Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5

Complete genome of Polaribacter huanghezhanensis KCTC 32516T isolated from glaciomarine fjord sediment of Svalbard

Polaribacter huanghezhanensis KCTC 32516T is an aerobic, non-flagellated, Gram-negative, orange-colony-forming bacterium that was isolated from the surficial glaciomarine sediment of inner basin of Kongsfjorden, Svalbard. The sampling site is characterized by a sedimentation of organic depleted lithogenous particles from the nearby glaciers, resulting in reduction of organic matter concentration. In order to understand microbial adaptation to the oligotrophic environment, we here sequenced the complete genome of the P. huanghezhanensis KCTC 32516T. The genome consists of 2,587,874 bp (G + C content of 31.5%) with a single chromosome, 2391 protein-coding genes, 39 tRNAs, and 2 rRNA operons. Our comparative analysis revealed that the P. huanghezhanensis possess the smallest genome in fifteen Polaribacter species with genome. The streamlined genome of this species, required less resource in replication, could evolved by the nutrient deficiency in surrounding environment. Simultaneously, the 15 KOs involved in amino acid biosynthesis and anaplerotic carbon fixation is uniquely absent in the P. huanghezhanensis. In addition, although the advantage of small genome, other 15 KOs involved in resource recycling and stress resistance is uniquely present in sequenced genome. This result demonstrates that the sequenced genome serves as a valuable model for further studies aimed at elucidating the molecular mechanisms associated with adaptation to oligotrophic habitat.

Colwellia maritima sp. nov. and Polaribacter marinus sp. nov., isolated from seawater

Two Gram-stain-negative, catalase- and oxidase-positive, and aerobic bacteria, strains MSW7^T and MSW13^T, were isolated from seawater. Cells of strains MSW7^T and MSW13^T are motile and non-motile rods, respectively. Strain MSW7^T optimally grew at 25 °C and pH 7.0 and in the presence of 3 % (w/v) NaCl, whereas strain MSW13^T optimally grew at 25 °C and pH 6.0-7.0 and in the presence of 2 % NaCl. As the sole respiratory quinone and the major fatty acids and polar lipids, strain MSW7^T contained ubiquinone-8, C_16 : 0, C_15 : 1  ω8c, C_17 : 1  ω8c and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), and phosphatidylethanolamine and phosphatidylglycerol, respectively, whereas strain MSW13^T contained menaquinone-6, C_15 : 1  ω6c, iso-C_15 : 0, anteiso-C_15 : 0, and iso-C_15 : 0 3-OH, and phosphatidylethanolamine, respectively. The DNA G+C contents of strains MSW7^T and MSW13^T were 37.3 and 29.9 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains MSW7^T and MSW13^T were most closely related to Colwellia echini A3^T and Polaribacter atrinae WP25^T with 98.8 and 98.1 % sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain MSW7^T and C. echini A3^T and between strain MSW13^T and P. atrinae KACC 17473^T were 73.6 and 22.6 % and 80.4 and 23.8 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic data, strains MSW7^T and MSW13^T represent novel species of the genera Colwellia and Polaribacter, respectively, for which the names Colwellia maritima sp. nov. and Polaribacter marinus sp. nov. are proposed, respectively. The type strains of C. maritima sp. nov. and P. marinus sp. nov. are MSW7^T (=KACC 22339^T=JCM 35001^T) and MSW13^T (=KACC 22341^T=JCM 35021^T), respectively.

Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats

The taxonomy of marine and non-marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean-to-land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non-marine adaptive genes. This included various Na⁺ -dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non-marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K⁺ scavenging ATPase was repeatedly gained whereas the corresponding low-affinity transporter repeatedly lost upon transitions, reflecting K⁺ ions are less available to non-marine bacteria. Strikingly, the central metabolism Na⁺ -translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H⁺ -translocating counterpart was repeatedly gained in non-marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non-marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non-marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.