Integrated microbiome and metabolome approaches reveal the resistant mechanisms of leaf blight resistant plum cultivar

Abstract Background Endophytic microbiome and metabolome are closely related to the plant resistance. Unravelling the compositional features of the endophytic microbiome and metabolome can help to understand plant resistant mechanisms. This study investigates the resistant mechanisms of leaf blight-resistant plum cultivars through comparative analysis of endophytic microbiome and metabolome features between leaf blight resistant (Mihuang Plum, RP) and susceptible (Pearl Plum, SP) cultivars. Results The results showed that higher microbial diversity and richness could be detected in RP cultivar than those of SP cultivar. Meanwhile, the endophytic bacterial genera, such as 1174-901-12 , Sneathia , Gardnerella , Bacteroides , Prevotella , Fastidiosipila , and the endophytic fungal genera, Paramycosphaerella , Epicoleosporium , Zasmidium , and Zeloasperisporium were enriched in the RP cultivar. Moreover, in comparison with SP cultivar, Flavonoid biosynthesis, Isoflavonoid biosynthesis, Phenylalanine metabolism, Phenylpropanoid biosynthesis, and Nucleotide metabolism showed high expression levels in RP cultivar, and the contents of (-)-Naringenin, 4-Coumaric acid, Epicatechin, Genistein, M-Coumaric acid, Dihydrokaempferol, and 4-Hydroxycinnamic acid were also significantly higher in RP cultivar. Conclusions Our findings had revealed that significant differences of endophytic microbiome and metabolome features could be found between leaf blight resistant (Mihuang Plum, RP) and susceptible (Pearl Plum, SP) cultivars. Meanwhile, positive correlations between potential functional microorganisms, metabolites and leaf blight resistant plum cultivar also had been identified. In future research, a deeper exploration of these microbial communities and metabolites is warranted to fully understand their functional roles in the resistance mechanisms. Identifying the specific microbial taxa and metabolites that contribute to leaf blight resistance could provide valuable insights into their potential applications in biological control. By harnessing these natural microbial and metabolic resources, it may be possible to develop sustainable, eco-friendly strategies for managing leaf blight, ultimately reducing the dependency on chemical pesticides. Graphical Abstract