The most important type of filtration in any aquarium is biological filtration. Put simply, this wonderful process converts the waste products of the reef inhabitants to a non-toxic state. This complex yet crucial process is carried out by various types of bacteria that live on every surface of your aquarium. In order to maximize the growth potential of the bacteria, aquarists utilize biological filters.
There are many types of biological filters on the market. Under gravel filters, bio-wheels, wet/dry or trickle filters all have the same goal, to house and grow nitrifying bacteria. These types of filters are essential for fish only systems. Without sufficient surface area for the bacteria to grow, the carrying capacity (i.e. the amount of animals the aquarium can safely support) quickly becomes very low. The reason for this is the presence of toxic ammonia.
In the aquarium, ammonia comes from two main sources. The first is the breakdown of organic material by heterotrophic bacteria. All of the excess food, fish waste, dead bacteria etc. is converted to its basic state of inorganic materials (including ammonia), CO2 and water. This process is called mineralization.
The second source (and a very important one) is the bi-product of animal respiration. Aquatic animals release ammonia directly into the aquarium water. This is a passive process. If the levels of ammonia in the surrounding water become too high, the animals cannot get rid of their own waste ammonia. This normally happens when an aquarium is has just been set up and the bacterial population has not become established or something has caused an existing population to die back. This is the number one killer of aquarium inhabitants.