Mechanistic insights into microbial and metabolomic responses in PAHs-contaminated soil derived from a coal gasification site

Microbial remediation offers a promising in situ solution for polycyclic aromatic hydrocarbons (PAHs)-contaminated soils at coal gasification sites, where these persistent pollutants cause long-term ecological risks. However, the mechanistic links between microbial metabolic processes, community dynamics, and degradation efficiency under realistic remediation conditions remain insufficiently understood. In this study, a large-scale soil column experiment evaluated an integrated bioremediation approach combining bacterial consortium inoculation, nutrient supplementation, and intermittent bio-ventilation (BA treatment). The BA treatment significantly accelerated the degradation of PAHs in soil, particularly high-concentration PAHs such as naphthalene (NAP), phenanthrene (PHE), pyrene (PYR) and benzo[a]pyrene (BaP), and resulted in pronounced changes in differential metabolites (DEMs), with notable enrichment of key transformation intermediates such as pyrene-1,6-dione and phenanthrene-1,2-oxide. KEGG pathway analysis indicated significant enrichment in xenobiotic biodegradation, amino acid metabolism, and lipid metabolism pathways, reflecting microbial functional expression associated with pollutant breakdown and cellular metabolic activity. Simultaneously, BA treatment enhanced dehydrogenase and fluorescein diacetate hydrolase activities while also increasing available phosphorus, which were strongly correlated with PAHs removal and metabolite profiles. Mantel tests and co-occurrence network analyses revealed strong linkages among microbial genera, PAHs, DEMs and soil biochemical properties, highlighting synergistic interactions underlying degradation. Specific bacterial genera exhibited close associations with PAH-related metabolites, suggesting functional contributions to pollutant transformation. Overall, the enhanced microbial treatment not only promoted PAHs removal but also altered soil metabolic profiles and biochemical activity, providing evidence of synergistic microbe–metabolite interactions that contribute to efficient bioremediation.