Do root mycobiota recruitment differ from the one acting for the bacterial microbiota? The tomato case

The current wealth of studies on the plant microbiota reflects the widespread interest in this topic, since root-microbe interactions are not only crucial for better understanding plant growth and health, but also for sustainable crop production in a changing world. To date, such studies focus almost exclusively on the bacterial dimension of the root-associated microbiota. However, given the unique biological and ecological features of fungi, recruitment of the fungal microbiota may deviate from the relationships documented for bacteria. For instance, due to the mycelial growth form, the distinction among the different rhizosphere compartments (root surface/tissues vs rhizosphere soil) may be less clear-cut for fungi than for bacteria. Within the framework of a project combining meta-barcoding and systems biology to infer the principles underlying the interactions between tomato and its root mycobiota (Mycoplant), we addressed the relative importance of different factors (soil type, cultivar-specificity, abundant pathogen presence) shaping this fungal microbiota. Approx. 900 000 ITS2 and EF1-alpha amplicons obtained from the roots of four tomato cultivars grown in two different soils under greenhouse conditions were analyzed. Tomato genotypes either susceptible (Moneymaker, Cuore di Bue) or resistant (Heinz; Battito) to Fusarium oxysporum f. sp. lycopersici were used; the two resistant cultivars had been grown either in the presence or in the absence of the pathogen. Rhizosphere and bulk soil samples were also analyzed. Both soil type and plant genotype were significant drivers of the structure of root mycobiota, the magnitude of the impact of the two factors being comparable in some cases. Inoculation with the pathogen also significantly affected the communities associated with the resistant cultivars.