Genome recovery and metatranscriptomic confirmation of functional acetate-oxidizing bacteria from enriched anaerobic biogas digesters

In many cases, it is difficult to isolate the key microbial organisms from their communities present in natural environments. Metagenomic methods can recover near-complete genomes of the dominant microbial organisms in communities, and metatrancriptomic data could further reveal important genes and pathways related to their functions. In this study, three draft genomes of Clostridium ultunense-like bacteria were recovered based on metagenomic analyses, which is an essential syntrophic acetate-oxidizing bacteria (SAOB) member for maintaining high methane production in high-ammonium biogas digesters but difficult to isolate from its syntrophic partners. Firstly, syntrophic acetate-oxidizing bacteria in a microbial community series were enriched from a biogas digester by adding sodium acetate in the medium. Global analyses of C. ultunense suggested that it would combine the pyruvate-serine-glycine pathway and part of the Wood–Ljungdahl pathway for syntrophic acetate oxidization. Moreover, metatranscriptomic analyses showed that all of the genes of the proposed syntrophic acetate-oxidizing pathway present in the genome were actively transcribed in the microbiota. The functional bacterial enrichment and refined assembly method identify rare microbial genome in complex natural microbiota, which help to recover the syntrophic acetate-oxidizing pathway in C. ultunense strains in this study. [Display omitted] •Syntrophic acetate-oxidizing bacteria and their potential syntrophic acetate-oxidizing pathway were investigated.•A biogas digester series dominated with Clostridium ultunense were enriched from one biogas digester.•Three draft C. ultunense genomes were recovered from the enriched microbiota.•Syntrophic acetate-oxidizing pathway combined the pyruvate-serine-glycine pathway and part of the W-L pathway was proposed.•The new proposed pathway was demonstrated by the metatranscriptomic analyses of the enriched microbiota.