Interactions between plants and their root-associated microbiome are important for determining host fitness during periods of stress. During drought, monoderm bacteria are more abundant in sorghum roots than in those of watered controls. Additionally, a reversion from monoderm to diderm dominance occurs in drought-stressed roots one week after rewatering. However, the mechanisms driving this rapid microbiome composition shift is currently unknown. To understand if changes in host metabolism are correlated with this shift, we employed 16S amplicon sequencing and metabolomics of root, rhizosphere, and soil at the peak of a preflowering drought and 24 hours after rewatering. The microbiomes of droughted roots, rhizospheres, and soils differed from watered controls, and shifts in bacterial composition were observed in root and rhizosphere 24 hours after rewatering, highlighting the rapid response of microbes to the cessation of drought. Next, we performed metabolomic profiling to identify putative drivers of this process. During drought, we observed a high abundance of abiotic stress response factors, including antioxidants, osmolytes, amino acids, and plant hormones. After rewatering, large shifts in metabolite abundances were observed in rhizosphere, whereas shifts in root and soil were subtle. In addition, pipecolic acid, a well-characterized systemic acquired resistance signalling compound, was enriched in roots and rhizosphere during drought. We found that exogenous application of pipecolic acid suppresses root growth via a systemic acquired resistance-independent mechanism. Collectively, these data provide a comprehensive characterization of metabolite shifts across three compartments during drought, and elucidate a potential role of pipecolic acid in the sorghum drought response. ### Competing Interest Statement The authors have declared no competing interest.

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