Drains from coal mines remain a worrisome point-source of toxic metal/metalloid pollutions to the surface- and ground-waters worldwide, requiring sustainable remediation strategies. Understanding the microbial community subtleties through microbiome and geochemical data can provide valuable information on the problem. Furthermore, the autochthonous microorganisms offer a potential means to remediate such contamination. The drains from Onyeama coal mine in Nigeria contained characteristic sulphates (313.0 ± 15.9 mg l−1), carbonate (253.0 ± 22.4 mg l−1), and nitrate (86.6 ± 41.0 mg l−1), having extreme tendencies to enrich receiving environments with extremely high pollution load index (3110 ± 942) for toxic metals/metalloid. The drains exerted severe degree of toxic metals/metalloid contamination (Degree of contamination: 3,400,000 ± 240,000) and consequent astronomically high ecological risks in the order: Lead > Cadmium > Arsenic > Nickel > Cobalt > Iron > Chromium. The microbiome of the drains revealed the dominance of Proteobacteria (50.8%) and Bacteroidetes (18.9%) among the bacterial community, whereas Ascomycota (60.8%) and Ciliophora (12.6%) dominated the eukaryotic community. A consortium of 7 autochthonous bacterial taxa exhibited excellent urease activities (≥ 253 µmol urea min−1) with subsequent stemming of acidic pH to > 8.2 and sequestration of toxic metals (approx. 100% efficiency) as precipitates (15.6 ± 0.92 mg ml−1). The drain is a point source for metals/metalloid pollution, and its bioremediation is achievable with the bacteria consortium.

Drains from coal mine remain a worrisome point source of toxic metal/metalloid pollutions to surface- and ground-waters worldwide, requiring sustainable remediation strategies. Understanding the microbial community subtleties through integrated metagenomic and geochemical data elicit selection of autochthonous bacteria consortium, spurring decommissioning of drains before discharge to hydrosphere. The drains contained characteristic sulphates (313.0 ± 15.9 mg/l), carbonate (253.0 ± 22.4 mg/l), and nitrate (86.6 ± 41.0 mg/l), having extreme tendencies to enrich receiving environments with extremely high pollution load index (3110 ± 942) for toxic metals/metalloid. The drains exerted severe degree of toxic metals/metalloid contamination (3,400,000 ± 240,000) and consequent astronomically high ecological risks in the order: Lead > Cadmium > Arsenic > Nickel > Cobalt > Iron > Chromium. Metagenome of the drains revealed dominance of Proteobacteria (50.8%) and Bacteroidetes (18.9%) among bacterial community, whereas, Ascomycota (60.8%) and Ciliophora (12.6%) dominated the eukaryotic community. A consortium of 7 autochthonous bacterial OTUs exhibited excellent urease activities (≥ 253 µmol urea/min.) with subsequent stemming of acidic pH to > 8.2 and sequestration of toxic metals (approx. 100% efficiency) as precipitates (15.6 ± 0.92 mg/ml). The coal mine drain is a point source for metals/metalloid pollution to surrounding hydrosphere, and its bioremediation is achievable with the bacteria consortium.