Integrated multi-omics analysis reveals the mechanism of birnessite-enhanced phenanthrene degradation by Novosphingobium sp. HDJX-2 bacteria

Phenanthrene (PHE) is a typical polycyclic aromatic hydrocarbon (PAH) pollutant characterized by biological toxicity and environmental persistence. To enhance its degradation efficiency, a composite system combining birnessite with Novosphingobium sp. HDJX-2 was established to investigate the synergistic mechanism between minerals and functional bacteria. Gas chromatography-mass spectrometry (GC–MS), coupled with transcriptomic and metabolomic analyses, was employed to elucidate the molecular regulation and metabolic pathway reconstruction involved in PHE degradation in the composite system. The results demonstrated that PHE was metabolized by the strain through a series of reactions, including aromatic ring dioxygenation, ring cleavage, and decarboxylation, leading to the formation of acetyl-CoA via the phthalic acid pathway and ultimately achieving complete mineralization through the tricarboxylic acid (TCA) cycle. This degradation process was accompanied by extensive transcriptional regulation and metabolic pathway enrichment, with 967 differentially expressed genes and 125 significantly altered metabolites identified. Further analysis revealed the upregulation of genes associated with biofilm formation ( rcsA , 2.31-fold upregulation) and energy metabolism ( Rbs , 2.47-fold upregulation), along with enhanced pathways, such as arachidonic acid metabolism (1.85-fold upregulation) and riboflavin metabolism (1.13-fold upregulation). These changes contributed to improved membrane transport, oxidative stress response, and energy production, thereby significantly promoting PHE degradation. Notably, pathways related to amino acid metabolism and carbon fixation were significantly enriched, further enhancing the system's degradation capacity. This study established an efficient and stable mineral–microbial synergistic system and revealed its multilayered regulatory mechanisms in PAH bioremediation, offering theoretical insights and practical strategies for ecological restoration.