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During the drying period some of the stems of my mushies have turned a light brown color in some areas. Is this contamination? Also while they were drying they took on dark dark blue almost black colors around some of the bruised areas. Whaaat's up with thaaat?
It sounds normal to me. Are they actually drying in there? If they're still moist and are turning colors, there could be some bacterial action going on. Any smell to the darkening areas? If they're getting crispy dry there isn't much to worry about. To get the best use out of dessicant, only put mushrooms in when they're fairly dry already [fan-dried]. Once mostly dry, the dessicant can take over and there is little/no chance of contamination in the chamber.
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