Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals

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.

*Co is rarely found in natural waters; therefore the permissible limit for Ni was adopted for Co Values are mean (± SEM) of triplicate measures. Values are mean (± SEM) of triplicate sampling measurements. The pollution indexes and ecological risk assessment factors include: contamination factor (CF), enrichment factor (EF), geoaccumulation index (I geo ), potential ecological risk factor (Er), modified potential ecological risk factor (MEr), and risk quotient (RQ)

Computation of pollution indices and ecological risk assessments
Contamination factor (CF): determines addition of heavy metals (HMs) in the environment in relation to contents of the metals in unpolluted freshwater as the background values (Hakanson, 1980). It is calculated as: where C n is the concentration of the metal n and B n is the natural local background concentration of metal n. CF is categorized into four as low contamination, CF < 1; moderate contamination, 1 < CF ≤ 3; high contamination, 3 < CF ≤ 6; and very high contamination, CF > 6.  (2) Where C n and B n were as state earlier in Eq. (1) above, C Fe is the Fe content (mean, 10.2 mg l -1 ) in a river that receives the AMD and B Fe is the Fe content in background environment. EF is categorized into: no enrichment, EF < 1; less enrichment, 1 ≤ EF < 3; moderate enrichment, 3 ≤ EF < 5; moderately high enrichment, 5 ≤ EF < 10; high enrichment, 10 ≤ EF < 25; very high enrichment, 25 ≤ EF < 50; and exceptionally high enrichment, EF > 50.

Geo-accumulation index (I geo ): determines the level of HMs pollution based on HMs contents
and it was calculated following Muller (1969) methods as: where C n is the concentration of metal n and B n is as indicated above. The factor K is the background matrix correction factor due to lithospheric effects, which is usually defined as 1.5 according to Muller (1969). It was ranked as: no pollution, I geo < 0; moderate pollution, 0 ≤ I geo < 1; strong pollution, 1 ≤ I geo < 2; high pollution, 2 ≤ I geo < 3; very high pollution, 3 ≤ I geo < 4; severe pollution, 4 ≤ I geo < 5; and very severe pollution, I geo ≥ 5.

Pollution load index (PLI):
is the nth root of the multiplication of CF of individual HMs.

Pollution index (PI): involved using a weighted average based on the average and maximum
values of CF to determine the quality of the environmental samples (Nemerow, 1991), and thus calculated as: CF av and CF max are the average and maximum values of CF, respectively. It is classified as: no pollution, PI < 0.7; slight pollution, 0.7 < PI ≤ 1; moderate pollution, 1 < PI ≤ 2; high pollution, 2 < PI ≤ 3; and severe pollution, PI > 3.

Degree of contamination (C d ):
measures the extent to which HMs get introduced to an environment, and it is calculated as:
where is the toxic response factor for a given substance (see

Potential ecological risk index (RI):
is the summation of all risk factors for HMs in the environment (Hakanson, 1980) and it is calculated as: Categories of risk assessment are as: low risk, RI < 40; moderate risk, 40 < RI ≤ 80; considerate risk, 80 < RI ≤ 160; high risk, 160 < RI ≤ 320; and very high risk, RI > 320 of HMs.

HMs.
Risk quotient (RQ): is the calculated index of ecological risk assessment based ratio of measured environmental concentration to predicted no-effect concentration (PNEC). In the present study, PNEC was based on function of permissible limit of HMs in drinking water and the total organic carbon in the AMD. RQ was therefore calculated as: where C e (mg/l) is the environmental concentration of HMs, C pl is the permissible limit of HMs in surface waters that poses no danger to physiologies of living things, and F oc is the mean organic carbon in the AMD. A RQ ≥ 1 shows the risk posed by toxicants is high but the risk is low if RQ < 1.