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A Beginner's Guide to the Freshwater Aquarium Cycle

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What is the aquarium cycle?

The aquarium cycle is not really a cycle in the true sense of the word but refers to the part of the nitrogen cycle that plays a vital role in our aquariums. All animals produce ammonia as a waste product of metabolization and this ammonia is toxic to these animals. For land animals, getting rid of ammonia is a simple matter of converting it to urea and expelling it from the body. It's a simpler process with more complicated results when it comes to our fish; instead of converting it fish expell ammonia directly into the water from their gills. This ammonia builds up in your tank water and becomes deadly over time. The aquarium cycle is the process of establishing a way for this ammonia to be converted into substances that are safer for your fish. In most cases, what this means in particular is establishing colonies of beneficial bacteria that convert ammonia to nitrite, which is also quite toxic to fish and then ultimately to nitrate which can be tolerated in much greater concentrations.

In every cycling method other than the live plant method, the steps to the cycle are as follows: as ammonia builds up, Nitrosomonas bacteria begin to build up on the surfaces of your aquarium including the substrate, any decor, the walls of your tank and most importantly, in your filter. These bacteria convert ammonia to nitrite. Nitrite is still quite toxic to fish but its presence promotes the growth of a second type of bacteria, Nitrospira,* which also live on your tank's surfaces. These Nitrospira bacteria convert the nitrite into nitrate. In the oxygen-rich environment of the freshwater fish tank, this is where the cycle ends as there is no aerobic (oxygen-friendly) bacterium that converts nitrate into harmless nitrogen gas. In non-planted tanks, we must manually remove nitrate with water changes but in heavily planted tanks, plants can absorb nitrate and prevent it from building up in our tanks. Luckily, nitrate is safe at low levels so water changes and/or plants can prevent it from ever building up to problematic levels. The entire process takes anywhere from 4-8 weeks although cycle lengths shorter or longer than this time frame aren't rare.

Why do I need to cycle my aquarium?

Ammonia is very toxic to fish and can kill them in a matter of hours or, in high enough concentrations, minutes. Exposure to even relatively low levels of ammonia can cause long-term health problems for our fish or cause them stress which weakens their immune systems, opening the door to a host of illnesses. Preventing exposure to ammonia is extremely important for the health of your fish so keeping them in an environment that processes their ammonia excretions into safer by-products is essential. A common mistake new fishkeepers make is to let their tanks run for a day or two before adding fish or even adding fish to newly set up tanks. Without the safety net of beneficial bacteria (or live plants) in place, ammonia levels quickly rise and fish become sick or die. Cycling the aquarium prevents these problems and ideally, a tank should be cycled before placing fish into it so that your pet fish are never exposed to harmful ammonia or nitrite.

How do I cycle my aquarium?

There are five methods of cycling your aquarium but whichever method you choose, your best friends during the cycle are patience and a good liquid test kit. Because cycling involves levels of ammonia, nitrite and nitrate in your tank, you need to be able to measure the quantities of these chemicals in your tank. Paper test strips are notoriously inaccurate so a liquid test kit is preferred. Apart from the patience and test kit, any cycling method relies on a source of ammonia in your tank. Without an ammonia source, beneficial bacteria won't colonize the surfaces of your aquarium so no matter how long you've left the tank running it hasn't cycled until these bacteria colonies are established. In every method, you can decorate the tank completely before you start the cycle (including live plants) as these will provide more surfaces on which the beneficial bacteria can grow. You'll also want to run your heater and filters as if fish were in the tank. Heated water promotes quicker bacteria growth and the filter is the main site of bacterial colonization in your tank.

-The "Fish In" Cycle

This is the least-preferred method of cycling. Essentially, it involves using live fish as your ammonia source. The benefit to this method is that you get to stock the tank immediately, but the problems associated with this method far outweigh that single benefit. Fish recommended for the "fish-in" cycle are usually hardy species but aren't always fish that you want to keep in your tank on a long-term basis so you have to deal with the hassle of removing them once the cycle is complete. Second, water changes must be performed on a regular basis (sometimes daily or even more often) in order to keep ammonia and nitrite levels low so that the fish you're using to cycle don't die. Finally, and most importantly, cycling with fish can be stressful or even deadly to the fish you're using to cycle. Unfortunately, many new aquarists are unaware of the aquarium cycle or its importance and are thus essentially forced to do a "fish-in" cycle. When using this method, you should only choose hardy species (zebra danios are a popular choice) in small numbers. Monitor ammonia and nitrite levels daily, performing water changes with a good water conditioner that neutralizes ammonia and nitrite (Seachem's Prime is a good choice) whenever ammonia or nitrite levels exceed 0.5 ppm (0.25ppm is an even safer number). After a few days the ammonia should spike. As the Nitrosomonas bacteria increase in number the ammonia level will start to peter out, replaced by nitrite. The Nitrospira bacteria will then start to grow but since these reproduce more slowly than Nitrosomonas, the nitrite portion of the cycle can take a deal longer than the ammonia portion. Eventually both ammonia and nitrite will continually test at 0 ppm and you'll start seeing a reading for nitrate. At this point the cycle is complete. It's usually best to wait a bit just to make sure there aren't any straggling ammonia or nitrite spikes but after some time you can begin adding more fish to the tank, a few fish every week or two until the tank is stocked. The most important part of the "fish-in" cycle are the ammonia and nitrite tests and the water changes that are needed whenever these readings rear their ugly heads.

-The "Fishless" Cycle using Fish Food

This method is preferred over cycling with fish but is not without its disadvantages. Instead of using live fish as the ammonia source, here we use fish food, which decays in the tank, to supply ammonia. Essentially, all you have to do is "feed" the tank with a pinch of fish food every day as if there were fish in the tank. The decaying food produces ammonia which then promotes the growth of Nitrosomonas bacteria and so on as above. The major benefit to cycling without fish is that no fish are harmed during the cycle and you can elect not to keep the hardy species often used for cycling purposes. Another benefit is that, without fish in the tank, there's no need to do large water changes during the cycle. Ammonia and nitrite can reach toxic levels without any worry as there are no fish in the tank. The disadvantages to using fish food are that it's a somewhat unreliable ammonia dosing method and it can take some tweaking until you're sure you're adding the right amount of food (i.e. enough to supply a moderate level of ammonia that can be measured). Also, as one might guess, it can leave quite a mess in your tank that needs to be cleaned up before fish can be added. The steps to the cycle itself are the same as cycling with fish; you'll see ammonia spike, followed by a nitrite spike along with a decrease in ammonia, eventually followed by both ammonia and nitrite staying at 0 while nitrate starts to climb. Once ammonia and nitrite are pegged at zero for at least a couple of days, you can do a gravel vac to remove the fish food waste and bring the nitrate down to a reasonable level (10-20 ppm or less). At that point you can begin slowly stocking the tank with fish.

*Nitrospira have only recently been identified as the nitrite oxidizing bacteria responsible for converting nitrite to nitrate in freshwater aquaria. Previously another nitrite oxidizing bacterium, Nitrobacter, was thought responsible. See this study for more information: Nitrospira-Like Bacteria Associated with Nitrite Oxidation in Freshwater Aquaria
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-The "Fishless Cycle" Using Shrimp

This method is similar to the fish food method but instead of fish food, we supply ammonia using raw shrimp from the seafood section of the grocery store. One medium sized shrimp for every 20 or 30 gallons of water will decay and provide a steady flow of ammonia into the tank. The benefit to using shrimp vs. fish food is that you can put the shrimp into some sort of mesh bag (filter media bags or pantyhose work great) so that the waste can be removed easily at the end of the cycle. Using shrimp also provides a nice steady, even flow of ammonia, something that can be hard to accomplish using only fish food. The steps to the cycle itself are the same as described above. This is likely the easiest method of cycling a tank as all you have to do is add the shrimp, test the water parameters from time to time, remove the shrimp at the end of the cycle and do a water change and you're all set.

-The "Fishless Cycle" Using Pure Ammonia

This is the most precise method of cycling your tank. It is similar to the fish food and shrimp methods described above but the ammonia source is pure bottled ammonia. It is of utmost importance that you use only pure ammonia, not ammonia-based cleaning products that contain detergents, dyes, scents or any other chemicals as these can be harmful to your fish. How much ammonia to add depends on the concentration of the ammonia you're using but you want to add enough ammonia to bring the concentration of your tank to 3-5 ppm (this is usually 3-5 drops per ten gallons but can vary). Test the ammonia and nitrite levels every day, adding more ammonia daily as needed to keep the ammonia level at 3-5 ppm. Eventually, you'll notice that the ammonia concentration will start dropping, which goes along with an increase in nitrite. Continue dosing ammonia to the same concentration. Eventually, you'll reach the stage where enough ammonia added to bring the tank to a concentration of 3-5 ppm totally disappears within 24 hours, leaving you with nothing but nitrate. At this point the cycle is complete and you can proceed as above. The difficulty with this method is that testing and ammonia dosing have to be done at least daily. Pure ammonia can also be difficult to track down and the risks, should you use ammonia that contains other chemicals, are serious. Unlike the other methods, however, the pure ammonia method allows you complete control over the cycle and lets you know just how much ammonia your biofilter (i.e. the colonies of beneficial bacteria established during the cycle) can process in a given time period.

-The "Planted Tank" Method

This is the only one of the five cycling methods that doesn't involve establishing colonies of beneficial bacteria (or at least that doesn't focus solely on these bacteria as a means to remove harmful chemicals). Like Nitrosomonas bacteria, aquatic plants can use ammonia. However, unlike these bacteria, the plants simply absorb the ammonia and don't produce nitrite as a by-product. For this reason, plants can be thought of as "ammonia sinks" in your aquarium. Aquatic plants also absorb nitrates, but prefer ammonia. The planted tank method, then, is the practice of planting your tank heavily enough that any ammonia your fish might excrete can be absorbed directly by your plants. In other words, you plant the tank very heavily and immediately add a small number of fish, letting the plants take the place of beneficial bacteria as they normally would exist in a cycled tank. Beneficial bacteria will be present and as a result you will eventually get some nitrate readings in the tank (though often at such low concentrations to be of no concern). However, most of the ammonia is taken care of by the plants. This method can be risky as it's difficult to know exactly how much ammonia your plants are capable of absorbing. If the plants aren't receiving proper care in other arenas (lighting and other nutrients) they may not be capable of absorbing the quantities of ammonia that would be needed in order for your tank to be cycled using only plants. Because of the additional considerations of caring for the plants that provide the ammonia removal in this method, the "planted tank cycle" is only recommended to aquarists that have some experience in keeping live aquarium plants and who have some feel for the relationship between plant and fish stocking levels in terms of the plants' ability to utilize the ammonia that fish produce.

Which method is best for me?

If you've already got fish in the tank, you're essentially stuck with the "fish-in" cycle as your only option unless you're willing to return the fish and do a fishless cycle. Any of the fishless cycling methods described above will work but I find the shrimp method to be the easiest and least labor-intensive. Once you choose your cycling method and complete your cycle, you're ready to begin adding fish. While some of these methods theoretically allow you to fully stock your tank right away (especially the ammonia dosing method which should allow you to establish relatively huge numbers of beneficial bacteria), in practice it is always safer to stock your tank slowly no matter how the tank was cycled.

"Seeding" your tank to "kick start" the cycle:

As mentioned above, beneficial bacteria live almost exclusively on the surfaces in your aquarium, not in the aquarium water itself. Thankfully, this means that it's relatively easy to "kick start" the cycle, no matter which method you're using, by "seeding" your tank with bacteria from an already established tank. There are a number of ways to do this. The simplest is to simply move some of the decor (driftwood, rocks, plants, artificial decor) from the established tank into the cycling tank, bringing bacteria with it. You can put bacteria-rich substrate into a mesh bag and put this in your filter or in a high-flow area on top of the cycling tank's substrate. Perhaps the best seeding method is to literally move some filter media (sponges, ceramic rings, filter floss, etc.) from an established tank's filter into the cycling tank's filter. When moving decor, substrate or filter media from an established tank to the cycling tank, be sure to keep any of these materials wet as any beneficial bacteria they house will die if the material dries out. If it's not possible to physically move the filter media, you can squeeze the media into the cycling tank's filter, which deposits some bacteria on your new filter's media and on the other surfaces in your tank. Because very few bacteria actually live in the water column, moving water from an established tank to a new cycling tank is ineffective as a means of seeding the new tank. There are also "bacteria in a bottle" products designed to add beneficial bacteria directly to your tank, some even claiming that they'll instantly cycle your tank for you. If you choose to use one of these products, make sure that you go for the type that needs to be refrigerated (bacteria are living organisms, after all). Results seem to be mixed with some reporting great success and others saying the product didn't seem to make a difference. While seeding a tank can have observable positive effects on the aquarium cycle it is not a substitute for cycling but rather a means to aid it. For this reason, caution should be taken not to place too much stress on whatever bacteria might have been introduced as it takes time for them to multiply.

An extra tidbit:
The following was mentioned to me by Thunderloon via PM:

"I've found that one of the further risks in live cycling of a tank is that the Nitrospira will also eat ammonia until it is gone and won't switch to nitrite until then.
This is symptomatic from people who's cycle started but the nitrite is climbing off the scale with zero produced nitrate.

Also a nitrate over about 400ppm will stop spira and somona from being able to "poop"

This is simple in the fishless cycle but problematic otherwise."

I'm already quite the fishless cycle proponent, but this information is yet more reason to use a fishless method rather than a fish-in cycle, as dealing with the above effects with live fish in the tank would be stressful for both you and the fish.

Written and posted by: IamntBatman 3/04/2010
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