Abstract
<title>Abstract</title> <p>Functional recovery of petroleum-contaminated soils remains poorly characterized, as remediation success is often judged by contaminant reduction rather than ecosystem-level biochemical responses. This study applied integrated liquid chromatography-mass spectrometry (LC-MS) and ¹H nuclear magnetic resonance (¹H-NMR) metabolomics to track metabolic restructuring during field-scale bioremediation of a polluted farmland in the Niger Delta, Nigeria. Soil samples were collected over 185 days from uncontaminated reference soil, untreated contaminated soil, tillage-watered contaminated soil, and poultry-manure-amended contaminated soil. Integrated analyses generated 266 spectral features, including confidently and putatively annotated compounds associated with osmolytes, organic acids, aromatic signals, and lipid-associated resonances. Principal component analysis and PERMANOVA showed significant treatment- and time-associated metabolomic restructuring (p < 0.001). Soils undergoing remediation showed higher relative abundance of branched-chain amino acids, glutamic acid, alanine, serine, and nucleotide-related metabolites, whereas untreated contaminated soils showed stronger representation of aromatic and stress-associated metabolites. Pathway enrichment indicated significant representation of amino acid metabolism, central carbon metabolism, and hydrocarbon degradation pathways. These findings demonstrate that bioremediation is accompanied by substantial metabolic reorganization, highlighting metabolomics as a powerful complement to contaminant-based assessments for evaluating functional recovery in petroleum-impacted ecosystems.</p>