Long‐Term Fertilisation Shapes the Distribution and N 2 O Reduction Potential of Clade I and Clade II N 2 O Reducers Along the Soil Profile in Rice Paddies

Long‐term fertilisation alters nitrous oxide (N 2 O) emissions from paddy soils, but its effects on the ecological roles of distinct N 2 O‐reducing clades remain unclear. Here, we investigated Clade I and Clade II N 2 O reducers using a 20‐year field experiment with unfertilized control (CK), chemical fertilizer (NPK), and organic fertilizer (OF) treatments. Clade II dominated the community, accounting for 72.4% of nosZ reads and 83.3% of recovered nosZ ‐containing draft metagenome‐assembled genomes (MAGs), and was enriched in carbohydrate‐active enzyme (CAZy) genes. However, Clade I abundance explained more variation in soil N 2 O reduction potential than Clade II (R 2 = 0.38 vs. 0.28). Structural equation modelling showed that fertilisation enhanced soil carbon and nitrogen status, which strongly promoted Clade I abundance ( β = 0.90). Clade I fully mediated fertilisation effects on N 2 O reduction potential, whereas Clade II showed only partial mediation. The two clades also exhibited contrasting vertical distributions: Clade I was relatively uniform throughout the soil profile, while Clade II displayed niche stratification, with different taxa dominating surface, middle, and deep layers. These results suggest distinct ecological strategies of the two N 2 O‐reducing clades and long‐term fertilisation differentially influences their distribution and contribution to the N 2 O sink function of rice paddy soils during the period examined.