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Autotoxic ginsenosides have been implicated as one of the major causes for replant failure of Sanqi ginseng (Panax notoginseng), however, the impact of autotoxic ginsenosides on the fungal microbiome, especially on soil-borne fungal pathogens, remain poorly understood. In this study, we aimed to investigate the influence of ginsenoside monomers Rg1, Rb1, Rh1, and their mixture (Mix) on the composition and diversity of the soil fungal community as well as the abundance and growth of soil-borne pathogen Fusarium oxysporum in pure culture. The addition of autotoxic ginsenosides altered the composition of the total fungal microbiome as well as the taxa within the shared and unique treatment-based components, but not a-diversity. In particular, autotoxic ginsenosides enriched potentially pathogenic taxa, such as Alternaria, Cylindrocarpon, Gibberella, Phoma, and Fusarium, and decreased the abundances of beneficial taxa such as Acremonium, Mucor, and Ochroconis. Relative abundances of pathogenic taxa were significantly and negatively correlated with that of beneficial taxa. Among the pathogenic fungi, the Fusarium genus was most responsive to ginsenoside addition with the abundance of F. oxysporum consistently enhanced in the ginsenoside-treated soils. Validation tests confirmed that autotoxic ginsenosides promoted mycelial growth and conidial germination of the root-rot pathogen F. oxysporum. In addition, the autotoxic ginsenoside mixture exhibited synergistic effects on pathogen proliferation. Collectively, these results highlight that autotoxic ginsenosides are capable of disrupting the equilibrium of fungal microbiomes through the stimulation of potential soil-borne pathogens which presents a significant hurdle in remediating replant failure of Sanqi ginseng. [ABSTRACT FROM AUTHOR]