Maintaining A Healthy Bacterial Colony In Aquaponics

An aquaponics system relies heavily on nitrifying bacteria in preventing fish waste from reaching toxic levels. As bacteria serve as the bridge that connects fish waste to the plant fertilizer, making it possible for the plants to filter the water in the system.

Therefore, the parameters that affect bacterial growth should be considered in maintaining a healthy aquaponics system. This blog will discuss the importance of bacteria and how to maintain a healthy bacterial colony to get your aquaponics system up and running.

The Nitrifying Bacteria

The nitrifying bacteria are an essential component for the nitrification process that converts fish waste into nutrients for the plants. The nitrifying bacteria convert fish wastes, which enter the system as ammonia, into nitrates, which is fertilizer for the plants. This process involves the two groups of nitrifying bacteria, the Nitrosomonas and Nitrobacter. Nitrosomonas and Nitrobacter are important microorganisms that help keep an aquaponics system in balance. 

  • Nitrosomonas: Excess ammonia is produced in the water when there is too much fish waste and fish food wastes in the fish tank. The role of Nitrosomonas bacteria is to convert ammonia into nitrites. However, excessive nitrites can be fatal to the fish, so nitrites must be converted into nitrates.
  • Nitrobacter:  Nitrobacter feed on nitrites, and once Nitrobacter bacteria consume these nitrites, they are converted into nitrates. Nitrates become food for the plants to grow healthy in an aquaponics system. 

The process of converting fish waste into ammonia, then into nitrites, and finally into nitrates is called the nitrogen cycle. Nitrification in aquaponics provides nutrients for the plants and eliminates ammonia and nitrites that are toxic to the fish. Nitrification helps in establishing a healthy bacterial colony, which is essential for the proper functioning of an aquaponics system.

Nitrifying Bacteria In Aquaponics

Sourcing for the Nitrifying Bacteria

Nitrifying bacteria exist naturally in water and air and will colonize a new aquaponics system once system cycling is started. The nitrifying bacteria can be sourced in the following:

  1. Aquaponics and aquarium stores sell several liquid forms of nitrifying bacteria.
  2. Water, or biofilter materials from a mature and balanced aquaponics system.

The liquid forms of nitrifying bacteria can help establish a bacterial colony fast, but it is an option and can be difficult to source. The best way to start system cycling is using water or materials from an established and disease-free aquaponics system.

System Cycling

System cycling is the establishment of nitrifying bacteria colonies in new aquaponics systems. Cycling is necessary to allow the bacteria to colonize a newly built system. System cycling consists of gradually adding ammonia to the newly built aquaponics system. Adding ammonia provides food for the nitrifying bacteria and encourages the establishment of a bacterial colony. This method can be done with or without fish. The reproduction of nitrifying bacteria is relatively slow, so systems cycling can take two weeks to two months, depending on the method used. 

Parameters that Affect Bacterial Growth

The nitrifying bacteria are relatively slow to reproduce and establish colonies. It requires days and sometimes weeks to occur, so patience is essential in establishing a new aquaponics system. Many aquaponics farmers failed to maintain a healthy bacterial colony because of adding too many fish into the system before the bacterial colony was fully developed. Several parameters affect bacterial growth in an aquaponics system that should maintain a healthy bacterial colony. These parameters are:

1. Surface Area

Bacteria thrive in the surface area within the system. These surface areas are the grow media, commercial plastic biofilter balls, plant roots, fish tank walls, inside the pipes or rocks that are usually on the bottom of the fish tanks. The total available surface area for the bacteria to establish a colony will determine how much ammonia they can metabolize.

Depending on the system design and fish biomass, the plant roots and tank walls can provide enough surface area. To maintain a healthy bacterial colony, aquaponics systems with high fish stocking density require a separate biofilter where materials with a high surface area are contained. A large biofilter cannot harm an aquaponics system but would add additional expenses to the farmer.

2. Water pH

pH is how basic or acidic the water in the system is. The water’s pH level impacts the biological activity of the nitrifyingbacteria and their ability to convert ammonia and nitrite. The ideal water pH level range for an aquaponics system is 6-7 because this range is a compromise between all the living organisms within the system. The nitrifying bacteria also functions adequately between 6-7 pH level, and any decrease in bacterial activity has a negative effect on the system.

3. Water temperature

Water temperature is an essential parameter for bacteria and aquaponics. The ideal temperature range for bacterial growth and productivity in an aquaponics system is 60-85 F (15-34C). Bacterial productivity will decrease if the water temperature range drops below 17C (62F). Low temperatures will have a significant impact on maintaining a healthy bacterial colony. This is why it is essential to monitor the nitrite level during winter. 

4. Dissolved Oxygen

To maintain a high productivity level, nitrifying bacteria needs an adequate level of dissolved oxygen (DO). To ensure that an aquaponics system has adequate biofiltration, the level must be at an ideal level, which is 4-8 mg/liter. This level is also the level required by the plants and fish. It is recommended to add aeration through the flood and drain cycle in the grow beds or by air stones in the external biofilters to ensure that biofilters have enough biofiltration.

5. Ultraviolet Light

If you’re using an external biofilter, make sure that it is in a shaded area. Nitrifying bacteria are photosensitive organism, and sunlight can cause harm to the biofilter. In a new aquaponics system, the UV light from the sun can damage bacterial colony formation.

One way of solving this problem is to cover the fish and biofilter with UV protective material to ensure that no water in the system is exposed to the sun until the bacterial colonies are fully formed. Once the bacteria have colonized a surface, this cover can be removed because the UV light can no longer cause a problem in the system. 

Water Quality Test In Aquaponics

How to Maintain a Healthy Bacterial Colony

If all of these parameters are in their ideal range or level, then the bacteria present in an aquaponics system will function properly. The bacteria are so essential in aquaponics that it needs to be monitored to ensure that they are healthy.

In a well-functioning and balanced aquaponics system, the ammonia and nitrites should always be 0-1 mg/liter. If they are not at their ideal level then, it indicates a problem with the nitrifying bacteria. Issues with nitrifying bacteria show problems in the water quality or imbalance system. To maintain a healthy bacterial colony in your aquaponics system, it is essential to monitor the water quality by regularly doing a water quality test to see if the parameters are within their ideal range or level. 


In growing a healthy bacteria colony, it is essential to create a bacteria-friendly environment in your aquaponics systems that will encourage the growth of nitrifying bacteria. A healthy bacterial colony means a healthy and successful aquaponics system. So cycle your newly built aquaponics system properly and maintain a healthy bacterial colony to ensure the success of your aquaponics system. Thank you for reading our article; subscribe to our mailing list to get aquaponics updates.

1 Response



February 08, 2022

I thought of raising the nitrifying bacteria at home in a barrel with some fish and components of a biofilter and a swirlfilter. Leave this for week or months and obserb the nitrificstion provess. When the nitrification frocess is completed and the nitrifying bacteria colonized the water in barrel i can use the water and the materials from the biofilter to start the system circling of my aquaponics system. This may takes time. Does this makes sence? Can anyone help?

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