Good info in this post.
I would highly suggest a airpump, and Defusers in your reservoir, and in any
hydroponic system if at all possible. With a closed system it might be the reason your plant roots are having issues.. because them being wet wet wet and the fluid isn't oxygenated much. You can grow plants in 100% fluid as done with a DWC system (Deep Water Culture), but it has to be aerated to get the needed Oxygen to the roots. None will result in root rot, and thats what it looks like your experiencing there.
IF it's not to late, I would also suggest the Hydrogen peroxide method mentioned above for trying to clear up the problem, but I personally wouldn't use it on a regular basis, but thats a personal choice.
Also, if you have your air defuser near your fishtank heater, it will help to distribute your heat throughout your resevior