Present address: National Oceanography Centre, Southampton, UK.
Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean
Article first published online: 6 SEP 2011
© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: OMICS Driven Microbial Ecology
Volume 14, Issue 1, pages 52–66, January 2012
How to Cite
Gómez-Pereira, P. R., Schüler, M., Fuchs, B. M., Bennke, C., Teeling, H., Waldmann, J., Richter, M., Barbe, V., Bataille, E., Glöckner, F. O. and Amann, R. (2012), Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environmental Microbiology, 14: 52–66. doi: 10.1111/j.1462-2920.2011.02555.x
- Issue published online: 2 JAN 2012
- Article first published online: 6 SEP 2011
- Received 21 April, 2011; accepted 21 June, 2011.
Bacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolytic potential. In this study, we used a targeted metagenomic approach to investigate the degradation capabilities of distinct Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean, the Polar Biome (BPLR) and the North Atlantic Subtropical (NAST). We present here the analysis of 76 Bacteroidetes fosmids, of which 28 encode the 16S rRNA gene as phylogenetic marker, and their comparison to complete Bacteroidetes genomes. Almost all of the 16S rRNA harbouring fosmids belonged to clades that we previously identified in BPLR and NAST. The majority of sequenced fosmids could be assigned to Bacteroidetes affiliated with the class Flavobacteria. We also present novel genomic information on the classes Cytophagia and Sphingobacteria, suggesting a capability of the latter for attachment to algal surfaces. In our fosmid set we identified a larger potential for polysaccharide degradation and cell surface attachment in the phytoplankton-rich BPLR. Particularly, two flavobacterial fosmids, one affiliated with the genus Polaribacter, showed a whole armoury of enzymes that likely function in degradation of sulfated polysaccharides known to be major constituents of phytoplankton cell walls. Genes involved in protein and peptidoglycan degradation, although present in both fosmid sets, seemed to have a slight preponderance in NAST. This study provides support for the hypothesis of a distinct specialization among marine Bacteroidetes for the degradation of certain types of polymers.