It would have to be a zoonotic pathogen and those tend to be rare.
Fungal spores, however, can live forever even in deep space.
Valley fever, caused by Coccidioides immitis is a danger to Archeologists (and ATV enthusiasts) as it lives in the soil and if its spores are breathed in it can cause some symptoms.
So, there's some danger, but not much. And the people doing this work will likely know the details.