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Typical biological environmental clean up technologies include treatment of wastewater and waste by activated sludge process or by methane fermentation process, and clean up of contaminated soil and groundwater by bioremediation. Microorganisms play an important role in the biodegradation of pollutants in the above-mentioned processes, however, little is known of the mechanism of action of the microbial communities involved in these processes. Currently, Ebara Research is analyzing the structure of pollutant-degrading microbial consortia, which are regarded as a black box by molecular biological technique based on gene information of microorganisms. And also we are collecting fundamental data of microbial community structure to improve the efficiency and stability of biological treatment processes. Furthermore, we are developing the monitoring method of the effective bacterial group to diagnosis the pollutant-degrading ability of sludge and soil.