IDEAS home Printed from https://ideas.repec.org/a/eee/ecomod/v362y2017icp111-119.html
   My bibliography  Save this article

Ammonia-uptake kinetics and domain-level contributions of bacteria and archaea to nitrification in temperate forest soils

Author

Listed:
  • Lin, L.
  • Norman, J.S.
  • Barrett, J.E.

Abstract

Ammonia-oxidizing bacteria and archaea (AOA and AOB) perform the rate-limiting step of nitrification, a biogeochemical process that controls the availability of inorganic nitrogen in terrestrial and aquatic ecosystems. We sought to investigate field values of AOA and AOB ammonia-uptake kinetics along with domain-level contributions to ammonia oxidation in temperate forest soils. To accomplish this goal, we constructed an ecosystem model that simulates ammonia oxidation in temperate forest soils based only on inorganic nitrogen pools and AOA and AOB population dynamics observed during in situ incubations. The model used Bayesian Markov chain Monte Carlo procedure to choose the most likely combination of in situ ammonia-uptake parameters for AOA and AOB, including Km,AOA, Km,AOB, Vmax,AOA, and Vmax,AOB. Domain-level contributions to ammonia oxidation were extracted from the best-fit solution and the model-selected values indicate that AOB was responsible for 70.0% of the simulated ammonia oxidation across sites, while AOA was responsible for the remaining 30.0%. We believe that the approach we demonstrate here can be applied to microbially-mediated biogeochemical fluxes in other elemental cycles as well.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:ecomod:v:362:y:2017:i:c:p:111-119
    DOI: 10.1016/j.ecolmodel.2017.08.016
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0304380017303769
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.ecolmodel.2017.08.016?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. 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.
    2. Willm Martens-Habbena & Paul M. Berube & Hidetoshi Urakawa & José R. de la Torre & David A. Stahl, 2009. "Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria," Nature, Nature, vol. 461(7266), pages 976-979, October.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. Zhen-Zhen Zheng & Li-Wei Zheng & Min Nina Xu & Ehui Tan & David A. Hutchins & Wenchao Deng & Yao Zhang & Dalin Shi & Minhan Dai & Shuh-Ji Kao, 2020. "Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. Sharif Hossain & Christopher W. K. Chow & David Cook & Emma Sawade & Guna A. Hewa, 2022. "Review of Nitrification Monitoring and Control Strategies in Drinking Water System," IJERPH, MDPI, vol. 19(7), pages 1-31, March.
    11. Jie Zhou & Yanling Zheng & Lijun Hou & Zhirui An & Feiyang Chen & Bolin Liu & Li Wu & Lin Qi & Hongpo Dong & Ping Han & Guoyu Yin & Xia Liang & Yi Yang & Xiaofei Li & Dengzhou Gao & Ye Li & Zhanfei Li, 2023. "Effects of acidification on nitrification and associated nitrous oxide emission in estuarine and coastal waters," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    12. 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.
    13. 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.
    14. 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.
    15. Jingyi Dong & Liming Tian & Jiaqi Zhang & Yinghui Liu & Haiyan Li & Qi Dong, 2022. "Grazing Intensity Has More Effect on the Potential Nitrification Activity Than the Potential Denitrification Activity in An Alpine Meadow," Agriculture, MDPI, vol. 12(10), pages 1-17, September.
    16. 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.
    17. 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.
    18. 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.
    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.
    20. 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.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:ecomod:v:362:y:2017:i:c:p:111-119. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/ecological-modelling .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.