Characterization of inter-annual changes in soil microbial flora of Panax ginseng cultivation fields in Shimane Prefecture of Western Japan by DNA metabarcoding using next-generation sequencing.

Panax ginseng C.A.Mey. (Araliaceae) cultivation suffers from the inability to cultivate the same fields continuously for long durations due to replant failure. The main cause of replant failure is considered to be the annual change in the soil microbial flora, especially the invasion and settlement of pathogenic microorganisms of soil-borne diseases. We analyzed the soil bacterial and fungal flora and inter-annual changes in their composition over 5 years in ginseng cultivation fields on Daikonshima Island, Shimane Prefecture of Western Japan by DNA metabarcoding using next-generation sequencing. Bacteria such as Sphingomonas sp., Bacillus sp., and Betaproteobacteria and the fungus Mortierella sp. were consistently detected throughout the cultivation period. The inter-annual compositional changes of the bacterial flora, especially two members of the family Burkholderiaceae, one member of the phylum Actinobacteria, one member of the genus Candidatus Koribacter, and one member of the genus Sphingomonas, corresponded to the cultivation period, whereas those of the fungal flora showed random changes, suggesting that the growth of ginseng may be greatly affected by changes in the bacterial flora. Therefore, a greater understanding of the bacterial flora could provide valuable information for the cultivation of ginseng. The absence of pathogenic microorganisms associated with soil-borne diseases, which have been reported as causative agents of the main diseases of ginseng, in all soil sampling sites throughout the entire cultivation period in this study proves, for the first time, that traditional cultivation management employing empirical methods and chemical control is an effective approach to control these pathogens. Therefore, the DNA metabarcoding of the bacterial flora could provide valuable information for cultivation management, specifically in detecting and controlling soil-borne pathogens responsible for ongoing cultivation damage in long-term cultivation of medicinal plants.