The beneficial bacteria that filter your tank water do not live in the gravel.
This is a common misconception.
I will no doubt hear arguments on that. I don't deny there are likely some few of them living there, but the vast majority of BB colonies live in the filter media. Not the gravel, not the water, not the biofilm in the tank.
This is why you can take a mature filter off one tank, stick it on a brand new tank and have the new tank instantly cycled, because the BB are in the filter. Many keep bare bottom tanks, and if the BB lived mostly in gravel, those tanks would not work very well. But they work just fine with cycled filters.
BB require solid surfaces to attach themselves to, but they also need a constant food supply and they don't really get that on the tank bottom, because the filter draws the water out all the time, and removes the vast majority of the bacterial food supply as it does so.
The reason most filter media is made the way it's made is so it will provide maximum surface area in a small space, to allow for the greatest number of bacterial colonies to grow there, where food is always available from the water flowing by.
Gravel must be vacuumed regularly or this is what happens, and it can really play heck with the water parameters if you allow it build up too much.