BackgroundThe root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota.ResultsThe effects of an infection of greenhouse grown apple saplings with eitherVenturia inaequalisorPodosphaera leucotrichaas foliar pathogen, as well as the combined effect ofP. leucotrichainfection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant.ConclusionsFoliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40793-023-00502-z.