Responses of Root Microbiome and Metabolome Are Linked to Crop Disease Severity

ABSTRACT Plant microorganisms are an essential component of the host and perform critical functions in plant development and health. Emerging evidence shows that plants use their root exudates to recruit beneficial microbes that protect them against abiotic and biotic stresses, including diseases. However, the metabolic responses of plant under pathogen infection remain underexplored. In this study, using a manipulative experiment, we employed amplicon sequencing and untargeted metabolomics to investigate the response of rhizosphere microbial communities and metabolites of root exudates to potato‐wilt disease caused by Ralstonia solanacearum (RS) across two developmental stages (vegetative and tuber bulking). Our results revealed that β‐diversity showed distinct shifts in bacterial and fungal communities between healthy and diseased plants. Higher relative abundance of bacterial taxa from genera, Bradyrhizobium, Cadidatus, Paenibacillus and the fungal genus Terramyces were observed in the rhizosphere of healthy plants. Similarly, Burkholderia spp and the fungal Apiotrichum spp dominated the rhizosphere of diseased plants across the developmental stages. Further compared to healthy plants, microbial functional potentials and metabolomic profiles of root exudates linked to pathogen resistance were significantly enhanced in diseased plants. Particularly, metabolites from alkaloids, triterpenoids and polyketides were enriched in disease plants and exhibited associations with microbial groups known to influence host immunity, nutrient acquisition and stress adaptation. We observed that variations in disease index were associated with the identified enriched metabolites. Our integrative analysis provides evidence for multifaceted signalling, sensing between plants, pathogens and beneficial microbiota that may shape plant health status and microbiome assembly under pathogen pressure. These insights not only advance our understanding of crop pathophysiology but also lay the foundation for developing targeted biological strategies or metabolic markers for early disease detection and sustainable crop protection.