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Comparative single-nucleus RNA-seq analysis revealed localized and cell type-specific pathways governing root-microbiome interactions

Author

Listed:
  • Qiuhua Yang

    (Southern University of Science and Technology)

  • Zhuowen Li

    (Southern University of Science and Technology)

  • Kaixiang Guan

    (Southern University of Science and Technology)

  • Zhenghong Wang

    (Southern University of Science and Technology)

  • Xianli Tang

    (Southern University of Science and Technology)

  • Yechun Hong

    (Southern University of Science and Technology)

  • Zhijian Liu

    (Southern University of Science and Technology)

  • Jixian Zhai

    (Southern University of Science and Technology)

  • Ancheng Huang

    (Southern University of Science and Technology)

  • Yanping Long

    (Southern University of Science and Technology)

  • Yi Song

    (Southern University of Science and Technology)

Abstract

Roots can recognize and differentially respond to beneficial and pathogenic microbes, which are fundamental for maintaining root microbiome homeostasis, plasticity, and plant fitness. Meanwhile, roots are highly heterogeneous tissues with complex cell-type compositions and spatially distinct developmental stages. We found that beneficial microbe specifically induces the expression of translation-related genes in the proximal meristem cells, and diverse ribosome proteins and translation regulators are necessary for beneficial microbe-mediated growth promotion. Notably, the root maturation zone can still mount localized immune responses to root pathogens, including genes related to camalexin and triterpene biosynthesis. A triterpene biosynthesis mutant blocked the microbiome reshaping process upon GMI1000 infection. Our results indicate roots may have specialized immune responses in the maturation zone, and provide important insights and vital resources for further elucidating regulators of root-microbe interactions and microbiome reshaping.

Suggested Citation

  • Qiuhua Yang & Zhuowen Li & Kaixiang Guan & Zhenghong Wang & Xianli Tang & Yechun Hong & Zhijian Liu & Jixian Zhai & Ancheng Huang & Yanping Long & Yi Song, 2025. "Comparative single-nucleus RNA-seq analysis revealed localized and cell type-specific pathways governing root-microbiome interactions," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58395-0
    DOI: 10.1038/s41467-025-58395-0
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    References listed on IDEAS

    as
    1. Bruno Pok Man Ngou & Hee-Kyung Ahn & Pingtao Ding & Jonathan D. G. Jones, 2021. "Mutual potentiation of plant immunity by cell-surface and intracellular receptors," Nature, Nature, vol. 592(7852), pages 110-115, April.
    2. Guoyong Xu & George H. Greene & Heejin Yoo & Lijing Liu & Jorge Marqués & Jonathan Motley & Xinnian Dong, 2017. "Global translational reprogramming is a fundamental layer of immune regulation in plants," Nature, Nature, vol. 545(7655), pages 487-490, May.
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