Microbiome network connectivity and composition linked to disease resistance in strawberry plants

Abstract

Plants recruit diverse microbial communities from the soil to their roots. Inter-microbial interactions and connectivity in the root microbiome play essential roles in plant health by promoting resistance to soil-borne pathogens. Yet, the understanding of these interactions under field conditions is still scarce. Using a strawberry crop model, we characterized the prokaryotic and the fungal communities in the rhizosphere and the roots of three strawberry cultivars grown under field conditions and displaying varying degrees of resistance to the soil-borne fungal pathogen Macrophomina phaseolina. We tested the hypothesis that resistant cultivars assemble distinct bacterial and fungal communities that foster microbial connectivity and mediate disease resistance. Our results show that the soil-borne pathogen, M. phaseolina, does not alter the root microbiome of the three strawberry cultivars. Microbiome comparative analysis indicated that the highly susceptible cultivar, Sweet Ann, assembled a distinct rhizosphere and root microbiome, whereas the microbiome of the strawberry cultivars Marquis and Manresa, were more similar and enriched with potential beneficial microbes. Co-occurrence network analysis revealed that the fungal pathogen, M. phaseolina, was more peripheral in the microbial network of Sweet Ann compared to Manresa and Marquis. Collectively, these results stress the role of the plant microbiome in mediating resistance against soil-borne pathogens and further suggest the role of plant genetic traits in the assembly of beneficial microbiome members. Our study reinforces the eminent role of the plant microbiome as trait selection in breeding programs and the need for further understanding of the genetic and biological mechanisms that mediate microbiome assembly. Uncovering these mechanisms will be key for the future success of plant breeding programs in their fight against soil-borne pathogens.