I'm not even sure too much water is harmful. After all, people root clones straight in water. I think it's the bacterial slime building up with systems like rockwool cubes that give people trouble and make them think to get more sterile. I've noticed that it's generally the slower rooting clones that are more likely to get stem rot. By slow, I mean anything that takes more than 5-7 days. When a cut roots fast, it basically outgrows any bacteria growing. One thing that helps is to open the dome every day and move each cube over to a new spot while breathing plenty of CO2 on them (well, maybe you can omit the breathing part ). Also, transfer everyone to another dome and scrub the bottom tray of the dome weekly. Cleanliness is important, but no need for bleach or hydrogen peroxide IMO.