My first comment is that there are many species of bacteria in an aquarium, and killing them off "naturally" is not as easy or simple as we used to believe. Your question, benzenering, is probably with respect to the bacteria that handle ammonia and nitrite, what we call the nitrification bacteria. There are also the de-nitrification bacteria. There is more organic waste in a tank without live fish than you might think, and the nitrifying processes will continue for months. These bacteria can also go into a sort of hibernation, awaiting better times. This is all very simplistic, but the point is that they will not all disappear provided you leave the substrate. You can also leave the filter running; if you do shut it down, I would clean it before re-starting with new fish.
I have a permanent running tank that I use to quarantine new fish. This tank has some live plants and a sponge filter. I do a 50% water change weekly, and add a dose of liquid plant fertilizer after the water change. It can run like this for several months, even a year, without fish. Then when I add new fish, I have no nitrifying issues as the tank is established. The plants handle much of the ammonia of course, but there is no doubt but that the bacteria are able to continue very rapidly.
Byron.