Metagenomic and metatranscriptomic analysis of microbial communities to investigate syntrophic interactions in the anaerobic digestion process

Microbial communities enacting the anaerobic digestion process are sustained by syntrophic relationships, whereby an exchange of compounds occurs between microbes to mutual benefit. The degradation of acetate by syntrophic acetate oxidizing bacteria (SAOB) via the Wood-Ljungdahl pathway is thought to provide hydrogenotrophic methanogens with hydrogen and carbon dioxide. This conversion, together with the subsequent metabolites consumption for methane production, constitutes one major syntrophy in the community. However, pinpointing the exact mechanisms underlying such syntrophy in real microbial ecosystems is still a matter of research. To this end, simplified inocula from anaerobic digesters were fed with either acetate or hydrogen and carbon dioxide. We employed genome-centric metagenomics to study the community via DNA and RNA sequencing, reconstructing 46 putative high-quality microbial genomes and predicting their functional potential. Abundance trends for the dominant organisms were verified via qPCR. The community was largely represented by Methanothermobacter wolfeii, a hydrogenotrophic methanogenic archaeon. This organism represented the majority of the community regardless of the feeding. Additionally, methanogenesis was active in all conditions, suggesting the fundamental role of SAOB in the community. A putative bifunctional SAOB and homoacetogen was found among the most abundant members of the community. Genome-centric metagenomics and metatranscriptomics analysis of the dominant syntrophes gave us insights into the key metabolic routes of CO2 methanation. In particular, the SAOB/homoacetogenic bacteria were suggested to use a novel alternative pathway for acetate interconversion in the different feeding conditions.