Comparative Genomic Analysis of Two Limnohabitans Stains Comprising a Novel Subcluster, Isolated from an Oligotrophic Lake

초록

Genus Limnohabitans is one of major bacterial lineages in freshwater environment. Previous phylogenetic analyses of 16S rRNA gene sequences showed that the genus can be divided into five subclusters: LimA, B, C, D, and E. Nevertheless, only five valid-published species have been proposed so far. Therefore, the genus Limnohabitans was predicted to have high microdiversity. Here, we report the cultivation and genomic characteristics of two colonynon-forming Limnohabitans strains that is not affiliated with any of the previous subclusters. The IMCC26093 and IMCC26116 were isolated by dilution-to-extinction method from an oligotrophic freshwater lake in Korea. Genomic sequences of two strains were analyzed using SMRT technique, and single, circular contigs were obtained for both strains. The sizes of two genomes were 2.95 Mb and 3.37 Mb and the G + C contents were 53.3 and 59.9%, respectively. Comparing other Limnohabitans strains, only a novel strains IMCC26116 encoded the complete Calvin cycle that proceeds with CO2 fixation. In addition, the strain was found to harbor genes for the denitrification cycle, which is likely to be deeply involved in the nitrogen cycle in the ecosystem. In fragment recruitment analyses using > 100 various freshwater metagenomes, these novel strains showed distribution patterns distinct from other Limnohabitans strains. These results suggest that the genus Limnohabitans were highly microdiversified in their phylogenetic and genomic characteristics.