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

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.