Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching

The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities’ structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously “Proteobacteria”) (68–72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.