Characterization of the Localized Immune Responses at the Single Cell Resolution in Arabidopsis Roots

Abstract

Plant roots are organs with multiple zones and cell types grown underground, which are constantly exposed to various pathogen attacks. Root cells can initiate pattern-triggered immunity (PTI) after recognition of elicitor molecules by cell-surface-localized pattern recognition receptors (PRRs). Elicitors can be pathogen-derived (e.g., MAMPs) or self-derived (e.g, phytocytokines). Recent findings have indicated that different cell types may activate immune responses according to their cell identity; however, how PTI is coordinated in roots is poorly understood. Therefore, tissue- and cell type-specific studies are essential to understand how this sophisticated immune system works in roots. In this research, we employed single cell transcriptomic analysis coupled with high-resolution single cell-imaging to study transcriptional outputs in Arabidopsis thaliana, induced by five different elicitors, including two MAMPs and three phytocytokines. This revealed that the transcriptional responses are treatment-, tissue- and cell type-specific in roots. Moreover, phytocytokines induced stronger immune responses than MAMPs in different root cell types and root zones, suggesting that phytocytokines might be interpreted as a stronger “alarm signal” by the root to amplify defense responses initiated by MAMPs. Interestingly, the root cap has a more robust immune response than the meristematic zone and elongation zone in response to different elicitors, indicating that root caps may act as “sentries” that provide specialized protection to the root meristem cells. Importantly, phytocytokines induce differentiated immune responses at different cell types, which might provide a mechanism for coordinating diverse phytocytokines in activating immunity. Finally, gene regulatory network analysis identified the upstream transcriptional regulators and corresponding targets for each root cell type and revealed that the root cell type-specific transcriptomic responses are strongly correlated to cell identity. This study thus reveals that immune signaling in Arabidopsis root is characterized by treatment-, tissue- and cell type-specificity, which highlights a complex immune landscape within the root.