Or will that ruin the cycle?
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Do you have a well-established filter media?
How long has the tank been running?
There's very little beneficial bacteria in the gravel, so yes.
To second Adam... go fior it. Your filter houses 95% of the beneficial bacteria. Generally, your substrate needs to be very porous (the actual material, not the gaps between stones) to have any sizeable amount of beneficial bacteria.
Out of curiousity, what is the bare bottom tank for?
I agree with Adam and phishphin!
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I wouldn't worry about it. I did this last week to make my tank as clean as possible for my ailing betta.
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