Ammonia oxidizers offset acidification stress via adaptive substrate affinity in aquatic ecosystems

Ammonia oxidation, a critical nitrogen cycle process, exhibits contradictory responses to aquatic acidification, and the underlying mechanism remains unresolved. Here, through pH manipulation experiments across diverse ecosystems and with a model ammonia-oxidizing archaea species, Nitrosopumilus maritimus strain SCM1, we discover a unifying adaptive mechanism: acidification triggers a compensatory increase in substrate affinity in ammonia-oxidizing microorganisms. This enhancement counteracts the reduction in ammonia availability, with the magnitude of increase being significantly greater in ammonia-oxidizing archaea than in ammonia-oxidizing bacteria. Consequently, in ammonia-oxidizing archaea-dominated systems, this adaptation can sustain or even stimulate oxidation rates under moderate acidification, while ammonia-oxidizing bacteria-dominated systems experience a decline. By incorporating this affinity response into models, we accurately reconcile prior disparate field observations. We thus establish the regulation of substrate affinity as a key determinant of microbial resilience, providing a framework for predicting nitrogen cycle dynamics under future acidification.