Hello there,
Here's my 2 cents worth of what may have happen to your chili seedlings and how to overcome damping off or root rot.
Firstly, the optimum temperature for growing chili peppers are between 25-32 degrees celcius and need a minimum 8 hours of light.
Damping off/root rot is usually cause by fungus or bacteria ( in culture medium ie, rock wool) infecting your seedlings. Of course that could also happen to healthy adult chili pepper plants, you can view them here. To prevent this is to sterilize your culture medium. I sterilize mine with bleach or hydrogen proxide. The other root rot prevention is to keep the culture medium moist and not wet. (a little on the dry side will do no harm)
On your comment you did not specify what type of hydroponic system you're utilising i.e a passive system, NFT(Nutrients Film Technique), Aeroponics, Drip Irrigation, etc.
I will assume you're are using either NFT system or drip irigation since you did mention about your system's pump (also assuming it to be water pump).
With drip irrigation system (which is also similar to my hydro system), it is best to keep the rock wool moist. I water the medium (spaghum moss) once a day, sometimes twice (once in the morning and once in the afternoon).
Also on my hydro system, nutrients (fluids) occupies 1/3 of pipe spacing (diameter) and culture medium(spaghum moss) occupies the other 1/3. Leaving 1/3 of pipe (diameter) exposed to air. In short, there is a gap of moist air in the pipe between the roots and the nutrients. This (moist air) happens when evaporated fluid stays inside the pipe as temperature outside soars to 31 degrees celcius during the day and stays at 25 degrees during night. Hence , its less likely the roots will get burn. Also, excessive nutrients from watering daily are drained out via a "drain hole".
quote"You may want to check for excessive water/nutrients supplied to the rock wool.
I have the pumps turning off for 45 minutes out of ever hour at night but still fear damping off disease is getting my peppers. Any advice? "
Hope this helps.
Sam
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