Proving that the PhD work was done prior to someone else's patent
You are right to be worried about a patent in the same field as your thesis research. 

You do have some protection in the form of having "prior publication" that shows your work predates the thesis. But this is not necessarily sufficient to protect your future work.

I would get into immediate contact with your thesis advisor, as well as the legal department of your university. They are trained in handling such issues, and can advise you as how best to proceed so as to protect yourself.

Note that the goal of talking to the legal department is not to file a lawsuit. The goal is to understand what are your rights as a researcher working in an area with an existing patent, and how you can show that you are avoiding infringement.