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.