I recently heard that some, if not all, straw and hay out of the Pacific Northwest has a mold spore in it. The question that accompanied this information is how to counter act the affects of the mold on the bales so they can be used for constriction.
The answer is quite simple: keep the bales dry. Mold can only grow and therefore have an affect on the bales when there is moisture. As long as the bales are kept dry, the spores will not be able to grow and will eventually shrivel up. The walls, sealed with plaster, will not allow any of the spores to enter the habitable space.