A culturomics biobank decodes extremophile evolution and metabolism in acid mine drainage

Extreme environments such as acid mine drainage (AMD) host highly specialized microbial communities that drive profound biogeochemical cycles. Within these ecosystems, iron- and sulfur-metabolizing taxa catalyze mineral weathering, generating intense acidity and mobilizing heavy metals. However, more than 97% of these microorganisms remain uncultured "microbial dark matter," heavily restricting our understanding of extremophile metabolism and adaptation. Here we present the Microbial Biobank of AMD (mbAMD), a culturomics-derived collection of 652 isolates spanning 42 species—including 21 novel taxa—that achieves 86.7% coverage of the global AMD core microbiome. Functional validation demonstrates that 36 of these taxa possess active iron or sulfur metabolic capacities, including the discovery of the first pure cultures of acid-tolerant sulfate reducers. Comparative genomic analyses across these isolates reveal that extreme environmental adaptation is predominantly driven by pervasive horizontal gene transfer. Specifically, extremophiles preferentially acquire adaptive genes governing acid tolerance and metal resistance from phylogenetically proximal relatives rather than distant donors. These findings elucidate the modular evolutionary strategies of extremophiles and provide critical functional resources for advancing biohydrometallurgy and environmental bioremediation. This mbAMD resource will accelerate biohydrometallurgical process optimization and environmental bioremediation strategies while advancing evolutionary microbial ecology research.