amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions
Identifieur interne : 000524 ( Pmc/Curation ); précédent : 000523; suivant : 000525amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions
Auteurs : Michael Pester [Autriche] ; Thomas Rattei [Autriche] ; Stefan Flechl [Autriche] ; Alexander Gröngröft [Allemagne] ; Andreas Richter [Autriche] ; Jörg Overmann [Allemagne] ; Barbara Reinhold-Hurek [Allemagne] ; Alexander Loy [Autriche] ; Michael Wagner [Autriche]Source :
- Environmental Microbiology [ 1462-2912 ] ; 2012.
Abstract
Ammonia-oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their
Url:
DOI: 10.1111/j.1462-2920.2011.02666.x
PubMed: 22141924
PubMed Central: 3328746
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>amoA</italic>-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of <italic>amoA</italic> genes from soils of four different geographic regions</title><author><name sortKey="Pester, Michael" sort="Pester, Michael" uniqKey="Pester M" first="Michael" last="Pester">Michael Pester</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Rattei, Thomas" sort="Rattei, Thomas" uniqKey="Rattei T" first="Thomas" last="Rattei">Thomas Rattei</name><affiliation wicri:level="1"><nlm:aff id="au2"><institution>Department of Computational Systems Biology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Flechl, Stefan" sort="Flechl, Stefan" uniqKey="Flechl S" first="Stefan" last="Flechl">Stefan Flechl</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Grongroft, Alexander" sort="Grongroft, Alexander" uniqKey="Grongroft A" first="Alexander" last="Gröngröft">Alexander Gröngröft</name><affiliation wicri:level="1"><nlm:aff id="au4"><institution>Institute of Soil Science, University of Hamburg</institution><addr-line>Allende-Platz 2, D-20146 Hamburg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Allende-Platz 2, D-20146 Hamburg</wicri:regionArea></affiliation></author><author><name sortKey="Richter, Andreas" sort="Richter, Andreas" uniqKey="Richter A" first="Andreas" last="Richter">Andreas Richter</name><affiliation wicri:level="1"><nlm:aff id="au3"><institution>Department of Chemical Ecology and Ecosystem Research, University of Vienna</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Overmann, Jorg" sort="Overmann, Jorg" uniqKey="Overmann J" first="Jörg" last="Overmann">Jörg Overmann</name><affiliation wicri:level="1"><nlm:aff id="au5"><institution>Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen</institution><addr-line>Inhoffenstraße 7B, D-38124 Braunschweig, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Inhoffenstraße 7B, D-38124 Braunschweig</wicri:regionArea></affiliation></author><author><name sortKey="Reinhold Hurek, Barbara" sort="Reinhold Hurek, Barbara" uniqKey="Reinhold Hurek B" first="Barbara" last="Reinhold-Hurek">Barbara Reinhold-Hurek</name><affiliation wicri:level="1"><nlm:aff id="au6"><institution>Department of Microbe-Plant Interactions, University of Bremen</institution><addr-line>Postfach 330440, D-28334 Bremen, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Postfach 330440, D-28334 Bremen</wicri:regionArea></affiliation></author><author><name sortKey="Loy, Alexander" sort="Loy, Alexander" uniqKey="Loy A" first="Alexander" last="Loy">Alexander Loy</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Wagner, Michael" sort="Wagner, Michael" uniqKey="Wagner M" first="Michael" last="Wagner">Michael Wagner</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22141924</idno><idno type="pmc">3328746</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328746</idno><idno type="RBID">PMC:3328746</idno><idno type="doi">10.1111/j.1462-2920.2011.02666.x</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000524</idno><idno type="wicri:Area/Pmc/Curation">000524</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>amoA</italic>-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of <italic>amoA</italic> genes from soils of four different geographic regions</title><author><name sortKey="Pester, Michael" sort="Pester, Michael" uniqKey="Pester M" first="Michael" last="Pester">Michael Pester</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Rattei, Thomas" sort="Rattei, Thomas" uniqKey="Rattei T" first="Thomas" last="Rattei">Thomas Rattei</name><affiliation wicri:level="1"><nlm:aff id="au2"><institution>Department of Computational Systems Biology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Flechl, Stefan" sort="Flechl, Stefan" uniqKey="Flechl S" first="Stefan" last="Flechl">Stefan Flechl</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Grongroft, Alexander" sort="Grongroft, Alexander" uniqKey="Grongroft A" first="Alexander" last="Gröngröft">Alexander Gröngröft</name><affiliation wicri:level="1"><nlm:aff id="au4"><institution>Institute of Soil Science, University of Hamburg</institution><addr-line>Allende-Platz 2, D-20146 Hamburg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Allende-Platz 2, D-20146 Hamburg</wicri:regionArea></affiliation></author><author><name sortKey="Richter, Andreas" sort="Richter, Andreas" uniqKey="Richter A" first="Andreas" last="Richter">Andreas Richter</name><affiliation wicri:level="1"><nlm:aff id="au3"><institution>Department of Chemical Ecology and Ecosystem Research, University of Vienna</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Overmann, Jorg" sort="Overmann, Jorg" uniqKey="Overmann J" first="Jörg" last="Overmann">Jörg Overmann</name><affiliation wicri:level="1"><nlm:aff id="au5"><institution>Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen</institution><addr-line>Inhoffenstraße 7B, D-38124 Braunschweig, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Inhoffenstraße 7B, D-38124 Braunschweig</wicri:regionArea></affiliation></author><author><name sortKey="Reinhold Hurek, Barbara" sort="Reinhold Hurek, Barbara" uniqKey="Reinhold Hurek B" first="Barbara" last="Reinhold-Hurek">Barbara Reinhold-Hurek</name><affiliation wicri:level="1"><nlm:aff id="au6"><institution>Department of Microbe-Plant Interactions, University of Bremen</institution><addr-line>Postfach 330440, D-28334 Bremen, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Postfach 330440, D-28334 Bremen</wicri:regionArea></affiliation></author><author><name sortKey="Loy, Alexander" sort="Loy, Alexander" uniqKey="Loy A" first="Alexander" last="Loy">Alexander Loy</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author><author><name sortKey="Wagner, Michael" sort="Wagner, Michael" uniqKey="Wagner M" first="Michael" last="Wagner">Michael Wagner</name><affiliation wicri:level="1"><nlm:aff id="au1"><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Althanstrasse 14, A-1090 Vienna</wicri:regionArea></affiliation></author></analytic><series><title level="j">Environmental Microbiology</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Ammonia-oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their <italic>amoA</italic> genes as marker for their diversity and abundance. We present an archaeal <italic>amoA</italic> consensus phylogeny based on all publicly available sequences (status June 2010) and provide evidence for the diversification of AOA into four previously recognized clusters and one newly identified major cluster. These clusters, for which we suggest a new nomenclature, harboured 83 AOA species-level OTU (using an inferred species threshold of 85% <italic>amoA</italic> identity). 454 pyrosequencing of <italic>amoA</italic> amplicons from 16 soils sampled in Austria, Costa Rica, Greenland and Namibia revealed that only 2% of retrieved sequences had no database representative on the species-level and represented 30–37 additional species-level OTUs. With the exception of an acidic soil from which mostly <italic>amoA</italic> amplicons of the <italic>Nitrosotalea</italic> cluster were retrieved, all soils were dominated by <italic>amoA</italic> amplicons from the <italic>Nitrososphaera</italic> cluster (also called group I.1b), indicating that the previously reported AOA from the <italic>Nitrosopumilus</italic> cluster (also called group I.1a) are absent or represent minor populations in soils. AOA richness estimates on the species level ranged from 8–83 co-existing AOAs per soil. Presence/absence of <italic>amoA</italic> OTUs (97% identity level) correlated with geographic location, indicating that besides contemporary environmental conditions also dispersal limitation across different continents and/or historical environmental conditions might influence AOA biogeography in soils.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bates, St" uniqKey="Bates S">ST Bates</name></author><author><name sortKey="Berg Lyons, D" uniqKey="Berg Lyons D">D Berg-Lyons</name></author><author><name sortKey="Caporaso, Jg" uniqKey="Caporaso J">JG Caporaso</name></author><author><name sortKey="Walters, Wa" uniqKey="Walters W">WA Walters</name></author><author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name></author><author><name sortKey="Fierer, N" uniqKey="Fierer N">N Fierer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benson, Da" uniqKey="Benson D">DA 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Environ Microbiol</journal-id><journal-id journal-id-type="iso-abbrev">Environ. Microbiol</journal-id><journal-id journal-id-type="publisher-id">emi</journal-id><journal-title-group><journal-title>Environmental Microbiology</journal-title></journal-title-group><issn pub-type="ppub">1462-2912</issn><issn pub-type="epub">1462-2920</issn><publisher><publisher-name>Blackwell Publishing Ltd</publisher-name><publisher-loc>Oxford, UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22141924</article-id><article-id pub-id-type="pmc">3328746</article-id><article-id pub-id-type="doi">10.1111/j.1462-2920.2011.02666.x</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Articles</subject></subj-group></article-categories><title-group><article-title><italic>amoA</italic>-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of <italic>amoA</italic> genes from soils of four different geographic regions</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Pester</surname><given-names>Michael</given-names></name><xref ref-type="aff" rid="au1">1</xref></contrib><contrib contrib-type="author"><name><surname>Rattei</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="au2">2</xref></contrib><contrib contrib-type="author"><name><surname>Flechl</surname><given-names>Stefan</given-names></name><xref ref-type="aff" rid="au1">1</xref></contrib><contrib contrib-type="author"><name><surname>Gröngröft</surname><given-names>Alexander</given-names></name><xref ref-type="aff" rid="au4">4</xref></contrib><contrib contrib-type="author"><name><surname>Richter</surname><given-names>Andreas</given-names></name><xref ref-type="aff" rid="au3">3</xref></contrib><contrib contrib-type="author"><name><surname>Overmann</surname><given-names>Jörg</given-names></name><xref ref-type="aff" rid="au5">5</xref></contrib><contrib contrib-type="author"><name><surname>Reinhold-Hurek</surname><given-names>Barbara</given-names></name><xref ref-type="aff" rid="au6">6</xref></contrib><contrib contrib-type="author"><name><surname>Loy</surname><given-names>Alexander</given-names></name><xref ref-type="aff" rid="au1">1</xref></contrib><contrib contrib-type="author"><name><surname>Wagner</surname><given-names>Michael</given-names></name><xref ref-type="aff" rid="au1">1</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib><aff id="au1"><label>1</label><institution>Department of Microbial Ecology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></aff><aff id="au2"><label>2</label><institution>Department of Computational Systems Biology</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></aff><aff id="au3"><label>3</label><institution>Department of Chemical Ecology and Ecosystem Research, University of Vienna</institution><addr-line>Althanstrasse 14, A-1090 Vienna, Austria</addr-line></aff><aff id="au4"><label>4</label><institution>Institute of Soil Science, University of Hamburg</institution><addr-line>Allende-Platz 2, D-20146 Hamburg, Germany</addr-line></aff><aff id="au5"><label>5</label><institution>Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen</institution><addr-line>Inhoffenstraße 7B, D-38124 Braunschweig, Germany</addr-line></aff><aff id="au6"><label>6</label><institution>Department of Microbe-Plant Interactions, University of Bremen</institution><addr-line>Postfach 330440, D-28334 Bremen, Germany</addr-line></aff></contrib-group><author-notes><corresp id="cor1">*For correspondence. E-mail <email>wagner@microbial-ecology.net</email>; Tel. (+43) 1 4277 54390; Fax (+43) 1 4277 54389.</corresp><fn><p>Re-use of this article is permitted in accordance with the Terms and Conditions set out at <ext-link ext-link-type="uri" xlink:href="http://wileyonlinelibrary.com/onlineopen#OnlineOpen_Terms">http://wileyonlinelibrary.com/onlineopen#OnlineOpen_Terms</ext-link></p></fn></author-notes><pub-date pub-type="ppub"><month>2</month><year>2012</year></pub-date><volume>14</volume><issue>2</issue><fpage>525</fpage><lpage>539</lpage><history><date date-type="received"><day>19</day><month>10</month><year>2011</year></date><date date-type="rev-recd"><day>07</day><month>11</month><year>2011</year></date><date date-type="accepted"><day>07</day><month>11</month><year>2011</year></date></history><permissions><copyright-statement>© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd</copyright-statement><copyright-year>2011</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.5/"><license-p>Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.</license-p></license></permissions><abstract><p>Ammonia-oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their <italic>amoA</italic> genes as marker for their diversity and abundance. We present an archaeal <italic>amoA</italic> consensus phylogeny based on all publicly available sequences (status June 2010) and provide evidence for the diversification of AOA into four previously recognized clusters and one newly identified major cluster. These clusters, for which we suggest a new nomenclature, harboured 83 AOA species-level OTU (using an inferred species threshold of 85% <italic>amoA</italic> identity). 454 pyrosequencing of <italic>amoA</italic> amplicons from 16 soils sampled in Austria, Costa Rica, Greenland and Namibia revealed that only 2% of retrieved sequences had no database representative on the species-level and represented 30–37 additional species-level OTUs. With the exception of an acidic soil from which mostly <italic>amoA</italic> amplicons of the <italic>Nitrosotalea</italic> cluster were retrieved, all soils were dominated by <italic>amoA</italic> amplicons from the <italic>Nitrososphaera</italic> cluster (also called group I.1b), indicating that the previously reported AOA from the <italic>Nitrosopumilus</italic> cluster (also called group I.1a) are absent or represent minor populations in soils. AOA richness estimates on the species level ranged from 8–83 co-existing AOAs per soil. Presence/absence of <italic>amoA</italic> OTUs (97% identity level) correlated with geographic location, indicating that besides contemporary environmental conditions also dispersal limitation across different continents and/or historical environmental conditions might influence AOA biogeography in soils.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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