Nitrifying and denitrifying microbes exhibit distinct community structure and activity responses to different crop rotation systems in subtropical paddy soils

The adverse impacts of double-season rice cultivation on soil health and crop yield can be alleviated by crop rotation. However, the mechanisms by which biotic and abiotic factors influence microbial nitrogen cycling under different crop rotation systems remain unclear. Here, we evaluated the impact of crop rotation in paddy soils on the community abundance, composition, and activity of nitrifying microbes (ammonia-oxidizing archaea and bacteria (AOA and AOB)) and denitrifying microbes (nirK- and nirS-denitrifiers). A 6-year field experiment was performed with four crop rotation systems: (1) double rice as a control, (2) middle-season rice–fallow rotation (MR), (3) middle-season rice–oilseed rape rotation (MROR), and (4) middle-season rice–pak choi–oilseed rape rotation (MRPOR). AOB abundance increased significantly in MROR and MRPOR treatments, whereas AOA abundance decreased significantly in MROR. nirS gene abundance was significantly lower in MROR and MRPOR treatments, whereas nirK gene abundance was significantly lower in MR and MRPOR treatments. AOB and nirK gene community structures were significantly altered by crop rotation; this relationship was closely correlated with soil water content and NO₃⁻-N concentration. For MROR and MRPOR treatments, potential nitrification activity was significantly increased and positively correlated with AOB abundance, whereas denitrification enzyme activity was significantly decreased and correlated with nirK and nirS community structure. Therefore, nitrifiers and denitrifiers exhibit distinct responses to crop rotation in paddy soils, which may influence microbial nitrogen cycling. These findings have practical implications for selecting appropriate cropping regimes.