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

ABSTRACT: Ammonia (NH(3)) 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 NH(3) stress. With a high-NH(3) pre-adapted and un-adapted community, this study investigated responses to NH(3) inhibition both at the community-scale and down to individual taxa. The pre-adapted community performed methanogenesis under inhibitory NH(3) 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 NH(3). 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 NH(3) 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 NH(3) tolerance can be disadvantageous to fitness without selection pressure. This study demonstrates that methanogenesis under NH(3) 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. KEY POINTS: • Ammonia pre-adaptation allows for better methanogenesis under inhibitory conditions. • All functionally important prokaryote phyla have some ammonia tolerant individuals. • Methanogenesis was likely dependent on interactions between tolerant individuals. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00253-023-12752-5.