Comparative genome analysis of marine OM43 clade bacteria isolated from the coastal seas of Korea and the Antarctic Peninsula

초록

The OM43 clade within the family Methylophilaceae (order Burkholderiales) is known to metabolize C1 compounds as their sole carbon sources in marine water column, with streamlined genomes. Only few genomic comparison studies of this clade have been performed to date, largely due to difficulty in laboratory cultivation. Here, we report the isolation and genome characterization of fourteen novel isolates of the OM43 clade. The OM43 strains were isolated from surface water samples of coastal seas of South ??Korea and the Antarctic Peninsula, using dilution-to-extinction cultivation. The complete genomes of OM43 strains were obtained through whole-genome amplification followed by Illumina sequencing. Genome sizes and GC contents ranged from 1.26 to 1.34 Mbp and 33.2 to 36.2 mol%, respectively. Phylogenomic comparison and ANI analysis showed that these strains form eleven novel species, distinctly from previously-reported several OM43 strains. All genomes harbored genes for oxidizing methanol and formaldehyde, confirming the methylotrophic lifestyle of the OM43 clade. Genes for sulfide oxidation were found in two genomes. While some genomes have only xanthorhodopsin (DTE motif), like previously-reported OM43 strains, eight genomes have both proteorhodopsin and xanthorhodopsin in tandem, like the LD 28 clade (freshwater sister group of the OM43 clade). Interestingly, proteorhodopsin (DTE motif) in these genomes are phylogenetically distinct from those of the LD28 clade, and xanthorhodopsin in these genomes have GTE motif without retinal-binding lysine (i.e. Rh-noKs). This study contributes to better understanding of the genomic divergence within the marine OM43 clade.