Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
Identifieur interne : 000487 ( Main/Exploration ); précédent : 000486; suivant : 000488Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
Auteurs : Sarahi L. Garcia [Allemagne] ; Katherine D. Mcmahon [États-Unis] ; Manuel Martinez-Garcia [États-Unis] ; Abhishek Srivastava [Allemagne] ; Alexander Sczyrba [Allemagne, États-Unis] ; Ramunas Stepanauskas [États-Unis] ; Hans-Peter Grossart [Allemagne] ; Tanja Woyke [États-Unis] ; Falk Warnecke [Allemagne]Source :
- The ISME Journal [ 1751-7362 ] ; 2012.
Abstract
Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (∼42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (∼15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an
Url:
DOI: 10.1038/ismej.2012.86
PubMed: 22810059
PubMed Central: 3526179
Affiliations:
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Mcmahon</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Civil and Environmental Engineering, University of Wisconsin-Madison</institution>, Madison, WI,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Department of Bacteriology, University of Wisconsin-Madison</institution> Madison, WI,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Martinez Garcia, Manuel" sort="Martinez Garcia, Manuel" uniqKey="Martinez Garcia M" first="Manuel" last="Martinez-Garcia">Manuel Martinez-Garcia</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Bigelow Laboratory for Ocean Sciences</institution>, East Boothbay, ME,<country>USA</country></nlm:aff><country 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Grossart</name><affiliation wicri:level="1"><nlm:aff id="aff5"><institution>Department of Limnology of Stratified Lakes, Leibniz-Institute for Freshwater Ecology and Inland Fisheries</institution>, Stechlin,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff8"><institution>Institute for Biochemistry and Biology, Postdam University</institution>, Postdam,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name><affiliation wicri:level="1"><nlm:aff id="aff7"><institution>DOE Joint Genome Institute</institution>, Walnut Creek, CA,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Warnecke, Falk" sort="Warnecke, Falk" uniqKey="Warnecke F" first="Falk" last="Warnecke">Falk Warnecke</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Jena School for Microbial Communication (JSMC) and Microbial Ecology Group at Friedrich Schiller University Jena</institution>, Jena,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">The ISME Journal</title><idno type="ISSN">1751-7362</idno><idno type="eISSN">1751-7370</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (∼42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (∼15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an <italic>actinorhodopsin</italic> gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Allgaier, M" uniqKey="Allgaier M">M Allgaier</name></author><author><name sortKey="Bruckner, S" uniqKey="Bruckner S">S Brückner</name></author><author><name sortKey="Jaspers, E" uniqKey="Jaspers E">E Jaspers</name></author><author><name sortKey="Grossart, H P" uniqKey="Grossart H">H-P Grossart</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Allgaier, M" uniqKey="Allgaier M">M Allgaier</name></author><author><name sortKey="Grossart, H P" uniqKey="Grossart H">H-P Grossart</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arnosti, C" uniqKey="Arnosti C">C Arnosti</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barabote, Rd" uniqKey="Barabote R">RD 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Chisholm</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>États-Unis</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Garcia, Sarahi L" sort="Garcia, Sarahi L" uniqKey="Garcia S" first="Sarahi L" last="Garcia">Sarahi L. Garcia</name></noRegion><name sortKey="Grossart, Hans Peter" sort="Grossart, Hans Peter" uniqKey="Grossart H" first="Hans-Peter" last="Grossart">Hans-Peter Grossart</name><name sortKey="Grossart, Hans Peter" sort="Grossart, Hans Peter" uniqKey="Grossart H" first="Hans-Peter" last="Grossart">Hans-Peter Grossart</name><name sortKey="Sczyrba, Alexander" sort="Sczyrba, Alexander" uniqKey="Sczyrba A" first="Alexander" last="Sczyrba">Alexander Sczyrba</name><name sortKey="Srivastava, Abhishek" sort="Srivastava, Abhishek" uniqKey="Srivastava A" first="Abhishek" last="Srivastava">Abhishek Srivastava</name><name sortKey="Warnecke, Falk" sort="Warnecke, Falk" uniqKey="Warnecke F" first="Falk" last="Warnecke">Falk Warnecke</name></country><country name="États-Unis"><noRegion><name sortKey="Mcmahon, Katherine D" sort="Mcmahon, Katherine D" uniqKey="Mcmahon K" first="Katherine D" last="Mcmahon">Katherine D. Mcmahon</name></noRegion><name sortKey="Martinez Garcia, Manuel" sort="Martinez Garcia, Manuel" uniqKey="Martinez Garcia M" first="Manuel" last="Martinez-Garcia">Manuel Martinez-Garcia</name><name sortKey="Mcmahon, Katherine D" sort="Mcmahon, Katherine D" uniqKey="Mcmahon K" first="Katherine D" last="Mcmahon">Katherine D. Mcmahon</name><name sortKey="Sczyrba, Alexander" sort="Sczyrba, Alexander" uniqKey="Sczyrba A" first="Alexander" last="Sczyrba">Alexander Sczyrba</name><name sortKey="Stepanauskas, Ramunas" sort="Stepanauskas, Ramunas" uniqKey="Stepanauskas R" first="Ramunas" last="Stepanauskas">Ramunas Stepanauskas</name><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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