These are two of the biggest problems for producers and also for the final user, who opens the walnut and sees strange colonies inside the aliment. That with luck, because otherwise there's the risk of eating strange bodies without being noticed. Someone might ask now, what kind of bacteria and fungi? Are they dangerous?
Xanthomonas, a wide extended set of bacteria, are responsible for great losses in the walnut production, sometimes taking advantage of a vast quantity, like half of it. A target usually presents signs in the exterior shell with black marks, and an opening, so the walnut is not completely closed. They can ruin multiple fruits and vegetables for human consumption. As water allows their spread, you can easily imagine the great issues with the rain.
And, for sure, eating some of them is not safe. There are types that tend to infect and create colonies, with documented cases in several zones of the body. The immune system needs to work with these bacteria.
Aspergillus flavus is the other big name here, a set of fungi with extensive activity in the vegetal world. Growing in filaments —yes, those in your memory, decorating the walnut— is a characteristic of the aspergillus flavus. Sadly, it's another human pathogen. The contamination could produce aflatoxin, a very dangerous toxic with potential interaction toward DNA chains.
With doubts, it's time to ensure that the aliment doesn't carry pathogens with some technique like heating. There's no need to waste their properties once cooked! Aflatoxin destruction is a usual source of experiments, so there's for sure more info. A start.