My fears that bacteria were ground off gravel surfaces used to be exaggerated, until calmed by RTR's point about fluidized bed filters. I still think a floc of humus the same size as a grain of gravel offers enormously greater microzones for bacteria.
I prefer to leave the microhabitats of facultative bacteria that can switch between aerobic and anaerobic metabolisms-- and maybe even some obligate anaerobes-- to develop in peace, oxidizing any sulfides to harmless sulfates, creating acidic low-oxygen microzones where the iron in my substrates is ferrous and available to plant roots, maybe even giving me some de-nitrification (my nitrates typically run <10ppm). Besides, my older (5 or 6 year) substrates are probably quite laden with phosphates by now.
I keep reading "algae problems" threads in all the forums that reinforce my impression that algae problems are related to: overwashed "aquarium" gravel with no humus "crud"or silt, substrate disturbance and a snowstorm of flake feed. My tanks have many kinds of algae in them, but not much of any one kind.
Gravel-digging roles are taken up by Melania snails and Botia modesta hunting for them like truffle dogs, since I don't have any big earth-shifting Cichlids.
How would "crud" work its way down into the substrate if the fishkeeper didn't stir it all in, from time to time? What happens to detritus below the surface: doesn't it break down pretty completely, leaving only some dark "humus."
You see, there is a successful different way...