Disease-induced assemblage of the rhizosphere fungal community in successive plantings of wheat

Authors: Yin, Chuntao; Schlatter, Daniel; HAGERTY, CHRISTINA - Oregon State University; HULBERT, SCOT - Washington State University; Paulitz, Timothy

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/16/2022
Publication Date: 6/6/2023
Citation: Yin, C., Schlatter, D.C., Hagerty, C., Hulbert, S.H., Paulitz, T.C. 2023. Disease-induced assemblage of the rhizosphere fungal community in successive plantings of wheat. Phytobiomes Journal. 7 (1):100-112. https://doi.org/10.1094/PBIOMES-12-22-0101-R.
DOI: https://doi.org/10.1094/PBIOMES-12-22-0101-R

Interpretive Summary: Microorganisms from plant roots can protect plants against soilborne pathogens. Research on suppressive microbes has focused on bacterial communities. However, the dynamics and function of fungal communities in soilborne disease suppression are poorly understood. We grew a susceptible wheat cultivar in a soil inoculated with the soilborne pathogen Rhizoctonia solani AG8 for multiple generations. Then we transferred wheat root microbes to the following generation for multiple cycles until disease suppression occurred. We used high-throughput DNA sequencing to characterize the soil fungal communities. We found that successive wheat plantings and pathogen infection changed soil fungal community, and diseased plant roots enriched some beneficial fungi. The findings enhance our knowledge of how monoculture and disease stress alter soil microorganisms and provide information for using microorganisms to control plant disease.

Technical Abstract: Natural suppression of soilborne diseases occurs after severe disease outbreaks in areas cropped to continuous wheat in the dryland Pacific Northwest. Bacterial communities have been reported to contribute to disease suppression. However, the role of fungal communities on the development of disease suppressive microbiomes is largely unknown. In this greenhouse study, rhizosphere fungal communities from successive wheat plantings with infection of fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) were characterized using MiSeq sequencing targeting the ITS1 region of the rRNA gene. Sequence analyses revealed that distinct fungal groups clustered by wheat planting cycles with or without AG8 inoculation, but infection with AG8 enhanced the separation of fungal communities. Clusters of fungal communities were also observed in AG8-infected and non-infected rhizospheres, whereas there was no difference in fungal communities between the rhizosphere with the lowest wheat root disease and those with the worst wheat root disease. Fungal alpha diversity drastically decreased with planting cycles. The most abundant fungal genus was Mortierella, a potential disease suppression indicator, which increased with planting cycles in AG8-infected samples. A group of potential pathogenic fungal genera, including Pseudogymnoascus, Gibberella, Fusarium, Fusicolla, Exophiala, and Waitea, were reduced with successive plantings and AG8 infection. Together, this study revealed how the structure of fungal communities changed with successive wheat growth under the pressure of a soilborne fungal pathogen and identified several potential fungal taxa that may be associated with the suppression of wheat root rot disease.