Understanding The Aquarium Nitrogen Cycle

There is a critical process every new aquarium must go through to become hospitable to fish.

Without this process in place, ammonia levels can spike to unsafe levels and kill your fish. This process is known as the Aquarium Nitrogen Cycle.

This nitrogen cycle must be established before you can fully stock your aquarium with fish. In this article, I will give you all the information you need to understand this cycle. More importantly, I will explain how to get your aquarium properly cycled.

What is the Nitrogen Cycle?

Nitrogen cycle diagram

Also known as the biological cycle, the nitrogen cycle is the processing of ammonia and nitrites into the less toxic nitrate.  Ammonia and nitrites are highly toxic to fish and can kill them in small amounts.

Fortunately, nitrifying bacteria are able to transform ammonia and nitrites into far less harmful nitrogen compounds. This nitrogen cycle is a three-step process that takes anywhere from 2-6 weeks to become established.

Step 1 - Ammonia production

Ammonia is produced naturally in the aquarium once fish have been introduced. It is typically created in a couple of different ways;  during the breakdown of organic matter like uneaten fish food, and as a byproduct of protein metabolism in fish. This ammonia is primarily excreted across the gill membranes of a fish but is also excreted in the urine (source).

Ammonia is very harmful to fish and can rise to dangerous levels within just a few days in a new tank. Harmful levels of ammonia can cause “new tank syndrome” in fish. This is caused by the negative effect ammonia has on a fish’s central nervous system. In a short period of time this will lead to fish death.

Temperature and pH can also have an effect on ammonia toxicity in an aquarium. There are two forms of ammonia that are produced in an aquarium. They are ionized ammonia (NH4 +) and un-ionized ammonia (NH3 0). This un-ionized ammonia is far more harmful and is formed at pH levels above 7 and at higher rates the warmer the temperature.

Step 2 - Converting ammonia to nitrites

As the ammonia levels rise bacteria will begin to take hold and consume this ammonia. These bacteria are called nitrosomonas. They are present nearly everywhere and will find their way into your aquarium one way or another. However, they will colonize your aquarium much quicker if artificially “seeded” in.

These little guys transform ammonia into nitrites. While still harmful to your fish nitrites are much less harmful than ammonia. Once these bacteria take hold the spike of ammonia experienced in the beginning will recede and nitrite levels will rise.

Step 3 - Converting nitrites into nitrates

As nitrites become available the bacteria nitrobacter will soon colonize the tank. They are responsible for transforming nitrites into nitrates. Nitrates are only harmful to fish in very high concentrations.

At this point, the high nitrite levels produced in the previous step will drop to safe levels. Nitrate levels will rise and are responsible for algal blooms. While unsightly, these are not harmful to your fish. Nitrates can be kept in check with live plants and/or regular water changes. 

You should monitor this process in a new aquarium using a water testing kit. You will first see the ammonia level rise and then drop. That will be followed by a nitrite spike and then a drop. And finally, you will see the nitrate levels rise while ammonia and nitrate levels remain near zero.

Your water may turn a cloudy white color during this process. Don’t worry, this is normal and should eventually clear up.

Once an aquarium is fully cycled and stabilized ammonia and nitrite levels should be 0 ppm while nitrate levels can range from 5 to 40 ppm. If your nitrate levels are 40 ppm or above you need to perform a partial water change.

Nitrogen Graph with watermark

Getting the Nitrogen Cycle Started In Your Aquarium

There are many options to begin the biological cycle in your aquarium. I recommend the following three methods.

Cycling with fish

Cycling with fish used to be the only way an aquarium was conditioned. While some “experts” don’t recommend it have no problem doing so as long as it is done correctly. I have lost very few fish with this method, but I go slowly and follow some simple rules. 

Only add 1 fish per 10 gallons of water until the cycle is established. This ensures that the ammonia will not spike too high, too quickly in the tank. The rate at which a single fish releases ammonia is slow. This gives the nitrosomona bacteria a chance to colonize the tank before ammonia levels get too high.

The starter fish you have added will have to deal with some level of ammonia before the bacteria take hold. Therefore, you need to put some thought into what breed of fish you are going to add for this process. You will need to select the hardiest species you plan on stocking in your tank.

If none of the species you plan on keeping are considered hardy you may want to consider a fishless cycling method. Likewise if you plan on keeping rare or expensive fish.

Also, consider if the fish is a schooling fish. If a schooling fish is not kept with at least six other fish it may become stressed.

I would recommend testing your water daily, or at least every other day. This will help you to catch any potential issues and allow you the opportunity to make adjustments if ammonia levels get too high.

Fish-in cycling steps

  1. Set up the aquarium with all the needed equipment
  2. Dechlorinate your water if needed (chlorine kills good bacteria)
  3. Allow water temperature to stabilize, then add 1 hardy fish per 10 gallons.
  4. Feed your fish very lightly, in the beginning, every other day. Slowly increase the amount of food over the next 4-6 weeks.
  5. Test your ammonia, nitrite, and nitrate levels with an aquarium water test kit. This should be done at least every other day.
  6. When ammonia and nitrite levels are at 0 ppm and nitrate levels begin to rise your aquarium is now cycling ammonia.
  7. If ammonia or nitrite levels go above 0.2 ppm do a 25% water change

Great, can I add all of my fish now? Not so fast! Adding more fish is going to increase the amount of ammonia produced in the tank. This can lead to more ammonia spikes which can kill your more sensitive fish.

Add in additional fish slowly, not all at once. Add some fish and wait a week or two before adding more. Make sure to monitor your ammonia and nitrite levels while doing so.

Cycling with Plants

Java Fern Wood Substrate

This method involves setting up your aquarium with live plants before any fish are added. The amazing thing about aquatic plants is that they will uptake ammonia, nitrite and nitrate for growth. Even better they will feed on the toxic ammonia first before going on to the less toxic forms of nitrogen (source).

What about those great beneficial bacteria we’ve talked so much about? Don’t worry, they will be there too. They will likely be introduced into the tank on the plant’s roots.

Setting up your aquarium with live plants really is the best way to go. That toxic ammonia and nitrite don’t stand a chance against healthy plants and bacteria!

While I have successfully done a fish-in cycle with live plants I wouldn’t necessarily recommend it. Many rich substrates designed for aquarium plants will cause a spike in ammonia initially. These substrates can also make the water very cloudy at first.

So it’s best to let things settle and reach an equilibrium in the aquarium before adding fish.

How do you know when the tank is properly cycled? Once you see new growth in the plants or algae. When this happens you know your plants are consuming ammonia and nitrogen compounds and converting them into new leaves.

Test the water to ensure ammonia and nitrites are below 0ppm and nitrates are below 40 ppm. Then you may add new fish gradually.

Cycling without fish

This method has become increasingly popular and recommended by many different people. The main advantage of this method is that there is no risk to kill or stress fish. This is especially important if you want to stock sensitive or expensive breeds of fish.

Beginners sometimes have trouble with this method because they do it wrong or struggle with the process.

To jump start the aquarium’s nitrogen cycle without fish, a source of ammonia must be added. This is usually accomplished by adding fish food or ammonia into the aquarium.

Cycling With Fish Food Steps

  1. Set up the aquarium with all required equipment
  2. Dechlorinate your water if needed (chlorine kills good bacteria)
  3. Bring the water up to at least 80°F/27°C
  4. Add a small pinch of fish food per day
  5. Monitor ammonia, nitrites and nitrates at least every other day
  6. When ammonia and nitrates reach 0 ppm and nitrates have begun to increase the cycle is complete
  7. Do a partial water change and add fish!

A downside to this method is that fish food alone doesn’t add a lot of ammonia to the tank. This results in fewer bacteria colonizing it. When fish are added there is a temporary spike in the ammonia and nitrite levels.

Fortunately, there is already a beneficial bacteria colony present so it doesn’t take long for them to catch up. As a result, the ammonia spike is much smaller and shorter than with fish in cycling.

Cycling With Ammonia Steps

  1. Set up the aquarium with all required equipment
  2. Dechlorinate your water if needed (chlorine kills good bacteria)
  3. Bring the water up to at least 80°F/27°C
  4. Add 3-5 drops of pure ammonia per 10 gallons of water daily. This will bring the ammonia level in the water to 5ppm
  5. Monitor the nitrates daily and as soon as the ppm starts to rise reduce the ammonia input to 2-3 drops per day
  6. Keep measuring ammonia and nitrates and when both levels come down to 0ppm your tank has been cycled
  7. Do a partial water change and add fish!

Cycling with ammonia is one of the fastest methods to establish beneficial bacteria in a tank. This method can take as little as three weeks to complete as opposed to four or six weeks with fish in cycling.

An important thing to emphasize here is that you need to use pure ammonia. Do not use ammonia that has any perfumes or other additives. You can find aquarium ammonia just for this purpose at aquarium supply stores.

Methods to reduce the time and jumpstart the cycle

Six weeks seems like an awfully long time to wait for your tank to be ready for fish. Fortunately, there are ways to reduce this timeframe and jumpstart the nitrogen cycle. They all involve seeding tank with bacteria in one way or another.

Seeding bacteria from an existing aquarium

The best way to jump start the nitrogen cycle is by seeding bacteria from a healthy established aquarium. This can be done by adding gravel, decor, or filter media from a parent tank. This method is also referred to as seeding your aquarium; you are “planting seeds” of good bacteria into your new aquarium.

The best thing to use to seed a new aquarium is filter media. This is because it is porous and receives a lot of water flow. Thus most of the bacteria will live here.

Take a piece of this filter media (bio rings, filter sponge, or even charcoal filter) and place it in the filter compartment of your new aquarium.  It’s as easy as that.

Alternatively, I have also taken some gravel from an established aquarium and put it in the new filter compartment.

While this is an excellent method, the item from the established aquarium cannot come from just any aquarium. There could be a variety of diseases and pathogens such as Ich present. Thus it should come from one of your already established aquariums or from a trusted friend. Sometimes the store where you purchased fish will be able to offer you a seeding item.

If you don’t have a good source read on as there are products designed to seed your aquarium as well.  

Commercial Bacteria Starters

There are a variety of commercially available bacteria starters available. Most of these are in liquid form but some aquarium substrates also come with nitrifying bacteria. These are a good choice for most people who do not have a source of “seed” material from an established tank.

While these certainly jump start your aquarium you still need to be cautious. Many of these products advertise that you can immediately add fish. Even so, it’s best to go slow. Add a small number of fish and monitor your water quality for at least a couple of weeks.

If your ammonia and nitrite levels are 0 after this time period feel free to fully stock your tank.

Tips For Success

You will need to monitor the ammonia and nitrite levels during this process with a water test kit. These are relatively inexpensive and can be found online or at most pet stores. When both ammonia and nitrite levels are 0 ppm the aquarium is cycled and it is safe to add all your fish.

Below are some other tips to ensure your success. 

  • Provide somewhere for the bacteria to live and process the nitrogen. This is usually in the filter compartment. Add some bio rings or a filter sponge if there is room. These porous surfaces give your bacteria plenty of surface area to live
  • Dechlorinate your water if you are on a municipal water supply. Treated water contains chlorine which is harmful to beneficial bacteria and fish. 
  • Heat the tank water to 80°F/27°C or a little higher. This warm water will allow the bacteria to replicate and grow more quickly. You may need to decrease this temperature back down before you add fish.
  • Provide adequate oxygen. The bacteria need oxygen to complete the nitrification process. So add a bubbler if you don’t have one already

Final Thoughts on the Nitrogen Cycle

If you made it this far you understand that this can be a somewhat complicated process. There are also a variety of ways to condition your tank correctly.

While it is important to get the cycle started correctly don’t let worry stop you. Pick a method and start enjoying the difficulties and joy of fishkeeping today!

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