Bacterial or perhaps fungal, but I agree to keep the substrate clean, run the water changer over all of it at each water change, lightly going into the substrate. Having some snails helps here, because they will eat any food that falls to the bottom, along with fish excrement, plant matter, anything organic basically, and this breaks it down faster for the various bacteria to get at it.
By snails I mean the small common ones like Malaysian Livebearing Snails (ideal), pond or acute bladder snails. Large snails have other issues.
Byron.