I agree with tropicbreezent. I don't see how you could sustain any seal around that root. I really think you'd be sorry.

Even if you could bond the liner to the root, the wood would act like a bundle of tiny straws wicking water out of the pond.

Cut it off, then drill a hole in a brick or large rock and in the bottom of the root, and mount using a metal rod. You will achieve the same effect without affecting your liner.

I can't think of any way to do what you're proposing that will not result in major problems. Do as hemlock140 suggests.

Do not try to do this. It's a disaster waiting to happen.

Cut off the root and stick it under a rock that's lying on top

of the pond edge. If you're planning on a rocked shelf around the pond,

you can have it on the shelf under water ( and again, under a rock )

Rock shelf example. (On the right side)

We cut it out. Thanks all for the advice.