How to Cycle an Aquaponics System: Aquaponics Startup


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The entire process by which aquaponics works is made possible by bacteria. They form the link between the symbiotic relationship both fishes and plants share.

Cycling in an aquaponic system is the process by introducing and cultivating a healthy bacteria population within the system before plants are added. It aids in the colonization of nitrifying bacteria required to break down the ammonia from fish waste to nitrates for plants to use.

Aquaponics systems can produce plants that can be harvested in short periods of time because of the constant amount of nutrients the system provides on a continuous basis to the plants. 

Before the plants are added to the system we firstly have to introduce the bacteria which produces the nutrients for the plants to grow. There are a few ways which we can do this and in this article we will discuss how to cycle an aquaponic system and what to pay attention to when cycling.

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What is Cycling in Aquaponics?

Cycling in aquaponics refers to the process by which nitrifying bacteria is added to a new system. The water is cycled or circulated in the system for a period of 2 to 6 weeks, allowing nitrifying bacteria to colonise the system. 

You keep reading the term nitrifying bacteria. But what kind of bacteria is nitrifying bacteria? 

Nitrifying bacteria, nitrosomonas and Nitrospira are bacteria which convert nitrogen compounds, in this case ammonia, into less harmful compounds such as Nitrites and Nitrates in a two step process.

How the Nitrification Process Works- 

The Ammonia compound (NH3) is broken down into Nitrites (NO2) by the nitrosomonas bacteria which is the first of a two step process. Nitrites are not used by plants and are also toxic to fishes. The second step of the process involves the Nitrospira bacteria which feeds on the nitrites and converts it into Nitrates which is beneficial to the plants.

In order for the ammonia (NH3) to be converted to nitrates (NO2). You will notice that the nitrogen (N) is broken from the ammonia and added to an oxygen (O) to make nitrite (NO2). This oxygen comes from the dissolved oxygen in the water. 

Dissolved Oxygen in the water is added by using an air pump which injects a stream of air into the water through air stones. The air stones then breaks the air into smaller bubbles which increases the surface area increasing its ability to be dissolved into the water. 

Here’s a detailed article on how to choose an air pump for an aquaponic system. 

Plants can only use nitrates to grow. Nitrates is a useful form of Nitrogen (N) and is one of the three macro ingredients which plants require to grow. (N, P, K). The Nitrogen helps plants produce green leafy branches which is why some plants such as lettuce, cabbage, cucumbers and Pak-Choi are best suited for aquaponic systems.

Nitrifying bacteria, nitrosomonas feed on ammonia to survive and will start showing up when the ammonia concentration in the system begins to build. As a result, the nitrites begin to build. As the Nitrites builds, this attracts the Nitrospira bacteria which breaks down the nitrites into Nitrates.

As these bacteria colonies are being established, plants can be added to the system.

Cycling can be done with or without fishes and we will discuss these later on. 

Graph of Nitrogen Cycle

How to Cycle an Aquaponic System?

In order to cycle an aquaponics system you firstly have to get the system fully set up. This means that the fishtank, mechanical filter, biofilter, sump and the plant system should be ready to have water circulating through them.

Once that is done you will need to fill the system with water. If you are using pipe borne water supply, the water should be allowed to settle for a short period of time to ensure that there isn’t any residual chlorine present in the water.

Both the water pump and the air pump can be started at this time. This will also help in conditioning the water and will speed up the process. The system should also be checked for leaks during this time. Small leaks can be fixed by use of aquarium grade silicone.

The fishes can now be added to the system. However, before they are added, you should allow them to acclimatize to the system water by placing them into the water after both the transporting water and the system water temperature are about the same. This is done to prevent sudden shock to the fishes.

At this point you should have air injection and water circulation taking place with the fishes in the system.

Monitor the fishes to ensure everything is ok and then you can start feeding them. 

As the fishes are being fed they will tend to produce waste. This is vital and will add the ammonia naturally in the system.

Now with everything setup and in service the cycling process has begun.

How do you Know When the Cycling Process is Taking Place – Testing Tools Required

An easy way to know when the cycling process is taking place is by testing. Testing can be done by the use of a water quality test kit.

We use the API Freshwater Master Test kit for the majority of our water testing. With this kit we can test high pH ranges, ammonia, nitrite and nitrate levels in the system. Each compound has its own respective color with its corresponding ppm concentration valve.

When the system is started you should do an initial test and note the test results to compare as time goes by. Each test result is compared to the color chart to determine the exact concentration of the compound being tested.

Note: All the various tests should be done at the same time to compare the results.

Initially, when cycling is started you will notice all the test colors are very light since there are small amounts of ammonia, nitrites and nitrates in the system. As the cycling advances and the fishes produce more waste the ammonia concentration will continue to build. This will show as the ammonia test result gets a darker green. This occurs until the ammonia concentration gets to a shade of green and doesn’t get any darker. Which leads to the next step of the process. 

As the ammonia concentration increases the bacteria will also build. The nitrosomonas bacteria will start to feed on the ammonia. This will cause the darker green ammonia test color to get lighter with time. At the same time the lighter nitrite colour will also begin to get to a darker purple as the ammonia color gets to a lighter green.

This would indicate that the nitrosomonas bacteria is doing their job by converting the ammonia to nitrites. 

As time passes, the Nitrites will follow the same pattern as the ammonia. The darker purple would tend to get lighter as the Nitrospira bacteria converts the nitrites into nitrates.

This would be shown as the nitrate test color turns from a lighter yellow to an orange and then a light red. 

When to Add Plants to the System?

Plants can be added to the system after the first week of cycling. This is recommended because you don’t want the nitrate compounds to build to an excessively high level before the plants are added. 

The plants can use the nitrates as they are being produced preventing excessive build up and perpetuating further nutrient conversion to take place.

How to Cycle an Aquaponic System Faster?

  1. Adequate aeration 

    Excess air can add that much needed oxygen required by the bacteria to convert the ammonia into nitrite and then nitrates. 

    The oxygen acts like a catalyst and stimulates the bacteria to carry out the Nitrification process. 
  2. Using ammonia chloride

    The process can be sped up using ammonia compounds such as ammonium chloride. The ammonium chloride is added in very small quantities at a time. 

    Adding this with fishes can cause ammonia spikes which can lead to fishes dying. Therefore, I would suggest that this method of speeding things up be done without fishes in the system. 

    With each addition the ammonia concentration should be measured until it reaches between 4 to 6ppm. This is then allowed to be cycled over a 6 week period. 

    Adding a quantity of water already colonised by nitrifying bacteria you can significantly speed up the process.
  3. Ensuring the pH is at 6.8

    During the initial stages as the amount of ammonia in the system increases the pH will tend to increase. 

    It is important to check the pH values during this time and try to bring it to the desired levels after cycling is completed. Lowing the pH can be done by use of pH lowering additives such as  API pH DOWN pH adjuster. 

    This should be done slowly to prevent overshooting and lowering the pH to dangerously low levels. 
  4. Keeping the water temperature warm

    Bacteria thrives in warm temperatures and produce the best results at temperatures between  77-86 F (25-30 C). Therefore, summer months are the best time for cycling an aquaponic system. 

    So just a precaution, you should not be cycling an aquaponic system during colder months or winter. If you have to cycle during these times you should use heaters to maintain the water temperature. 

Cycling Without Fishes

Cycling without fishes can be done using the same method as discussed above where you introduce an ammonia compound such as ammonium chloride into the water in small amounts. 

As with cycling with fishes, the water quality should also be monitored to ensure that there is proper pH, temperature and dissolved oxygen within the system. 

How Water temperature Affects Cycling?

Temperature can affect how fast the cycling process takes. These bacteria are living organisms; they tend to display similar traits as any other animal. In colder temperatures they are less active and the process takes longer. In warmer temperature water the process occurs much faster as the beateria are more active providing that there is enough “food” or ammonia for them to convert.

The water temperature is a key factor in the cycling process and it was found that the optimal temperature for cycling was between 77-86 F (25-30 C). At these temperatures the nitrifying bacteria showed the most activity meaning that the greatest amount of ammonia is converted to nitrates at these temperatures.

Common Cycling Mistakes and Correction

MistakesCorrections
Temperature below 70FMaintain Temperatures betwwen77-86 F
pH too low – below 6.0pH should be kept at 6.5 to 7
Too much ammoniaAmmonia concentrations kept between 4 to 6 ppm
Lack of oxygen – Slows Bacteria activityKeep system Aerated using an air pump
Too less cycling timeCycling should be between 2 to 6 weeks

JayLea

JayLea has a passion for plants and has been gardening since 2015. He has valuable knowledge about gardening and houseplant care and can answer everyday practical questions that every plant owner has.

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