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Background  Previous studies on the  Miscellaneous Crenarchaeota Group , recently assigned to the novel archaeal phylum  Bathyarchaeota , reported on the dominance of these  Archaea  within the anaerobic carbohydrate cycle performed by the deep marine biosphere. For the first time, members of this phylum were identified also in mesophilic and thermophilic biogas-forming biofilms and characterized in detail.    Results  Metagenome shotgun libraries of biofilm microbiomes were sequenced using the Illumina MiSeq system. Taxonomic classification revealed that between 0.1 and 2% of all classified sequences were assigned to  Bathyarchaeota.  Individual metagenome assemblies followed by genome binning resulted in the reconstruction of five metagenome-assembled genomes (MAGs) of  Bathyarchaeota . MAGs were estimated to be 65–92% complete, ranging in their genome sizes from 1.1 to 2.0 Mb. Phylogenetic classification based on core gene sets confirmed their placement within the phylum  Bathyarchaeota  clustering as a separate group diverging from most of the recently known  Bathyarchaeota  clusters. The genetic repertoire of these MAGs indicated an energy metabolism based on carbohydrate and amino acid fermentation featuring the potential for extracellular hydrolysis of cellulose, cellobiose as well as proteins. In addition, corresponding transporter systems were identified. Furthermore, genes encoding enzymes for the utilization of carbon monoxide and/or carbon dioxide via the Wood–Ljungdahl pathway were detected.    Conclusions  For the members of  Bathyarchaeota  detected in the biofilm microbiomes, a hydrolytic lifestyle is proposed. This is the first study indicating that  Bathyarchaeota  members contribute presumably to hydrolysis and subsequent fermentation of organic substrates within biotechnological biogas production processes.    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1162-4) contains supplementary material, which is available to authorized users.

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors