Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Archaea predominate among ammonia-oxidizing prokaryotes in soils

Abstract

Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity1,2. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Archaeal amoA genes outnumber bacterial amoA genes in topsoils and in deeper layers.
Figure 2: Isoprenoidal tetraether lipids in soils and correlation to amoA gene copies.
Figure 3: amoA cDNA copies and their AOA:AOB ratios in three different soils.
Figure 4: Identification of rRNA transcripts from crenarchaeota and AOB in 30 Mb of sequence determined from a RUD soil cDNA library (314,000 reads with an average length of 96.4 bp).

Similar content being viewed by others

References

  1. Kowalchuk, G. A. & Stephen, J. R. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu. Rev. Microbiol. 55, 485–529 (2001)

    Article  CAS  PubMed  Google Scholar 

  2. Prosser, J. I. & Embley, T. M. Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers. Antonie Van Leeuwenhoek 81, 165–179 (2002)

    Article  CAS  PubMed  Google Scholar 

  3. Bock, E. & Wagner, M. Oxidation of Inorganic Nitrogen Compounds as an Energy Source. in The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community (eds Dworkin, M. et al.) http://link.springer-ny.com/link/service/books/10125 (Springer, New York, 2001)

    Google Scholar 

  4. Purkhold, U. et al. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl. Environ. Microbiol. 66, 5368–5382 (2000)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Hermansson, A. & Lindgren, P. E. Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Appl. Environ. Microbiol. 67, 972–976 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Mendum, T. A., Sockett, R. E. & Hirsch, P. R. Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the beta subdivision of the class proteobacteria in arable soils to nitrogen fertilizer. Appl. Environ. Microbiol. 65, 4155–4162 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Phillips, C. J., Paul, E. A. & Prosser, J. I. Quantitative analysis of ammonia oxidising bacteria using competitive PCR. FEMS Microbiol. Ecol. 32, 167–175 (2000)

    Article  CAS  PubMed  Google Scholar 

  8. Treusch, A. H. et al. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol. 7, 1985–1995 (2005)

    Article  CAS  PubMed  Google Scholar 

  9. Schleper, C., Jurgens, G. & Jonuscheit, M. Genomic studies of uncultivated archaea. Nature Rev. Microbiol. 3, 479–488 (2005)

    Article  CAS  Google Scholar 

  10. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Konneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546 (2005)

    Article  ADS  PubMed  Google Scholar 

  12. Damste, J. S., Schouten, S., Hopmans, E. C., van Duin, A. C. & Geenevasen, J. A. Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota. J. Lipid Res. 43, 1641–1651 (2002)

    Article  PubMed  Google Scholar 

  13. 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)

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Stephen, J. R. et al. Analysis of beta-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64, 2958–2965 (1998)

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Kurola, J., Salkinoja-Salonen, M., Aarnio, T., Hultman, J. & Romantschuk, M. Activity, diversity and population size of ammonia-oxidising bacteria in oil-contaminated landfarming soil. FEMS Microbiol. Lett. 250, 33–38 (2005)

    Article  CAS  PubMed  Google Scholar 

  16. Okano, Y. et al. Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Appl. Environ. Microbiol. 70, 1008–1016 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Weigel, A., Russow, R. & Körschens, M. Quantification of airborne N-input in long-term field experiments and its validation through measurements using 15N isotope dilution. J. Plant Nutr. Soil Sci. 163, 261–265 (2000)

    Article  Google Scholar 

  18. Ochsenreiter, T., Selezi, D., Quaiser, A., Bonch-Osmolovskaya, L. & Schleper, C. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ. Microbiol. 5, 787–797 (2003)

    Article  CAS  PubMed  Google Scholar 

  19. De Rosa, M. & Gambacorta, A. The lipids of Archaebacteriaea. Prog. Lipid Res. 27, 153–175 (1988)

    Article  CAS  PubMed  Google Scholar 

  20. DeLong, E. F. et al. Dibiphytanyl ether lipids in nonthermophilic crenarchaeotes. Appl. Environ. Microbiol. 64, 1133–1138 (1998)

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Hopmans, E. C. et al. A novel proxy for terrestrial organic matter in sediments based on branched and isoprenoid tetraether lipids. Earth Planet. Sci. Lett. 224, 107–116 (2004)

    Article  ADS  CAS  Google Scholar 

  22. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  23. Hallam, S. J. et al. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol. 4, e95 (2006)

    Article  PubMed  PubMed Central  Google Scholar 

  24. Øvreås, L. & Torsvik, V. V. Microbial diversity and community structure in two different agricultural soil communities. Microb. Ecol. 36, 303–315 (1998)

    Article  PubMed  Google Scholar 

  25. Griffiths, R. I., Whiteley, A. S., O'Donnell, A. G. & Bailey, M. J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66, 5488–5491 (2000)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Weijers, J. W. et al. Membrane lipids of mesophilic anaerobic bacteria thriving in peats have typical archaeal traits. Environ. Microbiol. 8, 648–657 (2006)

    Article  CAS  PubMed  Google Scholar 

  27. Lane, D. J. et al. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl Acad. Sci. USA 82, 6955–6959 (1985)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank V. Torsvik for use of the qPCR machine, S. L. Jørgensen and V. Torsvik for discussions and L. Knudsen and L. Tomsho for technical assistance. K. Zink is acknowledged for running LC-APCI-MS analyses. We thank for help or support in soil sampling: V. Torsvik (for KRO and STO), E. Schulz (for L-l, L-n and L-h from a long-term field trial in Bad Lauchstädt, Germany), C. Emmerling (for R-nt and R-p), B. Winkler (for GSF), E. Vavoulidou (for B77V, B77T and E16 from the NAGREF Soil Science Institute of Athens). Most of this project was financed through an initial funding of the University of Bergen given to C.S. Part of the pyrosequencing project was paid through the Department of Health using Tobacco Settlement Funds to S.C.S. Author Contributions The project was conceived and the manuscript was written by C.S., assisted by co-authors. Soil samples were collected and characterized for general parameters by M.S., T.U. and S.L. DNA and RNA extractions were performed by M.S. and S.L. and real-time PCR by S.L.; MPN-PCR and clone libraries were performed by T.U.; GDGT analyses was carried out by L.S.; ds cDNA synthesis and high-throughput sequencing including data analyses was performed by T.U., J.Q. and S.C.S.; and amoA phylogeny was performed by G.W.N. and J.I.P.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to C. Schleper.

Ethics declarations

Competing interests

Sequences obtained in this study were deposited at GenBank (NCBI) with accession numbers DQ534808–DQ534888. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Methods

This file contains a detailed description of methods used in this study (extraction and preparation of nucleic acids; quantification of DNA; real-time PCR; AmoA gene amplification, sequence and phylogenetic analysis; most probable number (MPN) PCR; GDGT analysis; and construction of cDNA library, high-throughput sequencing and bioinformatic analysis). (PDF 83 kb)

Supplementary Notes

This file contains and additional reference list of literature cited in Supplementary Methods section (PDF 41 kb)

Supplementary Tables

This file contains Supplementary Tables 1–5. (PDF 93 kb)

Supplementary Figures

This file contains Supplementary Figures 1–6 and their accompanying legends. (PDF 190 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Leininger, S., Urich, T., Schloter, M. et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809 (2006). https://doi.org/10.1038/nature04983

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature04983

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing