Backyard Aquaponics
A place to discuss aquaponics

I have a problem of root rot fungi
Is there a solution to eliminate them

What kind of beds aggregate or DWC? Either way if you can increase the aeration that will probably help. For aggregate grow beds try not to stir the muck on the bottom up to much. Might not help enough so use plants that aren't as likely to get root rot to replant the area where you're having troubles.

I don't recall if you have red wrigglers or their equivalent there? I'd recommend that you get some to help break down the solids but I don't know if this is an option for you. Might be that you are accumulating solids in the grow beds and this is causing anaerobic areas to form. If this is the case also consider

1. Flushing the grow bed solids outside the system (not into the system it could be bad for the fish)
2. Adding more grow beds
3. Adding a Radial Flow Filter before the growbed to remove some of the solids (this will require regular maintenance).
4. Reducing the number of fish so you don't have solids build up. If your system isn't very old then you probably have to many fish for the filtration you have.

Hope this helps