Ammonia-oxidizing archaea as dominant and active ammonia oxidizers in agricultural soils from Yangtze River estuary by DNA-SIP

Nitrification is a pivotal nitrogen transformation process in agricultural ecosystems, playing a crucial role in maintaining soil nitrogen balance and ensuring food security. The conversion of ammonia to nitrite—a rate-limiting step in nitrification—is catalyzed by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammox Nitrospira). However, the specific characteristics of ammonia oxidation across different agricultural soils remain poorly understood. In this study, we investigated the community composition and metabolic activity of ammonia oxidizers in four agricultural soils, including green vegetable land (GVL), wasteland farmland (WF), orange planting land (OPL) and sesame planting land (SPL). The results indicate that AOA exhibit a higher abundance compared to AOB and comammox Nitrospira, with groups Ⅰ.1a and Ⅰ.1b identified as the dominant group. Salinity, NH₃ and pH were found to significantly influence the community structure of AOA. Neutral model analysis showed that the community assembly of ammonia oxidizers was a stochasticity process (drift) in agricultural soils. Co-occurrence network in GVL and OPL exhibited higher network density and average degree compared to those in WF and SPL. However, a higher proportion of negative correlations was observed in WF and SPL. Stable isotope probing (DNA-SIP) analysis confirmed that ¹³C was predominantly assimilated by AOA-Ⅰ.1b, with minimal incorporation by AOB-Nitrosomonas and -Nitrosospira. This study provides comprehensive insights into the spatial distribution and activity of ammonia oxidizers in the agricultural soils of the Yangtze River estuary, contributing to a deeper understanding of nitrogen cycling in these ecosystems.