Getting Started: Tank cycling and the Nitrogen Cycle

Improperly cycling your tank is the number one cause of failure for beginning aquarium keepers. Though the cycling of an aquarium is a quite simple process, ignorance of the process is widespread, especially among novices. So what does cycling a tank refer to? The word cycle actually has two meanings in keeping a freshwater aquarium. The first “cycle” that we are talking about is the nitrogen cycle. This is similar to the nitrogen cycle you may have learned about in high school biology, and is in fact a small section of the larger total nitrogen cycle. The second use of the word cycle refers to the process of nurturing and allowing the species of bacteria that convert nitrogenous wastes into less harmful chemicals to grow. A tank is fully cycled when all the necessary bacteria to convert ammonia ultimately into nitrate are living in the tank and keeping the ammonia and nitrite levels undetectable.

(Diagram credit to Ilmari Karonen)

The nitrogen cycle is the process in an aquarium by which extremely toxic nitrogenous wastes are converted into relatively harmless nitrogen compounds. This conversion is carried out by bacteria species that are ubiquitous, or everywhere around us (floating in the air, water, etc.). These bacteria that break down the nitrogenous wastes are what people are referring to when they talk about the biological filter of a tank. The first species is the bacteria that convert ammonia into nitrite, and the second type convert nitrite into nitrate. Sources often cite specific species of bacteria in discussing the nitrogen cycle. The microbiology of a fish aquarium is so complex, involving symbiotic and parasitic relationships between dozens or even hundreds of species of microbes, that it is beyond the scope of this blog. Studying the process in that much detail is also unnecessary to understanding what is happening in a tank and why it is happening, from a hobbyist’s point of view. For that reason, I will refer to the biological processes occurring in as simplistic a fashion as I can while imparting the necessary information.

Fish in an aquarium produce waste. There are many components of this waste, but the important one for our purposes is nitrogenous wastes. These wastes are excreted as ammonia, or are quickly turned into ammonia. Ammonia is extremely toxic to fish. One milligram per Liter (part per million, or ppm) of ammonia in water can be fatal to some fish species. Any amount of ammonia stresses fish, making them more susceptible to diseases. Ammonia levels are the number one cause of fish deaths in new aquariums (and a major cause of death in older aquariums) either directly by reaching deadly levels, or because they weaken a fish’s immune system so they cannot fight off disease. The good news is that these ubiquitous bacteria that I mentioned before need nothing more than a steady source of ammonia in your aquarium and a surface to grow on, preferably in the filter media. The bad news is they can take weeks or even months to establish themselves in sufficient quantities to convert the ammonia into nitrite as quickly as it is produced. Nitrite itself is quite toxic to fish, though less so than ammonia. Nitrite has the formula NO2, or one nitrogen bonded to two oxygen atoms. This means that since the formula for ammonia is NH3 (or NH4+ for the ammonium ion), one nitrogen and three hydrogens, that for every molecule of ammonia neutralized, a molecule of nitrite is created. This one-to-one relationship is constant throughout the nitrogen cycle. Once ammonia is being converted steadily into nitrite, a different species of bacteria can begin to establish colonies in your aquarium. Since this is a completely different species of bacteria, and it relies on the nitrite to grow, it cannot begin to establish itself in your tank until your ammonia consuming bacteria are well established. Like the first species, these new bacteria are slow to grow, meaning it can take several weeks to months for enough nitrifying bacteria to be in your tank to convert nitrite into nitrate as fast as it is produced. Just FYI, the only chemical difference between nitrite and nitrate is that nitrate has three oxygens, while nitrite only has two. Nitrate is much less toxic than nitrite, so levels of 20-40 ppm are acceptable to most fish, though the ideal level of nitrate is as close to 0 as you can reasonably keep it. Live plants can help keep nitrate levels lower, as they take nitrate up as a nutrient, but the main method of keeping your nitrate levels under control is through partial water changes.

So now that you know a bit about the nitrogen cycle and how it occurs, you are ready to begin cycling your tank. The common way to do this is to add a single fish of an inexpensive and hardy variety, feed it and let it produce your ammonia for you. This method often kills the fish. You also do NOT want to use feeder fish of any type to cycle your tank, as they are often ill-kept and can introduce diseases to your tank that will kill the fish you add once your tank is cycled. If you use this method, you need to keep measuring the ammonia and nitrite levels, and change part of the water on your tank if they rise to dangerous levels. Needless to say, if you are constantly removing the chemicals that the bacteria you are trying to establish require to grow, you are going to make cycling take longer, not to mention you are torturing and possibly killing a fish in the process. During the cycling of a tank, you will often have your water turn cloudy. This is normal, as there will be a bacteria explosion. This cloudiness will clear up, so don't do multiple water changes to try to eliminate it. You are just removing beneficial bacteria. If cycling with fish, the only thing you should base your water changes on is the nitrite and ammonia levels.

It is for this reason that many hobbyists suggest a fishless method of cycling your aquarium. There are different methods, some involve hanging a dead shrimp in the tank and letting it decay to produce the ammonia, some have you add actual liquid ammonia solution from a bottle to the tank each day, while my preferred method is the “feeding the tank” method. Very basically, you add some fish food to the tank, and in the process of decaying this food produces ammonia in a steady enough supply to create the necessary bacterial culture. To use this method, buy a small bottle of the cheapest flake fish food you can find. Your tank should be filled with water, dechlorinated and have the heater, filter, etc. running by now. To start this method, simply add a pinch of food, very small if you have a small tank, larger if you have a big tank, twice a day. Keep the heater set in the 70 to 80 degrees F range. Every week or so, test the water for ammonia and nitrites. If you don’t register any ammonia OR nitrites, increase the food you add a bit. If you get a reading of either chemical over 5ppm, cut back on how much food you put in the tank. After a week to a couple months, the ammonia level will be 0, and you will get nitrite readings only. At this point you can stop testing for the ammonia. Keep feeding the tank and testing for nitrite until you stop measuring any of that either. When you no longer measure nitrite, start testing every couple days for all three chemicals. Once you can measure 0 ammonia and 0 nitrite, and only nitrate for a week at least, your tank is cycled. While cycling your tank without fish, you don’t need to do water changes as the tank has nothing that will be harmed by too-high levels of nitrogenous wastes. During the cycling process though, you should rinse out your filter media every week or two. Don’t wash it in chlorinated water, as that will kill off the bacteria you are trying to culture. You can just rinse it out in the tank, as there are no fish you need to keep the water clear for, and the gunk will both produce more ammonia for the bacteria to feed on, and likely contains bacteria that will spread throughout the tank and speed up the colonization process. Once you are done with the cycling process, you will need to clean out the decaying food via a series of partial water changes. The next section will cover the procedure for doing these. These water changes should only be started when you are ready to go out to buy your first fish, since if you remove all the gunk that is producing ammonia, your bacteria will starve and your tank will have to cycle all over again when you add your fish. There will be a ton of decaying food in the gravel of your tank by this time, so when you do your water change, you will stir a ton of gunk up. Suck as much as you can up, but you will need to do several changes before you get it all. Since you don’t have to worry about stressing your fish, you can change up to 75% of the water at a time, and just wait long enough between changes for the gunk to settle. On your last water change, take the media out of the filter one last time and rinse it out in the water you removed. Now you need to go get your fish as quickly as possible. Stocking your aquarium with fish is covered here.

There are methods for speeding up your cycling process. If you have an established tank, move some gravel or filter media from that tank to your new one when you add your first fish. There should be enough bacteria in it so you never get any measurable ammonia or nitrite, but test to make sure. You can also borrow media or gravel from a friend's tank, or even a fish store. I personally would avoid a fish store's gravel or filter media as it may contaminate your tank with diseases. There are a number of products such as Cycle on the market, which are essentiall bottled bacteria that can quickly establish the necessary nirtifying bacteria colonies. People have reported mixed results with these. In theory they are perfect, but in reality they need to be kept in special conditions to keep the bacteria alive, such as refrigerated. If they are mishandled in shipping and storage, or too old, you are basically buying a bottle of dirty water that will do nothing to speed up your cycling process. Whether they are worth the money is up to you though.