Functional metabolite signatures reveal biochemical recovery trajectories in oil-polluted soils undergoing bioremediation.

Reliable candidate indicators of recovery following petroleum contamination remain limited, as remediation success is commonly assessed using hydrocarbon removal alone rather than restoration of soil characteristics. This study integrated physicochemical profiling with untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to resolve biochemical recovery trajectories across polluted soil (PS), soil undergoing bioremediation (UB), bioremediated soil (BS), and uncontaminated reference soil (CNTR) in Ogoniland, Nigeria. Total petroleum hydrocarbon (TPH) concentrations decreased progressively from 78.26 ± 6.04 mg/kg in PS to 41.23 ± 1.40 mg/kg in UB and 23.38 ± 1.81 mg/kg in BS, corresponding to an overall 70.1% reduction in BS relative to the PS. Sulphur decreased from 6.36 ± 0.70 wt% to 0.152 ± 0.052 wt%, whereas phosphorus increased from 0.068 ± 0.006 wt% to 0.325 ± 0.025 wt% after remediation. Principal component analysis of physicochemical variables explained 99.3% of total variance and resolved a directional restoration gradient (PS → UB → BS → CNTR). Untargeted metabolomics similarly separated treatment states, with PCA explaining 73.7% of total biochemical variance. Polluted and transitional soils were enriched in aromatic stress metabolites, including fluorene, triphenylphosphine oxide, quinolinic acid, and 2,4-dinitrophenol, whereas remediated soils accumulated recovery-associated metabolites such as citric acid, aconitic acid, ectoine, pyridoxamine, lipoic acid, and geranic acid. Integrated analyses showed strong positive correlations between TPH and fluorene (r = 0.88) and Triphenylphosphine oxide (TPPO) (r = 0.84), but negative correlations with citric acid (r = -0.82) and pyridoxamine (r = -0.78). These results demonstrate that hydrocarbon attenuation is tightly coupled to coordinated metabolic reprogramming and nutrient restoration. Functional metabolite signatures may provide a framework for the assessment of biochemical changes associated with soil recovery following petroleum contamination. Thus, our study demonstrates coordinated physicochemical and metabolomic shifts associated with soil recovery during bioremediation.