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

The recently discovered complete ammonia oxidizer (comammox Nitrospira ) contains clades A and B that were established 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 multi-site research on comammox Nitrospira in paddy soils. In this study, we conducted a survey of 36 paddy soil sites, aiming to understand the comammox Nitrospira community structure, abundance, and diversity and the degree to which they are affected by environmental factors at a large scale. Comammox Nitrospira was 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 the abundance of comammox Nitrospira including pH, soil organic matter, total carbon, total nitrogen, latitude, mean annual temperature and mean annual precipitation ( P < 0.05). 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 habitat. 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; this may be related to the unique habitat of the paddy field. In contrast, comammox Nitrospira clade B showed no clear habitat dependence. These results support the wide distribution and high abundances of comammox Nitrospira in paddy soils, and provide novel insight into nitrogen cycling and nutrient management in agricultural ecosystems.