Reversible Inhibition of Ammonia Monooxygenase by 1,9-Decanediol Triggers a RegB-RegA-Associated Energy Crisis and Stress Response in Nitrosomonas europaea

Abstract 1,9-decanediol, a rice-derived biological nitrification inhibitor (BNI) suppresses soil nitrification and nitrous-oxide emissions, but the mechanisms of action against ammonia-oxidizing bacteria remain unclear. Combining physiology and transcriptomics in Nitrosomonas europaea, we show that a dose-dependent and reversible inhibition of ammonia oxidation by 1,9-decanediol by up to 44.7%, while maintaining high cell viability. Transcriptomics reveal that inhibition of ammonia monooxygenase (AMO) triggered an energy crisis, downregulating the respiratory complexes (nuo, coxA/B, atp). We propose that the RegB-RegA two-component system senses the redox imbalance and contributes to a biosynthesis-to-defense transition, marked by an 8.9-fold induction of amoC3 and suppression of ribosomal and amino-acid synthesis. Activation of RND-efflux pumps and chemotaxis enable active counteraction and escape from the stressor. This study provides crude-enzyme-based evidence for AMO as a primary target of a reversible BNI and integrates it with genome-wide transcriptomics, offering molecular insight into designing nature-based nitrification inhibitors and BNI-enhanced crops.