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Background  Only a fraction of the microbial species used for anaerobic digestion in biogas production plants are methanogenic archaea. We have analyzed the taxonomic profiles of eubacteria and archaea, a set of chemical key parameters, and biogas production in samples from nine production plants in seven facilities in Thuringia, Germany, including co-digesters, leach-bed, and sewage sludge treatment plants. Reactors were sampled twice, at a 1-week interval, and three biological replicates were taken in each case.    Results  A complex taxonomic composition was found for both eubacteria and archaea, both of which strongly correlated with digester type. Plant-degrading  Firmicutes  as well as  Bacteroidetes  dominated eubacteria profiles in high biogas-producing co-digesters; whereas  Bacteroidetes  and  Spirochaetes  were the major phyla in leach-bed and sewage sludge digesters.  Methanoculleus  was the dominant archaea genus in co-digesters, whereas  Methanosarcina  and  Methanosaeta  were the most abundant methanogens in leachate from leach-bed and sewage sludge digesters, respectively.    Conclusions  This is one of the most comprehensive characterizations of the microbial communities of biogas-producing facilities. Bacterial profiles exhibited very low variation within replicates, including those of semi-solid samples; and, in general, low variation in time. However, facility type correlated closely with the bacterial profile: each of the three reactor types exhibited a characteristic eubacteria and archaea profile. Digesters operated with solid feedstock, and high biogas production correlated with abundance of plant degraders ( Firmicutes ) and biofilm-forming methanogens ( Methanoculleus  spp.). By contrast, low biogas-producing sewage sludge treatment digesters correlated with high titers of volatile fatty acid-adapted  Methanosaeta  spp.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-015-0271-6) contains supplementary material, which is available to authorized users.

Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany