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.
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?