Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans
Identifieur interne : 000418 ( Ncbi/Merge ); précédent : 000417; suivant : 000419Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans
Auteurs : Ilnam Kang ; Hyun-Myung Oh ; Dongmin Kang ; Jang-Cheon ChoSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2013.
Abstract
The abundance, genetic diversity, and crucial ecological and evolutionary roles of marine phages have prompted a large number of metagenomic studies. However, obtaining a thorough understanding of marine phages has been hampered by the low number of phage isolates infecting major bacterial groups other than cyanophages and pelagiphages. Therefore, there is an urgent requirement for the isolation of phages that infect abundant marine bacterial groups. In this study, we isolated and characterized HMO-2011, a phage infecting a bacterium of the SAR116 clade, one of the most abundant marine bacterial lineages. HMO-2011, which infects “
Url:
DOI: 10.1073/pnas.1219930110
PubMed: 23798439
PubMed Central: 3725092
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<author><name sortKey="Kang, Ilnam" sort="Kang, Ilnam" uniqKey="Kang I" first="Ilnam" last="Kang">Ilnam Kang</name>
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<author><name sortKey="Oh, Hyun Myung" sort="Oh, Hyun Myung" uniqKey="Oh H" first="Hyun-Myung" last="Oh">Hyun-Myung Oh</name>
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<author><name sortKey="Kang, Dongmin" sort="Kang, Dongmin" uniqKey="Kang D" first="Dongmin" last="Kang">Dongmin Kang</name>
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<author><name sortKey="Cho, Jang Cheon" sort="Cho, Jang Cheon" uniqKey="Cho J" first="Jang-Cheon" last="Cho">Jang-Cheon Cho</name>
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<series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title>
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<front><div type="abstract" xml:lang="en"><p>The abundance, genetic diversity, and crucial ecological and evolutionary roles of marine phages have prompted a large number of metagenomic studies. However, obtaining a thorough understanding of marine phages has been hampered by the low number of phage isolates infecting major bacterial groups other than cyanophages and pelagiphages. Therefore, there is an urgent requirement for the isolation of phages that infect abundant marine bacterial groups. In this study, we isolated and characterized HMO-2011, a phage infecting a bacterium of the SAR116 clade, one of the most abundant marine bacterial lineages. HMO-2011, which infects “<italic>Candidatus</italic>
Puniceispirillum marinum” strain IMCC1322, has an ∼55-kb dsDNA genome that harbors many genes with novel features rarely found in cultured organisms, including genes encoding a DNA polymerase with a partial DnaJ central domain and an atypical methanesulfonate monooxygenase. Furthermore, homologs of nearly all HMO-2011 genes were predominantly found in marine metagenomes rather than cultured organisms, suggesting the novelty of HMO-2011 and the prevalence of this phage type in the oceans. A significant number of the viral metagenome sequences obtained from the ocean surface were best assigned to the HMO-2011 genome. The number of reads assigned to HMO-2011 accounted for 10.3%–25.3% of the total reads assigned to viruses in seven viromes from the Pacific and Indian Oceans, making the HMO-2011 genome the most or second-most frequently assigned viral genome. Given its ability to infect the abundant SAR116 clade and its widespread distribution, <italic>Puniceispirillum</italic>
phage HMO-2011 could be an important resource for marine virus research.</p>
</div>
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<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id>
<journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id>
<journal-id journal-id-type="hwp">pnas</journal-id>
<journal-id journal-id-type="pmc">pnas</journal-id>
<journal-id journal-id-type="publisher-id">PNAS</journal-id>
<journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title>
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<issn pub-type="ppub">0027-8424</issn>
<issn pub-type="epub">1091-6490</issn>
<publisher><publisher-name>National Academy of Sciences</publisher-name>
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<article-meta><article-id pub-id-type="pmid">23798439</article-id>
<article-id pub-id-type="pmc">3725092</article-id>
<article-id pub-id-type="publisher-id">201219930</article-id>
<article-id pub-id-type="doi">10.1073/pnas.1219930110</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject>
<subj-group><subject>Ecology</subject>
</subj-group>
</subj-group>
<series-title>From the Cover</series-title>
</article-categories>
<title-group><article-title>Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans</article-title>
<alt-title alt-title-type="short">Bacteriophage infecting the SAR116 clade</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Kang</surname>
<given-names>Ilnam</given-names>
</name>
<xref ref-type="author-notes" rid="fn1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Oh</surname>
<given-names>Hyun-Myung</given-names>
</name>
<xref ref-type="author-notes" rid="fn1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kang</surname>
<given-names>Dongmin</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Cho</surname>
<given-names>Jang-Cheon</given-names>
</name>
<xref ref-type="corresp" rid="cor1"><sup>3</sup>
</xref>
</contrib>
<aff id="aff1">Division of Biology and Ocean Sciences,<institution>Inha University</institution>
, Incheon 402-751,<country>Korea</country>
</aff>
</contrib-group>
<author-notes><corresp id="cor1"><sup>3</sup>
To whom correspondence should be addressed. E-mail: <email>chojc@inha.ac.kr</email>
.</corresp>
<fn fn-type="edited-by"><p>Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved May 31, 2013 (received for review November 15, 2012)</p>
</fn>
<fn fn-type="con"><p>Author contributions: I.K., H.-M.O., and J.-C.C. designed research; I.K., H.-M.O., and D.K. performed research; I.K., H.-M.O., and J.-C.C. analyzed data; and I.K., H.-M.O., and J.-C.C. wrote the paper.</p>
</fn>
<fn fn-type="equal" id="fn1"><p><sup>1</sup>
I.K. and H.-M.O. contributed equally to this work.</p>
</fn>
<fn fn-type="present-address" id="fn2"><p><sup>2</sup>
Present address: Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 425-600, Korea.</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><day>23</day>
<month>7</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>24</day>
<month>6</month>
<year>2013</year>
</pub-date>
<volume>110</volume>
<issue>30</issue>
<fpage>12343</fpage>
<lpage>12348</lpage>
<self-uri xlink:title="pdf" xlink:type="simple" xlink:href="pnas.201219930.pdf"></self-uri>
<abstract><p>The abundance, genetic diversity, and crucial ecological and evolutionary roles of marine phages have prompted a large number of metagenomic studies. However, obtaining a thorough understanding of marine phages has been hampered by the low number of phage isolates infecting major bacterial groups other than cyanophages and pelagiphages. Therefore, there is an urgent requirement for the isolation of phages that infect abundant marine bacterial groups. In this study, we isolated and characterized HMO-2011, a phage infecting a bacterium of the SAR116 clade, one of the most abundant marine bacterial lineages. HMO-2011, which infects “<italic>Candidatus</italic>
Puniceispirillum marinum” strain IMCC1322, has an ∼55-kb dsDNA genome that harbors many genes with novel features rarely found in cultured organisms, including genes encoding a DNA polymerase with a partial DnaJ central domain and an atypical methanesulfonate monooxygenase. Furthermore, homologs of nearly all HMO-2011 genes were predominantly found in marine metagenomes rather than cultured organisms, suggesting the novelty of HMO-2011 and the prevalence of this phage type in the oceans. A significant number of the viral metagenome sequences obtained from the ocean surface were best assigned to the HMO-2011 genome. The number of reads assigned to HMO-2011 accounted for 10.3%–25.3% of the total reads assigned to viruses in seven viromes from the Pacific and Indian Oceans, making the HMO-2011 genome the most or second-most frequently assigned viral genome. Given its ability to infect the abundant SAR116 clade and its widespread distribution, <italic>Puniceispirillum</italic>
phage HMO-2011 could be an important resource for marine virus research.</p>
</abstract>
<counts><page-count count="6"></page-count>
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<affiliations><list></list>
<tree><noCountry><name sortKey="Cho, Jang Cheon" sort="Cho, Jang Cheon" uniqKey="Cho J" first="Jang-Cheon" last="Cho">Jang-Cheon Cho</name>
<name sortKey="Kang, Dongmin" sort="Kang, Dongmin" uniqKey="Kang D" first="Dongmin" last="Kang">Dongmin Kang</name>
<name sortKey="Kang, Ilnam" sort="Kang, Ilnam" uniqKey="Kang I" first="Ilnam" last="Kang">Ilnam Kang</name>
<name sortKey="Oh, Hyun Myung" sort="Oh, Hyun Myung" uniqKey="Oh H" first="Hyun-Myung" last="Oh">Hyun-Myung Oh</name>
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