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Effects of heavy metals on aerobic denitrification have been poorly understood compared with their impacts on anaerobic denitrification. This paper presented effects of four heavy metals (Cd(II), Cu(II), Ni(II), and Zn(II)) on aerobic denitrification by a novel aerobic denitrifying strain Pseudomonas stutzeri PCN-1. Results indicated that aerobic denitrifying activity decreased with increasing heavy metal concentrations due to their corresponding inhibition on the denitrifying gene expression characterized by a time lapse between the expression of the nosZ gene and that of the cnorB gene by PCN-1, which led to lower nitrate removal rate (1.67∼6.67 mg L h), higher nitrite accumulation (47.3∼99.8 mg L), and higher NO emission ratios (5∼283 mg L/mg L). Specially, promotion of the nosZ gene expression by increasing Cu(II) concentrations (0∼0.05 mg L) was found, and the absence of Cu resulted in massive NO emission due to poor synthesis of NO reductase. The inhibition effect for both aerobic denitrifying activity and denitrifying gene expression was as follows from strongest to least: Cd(II) (0.5∼2.5 mg L) > Cu(II) (0.5∼5 mg L) > Ni(II) (2∼10 mg L) > Zn(II) (25∼50 mg L). Furthermore, sensitivity of denitrifying gene to heavy metals was similar in order of nosZ > nirS ≈ cnorB > napA. This study is of significance in understanding the potential application of aerobic denitrifying bacteria in practical wastewater treatment.