Root rot-infected Sanqi ginseng rhizosphere harbors dynamically pathogenic microbiotas driven by the shift of phenolic acids

Background and aims Root rot is a catastrophic disease of perennial medicinal plants which could be caused by various soil-borne fungal pathogens. However, the understanding of the composition and diversity of root rot pathogenic fungi, their successions and potential drivers remains limited. Methods Sanqi ginseng ( Panax notoginseng ) was selected as a model plant and the rhizosphere soils of root rot-infected Sanqi ginseng at different growth years were collected. Phenolic acid content, pathogen abundance, and fungal microbiota were examined by using the high-performance liquid chromatography (HPLC), real-time PCR and Miseq sequencing. Results Pathogenic agents dominated in the rhizospheric fungal microbiota of rotten Sanqi ginseng and mainly comprised of Ilyonectria , Plectosphaerella , Clonostachys , Gibberella , Pestalotiopsis , Fusarium , and Chalara , with Ilyonectria and Fusarium being most abundant. The composition of pathogenic microbiota, but not α-diversity indices, changed considerably with Sanqi ginseng growth. The shifts of phenolic acid profile were an important driver in changes of rhizosphere pathogenic microbiota, and same phenolic acid exerted distinct functions on differential pathogenic taxa. Particularly, the contents of p -coumaric acid, ferulic acid, and benzoic acid were positively correlated with the abundance of genus Fusarium and negatively correlated with the abundance of genus Ilyonectria . Conclusions Root rot-infected Sanqi ginseng rhizosphere harbors dynamically pathogenic microbiota driven by the shift of phenolic acids. This study provides insights into the composition, variation, and driver of root rot pathogenic microbiota; these insights are important for the development of targeted measure for the prevention and control of root rot diseases.