Excess inorganic fertilizers (salt...) Can absolutely kill some soil microorganisms. Most of which we have little to no understanding of.
Another posibility is the the soil becomes so fertile that the tree no longer has a mineral need for symbionts such as mycorrhizea and the relationship is ended. This can open up the tree to potential root rot pathogens as the fungi are no longer there to out-compete the bad guys. Another negative could be increased drought damage as I believe at least some mycorrhizael fungi also have a role in water uptake
Feed the soil, don't "feed" the plant.