Upon checking the roots this morning, I found that they have a slight discoloring. Upon closer inspection, it became clear that they had a deposit of some kind of material sticking to them.
In hypothesing what it might be, I came up with two possible causes.
The first, is that it could be a deposit of clay from the media bed. There are deposits of clay in the floating rafts where the water shows down – you can make it out in the photo above on the tank floor.
The other, is that it could be the quality of the fish food which is not being digested properly – I read stories about that.
In thinking about it a little more I believe it is the latter. In the micro aquarium when I switched to the large bucket of cheaper food, the gold fishes poo’s were coagulated and they floated. I read about this being a problem with not being able to digest the food well, consequently jamming up the rest of the system.
It’s not a critical problem for the system yet, I don’t believe – the roots aren’t as bad as they look in the photo. I am changing the fish back to their original food and will continue the search for something better.