Genome-Resolved Metagenomics Suggests Site-Specific Microbial Adaptations in Urban Soils Co-Contaminated with Hydrocarbons and Heavy Metals

This study explores the physicochemical properties and microbiological community structure of oil-contaminated soils from Midrand and Roodepoort, South Africa. Due to sample pooling, the analysis provides a composite profile for investigating site-specific microbial adaptations rather than replicated ecological inference. The soils of Midrand exhibited acidity (pH around 5.5–5.9), elevated levels of heavy metals (e.g., Zn exceeding 1000 mg/kg), and the presence of 5–6 ring polycyclic aromatic hydrocarbons (PAHs). The soils in Roodepoort exhibited a near-neutral pH (about 6.2–7.2), characterized by specific metal concentrations (e.g., Cr exceeding 150 mg/kg) and an elevated presence of four-ring polycyclic aromatic hydrocarbons (PAHs). Metagenomic analysis indicated distinct microbial communities: Pseudomonas spp. were prevalent in Midrand, while Bacillus spp. were dominant in Roodepoort. Correlation analysis suggested connections between pollutants and microbial taxa; however, these findings are tentative. Recovered metagenome-assembled genomes (MAGs) indicated genetic potential for polycyclic aromatic hydrocarbon (PAH) degradation in Midrand and for metal resistance in Roodepoort. The findings suggest that localised pollution profiles are associated with unique microbial community structures and genetic potentials, providing a genomic basis for proposing site-specific bioremediation strategies. The research underscores the necessity for measures that take into account pollutant composition, soil pH, and microbial adaptation.