Yeah, I can't think of a reason why that would be true. The bacteria will live almost anywhere if the conditions are right. You could still layer them if you really like the look, it's obviously completely up to you. I would think through if you really want the marbles though because it's dramatically different from their "natural" environment, especially if they're the really shiny or opalesque kind. That might be the reason many serious hobbyist don't use them - as far as the fish is concerned, not the best option. But your tank will still cycle, it will just make vaccuuming a bit trickier.