Genotype-Dependent Recruitment of the Strawberry Holobiome
BackgroundCultivated strawberry (Fragaria × ananassa Duch., fam. Rosaceae) is an important fruit crop, greatly appreciated for its aroma and nutraceutical properties. Niche-specific characterisation of plant microbiome, from rhizosphere to aboveground plant organs, is crucial to understand the influence of structure and function of the microbial communities on plant phenotype, performances and disease resistance. Strawberry cultivation is challenged by a large variety of pathogens, which cause
... ogens, which cause substantial economic losses and require the frequent application of pesticides. Biological control is a promising and safer alternative to the use of xenobiotic pesticides. Biological control agents isolated from the microbiome of the host plant may have a superior efficacy in comparison to non-indigenous microbial inoculants. Therefore, the characterization of the native microbiome along different plant compartments is a key step for the successful microbial manipulation in farmlands. Results Here, we provide the first comprehensive description of the soil, rhizosphere, root and aerial parts microbiome of three commercially important strawberry cultivars ('Darselect', 'Elsanta' and 'Monterey') under cultural conditions. The fungal and bacterial microbiomes were functionally characterised to investigate their influence on plant disease tolerance, plant mineral nutrient content and fruit quality. The core microbiome included 24 bacteria and 15 fungal operative taxon units which were present in all compartments and plant genotypes. However, both plant organ and genotype had a significant role in assembling the microbial communities. The microbial community assemblage across different soil and plant compartments significantly correlated with disease resistance, mineral nutrient content in the plant and with fruit quality parameters. Interestingly, only the disease tolerant genotype 'Monterey' was able to recruit Pseudomonas fluorescens in all plant organs and to establish symbiosis with the arbuscular mycorrhiza Rhizophagus irregularis. These two species include several strains acting as pathogen biocontrol agents, plant growth promoters and plant defence inducers. Conclusions Altogether, our study provides the first comprehensive view of strawberry microbiome in relation to plant genotype, health and nutritional status and fruit quality parameters, shedding light on potential practical applications to increase the sustainability of crop production.