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.
Subscribe to Journal
Get full journal access for 1 year
only $14.08 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Könneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546 (2005).
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E. & Oakley, B. B. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl Acad. Sci. USA 102, 14683–14688 (2005).
Wuchter, C. et al. Archaeal nitrification in the ocean. Proc. Natl Acad. Sci. USA 103, 12317–12322 (2006).
Leininger, S. et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809 (2006).
He, J. Z. et al. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ. Microbiol. 9, 2364–2374 (2007).
Schauss, K. et al. Dynamics of functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ. Microbiol. 11, 446–456 (2009).
Nicol, G. W. & Schleper, C. Ammonia-oxidising Crenarchaeota: Important players in the nitrogen cycle? Trends Microbiol. 14, 207–212 (2006).
Prosser, J. I. & Nicol, G. W. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ. Microbiol. 10, 2931–2941 (2008).
Francis, C. A., Beman, J. M. & Kuypers, M. M. New processes and players in the nitrogen cycle: The microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J. 1, 19–27 (2007).
Di, H. J. & Cameron, K. C. The use of a nitrification inhibitor, dicyandiamide (DCD), to reduce nitrate leaching from cow urine patches in a grazed dairy pasture under irrigation. Soil Use Manag. 18, 395–403 (2002).
Di, H. J. & Cameron, K. C. Mitigation of nitrous oxide emissions in spray-irrigated grazed grassland by treating the soil with dicyandiamide, a nitrification inhibitor. Soil Use Manag. 19, 284–290 (2003).
Amberger, A. Research on dicyandiamide as a nitrification inhibitor and future outlook. Commun. Soil Sci. Plant Anal. 20, 1933–1955 (1989).
Shen, J. P., Zhang, L. M., Zhu, Y. G., Zhang, J. B. & He, J. Z. Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ. Microbiol. 10, 1601–1611 (2008).
Hatzenpichler, R. et al. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl Acad. Sci. USA 105, 2134–2139 (2008).
Valentine, D. L. Adaptation to energy stress dictate the ecology and evolution of the Archaea. Nature Rev. Microbiol. 5, 316–323 (2007).
Mahmood, S. & Prosser, J. I. The influence of synthetic sheep urine on ammonia oxidizing bacterial communities in grassland soil. FEMS Microbiol. Ecol. 56, 444–454 (2006).
Stephen, J. R., McCaig, A. E., Smith, Z., Prosser, J. I. & Embley, T. M. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62, 4147–4154 (1996).
Kowalchuk, G., Stienstra, A., Heilig, G., Stephen, J. & Woldendorp, J. Changes in the community structure of ammonia-oxidizing bacteria during secondary secession of calcareous grasslands. Environ. Microbiol. 2, 99–110 (2000).
Horz, H. P., Barbrook, A., Field, C. B. & Bohannan, B. J. M. Ammonia-oxidizing bacteria respond to multifactorial global change. Proc. Natl Acad. Sci. USA 101, 15136–15141 (2004).
Di, H. J., Cameron, K. C. & Sherlock, R. R. Comparison of the effectiveness of a nitrification inhibitor, dicyandiamide (DCD), in reducing nitrous oxide emissions in four different soils under different climatic and management conditions. Soil Use Manag. 23, 1–9 (2007).
Rotthauwe, J. H., Witzel, K. P. & Liesack, W. The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63, 4704–4712 (1997).
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.
About this article
Cite this article
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). https://doi.org/10.1038/ngeo613
Responses of soil ammonia-oxidizing bacteria and archaea to short-term warming and nitrogen input in a semi-arid grassland on the Loess Plateau
European Journal of Soil Biology (2021)
Biological nitrification inhibition by sorghum root exudates impacts ammonia-oxidizing bacteria but not ammonia-oxidizing archaea
Biology and Fertility of Soils (2021)
N2O and NOy production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers
Water Research (2021)
Effects of biochar and 3,4-dimethylpyrazole phosphate (DMPP) on soil ammonia-oxidizing bacteria and nosZ-N2O reducers in the mitigation of N2O emissions from paddy soils
Journal of Soils and Sediments (2021)
Soil extracellular enzyme activities and the abundance of nitrogen-cycling functional genes responded more to N addition than P addition in an Inner Mongolian meadow steppe
Science of The Total Environment (2021)