Microhabitats are associated with bacterial and archaeal community structure in acid mine drainage from an abandoned mine

Abstract

Acid mine drainage (AMD) is a severe environmental problem and a heterogeneous low-pH ecosystem containing diverse microbial communities. Microbial community structure across visually distinct AMD microhabitats remains poorly understood, particularly in South Korea, where field-based microbial studies are scarce and AMD research has mainly focused on contaminated soils and remediation. Here, in an exploratory survey, we analyzed 16S rRNA gene amplicon sequencing data from water, wall-attached biofilm, and AMD precipitate-associated biofilm microhabitats in AMD from the abandoned Ilgwang mine, Korea. The final dataset comprised 716,915 reads assigned to 663 ASVs across seven samples. Alpha diversity did not differ significantly among microhabitat types (all Kruskal-Wallis P > 0.10). A Type-constrained principal coordinates analysis of square-root-transformed Bray–Curtis dissimilarities, rarefied to the minimum library size, accounted for 50.3% of total variation (adjusted R² = 25.4%, P = 0.025 by exact permutation), although multivariate dispersion differed among Types. The largest genus-display category was Unclassified Gammaproteobacteria (24.96% of pooled reads); the dominant ASV in this category exactly matched a SILVA V4 sequence annotated as Ferrovum but remained formally unclassified at genus because its bootstrap support was 46%, below the 80% threshold. Overall, 57.91% of pooled reads remained unclassified at genus; among confidently assigned genera, Metallibacterium and Leptospirillum were the most abundant. The descriptive compositional summaries are consistent with visible AMD sample matrices being associated with shifts in the relative abundance of a partially shared acidophilic bacterial–archaeal assemblage, rather than with fully discrete communities. These exploratory findings suggest that sample matrix is an important context for interpreting AMD community composition and highlight candidate bacterial and archaeal lineages for future genome-resolved and activity-based studies.