Unraveling the genomic and metabolic mechanisms of pyrene and phenanthrene degradation by Mycolicibacterium sp. SCSIO 43805: A high-Efficiency bacterium isolated from seagrass sediment

The ability of microorganisms to break down persistent organic pollutants in the environment has sparked significant interest in bioremediation, as it provides a firm foundation for implementing an effective, robust, and eco-friendly approach. In this study, we isolated a bacterium, identified as Mycolicibacterium sp. SCSIO 43805, from seagrass sediments and studied its potential for degrading pyrene and phenanthrene. The stain effectively degraded pyrene and phenanthrene, both provided at a concentration of 50 mg/L, within 12 days of incubation, as evidenced by the absence of any noticeable peaks related to pyrene and phenanthrene in the GC-MS profile of the 12-day extract. Moreover, the whole genome sequence analysis unveiled a comprehensive array of genes crucial for the complete degradation of polycyclic aromatic hydrocarbons. Multiple copies of dioxygenases such as nidA, nidB and nidD and monooxygenase such as cytochrome P450, which are essential for initial cleavage of aromatic rings, were detected in the genome of the Mycolicibacterium sp. SCSIO 43805. Furthermore, based on the gene contents and metabolic profiling of the extracts, we speculated that Mycolicibacterium sp. SCSIO 43805 could degrade pyrene, phenanthrene and other PAHs via phthalate and β-Ketoadipate pathway. The comparative genomics with other member of the genus Mycolicibacterium showed that Mycolicibacterium sp. SCSIO 43805 possessed a maximum number of genes involved in polycyclic aromatic hydrocarbon degradation. Hence, based on results of genomic, comparative genomics and metabolic profiling, Mycolicibacterium sp. SCSIO 43805 demonstrated high ability in degrading persistent organic pollutants and is an excellent biological agent for bioremediation of contaminated environment.