This study investigates the physiological response to salinity stress in a Candidatus Methanoperedens enriched freshwater bioreactor

Climate change driven sea level rise threatens freshwater ecosystems and elicits salinity stress in native microbiomes. Methane emissions in those systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. Direct exposure to salt suggested that methanotrophic archaea were already inhibited at 1%. However, during gradual increase of salt to 3% in a laboratory-scale reactor over 12 weeks, the culture continued to oxidize methane. Gene expression profiles and dedicated metabolomics identified the pathway for salt stress response and the osmolyte of anaerobic methanotrophic archaea: N(e)-acetyl-ß-L-lysine. An extensive phylogenomic analysis on N(e)-acetyl-ß-L-lysine producing enzymes revealed that they are widespread across the tree of life, and indicates a potential horizontal gene transmission and link to giant BORG extrachromosomal elements. Physicochemical analysis of the bioreactor biomass indicated the presence of sialic acids and intracellular polyhydroxyalkanoate consumption by anaerobic methanotrophs during salt stress.