Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade

Abstract

The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea: one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter.

High contribution ofPelagibacteralesto bacterial community composition and activity in spring blooms off Kerguelen Island (Southern Ocean)

“…At the Atlantic time series site BATS, subclade Ib is usually found in surface water in late spring and early summer, while Ic is found in deeper water (Vergin et al , 2013). Subclade Ib has also been reported in epi- and bathypelagic waters in the Red Sea where it blooms following water mixing (Jimenez-Infante et al , 2017). Subgroup Ia.3 was more abundant in the deep layers, while Ia.1 and Ia.2 had higher relative abundances in surface and intermediate layers (Fig.…”

Red Sea SAR11 andProchlorococcusSingle-cell Genomes Reflect Globally Distributed Pangenomes

“…Following collection of surface seawater from the east-central Red Sea, flow sorting, and amplification, we sequenced and assembled 21 SAR11 and 5 Prochlorococcus single-cell amplified genomes (SAGs). These SAGs represent reference genomes in an ocean region with sparse coverage: only one cultured Prochlorococcus genome (27) and two cultured SAR11 genomes (46) are currently available from the Red Sea. The SAR11 SAGs also represent genomes from clades without other sequenced representatives: two SAGs from subclade Ib and three SAGs from subclade IId (Fig.…”

“…After the major analyses had been completed for this study, two SAR11 genomes (46) and one Prochlorococcus genome (27) derived from cultivated strains were sequenced, and four Prochlorococcus genomes were assembled from metagenomes (57). Of the SAR11 genomes, one was assigned to subclade Ia and the other to subclade Ib (46).…”

“…After the major analyses had been completed for this study, two SAR11 genomes (46) and one Prochlorococcus genome (27) derived from cultivated strains were sequenced, and four Prochlorococcus genomes were assembled from metagenomes (57). Of the SAR11 genomes, one was assigned to subclade Ia and the other to subclade Ib (46). Of note, the subclade Ia genome (RS39) contained several OGs also found among the Red-Sea-associated SAR11 OGs: 3-oxoacyl-acyl-carrier-protein synthase, ABC branched amino acid transporter, arylsulfotransferase, formate dehydrogenases, glycosyl transferases, methyltransferases, sialic acid synthase, sucrose synthase, sulfotransferases, and a type II restriction–modification system.…”

“…Of note, the subclade Ia genome (RS39) contained several OGs also found among the Red-Sea-associated SAR11 OGs: 3-oxoacyl-acyl-carrier-protein synthase, ABC branched amino acid transporter, arylsulfotransferase, formate dehydrogenases, glycosyl transferases, methyltransferases, sialic acid synthase, sucrose synthase, sulfotransferases, and a type II restriction–modification system. Several of these functions may play roles in one-carbon and sugar metabolism by SAR11 in the Red Sea (46). The Prochlorococcus genome was assigned to the HLII ecotype and notably contained a pathway for biosynthesis of the osmolyte (compatible solute) glucosylglycerol (27).…”