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More on the Nitrogen Cycle:
Ammonia, Nitrite and Nitrate

The basics of cycling are covered in a separate article. This article discusses aspects of the nitrogen cycle in more detail.


The ammonia level should always be zero (that is, undetectable by conventional test kits) in a mature aquarium. Fish waste, uneaten food and decaying plant matter will all contribute to the level of ammonia in the tank. However, in a mature tank, there are usually enough ammonia-converting bacteria to ensure that it never rises to detectable levels. However, there are situations which may result in a temporary rise in ammonia levels, even in a mature tank. These include:

  • Filter failure, or lack of maintenance
  • Use of medications
  • The addition of a large number of fish at the same time
  • Over-feeding
  • Over-enthusiastic cleaning of 'biological' filter media.
In such circumstances, the bacterial population will need time to increase or recover to cope with the demand. If fish appear unwell, testing for the presence of ammonia should be a priority.

The total ammonia in an aquarium will be present in two forms: ammonia (NH3) and the ammonium ion (NH4+). The proportion will depend mainly on pH, and to a lesser extent temperature. At alkaline pH, more of the ammonia will be present as the more toxic NH3, while at acidic pH, more of the less toxic ammonium (NH4) will be present. Ammonia poisoning is therefore more common at alkaline pH.

Ammonia can cause damage at levels of only 0.1 ppm (which is below the level detected by many kits!). There may be haemorrhaging and destruction of mucus membranes, the gills are particularly likely to be damaged, and may appear reddened. As with nitrite poisoning, fish may apppear to gasp for air at the surface, and show rapid gill movement. Higher levels, of several ppm, can be fatal.

In a mature aquarium, ammonia is oxidised by bacteria to form nitrites. The chemical reaction which occurs is shown below:

+ 2 H2O
>>> NO2-
+ 8 H+
(hydrogen ions)

For many years the bacteria responsible were thought to be Nitrasomonas species, but more recent research indicates that these bacteria may do little or nothing in freshwater aquaria, and that bacteria known as Nitrosococcus may be the true ammonia-oxidisers in our aquaria.


The nitrite level should always be zero in a mature tank. A temporary rise in nitrite levels may be seen for the same reasons as listed for ammonia above. However, the nitrite spike may persist longer, so if there is a delay in testing after a problem has occurred, it is more likely that nitrite will be detected. A nitrite level of only 0.1 ppm could prove harmful if exposure is prolonged. Symptoms of nitrite poisoning include gasping and rapid gill movements, which could be mistaken for a shortage of oxygen. In extreme cases, fish can actually die of suffocation because nitrite binds to the oxygen-carrying component (haemoglobin) in the blood.

In a mature aquarium, nitrite is oxidised by bacteria to form nitrate. The chemical reaction which occurs is shown below:

+ H2O
>>> NO3-
+ 2 H+
(hydrogen ions)

It was originally thought to be Nitrobacter species which were responsible for nitrite conversion to nitrate in aquaria, but again, recent research (by Dr. Timothy Hovanec and others) indicates a different group of bacteria - Nitrospira - are responsible.


In the past, nitrate was considered essentially harmless to fish; certainly it is far less toxic than ammonia or nitrite. It has been shown that levels of up to 1000 ppm may be required to cause death, but the effects of lower levels on long term health are not well understood. The sensitivity of different species to nitrate levels varies, and there may be long term effects on general health, growth and breeding ability.

Generally, many aquarists seem to agree that keeping nitrates below 50 ppm is necessary to prevent any long-term effects on fish health, but below 25 ppm is more desirable. Remember that many fish may come from a natural environment where there is little or no detectable nitrate. Fish which have been aquarium bred for generations are more likely to tolerate nitrates.

Fishless cycling

This is a method which uses pure ammonia to start the nitrogen cycle in a new aquarium, rather than the wastes of a few unlucky fish! The method was popularised by Dr. Chris Cow.
Essentially, the ammonia solution is added to the aquarium daily. When the ammonia-converting bacteria have established, the ammonia reading should fall back to zero overnight. The addition of ammonia is continued at a reduced level to keep the process going as nitrites rise and then subsequently fall as the nitrite-converting bacteria become established. When nitrites read zero, the tank is cycled and a water change is carried out to reduce any resulting nitrate before fish are added.
The advantages of this method are obvious - no fish are exposed to the toxic waste products during the cycling process. It also means the aquarium can be stocked with more fish straight away, as there is a full compliment of bacteria established. The fish wastes essentially take the place of the ammonia additions.

More details on fishless cycling can be found in Dr. Chris Cow's article

An example of an actual Fishless Cycle can be found here.




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