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I've got a couple plants on a piece of driftwood, just using the water column. The roots are getting pretty long and, to be honest, they're not the most visually appealing thing.

I'm not too fussed, but I was wondering if anyone's had any success manipulating the roots around the driftwood to make them less noticeable, or if it's okay to trim them back at some point?

Snipping the roots might not be the best idea, I'm not sure what damage it could cause, but I'm skeptical. You could try rearranging them to sit behind the driftwood instead, that might be a better option. I've had anubias and java fern mounted on rocks and wood, and I quite like the way the roots wrap around, it's a pretty natural look, but that's just my take on it.

I've had good luck with trimming the roots on my anubias and Java fern. Their roots are mainly for anchoring, so it doesn't seem to hurt them.