Microdiversity and fine-scale niche differentiation support persistence and coexistence of acidophiles in acid mine drainage

Community structure was primarily shaped by pH and habitat type (water vs. sediment), with low-pH conditions selecting for persistent, abundant taxa dominated by specialized acidophiles. Within this group, we identified significant fine-scale niche partitioning and intra-genus microdiversity, both of which were associated with greater persistence across heterogeneous conditions. Co-occurrence and niche analyses revealed that closely related taxa often occupy distinct ecological niches structured by gradients of metals, redox potential, and oxygen availability. Ecological assembly modeling indicated that deterministic homogeneous selection and stochastic drift dominate under the harshest conditions. In contrast, dispersal limitation becomes more important in less chemically-stressed sites, indicating that spatial constraints gain importance when environmental filtering weakens. Our findings reveal that AMD microbial communities are shaped by a dynamic interplay between strong environmental selection, stochasticity, and spatial factors. These insights advance fundamental understanding of microbial community organization in extreme habitats and have practical implications for predicting ecosystem responses to environmental change and optimizing bioremediation strategies in contaminated systems.