Composition, Structure, and Diversity of Rhizosphere Soil Microbial Community in Saffron (Crocus sativus) Affected by...

Fusarium oxysporum, first identified in Yunnan Province as the causal agent of saffron corm rot, causes a destructive soilborne disease that has become a devastating threat to saffron cultivation in Shangri-La, causing over 50% mortality. This pathogen infects saffron corms, leading to vascular browning and rot, ultimately causing plant death and severe production losses. Given the crucial role of the rhizosphere microbiome in plant immunity and soil ecology, deciphering pathogen-microbiome interactions is essential for developing sustainable disease-control strategies. High-throughput sequencing of ITS/16S rRNA (Illumina MiSeq) was combined with arbuscular mycorrhizal fungi (AMF) analysis to compare the community structures of fungi, bacteria, and AMF in the rhizosphere of healthy and diseased saffron. The effects of soil physicochemical factors on microbiome assembly were systematically evaluated. The rhizosphere microbiome of diseased plants was significantly dysregulated: (i) pathogen-related taxa (e.g., Lauriomyces) proliferated, while saprotrophic functional taxa (e.g., Mortierella elongata) underwent community restructuring; (ii) disease-suppressive taxa (e.g., Fusidium) were enriched, while symbiotic mycorrhizal fungi essential for nutrient acquisition sharply declined; (iii) the soil parameter-microbiome relationship changed under different health conditions: available phosphorus and available potassium drove the aggregation of pathogenic soil fungi, while pH and organic matter dominated the aggregation of healthy soil fungi; and (iv) Knufia and Phomopsis were important taxa regulating soil ammonia oxidation and plant vitality. Fusarium infection disrupts the rhizosphere balance by inhibiting beneficial symbionts and promoting the colonization of pathogenic or saprotrophic microorganisms, ultimately compromising the innate resistance of saffron. Our findings reveal the rhizosphere ecological mechanism underlying corm rot progression and provide a microbiome informatics framework for the selection of biocontrol agents and rhizosphere engineering.