Linking microbial community reassembly to multi-element metabolic potential across community and genome scales in...

Ion-adsorption rare earth element (REE) mining can create a composite pollution environment characterized by acidification and enrichment of NH₄⁺, SO₄²⁻, and REEs, yet its effects on riverine microbial community assembly and multi-element metabolic potential remain poorly understood. Here, we combined 16S rRNA amplicon sequencing, metagenomic sequencing, and metagenome-assembled genomes (MAGs) to characterize microbial community assembly and functional reorganization across a mining-disturbance gradient. At the community level, bacterial and archaeal richness and diversity declined significantly with increasing pollution, accompanied by clear community differentiation. Compared with bacteria, archaea exhibited greater environmental specificity, with larger contributions of homogeneous selection and dispersal limitation to community assembly. Meanwhile, microbial functional genes formed a modular network linking carbon, nitrogen, sulfur, iron, arsenic, and methane transformation processes, with particularly prominent cross-module associations among carbon-, nitrogen-, and sulfur-related functions. At the genome level, mining-associated MAGs showed multifunctional integration within individual genomes and potential functional division of labor and complementarity among different microbial members. Together, the community- and genome-level results revealed a cross-scale organization of multi-element metabolic potential, extending from functional network connectivity at the community level to functional configuration at the genome level. Such mining-driven reorganization of microbial communities and metabolic functions may further influence greenhouse-gas-related processes and the mobility and transformation of metal(loid)s, providing new insights into microbial ecological processes and potential ecological risks in mining-impacted rivers.