Quantification of indicator and pathogenic bacteria in manures and digestates from three agricultural biogas plants over a one-year period

•The fate of FIB and of pathogenic bacteria though AD varied with the biogas plant.•log10 reductions of pathogenic bacteria though AD varied over time.•Campylobacter and Salmonella were less persistent than L. monocytogenes.•The reduction of C. botulinum and C. difficile were less than or equal to 0.5 log10. Interest in the conversion of manure in biogas via anaerobic digestion (AD) is growing, but questions remain about the biosafety of digestates. For a period of one year, we monitored the impact of three mesophilic agricultural biogas plants (BPs) mainly fed with pig manure (BP1, BP3) or bovine manure (BP2) on the physicochemical parameters, the composition of the microbial community and the concentration of bacteria (E. coli, enterococci, Salmonella, Campylobacter, Listeria monocytogenes, Clostridium perfringens, Clostridium botulinum and Clostridioides difficile). The BP2 digestate differed from those of the two other BPs with a higher nitrogen content, more total solids and greater abundance of Clostridia MBA03 and Disgonomonadacea. Persistence during digestion ranked from least to most, was: Campylobacter (1.6 to >2.9 log10 reduction, according to the BP)