Phylogenomic analysis and characterization of a novel metagenome-assembled genome from the Bay of Bengal and description of Candidatus Niobacter visakhapatnamensis gen. nov., sp. nov.

A metagenome-assembled genome (NIO.Bin9T) belonging to the family Nannocystaceae was generated from a marine sample collected from the Bay of Bengal coastal water, Visakhapatnam, India. Phylogenetic analysis based on the 16 S rRNA gene placed NIO.Bin9T within the family Nannocystaceae, showing the sequence similarity (92.4%) to Pseudenhygromyxa salsuginis SYR-2T. Genome-wide comparisons revealed average amino acid identity (AAI) values ranging from 52.2% to 53.4% and average nucleotide identity (ANI) values between 75.8% and 75.9%, relative to closely related genera, including Nannocystis, Pseudenhygromyxa, Plesiocystis, and Enhygromyxa. Phylogenomic and 16 S rRNA gene-based analysis consistently supported the placement of NIO.Bin9T within the Nannocystaceae but distinct from existing taxa. Comprises complete pathways for carbohydrate degradation, glycolysis, the TCA cycle, nitrogen assimilation, sulfur metabolism, and biosynthesis of vitamins and cofactors. In particular, 29 biosynthetic gene clusters and an expanded CAZyme repertoire indicated robust potential for secondary metabolite production and complex carbohydrate utilization. Distinctive characteristics, such as the Csa3-type CRISPR component, the rifampin-resistance gene (arr), and an enriched suite of flagellar chemotaxis genes, differentiate the lineage from closely related taxa. Genome-relatedness analyses showed that NIO.Bin9T was distinct from members of genera of Nanocystaceae, with both AAI and ANI values falling below the established genus threshold (< 65% AAI and < 80-83% for ANI), supporting its designation as a novel genus and species, for which we propose the name "Candidatus Niobacter visakhapatnamensis" gen. nov., sp. nov.