Drought shifts sorghum root metabolite and microbiome profiles and enriches for pipecolic acid

Plant-associated microbial communities shift in composition as a result of environmental perturbations, such as drought. Recently, it has been shown that Actinobacteria are enriched in plant roots and rhizosphere during drought stress, however, the correlations between microbiome dynamics and plant response to drought are poorly understood. Here we apply a combination of bacterial community composition analysis and plant metabolite profiling in Sorghum bicolor root, rhizosphere, and soil during drought and drought-recovery to investigate potential contributions of host metabolism towards shifts in bacterial composition. Our results provide a detailed view of metabolic shifts across the plant root during drought and show that the response to rewatering differs between root and soil; additionally, we identify drought-responsive metabolites that are highly correlated with the observed changes in Actinobacteria abundance. Furthermore, our study reports that pipecolic acid is a drought-enriched metabolite in sorghum roots, and that exogenous application of pipecolic acid inhibits root growth. Finally, we show that this activity functions independently from the systemic acquired resistance pathway, and has the potential to impact Actinobacterial taxa within the root microbiome.