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Application of animal manure is restricted in water protection areas in Germany to avoid microbial contamination of drinking water supplies. The potential of a newly designed AD process scheme for the control of pathogens in cattle manure is being investigated in a joint project of Bavarian research institutions and local water suppliers. Experiments are being conducted in a pilot plant (total digester volume: 250 m3) located on a dairy cattle farm sized for the treatment of semiliquid manure (7 to 10 % m/m dry matter) from 100 livestock units (approximately 2,000 m3/a). The plant consists of a sequence of three anaerobic digesters operating at different temperature levels (mesophilic-thermophilic-mesophilic "MesTherMes") to optimize the destruction of a wide range of pathogenic organisms.

Using solely semi-liquid cattle manure as it was produced on the farm, the AD process in the pilot biogas plant could be established within about 2.5 months. Technical and operational problems particularly with the heating system prevented the plant from reaching steady-state conditions during the time period reported here. In preliminary experiments the quantitative real-time polymerase chain reaction (qPCR)-method in parallel with conventional cultivation techniques was successfully applied to determine the fate of indicator microorganisms in the pilot biogas plant. The required time for a complete qPCR-analysis was only 6-8 h as opposed to 24-72 h for cultivation. Higher values from the qPCR-analyses compared to cultivation assays for certain bacteria / bacterial groups indicated differences in specificity, and detection of microorganisms in a dormant, non-cultivable state by the qPCR-method.