Worldwide, anaerobic digestion for sanitation and utilization of the produced biogas as energy carrier have a long-standing history. Concomitantly, digested residues from biogas plants are utilized as valuable fertilizers in crop production. In Germany, guaranteed prices for electricity generated from renewable sources pushed the number of biogas plants from about 140 in 1992 to about 7,720 by the end of 2013, and the share of electricity supply from biogas close to 4.5%. In the midterm, biogas is given considerable potential to fill up the residual load from electricity generation based on wind and photovoltaic. In this review, we give an overview of the state-of-the-art of biogas technology for energy supply from agricultural inputs, based mainly on the situation in Germany. Focus is placed on the monitoring and control (M&C) of biogas plants as a means of meeting the growing demands for productivity and reliability of biogas supply. We summarize prominent factors for the stability and productivity of the anaerobic digestion (AD) process, and present latest findings about molecular biology tools, bioindicators, the ‘metabolic quotient’ and cDNA/DNA ratios for process analysis. In view of the large diversity of agricultural biogas installations, we discuss the cost-benefit ratio of M&C effort and equipment. In the light of the transformation of the energy system in Germany towards renewable sources (‘Energiewende’), we give an outlook on prospects and concepts for the future role of biogas technology in agriculture and energy supply. We also address recent misguided developments, as the sustainable development of biogas technology in agriculture can only be realized within the ecological, economical, and social boundaries of underlying agro-ecological systems.

Biogas production from renewable resources is an alternative to generate energy and concomitantly save fossil fuels and mitigate greenhouse gas emissions. As methanogenesis is a major bottleneck in the biogas process, the determination of the specific activity of methanogenic Archaea can be a good indicator of the process state. A new parameter, the metabolic quotient (MQ), was developed to evaluate the specific activity of methanogens. A standard was created from mesophilic maize-fed fermenters to calculate the expected concentration of methanogens for a given methane productivity at stable process stages. The MQ, the ratio of the predicted to the actual concentration of methanogens, defines their metabolic activity. The MQ was able to indicate methanogenic cell stress metabolism and imminent process failure before conventional chemical parameters. As a further approach, the methanogenic activity was determined by quantification of mRNA transcripts in relation to the mcrA/mrtA-gene, coding for a key enzyme subunit of methanogenesis. The cDNA/DNA ratio reflected the specific actual process activity of the methanogens. As both methods are potent parameters for the early detection of process failure, biogas plant operators may avoid economical losses by their preventive application.