Deciphering Conserved Rhizosphere Metabolite–Microbiome Interactions for Crop Drought Resistance

Drought stress is a major threat to global food security. It remains uncertain whether conserved drought-responsive microbes can be recruited by different crop species to help their adaptation to drought and how this recruitment occurs. Herein, we identified drought-responsive rhizosphere microbial genera conserved across multiple crop species under drought stress and elucidated their in situ regulatory mechanisms. Integrated amplicon sequencing of rhizosphere microbiomes from 26 crop species indicated 6 core genera (Streptomyces, Glycomyces, Inquilinus, Amycolatopsis, Acinetobacter, and Promicromonospora) consistently enriched under drought. Soil conditioning with 46 shared rhizosphere metabolites among multiple crops demonstrated that trehalose, myo-inositol, and phenylalanine synergistically enrich the six genera. The soil microbiome conditioned with three compounds significantly increased root length and leaf water content when evaluated in greenhouse trials (tomato, cucumber, and watermelon) and sorghum field studies. Furthermore, the conditioned soil microbiome exhibited enrichment in pathways related to energy supply, protective compound synthesis, and plant interaction signaling, driven by six core genera. Pure culture experiments revealed a potential cross-phylum interaction; that is, Streptomyces could synthesize phenylalanine to recruit Acinetobacter. Our findings reveal a potential conserved rhizosphere metabolite-microbiome interactions across multiple crops, offering a talent pathway to steer soil microbiome for drought resistance.