There are so many little things that you don't think about when you're planning a colony. Fortunately, somebody else is thinking about some of these things.
The example I'm thinking of is a Phase II SBIR award that was recently granted by NASA to Sol-gel Solutions, LLC, of Gainesville, Florida. The title?
"Photocatalytic and Adsorptive System for Odor Control in Lunar Surface Systems Using Silica-Titania Composites".
That's right... odor control. You don't really think about it much, but a closed environmental system is going to start to stink after a while. Not just stale sweat and the odor of humanity, but the odor of your restrooms and industrial processes. It would make a colony somewhat unbearable after a while, unless somebody found a way to neutralize the odors, and you'd have to do it with the resources you have on-hand. In this case, they are planning to use compounds from the lunar soil, combined with ultraviolet light, to bind, break down, and neutralize the volatile organic compounds (VOCs) that are the source of the odors.