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I always bake my sifted dirt in a low temperature (350 degrees f) for a few hours. This dryes the dirt out, makes it easy to sift and kills kills some bacteria. If you are a real stickler for using clean dirt, pop this in the microwave after slow baking and nuke it on high for a couple of minutes or shorter. That will almost sterilize it. Apart from the fact that it's dirt, it's pretty clean.
I feel pretty stupid baking dirt, so I wait until noone is around and bake enough to keep me in dirt for several dioramas. My wife found my dirt stash and asked what it was, said she was throwing it out because I could always get dirt. I stopped her, telling her that it was really special dirt (actually it was cause I had to sift through the clay we call dirt and get rid of the clay. She looked at me pretty funny, one of those looks that makes a man feel like a little boy, but we have stayed married.