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Episode 14: The Nitrogen Cycle

Show Notes

Today we’re going to discuss the nitrogen cycle. The nitrogen cycle can be confusing, so today we’re going to explain it in a way that is simple and understandable.
Before we get started, I want to remind you that reviews are important to us. They help us expand the reach of this podcast.

The Basics of Nitrogen

Nitrogen exists in systems in different forms- usually as a gas or as a solid. When we talk about solids, we’re talking about fish solids, dead organisms, really anything that is releasing nitrogen through metabolism or through decaying.
Nitrogen is a key nutrient to plants and animals, especially in aquaponics systems. The availability of nitrogen is a deciding factor of the productivity of your system. It’s also the main player when it comes to problems with your system.

Enter the nitrogen

Nitrogen enters the system as a protein- usually through fish food. You can influence how much nitrogen goes into your system by choosing feed with higher or lower protein content and by changing how much you feed.
All of the processes that nitrogen goes through is mediated by microbes. It starts when the fish consumes the food, and as it is digested in the gut, broken down into amino acids that the fish can use. (Many of the proteins pass straight through and enter the system as organic solids.) One main product of this process is ammonia.
In mammals, ammonia is processed into urea, which is easier for us to use because it has a charge. Ammonia, on the other hand, is neutral.
Ammonia leaves the fish and moves into the water by a diffusion gradient; it moves from an area of high concentration (inside the fish) to an area of low concentration (the water). If there is not a good diffusion gradient, this process can get messed up and revers. (If the water already has a high concentration of ammonia, the ammonia inside the fish will not move out, and will end up poisoning the fish.)
All of these processes are performed by bacteria. This speaks to the importance of bacteria- as the engine of the system, they are also at the core of most problems. You can support bacteria by providing them with a good habitat (lots of dissolved oxygen, CO2, and BSA.)

Ammonia/Ammonium (NH3 to NH4)

If you haven’t already, check out our video on ammonia on our Youtube channel.
Ammonia has no charge, so it can move across membranes; this includes fish, which are negatively affected at about 2 ppm. Most fish will die at around 5 ppm. Ammonia is nasty stuff that you don’t want in your system in higher amounts than are absolutely necessary. If your plants are leggy, it’s possible that you have too much ammonia in your system.
Ammonia’s magic number: Less than 2 ppm

Ammonia to Nitrite (NH3 to NO2)

Ammonia is turned into nitrite (NO2) through a oxidation reaction performed by a bacteria called nitrosomonas. It’s often call nitrosofication. Nitrite has a negative charge and is actually even more poisonous than ammonia. Ideally, both ammonia and nitrite are oxidized very quickly so that it doesn’t have the chance to harm your organisms.
Nitrite’s magic number: Less than 1 ppm, ideally less than .5 ppm

Nitrite to Nitrate (NO2 to NO3)

This is performed by bacteria- especially nitrobacter, which oxidizes NO2 into NO3, nitrate. It’s relatively non-toxic to fish and is the end product that we’re looking for.
Nitrate’s magic number: up to 160 ppm (You can tell that you have too many if your fish start getting lethargic.) Note that high nitrates means more aphid problems.

Hydronium ions

Because NH4 ends up being NO3, you end up with a lot of hydronium ions as a bi-product. Hydronium ions essentially acidify your solution, so as nitrification happens, your pH is dropping. This is why system tend to get more acidic over time. You need to be aware of this so that you can adjust pH accordingly. If your pH is high, this can be the most effective way to get that pH back down.


De-nitrification only happens if you have anaerobic zones. This is not likely to be a problem, but if it is, look for decaying organic matter and get it out.

How does nitrogen leave the system?

Minimize these causes of nitrogen loss as much as possible:

  • Harvesting plants
  • Harvesting fish
  • Water changes & leaks
  • De-nitrification
  • Algae use

Tips on managing nitrogen:

In a smaller system, if a fish dies, stop feeding for at least a day. This is because fish death causes a peak of ammonia, which created ammonia stress, and fish will not feed.

Temperature: the rate of microbial processes are affected by temperature. Warmer water speeds up the process and cooler water slows it down.

BSA: High BSA supports microbial populations and allows nitrification to happen quickly.

Intermediate cycles: when nitrogen is used in other life cycles, like duckweed or crayfish, it leaves less control over the nitrogen cycle.

Inputs: high protein feed (fish meal is your friend) causes more nitrates, and low protein feed means fewer nitrates.


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