Understand The Nitrogen Cycle – Your Livestock Depend On It


Whatever type of marine aquarium is kept, reef system or fish only system, there is one function that is totally essential. It isn’t a modern natural ‘invention’ either, it applied to those earlier aquarists just as much. The difference is that in the very early days the aquarists didn’t know anything about it. Before my time a pioneer marine aquarist thought he could keep his aquarium clean more easily by using what turned later into the much used under gravel-filter. I believe his name was Straughan. He was amazed about the length of time he was able to keep livestock, and put it down to better cleanliness. Investigations showed that in fact he had stumbled onto the secret of keeping any marine system basically healthy. In a way it was due to better cleanliness.

Livestock in an aquarium continue with their normal life functions. They are fed. Algae can die and rot as can uneaten food. This protein breaks down into a deadly toxin – ammonia. In the presence of not a great amount of ammonia livestock can be badly affected or die. Fish could hang quietly at the water surface, or swim in a very erratic manner, even upside down, or sit on the aquarium bottom leaning against a rock, and breathing could be rapid. This situation is very serious.

Yet in the modern aquarium the problem of toxins hardly arises, except perhaps in the case of a beginner who does not use patience and stocks too rapidly.

The saviours and the servants of the aquarist are bacteria. These bacteria break down toxins and the process is generally known as the nitrogen cycle.

Ammonia is very toxic and is broken down by bacteria called Nitrosomonas. The toxic ammonia is converted to nitrite, which is also toxic and nearly as bad as ammonia. That’s a lot of good! Well, another bacteria then comes into play and converts the nitrite into nitrate. These bacteria are called Nitrobacter. Nitrate can be bad at high levels, but is safe in comparison to ammonia and nitrite. The nitrogen cycle does not stop at this point, but continues when the nitrate is converted to nitrogen gas. The gas escapes from the aquarium and the cycle is complete.

Simple, nature saves the day!

Yes, it does, but there has to be a catch and here it is – the ammonia/nitrite conversion bacteria need a different environment to the nitrate bacteria.

The ammonia/nitrite bacteria require an environment that provides obviously ammonia and nitrite, and in addition they need a good supply of oxygen. This oxygen can only come from the water (except in one instance) so the aquarist has to provide plenty of water circulation to ensure good gas exchange at air/water interfaces such as the surface of the seawater. The home for the oxygen hungry bacteria can be in a canister filter and the like with suitable media. What is the exception mentioned – this is the so-called trickle filter. As the seawater running down is exposed to the air, oxygen is plentiful.

Providing a suitable home for the ammonia and nitrite bacteria is easy. The aquarist needs to ensure that the canister etc filters are properly matured, and this is achieved by using a prepared commercial maturation fluid. Using test kits, once the nitrite has disappeared the filter is initially mature. The instructions with the fluid will give details which are very straightforward. The nitrite showing as cleared means that there is a presence of bacteria which will deal with ammonia and nitrite. When the filter is initially mature, stocking can commence, but with great care and patience, as the filter is still unstable and needs to adjust to the bio load placed upon it.

The problem – here we go again – with canister etc filters is that the complete nitrogen cycle is not achieved. This is because they operate in an oxygen rich environment. Bacteria that deal with nitrate can live in an oxygen rich environment too, but under this circumstance they will not deal with the nitrate. An environment must be created where there is a lack of oxygen, and in this circumstance the bacteria will turn to the nitrate. The bacteria need oxygen, and the only way they can obtain it is to extract it from the nitrate, which breaks the nitrate down.

So there is no reason why a marine system cannot use a canister etc filter. It does mean though that the aquarist must keep a careful watch on nitrate levels as well as other parameters. Routine seawater changes will control nitrate to a degree, as will good husbandry such as a proper feeding discipline. There are other ways to control nitrates which will not be dealt with here.

There is a way of achieving the full nitrogen cycle, and that is to use live rock. This live rock (LR) can be used in fish only and reef aquariums. In the reef aquarium it has the secondary benefit of providing a material with which to construct the reef.

LR works as filtration because it is porous and provides a home for the bacteria. On the surface and inside toward the surface dwell the bacteria that use oxygen and deal with ammonia and nitrite. Deeper inside, where oxygen levels are depleted, dwell the bacteria that can only obtain oxygen from nitrate. Therefore the total nitrogen cycle is achievable. It is important that sufficient live rock of good quality is provided.

Using LR the aquarist still needs to monitor seawater parameters. Nitrate is included in those parameters, as LR has limits the same as anything else. That said, it is a wonderful filtration media.

Whatever type of bio filtration the aquarist uses, the bacteria will not make many demands, and the demands they do make are easily met. Fail to meet those demands, or pass the point where the bacteria do not have the capacity to deal with toxics, and the consequences could be very serious.

Provide suitable media and well oxygenated seawater, have patience with stocking and do not overstock, and nature’s bacteria will work silently and unseen providing life support.

Understand The Nitrogen Cycle – Your Livestock Depend On It
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  1. Would it be wise to use an under gravel filtrations along with a bio canister and pump if you are planning to start a system with live gravel and live rock? I have read some books on mini reef systems and their doesn’t seem to be anyone talking about using combinations. I am just in the planning phase and I already own a 75G tank with an under grave system, however I am planning to get a cannister bio filter and I plan to have a lot of shrimp, snails, and Mollusks, 30+ with Live gravel and Live Rock and I don’t plan for many fish. I would like more plants and corrals with the proper fish that are compatible. Would it be wise to use all those filters?

  2. Hello Frank.

    I believe that some aquarists still use undergravel filtration though they are very much in the minority.

    The following is my opinion only. Using canister filters for bio support has drawbacks, the main one is nitrate. If the canister is well maintained, that is, there is sufficient mechanical filtration to protect the bio media and the mechanical area is cleaned regularly, the canister will give little trouble.

    The undergravel filter has bacteria which rely on oxygen, as does the canister. It is necessary with both to ensure good seawater gas exchange to ensure a high ongoing oxygen presence.

    The canister can be easily serviced. However the undergravel cannot. Having the seawater constantly drawn down through the sand inevitably draws in detritus, and the sand becomes very dirty. This can slow down water flow etc. The only way to deal with this is to clean the sand. Removing it and washing it with tap water kills all the bacteria. Washing it gently in seawater is better but what a slow and tedious job to rmove the sand from the aquarium! And will it be clean?

    It is better to use a properly sized canister filter on its own, containing a sufficient amount of a good bio media (such as sintered glass) which in turn is protected by adequate mechanical filtration. As said, properly maintained there should not be a problem.

    Having said all that, if there is sufficient live rock of good enough quality then the need for a bio canister filter should not arise. The canister filter could be used for pure mechanical filtration.

  3. Hi Mr. John Cunningham,

    Thank you for your article, it has been a great ease to my puzzled mind on the types of bacteria and its abilities on the filter types.

    One thing i’d like to ask is how do the Nitrobacter get into the canister bio-filter media? or has it been in normal tap-water all along?

    For me i’ve been using holland sand as bedding for my aquarium with under gravel filter run by a powerhead. As well as a canister filter.

    So to describe the effect, the nitrosomonas are actually living on the holland sand bedding converting ammonia to nitrite and taking up oxygen from the oxygenated water (its source from any nearby airstone providing the oxygen?)
    After of which the Nitrobacters on the holland sand also break the nitrite to nitrate.

    Then the nitrate is free floating in the water and eventually gets sucked into the canister where the bio-media filter, within containing the nitrobacter are very constrained of oxygen and rely on breaking down the nitrate for oxygen to survive. Which then the nitrate broken into nitrogen gas which exits the canister filter is released back into the aquarium and then goes upwards (since its so light) and goes out of the aquarium.

    Would that be correct?

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