We all have heard of cycling your tank, curing your live rock and ammonia spikes but do you really understand what that means? Tragically, ammonia is deadly poisonous to fish. It inhibits their breathing, rather as carbon monoxide does in humans, and they slowly start to suffocate . At low levels ammonia acts as an irritant to the gills of your fish leading to respiratory distress and permanent damage. At higher levels (even for a short time) this can lead to skin, gill and eye damage it can also impede the normal excretion of ammonia damaging internal organs. The problem with this is if we are not careful we can misdiagnose ammonia poisoning for bacterial infections or parasites. Our fish show signs of poisoning by rubbing against decorations, rock and sand. They may also have rapid breathing or gill movement, clamped fins and lethargy.
They way to control ammonia is to allow the nitrogen cycle to complete, allowing the nitrification bacteria to grow and handle the bio-load to be introduced. Remember every time you add livestock to the tank the amount of waste increases which means the bacteria will need to grow to handle the load, every time you remove something from the tank the bio-load will lower. This process is slow growing so just because you aren't adding everything the same day doesn't mean the tank is ready. Depending on stocking procedure you can cause the tank to cycle again. Large amounts of live rock or sand, too many fish can overload the tank producing too much ammonia and affecting the inhabitants in the tank and worse yet killing them. One of the things that misdiagnosing ammonia poisoning can lead to is a catastrophic effect, say you think the reason the fish are rubbing and gasping is Ich or some other illness. You add a medication the fish do not get better but other fish get worse not because your medication is not working but because it is working too well in a healthy tank and is attacking the healthy bacteria base and killing it which increases the ammonia in the tank and is the true cause of illness. In reef environment we should not medicate in-tank but some still due and this can lead to disaster!
What can we do to prevent ammonia poisoning? Allow the tank to cycle completely, Add livestock slowly and follow a plan, do not over feed (decaying food leads to ammonia and more food more waste), and following a water change maintenance schedule. It may be the first step in starting a tank but ammonia is something that should be monitored the whole life of the tank and not be taken for granted.
Some websites that were used as reference and provide good reading:
http://groups.msn.com/FishHealth/envronmental.msnw http://fish.orbust.net/cycling.html http://www.fishdoc.co.uk/water/ammonia.htm 
Thanks for reading,
Phil Sosnowski
