The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
Identifieur interne : 000690 ( Pmc/Checkpoint ); précédent : 000689; suivant : 000691The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
Auteurs : Douglas B. Rusch [États-Unis] ; Aaron L. Halpern [États-Unis] ; Granger Sutton [États-Unis] ; Karla B. Heidelberg [États-Unis] ; Shannon Williamson [États-Unis] ; Shibu Yooseph [États-Unis] ; Dongying Wu [États-Unis] ; Jonathan A. Eisen [États-Unis] ; Jeff M. Hoffman [États-Unis] ; Karin Remington [États-Unis] ; Karen Beeson [États-Unis] ; Bao Tran [États-Unis] ; Hamilton Smith [États-Unis] ; Holly Baden-Tillson [États-Unis] ; Clare Stewart [États-Unis] ; Joyce Thorpe [États-Unis] ; Jason Freeman [États-Unis] ; Cynthia Andrews-Pfannkoch [États-Unis] ; Joseph E. Venter [États-Unis] ; Kelvin Li [États-Unis] ; Saul Kravitz [États-Unis] ; John F. Heidelberg [États-Unis] ; Terry Utterback [États-Unis] ; Yu-Hui Rogers [États-Unis] ; Luisa I. Falc N [Mexique] ; Valeria Souza [Mexique] ; Germán Bonilla-Rosso [Mexique] ; Luis E. Eguiarte [Mexique] ; David M. Karl [États-Unis] ; Shubha Sathyendranath [Canada] ; Trevor Platt [Canada] ; Eldredge Bermingham ; Victor Gallardo [Chili] ; Giselle Tamayo-Castillo [Costa Rica] ; Michael R. Ferrari [États-Unis] ; Robert L. Strausberg [États-Unis] ; Kenneth Nealson [États-Unis] ; Robert Friedman [États-Unis] ; Marvin Frazier [États-Unis] ; J. Craig Venter [États-Unis]Source :
- PLoS Biology [ 1544-9173 ] ; 2007.
Abstract
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the
Url:
DOI: 10.1371/journal.pbio.0050077
PubMed: 17355176
PubMed Central: 1821060
Affiliations:
- Canada, Chili, Costa Rica, Mexique, États-Unis
- Californie, Hawaï, Maryland, New Jersey
- Los Angeles, New Brunswick (New Jersey)
- Université Rutgers, Université de Californie du Sud
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:1821060Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The <italic>Sorcerer II</italic>
Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific</title>
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<author><name sortKey="Kravitz, Saul" sort="Kravitz, Saul" uniqKey="Kravitz S" first="Saul" last="Kravitz">Saul Kravitz</name>
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<author><name sortKey="Heidelberg, John F" sort="Heidelberg, John F" uniqKey="Heidelberg J" first="John F" last="Heidelberg">John F. Heidelberg</name>
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<affiliation wicri:level="4"><nlm:aff id="aff2"> Department of Biological Sciences, University of Southern California, Avalon, California, United States of America</nlm:aff>
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<author><name sortKey="Utterback, Terry" sort="Utterback, Terry" uniqKey="Utterback T" first="Terry" last="Utterback">Terry Utterback</name>
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<author><name sortKey="Rogers, Yu Hui" sort="Rogers, Yu Hui" uniqKey="Rogers Y" first="Yu-Hui" last="Rogers">Yu-Hui Rogers</name>
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<author><name sortKey="Falc N, Luisa I" sort="Falc N, Luisa I" uniqKey="Falc N L" first="Luisa I" last="Falc N">Luisa I. Falc N</name>
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<country xml:lang="fr">Mexique</country>
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<author><name sortKey="Souza, Valeria" sort="Souza, Valeria" uniqKey="Souza V" first="Valeria" last="Souza">Valeria Souza</name>
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<author><name sortKey="Bonilla Rosso, German" sort="Bonilla Rosso, German" uniqKey="Bonilla Rosso G" first="Germán" last="Bonilla-Rosso">Germán Bonilla-Rosso</name>
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<author><name sortKey="Eguiarte, Luis E" sort="Eguiarte, Luis E" uniqKey="Eguiarte L" first="Luis E" last="Eguiarte">Luis E. Eguiarte</name>
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<author><name sortKey="Karl, David M" sort="Karl, David M" uniqKey="Karl D" first="David M" last="Karl">David M. Karl</name>
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<author><name sortKey="Sathyendranath, Shubha" sort="Sathyendranath, Shubha" uniqKey="Sathyendranath S" first="Shubha" last="Sathyendranath">Shubha Sathyendranath</name>
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<author><name sortKey="Platt, Trevor" sort="Platt, Trevor" uniqKey="Platt T" first="Trevor" last="Platt">Trevor Platt</name>
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<author><name sortKey="Bermingham, Eldredge" sort="Bermingham, Eldredge" uniqKey="Bermingham E" first="Eldredge" last="Bermingham">Eldredge Bermingham</name>
<affiliation><nlm:aff id="aff8"> Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama</nlm:aff>
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<author><name sortKey="Gallardo, Victor" sort="Gallardo, Victor" uniqKey="Gallardo V" first="Victor" last="Gallardo">Victor Gallardo</name>
<affiliation wicri:level="1"><nlm:aff id="aff9"> Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile</nlm:aff>
<country xml:lang="fr">Chili</country>
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<author><name sortKey="Tamayo Castillo, Giselle" sort="Tamayo Castillo, Giselle" uniqKey="Tamayo Castillo G" first="Giselle" last="Tamayo-Castillo">Giselle Tamayo-Castillo</name>
<affiliation wicri:level="1"><nlm:aff id="aff10"> Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica</nlm:aff>
<country xml:lang="fr">Costa Rica</country>
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<author><name sortKey="Ferrari, Michael R" sort="Ferrari, Michael R" uniqKey="Ferrari M" first="Michael R" last="Ferrari">Michael R. Ferrari</name>
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<author><name sortKey="Strausberg, Robert L" sort="Strausberg, Robert L" uniqKey="Strausberg R" first="Robert L" last="Strausberg">Robert L. Strausberg</name>
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<author><name sortKey="Nealson, Kenneth" sort="Nealson, Kenneth" uniqKey="Nealson K" first="Kenneth" last="Nealson">Kenneth Nealson</name>
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<affiliation wicri:level="4"><nlm:aff id="aff12"> Department of Earth Sciences, University of Southern California, Los Angles, California, United States of America</nlm:aff>
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</affiliation>
</author>
<author><name sortKey="Friedman, Robert" sort="Friedman, Robert" uniqKey="Friedman R" first="Robert" last="Friedman">Robert Friedman</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Frazier, Marvin" sort="Frazier, Marvin" uniqKey="Frazier M" first="Marvin" last="Frazier">Marvin Frazier</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Venter, J Craig" sort="Venter, J Craig" uniqKey="Venter J" first="J. Craig" last="Venter">J. Craig Venter</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">17355176</idno>
<idno type="pmc">1821060</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821060</idno>
<idno type="RBID">PMC:1821060</idno>
<idno type="doi">10.1371/journal.pbio.0050077</idno>
<date when="2007">2007</date>
<idno type="wicri:Area/Pmc/Corpus">000593</idno>
<idno type="wicri:Area/Pmc/Curation">000593</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000690</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The <italic>Sorcerer II</italic>
Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific</title>
<author><name sortKey="Rusch, Douglas B" sort="Rusch, Douglas B" uniqKey="Rusch D" first="Douglas B" last="Rusch">Douglas B. Rusch</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Halpern, Aaron L" sort="Halpern, Aaron L" uniqKey="Halpern A" first="Aaron L" last="Halpern">Aaron L. Halpern</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Sutton, Granger" sort="Sutton, Granger" uniqKey="Sutton G" first="Granger" last="Sutton">Granger Sutton</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Heidelberg, Karla B" sort="Heidelberg, Karla B" uniqKey="Heidelberg K" first="Karla B" last="Heidelberg">Karla B. Heidelberg</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff2"> Department of Biological Sciences, University of Southern California, Avalon, California, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> Department of Biological Sciences, University of Southern California, Avalon, California</wicri:regionArea>
<placeName><region type="state">Californie</region>
<settlement type="city">Los Angeles</settlement>
</placeName>
<orgName type="university">Université de Californie du Sud</orgName>
</affiliation>
</author>
<author><name sortKey="Williamson, Shannon" sort="Williamson, Shannon" uniqKey="Williamson S" first="Shannon" last="Williamson">Shannon Williamson</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yooseph, Shibu" sort="Yooseph, Shibu" uniqKey="Yooseph S" first="Shibu" last="Yooseph">Shibu Yooseph</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wu, Dongying" sort="Wu, Dongying" uniqKey="Wu D" first="Dongying" last="Wu">Dongying Wu</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="aff3"> Genome Center, University of California Davis, Davis, California, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> Genome Center, University of California Davis, Davis, California</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="aff3"> Genome Center, University of California Davis, Davis, California, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> Genome Center, University of California Davis, Davis, California</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Hoffman, Jeff M" sort="Hoffman, Jeff M" uniqKey="Hoffman J" first="Jeff M" last="Hoffman">Jeff M. Hoffman</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Remington, Karin" sort="Remington, Karin" uniqKey="Remington K" first="Karin" last="Remington">Karin Remington</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="aff4"> Your Genome, Your World, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> Your Genome, Your World, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Beeson, Karen" sort="Beeson, Karen" uniqKey="Beeson K" first="Karen" last="Beeson">Karen Beeson</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Tran, Bao" sort="Tran, Bao" uniqKey="Tran B" first="Bao" last="Tran">Bao Tran</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Smith, Hamilton" sort="Smith, Hamilton" uniqKey="Smith H" first="Hamilton" last="Smith">Hamilton Smith</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Baden Tillson, Holly" sort="Baden Tillson, Holly" uniqKey="Baden Tillson H" first="Holly" last="Baden-Tillson">Holly Baden-Tillson</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Stewart, Clare" sort="Stewart, Clare" uniqKey="Stewart C" first="Clare" last="Stewart">Clare Stewart</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Thorpe, Joyce" sort="Thorpe, Joyce" uniqKey="Thorpe J" first="Joyce" last="Thorpe">Joyce Thorpe</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Freeman, Jason" sort="Freeman, Jason" uniqKey="Freeman J" first="Jason" last="Freeman">Jason Freeman</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Andrews Pfannkoch, Cynthia" sort="Andrews Pfannkoch, Cynthia" uniqKey="Andrews Pfannkoch C" first="Cynthia" last="Andrews-Pfannkoch">Cynthia Andrews-Pfannkoch</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Venter, Joseph E" sort="Venter, Joseph E" uniqKey="Venter J" first="Joseph E" last="Venter">Joseph E. Venter</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Li, Kelvin" sort="Li, Kelvin" uniqKey="Li K" first="Kelvin" last="Li">Kelvin Li</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Kravitz, Saul" sort="Kravitz, Saul" uniqKey="Kravitz S" first="Saul" last="Kravitz">Saul Kravitz</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</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="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff2"> Department of Biological Sciences, University of Southern California, Avalon, California, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> Department of Biological Sciences, University of Southern California, Avalon, California</wicri:regionArea>
<placeName><region type="state">Californie</region>
<settlement type="city">Los Angeles</settlement>
</placeName>
<orgName type="university">Université de Californie du Sud</orgName>
</affiliation>
</author>
<author><name sortKey="Utterback, Terry" sort="Utterback, Terry" uniqKey="Utterback T" first="Terry" last="Utterback">Terry Utterback</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Rogers, Yu Hui" sort="Rogers, Yu Hui" uniqKey="Rogers Y" first="Yu-Hui" last="Rogers">Yu-Hui Rogers</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Falc N, Luisa I" sort="Falc N, Luisa I" uniqKey="Falc N L" first="Luisa I" last="Falc N">Luisa I. Falc N</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"> Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico</nlm:aff>
<country xml:lang="fr">Mexique</country>
<wicri:regionArea> Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City</wicri:regionArea>
<wicri:noRegion>Mexico City</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Souza, Valeria" sort="Souza, Valeria" uniqKey="Souza V" first="Valeria" last="Souza">Valeria Souza</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"> Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico</nlm:aff>
<country xml:lang="fr">Mexique</country>
<wicri:regionArea> Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City</wicri:regionArea>
<wicri:noRegion>Mexico City</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Bonilla Rosso, German" sort="Bonilla Rosso, German" uniqKey="Bonilla Rosso G" first="Germán" last="Bonilla-Rosso">Germán Bonilla-Rosso</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"> Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico</nlm:aff>
<country xml:lang="fr">Mexique</country>
<wicri:regionArea> Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City</wicri:regionArea>
<wicri:noRegion>Mexico City</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Eguiarte, Luis E" sort="Eguiarte, Luis E" uniqKey="Eguiarte L" first="Luis E" last="Eguiarte">Luis E. Eguiarte</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"> Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico</nlm:aff>
<country xml:lang="fr">Mexique</country>
<wicri:regionArea> Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City</wicri:regionArea>
<wicri:noRegion>Mexico City</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Karl, David M" sort="Karl, David M" uniqKey="Karl D" first="David M" last="Karl">David M. Karl</name>
<affiliation wicri:level="2"><nlm:aff id="aff6"> Department of Oceanography, University of Hawaii, Honolulu, Hawaii, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> Department of Oceanography, University of Hawaii, Honolulu, Hawaii</wicri:regionArea>
<placeName><region type="state">Hawaï</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Sathyendranath, Shubha" sort="Sathyendranath, Shubha" uniqKey="Sathyendranath S" first="Shubha" last="Sathyendranath">Shubha Sathyendranath</name>
<affiliation wicri:level="1"><nlm:aff id="aff7"> Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea> Bedford Institute of Oceanography, Dartmouth, Nova Scotia</wicri:regionArea>
<wicri:noRegion>Nova Scotia</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Platt, Trevor" sort="Platt, Trevor" uniqKey="Platt T" first="Trevor" last="Platt">Trevor Platt</name>
<affiliation wicri:level="1"><nlm:aff id="aff7"> Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea> Bedford Institute of Oceanography, Dartmouth, Nova Scotia</wicri:regionArea>
<wicri:noRegion>Nova Scotia</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Bermingham, Eldredge" sort="Bermingham, Eldredge" uniqKey="Bermingham E" first="Eldredge" last="Bermingham">Eldredge Bermingham</name>
<affiliation><nlm:aff id="aff8"> Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama</nlm:aff>
<wicri:noCountry code="subfield">Republic of Panama</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Gallardo, Victor" sort="Gallardo, Victor" uniqKey="Gallardo V" first="Victor" last="Gallardo">Victor Gallardo</name>
<affiliation wicri:level="1"><nlm:aff id="aff9"> Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile</nlm:aff>
<country xml:lang="fr">Chili</country>
<wicri:regionArea> Departamento de Oceanografía, Universidad de Concepción, Concepción</wicri:regionArea>
<wicri:noRegion>Concepción</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Tamayo Castillo, Giselle" sort="Tamayo Castillo, Giselle" uniqKey="Tamayo Castillo G" first="Giselle" last="Tamayo-Castillo">Giselle Tamayo-Castillo</name>
<affiliation wicri:level="1"><nlm:aff id="aff10"> Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica</nlm:aff>
<country xml:lang="fr">Costa Rica</country>
<wicri:regionArea> Escuela de Química, Universidad de Costa Rica, San Pedro</wicri:regionArea>
<wicri:noRegion>San Pedro</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ferrari, Michael R" sort="Ferrari, Michael R" uniqKey="Ferrari M" first="Michael R" last="Ferrari">Michael R. Ferrari</name>
<affiliation wicri:level="4"><nlm:aff id="aff11"> Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey</wicri:regionArea>
<placeName><region type="state">New Jersey</region>
<settlement type="city">New Brunswick (New Jersey)</settlement>
</placeName>
<orgName type="university">Université Rutgers</orgName>
</affiliation>
</author>
<author><name sortKey="Strausberg, Robert L" sort="Strausberg, Robert L" uniqKey="Strausberg R" first="Robert L" last="Strausberg">Robert L. Strausberg</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Nealson, Kenneth" sort="Nealson, Kenneth" uniqKey="Nealson K" first="Kenneth" last="Nealson">Kenneth Nealson</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff12"> Department of Earth Sciences, University of Southern California, Los Angles, California, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> Department of Earth Sciences, University of Southern California, Los Angles, California</wicri:regionArea>
<placeName><region type="state">Californie</region>
<settlement type="city">Los Angeles</settlement>
</placeName>
<orgName type="university">Université de Californie du Sud</orgName>
</affiliation>
</author>
<author><name sortKey="Friedman, Robert" sort="Friedman, Robert" uniqKey="Friedman R" first="Robert" last="Friedman">Robert Friedman</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
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<author><name sortKey="Frazier, Marvin" sort="Frazier, Marvin" uniqKey="Frazier M" first="Marvin" last="Frazier">Marvin Frazier</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea> J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
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<author><name sortKey="Venter, J Craig" sort="Venter, J Craig" uniqKey="Venter J" first="J. Craig" last="Venter">J. Craig Venter</name>
<affiliation wicri:level="2"><nlm:aff id="aff1"> J. Craig Venter Institute, Rockville, Maryland, United States of America</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<series><title level="j">PLoS Biology</title>
<idno type="ISSN">1544-9173</idno>
<idno type="eISSN">1545-7885</idno>
<imprint><date when="2007">2007</date>
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<front><div type="abstract" xml:lang="en"><p>The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the <italic>Sorcerer II</italic>
Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene <italic>PstS</italic>
.</p>
</div>
</front>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS Biol</journal-id>
<journal-id journal-id-type="publisher-id">pbio</journal-id>
<journal-title>PLoS Biology</journal-title>
<issn pub-type="ppub">1544-9173</issn>
<issn pub-type="epub">1545-7885</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">17355176</article-id>
<article-id pub-id-type="pmc">1821060</article-id>
<article-id pub-id-type="doi">10.1371/journal.pbio.0050077</article-id>
<article-id pub-id-type="publisher-id">06-PLBI-RA-1263R2</article-id>
<article-id pub-id-type="sici">plbi-05-03-22</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline"><subject>Computational Biology</subject>
<subject>Computational Biology</subject>
<subject>Computational Biology</subject>
<subject>Ecology</subject>
<subject>Evolutionary Biology</subject>
<subject>Genetics and Genomics</subject>
<subject>Genetics and Genomics</subject>
<subject>Genetics and Genomics</subject>
<subject>Genetics and Genomics</subject>
<subject>Genetics and Genomics</subject>
<subject>Microbiology</subject>
<subject>Microbiology</subject>
<subject>Microbiology</subject>
<subject>Virology</subject>
</subj-group>
<subj-group subj-group-type="System Taxonomy"><subject>Eubacteria</subject>
<subject>Archaea</subject>
<subject>Viruses</subject>
</subj-group>
<series-title>Oceanic Metagenomics</series-title>
</article-categories>
<title-group><article-title>The <italic>Sorcerer II</italic>
Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific</article-title>
<alt-title alt-title-type="running-head"><italic>Sorcerer II</italic>
GOS Expedition</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Rusch</surname>
<given-names>Douglas B</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Halpern</surname>
<given-names>Aaron L</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sutton</surname>
<given-names>Granger</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Heidelberg</surname>
<given-names>Karla B</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Williamson</surname>
<given-names>Shannon</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yooseph</surname>
<given-names>Shibu</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wu</surname>
<given-names>Dongying</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Eisen</surname>
<given-names>Jonathan A</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hoffman</surname>
<given-names>Jeff M</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Remington</surname>
<given-names>Karin</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Beeson</surname>
<given-names>Karen</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tran</surname>
<given-names>Bao</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Smith</surname>
<given-names>Hamilton</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Baden-Tillson</surname>
<given-names>Holly</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stewart</surname>
<given-names>Clare</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Thorpe</surname>
<given-names>Joyce</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Freeman</surname>
<given-names>Jason</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Andrews-Pfannkoch</surname>
<given-names>Cynthia</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Venter</surname>
<given-names>Joseph E</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Kelvin</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kravitz</surname>
<given-names>Saul</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Heidelberg</surname>
<given-names>John F</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Utterback</surname>
<given-names>Terry</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rogers</surname>
<given-names>Yu-Hui</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Falcón</surname>
<given-names>Luisa I</given-names>
</name>
<xref ref-type="aff" rid="aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Souza</surname>
<given-names>Valeria</given-names>
</name>
<xref ref-type="aff" rid="aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bonilla-Rosso</surname>
<given-names>Germán</given-names>
</name>
<xref ref-type="aff" rid="aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Eguiarte</surname>
<given-names>Luis E</given-names>
</name>
<xref ref-type="aff" rid="aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Karl</surname>
<given-names>David M</given-names>
</name>
<xref ref-type="aff" rid="aff6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sathyendranath</surname>
<given-names>Shubha</given-names>
</name>
<xref ref-type="aff" rid="aff7">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Platt</surname>
<given-names>Trevor</given-names>
</name>
<xref ref-type="aff" rid="aff7">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bermingham</surname>
<given-names>Eldredge</given-names>
</name>
<xref ref-type="aff" rid="aff8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gallardo</surname>
<given-names>Victor</given-names>
</name>
<xref ref-type="aff" rid="aff9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tamayo-Castillo</surname>
<given-names>Giselle</given-names>
</name>
<xref ref-type="aff" rid="aff10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ferrari</surname>
<given-names>Michael R</given-names>
</name>
<xref ref-type="aff" rid="aff11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Strausberg</surname>
<given-names>Robert L</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Nealson</surname>
<given-names>Kenneth</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff12">12</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Friedman</surname>
<given-names>Robert</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Frazier</surname>
<given-names>Marvin</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Venter</surname>
<given-names>J. Craig</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
J. Craig Venter Institute, Rockville, Maryland, United States of America</aff>
<aff id="aff2"><label>2</label>
Department of Biological Sciences, University of Southern California, Avalon, California, United States of America</aff>
<aff id="aff3"><label>3</label>
Genome Center, University of California Davis, Davis, California, United States of America</aff>
<aff id="aff4"><label>4</label>
Your Genome, Your World, Rockville, Maryland, United States of America</aff>
<aff id="aff5"><label>5</label>
Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico</aff>
<aff id="aff6"><label>6</label>
Department of Oceanography, University of Hawaii, Honolulu, Hawaii, United States of America</aff>
<aff id="aff7"><label>7</label>
Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada</aff>
<aff id="aff8"><label>8</label>
Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama</aff>
<aff id="aff9"><label>9</label>
Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile</aff>
<aff id="aff10"><label>10</label>
Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica</aff>
<aff id="aff11"><label>11</label>
Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, United States of America</aff>
<aff id="aff12"><label>12</label>
Department of Earth Sciences, University of Southern California, Los Angles, California, United States of America</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Moran</surname>
<given-names>Nancy A</given-names>
</name>
<role>Academic Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">University of Arizona, United States of America</aff>
<author-notes><corresp id="cor1">* To whom correspondence should be addressed. E-mail: <email>DRusch@venterinstitute.org</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>3</month>
<year>2007</year>
</pub-date>
<pub-date pub-type="epub"><day>13</day>
<month>3</month>
<year>2007</year>
</pub-date>
<volume>5</volume>
<issue>3</issue>
<elocation-id>e77</elocation-id>
<history><date date-type="received"><day>14</day>
<month>7</month>
<year>2006</year>
</date>
<date date-type="accepted"><day>16</day>
<month>1</month>
<year>2007</year>
</date>
</history>
<copyright-statement><bold>Copyright:</bold>
© 2007 Rusch et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</copyright-statement>
<copyright-year>2007</copyright-year>
<related-article xlink:href="10.1371/journal.pbio.0050083" related-article-type="companion" xlink:title="Editorial" vol="5" page="e83" id="N0x90542a0N0x8d797d0" ext-link-type="doi"><article-title>Global Ocean Sampling Collection</article-title>
</related-article>
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The Search for Microbial Diversity Roils the Waters</article-title>
</related-article>
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Global Ocean Sampling Expedition: Expanding the Universe of Protein Families</article-title>
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<abstract><p>The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the <italic>Sorcerer II</italic>
Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene <italic>PstS</italic>
.</p>
</abstract>
<abstract abstract-type="summary"><title>Author Summary</title>
<sec id="st1"><title></title>
<p>Marine microbes remain elusive and mysterious, even though they are the most abundant life form in the ocean, form the base of the marine food web, and drive energy and nutrient cycling. We know so little about the vast majority of microbes because only a small percentage can be cultivated and studied in the lab. Here we report on the Global Ocean Sampling expedition, an environmental metagenomics project that aims to shed light on the role of marine microbes by sequencing their DNA without first needing to isolate individual organisms. A total of 41 different samples were taken from a wide variety of aquatic habitats collected over 8,000 km. The resulting 7.7 million sequencing reads provide an unprecedented look at the incredible diversity and heterogeneity in naturally occurring microbial populations. We have developed new bioinformatic methods to reconstitute large portions of both cultured and uncultured microbial genomes. Organism diversity is analyzed in relation to sampling locations and environmental pressures. Taken together, these data and analyses serve as a foundation for greatly expanding our understanding of individual microbial lineages and their evolution, the nature of marine microbial communities, and how they are impacted by and impact our world.</p>
</sec>
</abstract>
<abstract abstract-type="toc"><p>The<italic>Sorcerer II</italic>
GOS expedition, data sampling, and analysis is described. The immense diversity in the sequence data required novel comparative genomic assembly methods, which uncovered genomic differences that marker-based methods could not.</p>
</abstract>
<counts><page-count count="34"></page-count>
</counts>
<custom-meta-wrap><custom-meta><meta-name>citation</meta-name>
<meta-value>Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The <italic>Sorcerer II</italic>
Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol 5(3): e77. doi:<ext-link ext-link-type="doi" xlink:href="10.1371/journal.pbio.0050077">10.1371/journal.pbio.0050077</ext-link>
</meta-value>
</custom-meta>
<custom-meta><meta-name>article-logo</meta-name>
<meta-value>oceaniclogo.jpg</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Canada</li>
<li>Chili</li>
<li>Costa Rica</li>
<li>Mexique</li>
<li>États-Unis</li>
</country>
<region><li>Californie</li>
<li>Hawaï</li>
<li>Maryland</li>
<li>New Jersey</li>
</region>
<settlement><li>Los Angeles</li>
<li>New Brunswick (New Jersey)</li>
</settlement>
<orgName><li>Université Rutgers</li>
<li>Université de Californie du Sud</li>
</orgName>
</list>
<tree><noCountry><name sortKey="Bermingham, Eldredge" sort="Bermingham, Eldredge" uniqKey="Bermingham E" first="Eldredge" last="Bermingham">Eldredge Bermingham</name>
</noCountry>
<country name="États-Unis"><region name="Maryland"><name sortKey="Rusch, Douglas B" sort="Rusch, Douglas B" uniqKey="Rusch D" first="Douglas B" last="Rusch">Douglas B. Rusch</name>
</region>
<name sortKey="Andrews Pfannkoch, Cynthia" sort="Andrews Pfannkoch, Cynthia" uniqKey="Andrews Pfannkoch C" first="Cynthia" last="Andrews-Pfannkoch">Cynthia Andrews-Pfannkoch</name>
<name sortKey="Baden Tillson, Holly" sort="Baden Tillson, Holly" uniqKey="Baden Tillson H" first="Holly" last="Baden-Tillson">Holly Baden-Tillson</name>
<name sortKey="Beeson, Karen" sort="Beeson, Karen" uniqKey="Beeson K" first="Karen" last="Beeson">Karen Beeson</name>
<name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name>
<name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name>
<name sortKey="Ferrari, Michael R" sort="Ferrari, Michael R" uniqKey="Ferrari M" first="Michael R" last="Ferrari">Michael R. Ferrari</name>
<name sortKey="Frazier, Marvin" sort="Frazier, Marvin" uniqKey="Frazier M" first="Marvin" last="Frazier">Marvin Frazier</name>
<name sortKey="Freeman, Jason" sort="Freeman, Jason" uniqKey="Freeman J" first="Jason" last="Freeman">Jason Freeman</name>
<name sortKey="Friedman, Robert" sort="Friedman, Robert" uniqKey="Friedman R" first="Robert" last="Friedman">Robert Friedman</name>
<name sortKey="Halpern, Aaron L" sort="Halpern, Aaron L" uniqKey="Halpern A" first="Aaron L" last="Halpern">Aaron L. Halpern</name>
<name sortKey="Heidelberg, John F" sort="Heidelberg, John F" uniqKey="Heidelberg J" first="John F" last="Heidelberg">John F. Heidelberg</name>
<name sortKey="Heidelberg, John F" sort="Heidelberg, John F" uniqKey="Heidelberg J" first="John F" last="Heidelberg">John F. Heidelberg</name>
<name sortKey="Heidelberg, Karla B" sort="Heidelberg, Karla B" uniqKey="Heidelberg K" first="Karla B" last="Heidelberg">Karla B. Heidelberg</name>
<name sortKey="Heidelberg, Karla B" sort="Heidelberg, Karla B" uniqKey="Heidelberg K" first="Karla B" last="Heidelberg">Karla B. Heidelberg</name>
<name sortKey="Hoffman, Jeff M" sort="Hoffman, Jeff M" uniqKey="Hoffman J" first="Jeff M" last="Hoffman">Jeff M. Hoffman</name>
<name sortKey="Karl, David M" sort="Karl, David M" uniqKey="Karl D" first="David M" last="Karl">David M. Karl</name>
<name sortKey="Kravitz, Saul" sort="Kravitz, Saul" uniqKey="Kravitz S" first="Saul" last="Kravitz">Saul Kravitz</name>
<name sortKey="Li, Kelvin" sort="Li, Kelvin" uniqKey="Li K" first="Kelvin" last="Li">Kelvin Li</name>
<name sortKey="Nealson, Kenneth" sort="Nealson, Kenneth" uniqKey="Nealson K" first="Kenneth" last="Nealson">Kenneth Nealson</name>
<name sortKey="Nealson, Kenneth" sort="Nealson, Kenneth" uniqKey="Nealson K" first="Kenneth" last="Nealson">Kenneth Nealson</name>
<name sortKey="Remington, Karin" sort="Remington, Karin" uniqKey="Remington K" first="Karin" last="Remington">Karin Remington</name>
<name sortKey="Remington, Karin" sort="Remington, Karin" uniqKey="Remington K" first="Karin" last="Remington">Karin Remington</name>
<name sortKey="Rogers, Yu Hui" sort="Rogers, Yu Hui" uniqKey="Rogers Y" first="Yu-Hui" last="Rogers">Yu-Hui Rogers</name>
<name sortKey="Smith, Hamilton" sort="Smith, Hamilton" uniqKey="Smith H" first="Hamilton" last="Smith">Hamilton Smith</name>
<name sortKey="Stewart, Clare" sort="Stewart, Clare" uniqKey="Stewart C" first="Clare" last="Stewart">Clare Stewart</name>
<name sortKey="Strausberg, Robert L" sort="Strausberg, Robert L" uniqKey="Strausberg R" first="Robert L" last="Strausberg">Robert L. Strausberg</name>
<name sortKey="Sutton, Granger" sort="Sutton, Granger" uniqKey="Sutton G" first="Granger" last="Sutton">Granger Sutton</name>
<name sortKey="Thorpe, Joyce" sort="Thorpe, Joyce" uniqKey="Thorpe J" first="Joyce" last="Thorpe">Joyce Thorpe</name>
<name sortKey="Tran, Bao" sort="Tran, Bao" uniqKey="Tran B" first="Bao" last="Tran">Bao Tran</name>
<name sortKey="Utterback, Terry" sort="Utterback, Terry" uniqKey="Utterback T" first="Terry" last="Utterback">Terry Utterback</name>
<name sortKey="Venter, J Craig" sort="Venter, J Craig" uniqKey="Venter J" first="J. Craig" last="Venter">J. Craig Venter</name>
<name sortKey="Venter, Joseph E" sort="Venter, Joseph E" uniqKey="Venter J" first="Joseph E" last="Venter">Joseph E. Venter</name>
<name sortKey="Williamson, Shannon" sort="Williamson, Shannon" uniqKey="Williamson S" first="Shannon" last="Williamson">Shannon Williamson</name>
<name sortKey="Wu, Dongying" sort="Wu, Dongying" uniqKey="Wu D" first="Dongying" last="Wu">Dongying Wu</name>
<name sortKey="Wu, Dongying" sort="Wu, Dongying" uniqKey="Wu D" first="Dongying" last="Wu">Dongying Wu</name>
<name sortKey="Yooseph, Shibu" sort="Yooseph, Shibu" uniqKey="Yooseph S" first="Shibu" last="Yooseph">Shibu Yooseph</name>
</country>
<country name="Mexique"><noRegion><name sortKey="Falc N, Luisa I" sort="Falc N, Luisa I" uniqKey="Falc N L" first="Luisa I" last="Falc N">Luisa I. Falc N</name>
</noRegion>
<name sortKey="Bonilla Rosso, German" sort="Bonilla Rosso, German" uniqKey="Bonilla Rosso G" first="Germán" last="Bonilla-Rosso">Germán Bonilla-Rosso</name>
<name sortKey="Eguiarte, Luis E" sort="Eguiarte, Luis E" uniqKey="Eguiarte L" first="Luis E" last="Eguiarte">Luis E. Eguiarte</name>
<name sortKey="Souza, Valeria" sort="Souza, Valeria" uniqKey="Souza V" first="Valeria" last="Souza">Valeria Souza</name>
</country>
<country name="Canada"><noRegion><name sortKey="Sathyendranath, Shubha" sort="Sathyendranath, Shubha" uniqKey="Sathyendranath S" first="Shubha" last="Sathyendranath">Shubha Sathyendranath</name>
</noRegion>
<name sortKey="Platt, Trevor" sort="Platt, Trevor" uniqKey="Platt T" first="Trevor" last="Platt">Trevor Platt</name>
</country>
<country name="Chili"><noRegion><name sortKey="Gallardo, Victor" sort="Gallardo, Victor" uniqKey="Gallardo V" first="Victor" last="Gallardo">Victor Gallardo</name>
</noRegion>
</country>
<country name="Costa Rica"><noRegion><name sortKey="Tamayo Castillo, Giselle" sort="Tamayo Castillo, Giselle" uniqKey="Tamayo Castillo G" first="Giselle" last="Tamayo-Castillo">Giselle Tamayo-Castillo</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>
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