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Notoginseng ( Panax notoginseng ), a valuable herbal medicine, has high death rates in continuous cropping systems. Variation in the soil microbial community is considered the primary cause of notoginseng mortality, although the taxa responsible for crop failure remains unidentified. This study used high-throughput sequencing methods to characterize changes in the microbial community and screen microbial taxa related to the death rate. Fungal diversity significantly decreased in soils cropped with notoginseng for three years. The death rate and the fungal diversity were significantly negatively correlated, suggesting that fungal diversity might be a potential bioindicator of soil health. Positive correlation coefficients revealed that Burkholderiales, Syntrophobacteraceae,  Myrmecridium ,  Phaeosphaeria ,  Fusarium , and  Phoma  were better adapted to colonization of diseased plants. The relative abundance of  Fusarium oxysporum  ( R  = 0.841,  P  < 0.05) and  Phaeosphaeria rousseliana  ( R  = 0.830,  P  < 0.05) were positively associated with the death rate.  F. oxysporum  was a pathogen of notoginseng root-rot that caused seedling death. Negative correlation coefficients indicated that Thermogemmatisporaceae, Actinosynnemataceae, Hydnodontaceae, Herpotrichiellaceae, and  Coniosporium  might be antagonists of pathogens, and the relative abundance of  Coniosporium perforans  was negatively correlated with the death rate. Our findings provide a dynamic overview of the microbial community and present a clear scope for screening beneficial microbes and pathogens of notoginseng.

Soil bacterial and fungal community dynamics in relation to Panax notoginseng death rate in a continuous cropping system