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Ammonia- and Methane-Oxidizing Bacteria: The Abundance, Niches and Compositional Differences for Diverse Soil Layers in Three Flooded Paddy Fields

Author

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  • Jian Zhang

    (College of Resources and Environment, SouthWest University, Beibei, Chongqing 400715, China)

  • Olusanya A. Olatunji

    (College of Geographical Science, Fujian Normal University, 32 Shangsan Road, Fuzhou 350007, China)

  • Kaiwen Pan

    (Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China)

  • Xianjun Jiang

    (College of Resources and Environment, SouthWest University, Beibei, Chongqing 400715, China)

  • Yao Meng

    (College of Resources and Environment, SouthWest University, Beibei, Chongqing 400715, China)

  • Jianjun Li

    (Guangdong Institute of Microbiology, Guangdong 510070, China)

  • Jiabao Li

    (Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China)

  • Si Shen

    (College of Resources and Environment, SouthWest University, Beibei, Chongqing 400715, China)

  • Dalu Guo

    (College of Resources and Environment, SouthWest University, Beibei, Chongqing 400715, China)

  • Hongyan Luo

    (College of Resources and Environment, SouthWest University, Beibei, Chongqing 400715, China)

Abstract

Ammonia oxidizing bacteria (AOB), Ammonia oxidizing archaea (AOA) and methane oxidizing bacteria (MOB) play cogent roles in oxidation and nitrification processes, and hence have important ecological functions in several ecosystems. However, their distribution and compositional differences in different long-term flooded paddy fields (FPFs) management at different soil depths remains under-investigated. Using qPCR and phylogenetic analysis, this study investigated the abundance, niches, and compositional differences of AOA, AOB, and MOB along with their potential nitrification and oxidation rate in three soil layers from three FPFs (ShaPingBa (SPB), HeChuan (HC), and JiDi (JD)) in Chongqing, China. In all the FPFs, CH 4 oxidation occurred mainly in the surface (0–3 cm) and subsurface layers (3–5 cm). A significant difference in potential methane oxidation and nitrification rates was observed among the three FPFs, in which SPB had the highest. The higher amoA genes are the marker for abundance of AOA compared to AOB while pmoA genes, which is the marker for MOB abundance and diversity, indicated their significant role in the nitrification process across the three FPFs. The phylogenetic analysis revealed that AOA were mainly composed of Nitrososphaera, Nitrosospumilus, and Nitrosotalea, while the genus Nitrosomonas accounted for the greatest proportion of AOB in the three soil layers. MOB were mainly composed of Methylocaldum and Methylocystis genera. Overall, this finding pointed to niche differences as well as suitability of the surface and subsurface soil environments for the co-occurrence of ammonia oxidation and methane oxidation in FPFs.

Suggested Citation

  • 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.
    • Handle: RePEc:gam:jsusta:v:12:y:2020:i:3:p:953-:d:313842
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    References listed on IDEAS

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    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. Paul L. E. Bodelier & Peter Roslev & Thilo Henckel & Peter Frenzel, 2000. "Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots," Nature, Nature, vol. 403(6768), pages 421-424, January.
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    Keywords

    AOA; AOB; MOB; q-PCR; Paddy field;
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