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Blasting and fracking of rock in mines exposes fresh rock surfaces to the local water and microbial communities. This may lead to leaching of metals from the rock by chemical or biological means and can cause acidification of the water system in the mine, i.e., acid rock drainage (ARD). Failure to prevent leakage of metal contaminated mine water may be harmful for the environment, especially to the local groundwater. In the Rudna mine, Poland, an in situ bioleaching pilot test at approximately 1 km depth was performed in the H2020 BIOMOre project (Grant Agreement #642456). After the leaching stage, different methods for irreversible inhibition of acidophilic iron oxidizing microorganisms used for reoxidation of reduced iron in the leaching solution were tested and were shown to be effective. However, the potential of the natural mine water microbial communities to cause leaching of copper or acidification of the mine waters has not been tested. In this study, we set up a microcosm experiment simulating the exposure of freshly fractionated Kupferschiefer sandstone or black schist to two different chloride-rich water types in the Rudna mine. The pH of the microcosms water was measured over time. At the end of an 18-week incubation, the bacterial community was examined by high throughput sequencing and qPCR, and the presence of copper tolerant heterotrophic bacteria was tested by cultivation. The dissolution of copper into the chloride rich microcosm water was measured. The pH in the microcosms did not decrease over the time of incubation. The sandstone increased the number of bacteria in the microcosms with one or over two orders of magnitude compared to the original water. The bacterial communities in the two tested mine waters were diverse and similar despite the difference in salinity. The bacterial diversity was high but changed in the less saline water during the incubation. There was a high content of sulphate reducing bacteria in the original mine waters and in the microcosms, and their number increased during the incubation. No acidophilic iron oxidizers were detected, but in the microcosms containing the less saline water low numbers of Cu tolerant bacteria were detected. Copper to a concentration of up to 939 mg L−1 was leached from the rock also in the microbe-free negative controls, which was up to 2.4 times that leached in the biotic microcosms, indicating that the leaching was also abiotic, not only caused by bacteria. [ABSTRACT FROM AUTHOR]