Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov.

A Gram-staining-negative, aerobic bacterium, designated strain PT3(T) was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3(T) was closely related to Amphritea ceti RA1(T) (= KCTC 42154(T) = NBRC 110551(T)) and Amphritea spongicola MEBiC05461(T) (= KCCM 42943(T) = JCM 16668(T)) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3(T). Furthermore, the average amino acid identity (AAI) values of PT3(T) against other Amphritea species were on the reported genus delineation boundary (64–67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3(T), Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3(T), A. ceti KCTC 42154(T) and A. spongicola JCM 16668(T)) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1(T) = KCTC 42154(T) = NBRC 110551(T)), Aliamphritea spongicola comb. nov. (type strain MEBiC05461(T) = KCCM 42943(T) = JCM 16668(T)), and Aliamphritea hakodatensis sp. nov. (type strain PT3(T) = JCM 34607(T) = KCTC 82591(T)) were suggested.