Analysis of field-grown Panax ginseng rhizosphere microbiome provides clues for preventing red skin root syndrome

Abstract

Background Ginseng red skin root syndrome (GRS) is one of the most common ginseng diseases. It leads to a severe decline in ginseng quality and seriously affects the ginseng industry in China. However, as a root disease, the characteristics of GRS rhizosphere microbiome are still unclear. Methods The amplicon sequencing technology, combined with bioinformatics analysis, was used to explore the relationship between soil ecological environment and GRS. Results There were significant differences in the diversity and richness of soil microorganisms between the rhizosphere with different degrees of disease, especially between healthy ginseng (HG) and heavily diseased groups. We also found that bacterial communities underwent multiple changes between complex stability and simple instability in different ginseng rhizospheres through the established interaction networks. The GRS group also had more competition with each other and ecological niche separation than the HG group. The fungal community's stability decreased significantly in the early stages of the disease, followed by the formation of a stable and complex fungal community. The GRS groups significantly increased interspecies cooperation and ecological niche overlap in the fungal network than the HG group. Microbes closely related to potential pathogenic fungi were also identified according to the interaction network, which provided clues for looking for biological control agents. Finally, the Distance-based redundancy analysis (dbRDA) results indicated that total P (TP), available K (AK), available P (AP), catalase (CAT), invertase (INV) are the key factors that influence the microbial communities. Conclusions This study collectively analyzed the changing characteristics in ginseng rhizosphere and provided the basis for soil improvement and biological control of field-grown ginseng.