Different roles of rhizosphere effect and long-term fertilization in the activity and community structure of ammonia oxidizers in a calcareous fluvo-aquic soil

► N fertilizations increased PNA and AOB population size and diversity. ► Manure enhanced AOA population size in both bulk soil and the rhizosphere. ► PNA was correlated with the abundance and community structure of AOB rather than AOA. ► Rhizosphere effect, not fertilization, plays a key role in shaping the AOA community.