Nitrification, an essential process in global nitrogen cycling, has long been considered as a two-step process carried out by ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria (NOB), respectively. However, the discovery of complete ammonia oxidizers (“comammox”) revealed a new kind of nitrifiers in a recirculation aquaculture system and a deep oil exploration well system, and later studies showed that comammox may also exist in other ecosystems. This raised the question about the role of comammox in the nitrogen cycling and their specific niche compared to canonical nitrifiers. Here, we confirmed the existence of comammox in rice paddy soils sampled from a long-term free-air CO2 enrichment (FACE) plot by quantitative PCR. Then we conducted a microcosm experiment to investigate how different nitrifiers would response to various environment factors such as ammonia, oxygen and elevated CO2.
Results/Conclusions
We found that nitrifiers were all sensitive but responded differently to ammonia. The ammonia-oxidizing bacteria (AOB) preferred high ammonia concentrations while the comammox and ammonia-oxidizing archaea (AOA) could not tolerate such concentrations. However, compared to AOA, comammox were more resistant to high ammonia stress. Besides, we noticed that different nitrifiers had distinct responses to elevated CO2. Compared to the ambient soil group, we found that the abundance of AOB, AOA and clade A comammox decreased under the elevated CO2 group, while Nitrobacter were more abundant under the elevated CO2 group. Our work explored the niche differences among comammox and other nitrifiers and offered insights into the microbial mediation of soil N cycling under future climate change scenarios.