Chemistry of Nitrogen in Aquariums

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Father of Earth's Next Emperor
Apr 26, 2007
Port Arthur, TX
Nitrates, Nitrites and Ammonia are often discussed in the context of maintaining a tank or cycling a tank to prepare for inhabitants. But what are these things and why are they important? This article will discuss nitrogen and various nitrogen compounds, the chemistry behind nitrogen, and some of the effects of nitrogen and compounds on our tanks and inhabitants.

BTW: The chemical reactions look like crap in the forum text... sorry. If a number is in front of letters, it is regular, if it is after some letter, it should be subscripted.

First a quick lesson in the Nitrogen cycle.


Now, this shows land, but where the cycle is slightly different for fresh or saltwater, I'll note the changes.

We'll start with the fish, since this is mainly what the conversation is about. Fish need nitrogen for literally everything in their bodies. Nitrogen is a primary component of every protein and strand of genetic material (DNA and RNA) in every cell of every organism on the planet. However, there is plenty of nitrogen available and organisms (including fish) have no problem finding sufficient nitrogen in easily usable forms. There's generally some nitrogen left over and (in land animals) that is excreted in the form of uric acid (urea AKA pee-pee).

However, fish do something very different, they excrete an amide called glutamine from their gills. The glutamine is hydrolized in water to produce glutamic acid and ammonia. (

The appropriate reactions are (and enthalpies for the curious or insane):
[FONT=Courier, monospace]Glutamine (aq.) + [/FONT][FONT=Courier, monospace]H20 [/FONT][FONT=Courier, monospace]-* [/FONT][FONT=Courier, monospace]glutamate+ [/FONT][FONT=Courier, monospace]+ [/FONT][FONT=Courier, monospace]NH4+,[/FONT]
[FONT=Courier, monospace]AH= -5160±70cal.[/FONT]
[FONT=Courier, monospace]Glutamate' + H+ -+ glutamic acid,[/FONT]
[FONT=Courier, monospace]AH[/FONT][FONT=Courier, monospace]= [/FONT][FONT=Courier, monospace]-950[/FONT][FONT=Courier, monospace]± [/FONT][FONT=Courier, monospace]30 cal.[/FONT]

Now for the not so chemically literate that means that asglutamine is ejected from fish, it reacts with water to form glutamate ion and ammonium ion. The glutamate then reacts with hydrogen ions for form glutamic acid.

Other bacteria (called decomposers) also contribute to the nitrogen load of the aquarium. Uneaten food, fish poop, decaying plants, heck, even fish scales, are all consumed (slowly) by bacteria. This process releases ammonia.

Note for freshwater aquariests: It is true that plants will uptake ammonia, nitrates, and nitrites. This paper gives a lengthy discussion of the topic (

However, there is some blockage of the uptake of one form of nitrogen for others (some plants like ammonia, while some prefer nitrites). Also, the pH is an important moderator for the uptake of these nutrients into plants. The following discussion will note that the change of one form of nitrogen to another produces an acidic environment.

Here's where the bacteria get started (see chart above). First bacteria that nitrify ammonium for their energy source (generally of Nitrosomonas or Nitrosococcus genus (at least for aquariums)). Do the following:

NH3 + O2 + 2H+ + 2e− → NH2OH + H2O

NH2OH + H2O → NO−2 + 5H+ + 4e−

What this means it that the bacteria use a small amount of energy (2 electrons) and two hydrogen ions to create ammonium hydroxide and water. Then they convert the ammonium hydroxide into nitrites, 5 hydrogen ions, and more energy (4 electrons). It's not very efficient, but it's enough for these bacteria to live on. Note that there are 5 hydrogen ions produced for every 2 ions used... this increases the acidity of the water.

Now the nitrifying bacteria that work on nitrites go to work. These are generally Nitrobacter (freshwater and marine) or three other genuses in marine environments. They do the following:

NO−2 + H2O → NO−3 + 2H+ + 2e−

Basically, the is taking the nitrites and hydrolysing it to form nitrates, 2 more hydrogen ions and 2 electrons for the energy. Again, more hydrogen ions making the water more acidic.

This is where the nitrogen cycle in freshwater takes generally stops. These reactions take place in the presence of oxygen. Freshwater aquariests rarely go any further with this because the equipment necessary to create an anaerobic environment for the denitrifying bacteria is rare, expensive, homemade, or not needed because water changes are easier to do.

For the marine types, we'll take it one step further. The bacterial species Thiobacillus denitrificans, Micrococcus denitrificans and the genus Pseudomonas use oxygen as a terminal electron receptor which is why it must be in an anaerobic environment. Which, in marine tanks, is generally deep in the pores of the live rock and deep under the sand (lower than about 3-4 inches) which is why a 6 inch sand bed is recommended. Note that any flow to an area renders this chemical reaction impossible so there are no filters that can allow nitrifying bacteria to grow and flourish. The chemical reaction in these bacteria is as follows:

2NO3- + 10e- + 12H+ → N2 + 6H2O

Note the use of large numbers of hydrogen ions in this reaction. However, rememeber the above reactions, this only removes the hydrogen ions generated from the nitrite to nitrate step.

Also, something to keep in mind, cyanobacteria (often wrongly called an algae) does the reverse of this and converts gaseous nitrogen back into ammonium or one of the nitrogen species for use by itself and/or plants or true algaes. So if you have a cyano outbreak, all the nitrifying and denitrification bacteria in your tank are just keeping up with the cyano and not doing anything with fish waste, uneaten food, etc.

The introduction of these bacteria and their flourishing is what we call 'cycling the tank'. There are many, many articles on this process, so I won't go into depth. The point is that all the bacteria mentioned above are almost everywhere in the environment. So it's no problem getting the bacteria into the tank. But these bacteria must have food (the nitrogen compounds) to live on while they are populating your tank. Hence the recomendation that you add ammonia or drop a piece of shrimp into the tank. The shrimp will decompose (encouraged by other bacteria) thereby producing ammonia.

Now for the reason to keep the ammonia, nitrites, and nitrates in our tanks as low as possible.

This paper is critical for our discussion:

It describes the toxicity of various nitrogen products to the common guppy (Poecilia reticulus). {NOTE: This paper also describe the problems the researchers had in keping the ammonia levels constant in the tanks as evaporation of the water caused the ammonia concentration to increase by 5% over four days. The tests also observed a change in pH from 7.5 to 6.9 in four days.}

The final results are that 1.26mg of ammonia per liter has a LD50. That's lethal dose 50%... or the level at which 50% of the fish will die. 199 mg/L of nitrate will do the same thing. That's within a three day time frame.

When ammonia and nitrate are both present, LD50 occurs when the the concentrate of ammonia is .5mg/L and nitrate is 30mg/L at the same time.

Just because most Americans aren't familiar with the metric system... a grain of rice weighs between 20-30 milligrams. A ten gallon tank is roughly 30 liters. So if ammonia equivalent to the mass of a single grain of rice is added to a roughly 300 gallon tank, there is a 50% chance of killing every fish in the tank. That's not a lot of ammonia. If your tank already has nitrate problems, then the mass of ammonia needed drops... a lot.

What does this mean for the aquariest?

I hope that at least as far as nitrogen compounds are concerned, that nature isn't present in our tanks and that it is difficult to recreate the necessary conditions in our tanks. Keep in mind that many of you (like myself) really like Amazon species. The amazon has a flow rate of 7 million cubic feet (that's 52 million gallons) of water per SECOND. That's why they don't have any trouble with nitrogen build up. The river is constantly having the biggest water change in the world.

So, I hope that water changes are a part of your tank regime.

(thanks to sploke for suggesting this be an article.)