Comammox plays a functionally important role in the nitrification of rice paddy soil with different nitrogen fertilization levels

Abstract

Chemoautotrophic ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizers (comammox) catalyze ammonia oxidation; however, quantifying their individual gross ammonia oxidation activities in complex soil ecosystems remains elusive. In this study, we investigated the nitrifying population and community dynamics in response to fertilization in paddy soil under long-term treatment with different urea concentrations (0, 100, 200, and 300 kg N ha−1; designated N0, N100, N200, and N300, respectively). The community structure of nitrifiers, including comammox, was changed by long-term N fertilizers input, which also enhanced AOB abundance and comammox clade A/B abundance ratio, whereas it did not affect AOA abundance. Nevertheless, the microbial population sizes and community compositions remained largely similar following short-term fertilization throughout one rice-growing season. Furthermore, by employing a 15NO3− pool dilution technique in combination with chlorate and 1-octyne inhibition, we conducted a soil microcosm incubation without substrate supplementation to distinguish the relative contribution of comammox to gross ammonia oxidation from those of AOA and AOB. Comammox exhibited higher nitrification activity in soils treated with more N fertilizers, with the contribution increasing from 34 % (N0) to 75 % (N300), although its abundance was not dominant. This could be attributed to the repeated N-based fertilization, which reduced the soil pH, thereby decreasing the soil-free ammonia concentration. In contrast, the contribution of AOA declined from 57 % (N0) to 19 % (N300), while that of AOB only accounted for a minor fraction (<25 %) despite being in high abundance. Altogether, our findings provide evidence that the activity of nitrifying guilds is more valuable than their abundance and provide insights into the potential functional significance of comammox in the nitrification process in rice paddy systems.