Nitrifying bacteria need oxygen in order to break down ammonia. Unless you are circulating water (and oxygen) through the gravel the gravel is not contributing to your filtration. On the other hand, it is acting as a storage place for waste and non desired bacteria to accumulate. A thin layer of gravel will allow for the rays to hide and sift through looking for food. These activities keep the gravel stirred up enough that bad bacteria doesn't get established. If you need more filtration, you can always add on an external filter.
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