How and who makes these transformations? They are microscopic beings called nitrifying bacteria, whose role in nature is that of decomposers of nitrogen compounds. When we set up a new tank, these bacteria only exist in very small numbers (those few that happened to come with the water, with the gravel, etc). Therefore it is fundamental. in the first few weeks, to make this bacterial colony multiply until it reaches a population such that it can process the fish wastes to come. Thus, we depend on the formation of a good nitrifying bacterial colony in order to ensure a healthy life in our aquarium. In fishkeeping jargon, this initial period of colony formation is known as cycling the tank. A tank will only be ready to receive the main fish population when it is properly cycled. This process normally takes between 2 and 6 weeks to complete.

Let's understand how this cycle works. Nitrogen (N) is a chemical element that goes into the composition of two very important classes of organic molecules: proteins and nucleic acids. Although it is present in great quantities in the air, in the form of nitrogen gas (N₂), few living beings can assimilate it in this form. Only a special class of bacteria, mainly cyanobacteria (which is often called blue-green algae), are able to capture N₂, using it in the synthesis of nitrogen-based organic molecules. These bacteria are called nitrogen fixers. They end up being eaten by other organisms, who in turn get eaten by other animals, and so on until the nitrogen compounds are spread throughout the entire ecosystem.

When these nitrogen compounds are released (death of an organism, or part of it, or through its excrements), they are processed by decomposing bacteria, and one of the main products of this decomposing is Ammonia Gas (NH₃). Ammonia, in contact with water, forms Ammonium Hydroxide (NH₄OH), a highly toxic substance which in large concentrations is highly corrosive. Ammonia is a very dangerous substance for fish, and its toxicity depends on temperature, pH, and water salinity. For instance, the more acid the pH, more Ammonium Hydroxide is neutralized and so the ammonia toxicity is reduced. On the other hand, more alkaline pH means more dangerous Ammonia. Luckily, this substance is consumed by bacteria called Nitrosomonas, which in the presence of Oxygen transform Ammonia into Nitrite (NO₂^-), obtaining energy through the following process:

The HNO₂ (nitrous acid) also gets dissolved in water, releasing the nitrite ion (NO₂^-). Nitrite is another highly toxic substance for plants and animals, but luckily again it doesn't accumulate in a well set up tank, because bacteria called Nitrobacter transform it into Nitrate (NO₃^-), also obtaining energy through the reaction:

Only now, our nitrogen which started in the decomposing organic molecules has finally assumed a much less toxic form. In the aquarium, Nitrate begins to slowly accumulate as a result of this process. But we shouldn't let it accumulate too much because it may lead to excessive growth of algae which use it as a nutrient. To avoid this, we do regular partial water changes and, better yet, add natural plants to the tank, because nitrate is readily consumed by them. In fact, plants are also good consumers of ammonia, and therefore very helpful in keeping this toxin under control.

The nitrifying bacteria will become fixed in any location where theres a good supply of oxygen (since the main process of the cycle is aerobic, i.e., in the presence of oxygen). However, the colonies will prosper in places where there isn't too much light, and where the water current doesn't disturb them too much. This is the most important part of the Nitrogen Cycle in terms of fishkeeping, but actually it doesn't stop here. As an example, if oxygen runs short in the water, Nitrate can be transformed back into Nitrite or, through a process called denitrifying, it can be transformed by anaerobic bacteria back into nitrogen gas (N₂), and the cycle is complete.

Now that we know how the Nitrogen Cycle works, we may better understand how to proceed in a new aquarium, to ensure a healthy environment for our fish. The colonization process of these bacteria occurs without any necessary intervention. All they need is a source of organic matter. Once the tank is set up, filled with water and the filters turned on, we need to supply a little bit of ammonia to start the cycling process. Sometimes the tap water itself already contains ammonia, but in general its better to add some kind of incentive. Once again, a great way to start is by adding natural plants. Their own metabolism and the few leaves that fall off supply the initial nitrogen, and as we've already mentioned they help by preventing the ammonia level from getting too high. But you can also add a small pinch of flake food, or a very small slice of fish or shrimp, and there are several commercial products in the market which stimulate the cycle. Another good procedure is to use some gravel and/or water from an established tank, as long as you're sure that tank is healthy.

Another very common procedure is to use "cycling fish" to accelerate the process. 2 or 3 hardy fish are added (Zebra Danios, for instance) to live in the tank while its going through the cycling process. But this is not the best solution because you're submitting these fish to unnecessary stress. The ideal thing to do is buy a complete Freshwater Test Kit (pH, ammonia, nitrite, nitrate) and follow the ups and downs of ammonia and nitrite levels. When nitrite falls to zero after having gone up, the tank is ready to begin receiving fish. But even so the fish population should be added gradually, in order to allow the bacterial colony to adapt and grow according to the increased bioload.