Comparative metagenomic analyses of viral genomic diversity and ecosystem functions in extremely acidic copper mine...

Sulfidic mine tailings represent a major source of acid mine drainage (AMD), a significant environmental problem worldwide. While the prokaryotic communities in extremely acidic tailings have been extensively studied to reveal their adaptation strategies and roles in acid generation, the diversity and putative ecosystem functions of viruses potentially infecting these extremophilic prokaryotes remain unexplored. Here, we used comparative metagenomics to investigate the viral communities in a massive copper mine tailings impoundment. Our analyses identified 932 viral operational taxonomic units (vOTUs) in 22 tailings samples, with the majority of them being taxonomically unaffiliated. The viral communities were significantly more diverse in the surface tailings (mean = 531 vOTUs) than the deeper layers (mean = 249 vOTUs). Viral communities are shaped mainly by physicochemical factors related to tailings oxidation and salinity in the surface and deeper tailings, respectively. In silico prediction uncovered archaeal viruses significantly enriched in the deeper tailings layers as compared to the surface tailings, especially those putatively infecting Thermoplasmataceae. Predicted hosts included key functional microbes associated with Fe/S redox, linking the prevalent viral infection with AMD generation/bioremediation. Notably, viral-encoded auxiliary metabolic genes (AMGs) potentially contributing to the stress resistance of hosts were identified in the tailings, exhibiting higher abundance in the deeper layers. Global metatranscriptomic analyses further demonstrated the infective and functional activity of tailings viruses across diverse AMD-associated environments. Overall, our findings provide initial insights into the viral populations and putative ecosystem functions in this extreme habitat and have important implications for mitigating AMD generation in situ.