It looks like root rot to me! I would flush with h202 or chlorine to kill it, make sure your water is 19c or so, and start thinking about how you want to grow, if you are using salts, going sterile may be a better option and is compatible with throwing in h202 or chlorine anytime. If you want to use benificial bacteria, you can't use chlorine or h2o2. You add the bacteria and give it time to grow and establish before it becomes effective. It will out compete any bad stuff wanting to grow in there normally.