Aquaponics 4 – Building with bacteria

In ProAgri Zambia 32 we focused on two of the main building blocks of an aquaponic system, namely aquaculture (fish) and hydroponics (plants), and we compared it with traditional aquaculture and hydroponics.

In this issue we focus on bacteria as the third building block. To recap we shall briefly discuss aquaculture and hydroponics:

Aquaculture is the breeding, rearing, and harvesting of fish, shellfish, plants, algae and other organisms in all types of water environments. As our natural marine fish resources are becoming more and more depleted, farming with fish is becoming more important world-wide, showing exploding exponential growth. Methods include cages in the sea, rivers or dams, or dams specifically built to cultivate fish.

One of the challenges fish farmers face is water usage. In a traditional aquaculture system up to a third of the water has to be replaced regularly and everything has to be kept clean and sterile.

Hydroponics is a method of growing plants without using soil. In a traditional hydroponics system plants receive their nutrients through the application of growth mixes and chemical fertilisers. It is normally a single crop system because fertilisers are mixed for specific plants.

The waterflow systems include drip irrigation, nutrient film technique (NFT), deep water culture (DWC), ebb and flow and aeroponics. Hydroponics are usually practiced undercover in tunnels and nethouses with different degrees of climate control. It is an intensive form of farming, initially needing a lot of capital expenditure, but it delivers much higher yields per square meter than traditional soil based systems.

In a hydroponic system everything must be kept in a sterile state, and bacteria are not welcomed. Another challenge for hydroponic farmers is water usage. Once the water has run through the system, it usually has to be discarded or sterilised as one cannot be sure which nutrients have been used and what still remains in the water. The water may also contain harmful pathogens which it picked up on its way. So, clean water and a new batch of fertilisers are used every time.

In aquaponics you have to unlearn a lot of what you have learnt in traditional aquaculture and hydroponics. Suddenly bacteria become your best friends!

There are three basic bacterial systems at work:

Nitrification system

In this system ammonia is converted into useful nitrates, with an increase in acidity (in other words low pH rates). Two types of bacteria are always active when there is ammonia (NH³) present in nature, such as the ammonia released through fish gills. The more the ammonia, the more bacterial growth.

Nitrosomonas Bacteria: It changes ammonia into nitrites (NO²). Nitrobacter Bacteria: As soon as there is nitrite, these bacterias start to grow, changing the nitrites into nitrates (NO³); the nutrients plants need.

The nitrification process starts in the biofilter or bacteriological system where little plastic units (K2) are placed to enlarge the surface area to promote bacterial growth. When you start with an aquaponic system, you need time to “cycle up” the system, which means that you need to let the bacteria grow and do their work.

You do not need to add anything; all you need is for your fish to breath.

Bacteria will eventually grow on any surface in the system, it cannot be contained in a biofilter, and you also do not want to contain it. It is a case of the more, the merrier!

NB: Too much ammonia and nitrites in the water will kill the fish. Nitrite is toxic to tilapia at 5 mg/litre. Nitrate is less toxic, but can cause discomfort – the level should be below 300 mg/litre.

Nitrosomonas europaea is an obligate gram-negative chemolithoautotrophic ammonia-oxidizing Bacteria. TEM
Nitrobacter under a microscope. Photo:


This is the reverse process through which nitrates are converted into nitrogen gas causing alkaline conditions. This usually happens when anaerobic bacteria take over. You do not want this to happen, therefore it is important to limit the growth of anaerobic bacteria as far as possible. They tend to thrive in places where there is not regular movement of water and oxygen.

Heterotrophic bacteria system

This is the breakdown of solid organic material, such as fish waste and unused fish food, to release carbon dioxide, ammonia and inorganic material.

The solid organic material can be collected just after the outlet of the fish dam by using filters or swirl tanks in which the water slowly spins out leaving the solids at the bottom. The solids should be moved to a seperate tank for the breakdown process.

This process can be assisted by adding air and an activant which promotes aerobic bacterial growth (such as a composting agent). In an aquaponic system this is known as the mineralisation process and the mineralised water runs back into the system to add even more nutrients for the plants.

The remaining solids should be removed from the system. If gravel beds are used in a system, earthworms between the stones will also help to process the solid organic material that slipped through the filters.

Anaerobic bacteria under a microscope. Photo:
Anaerobic bacteria under a microscope. Photo:


There are many other forms of micro-life keeping nature in balance. In aquaponics we invite them in.

The organisms include fungi, algae, zooplankton, phytoplankton, nematodes and many more. The beauty of aquaponics is that it is a true ecosystem, so we encourage a diversity of naturally occurring elements. Eventually all contribute to the nutrients available to the plants.

The aquaponic cycle is all about the nitrification of the ammonia breathed out by the fish and the breakdown of solid organic fish waste to provide the nutrients for the plants. Healthy clean water is returned to the fish without any waste along the way.


Aquaponics is the integration of the three systems described above, namely aquaculture, hydroponics and bacteria to form a complete ECOSYSTEM.

The water is circulated the whole time; no part of the system functions in isolation or on its own. For example, the bacteria do not just stay in the biofilter where it is encouraged to grow, you will find it throughout the whole system. In the plant system you will find bacteria, lots of microbes and algae.

This is normal, as long as there is biological balance in the system. If you put your hand in the water, it should look like tea!

Bremner, CD & Bremner A, Introduction to Aquaponics, Kleinskuur Aquaponics Training Manual, 2017, Unpublished.

Algea under a microscope. Photo:
Daphnia Zooplankton under a microscope. Photo:
Holopedium Zooplankton under a microscope. Photo:

Phytoplankton. Photo:

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