Main environmental drivers of abundance, diversity and community structure of comammox Nitrospira in paddy soils

The recently discovered complete ammonia oxidizers comammox Nitrospira contain clades A and B that can establish an independent one-step nitrification process; however, little is known about their environmental drivers or habitat distributions in agricultural soils. Previous studies on comammox Nitrospira in paddy soils have mainly focused on small-scale samples, and there is a lack of multisite research on comammox Nitrospira in paddy soils. In this study, we conducted a survey of 36 paddy soils to understand the community structure, abundance, and diversity of comammox Nitrospira and the degree to which they are affected by environmental factors at a large scale. Comammox Nitrospira were found to be widely distributed among the paddy soils. The abundance of comammox Nitrospira clade A was mostly lower than that of clade B, whereas its diversity was mostly higher than that of clade B. Correlation analysis showed that multiple factors affected (P < 0.05) the abundance of comammox Nitrospira, including soil pH, organic matter, total carbon, and total nitrogen, latitude, mean annual temperature, and mean annual precipitation. Moreover, there was a clear relationship between the comammox Nitrospira community and habitat, indicating that some amplicon sequence variants (ASVs) had a unique dominant position in specific habitats. Phylogenetic analysis showed that the ASVs of comammox Nitrospira clade A clustered with the known sequences in the paddy soils and were significantly different from the known sequences in other habitats, which may be related to the unique paddy field habitat. In contrast, comammox Nitrospira clade B showed no clear habitat dependence. These results support the wide distribution and high abundance of comammox Nitrospira in paddy soils and provide novel insights into nitrogen cycling and nutrient management in agricultural ecosystems.