Over an over, I see too much emphasis placed on the toxicity of ammonia. The novice aquarist often simply ignores the role that nitrite plays in the overall absorption of nitrogen components within the new aquarium. This process is generally termed the Nitrogen Cycle. This wonderful system removes toxic nitrogenous compounds produced by most of the various organisms, included in an aquarium such as the fish and the bacteria fundamental in the decay and rot of excess organic materials within the habitat.
In a recent article on the Nitrogen Cycle titled The Nitrogen Cycle in Laymans Terms, www.swellUK.com attempts to give a description of the Nitrogen cycle, the problem here is that the focus is not on all three components of the cycle, rather the focus is on the ammonia production in the aquarium. Although this can be deadly if the pH is high – from a neutral 7.0 and higher. If the the aquarium is acid, there is no problem with the ammonium that is there. I much prefer to deal with the more pervasive killer, in my opinion, nitrite, which is not dependent on any other water characteristic to be deadly, and although nominally less dangerous than ammonia, it builds to much higher concentrations and for a longer period of time.
In a massive body of water like a lake, the ammonia would dissipate quite quickly, but in your fishtank it needs a helping hand. Especially in a new aquarium that hasn’t had time to mature, your ammonia levels will likely run high. Bacteria called nitrosomonas cause the ammonia to convert to nitrites (N02) which is better than ammonia but still bad for your fish.
The Nitrogen Cycle is not that complex, at least in its most simplistic description, ammonia (or the less toxic ammonium) is reduced to nitrite by bacteria called Nitrosomonas, then the nitrite is reduced to nitrate by Nitrobacter (in the article above the graphic calls it Nitrospira). While there are differences of opinion on which is the more common and most effective, the result is nitrate which remains in the aquarium and can build up to high concentrations as well. It takes very high concentrations to cause trouble in most cases, but regular water change techniques eliminate this problem when faithfully done.
The Nitrogen Cycle Ammonia -> Nitrite -> Nitrate
The Nitrogen Cycle is more fully discussed in its section at Freshwater-Tropical-Fish-Tanks where the roles of the various compounds produced in the aquarium are more carefully covered. Although ammonia can be important in an aquarium where the pH is 7.0 or above, I believe the bigger problem is nitrite. Granted it is less toxic initially, but it does build up to greater concentration and in a normal tank, hangs around much longer, so the damage it can do is greater as a result. The final by-product is nitrate – a common fertilizer for aquatic plants. It never dissipates and unless there is a strong population of live plants, all it can do is concentrate over time. This is the main reason partial water changes are so important. Nitrate can only be diluted by removing a highly concentrated aquarium water and replacing with low concentration tap water. When plants are involved, then a true cycle evolves where the nitrate is adsorbed into the roots and eventually the dead leaves create a new supply of ammonia when they rot.