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.

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

“…67) (parameter: -p meta) was used for gene prediction on the final set of contigs. Essential single-copy genes 68 among the protein predictions were detected as described 69 . Marker genes for phylogenetic analysis were predicted using Amphora2 (ref.…”

“…In the first pass, the parameters were ten minimum neighbourhood points and the Eps value was estimated based on the recommendations of the authors of DBSCAN. Number and multiplicity of essential genes 68,69 were used to judge completeness of clusters. Clusters with multiple copies of the same essential genes were divided further by analysing the metagenomic coverage depth of the essential genes using the Hartigans' diptest as implemented in the R package diptest.…”

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

“…GMD samples were stained with SYBR Green I and micromanipulated using techniques described previously (Chitsaz et al 2011;Dupont et al 2012). Briefly, we used an Olympus IX70 inverted microscope equipped with a TransferMan NK2 and CellTram Vario (Eppendorf) with sterile glass capillaries blunted to an I.D.…”

“…Single cells were flow sorted at JCVI as described previously (Chitsaz et al 2011;Dupont et al 2012) with additional precautions taken to ensure safe flow sorting in the presence of potentially biohazardous microorganisms (Schmid et al 2003). Briefly, a FACS (fluorescence activated cell sorting) Aria II flow sorter (BD) equipped with a 70-mm nozzle, an argon ion laser providing 100 mW at 488 nm, and a custom forward scatter photomultiplier tube (FSC-PMT) for high-sensitivity detection of microorganisms was used for sorting of single cells.…”

“…Single-cell amplifications were performed on the sorted single cells as previously described (Chitsaz et al 2011;Dupont et al 2012) with modifications being the 2-mL TE sorting volume and a total MDA reaction volume of 12.5 mL using the GenomiPhi HY Kit (GE Healthcare). Each frozen micromanipulated GMD was thawed on ice and placed in a thermocycler for 1 min at 65°C to melt the GMD and then briefly chilled on ice.…”