Genomic Analysis of Freshwater Polynucleobacter Strains Comprising a Novel Subcluster, Isolated from an Oligotrophic Freshwater Lake in South Korea

초록

The genus Polynucleobacter is one of major lineages of free-living bacteria in freshwater habitats. Since Polynucleobacter is ubiquitous in freshwater environments worldwide and relatively easy to grow, a number of studies on its phylogeny, biogeography, and evolution have been performed so far. Previous phylogenetic analyses of 16S rRNA gene sequences showed that the Polynucleobacter can be divided into four subclusters: PnecA, B, C, and D. This classification, however, was proposed based on the sequences collected from several lakes that are not distributed globally. Here, we report the cultivation and draft genome sequences of three novel Polynucleobacter strains that is not affiliated with any of the previous four subclusters. The strains IMCC30063T, IMCC29146 and IMCC30228 were isolated from Lake Soyang, an oligotrophic freshwater lake in South Korea, by the dilution-to-extinction culturing method. Phylogenetic trees built based on 16S rRNA genes and whole genomes showed that the three strains formed a new subcluster distinct from the four previously known subclusters, within the genus Polynucleobacter. The draft genomes of the strains consisted of 14?35 contigs with a total size of 2.4?2.5 Mb and an average G + C content of 44.5?44.8%, containing 2,322?2,492 cording sequences. In fragment recruitment analyses using >100 various freshwater metagenomes, these IMCC strains showed distribution patterns distinct from other Polynucleobacter strains. Genome-based inference suggested that all Polynucleobacter strains have diverse metabolic potentials for core carbohydrate and energy metabolism, nitrogen metabolism, sulfur metabolism and light utilization based on rhodopsin or aerobic anoxygenic photosynthetic gene cluster. Overall, these results suggest that the novel Polynucleobacter subcluster cultured from Lake Soyang had phylogenetic and genomic characteristics distinct from previously described subclusters, and thus these str