Auxiliary rapid identification of pathogenic and antagonistic microorganisms associated with Coptis chinensis root rot by high-throughput sequencing

Abstract

Root rot reduces the yield and medical quality of C. chinensis (Cc). Previous studies of Coptis root rot focused on the identification of pathogens and the rhizosphere microbial community composition. The present study aimed to identify potential pathogenic and antagonistic microorganisms associated with root rot based on a high-throughput sequencing technique to prevent this disease. Healthy and diseased Cc in the endosphere and rhizosphere from the same field were collected to investigate the differences in microbiome composition and function. The results showed that the composition and function of microbes were different. The numbers of animal pathogens, soil saprotrophs, plant saprotrophs, and wood saprotrophs in the endosphere of diseased Cc were higher than those in the healthy endosphere and were dominated by Phaeosphaeriaceae, Cladorrhinum, Fusarium, Exophiala, and Melanommataceae. Fusarium, Volutella, Cladorrhinum, Cylindrocarpon, and Exophiala were significantly enriched in the endosphere of the diseased plants. Co-occurrence network analysis showed that Bacillus was negatively correlated with Fusarium, Volutella, and Cylindrocarpon, indicating that Bacillus may be antagonistic microorganisms. To verify the sequencing results, F. solani and F. avenaceum were isolated and verified as pathogens, and 14 Bacillus strains were isolated, which displayed an apparent suppression effect against the two pathogens on PDA medium and detached roots. The strategy of high-throughput sequencing has the potential for the comprehensive identification of pathogenic and antagonistic microorganisms for plant disease. These results provide research ideas and microbial resources for future studies on mitigating or preventing root rot damage to Cc.

Multi-Omics Analysis Reveals the Resistance Mechanism and the Pathogens Causing Root Rot of Coptis chinensis

“…The results of the present study showed that Diaporthe eres , Fusarium avenaceum , and Fusarium solani were the dominant pathogens in the rhizosphere microbial community to cause root rot in C. chinensis . Among them, Fusarium avenaceum and Fusarium solani were consistent with the previous study's findings that both were pathogens closely related to C. chinensis root rot ( 11 ). And different from previous studies, the present study found that the abundance of Fusarium solani in healthy and diseased Coptis rhizosphere soils was significantly lower than that of Fusarium avenaceum .…”

“…However, similar to other tuberous medicinal plant, root rot is the main disease that harms the production and quality of C. chinensis . Previous studies have illustrated that plant metabolites and microflora contribute to host plant defense against pathogens ( 11 , 28 , 29 ). Recently, there has been increasing evidence that root/rhizosphere microbiota are directly or indirectly involved in host plant metabolic processes by regulating host secondary or specialized metabolism ( 30 ).…”

“…The fungal ITS2 region was amplified with the ITS3_KYO2 and ITS4 primers in this study. PCRs were conducted following a previously described protocol ( 11 ). Then, the 2% agarose gels and Trelief DNA Gel Extraction kit (TSINGKE, TSP601-200, China) were used to extract and purify PCR amplicons according to the manufacturer’s instructions, respectively.…”

“…Root rot is a severe plant-pathogenic fungus disease that generally causes the aboveground part of the plant to wilt and the whole plant to die, which is also the main factor constraining medicinal herb rhizome yield, the content of medicinal ingredients (quality), and marketability in China ( 10 – 12 ). In C. chinensis , root rot will seriously affect the use of medicinal effects and become a major threat to its production and industry development ( 13 ).…”

“…In C. chinensis , root rot will seriously affect the use of medicinal effects and become a major threat to its production and industry development ( 13 ). The brown speckle or progressive necrosis that emerges in the rhizomes or fibrous roots can cause mortality of the infected whole plants ( 11 ). A previous study has found that the annual infection rate of root rot disease is 10 to 20% in the largest production region of C. chinensis in Chongqing (Shizhu).…”