Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
There is not much bacteria in most of the substrate. Poor water flow, so the gravel is too low in oxygen.
The greatest population of nitrifying bacteria is in the filter, especially with extra media and a bio wheel.
If you want to be ultra conservative you can skim the top layer of gravel (about 2 rocks thick) and save this in several mesh bags or nylon stockings. (well, cut up stockings).
Hang these in the tank and remove one per week for a month. This will spread out the loss of the bacteria.
There is not much bacteria in the water. These bacteria colonize surfaces such as all the filter media, rocks, driftwood, plant parts, ceramic merpeople and so on.
I have done complete tank changes (substrate, hardscape) with saving just the filter and that was a bit much. Had to stay on top of water changes.
When I do big water changes (pretty close to 100%) there is no problem at all. (except the fish flopping around- oops).