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Complete nitrification by Nitrospira bacteria

Author

Listed:
  • Holger Daims

    (University of Vienna)

  • Elena V. Lebedeva

    (Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences)

  • Petra Pjevac

    (University of Vienna)

  • Ping Han

    (University of Vienna)

  • Craig Herbold

    (University of Vienna)

  • Mads Albertsen

    (Center for Microbial Communities, Aalborg University)

  • Nico Jehmlich

    (Helmholtz-Centre for Environmental Research - UFZ)

  • Marton Palatinszky

    (University of Vienna)

  • Julia Vierheilig

    (University of Vienna)

  • Alexandr Bulaev

    (Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences)

  • Rasmus H. Kirkegaard

    (Center for Microbial Communities, Aalborg University)

  • Martin von Bergen

    (Helmholtz-Centre for Environmental Research - UFZ
    Helmholtz-Centre for Environmental Research - UFZ)

  • Thomas Rattei

    (University of Vienna)

  • Bernd Bendinger

    (DVGW-Forschungsstelle TUHH, Hamburg University of Technology)

  • Per H. Nielsen

    (Center for Microbial Communities, Aalborg University)

  • Michael Wagner

    (University of Vienna)

Abstract

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.

Suggested Citation

  • Holger Daims & Elena V. Lebedeva & Petra Pjevac & Ping Han & Craig Herbold & Mads Albertsen & Nico Jehmlich & Marton Palatinszky & Julia Vierheilig & Alexandr Bulaev & Rasmus H. Kirkegaard & Martin vo, 2015. "Complete nitrification by Nitrospira bacteria," Nature, Nature, vol. 528(7583), pages 504-509, December.
    • Handle: RePEc:nat:nature:v:528:y:2015:i:7583:d:10.1038_nature16461
    DOI: 10.1038/nature16461
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    1. Yi Li & Xinqi Chen & Xinzi Wang & Jiahui Shang & Lihua Niu & Longfei Wang & Huanjun Zhang & Wenlong Zhang, 2022. "The Effects of Paroxetine on Benthic Microbial Food Web and Nitrogen Transformation in River Sediments," IJERPH, MDPI, vol. 19(21), pages 1-14, November.
    2. Ghazal Srivastava & Aparna Kapoor & Absar Ahmad Kazmi, 2023. "Improved Biological Phosphorus Removal under Low Solid Retention Time Regime in Full-Scale Sequencing Batch Reactor," Sustainability, MDPI, vol. 15(10), pages 1-22, May.
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    4. Hannaford, Naomi E. & Heaps, Sarah E. & Nye, Tom M.W. & Curtis, Thomas P. & Allen, Ben & Golightly, Andrew & Wilkinson, Darren J., 2023. "A sparse Bayesian hierarchical vector autoregressive model for microbial dynamics in a wastewater treatment plant," Computational Statistics & Data Analysis, Elsevier, vol. 179(C).
    5. Shengbo Gu & Leibin Liu & Xiaojie Zhuang & Jinsheng Qiu & Zhi Zhou, 2022. "Enhanced Nitrogen Removal in a Pilot-Scale Anoxic/Aerobic (A/O) Process Coupling PE Carrier and Nitrifying Bacteria PE Carrier: Performance and Microbial Shift," Sustainability, MDPI, vol. 14(12), pages 1-20, June.
    6. Li Meng & Jian Shi & Yuanzheng Zhai & Rui Zuo & Jinsheng Wang & Xueru Guo & Yanguo Teng & Jian Gao & Li Xu & Bingchi Guo, 2022. "Ammonium Reactive Migration Process and Functional Bacteria Response along Lateral Runoff Path under Groundwater Exploitation," Sustainability, MDPI, vol. 14(14), pages 1-20, July.
    7. 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.
    8. Ching Yi Hong & Khalida Muda & Hazlami Fikri Basri & Armstrong Ighodalo Omoregie & Jauharah Md Khudzari & Nur Shahidah Aftar Ali & Farhan Mohd Pauzi, 2024. "Discovering research evolution and emerging trends in ammonium wastewater treatment technologies: a bibliometric analysis," Environment, Development and Sustainability: A Multidisciplinary Approach to the Theory and Practice of Sustainable Development, Springer, vol. 26(9), pages 21877-21911, September.
    9. Qiong Wan & Qingji Han & Hailin Luo & Tao He & Feng Xue & Zihuizhong Ye & Chen Chen & Shan Huang, 2020. "Ceramsite Facilitated Microbial Degradation of Pollutants in Domestic Wastewater," IJERPH, MDPI, vol. 17(13), pages 1-13, June.
    10. Montaño San Agustin, Daniela & Orta Ledesma, Maria Teresa & Monje Ramírez, Ignacio & Yáñez Noguez, Isaura & Luna Pabello, Víctor Manuel & Velasquez-Orta, Sharon B., 2022. "A non-sterile heterotrophic microalgal process for dual biomass production and carbon removal from swine wastewater," Renewable Energy, Elsevier, vol. 181(C), pages 592-603.
    11. William C Nelson & Emily B Graham & Alex R Crump & Sarah J Fansler & Evan V Arntzen & David W Kennedy & James C Stegen, 2020. "Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome," PLOS ONE, Public Library of Science, vol. 15(1), pages 1-19, January.
    12. He, Yanying & Li, Yiming & Li, Xuecheng & Liu, Yingrui & Wang, Yufen & Guo, Haixiao & Hou, Jiaqi & Zhu, Tingting & Liu, Yiwen, 2023. "Net-zero greenhouse gas emission from wastewater treatment: Mechanisms, opportunities and perspectives," Renewable and Sustainable Energy Reviews, Elsevier, vol. 184(C).
    13. Ariel Freidenreich & Sanku Dattamudi & Yuncong Li & Krishnaswamy Jayachandran, 2022. "Influence of Leguminous Cover Crops on Soil Chemical and Biological Properties in a No-Till Tropical Fruit Orchard," Land, MDPI, vol. 11(6), pages 1-18, June.
    14. Aleksandra Wdowczyk & Agata Szymańska-Pulikowska & Magdalena Domańska, 2022. "Analysis of the Bacterial Biocenosis of Activated Sludge Treated with Leachate from Municipal Landfills," IJERPH, MDPI, vol. 19(3), pages 1-22, February.
    15. Huai Shi & Guohong Liu & Qianqian Chen, 2024. "Research Hotspots and Trends of Nitrification Inhibitors: A Bibliometric Review from 2004–2023," Sustainability, MDPI, vol. 16(10), pages 1-20, May.
    16. Agata Novara & Valentina Catania & Marco Tolone & Luciano Gristina & Vito Armando Laudicina & Paola Quatrini, 2020. "Cover Crop Impact on Soil Organic Carbon, Nitrogen Dynamics and Microbial Diversity in a Mediterranean Semiarid Vineyard," Sustainability, MDPI, vol. 12(8), pages 1-18, April.
    17. 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.

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