Comammox Nitrospira dominates autotrophic nitrification in paddy fields under long-term fertilization

Abstract

Fertilization significantly affects ammonia oxidation, a pivotal process governing nitrification in paddy soils. Nevertheless, the ecological niches of ammonia oxidizing-archaea (AOA), ammonia oxidizing-bacteria (AOB), and complete ammonia-oxidizers (Comammox), as well as their relative contributions to ammonia oxidation under long-term fertilization conditions, remain poorly understood. Here, the activity, community structure, and abundance of these ammonia-oxidizers were examined in rice fields under three long-term (35 years) fertilization treatments (CK: no fertilizer, NPK: inorganic fertilizer, SNPK: straw returning combined with inorganic fertilizer) across four rice growth periods. It was observed that AOB activity dominated ammonia oxidation under CK treatment, accounting for 52.65 % of the total ammonia oxidation activity. In contrast, Comammox activity dominated ammonia oxidation under both NPK and SNPK treatments, accounting for 65.44 % and 63.29 % of total ammonia oxidation activity, respectively. The contribution of AOA activity to ammonia oxidation was the lowest (0.67 %-2.25 %) under the three fertilization treatments. Compared to CK, both treatments significantly increased abundance of AOA, AOB, and Comammox, and AOB exhibited the strongest stimulation (943.59 %-1445.83 %) by fertilization. Community structure of AOB and Comammox showed a stronger response to fertilization compared with AOA. Partial least squares analysis indicated that fertilization indirectly affected the activity of three types of ammonia-oxidizers by changing the soil physicochemical properties (e.g., pH, organic carbon content, and NH₄⁺-N content) and the community structure of ammonia-oxidizers. Overall, our findings highlight the importance of Comammox in nitrification in long-term fertilized paddy soils, contributing to a better comprehension of the roles of different types of ammonia-oxidizers in nitrogen cycle.