Metabolic Segregation and Characteristic Gene clusters of the Key Functional Populations in Anaerobic Digestion Consortia

Enrichment experiment integrated with genome-centric meta-omics analysis revealed function partition among populations in the three functional niches of the anaerobic digestion bioprocess: primary fermentation, secondary fermentation (syntrophic acetogenesis), hydrogenotrophic and acetoclastic methanogenesis. Accumulation of H2 as a metabolic intermediate originates mainly from primary fermentation. Formate, rather than H2, plays a key role in secondary fermentation, mediating interspecies electron transfer from the syntrophic oxidizing bacteria to the formate-utilizing methanogens. Both the flavin based electron bifurcating HydABC hydrogenase (Group A3 hydrogenase) and the ferredoxin-dependent GroupB hydrogenase are present and actively expressed in the primary fermenting bacteria, while both the cytosolic formate dehydrogenase and the membrane-bound formate dehydrogenase are absent in the primary fermenting bacteria; in comparison, the latter two types of formate dehydrogenase are present and actively transcribed in the secondary fermenting bacteria. Additionally, absence of the formate hydrogenlyase in both the primary fermenting bacteria and the secondary fermenting bacteria indicated limited interconversion of H2 and formate in those strict anaerobic bacteria. Such segregation of the electron carrier pools by H2 and formate in primary fermentation and in secondary fermentation, respectively, can benefit the syntrophic oxidizers with a higher tolerance to the accumulation of H2 from the co-occurring primary fermentation. In addition, metabolic specificity and characteristic gene clusters are noted for anaerobes of the different function niches enriched in this study, i.e., primary fermenting bacteria Clostridium FI21,22, syntrophic butyrate oxidizer Syntrophomoas FI3,4,7, syntrophic propionate oxidizer Smithellaceae DES18-25, formate- and H2-utilizing methanogen Methanobacteriaceae EA7, and acetoclastic methanogen Methanothrix soehngenii HA1,2,3.