Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

• Published in: The ISME Journal 2012-06, Vol.6 (6), p.1186-1199
• Main Authors: Dupont, Chris L, Rusch, Douglas B, Yooseph, Shibu, Lombardo, Mary-Jane, Alexander Richter, R, Valas, Ruben, Novotny, Mark, Yee-Greenbaum, Joyclyn, Selengut, Jeremy D, Haft, Dan H, Halpern, Aaron L, Lasken, Roger S, Nealson, Kenneth, Friedman, Robert, Craig Venter, J
• Format: Article
• Language: English
• Subjects: ATP; Bacteria; BASIC BIOLOGICAL SCIENCES; Biomedical and Life Sciences; Biosynthesis; Carbohydrates; Computational Biology; Ecology; ENVIRONMENTAL SCIENCES; Environmental Sciences & Ecology; Evolutionary Biology; Gammaproteobacteria - classification; Gammaproteobacteria - genetics; Gammaproteobacteria - metabolism; Genome, Bacterial; Genomic Library; Genomics; integrated genomics and post-genomics approaches in microbial ecology; Life Sciences; Lipids; metagenomic assembly; Metagenomics; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Oceans and Seas; Original; original-article; Phylogeny; Plankton - genetics; proteorhodopsin; Rhodopsin; Rhodopsins, Microbial; RNA, Ribosomal, 16S - genetics; SAR11; SAR86; Seawater - microbiology; single cell genomics; Sulfate reduction; Sulfates; tonB receptors
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/ismej.2011.189

Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25–1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.