Deep-Sea Bacteria in Crude Oil Biodegradation: A Genomic and Metagenomic Perspective

Microbes play a vital role in the natural attenuation of oil spills, offering a sustainable and cost-effective strategy for bioremediation. This study presents the first comprehensive report of Priestia flexa MB3165, a deep-sea isolate from 200 m depth in the Arabian Sea, capable of efficiently degrading complex crude oil components, including polycyclic aromatic hydrocarbons (PAHs), phthalates, and long-chain alkanes, under aerobic and minimal nutrient conditions. The isolate achieved near-complete degradation within 30 days, with GC-MS analysis showing a reduction of PAHs from 45.2–1.5% and complete phthalate breakdown. Genomic and functional analyses revealed the presence of key hydrocarbon-degrading genes such as CYP153 , AlmA , NdoB , and cbaA , supporting a reconstructed metabolic network leading to complete mineralization through β-oxidation and the TCA cycle. The novelty lies in the simultaneous degradation capacity of a single strain across multiple hydrocarbon classes and the in-depth genomic-functional correlation supporting this metabolic versatility. Additionally, metagenomic characterization of the native microbial community revealed a high abundance of Hydrocarbonoclastic bacteria and hydrocarbon degradation genes, reinforcing the ecological relevance of the isolate. This integrated approach highlights the potential of P. flexa MB3165 as a promising candidate for bioremediation and uncovers untapped microbial capabilities in deep-sea environments impacted by oil contamination.