Simple Summary
Petroleum pollution is a serious environmental problem because crude oil contains many toxic compounds that are difficult to break down naturally. Using bacteria to clean up oil spills is an eco-friendly approach, but no single bacterial strain can degrade all components of crude oil by itself. Scientists are therefore designing synthetic bacterial consortia—mixed groups of different bacterial species that work together. In this study, we analyzed the complete genomes of 15 representative oil-degrading bacteria to understand their genetic differences. We found that these strains share very few common genes, and the key genes responsible for oil degradation are mostly unique to individual strains. This diversity means different bacteria have different degradation skills that can complement each other. For instance, some strains are better at breaking down polycyclic aromatic hydrocarbons, while others excel at degrading alkanes. By understanding these genomic differences, we can rationally select and combine specific strains to build highly efficient bacterial communities for petroleum cleanup. Our work provides a theoretical foundation for designing tailored bioremediation strategies that are more effective than using single strains alone.
Abstract
Microbial remediation serves as a cost-effective and eco-friendly tactic for petroleum-contaminated sites. In real-world practices, petroleum-degrading microbial consortia display prominent superiority over single strains. To tap into their intrinsic synergistic degradation capacity, it is essential to dissect microbial commonalities, individual traits and functional complementarity for complicated bioremediation scenarios. This study applied bibliometric approaches to collect 15 well-documented representative petroleum-hydrocarbon-degrading strains, and summarized research progress via comparative genomic analysis. Pseudomonas aeruginosa, Bacillus subtilis and Rhodococcus erythropolis are the most frequently reported degraders with remarkable petroleum removal performance. Moreover, co-occurrence network analysis identifies Pseudomonas, Bacillus, Acinetobacter and Rhodococcus as core co-existing genera sustaining natural pollutant-degrading communities. Genomic evidence indicates these strains harbour abundant functional elements encoding diverse oxygenases, alcohol dehydrogenases, cytochrome P450 monooxygenases and key LuxR-, AraC- and GntR-family regulatory factors. P. aeruginosa has the highest copy numbers of catabolic enzyme genes, consistent with its outstanding degradation phenotype. Degraders from different genera exhibit high genetic heterogeneity, with accessory gene clusters significantly enriched in hydrocarbon degradation pathways. Six strains including P. aeruginosa and R. erythropolis assemble a complete gene cascade targeting recalcitrant polycyclic aromatic hydrocarbons. This work provides reliable genomic support for rational strain screening and synthetic-consortium optimization, facilitating knowledge-driven strategies for efficient petroleum bioremediation.