How should I clean mushrooms and what should I do with the stems? Will washing mushrooms under running water end up with waterlogged, soggy mushrooms?

Although I have not seen research to determine how much water mushrooms will or will not absorb and under what circumstances, I recommend wiping mushrooms with a damp paper towel rather than cleaning them under running water as wetting the surface of mushrooms turns them dark and slimy only minutes after exposing them to the air.

And what about those stems? The stems of most mushrooms are tender and edible. However when it comes to shiitake mushrooms, I recommend cutting off the stems before cooking. It seems that the wide cap of the shiitake, along with the woody environment in which it is cultivated, requires a sturdy, tough stem to support its growth. While the stems may be too tough to eat, I would think twice about discarding them because they make an excellent addition to soup stock!

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