Niche Adaptation of Ammonia-Oxidizing Bacteria Nitrosomonas in Partial Nitrification System: Keystone Species and Unique Survival Strategies

Partial nitrification (PN) is of practical significance for achieving autotrophic nitrogen removal with impressive economic and environmental benefits. While most studies focused on the selective suppression of nitrite-oxidizing bacteria, maintaining stable ammonia oxidation as the primary source of nitrite remains equally critical but largely underexplored. Herein, we identified Nitrosomonas eutropha as the keystone species dominating ammonia oxidation in free ammonia treatment-based PN systems, comprising over 40% of the nitrifier community. Combined metagenomic and metaproteomic analyses revealed that N. eutropha orchestrated multiple cellular processes and reallocated intracellular resources to adapt to the PN niche. Specifically, enhanced primary metabolism and stress response systems within N. eutropha were observed, alongside significant upregulation of the protein synthesis machine, such as ribosomal proteins and translation factors. Notably, overexpression of the cell division protein FtsA was detected, which is known to disrupt Z-ring formation and inhibit cell division. These results suggest a protein synthesis-centered survival strategy, wherein N. eutropha maintained robust protein synthesis capacity while retarding propagation. This strategy differs fundamentally from conventional microbial stress responses, which typically involve the downregulation of protein synthesis to conserve resources. These findings provide multidimensional insights into the survival strategies of Nitrosomonas in PN systems, with practical implications for both understanding molecular responses to environmental stress and optimizing engineering strategies for autotrophic nitrogen removal.