Being that they are the fleshy, spore-bearing fruiting body of a fungus and that they usually grow from decaying organic matter and (if that weren’t enough) that many varieties will kill you faster than Ebola, it is no wonder people are confused about eating mushrooms. While some of the best mushroom experiences come from the consumption of wild mushrooms, most of the mushrooms we consume are commercially grown on mushroom farms (note: wild mushrooms should always be foraged for by, or at least with, someone who is an expert/mycophagists and will not likely steer you toward an early and delicious grave). Still, even though these domesticated versions are as safe to eat as anything, many home chefs are totally baffled by how to perform the most basic and simple of tasks with them – cleaning and trimming.
Mushrooms are unlike any other produce item we purchase. They are neither vegetable nor fruit; they are very clearly a fungus that is about 90 percent water by weight. The myth is that you should never ever wash a mushroom, as it may destroy the delicate structure and texture of the fungus. This is not exactly true. While a mushroom should never be soaked (at least for any length of time) a light washing of a very dirty mushroom is advisable.
However, most commercially grown mushrooms (and even the ones you purchase at the local farmer’s market) are usually never so dirty that they would need anything more than a gentle rubbing from a paper towel to remove surface dirt and debris. The majority of the time, this is about all you would need to do to sufficiently clean and prepare a mushroom for cooking and consumption (especially with the simple button mushrooms and portobellos). Of course there are other varieties whose natural architecture make them a bit more challenging to clean (morels, hen of the woods, etc) and whose natural tendency is to serve as a safe haven for all sorts of insects. In this case, you may want to throw your mushrooms in a cool bath and gently agitate for just a few moments, but you really only want to do this if you get the sense that this delicious mushroom is more than just a colony for fungus. Afterwards you are going to lightly towel dry the mushrooms and set them on a wire rack to air-dry (I know it seems excessive, but slimy and musty mushrooms are pretty undesirable).
Most mushrooms don’t need to be peeled, but many people prefer to remove the gills (especially if open, like in a portobello) as it has a tendency to darken and discolor sauces. Gently and carefully scrape out the gills with a spoon and discard them in the compost. The stem is where a lot of confusion resides: where and when to cut. Shitakes tend to have a fairly tough stem and should be cut somewhat close to the cap of the mushroom. However, most mushrooms can be trimmed a little closer to the base of the stem. When in doubt, you could always cut them close to the cap without loosing too much of that mushroom goodness.
In general, mushrooms should be kept as dry as possible. If you absolutely need to get them wet, make sure you dry them quickly thereafter. They are best kept cool and dry in a paper bag (plastic tends to encourage humidity and will darken the cap of the mushroom) and should be consumed within a few days.