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Incomplete Nitrogen Cycle
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"Cycling" is the term aquarists use for allowing a tank's beneficial bacteria to grow in the substrate, on live rock and in the filter media. This nitrifying bacteria creates the aquarium's "biological filter," which performs the important task of converting ammonia into less harmful nitrites and nitrates, which are then removed from the water during water changes. Cycling is accomplished by allowing an aquarium to run without fish for two weeks or longer. An aquarium that has measurable ammonia may not have had time to build up enough beneficial bacteria. Or, it might need more places for the bacteria to grow, such as in a deep sand bed, in live rock or in a filter filled with sponge, biofloss or bioballs.
Inadequate Aquarium Maintenance
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Keeping an aquarium ammonia-free requires that all filters and protein skimmers are clean and working properly. Vacuuming the substrate monthly or bimonthly is necessary to remove fish waste and uneaten food. Maintaining a healthy pH is important: if pH drops below 6, nitrifying bacteria starts to die off. Conversely, a tank with high pH contains more toxic ammonia. According to Randy Holmes-Farley in "Ammonia and the Reef Aquarium," the ammonia in an aquarium is a combination of ammonium ions and the more toxic free ammonia. More free ammonia is present in water with a higher pH while more ammonium ions are present in water with a lower pH.
Overfeeding
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Consistently overfeeding fish produces an excess of fish waste and uneaten food. This can overload nitrifying bacteria and cause deadly spikes in ammonia.
Excessive Bioload
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"Bioload" refers to the amount of animals kept in an aquarium. Keeping too many fish in too small a tank, or having inadequate filtration for the size of a tank, is a recipe for ammonia.
New Tank Syndrome
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"New tank syndrome" may occur when something containing a great deal of beneficial bacteria---for example, the sand in the bottom of the aquarium or the media in a mechanical filter---is removed or replaced with new materials containing no beneficial bacteria. The result is that the nitrogen cycle fails and ammonia is not properly converted into nitrites and nitrates.
Corpses
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Decaying dead fish and other animals give off large amounts of ammonia. Sometimes, an aquarist will not notice a corpse if the animal died behind a rock or under the sand. An unnoticed corpse may cause an aquarium to "crash."
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High Levels of Ammonia in Saltwater Tanks
A healthy saltwater tank should have no measurable amount of ammonia. Ammonia is the chemical produced from decaying organic matter such as fish waste and food. Ammonia is highly toxic to fish and other animals, and spikes in ammonia will quickly cause a tank to "crash" and its inhabitants to go belly-up. Ammonia test kits can be purchased at any pet store, and conscientious aquarists should check their ammonia frequently, especially when the tank is new or after adding new animals or decorations. There are several reasons why a saltwater tank's ammonia might spike.