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

TLDR

SAR86 bacteria are among the most abundant uncultivated microbes in the surface ocean, are aerobic chemoheterotrophs that may use proteorhodopsin for ATP generation but lack retinal biosynthesis, highlighting limited genomic knowledge. Using bioinformatic assembly of metagenomes and single‑cell sequencing, the authors reconstructed two nearly complete and two partial SAR86 genomes. The reconstructed genomes reveal SAR86 as a basal, temperature‑dependent γ‑proteobacteria lineage with streamlined, small genomes lacking amino‑acid and vitamin synthesis pathways, yet possessing extensive lipid and carbohydrate degradation capabilities and a proteorhodopsin‑based ATP system, thereby expanding knowledge of non‑photosynthetic surface‑ocean bacteria.

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.