Comparative analysis of the rhizosphere and endophytic microbiomes across apple rootstock genotypes in replant orchard soils

Apple replant disease (ARD), caused by a complex of soil-borne pathogens, negatively impacts tree health and productivity in new orchard plantings at sites previously planted to apple. Use of new disease tolerant apple rootstock genotypes may diminish growth limiting effects of ARD, however the influence of rootstock genotype on modulating the rhizosphere and endophytic microbiome to enable ARD tolerance is not fully understood. Composition of the rhizosphere and root endophytic microbiomes was characterized across a diversity of apple rootstock genotypes. A series of tolerant (G.210, G.41, G.890, and G.935) and susceptible (M.26 and M.9) rootstock cultivars were consecutively planted into orchard replant soil containing a known pathogen complex. Amplicon sequencing was used to determine simultaneously the presence of a broad taxonomic range of organisms and their relative abundance. Microbial communities exhibited significant differences in composition between the rhizosphere and endophytic environments in terms of species diversity, content, and abundance. Significant differences in composition of the endophytic and rhizosphere microbiomes were observed between rootstock genotypes. Among rootstock endophytic fungal communities, rootstock G.890 samples consistently harbored the highest percentage of arbuscular mycorrhizal fungal species (>5% of total). Ilyonectria spp., which may function as a pathogen of apple, were detected at high relative abundance in the endosphere of all genotypes, with the highest relative abundance in M.26. These results provide further insight into rhizosphere and endophytic microbial communities of apple rootstocks, which could be exploited or manipulated to improve tree fruit agricultural management practices with respect to plant nutrition and disease control.