Direct ammonia oxidation (Dirammox) is favored over cell growth in <i>Alcaligenes ammonioxydans</i> HO‐1 to deal with the toxicity of ammonium

Bacteria capable of direct ammonia oxidation (Dirammox) play important roles in global nitrogen cycling and nutrient removal from wastewater. Dirammox process, NH 3 → NH 2 OH → N 2 , first defined in Alcaligenes ammonioxydans HO‐1 and encoded by dnf gene cluster, has been found to widely exist in aquatic environments. However, because of multidrug resistance in Alcaligenes species, the key genes involved in the Dirammox pathway and the interaction between Dirammox process and the physiological state of Alcaligenes species remain unclear. In this work, ammonia removal via the redistribution of nitrogen between Dirammox and microbial growth in A. ammonioxydans HO‐1, a model organism of Alcaligenes species, was investigated. The dnfA , dnfB , dnfC , and dnfR genes were found to play important roles in the Dirammox process in A. ammonioxydans HO‐1, while dnfH , dnfG , and dnfD were not essential genes. Furthermore, an unexpected redistribution phenomenon for nitrogen between Dirammox and cell growth for ammonia removal in HO‐1 was revealed. After the disruption of the Dirammox in HO‐1, more consumed NH 4 + was recovered as biomass‐N via rapid metabolic response and upregulated expression of genes associated with ammonia transport and assimilation, tricarboxylic acid cycle, sulfur metabolism, ribosome synthesis, and other molecular functions. These findings deepen our understanding of the molecular mechanisms for Dirammox process in the genus Alcaligenes and provide useful information about the application of Alcaligenes species for ammonia‐rich wastewater treatment.