The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by ¹³CO₂ after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the ¹³C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the ¹³C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that ¹³CO₂ assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested.

The impact of management practices on the net global warming potential (GWP) and greenhouse gas intensity (GHGI) of rice cropping systems is not well documented. A field experiment was established in 2009 to gain insight into the net ecosystem carbon budget and the net GWP and GHGI on the crop seasonal scale over two cycles of rice–wheat rotations. With the local farmer's practices (FP) as the control, three integrated soil–crop system management (ISSM) practices at different nitrogen (N) application rates were established – ISSM-N1, ISSM-N2 and ISSM-N3 – for improvement of rice yield and agronomic nitrogen use efficiency (NUE). Compared with the FP, the rice yields significantly increased by 8.2%, 18% and 31%, while the agronomic NUE increased by 68%, 74% and 99% for ISSM-N1, ISSM-N2 and ISSM-N3, respectively. Within the three ISSM practices averaged over the two cycles, the soil organic carbon sequestration potentials, CH4 and N2O emissions were estimated to be 0.089–0.67tCha−1yr−1, 166–288kgCH4Cha−1yr−1 and 4.27–5.47kgN2ONha−1yr−1, respectively. Compared to the net GWPs (8.36tCO2eqha−1yr−1) and GHGI (0.58kgCO2eqkg−1 grain) from the FP, the ISSM-N1 and ISSM-N2 reduced both the net GWPs and GHGIs to some extent, indicating that GHG mitigation can be simultaneously achieved with improved food production and NUE. Although it produced similar GHGIs, the ISSM-N3 increased the net GWPs by 16% compared to the FP, indicating that more research is required on ISSMs for mitigating GHGs to further increase the grain yield and NUE in rice agriculture