Evidence of complete ammonia-oxidizing microbial communities and their contribution to N2O emissions in typical vegetable fields across China

No information is available for the newly found complete ammonia-oxidizing bacteria (COX) under globally intensified agriculture. In addition to the canonical ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), few studies have evaluated the structure and ecological niche of the community of COX. No information is available on their relative contributions to the ammonia oxidation process and related nitrous oxide (N2O) emissions in intensively managed vegetable fields. Therefore, in this study, fourteen soil samples were collected from vegetable fields across mainland China covering four climatic zones with distinct soil pH conditions. Two sets of microcosm incubations were combined to determine the rate of ammonia oxidation and N2O emissions distinguishing AOA, AOB and COX. The results indicated that COX coexisted with canonical ammonia-oxidizing microorganisms and its abundance was 1–4 orders of magnitude higher than those of AOA and AOB. COX abundance was highest in the subtropics and lowest in the tropics, whereas the ratio of COX to total ammonia-oxidizing microorganisms was highest in the tropics. The average contribution of COX to ammonia oxidation rate and N2O emission was 17.0% and 19.5%, respectively, while AOA contributed 47.1% to ammonia oxidation and AOB contributed 43.2% to N2O emissions. Interestingly, the contribution of COX to N2O emissions exceeded that of AOB in tropic acidic and AOA in subtropic alkaline soils. Based on high-throughput sequencing, the dominant genera of AOA, AOB, and COX were Nitrosopumilus, Nitrosospira, and Nitrospira, respectively. Reyranella and Rudaea were detected as a novel genus from COX. Furthermore, the N2O emissions were significantly positively correlated with Ktedonobacter in AOB, and negatively correlated with Nitrosomonas in AOB and Nitrospira in COX. In summary, COX coexisted with AOA and AOB while showed limited direct influence, but competed with AOA and AOB through ecological niche, which altered nitrification and N2O emissions in intensified vegetable fields.