Marine pollution driven by industrial activities poses a significant threat to aquatic ecosystems and human health, with bilge water (BW) representing a complex and persistent waste stream due to its heterogeneous composition of hydrocarbons, surfactants, and heavy metals. Microbial fuel cells (MFCs) offer a promising approach for simultaneous wastewater treatment and energy recovery; however, the influence of substrate complexity on bioelectrochemical performance and microbial adaptation remains poorly understood. Single-chamber MFCs inoculated with mixed microbial consortia were sequentially operated using synthetic (SBW), low-strength raw (LBW), and raw high-strength BW (RBW) to assess increasing complexity. Among BW types, LBW exhibited the highest power density (77.3 mW/m2). Performance declined under RBW, consistent with reduced substrate bioavailability and constrained electron transfer. Nevertheless, electricity generation was sustained for 95 days under 20% RBW, indicating sustained electrochemical activity following prolonged exposure. Microbial community analysis revealed stage-dependent restructuring, including enrichment of Pseudomonas, while predicted functional profiling indicated shifts in central carbon metabolism and hydrocarbon degradation pathways during sequential BW treatment. Molecular docking and molecular dynamics analyses provided complementary support for the potential interaction of dodecanoate with quinohemoprotein alcohol dehydrogenase from Pseudomonas putida. Overall, the results suggest that increasing BW complexity drives microbial community and functional reorganization, while biodegradation potential, contaminant removal, and electrochemical performance respond in a partial and functionally heterogeneous manner.
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