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Archaea predominate among ammonia-oxidizing prokaryotes in soils

Nature volume 442, pages 806809 (17 August 2006) | Download Citation

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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.

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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

Affiliations

  1. Department of Biology, University of Bergen, Jahnebakken 5, N-5020 Bergen, Norway

    • S. Leininger
    • , T. Urich
    •  & C. Schleper
  2. Institute of Soil Ecology, GSF-National Research Center for Environment and Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany

    • M. Schloter
  3. Institute of Geology and Mineralogy, University of Cologne, Zuelpicher Strasse 49a, 50674 Cologne, Germany

    • L. Schwark
  4. Penn State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA

    • J. Qi
    •  & S. C. Schuster
  5. School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK

    • G. W. Nicol
    •  & J. I. Prosser

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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.

Corresponding author

Correspondence to C. Schleper.

Supplementary information

PDF files

  1. 1.

    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).

  2. 2.

    Supplementary Notes

    This file contains and additional reference list of literature cited in Supplementary Methods section

  3. 3.

    Supplementary Tables

    This file contains Supplementary Tables 1–5.

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    Supplementary Figures

    This file contains Supplementary Figures 1–6 and their accompanying legends.

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DOI

https://doi.org/10.1038/nature04983

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