An Assessment of the Degradation Potential and Genomic Insights Towards Hydroxylated Biphenyls by Rhodococcus opacus Strain KT112-7.

Background: Hydroxylated biphenyls are currently recognized as secondary pollutants that are hazardous to animals and humans. Bacterial degradation is the most effective method for the degradation of hydroxylated biphenyls. Several strains capable of degrading polychlorinated biphenyls have been described, which also degrade hydroxylated biphenyls. Objectives: 1) To study the biodegradative properties of the Rhodococcus opacus strain KT112-7 towards mono-hydroxylated biphenyls. 2) To analyze the genome of the Rhodococcus opacus strain KT112-7. 3) To identify the genetic basis for the unique biodegradative potential of the Rhodococcus opacus strain KT112-7. Methods: A genome analysis of the strain KT112-7 was conducted based on whole-genome sequencing using various programs and databases (Velvet, CONTIGuator, RAST, KEGG) for annotation and identification of protein-coding sequences. The strain KT112-7 was cultivated in a K1 mineral medium supplemented with mono-hydroxy biphenyls or mono-hydroxybenzoic acids as the carbon source. For the growth test mono-hydroxybiphenyls or mono-hydroxybenzoic acids were dosed at concentrations of 0.5 g/L and 1.0 g/L correspondently, and the bacterial growth was monitored by the optical density. For the biodegradative activity test, mono-hydroxybiphenyls were dosed at a concentration of 0.1 g/L in vials, inoculated with late exponential phase bacteria previously acclimated on biphenyl. Compound analysis was performed using GC-MS, HPLC, and spectrophotometry. Results: It was found that the genome of strain KT112-7 consists of a chromosome and 2 plasmids. Biphenyl degradation genes (bph genes) were identified on plasmid PRHWK1 and the chromosome, as well as hydroxybenzoic acid degradation genes on the chromosome. The strain KT112-7 was shown to degrade mono-hydroxylated biphenyls to basal metabolic compounds of the cell, with the highest destructive activity observed towards 3- and 4-hydroxylated biphenyls (98%). Discussion: Analysis of the translated sequences of the bph genes from strain KT112-7 revealed that the amino acid sequences of the bph operon, located on plasmid pRHWK1, exhibit high similarity to homologous enzymes of the "upper" pathway for biphenyl degradation in Rhodococcus jostii RHA1, whose bph genes are also plasmid-borne. The deduced amino acid sequences encoded by the bphA1A2B genes, located on the chromosome of strain KT112-7, show a high degree of similarity to enzymes from Rhodococcus strains that mediate naphthalene degradation. The genes of the "lower" biphenyl pathway in strain KT112-7 are located on the chromosome and share a high level of similarity with the bph genes of Acidovorax sp. KKS102. Analysis of the deduced sequences of the pcaGHBCDF, pcaIJfadA, and catABC genes, along with the metabolites identified during the cultivation of strain KT112-7 on hydroxylated biphenyls, suggests the presence of both classical and unique metabolic pathways for hydroxylated benzoic acids in strain KT112-7. Conclusion: The Rhodococcus opacus strain KT112-7 is characterized by genetic systems that contribute to its high biodegradative potential towards mono-hydroxylated biphenyls and their metabolites. Thus, the strain KT112-7 is promising for use in hydroxybiphenyl degradation technologies.