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

The plant is one of the primary drivers of microbial communities in the rhizosphere. The consistent presence of same plant species over time, such as in monocropping in agriculture can drive significant changes in plant-associated microbiomes. Most of the studies with monocropping have focused on bacteria, which are involved in the natural suppression of a number of soilborne diseases, including Rhizoctonia root rot and take-all. However, few studies have examined how monocropping and root rot pathogens jointly affect the structure of fungal communities in the rhizosphere. In this greenhouse study, rhizosphere fungal communities from successive wheat plantings infected with the fungal pathogen Rhizoctonia solani AG8 were characterized using MiSeq sequencing targeting the ITS1 region of the rRNA gene. Sequence analyses revealed that distinct fungal groups clustered by 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 least root disease and those with the worst root disease. Planting cycles significantly reduced fungal alpha diversity. The most abundant fungal genus was Mortierella which increased in relative abundance with planting cycles in AG8-infected samples. In contrast, a group of fungal genera, including Pseudogymnoascus, Gibberella, Fusarium, Fusicolla, Exophiala, and Waitea, were reduced in relative abundance with successive plantings and AG8 infection. Together, this study revealed how fungal communities change with successive wheat growth under the pressure of a soilborne fungal pathogen.