Before we can start putting fish and corals into our tank, we must first take the time to properly cycle the aquarium. Nitrogen cycling the tank is the first major test of an aquarist's patience.

The nitrogen cycle has four steps:
1. Ammonia (NH3)
2. Nitrite (NO2)
3. Nitrate (NO3)
4. Nitrogen Gas (N2)

When you first start a reef tank, there are no nitrogen-producing organisms. Similarly, there are no nitrogen processing bacteria or algae. Once you put a fish, coral, or piece of live rock into the tank, there is now a nitrogen source without any nitrogen processors. The level of ammonia will steadily increase to harmful levels as the newly introduced organisms produce waste. It is for this reason that we recommend initiating the cycle with a piece of live rock or a large piece of shrimp rather than a fish or coral. The nitrogen cycle is a very stressful process that lasts well over a month, and can kill more sensitive fish and corals. Once the nitrogen cycle has started, it is a good idea not to add any new inhabitants until it has completed. Any new additions during this period will likely die from the toxic levels in the tank.

As the levels of ammonia increase, so does the population of nitrobacteria. These aerobic bacteria break down ammonia to a slightly less harmful nitrite compound and again to an even less harmful nitrate compound.

This initial cycle may take up to a month to complete. You should purchase a reliable test kit to determine the levels of ammonia, nitrite, and nitrate to see how the cycle is progressing. In the first week, the ammonia level will spike, and then start to diminish as the level of nitrite increases. As time passes, the ammonia levels in the tank will fall to undetectable levels, and the nitrite level will peak. After another week, you should expect to see the nitrite level fall as the nitrate level increases. Fish are not affected much by high nitrate levels; however, it is toxic to corals in high concentrations.

It is at this time that we recommend doing a water change to dilute the accumulated pollutants. After the water change, you can start to slowly stock the tank. You must be careful to not add inhabitants too quickly or you run the risk of starting another ammonia spike.

While it was a simple task of waiting for ammonia and nitrite to be processed, it is a more difficult task to deal with nitrate. Nitrate can be removed via water changes, anaerobic bacteria, or algae. Water changes as stated above dilute the concentration of nitrate in addition to replenishing trace elements. Anaerobic bacteria can break down nitrate into nitrogen gas, however they require special low oxygen areas in order to flourish. Algae binds nitrate as it grows. By harvesting algae from the tank from time to time, it is possilbe to physically remove the nitrates. Please read the section on reef filtration for a more in-depth discussion of de-nitrification.