When starting a new aquarium there are some very important things you need to know before adding fish to the aquarium. Understanding the nitrogen cycle and how it works is fundamental if you plan on being a successful aquarium hobbyist. Having a large filter on your aquarium in itself will not keep your fish alive. Aerobic beneficial bacteria are required to keep your aquarium hospitable for fish. These beneficial bacteria live on all surface area within the aquarium including the parts of the filtration system that is in contact with oxygen rich water. These aerobic bacteria are what is often referred to a biological filtration.
When starting a new aquarium, the tank is nearly sterile. During the first 35 days after the aquarium was set up (with fish) is the most difficult time for fish to survive. During this time bacteria population try to catch up with the fish population load. There are three chemicals that make up the nitrogen cycle the hobbyist needs to monitor, ammonia, nitrite, and nitrate. Ammonia, nitrite, and nitrate concentrations can be monitored with aquarium test kits. Every aquarist should have a aquarium test kit available that can test for ammonia, nitrite, nitrate, and pH. Master test kits are available from many companies that include tests for ammonia, nitrite, nitrate, and pH.
Fish excrete ammonia through respiration and waste. Ammonia at high enough concentrations can damage the fish's gills and other organs, making it difficult to take in oxygen. Bacteria known as Nitrosospira and Nitrosomonas help oxidize ammonia into nitrite in the aquarium. When you test for ammonia with your aquarium test kit, the reading you actually have is a combination of ammonium (NH4+ or ionized ammonia) and ammonia (NH3 or unionized ammonia) known as Total Ammonia Nitrogen (TAN). Ammonia is the toxic part of the TAN.
Ammonium even at highest concentrations you would see in the aquarium does not cause mortality in fish. Understanding the difference between the two is crucial to figuring out how much toxic ammonia you really have in your system. Ammonia concentration of as little as .6 ppm is toxic to many species of fish.