Nitrogen Cycle

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Aquarium Nitrogen Cycle.png
A simplified diagram of the nitrogen cycle in the aquarium


The nitrogen cycle is the biogeochemical cycle which describes the transformation of nitrogen and nitrogen compounds in living ecosystems. The element nitrogen is used by living organisms to produce complex organic molecules, such as proteins. However, most nitrogen is in the atmosphere and cannot be used by organisms in this form. Processing, or fixation, is necessary to convert gaseous nitrogen into forms usable by living organisms. Most such fixation is done by free-living or symbiotic bacteria.

These bacteria have an enzyme which combines gaseous nitrogen with hydrogen to produce ammonia and other nitrogen compounds. These compounds are then absorbed by plants either through symbiotic exchanges with bacteria or, more commonly, by absorbing ions through their roots (or root like) structures. All nitrogen obtained by animals has its origin in the consumption of plant life. When organisms die or produce waste, the processing of nitrogenous waste into nitrogen gas completes the nitrogen cycle.

In the marine aquarium setting, managing the levels of nitrogen compounds by facilitating the nitrogen cycle is referred to as biological filtration. Because the nitrogen cycle requires the presence of bacteria, marine tanks are typically cycled before livestock is added to the system, thereby giving the bacterial cultures time to become established.

The Nitrogen Cycle

A simplified diagram of the nitrogen cycle in the aquarium

Nitrogen Fixation and Uptake

In order for organisms to absorb nitrogen, it must be converted from atmospheric nitrogen (N2) into ammonium (NH4+). This is done either through bacterial metabolic process, natural events (lighting), or human activities. Once so converted, the ammonia is consumed by the bacteria itself, plants or other organisms. Nitrogen is stored by living things in an organic form, for example, as an amino acid or a protein.

In the marine aquarium, the main source of organic nitrogen comes from feeding.


Main Article: Ammonia

When an animal dies, organic nitrogen is converted to ammonia by heterotrophic bacteria in a process called mineralisation, otherwise known as decay. Marine fish also release ammonia as a waste product, together with a number of other nitrogen compounds, both through their gills and in their urea. Ammonia is highly toxic to the inhabitants of an aquarium. For this reason, an aquarium requires sufficient biological filtration to process ammonia into less toxic compounds. The process by which this occurs is called nitrification.


Main Article: Nitrite

Nitrification describes the bacterial oxidation of ammonium to nitrite and then to nitrate. The process is facilitated by autotrophic nitrifying bacteria in a reaction which, in an established aquarium, prevents ammonia reaching toxic concentrations. There are two separate reactions which occur.

NH4 (ammonium) + 3/2 O2 → NO2 (nitrite) + H2O + 2H+
NO2 (nitrite) + 1/2 O2 → NO3 (nitrate) + 2H+

Note that both reactions require oxygen (O2). This is because nitrifying bacteria are aerobic, and require the presence of oxygen to metabolise nitrogen compounds. Note also that the process of nitrification produces hydrogen ions (H+), which will cause the pH to fall and will deplete alkalinity over time.

Older literature about the aquarium hobby will indicate that there are two genera of nitrifying bacteria in aquariums. Some literature even identifies two species as being primarily responsible for nitrification (typically, Nitrosomonas europaea and Nitrobacter winogradskyi). Recent studies have shown however that this is not correct, and that there is a considerable number of different nitrifying species that may be present in marine tanks.[1]

In the aquarium, nitrite is significantly less toxic than ammonia and far less toxic in a marine environment than in a freshwater environment. Likewise, nitrate, at least compared to ammonia and nitrite, is relatively harmless to fish. However, invertebrates are not tolerant of high nitrate concentrations and thus it needs to be removed from aquariums containing these species.


The nitrate produced by nitrification is removed in one of two basic processes; dissimilatory and assimilatory nitrate reduction.

The first is called dissimilatory nitrate reduction. This is where nitrate is used as part of the biochemical respiration of anaerobic bacteria, but is not absorbed by the bacteria. Instead it is released as nitrogen gas (N2). There are a large number of heterotrophic bacteria which can function as denitrifiers.[2] Importantly, this type of bacteria requires a separate food source. In the example reaction given below, the food provided is methanol.

NO3 (nitrate) + 5/6 CH3OH (methanol) → 1/2N2 (nitrogen gas) + 5/6 CO2 + 7/6 H2O + OH

Note that denitrification liberates an hydroxide ion (OH) which raises pH and alkalinity thereby offsetting the hydrogen ion liberated by nitrification.

The second denitrification process is called assimilatory nitrate reduction. This is where the nitrate is directly absorbed into the tissue mass of algae or bacteria. In an aquarium, algae may be cultured for this purpose in a refugium or an algae turf scrubber. The nitrogen is permanently removed from the system when algae is manually harvested by the aquarist and discarded.



  1. (Delbeek Sprung 2005): Delbeek, J.C., Sprung, J., The reef aquarium: Science, Art, and Technology, Ricordea Publishing: Coconut Grove, 2005, p 256-258.
  2. (Spotte 1992): Spotte, S., Captive Seawater Fishes: Science and Technology, Wiley Interscience, John Wiley and Sons: New York, 1992, p 942.


Where do nitrifying and denitrifying bacteria come from?

Nitrifying and denitrifying bacteria are near ubiquitous in the biosphere. Provided that a nitrogen source is available, the bacteria will populate on any material which is not kept sterile. In a marine tank, bacteria is imported by live rock, live sand and even the water used in the tank. However, the bacteria in question actually cultures rather slowly. This is why a marine tank must be cycled for a number of weeks before livestock can be added. It is also why using filters with established bacterial cultures on a new tank will aid the rapid establishment of bacterial populations.

Do I need to add them to my tank?

There are a number of products available which "speed up" the establishment of bacterial populations. These products fall into one of two categories. The first simply keeps ammonia and nitrite at a manageable level so that naturally occurring bacteria can become established. The second is a highly concentrated pure culture of Nitrosomonas and Nitrobacter bacteria. Whether these products are effective or not is a matter of some controversy.