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What is a Biological Filter?

By R. Kayne
Updated May 16, 2024
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The first step in setting up a healthy aquarium is to establish a biological filter. A biological filter is a natural filtering system consisting of helpful bacterial colonies that, through a cycling process, convert pollutants in water to harmless nitrate. Nitrate is nitrogen, therefore this cycling process is also referred to as the nitrogen cycle, or cycling a tank.

A basic understanding of a biological filter is necessary for any successful aquarist. When an aquarium is initially set up there is no biological filter present in the water because the colonies of bacteria responsible for it have yet to be established. When fish are added to the new tank they immediately begin to pollute the water with highly toxic ammonia exuded from breathing and waste. The water will look clean, but it is quickly becoming poisonous to the fish.

During the first 7-14 days ammonia will soar to deadly levels in a new tank, causing some fish to succumb and others to be weakened and take ill. Finally this overabundance of ammonia triggers the natural development of a good bacteria called nitrosomonos which feeds on ammonia, converting it through oxidation to nitrite.

Nitrite is less toxic than ammonia, but still deadly to fish. For the next 10-14 days nitrite levels rise as more and more ammonia is converted, with new ammonia being converted as well. When nitrite builds to deadly levels, the last stage of the nitrogen cycle kicks in and nitrobacter, another good bacteria, spontaneously blooms to thrive on the toxic nitrite, converting it to harmless nitrate. That "a" makes all the difference.

Nitrobacter takes longer to establish than nitrosomonos, so toxic nitrite will drop only slowly. But eventually both bacteria colonies will catch up to production, and keep up, canceling pollutants as they are created. When nitrite and ammonia levels both test at zero, and nitrate is measurable, the nitrogen cycle is complete and a biological filter has been established. This process of establishing the biological filter normally takes 4-6 weeks.

Not soon enough for many fish! Due to a compromised immune system, those that do not succumb directly during this stressful period will often develop split fins, ich, or other diseases, and succumb in the weeks following. High ammonia levels can also cause permanent damage to delicate gill tissues, resulting in eventual death.

For these reasons experienced aquarists normally test the water daily for ammonia and nitrite levels, making 10-20% partial water changes to dilute the high levels of ammonia and/or nitrite in an attempt relieve conditions for the fish, even though this slows down the establishment of the biological filter. But there's been a better way since 1999: fishless cycling.

Fishless cycling is an alternate method for establishing the biological filter in a new tank without using fish at all. In this method, pure ammonia, minus any detergents or colors, is added daily to a fishless aquarium to trigger the nitrogen cycle. The biological filter is established over a period of about 7-10 days without fish. Once the tank has cycled, the fish are added all at once, because the tank has been cycled to handle a full bioload.

Once a tank is cycled and its inhabitants established, the size of the bacterial colonies will adjust to be in direct proportion to the amount of ammonia being produced. If you add another fish later, you are adding to the bioload and the bacterial colonies will need to grow to accommodate it. If you add too many fish at once, there will be a lag time between the extra ammonia and the ability to convert it. Ammonia and nitrite will spike, possibly triggering an outbreak of disease. Therefore the general rule is to only add only a few very small fish at a time, for example small tetras, and fewer fish if the fish are larger.

The only exception to this rule is the one-time event of adding all fish at once after cycling a tank using the fishless method.

Nitrosomonos and nitrobacter will colonize in manufactured filter medium, on the walls of the tank, gravel bottom, decorations, plants, and exist in the water as well. However their highest concentration will be found in the tank's filters which are designed to maximize their colonization. Therefore dirty filters should only be gently rinsed in tank water drawn into a bucket, never under the faucet. Any change in temperature or water parameters will cause the bacteria to die back, which will cause ammonia and nitrite to spike.

Aquarium test kits are available for testing ammonia levels, nitrite, nitrate, and other water parameters including hardness and pH. A newly established tank should continue to be tested weekly for the first few months, and monthly thereafter.

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Discussion Comments
By anon171580 — On Apr 30, 2011

When setting up a new aquarium, or one which has been thoroughly cleaned for some reason, connect the new canister filter 'in series' with the existing established one. That is, the output of the existing colonized one connects to the input of the new 'clean' filter whose output goes back into the tank to complete the loop.

Water and bacteria from the existing colonized tank will flow through the existing filter taking some bacteria into the new filter and an extension of the colony will established in the new filter. You could also go a step further and gradually take some water each day from the established tank and put this in the new tank with the filter that you prepared as above.

I do this by filling the new aquarium with clean water and replacing this with water from the colonized aquarium as above. Start by setting up the 'series' filter described above, then after two or three weeks (or more) set this filter up one the new tank now filled with water from the first tank. It is all about gradual changes that the bacteria can handle.

By anon107271 — On Aug 29, 2010

you can also cycle a tank very quickly using media from a healthy established tank. you can use the gravel, filter and some water to jump start a new tank. let it run with filters for a day or two then add fish and continually check nitrite levels several times a day.

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