Drought stress modifies the community structure of root-associated microbes that improve growth and medicinal compound accumulation.

is an important medicinal plant in traditional Chinese medicine, its rhizome is rich of volatile secondary metabolites with medicinal values and is largely demanded in modern markets. Currently, supply of high-yield, high-quality is mainly achieved cultivation. Certain soil microbes can benefit plant growth, secondary metabolism and induce resistance to environmental stresses. Hence, studies on the effects of soil microbe communities and isolates microorganisms on is extremely meaningful for future application of microbes on cultivation. Here we investigated the effects of the inoculation with an entire soil microbial community on the growth, resistance to drought, and accumulation of major medicinal compounds (hinesol, β-eudesmol, atractylon and atractylodin) of . We analyzed the interaction between and the soil microbes at the phylum and genus levels under drought stress of different severities (inflicted by 0%, 10% and 25% PEG6000 treatments). Our results showed that inoculation with soil microbes promoted the growth, root biomass yield, medicinal compound accumulation, and rendered drought-resistant traits of , including relatively high root:shoot ratio and high root water content under drought. Moreover, our results suggested drought stress was more powerful than the selectivity of in shaping the root-associated microbial communities; also, the fungal communities had a stronger role than the bacterial communities in protecting from drought. Specific microbial clades that might have a role in protecting from drought stress were identified: at the genus level, the rhizospheric bacteria , and , and rhizospheric fungi , , and , the root endophytic bacteria , , and , and the root endophytic fungus were closely associated with under drought stress. Additionally, we acquired several endophytic , and strains and verified they had differential promoting effects on the medicinal compound accumulation in root. This study reports the interaction between and soil microbe communities under drought stress, and provides insights for improving the outcomes in farming applying microbe inoculation.