Longitudinal zone- and cell type-specific pattern-triggered immune responses in Arabidopsis roots

Roots, composed of diverse cell types across longitudinal developmental zones, are vital for plant survival against microbial challenges. Leveraging single-cell transcriptomics and live-cell imaging of Arabidopsis roots, we reveal here that plant-derived phytocytokines elicit more potent immune responses than microbe-derived patterns across root cell types and zones. The differential expression of receptors and key signaling modules in distinct cell types and zones contributes to the response intensity to specific elicitors. Phytocytokines sustain growth-defense trade-offs by suppressing the expression of receptor-like kinase genes associated with root cell division and elongation. The intensity of immune responses in different root zones is associated with fungal and bacterial pathogen invasion sites. Furthermore, motif-informed network inference highlighted key transcriptional regulators driving cell identity-specific transcriptomic immune responses. Our study provides a comprehensive landscape of transcriptional responses in plant roots in response to diverse immune elicitors, highlighting how distinct phytocytokines orchestrate stage- and cell type-dependent transcriptional reprogramming.