Methanogenesis in biogas reactors under inhibitory ammonia concentration requires community-wide tolerance

Ammonia (NH₃) inhibition represents a major limitation to methane production during anaerobic digestion of organic material in biogas reactors. This process relies on co-operative metabolic interactions between diverse taxa at the community-scale. Despite this, most investigations have focused singularly on how methanogenic Archaea respond to NH₃ stress. With a high-NH₃ pre-adapted and un-adapted community, this study investigated responses to NH₃ inhibition both at the community-scale and down to individual taxa. The pre-adapted community performed methanogenesis under inhibitory NH₃ concentrations better than the un-adapted. While many functionally important phyla were shared between the two communities, only taxa from the pre-adapted community were robust to NH₃. Functionally important phyla were mostly comprised of sensitive taxa (≥ 50%), yet all groups, including methanogens, also possessed tolerant individuals (10–50%) suggesting that potential mechanisms for tolerance are non-specific and widespread. Hidden Markov Model–based phylogenetic analysis of methanogens confirmed that NH₃ tolerance was not restricted to specific taxonomic groups, even at the genus level. By reconstructing covarying growth patterns via network analyses, methanogenesis by the pre-adapted community was best explained by continued metabolic interactions (edges) between tolerant methanogens and other tolerant taxa (nodes). However, under non-inhibitory conditions, sensitive taxa re-emerged to dominate the pre-adapted community, suggesting that mechanisms of NH₃ tolerance can be disadvantageous to fitness without selection pressure. This study demonstrates that methanogenesis under NH₃ inhibition depends on broad-scale tolerance throughout the prokaryotic community. Mechanisms for tolerance seem widespread and non-specific, which has practical significance for the development of robust methanogenic biogas communities.