The Biological Nitrogenous Cycle: A Must for Freshwater Aquarists

This page describes the biological processes that occur within an aquarium and reinterates the imporatnce of cycling an aquarium before adding fish to the aquarium.

Biological Processes


Biological processes occur whenever you are dealing with anything that lives. The basics of these processes can be broken down into each organism’s requirements and wastes. For instance, fish require food and oxygen and produce organic wastes in the form of excreta, carbon dioxide, and feces. Alternatively, plants require nutrients in the form of nitrogen compounds, various minerals, and carbon dioxide and/or oxygen (plants absorb carbon dioxide during the day but use oxygen all the time as a part of cellular respiration)4,B. In turn, plants produce oxygen and carbon dioxide (depending on the time of day) as a net result of their biological processes. Processes such as these occur continuously in a given environment and represent a biological cycle.

In addition to plants and complex animals (i.e., the fish), there is another group of living things that cannot be excluded from aquaculture—bacteria. Bacteria provide a vital role in the natural environment of fish in that they are decomposers—organisms that break organic matter down into substances that can either be used by other living things or removed from the life cycle completely. Bacteria require the waste from other organisms to survive. Accordingly, bacteria alter the organic matter they take in so that it can be made useful again. In nature, the producers, consumers, and decomposers are balanced by the environment. Nature does not allow an excess of waste from plants, fish, or bacteria. Instead, they occur in proportions that allow everything to function normally and correctly. This balance even extends down to the types of bacteria present. Not all bacteria are the same and therefore do not do the same thing to organic waste.

The first major class of bacteria are aerobic bacteria and consist of all the forms that require dissolved oxygen to carry out their biological functions. These bacteria are the primary ones responsible for altering waste compounds in a freshwater aquarium. Nonetheless, one type of aerobic bacteria cannot process all the waste alone. This is where the different subclasses of aerobic bacteria come into play.

The first subclass is the group of aerobic bacteria that produces ammonia as a result of its actions (the fish will also produce ammonia naturally)4,7. Ammonia (NH3) can be toxic to fish in even minute quantities (generally toxic at 3ppm, harmful above 0.5-0.25ppm), but it is an important plant fertilizerA,B,7. After ammonia has been formed, it will react with the water and a portion of it will be converted into ammonium hydroxide (NH4OH), which is less harmful than raw ammonia8. One thing to note about ammonia is that acidic water will covert a larger portion of it into ammonium than alkaline water will. This is because acidic water has an excess of hydrogen ions (H+) necessary to produce ammonium from ammonia8. However, this can lead to problems when an aquarist completes an overdue water change. While acidic water produces the less harmful ammonium, alkaline water (which the tap water used to replace extracted aquarium water often is) has the opposite effect7. Alkaline water does not have many hydrogen ions and thus extracts them from the ammonium. This results in the extremely detrimental ammonia and could kill fish that seemed fine before the water change.

After ammonium is formed, it is made into nitrite (NO2-) by another subclass of aerobic bacteria4,7. Nitrite is as toxic as ammonia and should never be allowed to accumulate in an aquarium that has anything you want to keep alive in it4,7. On the other hand, nitrite is often measurable in an aquarium that has not been given time to matureA,B,4,7. This is not necessarily a bad sign, just an indication that the bacteria populations are not balanced out yet and that the setup is not ready for fish.



The last group of aerobic bacteria convert nitrite into nitrate (NO3-)7. Nitrate is relatively undamaging and levels as high as 150ppm can be reached before it is harmful to some freshwater aquarium fish (with 40ppm being the generally recognized maximum recommendation for most species of fish)A,B,7. Nevertheless, it is still unwise to allow nitrate to accumulate. Nitrate, while a terrestrial plant fertilizer (in fact, most nitrogen compounds are), can damage aquatic plants at high concentrations and can eventually kill your fish (if not stunt their growth)A,B,1,3,4,7. It is possible to rid the water of nitrate through biological means, but this requires extra care, knowledge, and often expense. This being the case, most freshwater aquarists prefer to go another route and simply use water changes to rid the water of nitrate. Since tap water can easily be made into suitable aquarium water and it is economical to do so, freshwater aquarists rely on this means of ridding the water of harmful substances more than any other sort of aquaristA,4,7.

The step from nitrate to inert substances, if present in your aquarium, is made by the second major class of bacteria--anaerobic bacteria. These bacteria only occur in areas devoid of oxygen. If these bacteria are not too far removed from a source of nitrate, they will denitrify it. This means that they will break it up into nitrogen and oxygen gases8. In this way, the bacteria receive oxygen in an environment that normally does not have it and there will be no more nitrate or nitrogen compounds in the water. However, if these bacteria exist in an area that does not have nitrate, they will find the next best substitute and the result will be poisonous substances (often sulfur-based compounds) that will kill your fishB,8. Additionally, it is almost impossible to sustain a large enough population of anaerobic bacteria to process all the nitrate a freshwater aquarium will produceA,B.

It is crucial that you understand all of these biological processes are reversible under certain conditions7. This means that aerobic bacteria or water conditions can convert nitrate and ammonium into nitrite and ammonia, respectively, if there is not enough oxygen in the water or the water chemistry changes4,7,8. Additionally, as mentioned before, anaerobic bacteria will use alternatives if there is not enough nitrate around. What is more, the very plants that absorb nitrogen compounds may release them into the water if they become shocked (replanting can cause this)7. Also understand that changes in the dynamics of your aquarium will upset the bacterial balance. This means that if a significant number of fish are added to the setup, then the biological processes that follow such an event will not occur in the correct proportions and subsequently will result in substances that could kill all your fish. New fish are not the only factor that could upset the biological balance—the list includes overfeeding, dead fish that have not been removed, overdue water changes, decaying plants, and filtration/aeration systems that have ceased to function for one reason or another. I mention these possibilities not to deter you from making any changes or reinforcing a need for constant care of the aquarium, but to simply provide you with reasons for not making any change too drastic. Fish can tolerate change, but it is better to make these changes slowly and in progressive steps.




A. MOA Fishkeeper. Personal experience working at a pet shop, having experimented with various systems, and having worked in fields that rely upon bacterial activity approximations.

B. FishChannel. [Internet]. Home; 2008. Available from: Accessed 2008 Mar 28. (Discussion board on general aquarium husbandry).

C. Hailey. Experienced fishkeeper who can be contacted via


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3. Wikipedia. [Internet]. Aquarium; 2008. Available from: Aquarium. Accessed 2008 Mar 28.

4. Levine JS. The complete fishkeeper: everything aquarium fishes need to stay happy, healthy, and alive. New York: W Morrow; 1991.

5. Benke AC. Production dynamics of riverine chironomids: extremely high biomass turnover rates of primary consumers. Ecology 1998; 79.n3: pp899(12).

6. Jewell, EJ. The oxford desk dictionary and thesaurus. New York: Oxford University P; 2002. (second ed.).

7. Scheurman, I. The natural aquarium handbook. New York: Barron’s; 2000.

8. Silberberg, MS. Chemistry: the molecular nature of matter and change. Boston: McGraw-Hill; 2006. (fourth ed.).