Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif

Abstract

The Kilianstollen Marsberg (Rhenish Massif, Germany) has been extensively mined for copper ores, dating from early medieval period until 1945. The exposed organic-rich alum shale rocks influenced by the diverse mine drainages at an ambient temperature of 10 ∘C could naturally enrich biogeochemically distinct heavy metal resistant microbiota. This amplicon-sequence-based study evaluates the microbially colonized subterranean rocks of the abandoned copper mine Kilianstollen to characterize the colonization patterns and biogeochemical pathways of individual microbial groups. Under the selective pressure of the heavy metal contaminated environment at illuminated sites, Chloroflexi (Ktedonobacteria) and Cyanobacteria (Oxyphotobacteria) build up whitish–greenish biofilms. In contrast, Proteobacteria, Firmicutes and Actinobacteria dominate rocks around the uncontaminated spring water streams. The additional metagenomic analysis revealed that the heavy metal resistant microbiome was evidently involved in redox cycling of transition metals (Cu, Zn, Co, Ni, Mn, Fe, Cd, Hg). No deposition of metals or minerals, though, was observed by transmission electron microscopy in Ktedonobacteria biofilms which may be indicative for the presence of different detoxification pathways. The underlying heavy metal resistance mechanisms, as revealed by analysis of metagenome-assembled genomes, were mainly attributed to transition metal efflux pumps, redox enzymes, volatilization of Hg, methylated intermediates of As3+, and reactive oxygen species detoxification pathways.