Hi, so I'm starting a PhD this October in the field of Molecular Plant Pathology.

I've got a great offer so far from one of the two top places in the country for what I do and have accepted it on account of them needing an answer quickly. My problem is that I'm still in the running for the other best place in the country for what I want to do. If I were to receive an offer from them I'd really want to consider both side by side but don't want to burn bridges with the place I've accepted an offer from... I may want to work there in the future. If it comes to it, do I just have to be true to what I want to do or should I take into account my potential supervisors/research institutions as well?

Be true to what you want to do but treat others with care as you never know what the future holds.

Most PhD supervisors are very understanding of this situation - they're used to students having to juggle offers, so it shouldn't be a problem if you do decide to go to the other place. The main thing is to be upfront (but polite) about it and to let them know as soon as you're able to, so they can find someone else to fill the place. Might be worth mentioning to them (if you haven't already) that you're still being considered for another institution, though, just so they're aware. I was in a similar position, and ended up having to choose - the other institution was fine about it, and I've actually been co-authoring a paper with the person who would have been my supervisor had I gone there, so it doesn't need to sour anything. Good luck!