Fragrant rice gains enhanced 2-acetyl-1-pyrroline and multi-stress resistance through a JA-proline module induced by a Rhizopus fungus

Rhizosphere microorganisms play crucial roles in regulating crop secondary metabolism and stress adaptation, yet the mechanisms by which they coordinately enhance both 2-acetyl-1-pyrroline (2-AP) and stress resistance in fragrant rice remain unclear. Here, we report a newly isolated a Rhizopus strain TYR1 (CGMCC NO: 42112) from fragrant rice rhizosphere. Through field trials, pot experiments, hydroponics, and plate assays combined with transcriptomics, qRT-PCR, metabolite quantification, and enzyme activity analysis, we show that TYR1 specifically colonizes rice roots and simultaneously increases grain 2-AP content by 38.04% (2023 field) and 48.37% (2024 field), and enhances tolerance to five abiotic stresses (phosphorus deficiency, iron deficiency, cadmium toxicity, salt, and drought), with shoot fresh weight increased by 25–62% and SPAD value by 18–35% under stress conditions. Importantly, TYR1 treatment did not compromise yield traits (1000-grain weight, seed-setting rate) but significantly improved milling quality (brown rice rate, milled rice rate) and eating quality (taste value). Mechanistically, TYR1 secretes bioactive compounds that activate the jasmonic acid (JA) signaling pathway (JA and JA-Ile increased by 2.8- and 3.2-fold), which in turn upregulates proline biosynthesis ( sP5CS1 / OsP5CS2 ) and catabolism ( OsProDH ), leading to proline accumulation (2.1-fold). Proline serves a dual function: as an osmoprotectant and ROS scavenger to reinforce stress tolerance, and as a direct precursor for 2-AP synthesis via non-enzymatic reaction with methylglyoxal. JA inhibition by diethyldithiocarbamic acid (DIECA) abolishes both proline accumulation and 2-AP enhancement, demonstrating that JA signaling bridges induced defense response and aroma synthesis within a unified physiological module. This study reveals a JA-proline metabolic hub that synchronously optimizes stress adaptation and flavor formation in fragrant rice, providing a microbial resource for green biofertilizer development.