“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis
Identifieur interne : 000001 ( Main/Exploration ); précédent : 000000; suivant : 000002“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis
Auteurs : Marco Fondi [Italie] ; Antti Karkman [Finlande] ; Manu V. Tamminen [Suisse] ; Emanuele Bosi [Italie] ; Marko Virta [Finlande] ; Renato Fani [Italie] ; Eric Alm [États-Unis] ; James O. Mcinerney [Irlande (pays), Royaume-Uni]Source :
- Genome Biology and Evolution [ 1759-6653 ] ; 2016.
Abstract
The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as “everything is everywhere but the environment selects.” While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.
Url:
DOI: 10.1093/gbe/evw077
PubMed: 27190206
PubMed Central: 4898794
Affiliations:
- Finlande, Irlande (pays), Italie, Royaume-Uni, Suisse, États-Unis
- Angleterre, Canton de Zurich, Grand Manchester, Massachusetts, Uusimaa
- Cambridge (Massachusetts), Helsinki, Manchester, Zurich
- Massachusetts Institute of Technology, Université d'Helsinki, Université de Manchester, École polytechnique fédérale de Zurich
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Mcinerney</name><affiliation wicri:level="1"><nlm:aff id="evw077-aff7">Department of Biology, National University of Ireland Maynooth, County Kildare, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Department of Biology, National University of Ireland Maynooth, County Kildare</wicri:regionArea><wicri:noRegion>County Kildare</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:aff id="evw077-aff8">Computational Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, United Kingdom</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Computational Evolutionary Biology, Faculty of Life Sciences, The University of Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="nation">Angleterre</region><region nuts="2" type="region">Grand Manchester</region></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author></analytic><series><title level="j">Genome Biology and Evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as “everything is everywhere but the environment selects.” While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alvarez Ponce, D" uniqKey="Alvarez Ponce D">D Alvarez-Ponce</name></author><author><name sortKey="Lopez, P" uniqKey="Lopez P">P Lopez</name></author><author><name sortKey="Bapteste, E" uniqKey="Bapteste E">E Bapteste</name></author><author><name sortKey="Mcinerney, Jo" uniqKey="Mcinerney J">JO. 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Xu</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Finlande</li><li>Irlande (pays)</li><li>Italie</li><li>Royaume-Uni</li><li>Suisse</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Canton de Zurich</li><li>Grand Manchester</li><li>Massachusetts</li><li>Uusimaa</li></region><settlement><li>Cambridge (Massachusetts)</li><li>Helsinki</li><li>Manchester</li><li>Zurich</li></settlement><orgName><li>Massachusetts Institute of Technology</li><li>Université d'Helsinki</li><li>Université de Manchester</li><li>École polytechnique fédérale de Zurich</li></orgName></list><tree><country name="Italie"><noRegion><name sortKey="Fondi, Marco" sort="Fondi, Marco" uniqKey="Fondi M" first="Marco" last="Fondi">Marco Fondi</name></noRegion><name sortKey="Bosi, Emanuele" sort="Bosi, Emanuele" uniqKey="Bosi E" first="Emanuele" last="Bosi">Emanuele Bosi</name><name sortKey="Bosi, Emanuele" sort="Bosi, Emanuele" uniqKey="Bosi E" first="Emanuele" last="Bosi">Emanuele Bosi</name><name sortKey="Fani, Renato" sort="Fani, Renato" uniqKey="Fani R" first="Renato" last="Fani">Renato Fani</name><name sortKey="Fani, Renato" sort="Fani, Renato" uniqKey="Fani R" first="Renato" last="Fani">Renato Fani</name><name sortKey="Fondi, Marco" sort="Fondi, Marco" uniqKey="Fondi M" first="Marco" last="Fondi">Marco Fondi</name></country><country name="Finlande"><region name="Uusimaa"><name sortKey="Karkman, Antti" sort="Karkman, Antti" uniqKey="Karkman A" first="Antti" last="Karkman">Antti Karkman</name></region><name sortKey="Virta, Marko" sort="Virta, Marko" uniqKey="Virta M" first="Marko" last="Virta">Marko Virta</name></country><country name="Suisse"><region name="Canton de Zurich"><name sortKey="Tamminen, Manu V" sort="Tamminen, Manu V" uniqKey="Tamminen M" first="Manu V." last="Tamminen">Manu V. Tamminen</name></region><name sortKey="Tamminen, Manu V" sort="Tamminen, Manu V" uniqKey="Tamminen M" first="Manu V." last="Tamminen">Manu V. Tamminen</name></country><country name="États-Unis"><region name="Massachusetts"><name sortKey="Alm, Eric" sort="Alm, Eric" uniqKey="Alm E" first="Eric" last="Alm">Eric Alm</name></region></country><country name="Irlande (pays)"><noRegion><name sortKey="Mcinerney, James O" sort="Mcinerney, James O" uniqKey="Mcinerney J" first="James O." last="Mcinerney">James O. Mcinerney</name></noRegion></country><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Mcinerney, James O" sort="Mcinerney, James O" uniqKey="Mcinerney J" first="James O." last="Mcinerney">James O. Mcinerney</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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