10/01/2018 · Explanation of nitrogen cycle



The aquarium nitrogen cycle is simply put the method by which diffusion from the gills of the fish and their wastes, as well as other decomposing organic matter (such as uneaten fish food) is converted from Ammonia or Ammonium to Nitrites to Nitrates.
Then Nitrates are then either converted to free nitrogen (which is a gas that will not remain in the water) by plants or de-nitrifying anaerobic bacteria, or you remove/lower your nitrates by way of regular water changes, or by using chemical absorbents such as Purigen.

Without this process going on in your aquarium/pond the keeping of fish or other inhabitants would be nearly impossible as ammonia is highly toxic in even small quantities (ammonium is not, but is quickly converted to ammonia at higher pH), nitrites are also toxic although not as much as ammonia. Nitrates are not toxic to most freshwater fish except in high amounts with long term exposure (this is not the case for many saltwater inhabitants though).
So with this in mind it is important to have an “established aquarium nitrogen cycle” in your aquarium or pond.




Nitrogen is an element vital to all life processes on Earth. Nitrogen is very important in our biosphere, where nitrogen comprises 78% of the atmosphere, and is part of every living tissue. It is a component of amino acids, proteins and nucleic acids. With the exception of carbon, nitrogen is the most universal element of life. Life could not exist without nitrogen. .
Nitrogen is essential for organic development; nitrogenous compounds are also required by some organisms for metabolic functions and respiration. Unfortunately, free nitrogen in the atmosphere is not in a form that is usable by plants or animals. Because of its stable structural formula, it is relatively inert and does not combine readily with other elements.

All living organisms, from fish to plants, have great quantities of assimilated nitrogen in their tissues. Nitrogen is a fundamental ingredient for the formation of proteins and nucleic acids. Every organism you place in your aquarium adds nitrogen based compounds; from fish to coral, to live rock, to plants.
The introduction of food also adds nitrogen. Dead or alive, they are organic masses, and possess the same nitrogenous attributes as the fish, plants, invertebrates you added to your aquarium.
Inorganic nitrogen is added two ways: the atmosphere and new water. Atmospheric nitrogen (N2) is incorporated into our aquarium water by way of nitrogen fixing bacteria and by Cyanobacteria (bacteria that obtain their energy through photosynthesis) as ammonia (NH3). Some Cyanobacteria fix nitrogen gas, which cannot be used by plants, into ammonia, nitrites (NO2-) or nitrates (NO3-). Nitrates can then be utilized by plants and converted to nucleic acids and protein.
Inorganic nitrogenous compounds from our tap or well water also enter our aquarium, often as Nitrites or Nitrates. Reverse Osmosis can remove much of this.
For more about tap water, please see this article:

 The nitrogen balance is an indication of protein synthesis and degradation.

FIGURE 14–8 Urea cycle and reactions that feedamino groups into the cycle. The enzymes catalyzing these reactions(named in the text) are distributed between the mitochondrial matrixand the cytosol. One amino group enters the urea cycle as carbamoylphosphate, formed in the matrix; the other enters as aspartate, formedin the matrix by transamination of oxaloacetate and glutamate, catalyzedby aspartate aminotransferase. The urea cycle consists of foursteps.
1 Formation of citrulline from ornithine and carbamoyl phosphate(entry of the first amino group); the citrulline passes into the cytosol.
2 Formation of argininosuccinate through a citrullyl-AMP intermediate(entry of the second amino group).
3 Formation of argininefrom argininosuccinate; this reaction releases fumarate, which entersthe citric acid cycle.
4 Formation of urea; this reaction also regenerates,ornithine. The pathways by which NH4  arrives in the mitochondrialmatrix of hepatocytes were discussed in Section 18.1.


Nitrogen is essential to synthesis of protein

A positive nitrogen balance correlates with a net synthesis of proteins and nucleic acids.

Nitrogen is an element vital to all life processes on Earth. Nitrogen is very important in our biosphere, where nitrogen comprises 78% of the atmosphere, and is part of every living tissue. It is a component of amino acids, proteins and nucleic acids. With the exception of carbon, nitrogen is the most universal element of life. Life could not exist without nitrogen. .
Nitrogen is essential for organic development; nitrogenous compounds are also required by some organisms for metabolic functions and respiration. Unfortunately, free nitrogen in the atmosphere is not in a form that is usable by plants or animals. Because of its stable structural formula, it is relatively inert and does not combine readily with other elements.

All living organisms, from fish to plants, have great quantities of assimilated nitrogen in their tissues. Nitrogen is a fundamental ingredient for the formation of proteins and nucleic acids. Every organism you place in your aquarium adds nitrogen based compounds; from fish to coral, to live rock, to plants.
The introduction of food also adds nitrogen. Dead or alive, they are organic masses, and possess the same nitrogenous attributes as the fish, plants, invertebrates you added to your aquarium.
Inorganic nitrogen is added two ways: the atmosphere and new water. Atmospheric nitrogen (N2) is incorporated into our aquarium water by way of nitrogen fixing bacteria and by Cyanobacteria (bacteria that obtain their energy through photosynthesis) as ammonia (NH3). Some Cyanobacteria fix nitrogen gas, which cannot be used by plants, into ammonia, nitrites (NO2-) or nitrates (NO3-). Nitrates can then be utilized by plants and converted to nucleic acids and protein.
Inorganic nitrogenous compounds from our tap or well water also enter our aquarium, often as Nitrites or Nitrates. Reverse Osmosis can remove much of this.
For more about tap water, please see this article:


Glossary | Linus Pauling Institute | Oregon State University

When an organism dies, nitrogen is moved from plant or animal into the inorganic chemical ammonia by the process of bacterial decay. Ammonia is also produced by bacteria in the breakdown of protein. This process is called Mineralization and is the end result of the metabolism of food.
However, ammonia is produced from both metabolism and mineralization. The decomposition (mineralization) process produces large quantities of ammonia (NH3) through the process of ammoniafication.
Heterotrophic microbes (organisms that require organic substrates to get its carbon for their growth and development) utilize the organic compounds of decomposing matter as their carbon source. Ammonia (NH3) is the byproduct of this consumption.

The process of nitrogen cycle was once thought to be a complete linear process, however newer scientific evidence (2008) indicates otherwise.

Newer research indicates that there are three more dynamic processes involved in our aquarium nitrogen cycle, in particular marine aquaria.
I have noticed this in my many both anecdotal observations as well as tests I have performed where many variables were changed, especially during the establishment of a new tanks bio filter (adding plants early on being one), so this new science based theory really helps explain this:

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