Functional genomic and metabolomics characterisation of bioleaching fungi from mine tailings

Abstract

Bioleaching is a biological and an environmentally friendly alternative to traditional leaching methods for extracting metals from ores or wastes. However, its reliance on microorganism, which are sensitive to bioleaching extreme conditions, result in challenges of slow kinetics and low metal recovery that limit its potential. This study applied functional genomics to gain insights into the bioleaching process. The focus was on fungal communities that can survive in extreme conditions. Tailing samples, which represent an extreme environment, with high metal concentration and low pH, similar to bioleaching conditions, were used to profile, isolate and identify fungal communities. Genera such as Trichoderma, Penicillium, and Talaromyces, were obtained. Further screening of this organisms for metal tolerance, growth rates, carbon utilisation and organic acid production revealed Trichoderma as the most promising bioleaching fungus. Trichoderma exhibited high growth rates in the presence of metals, likely due to its high metal tolerance index of >1 to 300 mg/l Al, 100 mg/l Zn and Ni, with a minimum inhibitory concentration of 1600 mg/l for Al, 1000 mg/l for Zn and 400 mg/l for Ni. When grown in glucose media, the organism produced up to 300 g/l of citric acid. Thus, the fungus's bioleaching capacity to extract metals from two different metal-containing samples, namely tailings and ore samples, was assessed using one-step, two-step, and spent media approaches. The results showed that the fungus's bioleaching efficiency was unaffected by the sample type and led to the recovery of various metals (>62% of Ni in ore samples and >54% Zn in tailings samples). Other metals such as Mg, As, Mn, Cu and Co were leached in both tailing and ore samples. Metabolite analysis during bioleaching revealed that Trichoderma produced oxalic acid (up to 930.13 mg/l) as the main bioleaching agent, while citric acid was produced in low amounts. Transcriptomics analysis revealed that genes related to biological processes, cellular components, and molecular functions were differentially expressed. Further enrichment of the differentially expressed genes revealed that genes associated with the structure and function of the cell membrane were consistently upregulated, indicating how Trichoderma tolerates high metal exposure. Notably, the genes related to organic acid production were not differentially expressed, and we further concluded that Trichoderma's metal toxicity defence mechanism does not disrupt the metabolic activities involved in the production of organic acid.