The Nitrogen Cycle
"Cycling" an aquarium means preparing it to achieve a balance between fish waste and bacteria which eat that waste. Bacteria living in the filter and substrates transform fishes nitrogenous waste, ammonia, into less toxic substances. This is how nature cycles waste nutrient and it doesn't accumulate. Without the bacteria, ammonia builds in an aquarium over the first few weeks. During this time, adding prebottled de-nitrifying bacteria as well as live sand and/or live rock can kick start the nitrogen cycle. Adding fish or food to the tank too fast causes ammonia spikes, you need to give the bacteria time to build up incrementally. Otherwise the fish end up in toxic water of their own waste.
There are three phases to the ammonia cycle:
1) The first phase entails bacteria "eating" fish waste and turning it into less toxic substances. These bacteria initially seed the tank by hitching a ride on fish, inverts, live rock, or anything that comes from an established tank without being rinsed. The bacteria transform ammonia, the nitrogenous waste produced by the fish (primary from their gills), into Nitrite. As ammonia eating bacteria grow in number and reduce the ammonia levels down, the nitrite levels begin to rise.
2) The second phase of the cycle, which in an established system runs continuously and proportionally to the first, is based on another group of bacteria changing Nitrite to Nitrate.
3) Lastly, there is a third group of bacteria, which are called de-nitrifying bacteria, turn Nitrate into nitrogen gas thus completing the cycle of organic solid nitrogen to inorganic gas. These de-nitrifying bacteria live both within live rock and a layer within the substrate/gravel where the oxygen levels are almost zero.
How to initiate the cycling
On top of buying de-nitrifying bacteria in a bottle, a common way to speed up the cycle and reduce how drastic levels of ammonia and nitrite get is by using live rock. When starting a tank with live rock, make sure that the rock isn't too dirty ( see curing live rock) otherwise the nutrient that goes from the rock to the water will likely result in the growth of more algae. Starting a 55 gallon tank with 10 lbs of live rock, one damsel or clownfish or whatever you are willing to pay for that is small, and a dozen blue legged hermit crabs is a relatively safe bet. If available and you are willing to pay a bit more, other good “clean up crew” options include a brittle starfish or cleaner shrimp. A successful strategy to eliminate algal growth and allow nutrient to be used by other beneficial microorganisms is to provide no light for the first 3 weeks. The nutrient coming from stuff dying on the rock should go back to the animals which lived from the rock; bacteria, worms, sponges, etc. To an extent they integrate the nitrates and phosphates (another end product of all food and organic stuff that dies) which would otherwise end up growing algae. It is also possible to use chemical filtration if your tests show excess phosphates. Options to chemically bind phosphates include the phosphate removing pad or Iron Oxide (granulated ferric oxide; the red stuff used in a phosban reactor).
When the lights go on after three weeks there is often a bloom of light brown diatom algae on all lit surfaces (these microalgaes use silica in the water) and there is a chance, depending on the amount of nitrate and phosphate in the tank, that hair algae grows. To fix this you can use snails and urchins (a common snail is the astrea: Lithopma sp. and a good hair algae eater is the tuxedo urchin). There are a number of algae eating fish which can also help. More live rock can be added in batches with less effect on the cycle each time. See the lighting section about what types of lights are good for what tanks. Remember, try to treat the system naturally and patiently. Impulse is the bane of marine tanks.
Consequences of failing to cycle the tank
It is essential that the two phases of the cycle are in balance because an excess of some components (ammonia, or Nitrate) is harmful to fish.
● Ammonia hurts fishes gills starting around .5 parts per million. When ammonia builds you can often see a cloudy tint to the water and fish generally stop eating, go to the bottom, breath hard, and exhibit stress color patterns. This often happens within a few days of starting a tank, especially if you put too many fish in or feed the fish food which doesn't get eaten and rots on the bottom.
● Nitrate at concentrations greater than 50 ppm can mess with sharks thyroid metabolism causing iodine deficiency and subsequent immunocompromised state in which they aremore likely to get sick. High nitrates can also cause browning of coral (their internal symbiotic algae overgrow) and can cause algal blooms.