Bioleaching of a low-grade copper ore, linking leach chemistry and microbiology

•Distinct microbial communities dominate solids and liquids from heap.•Cell numbers decline rapidly when [Fe3+] and [(SO4)2−] exceed 25 and 75gL−1 respectively.•Leptospirillum – the primary iron(II) oxidiser in solution and residue samples from the heap. Three largely-independent studies were undertaken on the same heap leach system during the period of transition from processing oxidised ores to sulfide ores: monitoring of heap solutions for microorganisms, analysis of samples from a spent heap, and column tests. Microbial cell numbers and diversity were monitored in process water samples from the transition heap over a four-year period. Cell numbers remained low throughout, 1–30×104cells mL−1, possibly reflecting growth inhibition by the high element concentrations in process water. High iron, magnesium and aluminium concentrations in spent heap pregnant leach solution (PLS) are attributed to siderite and clinochlore dissolution and would be expected to impact on microbial growth. Planktonic cell numbers in a column leachate declined rapidly by two orders of magnitude when concentrations of ferric ion and sulfate exceeded 30 and 75gL−1, respectively. Nevertheless, a variety of bacterial strains closely related to Acidithiobacillus (At.) ferrooxidans, At. caldus, Leptospirillum (L.) ferriphilum, Acidimicrobium (Am.) ferrooxidans, Acidiphilium (Ap.) cryptum, an Alicyclobacillus-related strain and Sulfobacillus (S.) thermosulfidooxidans, and the archaeon Ferroplasma (F.) acidiphilum were isolated, mainly from the more acidic intermediate leach solutions (ILS). Overall, the results obtained from the use of culture-dependent and culture-independent methods of community analysis were complementary and consistent. The majority of identified genera and species were present in both the process water samples from the operating heap and the solutions and ore samples from the spent heap. In the spent heap, distinct populations dominated different sample types. Leptospirillum- and Acidithiobacillus-like strains dominated PLS samples and Leptospirillum also dominated seven of eight spent ore samples and all of the heap sediment samples, making it the primary iron(II) oxidising species.