I just came up with an interesting theory regarding the Shivering Isles and the supposed living root system and the religion of Gyub, Lord of the Pit. My supposition is that this living root system that is growing beneath the Shivering Isles is Gyub. This entity is mentioned as some kind of Lovecraftian being most likely as the texts mention its tentacles. Those tentacles are the roots beneath the land. Further evidence of this living underground system can be seen in the likes of the Gardens of the Flesh and Bone.

So, for what it's worth, Gyub is the living root system that the Gnarls use.

For more info check out the following articles:

http://uesp.net/wiki/Lore:Bark_and_Sap

http://uesp.net/wiki/Lore:Fain