Several ideas for linking these two areas would be:
1 - See if there are different species or strains of bacteria in closely to distantly related plant species.
2 - Are there very specific strains of bacteria that live with different but related members of a genus of plants.
3 - Do different bacterial species associate with the seeds of closely related plants. Some seed associated bacteria might be very specific to the plant species.
4 - Does it take different strains of bacteria to degrade closely related plant species.