Mills, D. The Marine Aquarium.
Of primary concern to the aquarist is management of the biological waste produced by an aquarium's inhabitants. Fish, invertebrates, fungi, and some bacteria excrete nitrogen waste in the form of ammonia (which may convert to ammonium, depending on water chemistry) which must then pass through the nitrogen cycle. Ammonia is also produced through the decomposition of plant and animal matter, including fecal matter and other detritus. Nitrogen waste products become toxic to fish and other aquarium inhabitants at high concentrations.
A well-balanced tank contains organisms that are able to metabolize the waste products of other aquarium residents. The nitrogen waste produced in a tank is metabolized in aquaria by a type of bacteria known as nitrifiers (genus Nitrosomonas). Nitrifying bacteria capture ammonia from the water and metabolize it to produce nitrite. Nitrite is also highly toxic to fish in high concentrations. Another type of bacteria, genus Nitrospira, converts nitrite into nitrate, a less toxic substance to aquarium inhabitants. (Nitrobacter bacteria were previously believed to fill this role, and continue to be found in commercially available products sold as kits to "jump start" the nitrogen cycle in an aquarium. While biologically they could theoretically fill the same niche as Nitrospira, it has recently been found that Nitrobacter are not present in detectable levels in established aquaria, while Nitrospira are plentiful.) This process is known in the aquarium hobby as the nitrogen cycle.
In addition to bacteria, aquatic plants also eliminate nitrogen waste by metabolizing ammonia and nitrate. When plants metabolize nitrogen compounds, they remove nitrogen from the water by using it to build biomass. However, this is only temporary, as the plants release nitrogen back into the water when older leaves die off and decompose.
Although informally called the nitrogen cycle by hobbyists, it is in fact only a portion of a true cycle: nitrogen must be added to the system (usually through food provided to the tank inhabitants), and nitrates accumulate in the water at the end of the process, or become bound in the biomass of plants. This accumulation of nitrates in home aquaria requires the aquarium keeper to remove water that is high in nitrates, or remove plants which have grown from the nitrates.
Aquaria kept by hobbyists often do not have the requisite populations of bacteria needed to detoxify nitrogen waste from tank inhabitants. This problem is most often addressed through two filtration solutions: Activated carbon filters absorb nitrogen compounds and other toxins from the water, while biological filters provide a medium specially designed for colonization by the desired nitrifying bacteria.