You can treat vermiculite to reduce algae, but I'm not sure doing so has any value. The problem is, I'm unsure what effect treatments might have on the vermiculite OR the liner. The algae -- if it's not bleeding through as black stains -- is not a problem, underneath the liner.
Is there a specific reason you want to get rid of the liner . . . or just because the idea of 'dirty' dirt under the liner bothers you? If it's just the latter, I think your best bet would be to suck it up and pretend it's not there.
If you REALLY want to get rid of under-liner algae and fungus -- and fungus CAN produce staining that shows through -- you'll probably have to remove the vermiculite, and replace it with a new bottom, into which anti-algae treatment have been incorporated while mixing the vermiculite-cement mix.
But . . . I don't know if doing so will work. In years past, I've seen anti-fungal under-liner treatments advertised, but I don't know if they work, and I do know that MOST of the 'innovative' swimming pool products do NOT work well.
My guess is you could add a pH neutral blend of borax + boric acid to the mix, and end up with an algae resistant bottom. BUT I don't know how the borax would effect the vermiculite/cement mix, so you'd be taking a risk. I think people have used copper sulfate for this purpose, but I don't know how that worked out.
Probably the most effective approach that would NOT potentially compromise the verm. bottom, would be to put drains leading to a sump pump under the vermiculite, and then recoat. Dry verm. doesn't grow algae. BUT that would be a complex and expensive project.
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