Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery

During anaerobic digestion (AD) the microbial population is key to methane production in biogas plants, yet its composition is poorly characterized. This study aimed to uncover microbial dynamics and transcriptional adaptations during mesophilic AD of maize silage and slurry. While one digester performed under optimal conditions, we also evaluated the microbiome during a temperature drop mediated process failure accompanied by acidification and how it contributed to a process recovery. Composition and pathway activities were analyzed by whole genome shotgun (WGS) and metatranscriptome sequencing, respectively. A biodiversity of 112 species was observed with noticeable shifts over process time. Although we could identify four distinct groups of microbes with a correlating versatility according to substrate and to process disturbance, we also monitored tremendous effects on gene expression especially of the archaeal methane metabolism. Particularly, the expression of acetogenotrophic methanogenesis related genes was identified to be relevant for process regeneration.