A Beginner's Guide to the Freshwater Aquarium Cycle

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