title: Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.
abstract: 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.
authors.affiliation: Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA 92121, USA. cdupont@jcvi.org
authors.forename: Chris L
authors.initials: CL
authors.lastname: Dupont
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Rusch
authors.forename: Shibu
authors.initials: S
authors.lastname: Yooseph
authors.forename: Mary-Jane
authors.initials: MJ
authors.lastname: Lombardo
authors.forename: R Alexander
authors.initials: RA
authors.lastname: Richter
authors.forename: Ruben
authors.initials: R
authors.lastname: Valas
authors.forename: Mark
authors.initials: M
authors.lastname: Novotny
authors.forename: Joyclyn
authors.initials: J
authors.lastname: Yee-Greenbaum
authors.forename: Jeremy D
authors.initials: JD
authors.lastname: Selengut
authors.forename: Dan H
authors.initials: DH
authors.lastname: Haft
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Halpern
authors.forename: Roger S
authors.initials: RS
authors.lastname: Lasken
authors.forename: Kenneth
authors.initials: K
authors.lastname: Nealson
authors.forename: Robert
authors.initials: R
authors.lastname: Friedman
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
mesh_terms: D019295:Computational Biology; D020563:Gammaproteobacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D016680:Genome, Bacterial; D015698:Genomic Library; D056186:Metagenomics; D009792:Oceans and Seas; D010802:Phylogeny; D010933:Plankton / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012243:Rhodopsin; D025604:Rhodopsins, Microbial; D012623:Seawater / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S; D025604:Rhodopsins, Microbial; C413548:proteorhodopsin; D012243:Rhodopsin