Composition and function of soil mycobiomes associated with Rhizoctonia root and crown rot in sugar beet

Rhizoctonia root and crown rot (RRCR) is one of the major soilborne diseases of sugar beet that causes significant yield loss and exacerbates postharvest losses in the storage piles. To investigate the soil fungal communities (mycobiomes) influencing Rhizoctonia root rot (RRR), we used Illumina sequencing of the ITS rRNA gene to analyze field soils collected over three years (2016–2018) representing different levels of disease severity. Our analysis revealed that overall fungal diversity (alpha-diversity) and community composition (beta-diversity) did not correlate significantly with disease severity. This suggests that disease management strategies focused solely on broad-spectrum shifts in fungal diversity are unlikely to be effective. The soil mycobiome was consistently dominated by the phyla Ascomycota (mean relative abundance: 57.1%) and Basidiomycota (mean relative abundance: 21.1%), with Mrakia and Mortierella among the most prevalent genera. While the pathogen Rhizoctonia was ubiquitous, its relative abundance was generally low (∼2%). The RRR suppressiveness was associated with high abundance and significant expression of biocontrol and symbiotrophic fungal taxa. The current study provides in depth understanding of soil mycobiomes and functions that might be important indicators of Rhizoctonia suppressiveness in sugar beet. Future studies should focus on isolating and characterizing the specific biocontrol (e.g., Cladorrhinum , Chaetomium , and Cladorrhinum spp.) and symbiotrophic fungal taxa identified in this study to test their efficacy against R. solani AG 2–2. Further research is needed to determine the optimal conditions for inoculating sugar beet fields with these candidate microbes, and to assess their impact on RRR severity under field conditions.