Biofumigation affects the root and rhizosphere soil fungal microbiome of strawberry

Biofumigation has been proposed as an environmentally friendly method of plant protection against soil-borne pathogens but its effects on soil microbial communities remain poorly understood. The aim of this study was to investigate the effects of biofumigation with oilseed radish on rhizosphere soil and root associated fungal microbiomes of strawberry in the presence and absence of a soil-borne fungal pathogen, Verticillium dahliae. High throughput DNA sequencing was used to analyse possible changes in fungal community structure following biofumigation. Early flowering occurred in response to biofumigation, suggesting a stress-response of the plant and there was a significant decrease in berry yield. Fungal communities in the roots and rhizosphere soil were statistically distinct from each other. Biofumigation had a significant effect on the rhizosphere soil fungal microbiome but there was no significant effect of the pathogen. The fungal microbiome associated with roots was significantly restructured by both biofumigation and inoculation with Verticillium. An assessment of the fungal functional guilds associated with roots showed a significant reduction in abundance of arbuscular mycorrhizal guild in response to biofumigation or Verticillium inoculation. Though alpha diversity patterns of fungi associated with roots were not affected by either biofumigation or Verticillium, the combined effect of these two treatments resulted in a significant reduction in fungal species richness in the rhizosphere soil. This study highlights the importance of analysing both soil and root compartments as these communities may respond differently to soil management practices. Further investigations should reveal whether negative effects of biofumigation on symbiotic mycorrhizal fungi are host-genotype or soil dependent.