Analysis of rhizosphere bacterial and fungal communities associated with rusty root disease of Panax ginseng

Rusty root is a widespread problem in ginseng production, which can reduce ginseng quality and root price. The formation of rusty root is a complex process caused by multiple factors, primarily soil physicochemical factors and microorganisms. However, the precise roles played by these factors in the development of this disease remain unclear, especially the role of microorganisms. Deciphering the structure of the rhizosphere microbial communities will provide a more comprehensive and deeper understanding of rusty root disease. Rhizosphere microbial communities from five ginseng fields with different rusty root grades and indices were characterized by MiSeq sequencing. The pattern of beta diversity indicated that rusty root disease might be positively correlated with bacterial community structure, but not with fungal community structure. Rusty root may be caused by excessive Fe (II) oxidation and Fe (III) deposition accompanied by aluminum (Al) and manganese (Mn), in which nitrate-dependent Fe (II)-oxidizing bacteria, including Acidobacteria, Chloroflexi, and Nitrospirae, play a driving role. Moreover, the accumulation of iron (Fe), Al, and Mn could enhance growth and weak invasion of some fungi, thus exacerbating the rust symptoms. However, no correlation was found between the relative abundance of the genus Ilyonectria and rusty root grade or index (P > 0.05); suggesting that Ilyonectria species may not be essential for rusty root disease. Thus, the oxidation and deposition of rhizosphere Fe, Al, and Mn facilitated by nitrate-dependent Fe (II)-oxidizing bacteria might be key factors contributing to rusty root disease. Further studies on the inhibition of Fe, Al, and Mn transformation and accumulation, and application of iron/nitrogen-cycling related bacteria in ginseng soil might elucidate effective methods for preventing rusty root.