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Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

Identifieur interne : 000711 ( Pmc/Curation ); précédent : 000710; suivant : 000712

Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

Auteurs : Jonathan Kennedy ; Burkhardt Flemer ; Stephen A. Jackson ; David P. H. Lejon ; John P. Morrissey [Irlande (pays)] ; Fergal O Ara [Irlande (pays)] ; Alan D. W. Dobson [Irlande (pays)]

Source :

RBID : PMC:2857354

Abstract

The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.


Url:
DOI: 10.3390/md8030608
PubMed: 20411118
PubMed Central: 2857354

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PMC:2857354

Le document en format XML

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<p>The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.</p>
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<biblStruct>
<analytic>
<author>
<name sortKey="Zeng, R" uniqKey="Zeng R">R Zeng</name>
</author>
<author>
<name sortKey="Zhang, R" uniqKey="Zhang R">R Zhang</name>
</author>
<author>
<name sortKey="Zhao, J" uniqKey="Zhao J">J Zhao</name>
</author>
<author>
<name sortKey="Lin, N" uniqKey="Lin N">N Lin</name>
</author>
</analytic>
</biblStruct>
<biblStruct>
<analytic>
<author>
<name sortKey="Acevedo, Jp" uniqKey="Acevedo J">JP Acevedo</name>
</author>
<author>
<name sortKey="Reyes, F" uniqKey="Reyes F">F Reyes</name>
</author>
<author>
<name sortKey="Parra, Lp" uniqKey="Parra L">LP Parra</name>
</author>
<author>
<name sortKey="Salazar, O" uniqKey="Salazar O">O Salazar</name>
</author>
<author>
<name sortKey="Andrews, Ba" uniqKey="Andrews B">BA Andrews</name>
</author>
<author>
<name sortKey="Asenjo, Ja" uniqKey="Asenjo J">JA Asenjo</name>
</author>
</analytic>
</biblStruct>
<biblStruct>
<analytic>
<author>
<name sortKey="Chavez Croocker, P" uniqKey="Chavez Croocker P">P Chavez Croocker</name>
</author>
<author>
<name sortKey="Sako, Y" uniqKey="Sako Y">Y Sako</name>
</author>
<author>
<name sortKey="Uchida, A" uniqKey="Uchida A">A Uchida</name>
</author>
</analytic>
</biblStruct>
<biblStruct>
<analytic>
<author>
<name sortKey="Collins, T" uniqKey="Collins T">T Collins</name>
</author>
<author>
<name sortKey="Meuwis, Ma" uniqKey="Meuwis M">MA Meuwis</name>
</author>
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<name sortKey="Stals, I" uniqKey="Stals I">I Stals</name>
</author>
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<name sortKey="Claeyssens, M" uniqKey="Claeyssens M">M Claeyssens</name>
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<name sortKey="Feller, G" uniqKey="Feller G">G Feller</name>
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<name sortKey="Gerday, C" uniqKey="Gerday C">C Gerday</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="review-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Mar Drugs</journal-id>
<journal-id journal-id-type="publisher-id">MD</journal-id>
<journal-title-group>
<journal-title>Marine Drugs</journal-title>
</journal-title-group>
<issn pub-type="epub">1660-3397</issn>
<publisher>
<publisher-name>Molecular Diversity Preservation International</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">20411118</article-id>
<article-id pub-id-type="pmc">2857354</article-id>
<article-id pub-id-type="doi">10.3390/md8030608</article-id>
<article-id pub-id-type="publisher-id">marinedrugs-08-00608</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Review</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Kennedy</surname>
<given-names>Jonathan</given-names>
</name>
<xref ref-type="aff" rid="af1-marinedrugs-08-00608">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Flemer</surname>
<given-names>Burkhardt</given-names>
</name>
<xref ref-type="aff" rid="af1-marinedrugs-08-00608">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jackson</surname>
<given-names>Stephen A.</given-names>
</name>
<xref ref-type="aff" rid="af1-marinedrugs-08-00608">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Lejon</surname>
<given-names>David P. H.</given-names>
</name>
<xref ref-type="aff" rid="af1-marinedrugs-08-00608">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Morrissey</surname>
<given-names>John P.</given-names>
</name>
<xref ref-type="aff" rid="af1-marinedrugs-08-00608">1</xref>
<xref ref-type="aff" rid="af2-marinedrugs-08-00608">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>O’Gara</surname>
<given-names>Fergal</given-names>
</name>
<xref ref-type="aff" rid="af1-marinedrugs-08-00608">1</xref>
<xref ref-type="aff" rid="af2-marinedrugs-08-00608">2</xref>
<xref ref-type="aff" rid="af3-marinedrugs-08-00608">3</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Dobson</surname>
<given-names>Alan D. W.</given-names>
</name>
<xref ref-type="aff" rid="af1-marinedrugs-08-00608">1</xref>
<xref ref-type="aff" rid="af2-marinedrugs-08-00608">2</xref>
<xref ref-type="corresp" rid="c1-marinedrugs-08-00608">*</xref>
</contrib>
</contrib-group>
<aff id="af1-marinedrugs-08-00608">
<label>1</label>
Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland; E-Mails:
<email>jonathan.kennedy@ucc.ie</email>
(J.K.);
<email>bflemer@web.de</email>
(B.F.);
<email>s.a.jackson@student.ucc.ie</email>
(S.A.J.);
<email>d.lejon@ucc.ie</email>
(D.P.H.L.);
<email>j.morrissey@ucc.ie</email>
(J.P.M.);
<email>f.ogara@ucc.ie</email>
(F.O.)</aff>
<aff id="af2-marinedrugs-08-00608">
<label>2</label>
Department of Microbiology, University College Cork, Cork, Ireland</aff>
<aff id="af3-marinedrugs-08-00608">
<label>3</label>
BIOMERIT Research Centre, University College Cork, Cork, Ireland</aff>
<author-notes>
<corresp id="c1-marinedrugs-08-00608">* Author to whom correspondence should be addressed; E-Mail:
<email>a.dobson@ucc.ie</email>
; Tel.: +353-21-4901946; Fax: +353-21-4901932.</corresp>
</author-notes>
<pub-date pub-type="collection">
<year>2010</year>
</pub-date>
<pub-date pub-type="epub">
<day>15</day>
<month>3</month>
<year>2010</year>
</pub-date>
<volume>8</volume>
<issue>3</issue>
<fpage>608</fpage>
<lpage>628</lpage>
<history>
<date date-type="received">
<day>20</day>
<month>1</month>
<year>2010</year>
</date>
<date date-type="rev-recd">
<day>4</day>
<month>2</month>
<year>2010</year>
</date>
<date date-type="accepted">
<day>12</day>
<month>3</month>
<year>2010</year>
</date>
</history>
<permissions>
<copyright-statement>© 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland</copyright-statement>
<copyright-year>2010</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0">
<license-p>
<pmc-comment>CREATIVE COMMONS</pmc-comment>
This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (
<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link>
).</license-p>
</license>
</permissions>
<abstract>
<p>The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.</p>
</abstract>
<kwd-group>
<kwd>metagenome</kwd>
<kwd>marine</kwd>
<kwd>microorganism</kwd>
<kwd>enzyme</kwd>
</kwd-group>
</article-meta>
</front>
<floats-group>
<fig id="f1-marinedrugs-08-00608" position="float">
<label>Figure 1</label>
<caption>
<p>Enzyme discovery from metagenomes: functional and sequence-based approaches.</p>
</caption>
<graphic xlink:href="marinedrugs-08-00608f1"></graphic>
</fig>
<fig id="f2-marinedrugs-08-00608" position="float">
<label>Figure 2</label>
<caption>
<p>Examples of positive lipase (A) and protease activities (B) from a
<italic>Haliclona simulans</italic>
metagenomic library.</p>
</caption>
<graphic xlink:href="marinedrugs-08-00608f2"></graphic>
</fig>
<table-wrap id="t1-marinedrugs-08-00608" position="float">
<label>Table 1</label>
<caption>
<p>Marine enzymes discovered from Microbial and Metagenomic sources.</p>
</caption>
<table frame="box" rules="cols">
<thead>
<tr>
<th align="left" rowspan="1" colspan="1">Activity</th>
<th align="left" rowspan="1" colspan="1">Source</th>
<th align="left" rowspan="1" colspan="1">Habitat</th>
<th align="center" rowspan="1" colspan="1">Reference</th>
</tr>
<tr>
<th colspan="4" align="left" rowspan="1">
<hr></hr>
</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" rowspan="1" colspan="1">Esterase</td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Deep-sea sediment</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b97-marinedrugs-08-00608">97</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Deep-sea basin</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b72-marinedrugs-08-00608">72</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Surface seawater</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b69-marinedrugs-08-00608">69</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Arctic sediment</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b98-marinedrugs-08-00608">98</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Vibrio</italic>
sp.</td>
<td align="left" rowspan="1" colspan="1">Sea Hare Eggs</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b99-marinedrugs-08-00608">99</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Pseudoalteromonas haloplanktis</italic>
</td>
<td align="left" rowspan="1" colspan="1">Antarctic Seawater</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b71-marinedrugs-08-00608">71</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Lipase</td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Tidal Flat</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b74-marinedrugs-08-00608">74</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Deep Sea sediment</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b75-marinedrugs-08-00608">75</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Baltic Sea sediment</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b67-marinedrugs-08-00608">67</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Pseudoalteromonas haloplanktis</italic>
TAC125</td>
<td align="left" rowspan="1" colspan="1">Antarctic Seawater</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b73-marinedrugs-08-00608">73</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Aureobasidium pullulans</italic>
HN2.3</td>
<td align="left" rowspan="1" colspan="1">Sea saltern</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b100-marinedrugs-08-00608">100</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Cellulase</td>
<td align="left" rowspan="1" colspan="1">
<italic>Pseudoalteromonas</italic>
sp. DY3</td>
<td align="left" rowspan="1" colspan="1">Deep-sea sediment</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b77-marinedrugs-08-00608">77</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Pseudoalteromonas haloplanktis</italic>
</td>
<td align="left" rowspan="1" colspan="1">Antarctic Seawater</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b78-marinedrugs-08-00608">78</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Teredinibacter turnerae</italic>
T7902T</td>
<td align="left" rowspan="1" colspan="1">Shipworm</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b79-marinedrugs-08-00608">79</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<underline>
<italic>Marinobacter</italic>
sp. MSI032.</underline>
</td>
<td align="left" rowspan="1" colspan="1">Marine sponge</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b76-marinedrugs-08-00608">76</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Chitinase</td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Estuary</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b80-marinedrugs-08-00608">80</xref>
]
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Arthrobacter</italic>
sp. TAD20</td>
<td align="left" rowspan="1" colspan="1">Antarctic ice</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b101-marinedrugs-08-00608">101</xref>
]
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Rhodothermus marinus</italic>
</td>
<td align="left" rowspan="1" colspan="1">Marine hot spring</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b81-marinedrugs-08-00608">81</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Amidase</td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Marine sediments/sludges</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b102-marinedrugs-08-00608">102</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Amylase</td>
<td align="left" rowspan="1" colspan="1">
<italic>Aureobasidium pullulans</italic>
N13d</td>
<td align="left" rowspan="1" colspan="1">Deep-sea sediment</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b103-marinedrugs-08-00608">103</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Deep sea hydrothermal vent</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b66-marinedrugs-08-00608">66</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Phytase</td>
<td align="left" rowspan="1" colspan="1">
<italic>Kodomaea ohmeri</italic>
BG3</td>
<td align="left" rowspan="1" colspan="1">Fish gut</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b104-marinedrugs-08-00608">104</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Protease</td>
<td align="left" rowspan="1" colspan="1">
<italic>Pseudomonas</italic>
strain DYA</td>
<td align="left" rowspan="1" colspan="1">Deep-sea sediment</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b105-marinedrugs-08-00608">105</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">Marine bacterium</td>
<td align="left" rowspan="1" colspan="1">Antarctic Seawater</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b106-marinedrugs-08-00608">106</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">
<italic>Aerpyrum pernix</italic>
K1</td>
<td align="left" rowspan="1" colspan="1">Coastal solfataric vent</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b107-marinedrugs-08-00608">107</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Alkane hydroxylase</td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Hydrocarbon seep</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b82-marinedrugs-08-00608">82</xref>
]</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1"></td>
<td align="left" rowspan="1" colspan="1">Metagenome</td>
<td align="left" rowspan="1" colspan="1">Deep sea sediment</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b68-marinedrugs-08-00608">68</xref>
]</td>
</tr>
<tr>
<td colspan="4" align="left" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="1" colspan="1">Xylanase</td>
<td align="left" rowspan="1" colspan="1">
<italic>Pseudoalteromonas haloplanktis</italic>
</td>
<td align="left" rowspan="1" colspan="1">Antarctic Seawater</td>
<td align="center" rowspan="1" colspan="1">[
<xref ref-type="bibr" rid="b108-marinedrugs-08-00608">108</xref>
]</td>
</tr>
</tbody>
</table>
</table-wrap>
</floats-group>
</pmc>
</record>

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