Bacillus amyloliquefaciens orchestrates cell type-specific responses underlying drought tolerance in Arabidopsis

Plant growth-promoting rhizobacteria (PGPRs) play an essential role in maintaining plant health. However, the mechanism of PGPR-mediated plant tolerance to drought stress at single-cell resolution remains enigmatic. Here, we establish the single-cell transcriptome landscape of Arabidopsis thaliana leaves to uncover cell type-specific responses to drought stress in plants mediated by Bacillus amyloliquefaciens Ba13. Pot experiments show that inoculated plants have greater tolerance to simulated drought than non-inoculated plants. This is indicated by increases in plant biomass, photosynthetic performance, osmolyte contents, and antioxidant enzyme activity upon inoculation under osmotic stress, along with a decrease in membrane lipid peroxidation. Single-cell RNA sequencing uncovers that the gene expression profiles of various leaf cell types respond differently to inoculation, with stronger transcriptional responses under osmotic stress than under non-stressed conditions. Cell subclustering reveals nuanced functional differences in cell subpopulations that enhance stress tolerance in response to inoculation. Gene co-expression network analysis identifies RHA1 as a key transcription factor gene, which is targeted by B. amyloliquefaciens Ba13 to bolster plant stress tolerance. This study demonstrates PGPR-induced functional heterogeneity of Arabidopsis leaf cells in response to simulated drought and contributes to the mechanistic understanding of plant drought tolerance.