The nitrogen cycle

Anyone starting an aquarium soon hears it: ‘let your tank cycle first’. Behind that advice is the nitrogen cycle: an invisible process in which bacteria convert your fish’s toxic waste into far less harmful substances. Once you understand how it works, you also understand why fish in a new tank so often fall ill, why you never rinse your filter under the tap and why water changes are indispensable.

Where it starts: ammonia

Fish excrete most of their waste as ammonia (NH₃), mainly through their gills. Ammonia is also released when uneaten food, droppings, dead plant matter or a dead fish break down. In nature it is diluted in a huge volume of water; in an aquarium it builds up.

Ammonia is toxic even in small amounts: it damages gills and skin and disrupts breathing. In water it exists in balance with much less toxic ammonium (NH₄⁺). The higher the pH and temperature, the more of it is in the toxic form. At 25 °C that is about 0.5% at pH 7, but over 5% at pH 8. The same test reading is therefore ten times as dangerous in a Malawi or marine aquarium as in a soft, acidic discus tank.

Step 1: from ammonia to nitrite

Fortunately, there are microorganisms that live on ammonia. Nitrifying bacteria such as Nitrosomonas, together with ammonia-oxidising archaea, get their energy from converting ammonia into nitrite (NO₂⁻). They need oxygen to do so.

Nitrite, however, is still toxic. It is taken up through the gills and turns the haemoglobin in the blood into methaemoglobin, which can no longer carry oxygen. Fish then hang gasping at the surface, even though there is enough oxygen in the water. Nitrite is taken up along the same route as chloride; in freshwater fish, a small dose of salt (chloride) therefore partly blocks its uptake. That is an emergency measure, not a solution.

Step 2: from nitrite to nitrate

A second group of bacteria converts nitrite into nitrate (NO₃⁻). For a long time Nitrobacter was thought to be the main player, but research shows that in aquarium filters this work is mostly done by Nitrospira. Some Nitrospira species can even carry out both steps on their own.

Nitrate is much less toxic than ammonia and nitrite, but it isn’t harmless. High levels weaken fish’s resistance, slow the growth of young fish, feed algae and harm corals and many invertebrates. Guideline values:

• Community and Malawi aquariums: below 25 mg/l, preferably lower
• Discus and other sensitive species: below 10 to 20 mg/l
• Reef aquariums: below 10 mg/l for soft corals; hard corals (SPS) often do best at 1 to 5 mg/l, but not at zero

Removing nitrate

In most aquariums, the conversion stops at nitrate. It keeps building up until you remove it:

• Water changes are the simplest and most important method: changing 20 to 30 percent every week keeps nitrate low.
• Plants and algae take up nitrogen as a nutrient; fast-growing and floating plants do this best.
• Denitrification: in low-oxygen spots – deep inside live rock, a thick sand bed or a dedicated denitrification filter – other bacteria convert nitrate into nitrogen gas, which escapes from the water. This closes the cycle and mainly matters in marine aquariums.

Where do these bacteria live?

Not in the water, but as a thin layer (biofilm) on every surface: filter media, substrate, rocks, decoration and plant leaves. The filter is the most important place, because oxygen-rich water carrying waste flows past the bacteria there all the time. A few practical rules follow from that:

• Never rinse filter media under the tap: chlorine and chloramine in tap water kill the bacteria. Rinse it in a bucket of aquarium water that you are changing anyway.
• Never replace all filter media at once, but in stages, spread over several weeks.
• Never switch the filter off for more than a few hours. Without oxygen-rich flow the bacteria die, and when you switch it back on, the rotting material is flushed into the tank.
• Be careful with medication, especially antibiotics: they can kill the filter bacteria too.

Cycling a new aquarium

A new tank doesn’t have these bacteria yet. They multiply slowly: even in good conditions their number only doubles after about a day. Cycling therefore usually takes 4 to 6 weeks and follows a fixed pattern:

1. First ammonia rises, while there is hardly any nitrite yet.
2. After a week or two ammonia drops and nitrite rises quickly, often beyond what your test kit can measure.
3. Then nitrite drops too, while nitrate rises.
4. Once ammonia and nitrite have been at zero for a few days while nitrate keeps rising, the cycle is established.

Fishless cycling

The most animal-friendly method is fishless cycling. You feed the bacteria yourself with a source of ammonia: a small dose of pure ammonia (up to about 2 mg/l) or some fish food left to break down. A bacteria starter or a handful of filter media from a healthy aquarium speeds things up considerably.

The tank is ready when it fully converts 2 mg/l of ammonia within 24 hours without any nitrite remaining. Then change a large part of the water to lower the accumulated nitrate, and add your fish gradually: not all at once, as the bacteria population needs to grow along with the amount of waste.

What helps cycling

• A temperature of 25 to 30 °C
• Plenty of oxygen and water movement
• A pH above 7 and enough carbonate hardness (KH): nitrification consumes KH, and with too little KH the pH can suddenly crash, after which the bacteria stop working
• Patience: adding more ammonia doesn’t make it faster

When things go wrong

An established aquarium can also lose its balance: after adding too many new fish, cleaning the filter too thoroughly, a power cut, a dead fish nobody noticed or overfeeding. If you measure ammonia or nitrite, do the following:

1. Change 30 to 50 percent of the water right away, using dechlorinated water at the same temperature.
2. Feed little or nothing for a few days: less food means less ammonia.
3. Check the filter and remove dead animals and rotting material.
4. Test daily and repeat the water change until ammonia and nitrite are back at zero.

Measure, don’t guess

The nitrogen cycle is invisible: crystal-clear water can be full of ammonia or nitrite. So test ammonia/ammonium, nitrite and nitrate regularly, especially while cycling and in the first months. Liquid tests are more accurate than test strips. With the Water log tool on Yawar you can record your results and follow each parameter in a chart.

In short

• Fish and decay produce toxic ammonia.
• Bacteria convert it into toxic nitrite, and then into much less toxic nitrate.
• These bacteria live mainly in your filter: treat it with care.
• A new aquarium needs 4 to 6 weeks of cycling before fish can go in.
• You remove nitrate with water changes, plants and – in marine tanks – denitrification.