The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C 1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.
Methylotrophs are a taxonomically diverse group of microorganisms that use reduced one-carbon (C 1 ) compounds as their sole carbon and energy sources (1, 2). Unlike methanotrophs, non-methane-utilizing methylotrophs (here simply denoted methylotrophs) cannot oxidize methane but instead degrade more oxidized C 1 compounds, like methanol, methylamine, and formaldehyde, using different pathways for their oxidation, demethylation, and assimilation into biomass (1-3). Marine methylotrophs play an important role in the metabolism and assimilation of C 1 compounds like methanol and methylated compounds containing amino, halide, and/or sulfur moieties in the oceans (4).Many model methylotrophs have been cultured, which has facilitated studies on their genomic and functional characteristics and diversity (3). Among the marine methylotrophs, the OM43 clade belonging to the Betaproteobacteria occurs abundantly in productive aquatic environments from coastal waters to brackish and freshwater ecosystems (5, 6). The occurrence of close relatives of the marine OM43 clade in freshwater habitats, which form a closely related, but separate, lineage known as the LD28 clade (5, 7), also implies that OM43-like organisms have a broader biogeographical distribution. Surveys in the western Atlantic determined that OM43 clade members represented 5% of the b...