Even though aquarium systems are essentially artificial ecosystems, they are nevertheless ecosystems. As such, to be hospitable to the sorts of things we like to keep in them (fishes, corals, etc.), they must be “in balance” naturally. Striking this balance requires a bit of action as well as some patience. During a critical break-in period, biological and biochemical processes rapidly and dramatically alter the aquarium water chemistry.
Stabilization follows the establishment of key microbes. Most important of these for aquarists are the nitrifying bacteria. These bacteria play a huge role in the nitrogen cycle, as they work together to convert really toxic ammonia (produced mainly from animal wastes) to less toxic nitrite to relatively harmless nitrate.
Nitrifying bacteria do not assimilate this nitrogen, but rather oxidize it as a product in their metabolisms. The end product, nitrate, quickly reenters the food chain as a plant nutrient. To prevent algal blooms that accompany nitrate spikes, aquarists commonly cultivate “nutrient sponge” macroalgae such as Ulva.
Though it is a slower (and less conspicuous) part of the nitrogen cycle, some nitrate is simply made to gas off. Through a process called denitrification, certain anaerobic bacteria convert nitrate to dinitrogen (nitrogen gas).
The nitrogenous wastes in aquarium water originate mostly from fish foods. So, obliviously, the first step in controlling nutrient levels in aquaria is feeding sparsely and keeping stocking densities low. But having a large, heavily colonized biofilter will go further to protect your animals from deadly spikes of nitrite or, especially, ammonia. With sizable populations of nitrifying and denitrifying bacteria, as well as a lush bed of macroalgae, your aquarium system will be completely cycled and provide a safe and healthy home for your most delicate livestock.