The nitrogen cycle is a critical factor in the establishment of a crystal clear, well-balanced aquarium. This phenomenon is, however, little understood by aquarists. Poor functioning of the nitrogen cycle upon establishing a new aquarium is undoubtedly the most common reason for later failures and losses of animals.

In simplified terms, the nitrogen cycle is the conversion of nitrogen to several organic compounds that are then utilized by various organisms as food. Nitrogen enters aquatic systems via dead animals and plants, uneaten food, and the excretory products of animals. The most toxic nitrogenous compound that is added to aquariums in this matter is ammonia. Ammonia exists in aquatic environments in two forms: ionized ammonia and unionized ammonia. The unionized compound is extremely toxic to aquatic organisms, and its proportion of the total ammonia increases as temperature rises and as the water becomes more alkaline.

Two basic types of bacteria control the functioning of the nitrogen cycle.

Both of these bacteria species are aerobic, which means that they require oxygen to survive and reproduce. The bacteria develop and thrive on substrates that are exposed to oxygenated water, most especially in the various materials used in aquarium filters, and on the walls of the filters themselves.

The process by which these bacteria convert ammonia to less-harmful compounds basically occurs in two parts. Nitrosomas spp. convert ammonia to compounds known as nitrites. Nitrites, while still dangerous to aquatic life, are less toxic than is ammonia. In the second stage of the process, bacteria of the genus Nitrobacter use the nitrites as food, thus converting them to nitrates. Nitrates are the end product of the nitrogen cycle and are the least toxic of the compounds involved.

Nitrogenous bacteria exist in huge populations in nature and in healthy aquariums. Until such populations are established, the levels of all nitrogen-based compounds in the aquarium will be toxic to most fish and invertebrates.

The period of time from the setting up of the aquarium until the establishment of healthy populations of aerobic, nitrogenous bacteria is often referred to as the conditioning period. As a general rule, one can expect this period to last from one month to six weeks. However the actual timetable varies greatly depending upon the unique characteristics of each aquarium and of the inhabitants therein.

You can shorten the amount of time it takes to condition your aquarium by adding live aerobic bacteria that are now available at pet stores. The freeze-dried and liquid forms seem to work equally well. Alternatively, you can introduce used filter material from a well-conditioned tank into the filter of your new aquarium. Be sure to use material from healthy tanks only, as parasites or their eggs may be present in the filter beds of infected tanks. Natural materials such as rocks or sand often contain beneficial bacteria and offer another option. In the past, it was standard practice to use hardy fish, such as domino damselfish in marine aquariums or guppies in freshwater aquariums, to help hasten the conditioning period. The waste products produced by these fish provide the ammonia necessary to start and maintain the process. Today, however, you can purchase additives that provide food for the bacteria. This is both more effective and infinitely kinder than attempting to use fish to jump-start the process, as most fish subjected to this process did not survive.

While commercially available bacteria can be helpful, they do not eliminate the need for a proper conditioning period. The water quality must still be monitored carefully, and new animals should be introduced to the aquarium carefully and in small numbers.

Chemical test kits are essential during (and after) the conditioning period. Ammonia should be tested daily until you notice a rapid decrease. This decrease signals the presence of Nitrosomas bacteria. Nitrate levels will then follow the same pattern once the Nitrobacter bacteria become established. Be sure to regularly check the pH level during the conditioning period, as the water may become acidic at this time. The conditioning period may be considered at an end when the nitrate levels drop substantially. At this point you may begin to introduce fish and invertebrates into their new home. It is still safest to add animals in small quantities, so as not to overwhelm the nitrifying potential of the bacteria present. Observe the new animals and make further additions carefully.