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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche</title><author><name sortKey="Ricci, Jessica N" sort="Ricci, Jessica N" uniqKey="Ricci J" first="Jessica N" last="Ricci">Jessica N. Ricci</name><affiliation><nlm:aff id="aff1"><institution>Division of Biology, California Institute of Technology</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Coleman, Maureen L" sort="Coleman, Maureen L" uniqKey="Coleman M" first="Maureen L" last="Coleman">Maureen L. Coleman</name><affiliation><nlm:aff id="aff1"><institution>Division of Biology, California Institute of Technology</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Welander, Paula V" sort="Welander, Paula V" uniqKey="Welander P" first="Paula V" last="Welander">Paula V. Welander</name><affiliation><nlm:aff id="aff2"><institution>Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology</institution>, 77 Massachusetts Avenue, E25-633, Cambridge, MA 02139,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Sessions, Alex L" sort="Sessions, Alex L" uniqKey="Sessions A" first="Alex L" last="Sessions">Alex L. Sessions</name><affiliation><nlm:aff id="aff3"><institution>Division of Geological and Planetary Sciences, California Institute of Technology</institution>, MC100-23, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Summons, Roger E" sort="Summons, Roger E" uniqKey="Summons R" first="Roger E" last="Summons">Roger E. Summons</name><affiliation><nlm:aff id="aff2"><institution>Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology</institution>, 77 Massachusetts Avenue, E25-633, Cambridge, MA 02139,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Spear, John R" sort="Spear, John R" uniqKey="Spear J" first="John R" last="Spear">John R. Spear</name><affiliation><nlm:aff id="aff4"><institution>Department of Civil and Environmental Engineering, Colorado School of Mines</institution>, Golden, CO 80401,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Newman, Dianne K" sort="Newman, Dianne K" uniqKey="Newman D" first="Dianne K" last="Newman">Dianne K. Newman</name><affiliation><nlm:aff id="aff1"><institution>Division of Biology, California Institute of Technology</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><institution>Division of Geological and Planetary Sciences, California Institute of Technology</institution>, MC100-23, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff5"><institution>Howard Hughes Medical Institute</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24152713</idno><idno type="pmc">3930323</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930323</idno><idno type="RBID">PMC:3930323</idno><idno type="doi">10.1038/ismej.2013.191</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000015</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche</title><author><name sortKey="Ricci, Jessica N" sort="Ricci, Jessica N" uniqKey="Ricci J" first="Jessica N" last="Ricci">Jessica N. Ricci</name><affiliation><nlm:aff id="aff1"><institution>Division of Biology, California Institute of Technology</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Coleman, Maureen L" sort="Coleman, Maureen L" uniqKey="Coleman M" first="Maureen L" last="Coleman">Maureen L. Coleman</name><affiliation><nlm:aff id="aff1"><institution>Division of Biology, California Institute of Technology</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Welander, Paula V" sort="Welander, Paula V" uniqKey="Welander P" first="Paula V" last="Welander">Paula V. Welander</name><affiliation><nlm:aff id="aff2"><institution>Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology</institution>, 77 Massachusetts Avenue, E25-633, Cambridge, MA 02139,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Sessions, Alex L" sort="Sessions, Alex L" uniqKey="Sessions A" first="Alex L" last="Sessions">Alex L. Sessions</name><affiliation><nlm:aff id="aff3"><institution>Division of Geological and Planetary Sciences, California Institute of Technology</institution>, MC100-23, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Summons, Roger E" sort="Summons, Roger E" uniqKey="Summons R" first="Roger E" last="Summons">Roger E. Summons</name><affiliation><nlm:aff id="aff2"><institution>Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology</institution>, 77 Massachusetts Avenue, E25-633, Cambridge, MA 02139,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Spear, John R" sort="Spear, John R" uniqKey="Spear J" first="John R" last="Spear">John R. Spear</name><affiliation><nlm:aff id="aff4"><institution>Department of Civil and Environmental Engineering, Colorado School of Mines</institution>, Golden, CO 80401,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Newman, Dianne K" sort="Newman, Dianne K" uniqKey="Newman D" first="Dianne K" last="Newman">Dianne K. Newman</name><affiliation><nlm:aff id="aff1"><institution>Division of Biology, California Institute of Technology</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><institution>Division of Geological and Planetary Sciences, California Institute of Technology</institution>, MC100-23, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff5"><institution>Howard Hughes Medical Institute</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></nlm:aff></affiliation></author></analytic><series><title level="j">The ISME Journal</title><idno type="ISSN">1751-7362</idno><idno type="eISSN">1751-7370</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>Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of <italic>hpnP</italic>, the gene encoding the C-2 hopanoid methylase. Here we show that <italic>hpnP</italic> copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial <italic>hpnP</italic> genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether <italic>hpnP</italic> presence might track with particular variables. We found <italic>hpnP</italic> to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (<italic>P</italic>-value<10<sup>−6</sup>); in addition, we observed diverse <italic>hpnP</italic> types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">ISME J</journal-id><journal-id journal-id-type="iso-abbrev">ISME J</journal-id><journal-title-group><journal-title>The ISME Journal</journal-title></journal-title-group><issn pub-type="ppub">1751-7362</issn><issn pub-type="epub">1751-7370</issn><publisher><publisher-name>Nature Publishing Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24152713</article-id><article-id pub-id-type="pmc">3930323</article-id><article-id pub-id-type="pii">ismej2013191</article-id><article-id pub-id-type="doi">10.1038/ismej.2013.191</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject></subj-group></article-categories><title-group><article-title>Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche</article-title><alt-title alt-title-type="running">2-MeBHP production is niche specific</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ricci</surname><given-names>Jessica N</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Coleman</surname><given-names>Maureen L</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="author-notes" rid="note1"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Welander</surname><given-names>Paula V</given-names></name><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="author-notes" rid="note2"><sup>7</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sessions</surname><given-names>Alex L</given-names></name><xref ref-type="aff" rid="aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Summons</surname><given-names>Roger E</given-names></name><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Spear</surname><given-names>John R</given-names></name><xref ref-type="aff" rid="aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Newman</surname><given-names>Dianne K</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="aff" rid="aff5">5</xref><xref ref-type="corresp" rid="caf1">*</xref></contrib><aff id="aff1"><label>1</label><institution>Division of Biology, California Institute of Technology</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></aff><aff id="aff2"><label>2</label><institution>Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology</institution>, 77 Massachusetts Avenue, E25-633, Cambridge, MA 02139,<country>USA</country></aff><aff id="aff3"><label>3</label><institution>Division of Geological and Planetary Sciences, California Institute of Technology</institution>, MC100-23, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></aff><aff id="aff4"><label>4</label><institution>Department of Civil and Environmental Engineering, Colorado School of Mines</institution>, Golden, CO 80401,<country>USA</country></aff><aff id="aff5"><label>5</label><institution>Howard Hughes Medical Institute</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125,<country>USA</country></aff></contrib-group><author-notes><corresp id="caf1"><label>*</label><institution>Division of Biology, California Institute of Technology</institution>, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125, <country>USA</country>. E-mail: <email>dkn@caltech.edu</email></corresp><fn fn-type="present-address" id="note1"><label>6</label><p>Present address: Department of the Geophysical Sciences, University of Chicago, 5734 S. Ellis Avenue, Chicago, IL 60637</p></fn><fn fn-type="present-address" id="note2"><label>7</label><p>Present address: Department of Environmental Earth System Science, Stanford University, 473 Via Ortega Road, Rm 140, Stanford, CA 94305</p></fn></author-notes><pub-date pub-type="ppub"><month>03</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>24</day><month>10</month><year>2013</year></pub-date><volume>8</volume><issue>3</issue><fpage>675</fpage><lpage>684</lpage><history><date date-type="received"><day>14</day><month>07</month><year>2013</year></date><date date-type="rev-recd"><day>04</day><month>09</month><year>2013</year></date><date date-type="accepted"><day>22</day><month>09</month><year>2013</year></date></history><permissions><copyright-statement>Copyright © 2014 International Society for Microbial Ecology</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>International Society for Microbial Ecology</copyright-holder></permissions><abstract><p>Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of <italic>hpnP</italic>, the gene encoding the C-2 hopanoid methylase. Here we show that <italic>hpnP</italic> copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial <italic>hpnP</italic> genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether <italic>hpnP</italic> presence might track with particular variables. We found <italic>hpnP</italic> to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (<italic>P</italic>-value<10<sup>−6</sup>); in addition, we observed diverse <italic>hpnP</italic> types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche.</p></abstract><kwd-group><kwd>biomarker</kwd><kwd>2-methylhopanoid</kwd><kwd>plant–microbe interaction</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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