Oxidation, Nitrification, And The Nitrogen Cycle


We’ve all heard it, we all know it plays a part in keeping our aquariums and our fishes healthy, but do we really know how it works? What I’m referring to is the process of nitrification. Nitrification is a chemical process that is extremely important for our aquariums that’s achieved by oxidation.

What is oxidation? Well that’s not so easy to explain, but I’ll give it my best shot. Oxidation is basically a loss of hydrogen and a gain of oxygen, as opposed to a reduction, which is just the opposite, the loss of oxygen and gain of hydrogen. The oxidation that occurs with the ammonia waste from our fishes is what’s known as a redox reaction. That’s where oxidation and reduction is taking place at the same time.

The Nitrosomonas performs this by causing the ammonia (NH3) to lose it’s 3 hydrogen electrons, leaving just a lone nitrogen molecule (N) and then gain 2 oxygen electrons to create nitrite (NO- 2).

The Nitrobacter then takes the nitrite (NO- 2), and uses the oxygen electrons in the surrounding water molecules to take from, resulting in the creation of nitrate (NO- 3)

To be perfectly honest, I don’t fully understand the chemical formula aspect of it ( I haven’t done anything regarding chemistry since high school which seems like ages ago), but I do know it’s essentially the gaining and losing of hydrogen electrons and oxygen electrons.

Now here’s where the really interesting part comes in. There are actually bacteria that exist in marine and freshwater environments that reduce nitrate, however they’re iron oxidizing bacteria. In the research I did I found that these bacteria could utilize nitrate as an electron acceptor, which reduces it. Basically the nitrate is used for it’s oxygen electrons, which in the end after oxidization, leaves nothing but nitrogen remaining (which is known as denitrification).

I had thought these bacteria were aerobic, but it was brought to my attention that they’re anaerobic. I wondered how this could be since oxygen can damage or destroy anaerobic bacteria. I learned something fascinating, these bacteria are what’s known as facultative.

In a nutshell that means that it IS anaerobic bacteria, but it can rely on aerobic energy generation if oxygen is present.

It can use either method of energy generation and can survive in an oxygenated environment. It typically resides in the sediment of sea beds and the ocean floor and hasn’t been very thoroughly studied as of yet, but to my knowledge the research is ongoing.

A very knowledgeable member told me of his thoughts and theory of where they could possibly reside in his well developed and seasoned aquarium, and while doing this research he proved to be exactly right. He proposed that they could possibly have colonized his volcanic rock (lava rocks), and since volcanic rock has high concentrations of iron in it, this would be an ideal location for them as it would provide a excellent food source.

Since the bacteria is facultative, it can endure the conditions of the oxygen being present in the aquarium. I unfortunately don’t have any information regarding optimal condition data or growth rates for them, since the knowledge of them is fairly limited, however it stands to reason that eventually given enough time and supply of food they would naturally develop in an aquarium.

So... what do you think? Please leave me a comment.


  • Cloudy: Very interesting, thank you
  • Vale: Thanks for the part 2!
  • Gaz:

    Excellent Blog Rich.

    The only thing I believe that may be incorrect is the genus of the 2 bacteria when it comes to oxidation in water environments. I believe the Nitrosomonas and Nitrobacter are bacteria that are involved when talking about soil based environments.

    For water environments, it is Nitrosospira and Nitrospira I believe. Hope you understand me stating this. If you believe I’m wrong, please let us discuss it.

    In the last few weeks your research and threads/posts have taught me a thing or 2, so I applaud you for that and this Blog, and that is why I have given you a positive vote on this Blog.


    P.S. I wonder what is the true bacteria when we think about soiled based aquariums??? More food for thought?

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