Correlation between root exudate composition and beneficial bacteria underlies Fusarium wilt resistance in cucumber

Rhizosphere microbes regulated by root exudates play important roles in promoting plant growth and suppressing soil-borne diseases. However, their functions in monoculture systems are not well studied. Here, we integrated metabolomic and microbiome analyses to compare root exudate profiles and rhizosphere communities of Fusarium oxysporum f. sp. cucumerinum (Foc) resistant (CL11) and susceptible (ZN6) cultivars grown in naturally infested, continuous-cropping soil. The asymptomatic, resistant cultivar CL11 (CL11H) exhibited a metabolic signature enriched in defensive compounds (ganoderic acid I and L-isoleucine) and harbored a beneficial bacterial community dominated by Streptomyces, Cellvibrio, and Ensifer. While the asymptomatic susceptible cultivar ZN6 (ZN6H) showed elevated levels of primary metabolites (methylmalonic and succinic acids) and an enrichment in the relative abundance of Amycolatopsis and Flavobacterium. Upon symptom development, susceptible symptomatic ZN6 (ZN6D) mounted a "cry-for-help" response, accumulating L-tryptophan and citric acid, which correlated with recruitment of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. Conversely, resistant symptomatic CL11 (CL11D) deployed a metabolic profile (L-3-cyanoalanine, 4-hydroxybenzoyl glucose, D-fructose), which enriched Bacillus and Cellvibrio. Exogenous application of citric acid, L-isoleucine, L-tryptophan, hexadecanedioic acid, and succinic acid to susceptible ZN6 plants significantly suppressed wilt disease. These metabolites restructured the rhizosphere bacterial communities, demonstrated by enrichments of Pseudomonas, Burkholderia-Caballeronia-Paraburkholderia, and Comamonadaceae by L-tryptophan, as well as Pseudomonas and Bacillus promoted by L-isoleucine and citric acid, respectively. Moreover, succinic acid suppressed disease through microbiome-mediated mechanisms despite its in vitro positive effect on Foc growth. These findings demonstrate that root exudates are linked to cultivar-specific disease outcomes, and that target metabolite application can suppress Fusarium wilt through microbiome-mediated mechanisms or a combined antifungal mode.