Taxonomical and functional composition of strawberry microbiome is genotype-dependent

Introduction: Specific microbial communities are associated to host plants, influencing their phenotypeand fitness. Despite the rising interest in plant microbiome, the role of microbial communities associatedwith perennial fruit plants remains overlooked.Objectives: This work provides the first comprehensive description of the taxonomical and functionalbacterial and fungal microbiota of below- and above-ground organs of three commercially importantstrawberry genotypes under cultural conditions.Methods: Strawberry-associated fungal and bacterial microbiomes were characterised by NextGeneration Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria.Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineralnutrient content, and fruit quality was investigated.Results: Results showed that the strawberry core microbiome included 24 bacteria and 15 fungal operational taxonomic units (OTUs). However, plant organ and genotype had a significant role in determiningthe taxonomical and functional composition of microbial communities. Interestingly, the cultivar withthe highest tolerance against powdery mildew and leaf spot and the highest fruit productivity was theonly one able to ubiquitously recruit the beneficial bacterium, Pseudomonas fluorescens, and to establisha mutualistic symbiosis with the arbuscular mycorrhiza Rhizophagus irregularis.Conclusion: This work sheds light on the interaction of cultivated strawberry genotypes with a variety ofmicrobes and highlights the importance of their applications to increase the sustainability of fruit cropproduction