A beneficial bacterium mitigates drought stress by upregulating the flavonoid biosynthetic pathway in Arabidopsis

Drought stress hinders plant growth and causes major yield losses globally. This study investigated the mechanisms behind Pantoea species-induced drought tolerance in Arabidopsis. RNA-seq analyses revealed significant upregulation of the flavonoid biosynthesis pathway in Pantoea-inoculated plants under drought stress. The Pantoea strain, which is a plant growth-promoting rhizobacteria (PGPR), led to a significant increase in chlorophyll content and enhanced drought tolerance in wild-type Arabidopsis, but not in flavonoid pathway mutants (fls-1, tt4-2, and omt1), demonstrating the role of flavonoids in the interaction. Inoculation significantly upregulated flavonoid biosynthesis genes, including MYB11, CHI, CHS, F3H, F3'H, and FLS1, and significantly increased the flavonoid and anthocyanin contents in wild type plants compared to the mutants under drought stress, thus confirming that flavonoids are involved in Pantoea-induced drought stress. Wild type had higher colonization than the mutants, implicating flavonoids in root colonization. Pantoea species swarmed towards flavonoid soaked-agar plugs suggesting that flavonoids may be chemoattractants. To our knowledge, this is the first time that the flavonoid biosynthesis pathway has been implicated in Pantoea-induced drought tolerance. Overall, our findings revealed that Pantoea-mediated drought stress tolerance is largely regulated by the flavonoid biosynthesis pathway, providing insights into the role of flavonoids in plant-microbe interactions and drought stress tolerance.