Williamsia profundi sp. nov., a novel deep-sea Actinomycetota isolate with versatile metabolic potential and specialized ecological adaptability

The deep-sea biosphere hosts distinctive microbial communities with specialized adaptive traits, yet the mechanisms underpinning their physiological survival remain largely obscure. In this study a novel Gram-stain-positive, aerobic bacterium, designated strain SKLECPSW1T, was isolated from the Eastern Indian Ocean at a depth of 5318 m. The strain grows optimally at 32 °C and has a DNA G + C content of 70.0 mol%. Its major fatty acids are C16:0, C18:1 ω9c, and 10-methyl-C18:0. Genome analysis revealed a versatile metabolic repertoire, including complete central carbon metabolic pathways, dissimilatory nitrate reduction to ammonium (DNRA), anaplerotic CO₂ fixation, and multiple genes associated with environmental stress responses. Furthermore, CAZyme profiling and 12 putative biosynthetic regions suggested potential for complex carbohydrate processing and secondary-metabolite biosynthesis. Comparative 16S rRNA gene sequence analysis showed that strain SKLECPSW1T shared the highest sequence similarity with Williamsia aurantiaca B375T (98.3%). Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) values with related Williamsia species ranged from 71.15% to 83.35% and 18.8% to 26.6%, respectively, supporting its novel status. Metagenomic analysis of 25 deep-ocean datasets showed broad high-identity genome-wide recruitment in 2 samples, with breadths of 45.60% and 34.64% at ≥95% nucleotide identity, remaining 42.76% and 34.09% at ≥97.5%. Complementary marker-gene analyses further supported the occurrence of low-abundance environmental populations related to W. profundi in these two samples. Collectively, strain SKLECPSW1T represents a novel species, for which the name Williamsia profundi sp. nov. is proposed. The type strain is SKLECPSW1T (= MCCC 1K09832T = JCM 37991T).