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

Alejandro Palomo¹Bowei Li¹Zhixiong Huang¹Yunjie Ma¹Wenle Peng¹Weishi Wang¹Yan Zheng¹Yi Wen^2*Lihong Yang^1*

• ¹Southern University of Science and Technology, Shenzhen, China
• ²Ministry of Ecology and Environment Rural Ecological Environment Division, Beijing, China

Acid mine drainage (AMD) systems are extreme acidic environments characterized by low pH and high metal concentrations that shape unique microbial ecosystems. While acidophilic microorganisms are known to drive AMD biogeochemistry, the ecological processes governing their community assembly, niche partitioning, and stability remain incompletely resolved. By integrating high-resolution 16S rRNA gene amplicon sequencing with community ecology and null modeling approaches, here we investigated microbial diversity, structure, and assembly mechanisms in an AMD system in Zhejiang province, China. Community structure was primarily driven by pH and habitat type (water vs. sediment), with low-pH environments selecting for persistent abundant taxa comprising 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 demonstrated 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 demonstrate that AMD microbial communities are shaped by a dynamic interplay between strong environmental selection, stochasticity, and spatial factors. These insights clarify fundamental principles of microbial ecology in extreme environments and are critical for predicting community responses to change and developing effective bioremediation strategies.