Background: Syntrophic cooperation is essential for the efficient degradation of volatile fatty acids (acetate/propionate) in biogas reactors operating at high ammonia concentration. There is a shift in microbial community when biogas systems transits from no/low ammonia to high ammonia settings. When acetoclastic methanogens are inhibited by increasing ammonia levels, hydrogenotrophic methanogenesis in close syntrophic cooperation with acetate/propionate oxidizer shoulders the role as main microbes involved in the final steps of anaerobic digestions. But the molecular mechanisms underlying their ability to tolerate ammonia is not very well understood. How does the immediate response to a shock increase in ammonia differ to the long-term strategies to deal and prosper in high ammonia settings. Methodology/Experimental setup In this paper we aim to study the genetic expression after subjecting syntrophic acid degrading cultures(acetate/propionate) to a drastically increased ammonia concentration (0.1M -> 0.4M) and extracting RNA either shortly following the ammonia spike (hours) or after the communities has acclimatized to high ammonia concentration and resumed acid degradation (days/weeks) Negative controls in form of no ammonia spike will be extracted from at the point of the immediate RNA extraction after ammonia spiking. Differential expression analysis of mRNA transcripts between the negative control, immediate response and long-term response will be analysed using Deseq2. In addition NMR will be used to measure accumulation of compatible solutes/osmolytes under identical conditions to the RNA extraction experiment. This data will complement the gene expression patterns observed in the RNA data