Learning System

What are the bacteria in an aquaponic system?

What are the bacteria in an aquaponic system? Well, today’s episode is all about introducing the main bacterial players and their role in your aquaponic system.
In a nutshell, you can’t have an aquaponic system without these unseen forces helping you out!

You’re listening to Fish Grow Plants—A podcast all about practicing and sharing the love of aquaponics; hosted by Logan Schoolcraft.

Hello, and welcome to Fish Grow Plants! In today’s episode we’re answering the question, “What are the bacteria in an aquaponic system?”

It’s been a while since I first heard about the bacteria in an aquaponic system, but back then I was very much a component type of person. What that means is that I would break things down into components and analyze, inspect, or figure them out one at a time. While this method worked very well for my technical position at the time, I would now say that thinking might have been a bit flawed on my part. The bacteria can be separated out and analyzed, but for their role in aquaponics, looking at how everything interacts together is quite important. We are talking about a closed loop circuit that feeds back into itself, so understanding how things interact is very important.

I’ll be the first to say I don’t study this stuff, and am no expert, so if you want to know more, I am definitely not the one to help you. The point of this episode is to introduce you to the main bacteria players in your system water, their importance, and how to help them help you grow your best produce and keep your fish swimmingly happy.

I’ve seen and read various ideas about how bacteria play a role in aquaponics. Some call it a third “unseen” player between the fish and plants, some say it’s part of a “cycle” between the fish and plants, and others say it’s like a web or world of bacteria where the fish and plants are the smaller parts of the whole.

No matter what perspective works best for you, there are still some basic concepts that apply no matter what.

For instance, fish create ammonia. They create ammonia from their poop, urine, and breath. But this ammonia is toxic to them if left alone and allowed to accumulate. I don’t think anyone argues this. Oh, and dead stuff, like rotten plant roots, or even dead fish create ammonia; and as you might have guessed, the bigger the source, the larger amount of ammonia it puts out.

Another agreed upon concept: plants need nitrogen to grow. Without it, they will initially yellow, wilt, and then eventually die. It’s kind of like taking a nutrient out of your food—you can eat all day long, but still not get what you need to be healthy and grow.

So, the link, no matter how you like to look at it, is the bacteria in your aquaponic system water. These little unseen forces are what take the ammonia that can kill and transform it into a useable form of nitrogen that plants can thrive on.

So how is this done? Or should we ask, “what does this?”

Well, this process may seem magical, but is really pretty simple and accomplished in only two basic steps.

And there is a wonderful type of bacteria in the genus Nitrosomonas that loves ammonia! So what does it do? Well, it oxidizes, um, converts, ammonia into nitrite! Yes, nitrite is a form of nitrogen, but unfortunately it is not usable by plants, and it too, is toxic to fish, although less-so than ammonia. It’s toxic because it prevents blood from absorbing oxygen.

Sounds like a bad situation right? Well, yes, but no because of another wonderful type of bacteria in the genus Nitrobacter. This lovely bacteria oxidizes, err, converts nitrite to nitrate! And you guessed it, nitrate is the form of nitrogen plants love. And unless you somehow have created a super amount of nitrate, it is harmless to your fish. It’s kind of like a good thing—way too much of a good thing is not a good thing. But for the most part, it’s hard to have too much nitrate.

Pretty simple right? With the right mix of Nitrosomonas and Nitrobacter, your system will be robust and producing nitrate without any work on your part. Well, almost no work. Keeping these bacteria happy and healthy is really pretty simple—make sure they have plenty of oxygen in a comfortable temperature environment; think room temp somewhere in the 70F range. They are like you—too hot or too cold and they slow down; way too hot or cold, and they die. Make sure they are comfortable, and they will work 24-7 for you without complaint! Oh, your fish and plants like similar environmental conditions too, so it’s a true win-win-win for everyone.

But is that the only bacteria in your aquaponic system water?

The answer is no. Aquaponics is a living system, so there are going to be a LOT of things in your system you may not know about. But some of the lesser know bacteria are the mineralizing type. These bacteria are pretty aggressive in terms of reproduction and love to float around living off of decaying solids and gunk in your system. They vary by type, name, and lifestyle. Some are aerobic, that is they love oxygen, and some are anerobic, that is they love no oxygen.

I am not going to pretend I know anything beyond these basic facts, but my assumption is that having a small amount of them in wide variety is probably a good thing because they won’t overpower your Nitrosomonas and Nitrobacter bacteria, but they will bring their own positive spin to your system by breaking down certain gunk.

And on that note, I’ll say that’s all the bacteria I know about, and can even put sentences together to talk about them.

But I won’t leave you hanging after that lesson. There’s nothing like learning something and not having a concrete action to do, or an item to use afterward.

So my first item to tell you about is inoculating bacteria. Inoculate is kind of like a jump-start, or head start. There are multiple ways to get your bacteria colonies going in your system, and some do not require the purchase of anything at all. I’ve done that, but it does take a while. So, if you’d like to speed things up a bit, take a look at these products and see if they might work for your situation (see the blog for links):

Pentair has a bacteria startup for aquatic systems.

And Chewy offers some smaller, similar versions, for those of you looking to start on a smaller scale. Afterall, aquariums are a great place to start with aquaponics!

But the last tool I want to leave you with is how to see if you have any of these wonderful bacteria in your system. That means a test kit! There are various ways to test for nitrifying bacteria, but usually, you will find the strip test kit and the titration, or chemical mixing, tests.

Again, Pentair and Chewy are the links I’m going to share, but don’t feel obligated to them. There are many supplies and variations of these tests. Just use them as a springboard for ideas and information. The Pentair link is for the test strips of various kinds, while the Chewy link is the API Fresh Water Aquarium Master Test Kit. This kit will test for a lot more than you may need initially, but it’s good to have more information than less, usually.

Well, I hope now you know that there are basically two main types of bacteria running your aquaponic system with a scattering of various other bacteria players to make a beautiful concert of bacteria magic in your system water.

And with that, happy aquaponicing!


Questions! Let me have them! Do you need clarification, more information, or maybe you just have a tangent thought—send all your thoughts my way. See the website for episode details, or just fire off an email to and I’ll get back to you.


So, was this episode good, bad, ugly, or other? Let me know! Comment, email, smoke-signals it doesn’t matter! I love to hear from you. Your feedback is immense, and I am always grateful for it. Likewise, thank you for taking the time to listen and share your thoughts. Have a wonderful day.

This has been another episode of Fish Grow Plants—the podcast all about practicing and sharing the love of aquaponics; hosted by Logan Schoolcraft.

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