Every newly set up aquarium goes through a process of establishing beneficial bacterial colonies. This is called the Nitrogen cycle. A failure to understand this process is the largest contributing factor to the loss of aquarium livestock. Unlike nature, an aquarium is a closed environment. All wastes excreted from the livestock, uneaten food, and decaying plants stay inside the tank.
For a short period of time, a new aquarium becomes a toxic environment. The water may look clear, but don't be fooled! It's loaded with toxins. Beneficial bacterial colonies capable of converting wastes to safer by-products begin growing in the tank as soon as livestock is introduced. Unfortunately there isn't enough bacteria to eliminate all the toxins immediately, so for a period of several weeks or more, aquarium livestock is at great risk.
However, by understanding how the nitrogen cycle works and knowing the proper steps to take, you can get through this period with few problems. There are three stages of the nitrogen cycle. INITIAL STAGE
The cycle begins when turtles or fish are introduced to the aquarium. Their feces, urine, as well as any uneaten food, are quickly broken down into ammonia. Ammonia usually begins rising by the third day and is highly toxic to aquarium livestock. It’s only during the cycling of a tank that ammonia should be present. SECOND STAGE
During this stage Nitrosomonas bacteria begin to oxidize the ammonia, thus eliminating it. However, the by-product of ammonia oxidation is nitrite, which is also highly toxic to aquarium livestock. Nitrite usually begins rising by the end of the first week. Future ammonia and/or nitrite spikes would be due to excess waste accumulating within the tank and/or damaged bacterial colonies. If you do incur ammonia or nitrite spikes, the most effective way of reducing these toxins is to perform regular partial water changes.
In the last stage of the cycle, Nitrobacter bacteria convert the nitrites into nitrates. Nitrates are not highly toxic to aquarium livestock in low to moderate levels. Routine partial water changes will keep the nitrate levels within the safe range. Established tanks should be tested for nitrates frequently to ensure that levels are not becoming too high.