Do below-ground genotypes influence above-ground microbiomes of grafted tomato plants?

Bacteria and fungi form complex communities (microbiomes) in the phyllosphere and rhizosphere of plants, contributing to hosts’ growth and survival in various ways. Recent studies have suggested that host plant genotypes control, at least partly, microbial community compositions in the phyllosphere. However, we still have limited knowledge of how microbiome structures are determined in/on grafted crop plants, whose above-ground (scion) and below-ground (rootstock) genotypes are different with each other. By using eight varieties of grafted tomato plants, we examined how rootstock genotypes determine phyllosphere microbial assembly in field conditions. An Illumina sequencing analysis showed that both bacterial and fungal community structures did not significantly differ among tomato plants with different rootstock genotypes. Nonetheless, a further statistical analysis targeting respective microbial taxa suggested that some bacteria and fungi were preferentially associated with particular rootstock treatments. Specifically, a bacterium in the genus Deinococcus was found disproportionately from ungrafted tomato individuals. In addition, yeasts in the genus Hannaella were preferentially associated with the tomato individuals whose rootstock genotype was “Ganbarune”. Overall, this study suggests to what extent phyllosphere microbiome structures can be affected/unaffected by rootstock genotypes in grafted crop plants.