Objective Root rot has become a bottleneck restricting the industrial development of Monochasma savatieri, however, current understanding regarding its pathogenesis remains poorly understood. Methods This study took three groups of M. savatieri with different root rot progress and their rhizosphere soil as the research objects, and determined the soil physical and chemical properties of rhizosphere soil and the content of main active components of M. savatieri; metagenomic sequencing of the rhizosphere soil of M. savatieri. Results With the development of root rot, the physical and chemical properties of rhizosphere soil changed significantly. Among them, pH, electrical conductivity (EC) and available phosphorus increased significantly with the deepening of disease severity, while the contents of total carbon and total nitrogen showed the opposite trend. And the contents of total flavonoids, luteolin, apigenin and isoverbascoside were significantly reduced, while the content of verbascoside was increased. The microbial diversity increased with the deepening of disease severity, and the abundance of pathogenic bacteria related to soil-borne diseases in the soil, such as Fusarium, Cladosporium and Botrytis, as well as beneficial Trichoderma, increased in the later stage of the disease. The metabolic related pathways under KEGG annotation, such as fatty acid metabolism, glyoxylic acid and dicarboxylic acid metabolism, β-alanine metabolism and pyruvate metabolism, were more enriched than those in the healthy group and the mid-stage disease group. The pH value and EC value were significantly positively correlated with the abundance of potential pathogenic fungi. The genera such as Microbacterium, Drechslerella, Metarhizium and Trichoderma, which show significant positive correlations with total flavonoids of M. savatieri, luteolin, apigenin and verbascoside, may be involved in the improvement of soil microecology and the process of plant disease resistance. Conclusion Through a comprehensive correlation analysis of key indicators in the “M. savatieri -Microorganisms-Soil” system under different progression stages of root rot, this study systematically elucidates the patterns of change and interaction relationships among the three during the disease progression. The findings provide a basis for uncovering the microecological mechanisms underlying the occurrence of root rot in M. savatieri, as well as for developing control strategies through the regulation of soil and rhizosphere microorganisms.

Monochasma savatieri Franch. ex Maxim.  /  soil-borne diseases  /  metagenome  /  soil physicochemical factors  /  rhizosphere soil  /  luteolin  /  apigenin  /  verbascoside