Unraveling the characteristics of the microbial community and potential pathogens in the rhizosphere soil of Rehmannia glutinosa with root rot disease

The roots of R. glutinosa are a high-demand traditional Chinese medicine with many pharmacological functions and great economic value. However, root rot disease leads to a dramatic reduction in the yield and quality of R. glutinosa. Here, we combined high-throughput sequencing technologies and cultural approaches to investigate characteristics of the microbial community in the rhizosphere soil of R. glutinosa with root rot disease and identified potential pathogens. The results indicated the following: 1) Root rot of R. glutinosa had an intimate relationship with the imbalance of the microbial community. Some genera, such as Pseudomonas, Un-s-Sordariales and Un-s-Ascomycota, were more abundant in rhizosphere soil from diseased R. glutinosa than that from healthy R. glutinosa, while other genera, such as Sphingomonas, Streptomyces and Myrothecium, displayed the opposite trend. 2) The six isolates (Pseudomonas hibiscicola, Rhizopus stolonifer, Fusarium solani, Actinomucor elegans, Enterobacter aerogenes and Aspergillus tubingensis) from rotten roots were confirmed to be pathogens for root decay of R. glutinosa in pot experiments with different pathogenicities of 33.33%-100%, suggesting the potential synergy of several pathogens in causing root rot in R. glutinosa. Quantitative PCR and pathogenicity tests indicated that Pseudomonas hibiscicola of the genus Pseudomonas was probably the main microbe responsible for root rot in R. glutinosa.