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The Nitrogen Cycle

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#1 anchar

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  • Joined: 28-January 04
  • Location: Bullcreek

Posted 29 August 2006 - 12:59 PM

The Nitrogen Cycle
by Andrea Watts


One of the most common and freely available elements on Earth is nitrogen. The air that we breathe comprises of about 78% nitrogen and it appears in different forms throughout life's various biological cycles. Being an enclosed system, an aquarium requires careful monitoring to ensure that harmful forms of nitrogen do not impact negatively on it's occupants. An understanding of how the Nitrogen Cycle works is an essential component to successful fish keeping. The chemical reactions which take place in nature are complex and an aquarium is only a reconstruction of a part of the natural environment. The scale may be smaller, but essentially the fundamentals remain the same.

Hopefully the following article will explain the processes involved in cycling nitrogen.


The first stage in the Nitrogen Cycle begins as organic wastes start to decompose. These wastes originate from uneaten food, undetected fish corpses and excreta from the tank's inhabitants. The subsequent breakdown of the molecules in these wastes leads to the production of ammonia (if the pH of the water is neutral to alkaline) or ammonium ions (if the pH of the water is acidic). The bacteria responsible for the generation of ammonia are from the genera Bacillus, Bacterium or Micrococcus. The level of ammonia steadily increases as the tank ages, through the process of biochmical oxidation or ammonification. A peak of about 11mg/L is reached around day 7.

At this point in time, the bacteria responsible for the conversion of ammonia are numerous enough to reduce its concentration. The ammonia levels then drop abruptly and by day 11, its presence is virtually nil. If high levels are still detected beyond this time, or become apparent in an established tank several months later, a shortage of bacteria is indicated. There are two case scenarios to consider: increased ammonia is usually attributable to an excess of uneaten foood or undiscovered corpses. A mass destruction of bacteria is normally a direct result of over zealous water changes, the use of medications, replacement or the washing of filter media in tap water or a substrate change.

A little scientific notation for the chemistry buffs

As previously mentioned, the form of ammonia found in an aquarium is pH dependent. Free molecular ammonia (NH3), is a dissolved gas. It generally forms in tanks with a pH of 7 or greater (ie. neutral to alkaline environments). This is the form that keepers of Malawi and Tanganyikan type biotopes need to be most aware of. The toxity of ammonia is increased further in tanks with warmer water. Under these conditions, ammonia is extremely toxic to fish and becomes fatal in a very short period of time.

Biotopes that are acidic (ie. have a pH less than 7), ammonia combines with a water moleclue to form ammonium hydroxide (NH4OH). In this form, ammonia is approximately 100 times less dangerous to fish.

Therefore, African cichlids are at a higher risk than their South American counterparts due to the highly mineralised and alkaline environment. The presence of free ammonia is often indicated by a darkening of fish colour, skin damage and gill irritation (observed through fish gasping for air at the surface). It becomes fatal above a concentration of 0.02mg/L.

How do I rectify this situation?

Partial water changes will reduce the concentration of ammonia in the tank, whilst the addition of new bacteria will help re-populate the colony. Products such as Cycle, Environ-8, Nitrovec etc. are useful. An ammonia test kit, either colorimetric (colour scale) or electronic, is an essential addition to the home.


The second stage of the Nitrogen Cycle involves the activities of bacteria from the Nitrosomonas or Nitrosococcus genera. Nitrites (NO2), play an integral part in the decomposition cycle of nitrogenous waste in the aquarium. They are produced when the afore-mentioned bacteria decompose the ammoniacal derivatives (NH3 and NH4). From around day 6 to day 17, they convert the ammonia into nitrites. At around day 24, the nitrites begin to decline until such time that they are undetectable.

Although not quite as toxic as NH3 and NH4, nitrites are harmful to fish regardless of the pH. Therefore, fish should not be introduced into an aquarium that shows its presence. Nitrous bacteria are practically non-existent in new aquaria. To start the process, you can introduce micro-organisms that are readily sold at your LFS (Cycle, Environ-8, Nitrovec and so on). If you already have an established tank, you can call upon that reservoir of bacteria. Simply through the transfer of some filter material, aquarium decor or a handful of gravel, you can add some of the nitrous bacteria to your new tank. The transfer of water does not have the same beneficial effect as only a small amount of bacteria is suspended in the water column.

Nitrite levels should be checked regularly through the use of a colorimetric or electronic test kit. The slightest trace of nitrite can prove fatal and even when the levels register as zero, care should be taken to introduce fish gradually. Established aquariums are stable and all efforts to maintain the equilibrium must be observed. This includes not harming the bacteria through over zealous cleaning of the filter material. Do not use detergents or chlorinated water in the cleaning process and water changes should not involve replacing too large a volume of water. Fortnightly replacement of around 25% water is far more preferable to larger changes at less frequent inetrvals. Note that some medications (particularly antibiotics) can also destroy valuable bacteria. Isolating and medicating fish in a smaller tank is a better method of treatment.

Unless action is taken immediately, the fish's health will suffer drastically. The nitrite level should not exceed 0.01mg/L. Nitrites combine with haemoglobin (the oxygen carrying component in blood) and form methaemoglobin, thus preventing the transport of oxygen. The fish turns dark brown in colour and death ensues quite quickly. The presence of nitrites in the water is indicative of poor water quality, a situation that will aggrevate quite a number of diseases.

How do I rectify this situation?

A lack of balance can arise when a weakness in the bacteria or a rise in nitrates (through oxygen depletion) occurs. This situation can be rectified through a water change and the introduction of supplementary bacteria.


From about the 5th day after filling an aquarium, nitrates begin to form, although it is only after about day 25 that the different populations that bring about the Nitrogen Cycle are in large enough numbers for all stages of the cycle to take place similtaneously. The intermediate toxic compounds, ammonia and nitrite, should be no longer detectable. The bacteria responsible for this activity are from the genus Nictrobacter.

This is the stage at which fish can be successfully added to the aquarium. It should be noted, however, that even though plants assimilate the nitrates originating from the breakdown of organic wastes, they are rarely in sufficient numbers to absorb all that is produced. This fact becomes more apparent in many African type biotopes that are devoid of plants altogether. Over-populated, closed environments become subject to a steady build up of nitrates. An unattended tank can emass concentrations in excess of 1g/L over a 1 year interval (as opposed to a natural environment where the concentration rarely exceeds 5mg/L due to permanently changing water).

Excessive concentrations of nitrates are often termed 'silent killers'. This is because in small doses, these compounds are not deemd toxic. An accumulation that leads to concentrations in excess of 80-100mg/L will prove fatal to your fish. Only regular water changes will reduce their concentration. Certain species are more susceptible to nitrate poisoning than others. Amounts in excess of 50mg/L are often signalled by the explosive growth of algae. In a planted tank, preferred water plants are compromised by the algae that feed on the nitrogenous compounds. Affected fish will display signs of stress, hence making them more vulnerable to opportunistic diseases. Poor water quality can provoke such conditions as 'pop-eye' and fin rot. Care should be taken to keep nitrates under 15mg/L.

Additional latent risks can lead to dramatic consequences. For example, if the environment is oxygen depleted due to poor maintainance or a sudden rise in temperature, favourable conditions for the bacteria from the genus Bacillus develop. This, in turn, reverses the Nitrogen Cycle through denitrification hence producing ammonia and nitrite. If this is allowed to occur, the entire fish population can be decimated within a few hours.

How do I rectify this situation?

Commercial denitrifiers work on the principle of external denitrification. The nitrate charged water circulates through an anaerobic rich environment which breaks down the nitrates into molecular nitrogen. The provision of 'food' (for the bacterial colonies) is the only constraint and manufacturers have developed specially adapted foods in a number of different forms.

However, there is no substitute for regular water changes and testing for nitrate concentrations.


Ammonia is extremely toxic to fish. It causes swelling to the gills, leading to asphyxia and disruptive osmoregulatory functions. Nitrites become fatal by acting on the haemoglobin in the blood. Nitrates, however, are only toxic in high concentrations (between 50 and 300mg/L depending on the species).

Therefore, only when ammonia and nitrites have become undetectable, should fish be introduced into a newly installed tank. This usually occurs around week 3 - 4. Various test kits are available to monitor the levels of ammonia, nitrites and nitrates - it is vital to use them regularly in a newly set-up tank. Those of us who are impatient can help to speed up the natural processes by introducing gravel or filter media from an established aquarium.

#2 Blakey

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  • Joined: 11-October 04
  • Location: Scarborough, WA

Posted 10 February 2008 - 08:48 AM

When you start up a new tank it goes through a 'Nitrogen Cycle'
The nitrogen cycle of an aquarium is a chain reaction in nature resulting in the birth of various types of nitrifying bacteria, each with their own job to do. Each new bacteria born consumes the previous one, and in turn gives birth to the next bacteria.
The three components involved to make this happen are ammonia (NH³ or NH³+4), nitrite (NO²), and nitrate (NO³). In general the nitrogen cycling process usually takes about 30 days, but there is no exact time frame for this process to complete its task, as each aquarium is different. Factors such as how many fish, other livestock, and organic matter is present in the tank can vary the completion time, one way or the other

some links to visit and read (it even has an animation)



Phase 1 - Ammonia (NH³ or NH³+4)
The first component needed in the chain is ammonia, and it is only during the cycling process that ammonia readings should be present in an aquarium.

Once ammonia begins to accumulate in the aquarium, the process begins. So where do you get the ammonia from? It is produced by such things as fish and other livestock waste, excess food, and decaying organic matter from both animals and plants. Now putting live animals into a tank for the purpose of cycling is not easy, because they are exposed to highly toxic levels of ammonia and nitrite during the process. However, without ammonia present the cycle cannot begin, and if ammonia is removed, or the supply is disrupted during cycling, the process stops. As you see the ammonia level rise during the cycling period, if you think by adding an ammonia destroyer or doing a water change to bring it down is helping, it isn't! You are only delaying the cycling process and preventing it from completing its mission. If you use fish to cycle an aquarium, it's a catch 22! You don't want to put the animals in harms way by exposing them to toxic elements, but you need their waste as the ammonia source to get the job done

Phase 2 - Nitrite (NO²)
At about day 10 into the cycle, the nitrifying bacteria that convert ammonia into nitrite, nitrosomonas, should begin to appear and build. Just like ammonia, nitrite can be toxic and harmful to marine animals even at lower levels, and without nitrite present the cycling process cannot complete itself. Nitrite will continue to rise to a high level of about 15 ppm, the most critical stage, and at about day 25 the level should begin to fall off, although it's quite possible to run on for another 10 days. Most likely the nitrite reading will peak and fall off to less than 2 or 3 ppm by about day 30, and shortly thereafter to zero. If it does not, don't worry, it should drop sometime within the next 10 days or so.

Phase 3 - Nitrate (NO³)
Now that the ammonia has given birth to nitrite, the nitrite in turn give birth to the third and final nitrifying bacteria, nitrobacters These bacteria are living entities that require oxygen and food (an ammonia source) to survive, grow on the surfaces of everything in the tank, and the waste from nitrobacter are shown in the form of nitrate with a test kit. When nitrate readings begin to increase, you can tell that these beneficial nitrifying bacteria are starting to establish themselves, which is what you have painstakingly been going through the cycling process to achieve.

I suggest buying an ammonia test kit, a nitrite test kit and a nitrate test kit and actually run through the process properly for the first time as an experience and document your findings

#3 GaryA

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  • Joined: 13-November 08

Posted 27 November 2008 - 11:51 AM

ok I guess " Fishless cycle" is with out fish in tank and rely on mother nature to create the good bacteria (top of the class I go)
So would not it be better to set up an Aquarium and add bacteria to change Ammonia to Nitrite to Nitrate using Bacteria like Pond Max Clarifier Bacteria as this should speed up the process?
I have not grasped the concept of adding water in a tank that has a conditioner added and hope after 3 weeks it is going to turn into a safe environment for the fish as I am certain it will not but can you convince me!
Cawder adds "to do a fishless cycle you add Ammonia."
Question; The whole idea of this is to get rid of the Ammonia in your tanks am I right?

#4 Donna

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  • Joined: 14-October 07
  • Location: Rockingham

Posted 27 November 2008 - 12:42 PM

Hi Gary,

Cawdor adds "to do a fishless cycle you add Ammonia."
Question; The whole idea of this is to get rid of the Ammonia in your tanks am I right?

It is possible to have a fishless cycle, but not an ammonia-less cycle. You can add ammonia without fish if you like, but for the nitrifying process to begin, there must be ammonia, the ammonia is the "good" bacteria's food or fuel source. No ammonia, no bacteria. So adding bacteria before the ammonia is not going to work as the bacteria will die or diminish before the ammonia levels get high enough to sustain it.

I have not grasped the concept of adding water in a tank that has a conditioner added and hope after 3 weeks it is going to turn into a safe environment for the fish as I am certain it will not but can you convince me!

I agree with you. Adding a conditioner is probably not going to "kick start" the cycling process. There are some products that claim to be of help, but I would be suspicious of any substance that looks like it would not support "live" nitrosomanas and nitrobacter.

Bacteria is a living thing and is light, heat sensitive etc. It is also sensitive to chemicals and there are a number of inhibitors including lack of oxygen that will prevent its growth. I don't think it could survive well in a plastic container.

The only way around the cycle in my opinion that people say is reliable is to use an established filter with mature filter media in your new tank with fish added to produce ammonia or add ammonia.

Hope this has helped a little.

This link is a really good one that explains how to keep optimum conditions for nitrifying bacteria.




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