if you have a photo, it will help immensely in figuring out what exactly it is. It seems like it could also be sunburn or accumulation of fertilizer salts. But it's hard to say without seeing them.
A good way to diagnose bacterial rot: take a whiff. If it doesn't smell like anything in particular, it's definitely NOT bacteria. bacteria will usually smell nasty, once in a while it'll smell fruity (which means it's pseudomonas).