The nitrogen cycle is a common biological process that occurs in nature, and it also occurs in our aquariums. In aquariums it’s an essential process because it removes toxic waste products and coverts them to a much less toxic form. The process is performed by bacteria, which we call beneficial bacteria (or BB). These beneficial bacteria colonize any surface they can in the aquarium and in the filters. Special types of filter media, called biological media, are designed with as much surface area as possible to provide good places for these bacteria to colonize.
Ammonia is produced by fish waste, fish respiration, and uneaten fish food. It’s very toxic to fish, and becomes even more toxic at a higher pH. Ammonia toxicity causes symptoms like prominent red veins in fins, red splotches on the body, and gasping at the surface. It’s converted into nitrite by beneficial bacteria called nitrosomonas, so in a cycled aquarium, ammonia should always be zero.
These nitrosomonas produce nitrite. Nitrite is also very toxic to fish, causing symptoms like gasping at the surface, lethargy, hanging near the surface, and tan or brown gills. It impedes the ability of the fish’s blood to carry oxygen. Nitrite is converted into nitrate by beneficial bacteria called nitrobacter, so nitrite should always be zero in a cycled aquarium.
Bacteria called nitrobacter produce nitrate. Nitrate is much less toxic to fish, but is still harmful in great quantities. Nitrate toxicity can cause loss of proper swim bladder function and lethargy. In a cycled aquarium, nitrate will continue to accumulate. Live plants consume some nitrate, but mostly it is removed by regular water changes. You should typically not allow the nitrates to go above 20 ppm, but different species of fish have different ranges of nitrate tolerance.