Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
Identifieur interne : 000340 ( Ncbi/Checkpoint ); précédent : 000339; suivant : 000341Metabolic 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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<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>
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</author>
<author><name sortKey="Sczyrba, A" uniqKey="Sczyrba A">A Sczyrba</name>
</author>
<author><name sortKey="Lee, J" uniqKey="Lee J">J Lee</name>
</author>
<author><name sortKey="Rinke, C" uniqKey="Rinke C">C Rinke</name>
</author>
<author><name sortKey="Tighe, D" uniqKey="Tighe D">D Tighe</name>
</author>
<author><name sortKey="Clingenpeel, S" uniqKey="Clingenpeel S">S Clingenpeel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Woyke, T" uniqKey="Woyke T">T Woyke</name>
</author>
<author><name sortKey="Xie, G" uniqKey="Xie G">G Xie</name>
</author>
<author><name sortKey="Copeland, A" uniqKey="Copeland A">A Copeland</name>
</author>
<author><name sortKey="Gonzalez, Jm" uniqKey="Gonzalez J">JM González</name>
</author>
<author><name sortKey="Han, C" uniqKey="Han C">C Han</name>
</author>
<author><name sortKey="Kiss, H" uniqKey="Kiss H">H Kiss</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name>
</author>
<author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, K" uniqKey="Zhang K">K Zhang</name>
</author>
<author><name sortKey="Martiny, Ac" uniqKey="Martiny A">AC Martiny</name>
</author>
<author><name sortKey="Reppas, Nb" uniqKey="Reppas N">NB Reppas</name>
</author>
<author><name sortKey="Barry, Kw" uniqKey="Barry K">KW Barry</name>
</author>
<author><name sortKey="Malek, J" uniqKey="Malek J">J Malek</name>
</author>
<author><name sortKey="Chisholm, Sw" uniqKey="Chisholm S">SW Chisholm</name>
</author>
</analytic>
</biblStruct>
</listBibl>
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</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>
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