Insights Into Divergent Mechanisms of Pyrite Oxidation by Indigenous Fungi From Mine Tailings.

Fungi can oxidise pyrite, a process which has potential implications for metal bioleaching and acid mine drainage formation. However, this capacity has been demonstrated primarily using only a few model fungal strains. Diverse fungal communities are known to inhabit pyrite-rich mine tailings but how these indigenous fungi may mediate pyrite oxidation and by what mechanisms remain largely unexplored. Here, we isolated 51 pyrite-oxidizing fungal strains spanning 28 genera from three mine tailings areas in South China. From this native library, we selected three potent pyrite oxidisers, Pithomyces cynodontis DC37, Penicillium janthinellum ZJS52, and Aspergillus niger DBS124, for in-depth mechanistic characterisation. These indigenous strains solubilised 1.2%-1.8% of the total iron from pyrite in fungus-pyrite co-culture systems, exceeding values reported for model fungi under comparable conditions. They also acidified the medium to a pH as low as 2.15, providing dual lines of evidence for their robust oxidative capacity. Further analyses revealed distinct surface erosion features and changes in iron (Fe) and sulfur (S) speciation, confirming fungal-mediated pyrite oxidation. All three strains secreted organic acids (e.g., oxalic and citric acids) and showed peroxidase activity, but they exhibited divergent patterns. By combining hybrid genome sequencing (Illumina and Nanopore) with time-course transcriptomics, we uncovered the genetic basis for these divergent patterns. Genes coding for lignin and manganese peroxidases in P. cynodontis DC37 were co-induced by reactive oxygen species and metal ions released during pyrite oxidation. Furthermore, A. niger DBS124 employed an oxalic-acid-based mechanism upon pyrite exposure, driven by coordinated upregulation of central carbon metabolism and oxalate biosynthesis. Collectively, our findings highlight the underexplored biotechnological potential of mine-tailings fungi and establish a molecular foundation for understanding their roles in Fe- and S-cycling within mining environments and for developing fungal-mediated bioleaching technologies.