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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Metagenomic Sequencing of Prokaryotic Microbiota from Tropical Surface Seawater</title><author><name sortKey="Chan, Xin Yue" sort="Chan, Xin Yue" uniqKey="Chan X" first="Xin Yue" last="Chan">Xin Yue Chan</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Arumugam, Ramitha" sort="Arumugam, Ramitha" uniqKey="Arumugam R" first="Ramitha" last="Arumugam">Ramitha Arumugam</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Choo, Siew Woh" sort="Choo, Siew Woh" uniqKey="Choo S" first="Siew Woh" last="Choo">Siew Woh Choo</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Yin, Wai Fong" sort="Yin, Wai Fong" uniqKey="Yin W" first="Wai Fong" last="Yin">Wai Fong Yin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Chan, Kok Gan" sort="Chan, Kok Gan" uniqKey="Chan K" first="Kok Gan" last="Chan">Kok Gan Chan</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23950114</idno><idno type="pmc">3744670</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744670</idno><idno type="RBID">PMC:3744670</idno><idno type="doi">10.1128/genomeA.00540-13</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000236</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Metagenomic Sequencing of Prokaryotic Microbiota from Tropical Surface Seawater</title><author><name sortKey="Chan, Xin Yue" sort="Chan, Xin Yue" uniqKey="Chan X" first="Xin Yue" last="Chan">Xin Yue Chan</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Arumugam, Ramitha" sort="Arumugam, Ramitha" uniqKey="Arumugam R" first="Ramitha" last="Arumugam">Ramitha Arumugam</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Choo, Siew Woh" sort="Choo, Siew Woh" uniqKey="Choo S" first="Siew Woh" last="Choo">Siew Woh Choo</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Yin, Wai Fong" sort="Yin, Wai Fong" uniqKey="Yin W" first="Wai Fong" last="Yin">Wai Fong Yin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Chan, Kok Gan" sort="Chan, Kok Gan" uniqKey="Chan K" first="Kok Gan" last="Chan">Kok Gan Chan</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">Genome Announcements</title><idno type="eISSN">2169-8287</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Tropical seawater harbors a rich diversity of microorganisms as a result of its nutrient-rich environment, constant supply of sufficient sunlight, and warm climate. In this report, we present the complexity of the microbial diversity of the surface seawater of the Georgetown coast as determined using next-generation sequencing technology.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Whitman, Wb" uniqKey="Whitman W">WB Whitman</name></author><author><name sortKey="Coleman, Dc" uniqKey="Coleman D">DC Coleman</name></author><author><name sortKey="Wiebe, Wj" uniqKey="Wiebe W">WJ Wiebe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gutierrez, T" uniqKey="Gutierrez T">T Gutierrez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Azam, F" uniqKey="Azam F">F Azam</name></author><author><name sortKey="Fenchel, T" uniqKey="Fenchel T">T Fenchel</name></author><author><name sortKey="Field, J" uniqKey="Field J">J Field</name></author><author><name sortKey="Gray, J" uniqKey="Gray J">J Gray</name></author><author><name sortKey="Meyer Reil, L" uniqKey="Meyer Reil L">L Meyer-Reil</name></author><author><name sortKey="Thingstad, F" uniqKey="Thingstad F">F Thingstad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, J" uniqKey="Zhou J">J Zhou</name></author><author><name sortKey="Bruns, Ma" uniqKey="Bruns M">MA Bruns</name></author><author><name sortKey="Tiedje, Jm" uniqKey="Tiedje J">JM Tiedje</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Murray, Mg" uniqKey="Murray M">MG Murray</name></author><author><name sortKey="Thompson, Wf" uniqKey="Thompson W">WF Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chan, Xy" uniqKey="Chan X">XY Chan</name></author><author><name sortKey="Chua, Kh" uniqKey="Chua K">KH Chua</name></author><author><name sortKey="Puthucheary, Sd" uniqKey="Puthucheary S">SD Puthucheary</name></author><author><name sortKey="Yin, W F" uniqKey="Yin W">W-F Yin</name></author><author><name sortKey="Chan, K G" uniqKey="Chan K">K-G Chan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Seshadri, R" uniqKey="Seshadri R">R Seshadri</name></author><author><name sortKey="Kravitz, Sa" uniqKey="Kravitz S">SA Kravitz</name></author><author><name sortKey="Smarr, L" uniqKey="Smarr L">L Smarr</name></author><author><name sortKey="Gilna, P" uniqKey="Gilna P">P Gilna</name></author><author><name sortKey="Frazier, M" uniqKey="Frazier M">M Frazier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name></author><author><name sortKey="Mitra, S" uniqKey="Mitra S">S Mitra</name></author><author><name sortKey="Ruscheweyh, Hj" uniqKey="Ruscheweyh H">HJ Ruscheweyh</name></author><author><name sortKey="Weber, N" uniqKey="Weber N">N Weber</name></author><author><name sortKey="Schuster, Sc" uniqKey="Schuster S">SC Schuster</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="brief-report"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Announc</journal-id><journal-id journal-id-type="iso-abbrev">Genome Announc</journal-id><journal-id journal-id-type="hwp">ga</journal-id><journal-id journal-id-type="pmc">ga</journal-id><journal-id journal-id-type="publisher-id">GA</journal-id><journal-title-group><journal-title>Genome Announcements</journal-title></journal-title-group><issn pub-type="epub">2169-8287</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23950114</article-id><article-id pub-id-type="pmc">3744670</article-id><article-id pub-id-type="publisher-id">genomeA00540-13</article-id><article-id pub-id-type="doi">10.1128/genomeA.00540-13</article-id><article-categories><subj-group subj-group-type="heading"><subject>Prokaryotes</subject></subj-group></article-categories><title-group><article-title>Metagenomic Sequencing of Prokaryotic Microbiota from Tropical Surface Seawater</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chan</surname><given-names>Xin Yue</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Arumugam</surname><given-names>Ramitha</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Choo</surname><given-names>Siew Woh</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yin</surname><given-names>Wai Fong</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Chan</surname><given-names>Kok Gan</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><aff id="aff1">Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia<label>a</label></aff><aff id="aff2">Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia<label>b</label></aff></contrib-group><author-notes><corresp id="cor1">Address correspondence to Kok Gan Chan, <email>kokgan@um.edu.my</email>.</corresp></author-notes><pub-date pub-type="epub"><day>15</day><month>8</month><year>2013</year></pub-date><pub-date pub-type="collection"><season>Jul-Aug</season><year>2013</year></pub-date><volume>1</volume><issue>4</issue><elocation-id>e00540-13</elocation-id><history><date date-type="received"><day>18</day><month>6</month><year>2013</year></date><date date-type="accepted"><day>17</day><month>7</month><year>2013</year></date></history><permissions><copyright-statement>Copyright © 2013 Chan et al.</copyright-statement><copyright-year>2013</copyright-year><copyright-holder>Chan et al.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 Unported license</ext-link>.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="jga00413541001.pdf"></self-uri><abstract><p>Tropical seawater harbors a rich diversity of microorganisms as a result of its nutrient-rich environment, constant supply of sufficient sunlight, and warm climate. In this report, we present the complexity of the microbial diversity of the surface seawater of the Georgetown coast as determined using next-generation sequencing technology.</p></abstract><counts><page-count count="1"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>July/August 2013</meta-value></custom-meta><custom-meta><meta-name>access-type</meta-name><meta-value>free</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec><title>GENOME ANNOUNCEMENT</title><p>Seawater harbors a great diversity of living organisms, ranging from microscopic bacteria, <italic>Archaea</italic>, fungi, and <italic>Protista</italic> to macroscopic crustacean and fishes, each playing a major role in the biogeochemical cycle (<xref ref-type="bibr" rid="B1">1</xref>, <xref ref-type="bibr" rid="B2">2</xref>). South Channel, located at the tropical coast at the northern part of the Malacca Straits, Malaysia, is believed to harbor great oceanic biodiversity due to the warm seawater and consistent exposure to sunlight. According to several studies, the microbial diversity increases as one gets closer to the coastal area (<xref ref-type="bibr" rid="B3">3</xref>). Therefore, this study aims to investigate the marine microbial diversity of the surface seawater of the Georgetown coastal area.</p><p>A sterile amble bottle was used to collect 1 liter of water from the sea surface of the Georgetown coast (05°25.587′N, 100°19.591′E), Penang, Malaysia, and the water was filtered through a filter membrane (pore size of 0.22 µm) (Sartorius, Germany). Metagenomic DNA was extracted and purified with a modified cetyltrimethylammonium bromide (CTAB) DNA extraction method (<xref ref-type="bibr" rid="B4">4</xref>, <xref ref-type="bibr" rid="B5">5</xref>). The purified DNA was processed for sequencing-library preparation with the TruSeq DNA sample preparation kit (Illumina) prior to shotgun sequencing with MiSeq (Illumina). A total of 6,701,060 raw reads were channeled to the CLC Genomic Workbench 5.1 (CLC bio, Denmark) for trimming and <italic>de novo</italic> assembly (<xref ref-type="bibr" rid="B6">6</xref>). Assembled sequences were compared against the Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) for microbial diversity, and its outputs were imported into MEGAN4 software (version 4.64.2) for classifications (<xref ref-type="bibr" rid="B7">7</xref>, <xref ref-type="bibr" rid="B8">8</xref>). Microorganism abundance was assessed by counting the number of reads.</p><p>In terms of the kinds of organisms present, the majority were members of the <italic>Eubacteria</italic> and <italic>Archaea</italic>, making up 75% of the total organism presence. A total of 31 known bacterial phyla, together with a significant number of unclassified bacteria, were reported from this sample, suggesting rich bacterial diversity at the seawater surface of the Georgetown coast. Among the <italic>Eubacteria</italic>, the <italic>Proteobacteria</italic> (72%) make up the most abundance phylum, followed by the <italic>Bacteroidetes</italic> (9.4%), <italic>Firmicutes</italic> (5.1%), <italic>Actinobacteria</italic> (3.0%), <italic>Verrucomicrobia</italic> (1.8%), and <italic>Cyanobacteria</italic> (1.8%). On the other hand, the major phylum of the <italic>Archaea</italic> found in this sample was <italic>Euryarchaeota</italic>, contributing 65.2% of the <italic>Archaea</italic> diversity. Members of the <italic>Thaumarchaeota</italic> make up 17.4% and members of the <italic>Crenarchaeota</italic> make up 9.6% of the total <italic>Archaea</italic> presence in this sample, making these 2 of the most abundant phyla of <italic>Archaea</italic> found.</p><p>In this study, we report the rich microbial diversity found at the sea surface of the tropical Georgetown coast. The benefits of this great microbial diversity of the tropical marine waters, along with the diverse microbial gene activities, might be the key to enhancing the bioremediation dynamics of the polluted seaside.</p><sec id="h1"><title>Nucleotide sequence accession number.</title><p>The DNA sequences from this metagenomic project were deposited at DDBJ/EMBL/GenBank under the accession no. <ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/sra/?term=SRP014764">SRP014764</ext-link>.</p></sec></sec></body><back><fn-group><fn fn-type="other"><p><bold>Citation</bold> Chan XY, Arumugam R, Choo SW, Yin WF, Chan KG. 2013. Metagenomic sequencing of prokaryotic microbiota from tropical surface seawater. Genome Announc. 1(4):e00540-13. doi:10.1128/genomeA.00540-13.</p></fn></fn-group><ack><title>ACKNOWLEDGMENT</title><p>Kok Gan Chan thanks the University of Malaya for a High-Impact research grant (<funding-source id="GS1">HIR/MOHE</funding-source> grant no. <award-id rid="GS1">H-50001-A000001</award-id>) for funding this project.</p></ack><ref-list><title>REFERENCES</title><ref id="B1"><label>1.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Whitman</surname><given-names>WB</given-names></name><name><surname>Coleman</surname><given-names>DC</given-names></name><name><surname>Wiebe</surname><given-names>WJ</given-names></name></person-group><year>1998</year><article-title>Prokaryotes: the unseen majority</article-title>. <source>Proc. Natl. Acad. Sci. U. S. 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