Ammonia and nitrite are nitrogenous pollutants in aquaculture effluents, which pose a major threat to the health of aquatic animals. In this study, we developed a nitrogen conversion strategy based on synthesis of poly-γ-glutamic acid (γ-PGA) by Bacillus subtilis NX-2. The nitrogen removal efficiency of NX-2 was closely related to synthesizing γ-PGA, and was positively correlated with the inoculum level. The degradation rates of ammonia nitrogen and nitrite at 104 CFU/mL were 84.42 % and 62.56 %, respectively. Through adaptive laboratory evolution (ALE) experiment, we obtained a strain named ALE 5 M with ammonia degradation rate of 98.03 % and nitrite of 93.62 % at the inoculum level of 104 CFU/mL. Transcriptome analysis showed that the strain was more likely to produce γ-PGA after ALE. By enzyme activity and qPCR analysis, we confirmed that ALE 5 M degraded ammonia nitrogen through γ-PGA synthesis, which provided a new way for nitrogen removal in aquaculture water.