ON THE SURFACE
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For many hobbyists, the biological filter with the largest amount of surface area is obviously the best. In reality, a fair comparison of biological filters should be based on their effective surface area. Effective surface area is that which is actually available when comparing the surface for colonization by area of biological filters, it is nitrifying bacteria. As we shall see, the effective surface area can be much smaller than the actual surface area of the filter. And indeed, having more surface area does not automatically mean you will have more nitrifying bacteria.
Aquarists tend to assume that nitrifying bacteria increase in direct proportion to the amount of ammonia produced in the aquarium. However, it is not known for certain whether continuing to add ammonia means the population of nitrifying bacteria also continually increases, or if the numbers level off and those bacteria simply work more efficiently.
“More efficient” is defined as the same number of bacteria oxidizing more ammonia in the same amount of time. Thus, a very important piece of data that is critically important to our discussion is missing, demonstrating that there is still much to be learned about the ecology of nitrifying bacteria. However, what is known is that the nitrifying bacteria (or their efficiency) will not continue to increase unless there is a concurrent increase in ammonia production - the source of their energy.
When comparing the surface area of biological filters, it is important to consider factors which can limit the effectiveness of a biological filter and possibly reduce the value of larger surface areas. Oxygen, for example, is of prime importance.
The rate at which a colony of nitrifying bacteria can oxidize ammonia is determined by the amount of oxygen that is available, Therefore, when there is less oxygen, more surface area is needed to support the larger numbers of bacteria required to do the same work as smaller biofifters in which the bacteria have more oxygen available to them. This is the case, for instance, when comparing undergravel filters to wet/dry filters. Undergravel filters have been the standard biological filter for many years.They have a great amount of surface area, but are inefficient compared to, say, wet/dry filters, which perform the same work with less surface area because their media is exposed to the atmosphere. Air has a much greater amount of oxygen than that available in the aquarium water. In this way, fewer (or more efficient) bacteria an less surface area is needed to accomplish the same amount of work.
Only the upper inch or so of gravel on an undergravel filter contains nitrifying bacteria. This is due, in part, to the reduction in oxygen as the water passes through the gravel. Thus, when calculating the effective surface of an undergravel filter, only the top portion of the gravel layer really counts.
The same is true for the biological filtration media in canister filters. When clean, the media receives a lot of oxygen via the aquarium water, but as the canister clogs and the flow rate is reduced, less oxygen passes by the nitrifying bacteria. And as more organics are trapped in the canister, they also consume oxygen. This double negative significantly reduces the effective surface area of the biofilter media. Two other factors limiting the effective surface area of biofilters, are clogging and competition among types of bacteria. If the biofilter doubles as a mechanical filter it will clog even faster. As the media becomes increasingly clogged, less and less area is available for the nitrifying bacteria because much of the media is no longer exposed to the aquarium water.These areas of the media become dead spots. Of course, when the media is cleaned, such as during a siphon cleaning of an undergravel filter, the nitrifying bacteria can re-colonize it. But this leads to cyclic nitrifying populations - they first increase when the area is clean, but then decrease as the area clogs. This can manifest into periods of high ammonia concentrations in the aquarium, which is why it is important to keep the biological filter area clear of organic matter. Media that is prone to clogging has a less effective biological filtration surface area.