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Once your tank is set up with water, sand and live rock you will need to complete the initial nitrogen cycle before you add livestock. When you add livestock to the tank they produce ammonia as a waste product. Corals produce very little, fish produce quite a bit. Ammonia is toxic and burns gills and tissues. So how do we deal with this? By providing biological filtration based on the nitrogen cycle. There is often a lot of confusion about how to cycle a tank, how long it takes and exactly what it means.
Especially when using uncured live rock (LR) there may be enough die off to start the cycle. You can determine this by monitoring the ammonia. If you don't have any ammonia after a couple of days you can jump start the cycle by adding a big pinch of food or a RAW shrimp. If you use a shrimp it can be removed after a couple days. Tying it in a woman's nylon stocking will make it easy to remove.
In order to monitor cycling you will need ammonia, nitrite and nitrate test kits. You should buy kits that give you measurements in numbers, not in terms like high and low. The dipstick type of kits are not accurate and should be avoided. I test daily when a tank is cycling.
Once ammonia (NH4) is present in the tank aerobic nitrifing bacteria, Nitrosomonas, take over. As the ammonia rises the bacterial population explodes and begins converting the ammonia into nitrite (NO2). When this happens you will see the ammonia begin to fall and it will soon be zero. While the ammonia is falling the nitrite is going up and a second kind of bacteria, Nitrobacter, is building up to convert the nitrite. As the nitrite falls you will see nitrate (NO3) building up. This is the end of the aerobic bacteria's work. These aerobic bacteria live on the surface of your rock and sand and on bio media like bio-wheels, bio balls or ceramic rings.
As you see the end result of digestion by nitrifing bacteria is nitrate. Nitrate is well tolerated by fish but not by corals. If you have a fish only system filtration with bio-media is fine but not if you keep or want to keep corals. To complete the nitrogen cycle you need the anaerobic denitrifing bacteria, Pseudomonas. This bacteria lives in the lower layers of a DSB or deep in the LR. If you have an excess of surface area for aerobic nitrifing bacteria to colonize, i.e. bio-balls, compared to the area where anaerobic denitrifing bacteria live you will probably not be able to lower your nitrates below 10-20 ppm. Typically it takes some time to lower the nitrates to zero.
To recap, first you will see ammonia, it will peak and fall to zero. As it begins to fall you will start seeing nitrite which also peaks and falls to zero. During this time you will see nitrate start building. Once ammonia and nitrite have been at ZERO for several days you are ready to add your first livestock. I recommend adding hardy corals first. You can see why in this http://forum.marinedepot.com/Topic23945-9-1.aspx article.
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