If you know the answers to the above questions, you are definitely ahead of the game. Most hobbyists realize the importance of an established biological filter and the nitrogen cycle for maintaining optimal water quality. Members of the bacterial genus Nitrosomonas (and other related bacteria) help by converting ammonia, a waste product of fish eliminated through both the gills and urine into the tank water and a breakdown product of left over food, into nitrite. Nitrospira (and other related bacteria) convert nitrite to nitrate, which is much less toxic than either ammonia or nitrite. Both groups of bacteria need oxygen to metabolize, so good water flow and aeration are essential. Plants and water changes help reduce the nitrate load, as do specific anaerobic bacteria which transform nitrate into nitrogen gas. Continuous monitoring of both ammonia and nitrite levels are important, because subtle perturbations to the bio-filter can result in either the reduction in the numbers or efficiency of one or both groups of bacteria, or increased water or food may cause sudden rises in ammonia. Catfish ponds in the South, for example, seem to be more susceptible to nitrite toxicity after major temperature drops, possibly due to the sensitivity of Nitrospira (or related bacteria) to these changes. In addition to sudden temperature changes, lower oxygen levels in the water, reduction in alkalinity (especially bicarbonate ions), and drops in pH will also reduce the efficiency of the biofilter, causing increases in ammonia and/or nitrite

These are the ponds outside the Florida Aquaculture Lab that
Roy Yanong and Craig Watson work to improve what the
public gets for their tropical fish.

Okay, okay, so you know all of that already. So let's get a bit more specific. Ammonia occurs in water in two forms, the un-ionized form NH3, and the ionized form NH4+. The un-ionized form, NH3, is traditionally considered much more toxic than the ionized form NH4+ (although there is some debate over this). Most test kits measure the sum of the two forms, also known as total ammonia. So what determines the relative amount of each form? Temperature and pH are the most important parameters which decide this, with other factors, such as salinity also playing more minor roles. The higher the pH, the greater the percentage of ammonia which will be in the more toxic, or un-ionized, form NH3. The same holds true for temperature. So if you have two tanks each with a reading of 1 ppm (=1 milligram/liter) of total ammonia, the tank with a temperature of 72 degrees F and a pH of 7.0 has much less toxic un-ionized ammonia that the tank with a temperature of 78 degrees F and a pH of 8.0. Tables have been established so that you can determine the percent of your total ammonia (read from your test kit) which is actually present as the un-ionized form.

For example, if your temperature is 75.2 degrees F and your pH is 7.4, from the table your amount of un-ionized ammonia is 0.0131 or 1.3 percent. If your total ammonia reading was 2 ppm, then you would multiply 2 ppm by 0.0131 to get 0.0262 ppm as your amount of un-ionized ammonia. The rest would be present as the ionized form. Although there are definitely species differences when it comes to ammonia tolerance, the following guidelines can be used as a rough approximation: 0.05 ppm un-ionized ammonia or less is okay; 0.05 to 1.0 ppm un-ionized ammonia will lead to stress; 1.0 to 2.0 ppm with lead to death. Of course low levels of ammonia can cause chronic problems and lead to disease, so ideally no ammonia is best.

Okay, so you know ammonia in your aquarium is bad. But do you know why? There are numerous consequences of both acute and chronic ammonia exposure. You probably are familiar with some of these already: gasping fish, hemorrhages or other skin and tail lesions, abnormal swimming behavior such as whirling, and of course, acute death. We'll discuss many of them here, although there are probably many more subtle and not so subtle effects of ammonia which are still unknown.

Ammonia in a system is primarily a product of protein breakdown, whether it is by the fish or by bacterial processes in your tank (due to overfeeding for example). Excretion of the protein breakdown product ammonia in most fish is primarily through the gills, as opposed to the process in other animal groups, such as mammals, which excrete their protein breakdown product (urea, made from ammonia) primarily through the kidneys.

There are many racks like this
inside the lab to work with fish
on a smaller scale. Notice
how clean!

Even in fish, the form of ammonia excreted varies. Many marine fish excrete the ionized form NH4+ through their gills. Many freshwater fish may excrete a combination of NH3 and NH4+, depending upon numerous factors. Freshwater fish living in very acidic conditions excrete much of their ammonia as NH3 by diffusion through the gills.

By now you've probably already figured out that the gills are a primary target for disease resulting from ammonia toxicity, because of their function in ammonia excretion. You're right. In fact, the gills have numerous other important functions in addition to ammonia excretion: respiration (including oxygen and carbon dioxide exchange), acid-base balance (keeping the pH of the blood correct to allow for normal physiological processes), and monovalent ion exchange (keeping the correct amount of important ions such as sodium and chloride in the blood). Chronic exposure to low levels of ammonia results in a disruption of all these important processes because the ammonia acts as a chemical irritant and causes the gill epithelium to undergo hyperplasia (an increase in the number of cells on the gill) and hypertrophy (an increase in the size of the cells). You may think this would be a good thing, but it is not. The important surface-to-volume ratio of the gills is changed, so that oxygen must try to go through many more cells in order to diffuse into the blood. In addition, ammonia excretion, regulation of blood pH, and ion balance are impaired for the same reason - too many cells and an abnormal structure to the gill. The severity of these problems is multiplied by warmer temperatures and lower levels of oxygen in the water. Many fish die from the resulting dramatic decrease in oxygenation capacity of the gills. Acute exposure to high levels of ammonia damages the gill epithelium and causes excess mucus production, resulting in similar and life-threatening disruption of normal important physiological processes.

This disruption in the normal anatomy of the gill has also been implicated as a factor in the development of bacterial gill disease, with a resulting predisposition to bacterial invasion.

In addition to ammonia's role as a chemical irritant of the gill, it is also thought to be a chemical irritant of other organs, especially the skin, fins, and intestine, where disruption of normal mucous membranes may result in external and internal bleeding.

Other effects of chronic ammonia exposure include damage to kidneys, decreased growth, and immunosuppression (decreased ability to fight off disease), caused by a rise in corticosteroid levels in the blood, and a change in predator-prey interactions.

This is Roy's work room at the lab. If
you show this picture to anyone
we'll have to shoot you.....;-)

Ammonia also affects the nervous system. Ammonia depresses neuronal membrane activity, disrupts brain energy metabolism, and causes blood flow and pressure in the brain case to increase. The rise in corticosteroid production mentioned above, along with other factors, results in an increase in glucose production (the main energy source in the body) through breakdown of certain other parts of the body, such as specific amino acids (the building blocks of protein). The breakdown of proteins means even more ammonia in the blood and an increase in the production of abnormally high levels of certain chemicals in the brain and the rest of the nervous system which cause aberrant behavior such as whirling or spinning, and abnormal physiological processes.

Ammonia has also been implicated as a potential goitrogen (any chemical which induces a goiter - an increase in the size of the thyroid gland) in fishes, resulting in impaired thyroid function.

Different species have different ammonia tolerance levels, but regardless of the species, stress is always present under conditions of poor water quality. The damage will eventually occur if it has not already, so why risk it?

Make sure your bio-filters are working, do major water changes as needed, don't overfeed, keep your tanks clean, make sure aeration is good, and monitor ammonia, nitrite, alkalinity, and pH levels regularly.