Bacterial Degradation of Persistent Organic Pollutants: From Molecular Mechanisms to Synthetic Biology

Persistent organic pollutants (POPs) are among the most recalcitrant environmental contaminants due to their chemical stability, hydrophobicity, toxicity, and capacity for long-range transport, yet mechanistic understanding remains fragmented across molecular, cellular, and systems scales, hindering integrated bioremediation strategies. This study synthesizes recent advances in bacterial POP degradation by integrating evidence from aerobic oxidative, anaerobic reductive, and cometabolic pathways across molecular, genomic, regulatory, metabolic, and multi-omics levels. The analysis reveals that POP degradation is governed by highly modular and evolutionary dynamic networks involving catabolic operons, mobile genetic elements, regulatory hierarchies, and extensive metabolic rewiring. Notably, enzymatic promiscuity in aromatic-ring-hydroxylating dioxygenases and reductive dehalogenases, along with alternative pathway architectures and syntrophic microbial interactions, significantly enhances degradation efficiency. Systems-level insights further highlight the importance of coordinated redox balancing, membrane adaptation, efflux mechanisms, biosurfactant production, and biofilm-mediated resilience. Advances in synthetic biology, including pathway refactoring, enzyme engineering, designer consortia, and smart biosensors, provide new opportunities to expand substrate range, improve pathway control, and enable real-time monitoring. However, challenges related to genetic stability, biosafety, and field robustness persist. Overall, the field is transitioning toward predictive, systems-informed, and engineerable frameworks, emphasising the need for in situ multi-omics validation and environmentally robust bioremediation solutions.