Nitrogen fertilization induced changes in ammonia oxidation are attributable mostly to bacteria rather than archaea in greenhouse-based high N input vegetable soil

• Potential ammonia oxidation decreased significantly with increasing N fertilization rates.
• 49.9–77.2% of potential ammonia oxidation was inhibited in the presence of bacterial inhibitors.
• Abundance of AOB and AOA were significantly decreased at the highest N fertilization rate.
• PH is the predominant factor affecting potential ammonia oxidation and abundance of AOA.
• Changes in community composition were more pronounced in AOB than in AOA.

Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing bacteria (AOB) and archaea (AOA) and their differential contribution to ammonia oxidation, particularly in greenhouse-based high N input vegetable soils. Potential ammonia oxidation (PAO) of these vegetable soils was evaluated under five levels of N fertilization (with urea) in the presence or absence of the bacterial protein synthesis inhibitors kanamycin and gentamicin. Abundance and community composition of AOB and AOA were evaluated by quantitative polymerase chain reaction (PCR) and clone libraries. The five annual N fertilization rates studied were 100% (N870: 300, 270 and 300 kg N ha−1 for tomato, cucumber and celery, respectively), 80% (N696), 60% (N522), 40% (N348) and 0% (N0) of the conventional N rate. The PAO decreased significantly with increasing N fertilization rates irrespective of the presence of kanamycin plus gentamicin. PAO was significantly lower in the presence than in the absence of kanamycin plus gentamicin, and was decreased by 71.9% under N0, 77.2% under N348, 54.9% under N522, 49.9% under N696, and 51.6% under N870. The abundance of bacterial and archaeal amoA genes was significantly decreased at the highest N fertilization rate. The clone sequences of AOB and AOA were mostly affiliated with the genus Nitrosospira and group 1.1b thaumarchaeota. Changes in community composition were more pronounced in AOB than in AOA after long-term (6-year) N fertilization. Our results suggest that AOB may play a more important role than AOA in NH3 oxidation in such high N input vegetable soils.