The small genome of an abundant coastal ocean methylotroph

Abstract

OM43 is a clade of uncultured beta-proteobacteria that is commonly found in environmental nucleic acid sequences from productive coastal ocean ecosystems, and some freshwater environments, but is rarely detected in ocean gyres. Ecological studies associate OM43 with phytoplankton blooms, and evolutionary relationships indicate that they might be methylotrophs. Here we report on the genome sequence and metabolic properties of the first axenic isolate of the OM43 clade, strain HTCC2181, which was obtained using new procedures for culturing cells in natural seawater. We found that this strain is an obligate methylotroph that cannot oxidize methane but can use the oxidized C1 compounds methanol and formaldehyde as sources of carbon and energy. Its complete genome is 1304 428 bp in length, the smallest yet reported for a free-living cell. The HTCC2181 genome includes genes for xanthorhodopsin and retinal biosynthesis, an auxiliary system for producing transmembrane electrochemical potentials from light. The discovery that HTCC2181 is an extremely simple specialist in C1 metabolism suggests an unanticipated, important role for oxidized C1 compounds as substrates for bacterioplankton productivity in coastal ecosystems.

Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

“…The large subunit of the OM43 clade methanol dehydrogenase (MDH) (XoxF aka MxaF) was the best match to 2.3% of all the spectra identified, lending further support to recent findings that implicate methanol and other one carbon compounds as important substrates for bacterioplankton in coastal ecosystems (Giovannoni et al, 2008). A total of 168 spectra matching 33 eCDSs were closest matches to the OM43 clade MDH (Figure 4).…”

“…The betaproteobacterial OM43 clade is commonly found at low levels in coastal ecosystems and has been observed to increase in abundance to B2% of bacterial cells during phytoplankton blooms (Morris et al, 2006). Phylogenetic and genome analysis of the OM43 isolate HTCC2181 placed this organism among type I methylotrophs that can use methylated compounds as a sole carbon and energy source (Giovannoni et al, 2008). It was also shown that cell growth yield was proportional to the amount of methanol or formaldehyde added to sterile seawater media.…”

“…Peptides from marine microorganisms were detected using two-dimensional high-performance liquid chromatography coupled with electrospray tandem mass spectrometry (MS/MS). Peptides were identified by spectral comparison with translated environmental proteincoding sequences (eCDSs) collected from coastal environments during the GOS metagenomics project (GOS02-11) as well as the genomes of two coastal Bacterial isolates, Candidatus Pelagibacter ubique strain HTCC1062 of the SAR11 clade (Giovannoni et al, 2005b) and the OM43 clade strain HTCC2181 (Giovannoni et al, 2008). Our goal was to identify abundant proteins that could reveal the dominant metabolic processes occurring within marine bacterial communities.…”

Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton

“…Consistent with other coastal studies (Sowell et al, 2011;Williams et al, 2012), we detected the expression of methanol dehydrogenase large subunit proteins derived from the Beta-proteobacteria OM43 clade (Table 3). Methanol dehydrogenase was detected in all samples and exhibited highest similarity to homologs from two methylotrophic strains (HTCC2181 and KB13; Supplementary Table S8; Giovannoni et al, 2008). On the basis of previous genome analysis, OM43 bacteria use the RuMP pathway for the assimilation of carbon from C1 compounds (Giovannoni et al, 2008).…”

“…Methanol dehydrogenase was detected in all samples and exhibited highest similarity to homologs from two methylotrophic strains (HTCC2181 and KB13; Supplementary Table S8; Giovannoni et al, 2008). On the basis of previous genome analysis, OM43 bacteria use the RuMP pathway for the assimilation of carbon from C1 compounds (Giovannoni et al, 2008). Here, we also identified the expression of a key enzyme of the RuMP pathway, namely hexulose-6-phosphate synthase, in all samples (Table 3, Supplementary Table S8), suggesting OM43 may be assimilating carbon derived from methanol.…”