Nitrification- The Motor of Aquaponics

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Nitrification is the process that drives most aquaponic systems, and yet, it is oftentimes poorly understood- even by experts. *

Nitrogen in Aquaponics

nitrogen in aquaponicsNitrogen is one of the most important plant elements, but making it available depends very closely on the ability of system bacteria to add oxygen to ammonia and nitrite (both toxic) to produce nitrate- a relatively benign form of nitrogen that is plant available.

This process of oxidation is known as nitrification, and it serves a number of secondary functions in the system as well, including acidification of the system water.

You see, as the bacteria oxidize ammonia and nitrite, they release hydronium ions into the solution, making the system more acidic naturally.

For people who want to run their systems in the optimal nutrient availability pH range, nitrification is the single most important process towards lowering pH.

Nitrifying Bacteria in Aquaponics

There has always been a perceived balance between pH and nitrification efficiency, based on the assumption that nitrification activity in aquaponic systems was primarily a function of two different groups of bacteria: Nitrosomonas spp., and Nitrobacter spp. 

In lab trials, these bacterial species have showed sensitivity to pH, with changes in pH affecting their ability to oxidize ammonia (Nitrosomonas) and nitrite (Nitrobacter).  It should be noted, that most nitrifying bacteria (studied so far at least), are total wimps when it comes to changing environmental variables.  This is important to know for two reasons:

  1. Changing your pH rapidly will reduce your nitrification efficiency.
  2. Most nitrifiers are very hard to remove from the environment and culture in a lab.

Why Do I Need to Know This?

What does this have to do with the nitrification debate?  Well, point #1 tells us that perhaps many of the “system crashes” ascribed to running a system pH too low, may actually be attributed to decreasing system pH too quickly.

Point #2 tells us that Nitrosomonas and Nitrobacter may not really be the most important nitrifiers in systems- they’re simply the easiest groups to isolate and grow in a petri dish in a lab.

nitrification in aquaponics

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What does this mean? 

Well, it basically means that the hard and fast rules of nitrification may not be as hard and fast as they’re typically communicated.  There are many systems out there running very low pH ranges with great nitrification efficiency (including ours).  It may be that Nitrosomonas and Nitrobacter species are the primary nitrifiers in our system, but the reality is, we just don’t know.  What we do know is that our nitrification is efficient and excellent regardless of our system pH.

Nitrification in Soil

To put this in perspective- there are many acid soils and marine environments around the world, where nitrification occurs at remarkably low pH ranges.  Many of the nitrifiers in these environments aren’t members of the Nitrobacter or Nitrosomonas groups.  Many of them are unknown.

In a single shovel of soil, there’s an estimated 10,000 different species of bacteria, or roughly twice the number of bacteria currently known to science.  With that in mind, I think that it’s not just possible, but probable that there are some pretty interesting bacteria performing nitrifying functions in aquaponic systems around the world.

If you’re interested in more information on this subject, there are a number of resources out there, and I’ll plan on getting more information out as my time allows.  In the meantime, check out our BSA video detailing Biological Surface Area- arguably the most important system design element that fosters nitrification.


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  1. Hello, I was wondering how low can the PH go down before harm is done. I have a system pushing 9 months running and the PH will go down to 4, I will then add PH up to bring it back to mid 5’s to mid 6’s. It will go back down to 4 in about 3 days. Is it ok to run it at 4? Fish dont seem to care at all. ( FYI, I do add a teaspoon of Seabird guano (12-11-2) and 16 oz of worm tea every other day to boost nitrates, instead of adding more fish to my 150 gallon tank.) Never have ammonia nor nitrate readings to speak of. I grow tomatoes, cauliflower, broccoli, zucchini and lettuces.

    I also want you to know that I have enjoyed all the information that is on this website. It has been extremely helpful in my quest for aquaponic success.

    • Whoa! 4.0 is way too low. It’s impressive but way too low. I would keep an eye on your nitrification. If you’re not seeing a bump in ammonia, then I would say 5 is the lowest I would recommend with 5.5-6.5 being the ideal range for your plants. Your fish will likely like it higher than even 5.5 though. My typical recommended range is between 6.2 and 6.7. I will say though that different systems are different. Yours is unique. Make sure you don’t have testing error (4 is really really low), but be careful about how you bring pH up too. Think about converting over to more carbonates down the road. I very seldom recommend this, but in your case I do.



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