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

Qiuhua Yang, Zhuowen Li, Kaixiang Guan, Zhenghong Wang, Xianli Tang, Yechun Hong, Zhijian Liu, Jixian Zhai, Ancheng Huang (), Yanping Long () and Yi Song ()
Additional contact information
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

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: 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.

Date: 2025
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-58395-0 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58395-0

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-58395-0

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().