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

Abstract

A Gram-staining-negative, aerobic bacterium, designated strain PT3T 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 PT3T was closely related to Amphritea ceti RA1T (= KCTC 42154T = NBRC 110551T) and Amphritea spongicola MEBiC05461T (= KCCM 42943T = JCM 16668T) 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 PT3T. Furthermore, the average amino acid identity (AAI) values of PT3T 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 PT3T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3T, A. ceti KCTC 42154T and A. spongicola JCM 16668T) 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 RA1T = KCTC 42154T = NBRC 110551T), Aliamphritea spongicola comb. nov. (type strain MEBiC05461T = KCCM 42943T = JCM 16668T), and Aliamphritea hakodatensis sp. nov. (type strain PT3T = JCM 34607T = KCTC 82591T) were suggested.

Genomic Insights into the Symbiotic and Plant Growth-Promoting Traits of “Candidatus Phyllobacterium onerii” sp. nov. Isolated from Endemic Astragalus flavescens

“…In recent times, genomic approaches have been suggested as an alternative to traditional chemotaxonomy for identifying bacterial species [ 44 ]. An in silico chemotaxonomy methodology was initially applied to Corynebacterium and Turicella, and subsequently to Aliamphritea species [ 45 , 46 ]. In this study, we used genome sequences to predict chemotaxonomic characteristics of strain IY22.…”

“…However, there is a need for further advancements in predicting the structure of enzymes responsible for fatty acid metabolism and their biochemical kinetics. This is crucial because current methods are not well suited to accurately determine the quantitative amounts of predicted fatty acids [ 46 ].…”

Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter

“…The meta-pangenomics give us new insights into bacteria genome in its host and/or environmental metagenomes and its microbial functions related to host physiology and habitat preferences. Our meta-pangenomics of Sulfitobacter BL28 is just a beginning in the approach to understanding the role of specific bacteria in larval development [ 51 ], further exploration of other stage denoted microbes applied with meta-pangenomics could contribute to a more comprehensive and deep-seated knowledge of early life microbiome during sea cucumber ontogenesis.…”

Thalassotalea psychrophila sp. nov., Thalassotalea nanhaiensis sp. nov. and Thalassotalea fonticola sp. nov., three psychrophilic bacteria isolated from deep-sea sediment

“…Collectively, the data suggests that further examinations of the taxonomy of the family Colwelliaceae are necessary. All currently described members of the genus Thalassotalea were isolated from surface or shallow marine environments such as marine sediment [7,9,12,13], seawater [3,4,6,14,15], marine animals [1,5,8,11,[16][17][18][19], and sea sand [2,20]. In this study, three strains (SQ149 T , SQ345 T , and S1-1 T ) were isolated from deep-sea sediment collected at depths of over 1000 m in the South China Sea.…”