Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes
Identifieur interne : 000482 ( Pmc/Checkpoint ); précédent : 000481; suivant : 000483Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes
Auteurs : Ivaylo Kostadinov [Allemagne] ; Renzo Kottmann [Allemagne] ; Alban Ramette [Allemagne] ; Jost Waldmann [Allemagne] ; Pier Luigi Buttigieg [Allemagne] ; Frank Oliver Glöckner [Allemagne]Source :
- Microbial Informatics and Experimentation [ 2042-5783 ] ; 2011.
Abstract
DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine
We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool.
Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to
Url:
DOI: 10.1186/2042-5783-1-9
PubMed: 22587903
PubMed Central: 3372289
Affiliations:
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<series><title level="j">Microbial Informatics and Experimentation</title>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine <italic>Synechococcus </italic>
strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated.</p>
</sec>
<sec><title>Results</title>
<p>We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool.</p>
</sec>
<sec><title>Conclusions</title>
<p>Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to <italic>in situ </italic>
measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data.</p>
</sec>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Microb Inform Exp</journal-id>
<journal-id journal-id-type="iso-abbrev">Microb Inform Exp</journal-id>
<journal-title-group><journal-title>Microbial Informatics and Experimentation</journal-title>
</journal-title-group>
<issn pub-type="epub">2042-5783</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22587903</article-id>
<article-id pub-id-type="pmc">3372289</article-id>
<article-id pub-id-type="publisher-id">2042-5783-1-9</article-id>
<article-id pub-id-type="doi">10.1186/2042-5783-1-9</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research</subject>
</subj-group>
</article-categories>
<title-group><article-title>Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Kostadinov</surname>
<given-names>Ivaylo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>ikostadi@mpi-bremen.de</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Kottmann</surname>
<given-names>Renzo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>rkottman@mpi-bremen.de</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Ramette</surname>
<given-names>Alban</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>aramette@mpi-bremen.de</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Waldmann</surname>
<given-names>Jost</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>jwaldman@mpi-bremen.de</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Buttigieg</surname>
<given-names>Pier Luigi</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>pbuttigi@mpi-bremen.de</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A6"><name><surname>Glöckner</surname>
<given-names>Frank Oliver</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>fog@mpi-bremen.de</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany</aff>
<aff id="I2"><label>2</label>
Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany</aff>
<pub-date pub-type="collection"><year>2011</year>
</pub-date>
<pub-date pub-type="epub"><day>7</day>
<month>9</month>
<year>2011</year>
</pub-date>
<volume>1</volume>
<fpage>9</fpage>
<lpage>9</lpage>
<history><date date-type="received"><day>1</day>
<month>4</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>7</day>
<month>9</month>
<year>2011</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2011 Kostadinov et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2011</copyright-year>
<copyright-holder>Kostadinov et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.microbialinformaticsj.com/content/1/1/9"></self-uri>
<abstract><sec><title>Background</title>
<p>DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine <italic>Synechococcus </italic>
strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated.</p>
</sec>
<sec><title>Results</title>
<p>We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool.</p>
</sec>
<sec><title>Conclusions</title>
<p>Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to <italic>in situ </italic>
measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data.</p>
</sec>
</abstract>
<kwd-group><kwd>transcription factors</kwd>
<kwd>ecological metagenomics</kwd>
<kwd>interpolated environmental data</kwd>
<kwd>multivariate statistics</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Allemagne</li>
</country>
<region><li>Brême (Land)</li>
</region>
<settlement><li>Brême</li>
</settlement>
</list>
<tree><country name="Allemagne"><region name="Brême (Land)"><name sortKey="Kostadinov, Ivaylo" sort="Kostadinov, Ivaylo" uniqKey="Kostadinov I" first="Ivaylo" last="Kostadinov">Ivaylo Kostadinov</name>
</region>
<name sortKey="Buttigieg, Pier Luigi" sort="Buttigieg, Pier Luigi" uniqKey="Buttigieg P" first="Pier Luigi" last="Buttigieg">Pier Luigi Buttigieg</name>
<name sortKey="Buttigieg, Pier Luigi" sort="Buttigieg, Pier Luigi" uniqKey="Buttigieg P" first="Pier Luigi" last="Buttigieg">Pier Luigi Buttigieg</name>
<name sortKey="Glockner, Frank Oliver" sort="Glockner, Frank Oliver" uniqKey="Glockner F" first="Frank Oliver" last="Glöckner">Frank Oliver Glöckner</name>
<name sortKey="Glockner, Frank Oliver" sort="Glockner, Frank Oliver" uniqKey="Glockner F" first="Frank Oliver" last="Glöckner">Frank Oliver Glöckner</name>
<name sortKey="Kostadinov, Ivaylo" sort="Kostadinov, Ivaylo" uniqKey="Kostadinov I" first="Ivaylo" last="Kostadinov">Ivaylo Kostadinov</name>
<name sortKey="Kottmann, Renzo" sort="Kottmann, Renzo" uniqKey="Kottmann R" first="Renzo" last="Kottmann">Renzo Kottmann</name>
<name sortKey="Ramette, Alban" sort="Ramette, Alban" uniqKey="Ramette A" first="Alban" last="Ramette">Alban Ramette</name>
<name sortKey="Waldmann, Jost" sort="Waldmann, Jost" uniqKey="Waldmann J" first="Jost" last="Waldmann">Jost Waldmann</name>
</country>
</tree>
</affiliations>
</record>
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