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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.

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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).

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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.

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Correspondence to C. Schleper.

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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)

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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

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