Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche
Identifieur interne : 000015 ( Pmc/Corpus ); précédent : 000014; suivant : 000016Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche
Auteurs : Jessica N. Ricci ; Maureen L. Coleman ; Paula V. Welander ; Alex L. Sessions ; Roger E. Summons ; John R. Spear ; Dianne K. NewmanSource :
- The ISME Journal [ 1751-7362 ] ; 2013.
Abstract
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
Url:
DOI: 10.1038/ismej.2013.191
PubMed: 24152713
PubMed Central: 3930323
Links to Exploration step
PMC:3930323Le document en format XML
<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)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000015 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000015 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Pmc |étape= Corpus |type= RBID |clé= PMC:3930323 |texte= Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/RBID.i -Sk "pubmed:24152713" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
This area was generated with Dilib version V0.6.25. |