Backyard Aquaponics
A place to discuss aquaponics

In containers that small, I expect you will want to pull the roots out. Some people will cut the plant off near the gravel line and wait a little while (few days ta a week or so) to make the roots a little easier to pull out. You will have to decide how much time you dare leave parts of the system empty of plants though. You might be better off having an additional regular worm bin that you can throw the roots into. I find my tilapia will strip roots of all little rootlets but they don't seem to eat them completely. Same with plants like lettuce that I throw in, they leave the stem. Having some worms in those small beds would be nice but keeping a good population in such small containers might be tricky.