when dealing with plants, you have to learn some basic anatomy.
rhizome= green colored base root from which all the leaves stem.
In the case of the java fern, only the brown roots can be burried. With the anubias, only the thinnest green/white roots can be burried. If there is no thick root column (the rhizome) above the substrate, you've burried it too far and the plant is going to have a lot of trouble. Since java fern roots normally start off so small, we usually attach them to wood.