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Biotechnol Biofuels. 2018 Jun 19;11:167. doi: 10.1186/s13068-018-1162-4. eCollection 2018.

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

Author information

1
1Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany.
2
2Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany.
3
3Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany.
4
4Biochemical Conversion Department, Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany.
5
5Urban Water Management and Environmental Engineering, Faculty of Civil and Environmental Engineering, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany.
6
6Dept. Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
#
Contributed equally

Abstract

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.

KEYWORDS:

Anaerobic digestion; Archaea; Bathyarchaeota; Biomass conversion; Biomethanation; Genome binning; Hydrolysis; Metabolic pathway reconstruction; Metagenome-assembled genomes

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