Root and the Rhizosphere Microbiomes Associated with Productive Grafted Tomato Plants.

Grafted plants are becoming more popular with organic tomato growers, due to increased yield and lower incidence of soil-borne diseases. The success of grafted tomato plants, in part, could be a function of the root-associated microbiome, as microbes are critical for plant health and performance. We analyzed the impact of grafting and rootstock genotypes on the bacterial communities inhabiting the rhizosphere and the endosphere of tomatoes using high-throughput sequencing of 16S rRNA. Our study evaluated rootstocks representing non-graft (BHN589), self-graft, and two hybrid grafts: (Maxifort and RST-04-106), while the scion (BHN589) remained the same across the treatments. The experiment was repeated at three study sites at Kansas for two years. Diversity measures calculated based on OTUs (Operational Taxonomic Units) revealed significantly more diverse communities in the more productive hybrid rootstock (Maxifort) compared to the non-graft controls, while the bacterial community was similar to the controls for the other hybrid rootstock (RST-04-106). Grafting itself had a non-significant effect on the diversity of the bacterial community, and the associated bacterial community was resilient to the applied grafting treatment. In all the rootstock genotypes, the rhizosphere had higher diversity compared to the endosphere; however, the major shift in the number of bacterial taxa was revealed in the endosphere, with the maximum number of differentially abundant taxa in Maxifort. Ordinate analysis showed that compartment (i.e., endosphere vs. rhizosphere) is an important factor for explaining the variation in the bacterial community, while the rootstock genotypes explained a small, but significant, percentage of the variation. Evaluation of OTUs associated with each treatment identified microbial taxa specific to rootstock genotypes in both the endosphere and the rhizosphere. Further research on the taxa identified through analysis of microbial responses to rootstock management will ultimately support vegetable production, and inform efforts towards phytobiome-based crop breeding and disease management.