The worm may be something like a leech.  There is a particular type of leech that actually feeds on roots of plants.  In general its best to remove them when you see them if you're not sure what they are.  There are some types of worms that can be eaten by your fish as food that it could be too.  If you can remove it and take it to a local college's biology department (call first) they may be willing to help you identify it.