Auxiliary Rapid Identification of Pathogenic and Antagonistic Microorganisms for Coptis Chinensis Root Rot by High-throughput Sequencing

Root rot reduced the yield and medical quality of C. Chinensis . Previous studies of Coptis root rot focused on the identification of pathogens and the rhizosphere microbial community composition. In order to provide more evidence for preventing this disease, the present study was to identify the pathogenic and antagonistic microorganisms based on a high-throughput sequencing technique. The healthy and diseased C. chinensis in the endosphere and rhizosphere from the same field were collected to investigating the differences in microbiome composition and function. The results showed that the composition and function of microbes were different. The animal pathogen, soil saprotroph, plant saprotroph, and wood saprotroph in the endosphere of the diseased C. chinensis were higher than the healthy endosphere, which was dominated by Phaeosphaeriaceae, Cladorrhinum , Fusarium , Exophiala , and Melanommataceae. Fusarium , Volutella , Cladorhinum , Cylindrocarpon , and Exophiala were significantly enriched in the endosphere of diseased plants. Co-occurrence network analysis showed that Bacillus were negatively correlated with Fusarium , Volutella , and Cylindrocarpon , indicating that they may be antagonistic microorganisms. To verify the sequencing results, F. solani and F. avenaceum have been isolated and verified as pathogens, and 14 Bacillus bacteria have been isolated, which displayed an apparent suppression effect against the two pathogens on PDA medium and detached root. The strategy of high-throughput sequencing has the potential for the comprehensive identification of pathogenic and antagonistic microorganisms for plant disease. These results lay the foundation for future studies on mitigating or preventing root rot damage to C. chinensis .