Analysis of metabolome and microbiome revealed the resistance mechanisms in sugarcane cultivars with high resistance to pokkah boeng disease

Background Endophytes are reported to play a role in resistance against plant pathogens. Understanding the metabolite-mediated endophytic microbiota composition in plants provides insights to improve plant stress resistance. In this study, via metabolome and microbiome analyses, we aimed to elucidate the resistance mechanism of sugarcane cultivars with high resistance to sugarcane pokkah boeng disease (PBD). The endophytic microbial composition and metabolites in the stems of various sugarcane cultivars with high resistance (HR) or high susceptibility (HS) to PBD were analyzed.Results The results revealed that the endophytic fungi with biocontrol effects such as Shinella, Dechloromonas, and Microbacter were significantly enriched, and the abundance of pathogenic fungi such as Fusarium, Ramichloridium, Scleroramularia, Phaeosphaeriopsis, Sarocladium, Zygophiala, Gibberella, Pseudocercospora, Cyphellophora, Monocillium, Apiotrichum, Microsphaeropsis, and Scleroramularia significantly reduced in the stems of HR cultivars. Additionally, six metabolites [citric acid, isocitrate, malic acid, PC(16:0/0:0), phosphocholine, and lysoPC(16:0)] were significantly related to the endophytes in the stems of HR cultivars.Conclusions These results suggested that more abundance of antagonistic microbes and highly active metabolic functions of endophytes in the HR cultivars were the important mechanisms underlying their higher resistance to PBD.