The influence of environmental parameters on the diversity of methanogenic communities in 15 full-scale biogas plants operating under different conditions with either manure or sludge as feedstock was studied. Fluorescence in situ hybridization was used to identify dominant methanogenic members of the Archaea in the reactor samples; enriched and pure cultures were used to support the in situ identification. Dominance could be identified by a positive response by more than 90% of the total members of the Archaea to a specific groupor order-level probe. There was a clear dichotomy between the manure digesters and the sludge digesters. The manure digesters contained high levels of ammonia and of volatile fatty acids (VFA) and were dominated by members of the Methanosarcinaceae, while the sludge digesters contained low levels of ammonia and of VFA and were dominated by members of the Methanosaetaceae. The methanogenic diversity was greater in reactors operating under mesophilic temperatures. The impact of the original inoculum used for the reactor start-up was also investigated by assessment of the present population in the reactor. The inoculum population appeared to have no influence on the eventual population.Anaerobic digestion is a simple and effective biological process for the treatment of different organic wastes and the production of energy in the form of biogas (1). A number of full-scale anaerobic digesters for biogas production have been developed and installed in Denmark during the last 20 years (27). They have been designed mainly for the codigestion of manure with a smaller fraction of other waste as a supplemental substrate. Specific environmental and operating factors influence anaerobic conversion processes in these codigestion plants, and similar factors also have an influence on wastewater primary and activated sludge (WW sludge) digesters. Some of the more important factors are temperature (4), ammonia level (7), and loading rate, which affects overall process stability, generally as measured by the concentrations of volatile fatty acids (VFA) in the digester (2).Anaerobic digestion is a multistep microbial process mediated by functionally different microbial groups-saccharide and amino acid fermenters, VFA oxidizers, and methanogens (17, 21). The two functional groups of methanogens (hydrogenotrophic and aceticlastic) have been well described in terms of physiology and phylogeny (11). Hydrogenotrophic methanogenesis and aceticlastic methanogenesis are also the key processes within anaerobic digestion, as when these processes are inhibited, digestion is effectively blocked at acidogenesis. Optimization of methanogenesis is difficult, because of both low growth rates and the susceptibility of the organisms to toxins (6).Organisms described as mediating hydrogenotrophic and aceticlastic methanogenesis are found within five phylogenetic orders (12). One of the hydrogenotrophic orders, Methanopyrales, has only hyperthermophilic member species and will not be considered further. The main orders and t...