Abstract
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.
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Acknowledgements
This work was financially supported by the National Science Foundation of China (40971153 to ZJ), the National High-Tech R&D Program (863) (2009AA02Z310 to JX), the Knowledge Innovation Programs of the Chinese Academy of Sciences (KZCX2-YW-BR-06 to ZJ) and the E-Science Program of the Chinese Academy of Sciences (INFO-115-D01-Z006 to JX and ZJ). We want to extend our gratitude to Professor Weixing Ding for sampling assistance at the Feng Qiu State Key Experimental Station for Ecological Agriculture.
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Xia, W., Zhang, C., Zeng, X. et al. Autotrophic growth of nitrifying community in an agricultural soil. ISME J 5, 1226–1236 (2011). https://doi.org/10.1038/ismej.2011.5
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DOI: https://doi.org/10.1038/ismej.2011.5
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