Phenanthrene-induced proteomic adaptations in marine Pseudomonas oleovorans: insights into PAH biodegradation mechanisms

Environmental context Polycyclic aromatic hydrocarbons (PAHs) are toxic, persistent organic pollutants widely introduced into marine environments through oil spills, industrial effluents and incomplete combustion processes. Owing to their hydrophobic nature, PAHs readily accumulate in sediments and biota, posing serious ecological risks associated with their carcinogenic and mutagenic properties. In this study, we show that indigenous microbial assemblages contribute directly to PAH transformation in marine systems and underscore their relevance to intrinsic biogeochemical attenuation and environmentally compatible remediation approaches. Rationale Polycyclic aromatic hydrocarbons (PAHs) are persistent organic contaminants whose chemical stability and toxicity pose risks in marine environments. Phenanthrene (Phe) is used as a model PAH to elucidate transformation mechanisms relevant to more complex and carcinogenic compounds. Although microbial degradation of PAHs is recognised as a key attenuation process, chemically resolved evidence linking enzymatic activity to transformation intermediates in marine systems remains limited. This study investigates Phe degradation by a marine Pseudomonas oleovorans strain, integrating proteomic and metabolite analyses to resolve dominant degradation pathways. Methodology Pseudomonas oleovorans strain NIOSV8 was incubated in Luria–Bertani broth (LB) amended with Phe (100 mg L−1) for 48 h. Phe removal was quantified over time. Protein expression profiles under control and Phe-amended conditions were analysed using liquid chromatography–mass spectrometry (LC-MS) quadrupole time of flight (QToF)-based shotgun proteomics. Differentially expressed proteins were used to infer active metabolic pathways. Degradation intermediates were identified using gas chromatography–mass spectrometry (GC-MS) to validate proteomic interpretations. Results Approximately 55% of Phe was degraded within 48 h. Proteomic analysis identified 5902 proteins across all conditions, with 2486 proteins detected exclusively in Phe-amended cultures, indicating metabolic reprogramming. Enzymes associated with aromatic hydrocarbon transformation were enriched, particularly salicylate hydroxylase and catechol 2,3-dioxygenase-related proteins, consistent with a salicylate–catechol degradation sequence. Multiple oxidoreductases and dehydrogenases involved in xenobiotic metabolism were also upregulated. GC-MS analysis detected intermediates such as 1-naphthol and 8-methyl-1-naphthoic acid, which support the oxidative transformation of Phe to salicylate-related compounds. Discussion The combined proteomic and metabolite evidence demonstrates that Phe degradation proceeds by a salicylate-mediated pathway. The induction of oxidoreductases highlights oxidative reactions in PAH transformation and the maintenance of redox balance. Changes in energy metabolism indicate that Phe degradation is a metabolically demanding process. These findings provide mechanistic insight into microbial PAH transformation and contaminant fate in marine environments and sediments.