Abstract
Biofumigation has been proposed as an environmentally friendly method of plant protection against soil-borne pathogens, but its effects on microbial communities are still incompletely understood. Using high throughput DNA sequencing, we investigated the effects of oilseed radish residues on the root fungal microbiome of strawberry in the presence of a soil-borne fungal pathogen, Verticillium dahliae. Results of our greenhouse study show that early flowering occurred in response to residue addition, suggesting a plant stress-response and there was a significant decrease in berry yield. The fungal microbiome of roots was significantly restructured by both biofumigation and inoculation with Verticillium. In particular, the abundance of root endophyte- and arbuscular mycorrhizal functional guilds was reduced significantly as a result of biofumigant and V. dahliae addition, whereas the abundance of saprotrophs increased significantly when both treatments were applied together. Alpha diversity analyses of fungi associated with roots indicated a significant increase in species richness following Verticillium inoculation, whereas the biofumigant alone or in the presence of V. dahliae resulted in no significant effect, suggesting that apparently some rare taxa may have been enriched/stimulated in the presence of the pathogen. Further investigations should reveal whether negative effects of biofumigation on potentially beneficial root associated endophytes and arbuscular mycorrhizal fungi are host genotype- or soil-dependent.
Highlights
Microbial interactions in the rhizosphere play fundamental roles in influencing the growth, stress tolerance and health of plants
A significant decrease in berry yield was observed in response to biofumigant addition in the V. dahliae controls (+B–V) (ANOVA P = 0.024), but the reduction associated with biofumigant treatment in the presence of Verticillium (+B+V) was not statistically significant (Fig. S1)
Endophyte and arbuscular mycorrhizal guilds were signifi cantly abundant in the –B–V treatment and the saprotroph guild was significantly abundant in the +B+V treatment. To our knowledge this is the first study describing the effect of oilseed radish residues on the composition of the root fungal micro biome in strawberry plants
Summary
Microbial interactions in the rhizosphere play fundamental roles in influencing the growth, stress tolerance and health of plants. Current strategies for plant protection based on cultivation practices, including use of resistant cultivars and application of pesticides, are not always sufficient. Their hazardous effects on our environment and the European Directive 2009/128/EC (2009) on sustainable use of pesticides necessitate the development of alternative solutions that are environmentally sound and sustainable. In this context, use of biocontrol agents is being explored to control pathogens, soil-borne pathogens that are difficult to control with current practices. The effects of biocontrol agents have been shown to differ with respect to host geno type response, indicating a need to find better alternatives
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