Pythium and Fusarium are two common causes of root rot in Hydroponics. Whether on r/hydro, dedicated forums or papers dealing with these pathogens, it's a hot topic. Several Bacillus bacteria are used to suppress Pythium growth and trichoderma harzianum has proven useful in the treatment of Fusarium. This is referred to as using beneficials in amateur hydro or biological control in scientific literature.
In aquaponics root rot is not that big of a topic, few people report total collapse of their system. Why aquaponics has an edge here is not well studied. Some reasons given:
It's no magic bullet see picture below of some strawberry roots I pulled out of my system, constant flow bed on the left and nft netpot on the right, but they get by and already produced fruit. I didn't take any active steps to prevent root rot in my system.
Getting back to biocontrol, this study found zinc improved biocontrol of Fusarium Crown and root rot of tomato by Pseudomonas fluorescens. Zinc might be a key element in combating root rot.
The UVI aquaponics project reported mean zinc concentrations of 34 mg/L, much higher than the standard 0.05 mg/L.
The system used rainwater, which was captured by a plastic liner (high density polyethylene) and stored in a covered tank. The system had been running for 4 years without a water change event, only top ups. source paper
Zinc is usually abundant in aquaponic systems, it can even reach toxic levels when galvanized steel parts are present. The main sources are:
