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Plant roots host diverse microbes that are closely associated with root fitness. Currently, the relationship between microbes and rusty roots of  Panax ginseng  remains unclear. Here, we described the root-associated microbiome in rusty and healthy ginseng by metagenomic sequencing of 16S rRNA and ITS regions. Being enriched in Diseased-roots (Dr) of ginseng and their rhizosphere soil, the fungus of  Ilyonectria , was identified as the most probable cause of the disease after ITS analysis. Meanwhile, an increase of  Mortierella  was observed in Healthy-roots (Hr). Surprisingly, an enriched  Fusarium  was found in both Hr and their rhizosphere soil. Besides, in comparison with Hr, decreased relative abundance of  Actinomycetales  and increased relative abundance of  Pseudomonadales  was observed in Dr after 16S rRNA analysis. What’s more, we isolated several microorganisms as antagonists that showed strong inhibiting effects on  Ilyonectria  in plate assays. In field trials, inoculation of  Bacillus  sp. S-11 displayed apparent suppression effect against  Ilyonectria  and shifted microbial communities in rhizosphere soil. Our research identified key microbiota involved in rusty roots of  P. ginseng  and offered potential biocontrol solutions to rusty disease.

Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria