Complete genome sequence of Idiomarina sp. D18 from the Western Pacific Ocean reveals biosynthetic potential for β-lactone and RiPP-like compounds.
Idiomarina sp. D18 is a deep-sea marine bacterium isolated from seawater at a depth of 5069 m in the western Pacific Ocean. The complete genome of strain D18 consists of a circular chromosome of 2,765,208 bp and three plasmids, with a G + C content of 47.28%. Genome annotation identified 2587 predicted protein-coding genes, 57 tRNA genes, and 14 rRNA genes. Functional analysis revealed genes involved in diverse metabolic processes, including amino acid metabolism, signal transduction, and energy production. In addition, multiple carbohydrate-active enzymes were identified, suggesting the ability to utilize complex substrates in marine environments. Genome mining identified two biosynthetic gene clusters, including a RiPP-like cluster and a β-lactone cluster. These clusters are predicted to encode bioactive compounds, which may contribute to microbial competition and interaction through antimicrobial activity and enzyme inhibition. These findings suggest that strain D18 possesses adaptive strategies for survival in deep-sea environments and highlight its potential as a source of novel secondary metabolites.