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Background  High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, “Royal Gala,” “Golden Delicious,” and “Honey Crisp,” and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine if the microbiota differs in different rootstocks and apple varieties and (2) determine if specific rootstock-scion combinations influence the microbiota composition of either component.    Results  Results indicated that  Ascomycota  (47.8%),  Zygomycota  (31.1%), and  Basidiomycota  (11.6%) were the dominant fungal phyla across all samples. The majority of bacterial sequences were assigned to  Proteobacteria  (58.4%),  Firmicutes  (23.8%),  Actinobacteria  (7.7%),  Bacteroidetes  (2%), and  Fusobacteria  (0.4%). Rootstocks appeared to influence the microbiota of associated grafted scion, but the effect was not statistically significant. Pedigree also had an impact on the composition of the endophytic microbiota, where closely-related cultivars had a microbial community that was more similar to each other than it was to a scion cultivar that was more distantly-related by pedigree. The more vigorous rootstock (M.M.111) was observed to possess a greater number of growth-promoting bacterial taxa, relative to the dwarfing rootstock (M.9).    Conclusions  The mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known. The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the “holobiont” concept in which metaorganisms have co-evolved. Clearly, however, the present information is only suggestive, and a more comprehensive analysis is needed.    Electronic supplementary material  The online version of this article (10.1186/s40168-018-0403-x) contains supplementary material, which is available to authorized users.

Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence