It partly depends upon the intended plants, since some obviously need greater depth for their roots. But using my tanks as an example, in the 115g I have 3 to 3.5 inches sand depth; in the 33g it is around 2 inches; and the 70g is 1.5 to 2 inches. I would have more in this one, but when I was setting it up I thought I had more sand than I actually did, and being in the middle of rebuilding it I decided to go with what I had. There are no real large-root plants, this tank is covered with pygmy chain sword and micro sword, so it worked.
On this issue of substrate bacteria, here is an excerpt from an article I did on bacteria that may help explain things:
The greatest population of bacteria in a healthy balanced aquarium occurs in the substrate, not the filter. The floc or humic compost that collects in the substrate is the host for the biofilms; this is why the substrate in planted tanks should never be disturbed, and many aquarists apply this to non-planted tanks as well.
In very general terms, aerobic nitrification takes place in the top 1-2 inches of the substrate; anaerobic de-nitrification takes place approximately 2-4 inches down, and anaerobic bacteria producing hydrogen sulfide occurs in substrates deeper than 3-4 inches. In all three cases, it will be deeper in coarse substrates (like pea gravel) and more shallow in finer substrates such as sand. These generalities will also vary with the presence of live plant roots and substrate “diggers” such as snails and worms, since these factors result in more oxygen being made available in the substrate, reducing anaerobic bacteria activity. An oxygen level in the substrate of as little as 1 ppm promotes nitrogen reduction rather than sulfur reduction (hydrogen sulfide). [6]
Maintaining a substrate of fine gravel or sand no deeper than 4 inches, having live plants rooted in the substrate, and keeping Malaysian Livebearing snails are the best and safest methods of providing a healthy biological system for aerobic and denitrifying anaerobic bacteria.