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Your Aquarium’s Water Quality: Biological Filtration and The Nitrogen Cycle

By: Dr. Roy Yanong

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New aquariums undergo a cycling period of about 3 to 8 weeks during which time ammonia and nitrite levels can become lethal to fish. Luckily, biological filtration takes care of this.

Biological filtration is the process by which a group of bacteria known as nitrifiers converts toxic ammonia to less toxic nitrate. It's one of the most important aspects of keeping fish. Most hobbyists realize the importance of having an established biological filter but don't completely understand what it does or how it works. The entire process begins with ammonia.

New Tank Syndrome

In order for the biological filter to function properly, several things must occur. There must be ammonia present. The aquarium must have enough surface area for bacteria to live on. There must be enough oxygen in the water. And, water must flow through these bacterial colonies adequately.

One of the most common mistakes made by new hobbyists is adding too many fish too soon after setting up their aquarium. The causes ammonia levels to become excessively elevated, and after a few days or a week, all the fish die. This is called "new tank syndrome." What these hobbyists have failed to do is allow their tank to cycle.

When fish are first introduced into a new aquarium, there are very few bacteria present to remove ammonia. Consequently, the ammonia builds up to high concentrations that will kill most fish. After some time, enough ammonia-oxidizing bacteria are present to convert the ammonia into nitrite. The ammonia levels drop and the nitrite levels rise. Soon, nitrite levels become toxic, until the nitrite-oxidizing bacteria are present in high enough numbers to convert the nitrite into nitrate. It generally takes 3 to 8 weeks for enough bacteria to grow on the biofilter and in the tank before more fish can be added.

Cycling the Aquarium: Practical Suggestions

There are several ways to prevent "new tank syndrome." One method is to start with just a few hardy fish that can handle the ammonia and nitrite increases or "spikes." Danios and black tetras can be used to start freshwater tanks. Damselfish, sailfin mollies and hermit crabs can be used to start marine tanks. Hobbyists should determine when it's safe to add a few more fish by monitoring ammonia and nitrite levels once or twice a week.

The aquarium owner can speed up this process by using a small amount of gravel or some other biological filter media from an already established tank or system of the same type (i.e., marine or freshwater), preferably one that hasn't had any disease problems. Numerous bacteria will already be present on these media and can, therefore, multiply to adequate numbers much more rapidly.

An alternative method for cycling a tank requires no fish. Once a tank has been set up but before fish are introduced, adding very small amounts of straight household ammonia (without any additives) will provide food for growing the necessary bacteria. Monitoring levels of ammonia and nitrite will still be necessary to determine when the biofilter is ready to handle fish.

Each time fish are added, ammonia and nitrite levels should be monitored periodically (biweekly or weekly) to be sure the filter is handling the extra load.

The Beginning of the Cycle: Ammonia

Ammonia is a waste product of protein digestion. Most fish excrete ammonia through their gills. Excretion of ammonia requires a lot of water, but because fish live in water, they don't have to worry too much about wasting it. Fecal matter, uneaten food and decaying organisms also add ammonia to the water. Unfortunately, most fish can't survive in water with even very small amounts of ammonia. The biological filter is nature's way of removing this ammonia load.

The Biological Filter

The biological filter consists of nitrifying bacteria that remove ammonia from the water. These bacteria concentrate on media through which water from the tank flows. This medium can be a sponge, gravel, bioballs, sand or a foam pad. However, these bacteria will colonize any surface in the aquarium – such as plants and glass – and will also be present in the water.

The biological filter uses different groups of bacteria to breakdown the ammonia. The first group of bacteria, the ammonia-oxidizing group, converts ammonia to nitrite. Nitrite is still very toxic to most fish. A second group of bacteria, the nitrite-oxidizing group, converts this toxic nitrite into a much safer compound, nitrate. Both groups need oxygen in order to do their work. After the bacteria have converted ammonia to nitrite and nitrite to nitrate, a small amount of acid is released. Well-established tanks should have no measurable ammonia or nitrite. Ammonia and nitrite levels should be tested regularly, especially during the establishment of the biological filter.

Nitrate is relatively harmless but can be removed through routine water changes. If live plants are present, they can also take up nitrate. In nature and in some systems, another group of bacteria can convert the nitrate into nitrogen gas. Excess nitrate can lead to build up of unwanted algae and may be harmful to some invertebrates.

The actual bacterial species that make up the biological filter were misidentified in the early days of the hobby, according to some recent research. This means that some over-the-counter bacterial starter mixes may contain the wrong bacterial species. Additionally, freshwater nitrifying bacteria differ from marine nitrifying bacteria.

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