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Archaea predominate among ammonia-oxidizing prokaryotes in soils

Author

Listed:
  • S. Leininger

    (University of Bergen)

  • T. Urich

    (University of Bergen)

  • M. Schloter

    (Institute of Soil Ecology, GSF-National Research Center for Environment and Health)

  • L. Schwark

    (Institute of Geology and Mineralogy, University of Cologne)

  • J. Qi

    (Penn State University, Center for Comparative Genomics and Bioinformatics)

  • G. W. Nicol

    (University of Aberdeen)

  • J. I. Prosser

    (University of Aberdeen)

  • S. C. Schuster

    (Penn State University, Center for Comparative Genomics and Bioinformatics)

  • C. Schleper

    (University of Bergen)

Abstract

Soil bacteria yield to archaea Nitrification, the microbial conversion of ammonia to nitrate, is a key process in the global nitrogen cycle. It has been generally assumed that specialist bacteria are the main aerobic ammonia oxidizers on the soil. An analysis of the abundance of the amoA gene encoding a subunit of the key enzyme ammonia monooxygenase shows that in twelve different soil types from three different climatic zones, amoA gene copies from archaea of the kingdom Crenarchaeota were up to 3,000-fold more abundant than bacterial amoA. So in both pristine and agricultural soils, it seems that archaea are by far the dominant ammonia oxidizers.

Suggested Citation

  • S. Leininger & T. Urich & M. Schloter & L. Schwark & J. Qi & G. W. Nicol & J. I. Prosser & S. C. Schuster & C. Schleper, 2006. "Archaea predominate among ammonia-oxidizing prokaryotes in soils," Nature, Nature, vol. 442(7104), pages 806-809, August.
    • Handle: RePEc:nat:nature:v:442:y:2006:i:7104:d:10.1038_nature04983
    DOI: 10.1038/nature04983
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    1. Pok Man Leung & Rhys Grinter & Eve Tudor-Matthew & James P. Lingford & Luis Jimenez & Han-Chung Lee & Michael Milton & Iresha Hanchapola & Erwin Tanuwidjaya & Ashleigh Kropp & Hanna A. Peach & Carlo R, 2024. "Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Aixia Xu & Lingling Li & Junhong Xie & Subramaniam Gopalakrishnan & Renzhi Zhang & Zhuzhu Luo & Liqun Cai & Chang Liu & Linlin Wang & Sumera Anwar & Yuji Jiang, 2022. "Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization," IJERPH, MDPI, vol. 19(5), pages 1-18, February.
    3. R. Michael Lehman & Cynthia A. Cambardella & Diane E. Stott & Veronica Acosta-Martinez & Daniel K. Manter & Jeffrey S. Buyer & Jude E. Maul & Jeffrey L. Smith & Harold P. Collins & Jonathan J. Halvors, 2015. "Understanding and Enhancing Soil Biological Health: The Solution for Reversing Soil Degradation," Sustainability, MDPI, vol. 7(1), pages 1-40, January.
    4. Kehinde Abraham Odelade & Olubukola Oluranti Babalola, 2019. "Bacteria, Fungi and Archaea Domains in Rhizospheric Soil and Their Effects in Enhancing Agricultural Productivity," IJERPH, MDPI, vol. 16(20), pages 1-19, October.
    5. Massimo Zilio & Silvia Motta & Fulvia Tambone & Barbara Scaglia & Gabriele Boccasile & Andrea Squartini & Fabrizio Adani, 2020. "The distribution of functional N-cycle related genes and ammonia and nitrate nitrogen in soil profiles fertilized with mineral and organic N fertilizer," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-19, June.
    6. Jian Zhang & Olusanya A. Olatunji & Kaiwen Pan & Xianjun Jiang & Yao Meng & Jianjun Li & Jiabao Li & Si Shen & Dalu Guo & Hongyan Luo, 2020. "Ammonia- and Methane-Oxidizing Bacteria: The Abundance, Niches and Compositional Differences for Diverse Soil Layers in Three Flooded Paddy Fields," Sustainability, MDPI, vol. 12(3), pages 1-24, January.
    7. Alvarez-Yela, Astrid Catalina & Alvarez-Silva, María Camila & Restrepo, Silvia & Husserl, Johana & Zambrano, María Mercedes & Danies, Giovanna & Gómez, Jorge M. & González Barrios, Andrés Fernando, 2017. "Influence of agricultural activities in the structure and metabolic functionality of paramo soil samples in Colombia studied using a metagenomics analysis in dynamic state," Ecological Modelling, Elsevier, vol. 351(C), pages 63-76.
    8. X.X. Dong & L.L. Zhang & Z.J. Wu & H.W. Zhang & P. Gong, 2013. "The response of nitrifier, N-fixer and denitrifier gene copy numbers to the nitrification inhibitor 3,4-dimethylpyrazole phosphate," Plant, Soil and Environment, Czech Academy of Agricultural Sciences, vol. 59(9), pages 398-403.
    9. Xingjia He & Sen Li & Fengzhi Wu, 2021. "Responses of Ammonia-Oxidizing Microorganisms to Intercropping Systems in Different Seasons," Agriculture, MDPI, vol. 11(3), pages 1-17, February.
    10. Ping Han & Xiufeng Tang & Hanna Koch & Xiyang Dong & Lijun Hou & Danhe Wang & Qian Zhao & Zhe Li & Min Liu & Sebastian Lücker & Guitao Shi, 2024. "Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    11. Jordi Escuer-Gatius & Merrit Shanskiy & Ülo Mander & Karin Kauer & Alar Astover & Hanna Vahter & Kaido Soosaar, 2020. "Intensive Rain Hampers the Effectiveness of Nitrification Inhibition in Controlling N 2 O Emissions from Dairy Slurry-Fertilized Soils," Agriculture, MDPI, vol. 10(11), pages 1-18, October.
    12. Carla L. Abán & Giovanni Larama & Antonella Ducci & Jorgelina Huidobro & Michel Abanto & Silvina Vargas-Gil & Carolina Pérez-Brandan, 2022. "Soil Properties and Bacterial Communities Associated with the Rhizosphere of the Common Bean after Using Brachiaria brizantha as a Service Crop: A 10-Year Field Experiment," Sustainability, MDPI, vol. 15(1), pages 1-23, December.
    13. Mohammad Bahram & Mikk Espenberg & Jaan Pärn & Laura Lehtovirta-Morley & Sten Anslan & Kuno Kasak & Urmas Kõljalg & Jaan Liira & Martin Maddison & Mari Moora & Ülo Niinemets & Maarja Öpik & Meelis Pär, 2022. "Structure and function of the soil microbiome underlying N2O emissions from global wetlands," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    14. Jianfeng Ning & Yuji Arai & Jian Shen & Ronghui Wang & Shaoying Ai, 2021. "Effects of Phosphorus on Nitrification Process in a Fertile Soil Amended with Urea," Agriculture, MDPI, vol. 11(6), pages 1-12, June.
    15. Nagendranatha Reddy, C. & Venkata Mohan, S., 2016. "Integrated bio-electrogenic process for bioelectricity production and cathodic nutrient recovery from azo dye wastewater," Renewable Energy, Elsevier, vol. 98(C), pages 188-196.
    16. M. E. Marushchak & J. Kerttula & K. Diáková & A. Faguet & J. Gil & G. Grosse & C. Knoblauch & N. Lashchinskiy & P. J. Martikainen & A. Morgenstern & M. Nykamb & J. G. Ronkainen & H. M. P. Siljanen & L, 2021. "Thawing Yedoma permafrost is a neglected nitrous oxide source," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    17. Dhafer Alsalah & Nada Al-Jassim & Kenda Timraz & Pei-Ying Hong, 2015. "Assessing the Groundwater Quality at a Saudi Arabian Agricultural Site and the Occurrence of Opportunistic Pathogens on Irrigated Food Produce," IJERPH, MDPI, vol. 12(10), pages 1-21, October.
    18. Lin, L. & Norman, J.S. & Barrett, J.E., 2017. "Ammonia-uptake kinetics and domain-level contributions of bacteria and archaea to nitrification in temperate forest soils," Ecological Modelling, Elsevier, vol. 362(C), pages 111-119.
    19. Patricia Buškulić & Jelena Parlov & Zoran Kovač & Tomislav Brenko & Marija Pejić, 2023. "Determination of Nitrate Migration and Distribution through Eutric Cambisols in an Area without Anthropogenic Sources of Nitrate (Velika Gorica Well Field, Croatia)," Sustainability, MDPI, vol. 15(23), pages 1-19, December.

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