Genomic and functional insights into aromatic compound degradation by <i>Delftia</i> strain PS-11 isolated from freshwater pufferfish

This study describes the functional genomic features and aromatic compound degradation potential of <i>Delftia</i> strain PS-11, isolated from the skin mucus of a freshwater pufferfish (<i>Tetraodon cutcutia</i>). Whole-genome sequence analysis of strain PS-11 revealed genetic attributes associated with species distinctiveness. The overall genome-relatedness indices, such as <i>in silico</i> DNA-DNA hybridization, are below 70%, and average nucleotide identity and average amino acid identity were below the threshold value, that is, 95% to 96%, respectively. Phylogenomic analysis based on genome-wide core genes showed that strain PS-11 clustered with <i>Delftia acidovorans</i> NBRC 14950^T. Furthermore, genome analysis identified multiple gene clusters involved in the degradation of aromatic compounds, including phenol, benzoic acid, and hydroxybenzoic acid. We determined the specific activities of key metabolic enzymes in cell-free extracts, including catechol-1,2-dioxygenase, catechol-2,3-dioxygenase, protocatechuic acid 4,5-dioxygenase, and gentisate 1,2-dioxygenase. To our knowledge, the presence of <i>Delftia</i> strains associated with pufferfish has not been reported previously. These findings suggest that members of this genus occupy a broader and more diverse range of ecological habitats than previously recognized and may play a potential role in the remediation of aromatic pollutants.IMPORTANCE<i>Delftia</i> strain PS-11 described in this study associated with freshwater pufferfish skin is capable of degrading aromatic compounds. Gene clusters in the form of operons involved in degradation of phenol, benzoic acid, and hydroxybenzoic acid were present. Enzymatic studies support the proposed degradation pathways. Our study suggests that the presence of xenobiotics-degrading <i>Delftia</i> strain in the skin of pufferfish adds a new ecological niche to this bacteria. The observed metabolic pathway in the degradation of aromatic compounds indicates niche-specific adaptive evolution for this bacterium.