Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils


The oxidation of ammonia to nitrate, nitrification, is a key process in the nitrogen cycle. Ammonia-oxidizing archaea are present in large numbers in the ocean1,2,3 and soils4,5,6, suggesting a potential role for archaea, in addition to bacteria, in the global nitrogen cycle7,8. However, the importance of archaea to nitrification in agricultural soils is not well understood4. Here, we examine the contribution of ammonia-oxidizing archaea and bacteria to nitrification in six grassland soils in New Zealand using a quantitative polymerase chain reaction. We show that although ammonia-oxidizing archaea are present in large numbers in these soils, neither their abundance nor their activity increased with the application of an ammonia substrate, suggesting that their abundance was not related to the rate of nitrification. In contrast, the number of ammonia-oxidizing bacteria increased 3.2–10.4-fold and their activity increased 177-fold, in response to ammonia additions. Indeed, we find a significant relationship between the abundance of ammonia-oxidizing bacteria and the rate of nitrification. We suggest that nitrification is driven by bacteria rather than archaea in these nitrogen-rich grassland soils.

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Figure 1: AOA and AOB amoA gene copy numbers in the six soils in the control treatments at the start of the incubation experiment.
Figure 2: Dynamics of AOB and AOA populations and nitrification rate in the Waikato soil in the incubation study.
Figure 3: Relationships between the amount of NO3–N produced and ammonia oxidizer populations from the incubation study.
Figure 4: RNA copy numbers of the AOB and AOA populations in the WK soil as affected by applications of cow urine-N and DCD after 49 days of incubation.


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We would like to thank the New Zealand Foundation for Research, Science and Technology (FRST) for funding, R. Monaghan, S. Ledgard and M. Sheppard of AgResearch and B. Thorrold and D. Waugh of Dairy NZ for assistance with soil sampling, and E. Gerard and S. Brock of AgResearch and J. Lei, S. Moore, C. Barlow and T. Hendry of Lincoln University for technical support.

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The project was conceived and led by H.J.D. and K.C.C. The manuscript was written by H.J.D., assisted by the co-authors. J.P.S., C.S.W., M.O., S.B. and J.Z.H. contributed to the sample analysis.

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Correspondence to H. J. Di or J. Z. He.

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Di, H., Cameron, K., Shen, J. et al. Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nature Geosci 2, 621–624 (2009).

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