How pH Affects Microbes in Aquaponics

We left off with a question: can human actions affect microbial populations?

The answer is of practical importance, because it determines whether or not we can trip up microbes (the engine of aquaponics) by our mistakes.

A specific application of this question is pH. Does they way we run pH in our systems matter to microbes? 

In today's article, we're talking about how pH affects microbes in aquaponics systems.

pH Affects How Microbes Are Able to Metabolize Compounds.

One of the most important groups of microbes in an aquaponics system is the nitrifying bacteria- organisms like nitrobacter and nitrosomonas that turn ammonium and ammonia into nitrogen compounds that the plants can use.

It's important to note that nitrification is a beneficial side effect of the bacteria's processes.

The bacteria, of course, aren't nitrifying with the goal to create usable nitrogen for the plants.

That's not how the natural world works.

Organisms perform functions to achieve survival and reproduction.

These bacteria are nitrifying to gain energy that ultimately they will use to build and reproduce. Dr. Storey describes how nitrifying bacteria use ammonia to achieve this end:

"They're breaking it (ammonia) apart and they're stealing electrons and then they're using this energy that they're gaining from this little chemical process that they've hacked. All these little microbes have their specialty. They can hack these processes, and they can do it more efficiently than their neighbors.


The capabilities of a bacteria are far more varied than what we can observe in a lab setting.

They make a little money in the form of electrons and they use that money basically to fix carbon. CO2 is fixed in the water, and they're taking the CO2 out of the water and using it to build their own structures."

Now remember- there are hundreds of bacteria in the system. Some of them function better than others under certain circumstances.

Their chances of survival over the other bacterial species are constantly changing with the changing environment, which means that there is a lot of competition going on.

When microbes and pH react with each other, the rules of the game change.

"...So as (the microbes) complete these little processes, they're completely dependent on doing it efficiently. They're competing with each other; there's competition between different species, even within the same species, some microbes are different than others. They evolve and adapt incredibly quickly compared to other organisms. So there's this competition going on.

When we change the pH, we change the variables at which they're functioning. Microbe A is really good at converting ammonia into nitrate. Microbe B is good at taking ammonium and turning it into ammonia, and then turning it into nitrate. They each have their thing that they're really good at. And when we change the pH, it shifts that balance of power between the communities that are doing these operations for us. In the short term it impacts the stability and the efficiency of the system, but what we've found is that in the long term, it doesn't actually impact anything. Because you give these guys enough time to adapt, or enough time for another species to colonize the system that converts (for example) ammonia to nitrite at a pH value of 5.7 very efficiently... you give that guy enough time to get into your system and start doing your work, and he does it beautifully."

Conclusion: Does it matter how high or low you run the pH in your system?


pH testing is fairly simple to do with a test kit.

Well, yes and no.

As we've seen, long term affects will be nullified by the natural competition of bacterial populations, but there is a temporary effect.

A change in pH every now and then isn't really going to matter, but you don't want your pH to be changing constantly- your bacteria wouldn't have time to catch up.

We recommend a balanced approach: try to keep pH constant, but don't worry too much if it wavers a bit.

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