Rhizosphere microbiome assembly mediated by consecutive monoculture triggers the replant disease of Rehmannia glutinosa

Consecutive monoculture of Rehmannia glutinosa results in severe replant disease and remarkably reduces the yield and quality. Rhizosphere microbiome plays a crucial role in soil health and plant performance. In this study, high-throughput pyrosequencing combined with a culture-dependent approach were applied to analyze the changes in rhizosphere microbiome structure and bacteria-fungi inter-kingdom associations under R. glutinosa consecutive monoculture. The results revealed a distinct separation between the newly planted (NP) and the two-year monocultured (SM). R. glutinosa consecutive monoculture resulted in a significant decline in the Shannon and Simpson diversity indices for the fungal community, and a significant decrease in relative abundances of the phyla Actinobacteria, Chloroflexi and Basidiomycota. The relative abundances of the genera Streptomyces, Arthrobacter, Bacillus, Nocardioides and Lysobacter were significantly higher in NP than in SM, while the opposite was true for Fusarium. Quantitative PCR confirmed a significant reduction in the phylum Actinobacteria and the genus Bacillus, and a significant increase in Fusarium oxysporum. Furthermore, the abundances of Actinobacteria and Bacillus strains with antagonistic activities against Fusarium oxysporum were lower in extended monoculture soils. Most of the isolated antagonistic bacteria were found to be positive for different plant growth promotion activities such as solubilization of phosphate and potassium, production of siderophore and indolic compounds. In addition, it was found that phenolic acid mixture and catalpol, identified in the root exudates of R. glutinosa, could selectively inhibit or stimulate different microbes. Moreover, the culture filtrate and volatile organic compounds produced by F. oxysporum could in turn suppress the growth of certain antagonistic bacteria. In conclusion, these findings highlight the close association between R. glutinosa replant disease and rhizosphere microbiome assembly, which was mediated by root exudates and microbe-microbe interactions.