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.