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Cycling an Aquarium

The dream, a superb-looking display full of healthy plants and fishes © Filipe Oliveira

Mark G N Ferguson breaks down an essential process.

1. Sources of Ammonia

2. Sources of Bacteria

3. How to Cycle

4. The Science Bit


All living creatures excrete and for fish this is mainly in the form of ammonia which is constantly produced from their gills. There is also the more obvious solid waste. Unlike in the wild, where water currents remove the ammonia from the fish’s locality, an aquarium is a closed environment so there is nowhere for the ammonia to go. This then creates a problem for us as fishkeepers since ammonia is toxic to fish.

Fortunately a naturally occurring bacterium, Nitrosomonas sp., will reduce this ammonia to nitrIte as part of the nitrogen cycle. NitrIte is also toxic but a second bacterium, Nitrospira sp., then reduces this to nitrAte which can be removed by regular water changes.

It’s important to understand the nitrogen cycle when setting up an aquarium. © Ilmari Karonen

In a new aquarium however these bacteria are not present, so any fish will be exposed to high levels of ammonia and nitrIte until the colonies form and multiply sufficiently to cope with the waste produced. This process is termed the ‘cycle’.

Clearly therefore we want to avoid exposing any fish to harm caused by ammonia or nitrIte. But without any ammonia being present then the colonies required to deal with the ammonia produced by the fish can’t form. How do we resolve this Catch 22?

1. Sources of Ammonia

Contrary to what some shops still say, leaving the aquarium to stand for a week or two is not cycling it, since there is no source of ammonia present to feed the bacteria. There are however alternative ways to add ammonia to an aquarium and build up the colonies before introducing any fish.

If liquid ammonia is to be used ensure it is free of additives.

• Ammonia can be purchased for household cleaning and is available from chemists or hardware stores. Make sure it is pure ammonia and doesn’t contain any additives such as foaming agents and be careful when handling it. Small amounts of this can then be added using a pipette each day to feed the bacteria.

• A raw prawn or decaying fish food will produce ammonia. Whilst this is less precise than measuring the amount of ammonia added, the bacteria are only interested in ammonia being present rather than the source.

• All humans produce their own ammonia in the form of urine and this has been used in the past to cycle aquaria (proof the bacteria aren’t fussy about the source!).

• Plants will absorb ammonia and nitrIte from the water, so with heavy planting of quick growing types it is possible to stock very lightly and then build numbers up slowly, relying on the plants to deal with the initial ammonia and nitrIte before the bacteria colonies develop sufficiently. This only works under certain circumstances, so please ask on the forums for more detail if you are considering this option.

• Some people still suggest cycling with fish, adding a few to start with and then gradually building the numbers up over time. This is both unethical, since it exposes pioneer fish to elevated levels of ammonia and nitrIte, and hard work, since frequent (even daily) water changes are needed for several weeks in order to maintain acceptable levels.

2. Sources of Bacteria

Both Nitrosomonas sp. and Nitrospira sp. are naturally occurring and will colonise the aquarium in due course. However there are ways to speed the process up.

• If you know someone with an aquarium, ask them for squeezings from their filter media (the muckier the better). These will contain some of the bacteria needed, giving the cycle an instant boost. Just make sure their aquarium is disease free first.

Nitrosomonas bacteria play an important part in the aquarium cycling process. © Yuichi Suwa

• A small piece of their media works just as well, but don’t take too much as this will cause a mini-cycle in their aquarium. A mini-cycle is when the remaining bacteria are insufficient for the waste produced by the fish present and it takes time for the bacteria to multiply back to being able to cope.

• Alternatively ask your local fish shop for some squeezings or media. Not all shops do this however.

• A pinch of soil from an organic garden will contain the correct bacteria, but it needs to be organic to avoid any residual pesticides being introduced to the aquarium.

• Most of the ‘bacteria-in-a-bottle’ products should be avoided as few contain the correct Nitrospira sp. bacterium. There is also a question mark over how live bacteria can survive for weeks or even months with no oxygen or food source.

The bacteria will colonise any and every surface in the aquarium, but have a preference for the filter media because the through flow of water provides a constant supply of both ammonia/nitrIte and oxygen. Ultimately the size of the bacteria colonies is restricted by the availability of these, but other constraints on stocking will restrict the number of fish that can be kept before this limit is reached.

3. How to Cycle

This article will focus on the fishless cycle as using fish is damaging to their health. If you’re in the unfortunate position of having already bought fish for a brand new aquarium, then please ask in the forums and we’ll help you get them through the process if you are unable to return them to the shop.

You will need to make two purchases – one being a bottle of pure ammonia and the other test kits for ammonia, nitrIte, nitrAte and pH. Liquid kits are both more accurate and longer lasting than test strips and generally a master pack containing all the necessary tests is cheaper than buying individually.

The next step is to set up the aquarium and raise the water to a temperature of 80°F/27°C. Remember to dechlorinate the water first, as tap water contains chlorine or chloramine to kill bacteria, and the purpose of the cycle is to grow bacteria. During the cycle the filter should be left running with the outlet rippling the surface as this will help the colonies to grow by increasing the oxygen content of the water.

Ideally you should settle on a time when you will be able to test each day, as it is important to let 24 hours elapse between tests. Ammonia should be added carefully to the aquarium to achieve a reading of 5 ppm. Too high an ammonia level will kill the bacteria and too low will slow the cycle.

Despite what some may tell you, live fishes should not be added until the aquarium is fully-cycled. © Ricardo Kobe

Determining the correct amount of ammonia to add can be tricky, but the following calculation can be used as a starting point.

• Assuming a 100 L aquarium and a 10 % solution of ammonia, then the correct dosage is 5ml.

• Increase/decrease the dosage for larger/smaller aquaria, so a 150 L aquarium would need 7.5 ml [(150 L / 100 L) x 5 ml].

• Increase/decrease the dosage for weaker/stronger solutions of ammonia, so a 9% solution would need 5.56 ml [(10% / 9%) x 5 ml].

• So a 150 L aquarium and a 9 % solution requires 8.33 ml [(150 L / 100 L) x (10 % / 9 %) x 5 ml] and a 70 L aquarium with a 11 % solution is 3.18 ml [(70 L / 100 L) x (10 % / 11 %) x 5 ml].

It is best to add a little less than the calculated amount the first time. Note how much you have added, then wait for five minutes to let the ammonia circulate and then test to check the reading. If it is less than 5 ppm then it can be increased based on the amount you first added.

There are calculators available on the internet that will calculate how much ammonia to add if you don’t want to do the calculation yourself.

Each day at the same time you need to test the ammonia reading and then add only enough to raise this back to 5ppm, not by a further 5 ppm. For the first few days you may not notice any movement, especially if you didn’t have a source of bacteria at the start. Once the ammonia starts to drop between readings you can test for nitrIte.

When the nitrIte level begins to rise sharply there is no need to top the ammonia up to 5 ppm every day. Instead aim for a level of 2-3ppm as this will help speed up the growth of the Nitrospira sp. colonies. Nitrospira sp. is much slower to multiply than Nitrosomonas sp. and you’ll find that the nitrIte stays high for much longer than the ammonia did. However once it does start to fall it falls very quickly.

Typical patterns of ammonia, nitrite, and nitrate fluctuation in a new aquarium cycled using the ‘fishless’ method © Seriously Fish

It is worth testing the ph every few days as the bacteria will go dormant if this falls too far. Being aware that the pH is falling will enable you to prevent this happening. Check the kh of the tank first as this is likely to be very low.

Avoid ‘pH Up’ products and use bicarbonate of soda (found in the home baking aisle of a supermarket) to raise both the pH and kh. Again there are calculators available on the internet that will tell you the correct amount. The bacteria do best at a pH of 7.8 but there is no need to target this and anything over 6.5 is fine.

The inevitable question arises of how long this whole process takes. There is no clear answer as all aquaria cycle at their own speed, but generally anything between four and six weeks is normal. It can be quicker, especially if a source of bacteria is added at the start, but it is also not unknown for the cycle to take up to eight weeks.

This is an ideal time to plan your eventual stocking, so visit your local fish shop to see what they have in stock, note down what catches your eye and then read up on those species in the Knowledge Base. Ask on the forums about the fish you are considering and we can advise on their suitability and share experiences with you.

Live plants are useful since they consume nitrate. © Viktor Lantos

The cycle is complete when you have zero readings for both ammonia and nitrIte for more than a couple of days in a row. At this point you can test for nitrAte which will be very high. Keep topping up the ammonia to 2ppm after the daily test until you are ready to get fish. At that point do a very large water change (80-90 %) to remove the excess nitrAte, and remember to dechlorinate the fresh water before adding it. No ammonia should be added once fish are present.

The aquarium now has sufficiently large colonies of the correct bacteria to support fish and you are able to fully stock immediately. Remember that all stocking should be based on eventual adult sizes and there are no hard rules about stocking density (e.g., 25 mm of fish per gallon) due to the differing requirements of each species (water conditions, sociability, territoriality, predation, activity etc) which are highlighted in the Knowledge Base.

4. The Science Bit

There is an old saying in the hobby that we don’t keep fish, we keep water. So what does that mean?

In simple terms it means that we regularly test the water to monitor the levels of various substances, which allows any problems to be identified at an early stage before there is any impact on the health of the fish. Clean water is the fish equivalent of fresh air for us.

Water test kits are essential in moitoring the progress of an aquarium cycle. © sera GMBH

The key substances to monitor are:

• Ammonia (NH3)/Ammonium(NH4) – tests kits don’t distinguish between the two but, as a rule of thumb, in an aquarium with a pH above 7.0 there will more ammonia present whilst if the pH is below 7.0 then there will be more ammonium present. Ammonia is more dangerous to fish than ammonium, but as test kits don’t distinguish between them high readings (i.e., >0.5 ppm) must be avoided. When present in higher quantities skin, fin, eye and/or gill damage can occur quite rapidly which is referred to as ‘ammonia burn’.

Both are also more toxic at lower pHs and temperatures. Both ammonia and ammonium are the end result of the fish’s natural metabolic processes, so can’t be prevented and also arise from decaying matter such as faeces, dead livestock, or plants.

• NitrIte (NO2) – again this is harmful to fishes. They absorb nitrIte from the water and it combines with the haemoglobin in their blood to form methaemoglobin. This means that the fish’s blood is less able to transport oxygen and again is fatal at higher levels. NitrIte arises when the ammonia/ammonium present is consumed by the Nitrosomonas sp. bacterium.

• NitrAte (NO3) – this is the end stage of the cycling process and is produced by Nitrospira sp. bacterium consuming nitrIte. It is harmful to fishes only at very high concentrations (200 ppm+) but regular water changes will mean that the level never rises high enough to be a concern. There is no need to test for nitrAte during a fishless cycle as it will be removed by the large water change on completion, and the reading can be confused by the elevated nitrIte levels.

The normal level in an established aquarium should be no more than 20ppm above that of your tap water and if it is more than this you will need to increase both the size and frequency of the regular water changes. Live plants will consume nitrAte and help keep the reading down.

• pH, carbonate hardness (KH) – these should be considered together as they are linked. The pH of the aquarium is less important to the fish than it is to the bacteria as these become dormant if the pH falls below 5.5, at which point ammonia and nitrIte will start to accumulate. Unless you live in a hardwater area then you will find that the pH drops over time.

This is because the reduction of ammonia to nitrIte results in free hydrogen ions which lower pH. As long as there is sufficient carbonate present then this will react with the free hydrogen ions to form CO2 and water, which greatly reduces the pH decrease. Monitoring the carbonate hardness is therefore necessary to ensure that there is sufficient carbonate present to buffer the free hydrogen ions.

Once your tank is cycled livestock can be added, but you should continue to test the water regularly © Ryan O’Donnel

• General hardness (GH) – a stable gh is important for fish as changes in gh will alter the osmotic balance, resulting in minerals either leaving the fish or being absorbed by it, depending on whether the water content is lower or higher than that of the fish. Any change should therefore be made gradually as large changes in gh will cause potentially fatal osmotic shock because the fish is unable to adjust quickly enough to the new conditions.

This is particularly important if making a water change on a neglected tank and so a series of smaller changes should be performed in preference to one large one. Remember also that a neglected tank will typically have a low pH making the bacteria dormant, and ammonium can accumulate as a result. Such a large water change will raise the pH and in doing so convert the ammonium to more toxic ammonia – another good reason for several small changes being preferable.

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5 Responses to “Cycling an Aquarium”

  • SGielis

    Nice article.
    But why not adding nitrite at the start up?
    Natrium nitrite and especially potassium nitrite should work fine to give the Nitrospira a head start.

  • georg_fuss

    There is no need to use ammonia for an aquarium. You can use Ammon carbonate (salts of hartshorn) or urea instead.

    Ammon carbonate is a solid salt and much easear to handle. 1 Gramm substitute 10 ml 10 o/o liquid ammonia.

  • georg_fuss

    @ SGielis

    Nitrites is the following produkt of ammonia. So it make sense to start with ammonia.Nitrites are are higher poison as ammonia. You use a litle Nitrite to corn or cure meat.

  • SGielis

    I didn’t make myself very clear. I start my aquaria with ammonia and nitrite. This starts both bacteria cultures at the same time and so reduces the cycling time considerably.

  • […] bits in way i couldnt. Great read for newbies to the cycle ( like me ) and old veterans…. Cycling an Aquarium — Seriously Fish Enjoy […]

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