Call it cycling, nitrification, biological cycle, startup cycle, break-in cycle, or the nitrogen cycle. No matter what name you use, every newly set up aquarium goes through a process of establishing beneficial bacterial colonies. Older aquariums also go through periods during which the bacterial colonies fluctuate. Failure to understand this process is the largest contributing factor to the loss of fish. Learning what it is, and how to deal with critical periods during the nitrogen cycle, will greatly increase your chances of successful fish keeping.
The Waste Problem
Unlike nature, an aquarium is a closed environment. All the wastes excreted from the fish, uneaten food, and decaying plants, stay inside the tank. If nothing eliminated those wastes, your beautiful aquarium would turn into a cesspool in no time at all.
Actually, for a short period of time, a new aquarium does become a toxic cesspool. The water may look clear, but don't be fooled. It's loaded with toxins, much like a septic tank. Sounds awful, doesn't it? Fortunately, bacteria that are capable of converting wastes to safer by-products begin growing in the aquarium as soon as fish are added. Unfortunately, there aren't enough bacteria to eliminate all the toxins immediately, so for a period of several weeks to a month or more, your fish are at risk.
However, you need not lose them. Armed with an understanding of how the nitrogen cycle works and knowing the proper steps to take, you can sail through the break-in cycle with very few problems.
Stages of the Nitrogen Cycle
There are three stages of the nitrogen cycle, each of which presents different challenges.
Initial stage: The cycle begins when fish are introduced to the aquarium. Their feces, urine, as well as any uneaten food, are quickly broken down into either ionized or unionized ammonia. The ionized form, Ammonium (NH4), is present if the pH is below 7, and is not toxic to fish. The unionized form, Ammonia (NH3), is present if the pH is 7 or above, and is highly toxic to fish. Any amount of un-ionized Ammonia (NH3) is dangerous, however, once the levels reach 2 ppm, the fish are in grave danger. Ammonia usually begins rising by the third day after introducing fish.
Second stage: During this stage Nitrosomonas bacteria oxidize the ammonia, thus eliminating it. However, the by-product of ammonia oxidation is nitrite, which is also highly toxic to fish. Nitrites levels as low as 1 mg/L can be lethal to some fish. Nitrite usually begins rising by the end of the first week after introducing fish.
Third stage: In the last stage of the cycle, Nitrobacter bacteria convert the nitrites into nitrates.
Nitrates are not highly toxic to fish in low to moderate levels. Routine partial water changes will keep the nitrate levels within the safe range. Established tanks should be tested for nitrates every few months to ensure that levels are not becoming extremely high.