Knowledge of the microbial consortia participating in the generation of biogas, especially in methane
formation, is still limited. To overcome this limitation, the methanogenic archaeal communities in six full-scale
biogas plants supplied with different liquid manures and renewable raw materials as substrates were analyzed
by a polyphasic approach. Fluorescence in situ hybridization (FISH) was carried out to quantify the methanogenic
Archaea in the reactor samples. In addition, quantitative real-time PCR (Q-PCR) was used to support
and complete the FISH analysis. Five of the six biogas reactors were dominated by hydrogenotrophic Methanomicrobiales.
The average values were between 60 to 63% of archaeal cell counts (FISH) and 61 to 99% of
archaeal 16S rRNA gene copies (Q-PCR). Within this order, Methanoculleus was found to be the predominant
genus as determined by amplified rRNA gene restriction analysis. The aceticlastic family Methanosaetaceae was
determined to be the dominant methanogenic group in only one biogas reactor, with average values for Q-PCR
and FISH between 64% and 72%. Additionally, in three biogas reactors hitherto uncharacterized but potentially
methanogenic species were detected. They showed closest accordance with nucleotide sequences of the
hitherto unclassified CA-11 (85%) and ARC-I (98%) clusters. These results point to hydrogenotrophic methanogenesis
as a predominant pathway for methane synthesis in five of the six analyzed biogas plants. In addition,
a correlation between the absence of Methanosaetaceae in the biogas reactors and high concentrations of total
ammonia (sum of NH3 and NH4
) was observed.