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

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.

Fig. 1

Relative abundance of the classified phyla present in the biofilms of the sampled thermophilic (systems 1 and 3) and mesophilic (system 2) biogas reactor systems. Analyses were performed on metagenomic data using the LCA (lowest common ancestor) algorithm implemented in MEGAN6 [23]. UASS upflow anaerobic solid-state reactor, AF anaerobic filter; *relative abundance 0.1%

Fig. 2

Phylogenetic classification of the Bathyarchaeota MAGs ATB-1, -2, -3, -4, and -5 originating from thermophilic and mesophilic biogas-producing microbial communities. The phylogenetic tree is based on all core genes of the selected strains and MAGs from the phyla Euryarchaeota, Korarchaeota, Crenarchaeota, Aigarchaeota, Thaumarchaeota, and Bathyarchaeota as determined by means of phylosift [46, 47] and RAxML version 8.1.16 [30]. Red-colored lines indicate a 100% support, orange tones accordingly less. BA1, BA2: MAGs determined for samples from coal-bed methane wells within the Surat Basin, Australia [10]; RBG_16_48_13, RBG_13_60_20, RBG_13_38_9, RBG_13_46_16b, RBG_16_57_9, RBG_13_52_12: MAGs determined for groundwater and sediment samples from an aquifer adjacent to the Colorado river near Rifle, USA [35], SG8-32-1, SMTZ-80, DG-45, AD8-1, SG8-32-3, SMTZI-55: MAGs determined for sediment core samples of the White Oak river, USA [, –50]; further details on the MAGs are given in Additional file 2. The Euryarchaeota was chosen as outgroup. The bar represents the scale of sequence divergence

Fig. 3

Metabolic reconstruction of central carbon metabolism pathways in Bathyarchaeota MAG ATB-1. Predicted metabolic pathways for conversion of carbohydrates, proteins and amino acids into acetate, lactate, and tricarboxylic acid intermediates are presented. Determined genes are shown in yellow boxes, determined transport systems are displayed in blue, and missing but presumed transport systems are indicated by gray coloring. Central metabolic pathways are highlighted in green. The identification numbers (locus tags) of MAG ATB-1 genes included in this analysis are listed in Additional file 7

Fig. 4

Diversity of genes encoding carbohydrate-active enzymes (CAZymes) predicted to be involved in hydrolysis and/or rearrangement of glycosidic bonds for the Bathyarchaeota MAGs ATB-1, -2, -3, -4, and -5. The screening for the presence of CAZymes was accomplished applying the Hidden-Markov-Model (HMM)-based Carbohydrate-active-enzyme Annotation database dbCAN [37]. The numbers of genes belonging to a corresponding glycosyl hydrolase (GH) family are given in the fields

Fig. 5

Venn diagram representing the core genome of the Bathyarchaeota MAGs ATB-1, -2, -3, -4, and -5. The number of orthologous coding sequences (CDSs) shared by all bins is in the center. Numbers in non-overlapping portions of each oval show the number of CDSs unique to each bin