Unionised ammonia is extremely toxic to fish and other aquatic inhabitants but fortunately some of the fauna present in almost all bodies of water have the ability to oxidise ammonia in to nitrite. This isn't the full story because nitrite is still very toxic to fish. There are a number of bacteria which have the ability to oxidise nitrite (NO2) in to nitrate (NO3) which is far less toxic especially at low levels.
Depending on the pH and the temperature of the water most ammonia will be in the form of ammonium (NH4) which is ionised ammonia. The reaction to nitrate is as follows.
2NH4 + O2 → 2NH2OH + 2H (ammonium + oxygen becomes hydroxylamine + hydrogen gas).
The second stage of this process is as follows.
2NH2OH + 2O2 → 2H + 2H2O + 2NO2 (hydroxylamine + oxygen becomes hydrogen gas + water + nitrite).
For a long time it was thought that bacteria alone were responsible for the entire nitrification cycle:
(a) nitrosomonas and/or biospira where responsible for ammonia oxidisation.
(b) nitrobacter and/or nitrospira were responsible for nitrite oxidisation.
But new research has put this in to very much doubt. The discovery was made when researchers tested 27 fresh water aquarium bio filters from stand alone systems in homes and offices. They discovered that ammonia-oxidizing Achaea (AOA) were numerically dominant in 23 of those aquarium bio filters and that in 12 of the aquarium bio filters that AOA alone were oxidising all of the ammonia instead of ammonia-oxidizing bacteria (AOB) and that AOA are the dominant contributors to nitrification in most established freshwater aquaria.
The researchers also tested 8 marine aquariums and found that AOA out numbered AOB in 5 out of the 8 bio filters.
Ammonia-oxidizing archaea (AOA), belong to the newly proposed phylum Thaumarchaeota which so far contains four species two of which have the gene which allows them to oxidise ammonia. They are Nitrosopumilus maritimus and Nitrososphaera gargensis.
The study found that as the ammonia level went up the AOA population decreased showing that AOA do better in a low ammonia environment.
A preference for high ammonia concentrations by AOB suggests a possible role for their involvement in first establishing an aquarium when ammonia concentrations may approach levels associated with fish toxicity. In addition, ammonium concentration was positively and significantly correlated with the number of fish per gallon of aquarium water and, suggesting that AOB may also be important for heavily stocked tanks that experience chronic high ammonia concentrations.
Marine Crenarchaeota are the most abundant prokaryotes (cells that lack a membrane-bound nucleus) in the ocean, Their numbers relate to the level required for ammonia oxidation exactly and were one or two orders of magnitude (10 to 100x) higher than ammonia oxidising bacteria. Showing that they have a significant role in ammonia oxidation in the ocean.
Archaea seem to play a dominant role in fresh water aquariums which are well established and stocked normally. They may still have a significant role in heavily stocked aquariums but taking a less dominant role. Both AOA and AOB were found in marine aquarium bio filters but AOA were found in higher numbers in the majority of of the small sample tested.
Aquariums which are under going a cycle had less archaea and possibly relied more on ammonia oxidising bacteria which if true means that a freshly cycled aquarium which has been cycled using relatively high ammonia levels throughout the cycle will under go further maturing before it is considered to be fully established.
Most fish keepers are by now quite familiar with the nitrification process which occurs in all aquariums. But just to recap and in simple terms here it is again. When organic waste is left in an aquarium be it uneaten food, dead fish, fish waste or dead plant material it will be broken down by fungi and bacteria in a process known as mineralization. All the carbon from the organic material is used up in this process and all that is left is ammonia (NH3) and mulm which is organically and chemically inert solid material which is left as dust in the water column and substrate.