Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

Abstract

The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

“…S3c ) (12). The specific subgroup salinity preference resembles that described for SAR11 subclade IIIa (33). Overall, the high amount of overlap between the habitats of SAR11 and AEGEAN-169 likely explains the metabolic variation we observed between the two groups.…”

“…Nevertheless, SAR11 is the more successful group, with relative abundances that are usually much higher than that of AEGEAN-169 (e.g., (7)). In this context, it is notable that strain LSUCC0245 grew to much lower cell densities than SAR11 strains in the same medium, even though growth rates were similar (33,78). Since our defined media have numerous carbon compounds at similar concentrations, these yield differences either mean that SAR11 and AEGEAN-169 use a different set of compounds available in the medium, or there is something inherently different about growth physiology with AEGEAN-169.…”

“…We used SAR11 genomes collected previously from GTDB (30, 33) and AEGEAN-169 genomes from the IMG database, the GORG-TROPICS SAGs database, the Microbiomics database, and the OceanDNA MAG catalog (21, 28, 29, 39). We initially used the HIMB59 and LSUCC0245 genomes, as well as AEGEAN-169 SAGs from GORG-TROPICS and our SAR11 genome collection as a starting dataset, and used FastANI v1.33 (40) with default settings to identify additional SAR11 and AEGEAN-169 genomes from the Microbiomics and the OceanDNA MAG datasets.…”

“…Samples were harvested via 0.2 µm filtration (polycarbonate, Millipore) in late log phase. DNA was extracted using the Mobio PowerWater kit (Qiagen) with a 50 ml elution in water, and library preparation and sequencing were performed as described (33). Illumina HiSeq sequencing generated 1,925,078 paired-end, 150 bp reads.…”

Linking prokaryotic genome size variation to metabolic potential and environment

“…On the other side of the genome size spectrum, the representative MAG with the smallest estimated genome size belongs to class Alphaproteobacteria (family Pelagibacteraceae, 1.08 Mbp; Table 1). Bacteria from this family have been widely reported to be streamlined, abundant and ubiquitous across all salinity gradients [37,38].…”