Bacterial and archaeal community in a flooding uranium mine, Königstein (Germany)

The former uranium mine Königstein in Germany is currently in the process of remediation and represents an underground acid mine drainage (AMD) environment. Due to technical leaching with sulphuric acid, the mine water is characterized by low pH, high concentrations of toxic heavy metals and uranium (up to 3×10-4 M) (Arnold et al. 2011). Biofilms in the Königstein mine grew underground in the mine galleries in a depth of 250 m (50 above sea level) either as stalactite-like slime communities (snotites) or as acid streamers in the drainage channels (Zirnstein et al. 2012). Since 2010 the underground mine is no longer accessible because of flooding. Biomass of the mine water community was retrieved by three different in-situ systems: vacuum filtration of the mine water, flow cell with slides and reactor with PE carrier. The diversity of the planktonic microorganisms and of the biofilms of the Königstein samples of two consecutive years were characterized by catalysed reporter deposition fluorescence in-situ hybridization (CARD-FISH) and a bar-coded pyrosequencing approach.
The identified microbial communities showed low diversity. 24,630 archaeal sequences and 5,706 bacterial sequences could be classified into 5 classes (archaea) and 13 phyla (bacteria) including candidate divisions. CARD-FISH analysis showed that Bacteria were more abundant than Archaea. The dominating phylum of bacteria was Proteobacteria, especially Alphaproteobacteria and Gammaproteobacteria. Furthermore, sequences of Actinobacteria, Nitrospira, Firmicutes, Bacteroidetes, Verrucomicrobia, Acidobacteria, Chlorobi, Chloroflexi, Planctomyces, OD1, TM7 and Gemmatimonadetes were found. Most of the archaeal sequences belong to the class Thermoplasmata, especially Ferroplasma sp..
The obtained results for the microbial community in the flooded mine site is completely different in comparison to the microbial community observed in the underground environment before flooding. Before flooding the mine galleries were dominated by biofilms composed predominantly of Betaproteobacteria affiliated with Ferrovum myxofaciens, also designated “Ferribacter polymyxa”. Knowing more about the acidophiles in former uranium mines helps to explain how microorganisms live in such extreme environments and how they affect the water chemistry and how to use them for biomining and bioleaching technologies.