Since the beginning of the 20th century in Lusatia and in Central Germany the mining of lignite was performed. Therefore mining lakes exist and are characterised by a low pH value and increased sulphate concentrations. This process is harmful to the environment and called acid mine drainage (AMD). Aim of this study was the detection of acidophilic microorganisms in the mining areas in Lusatia and in central Germany. Furthermore, the connection between these leaching microorganisms and the AMD, the inhibition of AMD in the laboratory scale, and the mechanism of action of the surfactants to the microorganisms were examined.<br><br> From 66 sand samples, taken in 2006 and 2008, from three lignite mining areas in Lusatia and from two mining areas in central Germany iron- and sulphur- oxidizing microorganisms were detected by cultivation based technique at temperatures from 28 to 70°C. From 168 isolated pure cultures, the microorganisms were identified by sequencing of the 16S rRNA genes as 12 different species e.g. Acidithiobacillus ferrooxidans, A. thiooxidans, Leptospirillum ferrooxidans, L. ferriphilum, Ferrimicrobium acidiphilum, Acidiphilium acidophilum and Sulfobacillus thermosulfidooxidans. By the amplification of the 16S rRNA genes after extraction of the nucleic acids direct from the sand and purification from PCR inhibiting substances the species A. ferrooxidans, A. thiooxidans and Leptospirillum spp. were detected and supported the results derived from the classical method. Furthermore, microcalorimetric determination of the metabolic activity supported the results shown above. After examination of 42 drilling core samples after lowering the groundwater and 24 samples of drilling cores before lowering the ground water, taken in 2008 and 2009, the hypothesis was proposed that the biological pyrite oxidation starts by lowering the ground water and influx of air. <br><br> For the development of a strategy for the inhibition of leaching microorganisms, experiments were performed in columns in 20 mL and 20 L scale, filled with aquifer material, in the temperature range from 12 to 25°C and different surfactant regimes. The leaching was started by the addition of rainwater to the columns. By addition of SDS or Texapon N 70 an inhibition of the bioleaching was achieved in the 20 mL columns for up to 38 weeks. This was measured by an increased pH, missing detection of iron- and sulphur- oxidizing microorganisms in sand or solution. At all temperatures a reduction of the sulphate concentration was found, with a maximum of minus 70%. In 20 L columns, operated at constant 12°C or from 15 to 21°C, the bioleaching was successfully initiated and afterwards inhibited by surfactant treatment for up to 45 weeks. The surfactant addition achieved an inhibition of iron- and sulphur- oxidizing microorganisms, hence the occurrence of iron in the reduced form and an increasing pH of the leaching solution. Furthermore, the total sulphate release was decreased between 29 and 44% in comparison to the rainwater washed control, respectively.<br><br> By examinations of concentrated suspensions of A. ferrooxidans, A. thiooxidans and Ac. cryptum in comparison to E. coli and B. subtilis an induced lysis of the leaching bacteria by SDS and Texapon N70 treatment was observed. By SDS treatment a decrease in the cell count down to minus 75% for A. thiooxidans was found. Surfactant treatment of the three leaching bacteria caused a decrease in the optical density at 600nm by 80%, whereas only a slight decrease between 10 and 20% was measured for E. coli and B. subtilis, respectively. For all bacteria a release of DNA and RNA was found. Furthermore, a release of 50 to 80% of total protein content was measured for the leaching bacteria after the SDS treatment, whereas for E. coli only 0.35% was detected. These results indicate an induced lyis mechanism and explain the successful inhibition of the bioleaching in the columns by SDS and Texapon N70 addition.