Genome and cultural characteristics of strain IMCC19250, a cultured representative from the LD28 clade of freshwater Betaproteobacteria

초록

Methylotrophic bacteria are important players to maintain carbon budgets in aerobic environments such as coastal region of the ocean and freshwater lakes. Many members of the methylotrophic bacteria have been intermittently isolated from aquatic environments, however major freshwater methylotrophic clades such as the LD28 clade do not have any cultured representatives and marine counterpart clade, the OM43 clade, has only small number of isolates such as HTCC2181. The LD28 clade of the family Methylophilaceae is a betaproteobacterial lineage widely found in freshwater environments. Here we report cultivation and genome sequencing of strain IMCC19250 of the LD28 clade, isolated from surface layer of Soyang Lake. During an effort to cultivate the uncultured yet abundant bacterial populations inhabiting freshwater ecosystem, 62 bacterial strains belonging to the LD28 clade were obtained from Lake Soyang using the high throughput dilution-to-extinction culturing. Strain IMCC19250 was chosen as a representative strain among 62 strains affiliated with the LD28 clade. Strain IMCC19250 showed ≈95% 16S rRNA gene sequence similarity to HTCC2181, a representative isolate of the well-known marine methylotrophic OM43 clade found in coastal regions. We found that this strain is an obligate methylotrophic bacterium that cannot oxidize methane but can utilize C1 compounds such as methanol and formaldehyde as sources of carbon and energy. In contrast, no growth was observed in the presence of the methylated compounds including methyl chloride or dimethylsulfoniopropionate (DMSP). Growth rate and maximum cell density of IMCC19250 increased with methanol concentration, yielding a Ks value of 41μM. Optimum growth was observed at 25-30°C and in the presence of 0-0.1% of NaCl. The draft genome sequence of IMCC19250 was determined by Illumina sequencing (250-bp paired-end), resulting in 5 contigs.