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.
To setup these anaerobic regions I recommend the following:
Provide a substrate of sand which is no larger than 1-2mm and which can be finer. With this size of sand, a sand bed with approximately 2" of depth should be provided. This is sufficient to ensure that the deeper areas of the sand bed will become anaerobic and allow nitrate processing bacteria to colonize it. This is an area in which DSB
's (deep sand beds) are often recommended. However the same thing can be accomplished without the 4-6" deep sand beds which are recommended by DSB
Going against common wisdom in the literature these days, placing live rock directly on top of the substrate also helps to create these anaerobic regions. Many hobbyist spend a lot of effort to provide frameworks to keep the live rock off the sand to allow full circulation, but I believe this effort is misguided. For instance, I see people suspending their live rock on PVC
pipe so that they get full water circulation and then they install a DSB
to establish oxygen poor zones. Seems counter productive to me. The same thing can be accomplished by placing the live rock directly on a 2" deep sand bed. It is easier and it occupies less of the tank depth.
There are also some things to avoid that can tend to impair the nitrate conversion process:
Do not use a wet/dry filter with biomedia such as bioballs. It has been established that these filters do a good job of converting wastes into nitrate, but their use tends to cause nitrates to accumulate in the system. The reason why is not well understood, but many hobbyist have been able to cure nitrate problems by removing the biomedia from their filters. One school of thought is that when nitrates are created in the sand bed, they are created near the nitrate converting bacteria in the lower regions of the sand bed and therefore get processed more readily. It is recommended that anyone who is running a wet/dry and who has nitrate accumulation problems should consider slowly removing the biomedia over the course of a couple of weeks to give time for the system to adjust.
Do not use coarse crushed coral for the substrate. The large particle size allows too much water circulation which does not allow the necessary anaerobic regions to develop.
Do not disturb the deeper regions of the sand bed any more than necessary. This obviously disturbs the anaerobic regions. This typically means that you don't want to use a siphon to clean the sand bed. If you must for some reason, try to limit this actively to a small region of the tank only (10%?) so that the majority of the filtration process stays intact. A light stirring of the upper portion of the sand bed through the actions of sand sifter creatures or through the actions of the hobbyist are fine.