The Aquarium Nitrogen Cycle and Biological Filtration

Understand how nitrifying bacteria turn toxic ammonia into nitrite and then nitrate, where this happens in your filter, why you must never let media dry out, and how to cycle a tank to a steady 0 ammonia and 0 nitrite.

How the nitrogen cycle works

Fish waste, uneaten food and decaying matter release ammonia, which is highly toxic — the un-ionized form is roughly 100 times more toxic to fish than the ionized form, and it becomes more dangerous as pH and temperature rise. In a healthy tank, colonies of nitrifying bacteria continuously convert this ammonia to nitrite, and then nitrite to far less toxic nitrate, in a two-step process known as the nitrogen cycle.

• Step 1 — ammonia-oxidising bacteria (such as Nitrosomonas and Nitrosospira) convert ammonia (NH3/NH4+) to nitrite. Ammonia damages gills and tissues above about 0.05 mg/L, and around 2.0 mg/L will kill sensitive fish.
• Step 2 — nitrite-oxidising bacteria (such as Nitrobacter and Nitrospira) convert nitrite (NO2-) to nitrate (NO3-). Nitrite is toxic at levels as low as 0.10 mg/L.
• Target — in a cycled, healthy aquarium both ammonia and nitrite should always read 0; only nitrate accumulates, and it is exported by routine water changes.

Where it happens: the biofilter

The bacteria live on surfaces, so a biofilter simply provides a large, water-permeable surface area — sponge, ceramic media, sintered glass or plastic bio-media — for them to colonise. Nitrification is an aerobic process: the bacteria need a steady supply of oxygen and alkalinity, and the reaction releases hydrogen ions that gradually lower pH. Building up enough bacteria to fully process the tank's waste takes time — a new biofilter typically needs about six to eight weeks to mature.

You must cycle a tank before it can safely hold a full stock of fish. In fishless cycling you add an ammonia source (bottled ammonia or a pinch of fish food) and let the bacteria build until they clear ammonia and nitrite within a day; in fish-in cycling a very light stock produces the ammonia while you protect them with frequent water changes. Either way the principle is the same — keep testing, and only treat the tank as cycled once ammonia and nitrite both read 0 and nitrate is present.

Sources: ask.ifas.ufl.edu , en.wikipedia.org