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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A microarray for assessing transcription from pelagic marine microbial taxa</title>
<author><name sortKey="Shilova, Irina N" sort="Shilova, Irina N" uniqKey="Shilova I" first="Irina N" last="Shilova">Irina N. Shilova</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Robidart, Julie C" sort="Robidart, Julie C" uniqKey="Robidart J" first="Julie C" last="Robidart">Julie C. Robidart</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="James Tripp, H" sort="James Tripp, H" uniqKey="James Tripp H" first="H" last="James Tripp">H. James Tripp</name>
<affiliation><nlm:aff id="aff2"><institution>DOE Joint Genome Institute</institution>
, Walnut Creek, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Turk Kubo, Kendra" sort="Turk Kubo, Kendra" uniqKey="Turk Kubo K" first="Kendra" last="Turk-Kubo">Kendra Turk-Kubo</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wawrik, Boris" sort="Wawrik, Boris" uniqKey="Wawrik B" first="Boris" last="Wawrik">Boris Wawrik</name>
<affiliation><nlm:aff id="aff3"><institution>Department of Microbiology and Plant Biology, University of Oklahoma</institution>
, Oklahoma,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Post, Anton F" sort="Post, Anton F" uniqKey="Post A" first="Anton F" last="Post">Anton F. Post</name>
<affiliation><nlm:aff id="aff4"><institution>Marine Biological Laboratory</institution>
, Woods Hole, MA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Thompson, Anne W" sort="Thompson, Anne W" uniqKey="Thompson A" first="Anne W" last="Thompson">Anne W. Thompson</name>
<affiliation><nlm:aff id="aff5"><institution>Advanced Cytometry Group, BD Biosciences</institution>
, Seattle, WA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ward, Bess" sort="Ward, Bess" uniqKey="Ward B" first="Bess" last="Ward">Bess Ward</name>
<affiliation><nlm:aff id="aff6"><institution>Department of Geosciences, Princeton University</institution>
, Princeton, NJ,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hollibaugh, James T" sort="Hollibaugh, James T" uniqKey="Hollibaugh J" first="James T" last="Hollibaugh">James T. Hollibaugh</name>
<affiliation><nlm:aff id="aff7"><institution>Department of Marine Sciences, University of Georgia</institution>
, Athens, GA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Millard, Andy" sort="Millard, Andy" uniqKey="Millard A" first="Andy" last="Millard">Andy Millard</name>
<affiliation><nlm:aff id="aff8"><institution>Department of Marine Microbiology, University of Warwick</institution>
, Coventry,<country>UK</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ostrowski, Martin" sort="Ostrowski, Martin" uniqKey="Ostrowski M" first="Martin" last="Ostrowski">Martin Ostrowski</name>
<affiliation><nlm:aff id="aff8"><institution>Department of Marine Microbiology, University of Warwick</institution>
, Coventry,<country>UK</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="J Scanlan, David" sort="J Scanlan, David" uniqKey="J Scanlan D" first="David" last="J Scanlan">David J Scanlan</name>
<affiliation><nlm:aff id="aff8"><institution>Department of Marine Microbiology, University of Warwick</institution>
, Coventry,<country>UK</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Paerl, Ryan W" sort="Paerl, Ryan W" uniqKey="Paerl R" first="Ryan W" last="Paerl">Ryan W. Paerl</name>
<affiliation><nlm:aff id="aff9"><institution>Marine Biology Research Division, University of California San Diego</institution>
, San Diego, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stuart, Rhona" sort="Stuart, Rhona" uniqKey="Stuart R" first="Rhona" last="Stuart">Rhona Stuart</name>
<affiliation><nlm:aff id="aff10"><institution>Physical and Life Sciences, Lawrence Livermore National Laboratory</institution>
, Livermore, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zehr, Jonathan P" sort="Zehr, Jonathan P" uniqKey="Zehr J" first="Jonathan P" last="Zehr">Jonathan P. Zehr</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">24477198</idno>
<idno type="pmc">4069398</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069398</idno>
<idno type="RBID">PMC:4069398</idno>
<idno type="doi">10.1038/ismej.2014.1</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000016</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A microarray for assessing transcription from pelagic marine microbial taxa</title>
<author><name sortKey="Shilova, Irina N" sort="Shilova, Irina N" uniqKey="Shilova I" first="Irina N" last="Shilova">Irina N. Shilova</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Robidart, Julie C" sort="Robidart, Julie C" uniqKey="Robidart J" first="Julie C" last="Robidart">Julie C. Robidart</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="James Tripp, H" sort="James Tripp, H" uniqKey="James Tripp H" first="H" last="James Tripp">H. James Tripp</name>
<affiliation><nlm:aff id="aff2"><institution>DOE Joint Genome Institute</institution>
, Walnut Creek, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Turk Kubo, Kendra" sort="Turk Kubo, Kendra" uniqKey="Turk Kubo K" first="Kendra" last="Turk-Kubo">Kendra Turk-Kubo</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wawrik, Boris" sort="Wawrik, Boris" uniqKey="Wawrik B" first="Boris" last="Wawrik">Boris Wawrik</name>
<affiliation><nlm:aff id="aff3"><institution>Department of Microbiology and Plant Biology, University of Oklahoma</institution>
, Oklahoma,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Post, Anton F" sort="Post, Anton F" uniqKey="Post A" first="Anton F" last="Post">Anton F. Post</name>
<affiliation><nlm:aff id="aff4"><institution>Marine Biological Laboratory</institution>
, Woods Hole, MA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Thompson, Anne W" sort="Thompson, Anne W" uniqKey="Thompson A" first="Anne W" last="Thompson">Anne W. Thompson</name>
<affiliation><nlm:aff id="aff5"><institution>Advanced Cytometry Group, BD Biosciences</institution>
, Seattle, WA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ward, Bess" sort="Ward, Bess" uniqKey="Ward B" first="Bess" last="Ward">Bess Ward</name>
<affiliation><nlm:aff id="aff6"><institution>Department of Geosciences, Princeton University</institution>
, Princeton, NJ,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hollibaugh, James T" sort="Hollibaugh, James T" uniqKey="Hollibaugh J" first="James T" last="Hollibaugh">James T. Hollibaugh</name>
<affiliation><nlm:aff id="aff7"><institution>Department of Marine Sciences, University of Georgia</institution>
, Athens, GA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Millard, Andy" sort="Millard, Andy" uniqKey="Millard A" first="Andy" last="Millard">Andy Millard</name>
<affiliation><nlm:aff id="aff8"><institution>Department of Marine Microbiology, University of Warwick</institution>
, Coventry,<country>UK</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ostrowski, Martin" sort="Ostrowski, Martin" uniqKey="Ostrowski M" first="Martin" last="Ostrowski">Martin Ostrowski</name>
<affiliation><nlm:aff id="aff8"><institution>Department of Marine Microbiology, University of Warwick</institution>
, Coventry,<country>UK</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="J Scanlan, David" sort="J Scanlan, David" uniqKey="J Scanlan D" first="David" last="J Scanlan">David J Scanlan</name>
<affiliation><nlm:aff id="aff8"><institution>Department of Marine Microbiology, University of Warwick</institution>
, Coventry,<country>UK</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Paerl, Ryan W" sort="Paerl, Ryan W" uniqKey="Paerl R" first="Ryan W" last="Paerl">Ryan W. Paerl</name>
<affiliation><nlm:aff id="aff9"><institution>Marine Biology Research Division, University of California San Diego</institution>
, San Diego, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stuart, Rhona" sort="Stuart, Rhona" uniqKey="Stuart R" first="Rhona" last="Stuart">Rhona Stuart</name>
<affiliation><nlm:aff id="aff10"><institution>Physical and Life Sciences, Lawrence Livermore National Laboratory</institution>
, Livermore, CA,<country>USA</country>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zehr, Jonathan P" sort="Zehr, Jonathan P" uniqKey="Zehr J" first="Jonathan P" last="Zehr">Jonathan P. Zehr</name>
<affiliation><nlm:aff id="aff1"><institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<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="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. <italic>Prochlorococcus</italic>
 (eHLI), <italic>Synechococcus</italic>
 (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.</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">24477198</article-id>
<article-id pub-id-type="pmc">4069398</article-id>
<article-id pub-id-type="pii">ismej20141</article-id>
<article-id pub-id-type="doi">10.1038/ismej.2014.1</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>A microarray for assessing transcription from pelagic marine microbial taxa</article-title>
<alt-title alt-title-type="running">MicroTOOLs microarray for marine microbial taxa</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Shilova</surname>
<given-names>Irina N</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="corresp" rid="caf1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Robidart</surname>
<given-names>Julie C</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>James Tripp</surname>
<given-names>H</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Turk-Kubo</surname>
<given-names>Kendra</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wawrik</surname>
<given-names>Boris</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Post</surname>
<given-names>Anton F</given-names>
</name>
<xref ref-type="aff" rid="aff4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Thompson</surname>
<given-names>Anne W</given-names>
</name>
<xref ref-type="aff" rid="aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ward</surname>
<given-names>Bess</given-names>
</name>
<xref ref-type="aff" rid="aff6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hollibaugh</surname>
<given-names>James T</given-names>
</name>
<xref ref-type="aff" rid="aff7">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Millard</surname>
<given-names>Andy</given-names>
</name>
<xref ref-type="aff" rid="aff8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ostrowski</surname>
<given-names>Martin</given-names>
</name>
<xref ref-type="aff" rid="aff8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>J Scanlan</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="aff8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Paerl</surname>
<given-names>Ryan W</given-names>
</name>
<xref ref-type="aff" rid="aff9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stuart</surname>
<given-names>Rhona</given-names>
</name>
<xref ref-type="aff" rid="aff10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zehr</surname>
<given-names>Jonathan P</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<aff id="aff1"><label>1</label>
<institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, Santa Cruz, CA,<country>USA</country>
</aff>
<aff id="aff2"><label>2</label>
<institution>DOE Joint Genome Institute</institution>
, Walnut Creek, CA,<country>USA</country>
</aff>
<aff id="aff3"><label>3</label>
<institution>Department of Microbiology and Plant Biology, University of Oklahoma</institution>
, Oklahoma,<country>USA</country>
</aff>
<aff id="aff4"><label>4</label>
<institution>Marine Biological Laboratory</institution>
, Woods Hole, MA,<country>USA</country>
</aff>
<aff id="aff5"><label>5</label>
<institution>Advanced Cytometry Group, BD Biosciences</institution>
, Seattle, WA,<country>USA</country>
</aff>
<aff id="aff6"><label>6</label>
<institution>Department of Geosciences, Princeton University</institution>
, Princeton, NJ,<country>USA</country>
</aff>
<aff id="aff7"><label>7</label>
<institution>Department of Marine Sciences, University of Georgia</institution>
, Athens, GA,<country>USA</country>
</aff>
<aff id="aff8"><label>8</label>
<institution>Department of Marine Microbiology, University of Warwick</institution>
, Coventry,<country>UK</country>
</aff>
<aff id="aff9"><label>9</label>
<institution>Marine Biology Research Division, University of California San Diego</institution>
, San Diego, CA,<country>USA</country>
</aff>
<aff id="aff10"><label>10</label>
<institution>Physical and Life Sciences, Lawrence Livermore National Laboratory</institution>
, Livermore, CA,<country>USA</country>
</aff>
</contrib-group>
<author-notes><corresp id="caf1"><label>*</label>
<institution>Department of Ocean Sciences, University of California Santa Cruz</institution>
, 1156 High Street, Santa Cruz, CA 95064, <country>USA</country>
. E-mail: <email>iirina@ucsc.edu</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>07</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>30</day>
<month>01</month>
<year>2014</year>
</pub-date>
<volume>8</volume>
<issue>7</issue>
<fpage>1476</fpage>
<lpage>1491</lpage>
<history><date date-type="received"><day>29</day>
<month>05</month>
<year>2013</year>
</date>
<date date-type="rev-recd"><day>16</day>
<month>12</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>31</day>
<month>12</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>Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. <italic>Prochlorococcus</italic>
 (eHLI), <italic>Synechococcus</italic>
 (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.</p>
</abstract>
<kwd-group><kwd>marine</kwd>
<kwd>microbial</kwd>
<kwd>microarray</kwd>
<kwd>transcription</kwd>
<kwd>molecular</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>

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