The base chakra naturally governs all that is solid in the body such as the bones, teeth and nails. The sense of smell is associated with this level. All creatures that are very close to the earth have a strong sense of smell. We also see this in people; those who are very acute in material matters very often have prominent noses.
You smell these odors through your nose which is almost like a huge cave built to smell, moisten, and filter the air you breathe. As you breathe in, the air enters through your nostrils which contain tiny little hairs that filter all kinds of things trying to enter your nose, even bugs! These little hairs are called cilia and you can pretend that they sweep all the dirt out of the nasal cavity, which is the big place the air passes through on it's way to the lungs.
After passing through the nasal cavity, the air passes through a thick layer of mucous to the olfactory bulb. There the smells are recognized because each smell molecule fits into a nerve cell like a lock and key. Then the cells send signals along your olfactory nerve to the brain. At the brain, they are interpreted as those sweet smelling flowers or that moldy cheese.