Effects of root rot disease on the microbiome and metabolites in roots and rhizosphere soil of sweet cherry

• Root rot disease affects the nutrient absorption capacity of sweet cherry by altering the interactions between flavonoids, nitrogen-fixing bacteria, and NH 4 + -N within the roots. • Plants can activate their innate immune systems by regulating key metabolites, thereby effectively influencing the rhizosphere bacterial community to combat root rot disease. • Sweet cherry oot rot disease result from the combined action of multiple pathogenic fungi, which strategically breach the tree's defenses and cause root damage. • Investigating the characteristics of metabolites and microbial communities in the roots and rhizosphere soil of woody plants affected by root rot disease. Root rot is a devastating disease in sweet cherry. Rhizosphere, endophytic microbiome, and plant immunity are believed to contribute to plant disease suppression in soil. However, the interactions between plants, rhizosphere soil, and microbes are poorly understood in sweet cherry regarding to root rot disease. This study investigated the microbial community structures, metabolites, soil properties, plant physiological characteristics and their relationships in sweet cherries affected by root rot. Diseased trees exhibited substantially decreased tree height, total chlorophyll, and specific leaf area, but increased proline and H 2 O 2 content. Rhizosphere soil of diseased trees also showed changes with lower nitrogen, higher electrical conductivity (EC) and moisture. Notably, bacterial, and fungal community compositions differed significantly between healthy and diseased trees in roots and rhizosphere soil. Specific fungal genera like Ilyonectria, Cylindrocarpon and Fusarium emerged as potential infection indicators. We also found distinct metabolite profiles in roots and rhizosphere soil, with diseased roots showing decreased levels of key metabolite classes, particularly phenylpropanoids and polyketides, lipids and lipid−like molecules, and organic oxygen compounds. In contrast, the quantities of differential metabolites in the rhizosphere soil showed similar increases and decreases, primarily belonging to lipids and lipid−like molecules, organic oxygen compounds, and benzenoids. Network analysis revealed root rot disease affected nutrient uptake and immune signaling by influencing nitrogen-associated microbes in the roots, actinomycete bacteria in rhizosphere soil, and reactive oxygen species (ROS) in plants. This study provides new insights into root rot infection mechanisms, which could aid in developing novel control strategies.