Establishing the nitrogen cycle in the reef tank
It should be somewhat obvious that to establish the bacteria which convert ammonia to nitrites, a source of ammonia must be added to the tank. Once these bacteria start producing nitrites, the bacteria which convert nitrites into nitrates can start to establish themselves and of course, once nitrates are available, the nitrate converting bacteria can start to establish themselves, providing the hobbyist has taken steps to provide a suitable oxygen poor home for them.
The 'trick' to establishing the nitrogen cycle in the tank is to do it without endangering any tank inhabitants. This generally means that the part of the cycle which converts ammonia to nitrate should be established before any specimens are added. Fortunately a ready supply of ammonia is introduced with the live rock that is introduced into the system. As the live rock goes through its curing process, the decaying life forms on the rock provide the starter fuel for ammonia and nitrite consuming bacteria to colonize the rock. When live rock is being cured and this process is getting setup, toxic levels of ammonia and nitrite can form and specimens cannot be introduced until it is verified that both ammonia and nitrite have dropped to zero levels through the use of test kits. Typically, while this process in occurring, the hobbyist will measure an increase in ammonia and then it will start to drop as ammonia consuming bacteria start to grow. The hobbyist will then measure an increase in nitrites as the ammonia gets converted to nitrite. As the nitrite consuming bacteria start to grow, the nitrite level will also start to fall. When both ammonia and nitrite levels fall to zero levels, the cycling is complete. Typically, the nitrates will be high at this stage and the water that was involved in establishing the cycle should be replaced with new saltwater.
Once the live rock is cured, the basic tank cycle has been established and the live rock can be stacked in its final arrangement in the tank. Even though the basic bacteria types have been established, the number of bacteria will fluctuate depending on the bioload of the system. Also, there is probably not much bacterial colonization of the sand bed at this point. Therefore it is important to increase the bioload of the system slowly so that the bacteria colonies can grow to match the load of the system. If a lot of fish are added to a newly cycled tank, the sudden increase in waste products will cause a new mini cycle to start all over and since there are specimens in the tank, they are at risk of death or injury due to the ammonia or nitrite spikes that will occur. Corals and clams do not generally add bioload to the system, so they can be added more freely than fish or other critters that require constant feeding.
The final part of the nitrogen cycle (converting nitrates to nitrogen gas) has to be established after the tank is setup. The first thing that a hobbyist must do is to ensure that the reef tank provides oxygen poor regions in the live rock and sand. Old school was that this was to be avoided at all costs due to the concern over noxious gases, such as hydrogen sulfide, being formed. This concern seems to be overly exaggerated and can probably be ignored for the most part. It is important however, that once these oxygen poor zones are created, that they not be unduly disturbed.
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