Metabolic Segregation and Functional Gene Clusters in Anaerobic Digestion Consortia

Abstract

Enrichment experiment integrated with genome-centric meta-omics analysis revealed that metabolic specificity, rather than metabolic flexibility, governs the anaerobic digestion (AD) ecosystem. This study provides new insights into interspecies electron transfer in the AD process, highlighting a segregation in the metabolism of H2 and formate. Our findings indicate that H2 serves as the primary electron sink for recycling redox cofactors, NAD and oxidized ferredoxin (Fdox), during primary fermentation. In contrast, formate predominates in the co- occurring secondary fermentation, particularly under conditions of elevated H2 concentrations. Notably, no evidence of biochemical interconversion between H2 and formate was identified in the primary fermenting bacteria or in syntrophs enriched in this study. This segregation of H2 and formate metabolism likely benefit the anaerobic oxidation of butyrate and propionate with a higher tolerance to H2 accumulation. Furthermore, this study underscores the functional partitioning among microbial populations within key niches of the AD bioprocess: primary fermentation, secondary fermentation (syntrophic acetogenesis), hydrogenotrophic methanogenesis, and acetoclastic methanogenesis. Through genome-centric analysis of the AD microbiome, we identified several key functional gene clusters, highlighting the potential for improving genome-centric genotype-phenotype correlations, which is particularly valuable for strict anaerobes that remain challenging to isolate and characterize in pure culture.