Genetic characterization of a novel biphenyl degradation pathway in Extensimonas perlucida RM1 isolated from agricultural soil in Mosul city

Aims: Isolation of novel biphenyl degrading strains from Mosul, Iraq.Methodology and results: Extensimonas perlucida RM1 was isolated from agricultural soil in Mosul, Iraq for its ability to metabolize biphenyl as a sole source of carbon and energy.Extensimonas perlucida RM1 appeared as colorless transparent colonies on a nutrient agar medium.Molecular identification of E. perlucida was confirmed using 16S rRNA gene sequencing.The ribosomal 16S gene sequence of the E. perlucida strain was submitted to the National Center for Biotechnology Information (NCBI) and deposited in the GenBank database under the accession number OP161920.Growth curve experiments show this bacterium has a 9.6-h doubling time on biphenyl.The growth of biphenyl was due to the presence of several biphenyl-degrading genes that were detected using four sets of degenerate primers.Molecular studies showed that E. perlucida RM1 uses a Rieske non-heme iron dioxygenase which is responsible for the initial oxygenation of biphenyl involved in the first step of biphenyl degradation, and it was possible to amplify its Rieske cofactor sequence using a set of degenerate primers.Furthermore, this bacterium contains a ring cleavage dioxygenase used in biphenyl degradation.In addition, an angular dioxygenase not involved in biphenyl degradation was detected, suggesting this bacterium's ability to degrade other aromatics that require angular deoxygenation. Conclusion, significance and impact of study:This study shows for the first time worldwide the ability of E. perlucida to degrade biphenyl and detects multiple polyaromatic hydrocarbon degrading genes involved in this pathway.