This is a growing field. There are several initial studies suggesting that plant microflora see changes using these practices. There are even reports on vertical transfer of in plant microbiome. If your question was to ask how plant microflora behaves, then you have to investigate by yourself for specific plant type. But if it was to know whether community is changed after using these practices, then the answer is more likely yes...
Yes! Breeding also changes the root architectures and thus the micro-flora associated with the root traits.
Interestingly, recent study shows that microbiota is also influenced when we subject to change the root traits by mutating some essential genes responsible for phosphate homeostasis.
Article Root microbiota drive direct integration of phosphate stress...