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Are they slimy? Easy to pull off? Do they smell nasty? It looks like root rot to me. Could also be the brown algae, i think there is a thread stickied here. Whatever it is it doesn't look good. You want those roots pearly white.
Sounds like you had some problems before did you clean everything well afterward? I might get some physan 20 and clean with that next time.
Also in the second picture on the left side is there a long stem sticking down or is that roots? I have had problems when stems get submerged in water too long. Do you have them in DWC or...
I think I'd throw some h2o2 in there just to be safe and maybe change out the water
Would the nutrients turn the roots this color? I added sm-90 to the cloner a couple of days ago. Today most of the roots were white. So I decided to put them in a turbogarden. I only kept the ones with white roots. Out of 45, I only have 11 clones left. I think it was root rot. They were slimmy. Not so much smelly. Smelled like nutrients. I thought. The sm-90 covered the smell. Thanks for the advise!!