Biological Filtration: Understanding the Nitrogen Cycle in Aquariums

Drs. Foster & Smith Educational Staff

Understanding the nitrogen cycle is an important part of keeping a successful aquarium. The nitrogen cycle is responsible for
the biological filtration within the system. It keeps the water free of toxic compounds that are a result of the respiration of the
inhabitants, and the decay of any matter such as waste products and uneaten food. When we understand this cycle, we can
anticipate situations that may cause damage to this process, and prevent or avoid these situations that may lead to livestock
loss.
What is the nitrogen cycle?

In the nitrogen cycle, the waste products of the fish, plants, Figure 1. The nitrogen cycle
and invertebrates, along with any dead organisms or uneaten
food, are broken down by bacteria and fungi into the resulting
chemical, ammonia. Ammonia is extremely toxic to all of the
aquarium inhabitants. It is broken down by an oxygen-loving
bacteria, Nitrosomonas. The Nitrosomonas* bacteria feed
on both oxygen and ammonia, and with their biological
activities, they excrete a chemical called nitrite. Although
nitrite is not as toxic as ammonia, even at low concentrations
in the aquarium, it can be harmful to fish and invertebrates.
Another bacteria Nitrobacter*, which also utilizes oxygen in
its respiration, acts in a similar way as Nitrosomonas, and
essentially changes the nitrites into a relatively harmless
chemical called nitrate. The bacteria that will feed on nitrates
are anaerobic, meaning they grow in areas of little or no
oxygen. They require low-oxygenated stagnant water, and
can be found in more elaborate filtration systems and within
live rock. Here they breakdown nitrates into free nitrogen.
* Note: Recent research by one of the leading companies in
the aquatics industry has found that other bacteria (some of
which are still unnamed) are involved in the nitrogen cycle.
The company has isolated these strains of bacteria in the
freshwater systems and will be marketing them in a product
to be used as a cycling aid. A product containing the
saltwater strains is still in development, but is expected to be
available in the near future. In this article, I have used the
names of the bacteria commonly referred to in current
textbooks and journals, understanding these names may be
added to or changed as we learn more. For home aquarists,
the names of the specific bacteria are not as important as
Adapted from: Mills, D. The Marine Aquarium. Salamander Books LTD.
understanding the process and what may affect its efficiency. 8 Blenhein Ct., Brewery Rd. London N79NT; 1987.
The nitrogen cycle in new aquariums
Newly-set-up aquariums lack the colonies of bacteria that are necessary to perform the biological filtration. Because of this,
the aquarium must be "cycled." "Cycling" refers to the process of establishing and maturing the biological filtration. In order
to establish the system, we need to provide a source of ammonia for the Nitrosomonas bacteria in the filtration system so
they can live, reproduce, and colonize. To provide an ammonia source, it is best to add a few hardy fish that can withstand the
presence of ammonia and nitrites. Then we need to seed the aquarium with bacteria. There are commercially available cycling
aids that contain the bacteria. Otherwise, when purchasing the hardy fish, request a small amount of gravel from the aquarium
where the fish were held. This gravel should then be placed in the new aquarium along with the fish, and will provide the
bacteria that are necessary to seed the system. Figure 2 illustrates the process that occurs in an aquarium during the biological
filter maturing process.
As the fish in the new system are fed and begin to thrive, they will, through their biological activities, produce ammonia. The
Nitrosomonas bacteria, in turn, will begin to feed upon that ammonia and will start populating the aquarium. Their
population will be greatest in the media that contains the highest level of oxygen and surface area, which will normally be
within the filtration system. At this point, because the numbers of bacteria are limited, they will not be able to convert all of
the ammonia that is present in the system, so the ammonia levels will continue to rise. As the amount of ammonia increases,
the population of bacteria will also increase, but at a much slower rate than the ammonia. The ammonia level will eventually
reach a peak and then start to decline as the population of bacteria becomes large enough to break down the ammonia faster
than it is being produced. Because there is still ammonia within the system, however, the bacteria will continue to live and
feed on the ammonia until it reaches a level undetectable by testing. At this point, a balance has been achieved in which the
rate of ammonia production equals the rate at which it is broken down by the bacteria. The number of bacteria, from this point

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on, will change as the levels of ammonia (their food source) changes.
As we can see in Figure 2, the
nitrites go through a very Figure 2. Biological filtration cycling process
similar cycle as the ammonia.
Nitrites are produced through
the biological activities of the
Nitrosomonas bacteria as they
feed on the ammonia. As their
numbers increase, so does the
amount of their waste product,
nitrites. The Nitrobacter
bacteria, because of the
increasing supply of nitrites,
will multiply and increase in
numbers. They, too, will be
most densely populated in the
area with the greatest surface
area and oxygen content. The
nitrite levels will rise until the Adapted from: Mills, D. The Marine Aquarium. Salamander Books LTD.
number of bacteria has 8 Blenhein Ct., Brewery Rd. London N79NT; 1987.
increased to the point at which
they break down the nitrites faster than it is being produced. At this point, the peak level of nitrites has occurred, and the
bacteria will continue to metabolize and feed upon the nitrites that are produced. The nitrite level will decrease until it
becomes undetectable. As with the Nitrosomonas, the Nitrobacter will constantly alter their numbers as the amount of
nitrites changes, keeping a balance at which the nitrites are undetectable.
The end product of this whole process is nitrate. Nitrates, in low to moderate concentrations, are not toxic to fish and
invertebrates. Nitrates, however, can serve as a nutrient source for bacteria and plant life, and be the cause of other problems
in the aquarium, such as excess algae. The anaerobic bacteria will break down the nitrates. Plants within the system will also
feed on nitrates and are a good natural way of controlling this nutrient. Otherwise, the nitrate level needs to be controlled by
chemical filtration and partial water changes.
The length of time required for this cycle to be completed in the new aquarium depends on many factors. These factors
include: the amount of ammonia being produced during the cycling period; the efficiency of the biological filtration; and
whether live rock or live plants are used in this process. The typical time period in most aquariums is going to be 3 to 6
weeks. It is important that if any of the fish used during this process perish, that they be replaced with another hardy fish in
order to maintain the input of ammonia.
The nitrogen cycle in established aquariums
An established aquarium is one that the biological filtration has been matured. There are situations, however, that affect the
nitrogen cycle in established aquariums, such as: adding livestock; unnoticed death in the aquarium; overfeeding; medicating
the aquarium; and system maintenance.
Adding livestock
In the biological filter of an established aquarium, there are just enough bacteria to handle the biological load that is placed on
the system at that time. When we add livestock to this system, we are increasing the amount of ammonia for the bacteria in
the biological filter to metabolize. This situation brings us back to the cycling process (Figure 2), where the bacteria begin to
multiply to make up for the extra biological load. How high the toxins will become in the system is going to depend both on
the amount of livestock added to the aquarium at one time, and the size of the aquarium. If too much livestock is added at one
time, it is possible for the ammonia and nitrites to reach dangerous levels, which may lead to livestock losses. It is important
to minimize these levels by stocking the aquarium slowly over time, giving the biological filtration time to catch up to the
load.
Situations may arise where it is advantageous to stock the aquarium at a faster rate than the biological filtration can handle.
These situations include:
Buying livestock through the mail: Because of the price of shipping, most aquarists
will place large orders when purchasing their livestock through a mail order company.
Although they may offset the shipping cost in doing this, they are also placing the new
and existing livestock in jeopardy.
Adding many aggressive fish at the same time: It is best to acclimate aggressive fish
of the same species at the same time. Doing this will allow the fish to set their own
territories prior to one individual taking over the entire aquarium.
Transferring livestock to a hospital tank: The hospital tank is typically a small
aquarium with minimal filtration. Levels of toxins must be monitored closely when
any number of fish are added to this new system.

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Unnoticed death in the aquarium
It is possible in many aquariums, such as freshwater planted and saltwater reef aquariums, to have an inhabitant perish in a
place where it cannot be seen. When this happens, the organism begins to decay, which places a large load on the biological
filtration. Again, the nitrogen cycle can be thrown out of balance depending on both the amount of death in the system, and
the size of the aquarium. Having a large aquarium, in this case, is advantageous because the ammonia being produced by the
organism will be diluted by the large volume of water.
Overfeeding
When feeding the aquarium, it is important that the food that is added for the fish and invertebrates is consumed within a short
period of time. After a few hours, any food that is left uneaten in the aquarium will begin to be broken down by the bacteria
and fungi, resulting in ammonia added to the system. This ammonia in turn becomes part of the biological load and if the
amount of decaying food is great enough, can cause an imbalance in the biological filtration. If the aquarium has been
overfed, it is necessary to siphon out any uneaten food and to perform a 25% water change.
Medicating the aquarium
Many medications affect the ability of the bacteria to function in the biological filtration. For instance, anti-bacterial
medications act in the way the name describes, by killing many types of bacteria. Unfortunately, the biological filtration is
bacteria-based, and will be affected by these medications. Other medications such as copper, antibiotics, and ich treatments
will also affect the filtration in different degrees. It is important, when treating an aquarium, to closely monitor both the
ammonia and nitrite levels and to perform water changes or chemical filtration when necessary.
System maintenance
Water changes and filter maintenance will both affect the biological filtration to some degree. When performing water
changes, it is important that the replacement water is free of any toxic chemicals such as chlorine. These chemicals can kill
bacteria within the system and any water that is to be used, should be treated either by reverse osmosis, or by one of the many
available liquid dechlorinators. Filter maintenance, if not done properly, can have a large effect on the biological filtration.
Again, the beneficial bacteria responsible for the nitrogen cycle, populate in the greatest numbers where the water flow and
oxygen content of the water are the highest. This is typically within the filter. When performing maintenance on the filter, it is
ideal to leave the biological media untouched in order to preserve the bacteria. If there is no biological media within the filter,
it is wise to change only ½ of the mechanical media at a time. The remaining media that is to be reused should be rinsed in
water taken from the aquarium in order to preserve the bacteria colony.
Restoring the balance
All of the above situations can cause an imbalance in the nitrogen cycle, and make it necessary for us to monitor the level of
toxins in the system whenever they occur. If any level of either ammonia or nitrites is detected, it is important to control these
toxins either through partial water changes, or with one of the available toxin-absorbing resins.
When performing water changes, it is important to change no more than 25% of the aquarium water at a time. Changing more
than 25% of the aquarium water can cause rapid changes in both temperature and pH, which can result in added stress to the
aquarium inhabitants. Therefore, if toxins are present, it is best to perform small water changes frequently (even daily) rather
than performing large water changes at less frequent intervals. Again, the makeup water that is used to replace the aquarium
water should be treated by reverse osmosis, distillation, or at the very least using a liquid dechlorinator. It is ideal that the
makeup water is at the same temperature as the aquarium, and has been aerated prior to adding it to the aquarium.
There are many chemical medias available on the market that will help control sudden increases in ammonia. By stopping the
ammonia prior to it being broken down by the bacteria, we are reducing the biological load on the system. These products can
be useful in the situations that have been described above. Again, it is important when using these products to monitor the
water quality, and to perform water changes when any toxin levels are detected.
Know the warning signs
It is not practical to constantly test and monitor our water for ammonia and nitrites, but there are signs that we can see within
the aquarium. These signs are the actions of the fish and invertebrates. When ammonia or nitrites are present in the water, the
fish will show signs of stress. These signs can be in the form of erratic swimming behavior, gasping, or even laying on the
substrate. These activities can also be the sign of disease, but our first reaction should be to test the water for ammonia and
nitrites. Likewise, invertebrates such as corals will also show signs of distress. These signs are represented by the poor
expansion of the coral, losses in coloration, and deterioration. If these signs do show themselves within the aquarium, it is then
important to test the water for any amounts of ammonia or nitrites. If any levels are detected, then we must correct the
situation by the methods that I have described above.
Conclusion
Maintaining a healthy aquarium starts with understanding the nitrogen cycle and its effect on the inhabitants. This cycle takes
time to stabilize the water conditions both in the initial set-up, and after adding livestock. It is important to stock your new
aquarium slowly and to allow the cycle to be completed prior to adding any new inhabitants. If you understand this process,
pay attention to the warning signs, and take appropriate actions, there is no reason for catastrophic die offs in the aquarium

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prohibited under copyright law. Site content, including photography, descriptions, pricing, promotions, and availability are subject to change without
notice. These restrictions are necessary in order to protect not only our copyrighted intellectual property, but also the health of pets, since articles or
images that are altered or edited after download could result in misinformation that may harm companion animals, aquatic life, or native species.
pay attention to the warning signs, and take appropriate actions, there is no reason for catastrophic die offs in the aquarium
due to ammonia or nitrites.

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Unauthorized use of any images, thumbnails, illustrations, descriptions, article content, or registered trademarks of Foster & Smith, Inc. is strictly
prohibited under copyright law. Site content, including photography, descriptions, pricing, promotions, and availability are subject to change without
notice. These restrictions are necessary in order to protect not only our copyrighted intellectual property, but also the health of pets, since articles or
images that are altered or edited after download could result in misinformation that may harm companion animals, aquatic life, or native species.