Bacteria's Role In Aquaponics - Go Green Aquaponics

Bacteria's Role In Aquaponics

The first thing that comes to mind when people think of an aquaponics system is thefish and plants, as we often define aquaponics as a combination of raising fish and growing plants. However, bacteria is an equally important component of your aquaponics system. It is vital to have all the three components; fish, plants, and bacteria, to run a successful aquaponics system.

Close up Microscopic Bacteria

The Role of Bacteria in Aquaponics

An aquaponics system requires beneficial bacteria in order for the fish and plants to thrive. Bacteria break down the fish waste, keep the water clean for the fish, and turn the fish waste into a usable form ofnutrients for the plants. The plants remove the nutrients from the water, which then helps to clean the water for the fish to live in. Before the plants can absorb the nutrients, the nutrients must be converted into nitrates.

Bacteria usually live on the bottom of the fish tank and on the grow media in the grow beds. Fish waste and excess food settle at the bottom of the tank and the bacteria work on breaking down this waste. 

The Nitrification Process in Aquaponics

The nitrifying bacteria plays an important role in an aquaponics system. The nitrifying bacteria convert fish waste, which enters the system as ammonia into nitrates, that fertilizes the plants. Nitrification in aquaponics is a two-step process and involves two nitrifying bacteria:

1. Converting Ammonia Into Nitrites- This is done by the Nitrosomonas when there is an overload of food waste, it produces excess ammonia in water. Ammonia must be removed to keep the fish healthy. Nitrosomonas bacteria convert the ammonia into nitrites. 

2. Converting nitrites into nitrate- This is done by the Nitrobacter. Nitrobacter bacteria feed off nitrites. The nitrites are converted into nitrates once the nitrites are consumed by nitrobacter. Plants grow rapidly when they absorb nitrates. Excessive nitrites can kill the fish. In order to keep the fish and the plants healthy, nitrites must be converted into nitrates.

Nitrifying bacteria is slow to reproduce and establish colonies; It may take days, weeks, or even months. Nitrifying bacteria requires a dark location, good water quality, and adequate food and oxygen to colonize. There are five key parameters to support nitrifying bacteria. If these parameters are observed, it will be safe to assume that the bacteria are present and functioning well.

1. High surface area

Bio-filtration with a high specific surface area is important to develop extensive colonies of nitrifying bacteria. There are many materials that can be used in aquaponics, either as growing media or for biofiltration. Volcanic gravel,expanded clay pebbles, commercial plastic bio-filter balls, and plant roots all act as a surface area for the bacteria to live on. The smaller and more porous that the particles are, the greater the surface available for bacteria to colonize, which will cause a more efficient biofiltration.

2. Water pH

Nitrifying bacteria function properly when the pH levels are between 6 and 8.5. The ideal pH in aquaponics is usually 6-7, which is a compromise between all the organisms in the system. 

3. Water temperature

The ideal temperature range for the bacteria is 63 °F - 93 °F. This range encourages growth and productivity for bacteria. If the water temperature drops below this range, it will decrease the productivity of the bacteria. 

4. Dissolved Oxygen

Nitrifying bacteria needs an adequate level of dissolved oxygen in the water to grow healthy and maintain productivity. The optimum level of dissolved oxygen is 4 - 8 ppm. Nitrification does not happen if the dissolved oxygen concentration drops below 7.0 ppm. You can ensure adequate bio-filtration and dissolved oxygen by adding aeration by using either air stones or through flood-and-drain cycles in media beds. 

5. UV light

Nitrifying bacteria is photosensitive until they are fully established, and sunlight can cause harm to the bio-filter. Media beds protect the bacteria from the sunlight, but if you’re using a biofilter, keep it shaded from direct sunlight. 

Unwanted Bacteria

Nitrifying and mineralizing bacteria are important and useful to aquaponics, but there are some types of bacteria that are harmful to an aquaponic system, these are:

1.Sulphate-reducing bacteria

These bacteria are often found in anaerobic conditions and have an odor of rotten eggs. These bacteria have a grey-black color and grow only in anoxic conditions. It is important to provide adequate aeration and to increase mechanical filtration to prevent the accumulation of these bacteria. 

2. De-Nitrifying bacteria

These bacteria also thrive in anaerobic conditions and are responsible for denitrification. They convert nitrites back into atmospheric nitrogen that is unavailable to plants. In aquaponics systems, these bacteria can decrease efficiency by removing the nitrogen fertilizer. 

3. Pathogenic Bacteria

These bacteria can cause diseases in plants, fish and humans. It is important to have good gardening practices to minimize the risks of diseases in an aquaponic system. You can prevent pathogens from entering the system by keeping household pets, animals, and other fish away from your system. Placing your aquaponics system in an enclosed greenhouse will also help to prevent pathogenic bacteria from entering your system.

Fish in Aquaponics Fish Tank

System Cycling and Creating a Biofilter Colony

System cycling in aquaponics refers to establishing a healthy bacteria colony when starting your new aquaponics system. Cycling takes place once a new aquaponics system is built and usually takes 3-5 weeks. The process involves introducing an ammonia source (usually fish) into a new aquaponic system, feeding the new bacterial colony and creating a biofilter. The progress of your cycling is measured by monitoring nitrogen levels.

Without bacteria, the nitrogen cycle will not occur. The nitrogen cycle transforms the ammonia from fish waste into nutrient-rich fertilizer for plants. The nitrogen cycle will only take place when the nitrifying bacteria is present. For cycling to occur, ammonia must be added to the system. This ammonia can be added using the fish or using water from another aquaponics system where the bacteria colony is already established. As more ammonia is added, more bacteria are produced, which makes the system work efficiently. Once ammonia converting bacteria is established, it produces nitrites, which allows the bacteria to use nitrites and produce nitrates. A system is fully cycled once ammonia or nitrites are measurable during testing. 

Fishless Cycling 

This process is often used in new aquaponics systems or tanks because it can be done without concern related to the safety of the fish. To begin fishless cycling, you need to introduce ammonia without fish waste using anammonia solution

The process is simple; after the system is set up, begin by adding the ammonia solution to the water in the tank. The tank is fully cycled once the tank gets to the 0.2 ppm level. Once fully cycled, additional freshwater and fish can be added. 

Ways to Reduce System Cycling Time

System cycling is a slow process, but there are other ways to get your system quickly established. One method to get your system quickly established is to use water from another aquaponics system where the bacteria colony is already established. It is very helpful to share a part of the biofilter as a seed of bacteria to a new aquaponics system. This decreases the time necessary for cycling the system. Some prefer to add a little urea or a dead fish into the tank to start the decomposition process. Household ammonia products can also be used, but be sure that the product is 100 percent ammonia and does not include other ingredients like detergents or heavy metals that could damage the entire system.

Once ammonia and nitrite levels are below 1 ppm, you can start addingplants and fish to the system. Start adding the fish slowly, continue monitoring the levels of nitrogen, and be prepared to water exchanges if ammonia or nitrite levels rise above 1 ppm while the system continues to cycle.


Bacteria are the little microscopic creatures that do all the work in an aquaponics system by converting fish waste into food that the plants can absorb. Without them, the system would fail, the fish would die, and the plants won't grow. Bacteria are equally important as the fish and the plants in an aquaponics system. Subscribe to our Newsletter to stay updated on all the aquaponics related news, products, and content.


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