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

SUMMARY 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.