Genomic analysis of freshwater Limnohabitans strains comprising a novel subcluster, isolated from an oligotrophic lake in South Korea

초록

The genus Limnohabitans is one of major lineages of free-living bacteria in freshwater environments. Previous phylogenetic analyses of 16S rRNA gene sequences showed that the genus can be divided into five subclusters: LimA, B, C, D and E, with each subcluster presumably comprising multiple species. However, only five validly-published species have been proposed so far in this genus. Here, we report the cultivation and genomic characteristics of two colony-non-forming Limnohabitans strains that are not affiliated with any of the previously described subclusters and thus are candidates for novel species. The strains IMCC26093 and IMCC26116 were isolated by dilution-to-extinction method from an oligotrophic freshwater lake in South Korea. Genome sequencing of two strains were performed using single molecule real-time sequencing (SMRT) technique, resulting in single circular contigs for both strains. The sizes of two genomes were 2.95 Mbp and 3.37 Mbp and the DNA G+C contents were 53.3 and 59.9 mol%, respectively. The IMCC26116 genome encoded genes for the complete Calvin cycle of CO2 fixation and the denitrification pathway, suggesting diverse metabolic potential. In fragment recruitment analyses using >100 various freshwater metagenomes, these novel strains showed distribution patterns distinct from other Limnohabitans strains, showing endemism. Overall, these findings would contribute to expanding the opportunity to study more detailed ecophysiology and evolution of freshwater Limnohabitans.