Niche adaptation strategies of comammox Nitrospira in response to nitrogen addition in different types of soil

Comammox Nitrospira (CMX) is a novel discovered “one-step” nitrifying microorganism, and the understanding of its niche specialization and response to agricultural practices in intensive ecosystems is still in its infancy. In this study, we investigated the effect of CMX community activated by nitrogen (N) inputs and soil types on two long-term maize N fertilizer experiments in the main maize-producing areas of North China (calcareous fluvo-aquic soil) and Southwest China (acidic purple soil). CMX includes clade A and clade B, with clade B detected only in the purple soil. The results indicated that the abundance and alpha diversity of CMX in the purple soil were higher than those in fluvo-aquic soil. Greater network complexity and enhanced cooperation have led to a broader ecological niche for CMX in acidic purple soils, but not in fluvo-aquic soil. The clade A community were affected mainly by soil organic carbon (C), N contents in fluvo-aquic soil, while pH and the ratio of C:N were the primary factors for CMX in purple soil. Moreover, the alpha diversity and niche breadth of clade A in fluvo-aquic soil and clade B in the purple soil increased under optimal N application (148 kg N ha⁻¹ for fluvo-aquic soil,180 kg N ha⁻¹ for purple soil). Overall, these findings provide new insights into the adaptation mechanisms of CMX communities under distinct agricultural soil conditions and offers microbial perspective of optimizing N fertilizer management strategies. It refines our understanding of the microbial-soil nutrient cycling processes, promoting the development of future microbe-driven soil management strategies.