The brownish "fuzz" that occurs on floating plant roots is orgaqnic matter. I had an organic bloom in my 90g tank a few years ago, and the floating plants were unbelievably heavy with this. I had never noticed it previously, and I see very little now in any of my tanks. Microscopic food gets caught in this, and fish like pygmy cories, pencilfish, some tetras will be seen browsing through the plant roots looking for the food. I don't think this has any relation to ammonia, as I have seen this in tanks with a very minimal fish load, but not in tanks with much heavier fish loads.
You mention Equilibrium...I used this for three or so years, until a marine biologist convinced me it was unnecessary. I had consulted her concerning a fish disease and this came up in the discussion. I decided to stop the Equilibrium (I had started it because of my zero GH water, to provide sufficient calcium and it certainly made a difference to the plants), and used Seachem's Flourish Tabs instead. I've been doing this now ever since, some five or sic years, and the FT appear to be providing sufficient calcium as the large swords which were the main issue have been doing well; I can't say they are as "good" as they were with Equilibrium, but they are still growing well and that is all I care about, as the FT mean no excess minerals are getting into the water to bother the fish.