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

- Substrate and temperature specific groups of microbes identified.
- Methanoculleus sp. Eu01 impaired in hydrogenotrophic pathway by low temperature.
- Recovery from acidification through rapid induction of acetogenic pathway.
- Methanosarcina sp. Eu06 and novel taxon Eu43 essentially involved in recovery.
- Full compositional and functional restauration of microbiome within days.

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, the investigations 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 four distinct groups of microbes could be identified with a correlating versatility according to substrate and to process disturbance, also tremendous effects on gene expression were monitored especially of the archaeal methane metabolism. Particularly, the expression of acetogenotrophic methanogenesis related genes was identified to be relevant for process regeneration.