Integrated multi-omics analysis of chlorosis in Phyllostachys edulis seedlings

Moso bamboo ( Phyllostachys edulis ) is a forestry crop with a high economic and edible value. However, chlorosis in sexually propagated seedlings markedly reduces their survival rates. In this study, an integrated multi-omics approach was employed to investigate the underlying causes and molecular basis of chlorosis. The differentially expressed genes and metabolites in chlorotic seedlings were predominantly enriched in phenylpropanoid biosynthesis and plant-pathogen interaction pathways. Microbial analysis indicated that Scleroderma dominated the root microbiota in healthy seedlings, while the chlorotic roots were enriched with potential pathogens, such as Fusarium , which demonstrated pathogenic infection. Seven fungal and fifteen bacterial endophytic genera were isolated from chlorotic roots, among which three strains ( Pseudomonas spp. and Pantoea sp.) exhibited potential biocontrol activity. These findings provide mechanistic insights into the etiology of chlorosis and support the development of microbial biocontrol strategies in Moso bamboo cultivation. • Investigated the causative factors of chlorosis in Moso bamboo seedlings through integrated multi-omics analysis. • Identified pathogenic microbes as key drivers of chlorosis in Moso bamboo seedlings. • Elucidated critical pathways involved in the defense response of Moso bamboo against pathogen invasion. • Isolated multiple potential pathogenic fungi and antagonistic bacterial strains.