Taxonomical and functional composition of strawberry microbiome is genotype-dependent

Introduction Specific microbial communities are associated to host plants, influencing their phenotype and fitness. Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked. Objectives This work provides the first comprehensive description of the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organs of three commercially important strawberry genotypes under cultural conditions. Methods Strawberry-associated fungal and bacterial microbiomes were characterised by Next-Generation 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 mineral nutrient 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 determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highest tolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonas fluorescens, and to establish a mutualistic symbiosis with the arbuscular mycorrhiza Rhizophagus irregularis. Conclusion This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop production.