During the workshop 'healthy soil' at Cityplot I was triggered to look for information about mycorrhizae and other fungi in aquaponics. Unfortunately there's nothing to find, really. Some people say they put it in their system, but they don't elaborate.
I found an interesting article about fungi in hydroponics though: in Urban Garden Magazine
This is some of their research
There's also a research about mycorrhizae and aquatic plants, but I can't find it complete, only one page telling how the research was conducted. Maybe our scientist friends can help us here?