Beneficial Bacteria and the Biological Filter
The microbes behind the nitrogen cycle turn toxic ammonia into nitrate. Learn which bacteria do the work, where they live, what they need, how to seed a cycle and what kills them.
The biological filter is not really the box or sponge; it is the living colony of bacteria it houses. These microbes drive nitrification, the process that protects fish by turning their toxic ammonia waste into far safer nitrate. Understanding them is the key to cycling a tank successfully and never accidentally wiping out the colony.
Who does the work
Nitrification is the aerobic, oxygen-requiring oxidation of ammonia to nitrite and then to nitrate, carried out by a small group of specialised microbes. Ammonia-oxidising bacteria such as Nitrosomonas, along with ammonia-oxidising archaea, convert ammonia to nitrite. Nitrite-oxidising bacteria such as Nitrobacter and Nitrospira then convert nitrite to nitrate. Some Nitrospira are now known to perform both steps in a single organism, a process called comammox. Because these reactions release hydrogen ions, nitrification gradually acidifies the water unless buffered by alkalinity.
What they need
- A steady ammonia source to feed on; with no waste input the colony starves and shrinks.
- Oxygen, since nitrification is strictly aerobic; good flow and surface agitation keep media oxygenated.
- Plenty of surface area on porous media, substrate and decor.
- Stable temperature and pH, and adequate alkalinity; below about 20 mg/L total alkalinity, common nitrifiers function poorly.
- No chlorine or chloramine, which are toxic to the bacteria.
Seeding and speeding a cycle
Building a biofilter from scratch can take anywhere from a few weeks to a couple of months; aquaculture guidance often cites six to eight weeks for a filter to fully mature. You can accelerate it by seeding the new tank with bacteria from a mature one, most easily by transferring used filter media or substrate, by adding a bottled live-bacteria product, or by including live plants. Patience during this stage prevents the ammonia and nitrite spikes that kill fish in a new tank.
A note on denitrification
Nitrate is the safe end product of nitrification but still accumulates and is normally removed by water changes. A separate group of bacteria performs denitrification, the anaerobic conversion of nitrate into nitrogen gas, in low-oxygen zones such as deep sand beds and refugia. This is why some advanced systems use deep substrates to lower nitrate biologically.