09-30-2013, 10:59 AM
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The only way that I can see keeping the bio filter in the substrate (as your primary biofiltration) is if you constantly replace the media in the filter. By not allowing the bacteria to colonize the media, it will force the growth of the bacteria in the rest if the tank.
There is only ever 100% filtration, so any bacteria that grows on the filter media will do so at the expense of the colonies elsewhere in the tank. The fact that such a large volume of water passes through the filter (compared to the substrate) means the bacteria that grows in the filter is essentially being force fed. I know some people believe that the majority of bio filtration occurs in the substrate, but I am not really on board with that as a rule.
Much fuss is made about surface area for the bacteria, but real estate is not a limiting factor for bacteria growth in most aquariums. Availability of food determines the size of any population, be it bacteria, snails, ants, etc. The flow of water through the filter is greater than the flow of water through the substrate, so more bacteria lives in the filter than the substrate. The flow of water takes the path of least resistance, which means the current does not so much penetrate the substrate as it does flow over it.