Nowadays, the notoginseng supply mainly relies on intensive field cultivation under artificial shade structures with fertile and moist soils as the wild-type notoginseng disappeared many years ago . The long shade cultivation, pesticide spray, and chemical fertilizers are widely used in cultivation of notoginseng. To achieve higher yield, the frequencies of pesticide and fertilizer use increase more as the product price increases. These agricultural managements improve the productivity to some degree, but also cause other problems, such as being toxic to humans, animals, and other crops, and development of fungicide-tolerant pathogen strains . At the same time, they affect the structures and functions of microorganisms in bulk soil, rhizosphere soil, and endophytes. The harmful effects should be investigated for further reasonable agro-applications in notoginseng planting.