In-Depth Genome Characterization and Pan-Genome Analysis of Strain KMM 296, a Producer of Highly Active Alkaline Phosphatase; Proposal for the Reclassification of <i>Cobetia litoralis</i> and <i>Cobetia pacifica</i> as the Later Heterotypic Synonyms of <i>Cobetia amphilecti</i> and <i>Cobetia marina</i>, and Emended Description of the Species <i>Cobetia amphilecti</i> and <i>Cobetia marina</i>
Olga Nedashkovskaya,
Larissa Balabanova,
Nadezhda Otstavnykh,
Natalia Zhukova,
Ekaterina Detkova,
Aleksandra Seitkalieva,
Evgenia Bystritskaya,
Yulia Noskova,
Liudmila Tekutyeva,
Marina Isaeva
Affiliations
Olga Nedashkovskaya
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia
Larissa Balabanova
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia
Nadezhda Otstavnykh
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia
Natalia Zhukova
A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia
Ekaterina Detkova
Winogradsky Institute of Microbiology, Russian Academy of Sciences, Federal Research Centre “Fundamentals of Biotechnology”, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
Aleksandra Seitkalieva
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia
Evgenia Bystritskaya
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia
Yulia Noskova
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia
Liudmila Tekutyeva
Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, Ajax Bay 10, Russky Island, Vladivostok 690922, Russia
Marina Isaeva
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok 690022, Russia
A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of the mussel Crenomytilus grayanus, was investigated in detail due to its ability to produce a highly active alkaline phosphatase CmAP of the structural family PhoA. A previous taxonomic study allocated the strain to the species Cobetia marina, a member of the family Halomonadaceae of the class Gammaproteobacteria. However, 16S rRNA gene sequencing showed KMM 296’s relatedness to Cobetia amphilecti NRIC 0815T. The isolate grew with 0.5–19% NaCl at 4–42 °C and hydrolyzed Tweens 20 and 40 and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C18:1 ω7c, C12:0 3-OH, C18:1 ω7c, C12:0, and C17:0 cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and also an unidentified aminolipid, phospholipid, and a few unidentified lipids. The major respiratory quinone was Q-8. According to phylogenomic and chemotaxonomic evidence, and the nearest neighbors, the strain KMM 296 represents a member of the species C. amphilecti. The genome-based analysis of C. amphilecti NRIC 0815T and C. litoralis NRIC 0814T showed their belonging to a single species. In addition, the high similarity between the C. pacifica NRIC 0813T and C. marina LMG 2217T genomes suggests their affiliation to one species. Based on the rules of priority, C. litoralis should be reclassified as a later heterotypic synonym of C. amphilecti, and C. pacifica is a later heterotypic synonym of C. marina. The emended descriptions of the species C. amphilecti and C. marina are also proposed.
