Unless one is using an undergravel filter with the proper sized gravel, only the very top of the substrate is aerobic enough to host the nitrifying bacteria, somewhere around 1/2 inch things get dicey for them and by a small amount more there are none of these bacteria. Howevere, there are plenty of them in thet top layer of substrate. The exception to this is in tanks with live plants. These have their roots in the anaerobic zones of the substrate. What many plants do is to transport oxygen down to their roots where they release it. This turns that space into an aerobic zone which fosters ammonia creation and the result is nitrifying bacteria colonize.
What makes this even more interesting is things do not stop there. There are anaerobic zones often below and above the aerobic one created by the plants, And there are colonies of denitrifying bacteria which process the nitrate created by the nitrfyers.
Petersen, Nils Risgaard-, Jensen, Kim, (1997), Nitrification and denitrification in the rhizosphere of the aquatic macrophyte Lobelia dortmanna L.,
Limnology and Oceanography, 42, doi: 10.4319/lo.1997.42.3.0529.
Abstract
Nitrogen and O2 transformations were studied in sediments covered by Lobelia dortmanna L.; a combination of 15N isotope pairing and microsensor (O2, NO3−, and NH4+) techniques were used. Transformation rates and microprofiles were compared with data obtained in bare sediments. The two types of sediment were incubated in doublecompartment chambers connected to a continuous flow-through system.
The presence of L. dortmanna profoundly influenced both the nitrification-denitrification activity and porewater profiles of O2, NO3−, and NH4+ within the sediment. The rate of coupled nitrification-denitrification was greater than sixfold higher in L. dortmnanna-vegetated sediment than in bare sediment throughout the light–dark cycle. Illumination of the Lobelia sediment reduced denitrification activity by ∼30%. In contrast, this process was unaffected by light–dark shifts in the bare sediment. Oxygen microprofiles showed that O2 was released from the L. dortmanna roots to the surrounding sediment both during illumination and in darkness. This release of O2 expanded the oxic sediment volume and stimulated nitrification, shown by the high concentrations of NO3− (∼30 µM) that accumulated within the rhizosphere. Both 15N2 isotope and microsensor data showed that the root-associated nitrification site was surrounded by two sites of denitrification above and below, and this led to a more efficient coupling between nitrification and denitrification in the Lobelia sediment than in the bare sediment.
full paper here
https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.4319/lo.1997.42.3.0529
The above aside, I started using gravel when I had an RUGF in my first tank, My high tech co2 added planted tank used small gravel, But in the past decade most tanks have used sand. However, none of my tanks with sand have substrate plants (they have potted and attached plants). Most of the sand is about an inch deep. I am a big fan of the Carib Sea Torpedo Beach sand. I began usung it with my Altum angels because one of the admins on the wild angel site has been to many of the rivers with altums and posted that Torbedo beach looked the most like what he saw the Altums living over. I liked it so much I now have it in 12/20 tanks (it also in all 6 temp. tanks essentially outdoors, these are all coming down starting today and finished before Oct 1). The rest of the tanks have gravel, mostly Estes Bits of Walnut, which I cannot say is still sold. It is great for plants as it is a small sized, rounded gravel. (That is a Otocinclus cocama, aka zebra oto, on the leaf)