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Show Notes

Today we’re going to talk about microbes and the role that they play in your system’s nutrition. My goal is to give the overview that you need to go out and find the detailed information that you need to

A lot of people see aquaponic systems as aquaculture systems – fish-based systems, that is – that have plants and microbes. Or they see it as a plant-based system that uses fish and microbes. In reality, aquaponic systems are microbial systems that use fish and plants. 

 For this reason, it’s extremely important to understand microbes and how they perform within the ecosystem of your system.

How do microbes affect nutrition?

  • They absorb nutrients 
  • They  release nutrients
  • They free nutrient from organic compounds
  • They nitrify (oxidation)

Microbes are an incredible part of the nutrient cycle, and they’re involved with every part of the nutrition system.

Every organism is involved in trading electrons, but microbes trade electrons on a much more fundamental level. 

I hesitate to make generalizations about this diverse group of organisms, but I will say that for most of the decomposers and bacteria in our system that take organic matter and break it down, they’re doing to gain electrons and nutrients. 

Microbes form very specialized relationships with the plants and in the system, often doing a great portion of the heavy lifting in the nutrition cycle. (This is true of any system in the world.) 


Mineralization is essentially taking an organic compound and breaking is down into simpler compound. Often this means going from proteins to amino acids and amino acids to ammonia, then ammonia into nitrates. It can also mean breaking down compounds that contain phosphorus, potassium, etc. in a way that makes them plant available; mineralizing them.

There are two types of mineralization: the kind that takes place in aerobic environments, and the kind that takes place in anaerobic environments. 

Mot grower shoot for very aerobic environments. But some nutrients only become available in anaerobic environments. Iron is a tricky one since it becomes insoluble when exposed to oxygen, so we need some anaerobic decomposition. Now it’s something we want to be really careful about, but it’s important to note that some microbes function in anaerobic environments.

Another note too make is that red worms play a role in the system and can speed the process up. Red worms function as little bioreactors; a delivery system for gut microbes. In that contained and highly moderated environment, those microbes break solids down. This is beneficial because the amount of water soluble nutrients in the those worm castings is much higher than some of the other microbe interactions. This can speed up many nutrient cycles. 

Disturbance of microbe ecologies

Microbes, as a diverse group of organism, can form sub-ecologies on their own, each of which serve important roles both to each other and to the other organisms within the whole aquaponics systems.

This means that after a disturbance of the system, some of those ecologies can crash, which in turn effects the fundamental functions of your system.

This disturbance could be a change in pH, a change in temperature, physical disturbance of water or growing medium, etc. 

On the other hand, if you give your microbes the most steady, predictable habitat possible, you end up with much more stable and productive systems.

So how do we do that? What do microbes need?

Remember that microbes consume dissolved CO2, carbon compounds (ammonia) to break down, and lots (and lots) of oxygen.

Remember that as you add organic materials to your system, more oxygen is consumed, so adding organic matter to fast (like in compost tea, for example) an crash your oxygen and cause anaerobic environments on a large scale across your system. This means that you must understand how adding things to your system will affect your microbes.

For instance, overfeeding your fish can cause them to become oxygen starved. This is because you are not only causing a bump in a ammonia, but a drop in oxygen due to increased microbial activity. 

Microbes also impact pH, mostly through nitrification reactions in an aquaponics system. There are also other reactions that are releasing hydrogen ions into the system (acidifying solution) and many other reactions that drive pH down unless you have a lot of carbonates. For those who struggle with pH control, microbes are at the heart of the problem… and the heart of the solution. So think about how you can manipulate microbial populations to drive pH.

Another thing to think about is temperature. While many reactions in the microbial populations drive some heat, microbes don’t usually change the temperature significantly. Temperature does, however, have an affect on the speed of reactions. Think back to biology class… enzymes are used to speed up reactions. Microbes use enzymes quite often to speed up reactions. Temperature affect this because as temperature goes down, oxygen becomes less soluble in water. But as temperature goes up, enzymatic reactions (typically) increase.

In conclusion

Remember as you manage your system that every action you take impacts the microbes in your system, whether that action is feeding, moving stuff around, and even harvesting. Being aware of this will help you to keep your system stable and productive.

I hope that this is food for thought. If you have any questions about this stuff, we’d love to hear from you. You can read more about microbes and hear more great information on our Youtube channel and on the Bright Agrotech blog.


Thanks for joining us today! Stay tuned for more on nutrients in aquaponic systems.

View all our episodes here.

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