sarma-Rupavtarm</name></author><author><name sortKey="Klepac Ceraj, V" uniqKey="Klepac Ceraj V">V. Klepac-Ceraj</name></author><author><name sortKey="Polz, M F" uniqKey="Polz M">M. F. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Microbiol</journal-id><journal-id journal-id-type="iso-abbrev">Front Microbiol</journal-id><journal-id journal-id-type="publisher-id">Front. Microbiol.</journal-id><journal-title-group><journal-title>Frontiers in Microbiology</journal-title></journal-title-group><issn pub-type="epub">1664-302X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23518919</article-id><article-id pub-id-type="pmc">3603346</article-id><article-id pub-id-type="doi">10.3389/fmicb.2013.00052</article-id><article-categories><subj-group subj-group-type="heading"><subject>Microbiology</subject><subj-group><subject>Original Research Article</subject></subj-group></subj-group></article-categories><title-group><article-title>Metagenomic insights into the dominant Fe(II) oxidizing <italic>Zetaproteobacteria</italic> from an iron mat at Lō´ihi, Hawai´l</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Singer</surname><given-names>Esther</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Heidelberg</surname><given-names>John F.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dhillon</surname><given-names>Ashita</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Edwards</surname><given-names>Katrina J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Department of Earth Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></aff><aff id="aff2"><sup>2</sup><institution>Department of Biological Sciences, University of Southern California</institution><country>Los Angeles, CA, USA</country></aff><aff id="aff3"><sup>3</sup><institution>Genzyme Corporation</institution><country>Allston, MA, USA</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: <italic>Andreas Teske, University of North Carolina at Chapel Hill, USA</italic></p></fn><fn fn-type="edited-by"><p>Reviewed by: <italic>Craig L. Moyer, Western Washington University, USA; Runar Stokke, University of Bergen, Norway</italic></p></fn><corresp id="fn001">*Correspondence: <italic>Katrina J. Edwards, Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA. e-mail: <email xlink:type="simple">kje@usc.edu</email></italic></corresp><fn fn-type="other" id="fn002"><p>This article was submitted to Frontiers in Extreme Microbiology, a specialty of Frontiers in Microbiology.</p></fn></author-notes><pub-date pub-type="epub"><day>19</day><month>3</month><year>2013</year></pub-date><pub-date pub-type="collection"><year>2013</year></pub-date><volume>4</volume><elocation-id>52</elocation-id><history><date date-type="received"><day>05</day><month>11</month><year>2012</year></date><date date-type="accepted"><day>22</day><month>2</month><year>2013</year></date></history><permissions><copyright-statement>Copyright © Singer, Heidelberg, Dhillon and Edwards.</copyright-statement><copyright-year>2013</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p> This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.</license-p></license></permissions><abstract><p><italic>Zetaproteobacteria</italic> are among the most prevalent Fe(II)-oxidizing bacteria (FeOB) at deep-sea hydrothermal vents; however, knowledge about their environmental significance is limited. We provide metagenomic insights into an iron mat at the Lō´ihi Seamount, Hawai´l, revealing novel genomic information of locally dominant <italic>Zetaproteobacteria</italic> lineages. These lineages were previously estimated to account for ~13% of all local <italic>Zetaproteobacteria</italic> based on 16S clone library data. Biogeochemically relevant genes include nitrite reductases, which were previously not identified in <italic>Zetaproteobacteria</italic>, sulfide:quinone oxidases, and ribulose-1,5-bisphosphate carboxylase (RuBisCo). Genes assumed to be involved in Fe(II) oxidation correlate in synteny and share 87% amino acid similarity with those previously identified in the related <italic>Zetaproteobacterium</italic><italic>Mariprofundus ferrooxydans</italic> PV-1. Overall, <italic>Zetaproteobacteria</italic> genes appear to originate primarily from within the <italic>Proteobacteria</italic> and the Fe(II)-oxidizing <italic>Leptospirillum</italic> spp. and are predicted to facilitate adaptation to a deep-sea hydrothermal vent environment in addition to microaerophilic Fe(II) and H<sub>2</sub>S oxidation. This dataset represents the first metagenomic study of FeOB from an iron oxide mat at a deep-sea hydrothermal habitat.</p></abstract><kwd-group><kwd>iron oxidation</kwd><kwd>Lō´ihi Seamount</kwd><kwd>molybdopterin oxidoreductase</kwd><kwd>Rubisco</kwd><kwd><italic>Zetaproteobacteria</italic></kwd><kwd>hydrothermal vents</kwd><kwd>sulfide oxidation</kwd></kwd-group><counts><fig-count count="3"></fig-count><table-count count="1"></table-count><equation-count count="0"></equation-count><ref-count count="49"></ref-count><page-count count="9"></page-count><word-count count="0"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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