The plant-associated microbiome, as part of the extended plant phenotype, is expected to be influenced by plant genome. While accumulated evidence indicates that genetic variation within a host species (i.e. genotype) and among distinct host species drives microbial assemblies in phyllosphere and rhizosphere, we know little about how species hybridization affects the associated microbiome, and whether this effect is consistent across rhizosphere, phyllosphere and anthosphere. To address these questions, we used wild strawberries (Fragaria) as the model system, focusing on two pure species (F. chiloensis and F. virginiana ssp. platypetala) and their natural hybrid (F. ×ananassa ssp. cuneifolia, the wild relative of the cultivated strawberry), as hybridization has resulted in divergence among these species in sexual dimorphism and ecological niche, and perhaps the associated microbiota as well. Using 16s rRNA sequencing, we characterized the root, leaf and flower microbiomes of these three species in the broadly sympatric portion of their native ranges. Specially, we asked two key questions: 1) Does host species play the dominant role in structuring microbiota, compared to other factors (i.e. organ type and sexual phenotype)? 2) Does the hybrid species harbor intermediate microbiome relative to two pure species consistently across rhizosphere, phyllosphere and anthosphere?
Results/Conclusions
Relative to host species or host sex, organ type explained the largest variation of compositional and phylogenetic α- and β-diversity of bacterial communities associated with these plants. We then evaluated how the microbiome of the hybrid species diverged from those of two pure species in rhizosphere, phyllosphere and anthosphere separately. Both PERMANOVA and multivariate GLMs revealed that host species explained the largest source of variation in both compositional and phylogenetic structures of flower microbiome. In particular, the hybrid species possessed a flower microbiome resembling that of F. virginiana ssp. platypetala, which also shares more similarity in floral traits with the hybrid relative to the other pure species (F. chiloensis). In leaf microbiome, host species only affected the compositional structure of microbiota, with the hybrid being more similar to F. virginiana ssp. platypetala in microbiota. By contrast, root microbiome was similar among all three host species in both compositional and phylogenetic structures. Overall, our results reveal that plant hybridization can influence the associated microbiota, and this effect is strongest in anthosphere where divergence among species is essential for enhancing reproductive isolation, relative to rhizosphere and phyllosphere.