Objective To decipher the association between corm rot disease in Crocus sativus and the impairment of the functional synergistic network within the rhizosphere microbiome, and to identify core beneficial microorganisms, thereby providing a basis for the targeted design of synthetic microbial communities (SynComs). Methods Rhizosphere soil samples from healthy and diseased saffron plants were collected. Metagenomic sequencing was employed to analyze the microbial community structure and function, while multivariate statistical analyses were used to identify differentially enriched taxa and disease-resistant functional pathways. Results The diseased rhizosphere was characterized by the abnormal proliferation of pathogens such as Fusarium oxysporum (with a combined relative abundance of up to 21%), alongside a significant decrease in the abundance of beneficial microbes like Bacillus and Trichoderma. In contrast, the healthy rhizosphere was enriched with functional pathways related to signal transduction, biosynthesis of antimicrobial compounds (e.g., nonribosomal peptides), and defense mechanisms. Species-function correlation analysis revealed that the core beneficial microorganisms in the healthy rhizosphere were significantly positively correlated with these disease-resistant functions, forming a potential “functional synergistic network”, which collapsed under diseased conditions. Conclusion The occurrence of corm rot is closely related to the disruption of the functional synergistic network in the rhizosphere microbiome. This study reveals the functional synergistic network constituted by core beneficial microbes in the healthy rhizosphere, providing key theoretical foundations and microbial resources for targeted restoration of this network and the design of multi-mechanistic SynCom-based biocontrol strategies.

Crocus sativus L.  /  corm rot  /  rhizosphere microbiome  /  functional synergistic network  /  synthetic microbial communities (SynComs)  /  metagenomics