Temporal dynamics of abundant and rare nitrifying and denitrifying communities in paddy soils under wetting-drying cycles

Wetting-drying cycles, a common water-saving practice in paddy soils, significantly influence soil microbial communities that regulate nitrogen cycling through nitrification and denitrification. However, the responses of nitrifying and denitrifying communities to these cycles, especially the roles of abundant and rare subcommunities, remain poorly understood. Here, we used next-generation sequencing of functional genes (AOA, AOB, nirK, and nirS) to explore the temporal dynamics of nitrifier and denitrifier communities during wetting-drying cycles. Our results revealed divergent response patterns: nirS-type denitrifiers exhibited unique dynamics compared to AOA, AOB, and nirK communities. Abundant taxa in AOA, AOB, and nirS communities showed more pronounced changes than their rare counterparts, while nirK communities exhibited the opposite pattern. The higher abundance of AOB compared to AOA highlighted their dominant role in nitrification. Strong correlations among the four N-cycling genes indicated complex microbial interactions and coordinated responses to environmental fluctuations. These findings enhance our understanding of microbial-driven N cycling in paddy soils and inform strategies for sustainable agriculture management.