Substrate Affinity as a Key Adaptive Mechanism in Ammonia Oxidation under Acidification

Ammonia oxidation, mediated primarily by ammonia-oxidizing archaea (AOA) and bacteria (AOB), is a cornerstone of the nitrogen cycle of aquatic ecosystems. However, the impact of increasing acidification on this process remains unresolved, with field observations across diverse aquatic environments yielding contradictory results. Here, we present a comprehensive investigation combining pH manipulation experiments across multiple ecosystems—including a freshwater reservoir, estuaries, and the oligotrophic open ocean—and controlled laboratory experiments using the AOA isolate Nitrosopumilus maritimus SCM1. Our results reveal an unexpected adaptive response: both AOA and AOB enhance their substrate affinity under acidified conditions, counteracting the anticipated reduction in ammonia availability. This respense defies to traditional paradigm that predicts diminished ammonia oxidation under acidified conditions and highlights substrate affinity as a key regulator of microbial activity. Notably, in AOA-dominated environments, this adaptation sustains ammonia oxidation rates despite acidification-induced substrate scarcity. These results reconcile previously inconsistent observations and establish a mechanistic framework for predicting ammonia oxidizer dynamics in acidifying aquatic systems. By incorporating substrate affinity into predictive models of nitrogen cycling, this study offers critical insights into the resilience of biogeochemical processes under future acidification scenarios.