Abstract
The anaerobic digestion is a biological process that consists of four stages. At the final step of the biodegradation of the organics the most sensitive to the ambient factors group of microorganisms - the methanogens, produces biogas with main component methane. Common problems of these technologies are low biogas yield, production of biogas with low quality or situations in which the plant gets out of exploitation. These problems are related to the lack of biological indicators of the process used in the practice and lack of understanding of the structure and functioning of the methanogenic consortium. Different fluorescent techniques have the potential to fulfill this gap and to contribute to the deep understanding of the structure of the microbial communities. In this study it was applied fluorescence in situ hybridization analysis for identifying and localization of microorganisms by the Archaea domain in digesters of wastewater treatment plant "Kubratovo". High negative correlation between the quantity of Archaea and the biogas and methane production has been registered. This method has the potential to be used as a tool for analyzing the structure of the microbial communities in the digesters and thus to allow the adaptation of the consortium and the optimization of the whole process.