Microspatial gene expression patterns in the Amazon River Plume
Identifieur interne : 000410 ( Pmc/Curation ); précédent : 000409; suivant : 000411Microspatial gene expression patterns in the Amazon River Plume
Auteurs : Brandon M. Satinsky ; Byron C. Crump ; Christa B. Smith ; Shalabh Sharma ; Brian L. Zielinski ; Mary Doherty [États-Unis] ; Jun Meng ; Shulei Sun ; Patricia M. Medeiros ; John H. Paul ; Victoria J. Coles [États-Unis] ; Patricia L. Yager ; Mary Ann MoranSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2014.
Abstract
The microbial community of the Amazon River Plume determines the fate of the world’s largest input of terrestrial carbon and nutrients to the ocean. By benchmarking with internal standards during sample collection, we determined that each liter of plume seawater contains 1 trillion genes and 50 billion transcripts from thousands of bacterial, archaeal, and eukaryotic taxa. Gene regulation by taxa inhabiting distinct microenvironments provides insights into micron-scale patterns of transformations in the marine carbon, nitrogen, phosphorus, and sulfur cycles in this globally important ecosystem.
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DOI: 10.1073/pnas.1402782111
PubMed: 25024226
PubMed Central: 4121788
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Zielinski</name><affiliation><nlm:aff id="aff4">College of Marine Science,<institution>University of South Florida</institution>, St. Petersburg,<addr-line>FL</addr-line> 33701;</nlm:aff></affiliation></author><author><name sortKey="Doherty, Mary" sort="Doherty, Mary" uniqKey="Doherty M" first="Mary" last="Doherty">Mary Doherty</name><affiliation wicri:level="2"><nlm:aff wicri:cut="; and" id="aff5">Horn Point Laboratory,<institution>University of Maryland Center for Environmental Science</institution>, Cambridge, MD 21613</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>, Cambridge</wicri:cityArea></affiliation></author><author><name sortKey="Meng, Jun" sort="Meng, Jun" uniqKey="Meng J" first="Jun" last="Meng">Jun Meng</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author><author><name sortKey="Sun, Shulei" sort="Sun, Shulei" uniqKey="Sun S" first="Shulei" last="Sun">Shulei Sun</name><affiliation><nlm:aff id="aff6">Center for Research in Biological Systems,<institution>University of California, San Diego</institution>, La Jolla,<addr-line>CA</addr-line> 92093</nlm:aff></affiliation></author><author><name sortKey="Medeiros, Patricia M" sort="Medeiros, Patricia M" uniqKey="Medeiros P" first="Patricia M." last="Medeiros">Patricia M. 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Yager</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author><author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25024226</idno><idno type="pmc">4121788</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121788</idno><idno type="RBID">PMC:4121788</idno><idno type="doi">10.1073/pnas.1402782111</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000410</idno><idno type="wicri:Area/Pmc/Curation">000410</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Microspatial gene expression patterns in the Amazon River Plume</title><author><name sortKey="Satinsky, Brandon M" sort="Satinsky, Brandon M" uniqKey="Satinsky B" first="Brandon M." last="Satinsky">Brandon M. Satinsky</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Crump, Byron C" sort="Crump, Byron C" uniqKey="Crump B" first="Byron C." last="Crump">Byron C. Crump</name><affiliation><nlm:aff id="aff3">College of Earth, Ocean, and Atmospheric Science,<institution>Oregon State University</institution>, Corvallis,<addr-line>OR</addr-line> 97331;</nlm:aff></affiliation></author><author><name sortKey="Smith, Christa B" sort="Smith, Christa B" uniqKey="Smith C" first="Christa B." last="Smith">Christa B. Smith</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author><author><name sortKey="Sharma, Shalabh" sort="Sharma, Shalabh" uniqKey="Sharma S" first="Shalabh" last="Sharma">Shalabh Sharma</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author><author><name sortKey="Zielinski, Brian L" sort="Zielinski, Brian L" uniqKey="Zielinski B" first="Brian L." last="Zielinski">Brian L. Zielinski</name><affiliation><nlm:aff id="aff4">College of Marine Science,<institution>University of South Florida</institution>, St. Petersburg,<addr-line>FL</addr-line> 33701;</nlm:aff></affiliation></author><author><name sortKey="Doherty, Mary" sort="Doherty, Mary" uniqKey="Doherty M" first="Mary" last="Doherty">Mary Doherty</name><affiliation wicri:level="2"><nlm:aff wicri:cut="; and" id="aff5">Horn Point Laboratory,<institution>University of Maryland Center for Environmental Science</institution>, Cambridge, MD 21613</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>, Cambridge</wicri:cityArea></affiliation></author><author><name sortKey="Meng, Jun" sort="Meng, Jun" uniqKey="Meng J" first="Jun" last="Meng">Jun Meng</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author><author><name sortKey="Sun, Shulei" sort="Sun, Shulei" uniqKey="Sun S" first="Shulei" last="Sun">Shulei Sun</name><affiliation><nlm:aff id="aff6">Center for Research in Biological Systems,<institution>University of California, San Diego</institution>, La Jolla,<addr-line>CA</addr-line> 92093</nlm:aff></affiliation></author><author><name sortKey="Medeiros, Patricia M" sort="Medeiros, Patricia M" uniqKey="Medeiros P" first="Patricia M." last="Medeiros">Patricia M. Medeiros</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author><author><name sortKey="Paul, John H" sort="Paul, John H" uniqKey="Paul J" first="John H." last="Paul">John H. Paul</name><affiliation><nlm:aff id="aff4">College of Marine Science,<institution>University of South Florida</institution>, St. Petersburg,<addr-line>FL</addr-line> 33701;</nlm:aff></affiliation></author><author><name sortKey="Coles, Victoria J" sort="Coles, Victoria J" uniqKey="Coles V" first="Victoria J." last="Coles">Victoria J. Coles</name><affiliation wicri:level="2"><nlm:aff wicri:cut="; and" id="aff5">Horn Point Laboratory,<institution>University of Maryland Center for Environmental Science</institution>, Cambridge, MD 21613</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>, Cambridge</wicri:cityArea></affiliation></author><author><name sortKey="Yager, Patricia L" sort="Yager, Patricia L" uniqKey="Yager P" first="Patricia L." last="Yager">Patricia L. Yager</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author><author><name sortKey="Moran, Mary Ann" sort="Moran, Mary Ann" uniqKey="Moran M" first="Mary Ann" last="Moran">Mary Ann Moran</name><affiliation><nlm:aff id="aff2">Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Significance</title><p>The microbial community of the Amazon River Plume determines the fate of the world’s largest input of terrestrial carbon and nutrients to the ocean. By benchmarking with internal standards during sample collection, we determined that each liter of plume seawater contains 1 trillion genes and 50 billion transcripts from thousands of bacterial, archaeal, and eukaryotic taxa. Gene regulation by taxa inhabiting distinct microenvironments provides insights into micron-scale patterns of transformations in the marine carbon, nitrogen, phosphorus, and sulfur cycles in this globally important ecosystem.</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">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25024226</article-id><article-id pub-id-type="pmc">4121788</article-id><article-id pub-id-type="publisher-id">201402782</article-id><article-id pub-id-type="doi">10.1073/pnas.1402782111</article-id><article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Environmental Sciences</subject></subj-group></subj-group></article-categories><title-group><article-title>Microspatial gene expression patterns in the Amazon River Plume</article-title><alt-title alt-title-type="short">Gene expression in the Amazon River Plume</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Satinsky</surname><given-names>Brandon M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Crump</surname><given-names>Byron C.</given-names></name><xref ref-type="aff" rid="aff3"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Smith</surname><given-names>Christa B.</given-names></name><xref ref-type="aff" rid="aff2"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sharma</surname><given-names>Shalabh</given-names></name><xref ref-type="aff" rid="aff2"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zielinski</surname><given-names>Brian L.</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Doherty</surname><given-names>Mary</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author"><name><surname>Meng</surname><given-names>Jun</given-names></name><xref ref-type="aff" rid="aff2"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sun</surname><given-names>Shulei</given-names></name><xref ref-type="aff" rid="aff6"><sup>f</sup></xref></contrib><contrib contrib-type="author"><name><surname>Medeiros</surname><given-names>Patricia M.</given-names></name><xref ref-type="aff" rid="aff2"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Paul</surname><given-names>John H.</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Coles</surname><given-names>Victoria J.</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yager</surname><given-names>Patricia L.</given-names></name><xref ref-type="aff" rid="aff2"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Moran</surname><given-names>Mary Ann</given-names></name><xref ref-type="aff" rid="aff2"><sup>c</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><aff id="aff1">Departments of<sup>a</sup>Microbiology and</aff><aff id="aff2"><sup>c</sup>Marine Sciences,<institution>University of Georgia</institution>, Athens,<addr-line>GA</addr-line> 30602;</aff><aff id="aff3"><sup>b</sup>College of Earth, Ocean, and Atmospheric Science,<institution>Oregon State University</institution>, Corvallis,<addr-line>OR</addr-line> 97331;</aff><aff id="aff4"><sup>d</sup>College of Marine Science,<institution>University of South Florida</institution>, St. Petersburg,<addr-line>FL</addr-line> 33701;</aff><aff id="aff5"><sup>e</sup>Horn Point Laboratory,<institution>University of Maryland Center for Environmental Science</institution>, Cambridge, MD 21613; and</aff><aff id="aff6"><sup>f</sup>Center for Research in Biological Systems,<institution>University of California, San Diego</institution>, La Jolla,<addr-line>CA</addr-line> 92093</aff></contrib-group><author-notes><corresp id="cor1"><sup>1</sup>To whom correspondence should be addressed. Email: <email>mmoran@uga.edu</email>.</corresp><fn fn-type="edited-by"><p>Edited by Edward F. DeLong, Massachusetts Institute of Technology, Cambridge, MA, and approved June 23, 2014 (received for review February 14, 2014)</p></fn><fn fn-type="con"><p>Author contributions: B.M.S., B.C.C., J.H.P., P.L.Y., and M.A.M. designed research; B.M.S., B.C.C., C.B.S., B.L.Z., M.D., and J.M. performed research; P.M.M. and V.J.C. contributed new reagents/analytic tools; B.M.S., B.C.C., C.B.S., S. Sharma, M.D., S. Sun, P.M.M., P.L.Y., and M.A.M. analyzed data; and B.M.S. and M.A.M. wrote the paper.</p></fn></author-notes><pub-date pub-type="ppub"><day>29</day><month>7</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>14</day><month>7</month><year>2014</year></pub-date><volume>111</volume><issue>30</issue><fpage>11085</fpage><lpage>11090</lpage><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="pnas.201402782.pdf"></self-uri><abstract abstract-type="executive-summary"><title>Significance</title><p>The microbial community of the Amazon River Plume determines the fate of the world’s largest input of terrestrial carbon and nutrients to the ocean. By benchmarking with internal standards during sample collection, we determined that each liter of plume seawater contains 1 trillion genes and 50 billion transcripts from thousands of bacterial, archaeal, and eukaryotic taxa. Gene regulation by taxa inhabiting distinct microenvironments provides insights into micron-scale patterns of transformations in the marine carbon, nitrogen, phosphorus, and sulfur cycles in this globally important ecosystem.</p></abstract><abstract><p>We investigated expression of genes mediating elemental cycling at the microspatial scale in the ocean’s largest river plume using, to our knowledge, the first fully quantitative inventory of genes and transcripts. The bacterial and archaeal communities associated with a phytoplankton bloom in Amazon River Plume waters at the outer continental shelf in June 2010 harbored ∼1.0 × 10<sup>13</sup> genes and 4.7 × 10<sup>11</sup> transcripts per liter that mapped to several thousand microbial genomes. Genomes from free-living cells were more abundant than those from particle-associated cells, and they generated more transcripts per liter for carbon fixation, heterotrophy, nitrogen and phosphorus uptake, and iron acquisition, although they had lower expression ratios (transcripts⋅gene<sup>−1</sup>) overall. Genomes from particle-associated cells contributed more transcripts for sulfur cycling, aromatic compound degradation, and the synthesis of biologically essential vitamins, with an overall twofold up-regulation of expression compared with free-living cells. Quantitatively, gene regulation differences were more important than genome abundance differences in explaining why microenvironment transcriptomes differed. Taxa contributing genomes to both free-living and particle-associated communities had up to 65% of their expressed genes regulated differently between the two, quantifying the extent of transcriptional plasticity in marine microbes in situ. In response to patchiness in carbon, nutrients, and light at the micrometer scale, Amazon Plume microbes regulated the expression of genes relevant to biogeochemical processes at the ecosystem scale.</p></abstract><kwd-group><kwd>metatranscriptomics</kwd><kwd>metagenomics</kwd><kwd>biogeochemistry</kwd><kwd>gene expression ratios</kwd><kwd>marine bacteria</kwd></kwd-group><counts><page-count count="6"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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