Updated: Dec 13, 2022
This post will be about the ways in which ammonia is (most often) utilized within our aquariums, and why it can matter.
Ammonia can be very toxic in both freshwater and marine aquariums, and thus its removal is very important. There are both chemical and biological means to remove ammonia, however given how much can be produced daily, and how quickly chemical filter media can be exhausted, it is objectively better to rely on biological methods to remove ammonia. This is also, if you think about it, important when considering we do not always know when ammonia is no longer removed via chemical means, and we only need to miss one day where ammonia builds up and that can be enough to cause long term, permanent harm to fish, if not outright kill them.
So biological means of ammonia removal - there are essentially two (common) ways in our aquariums, as an energy or as a nitrogen source. Let's first talk about what that means.
When talking about physiological processes in the various fields of biology, there are different ways to categorize metabolic processes. One way of separation is whether a substrate is utilized for growth (as a carbon, nitrogen, phosphorous, sulfur, etc. source) or for respiration (as an energy source). Both processes are fundamental to life. All organisms need to assimilate elements into the body to grow and reproduce, and energy to power such processes.
Not surprisingly, metabolic processes involved in growth are also referred to as 'assimilatory processes' or 'assimilatory metabolism', while energy-producing processes are also often referred to as 'dissimilatory processes' or 'dissimilatory metabolism' because the substrates and products involved in such processes are often not then assimilated by the organism. Not always, but often the case. Some end products of dissimilatory processes can also be starting substrates for assimilatory processes for example, and vice versa. Nonetheless, biologists are still often able to separate the processes.
Also not surprisingly, there are a lot of arguments about how to categorize certain pathways. Luckily, for the utilization of nitrogenous compounds, this is not too big an issue, with pretty much full agreement in definitions.
Ammonia as an energy source
I want to first talk about ammonia utilization as an energy source. This is via a method that should sound very familiar - nitrification. How this process works is that nitrifiers will convert ammonia to nitrite via what is ultimately a redox reaction, and oxygen is converted to water in the process.
This is a very efficient process, as there are minimal steps that are involved. Ammonia acts as an electron donor for the reduction of oxygen, forming hydroxylamine and water in the process. Hydroxylamine is then oxidized, coupled with the reduction of water, producing nitrite. Thus ultimately, ammonia is converted to nitrite via a redox reaction. There is some belief that this at least can be a one-step process for some nitrifiers. For more information, see here. This is rather scientific and can be difficult to understand. Ultimately, the gist of it is this: there are only a few steps in the process, and importantly, it is energy-generative. The only limitation is the availability of the enzymes, presence of ammonia and oxygen, and that there are no inhibitors (or concentrations of any chemical that can inhibit the process).
This is why cycling an aquarium is such a desirable process. By establish a robust colony of nitrifiers, ammonia is efficiently and continuously converted to nitrite. This would also mean that yes, if ammonia is oxidized via nitrification, then one should see nitrite and/or nitrate (as nitrite can also rapidly convert to nitrate) as a result. Of course, if there are organisms that can consume nitrate, such as plants, in our aquariums, then there may be a decrease in ammonia witnessed but no corresponding increase in nitrite/nitrate.
P.S. A bit of a tangent, but denitrification is also an energy-generative process, and likely nitrification, is by definition dissimilatory. There is no such thing as 'assimilatory nitrification' or 'assimilatory denitrification'.
Ammonia as a nitrogen source
In the field of biology, when we refer to something as a 'nitrogen source', we mean it is a source of nitrogen that is assimilated into the body of an organism, differentiating such chemicals from an 'energy source' as defined above.
Every living being requires nitrogen. This is because it is an essential element, a necessary component of the genetic structures of every single living being.
The nitrogen source for humans is the food we consume everyday, particularly (but not limited to) proteins, which we can break down to 'recycle' the nitrogen present in the amino acids.
Ammonia can be utilized by many organisms as a nitrogen source, assimilating it into various compounds. One of the most common assimilatory pathway is for the biosynthesis of amino acids, specifically L-glutamate and L-glutamine. This is not the only way, but is very common. Many organisms, including bacteria, algae, and even plants consume ammonia as a nitrogen source via this or other assimilatory pathways.
This is why filterless planted aquariums can work, as the plants (and other organisms) can consume ammonia, potentially instead of nitrifiers.
However, there is a limitation to utilization of ammonia as a nitrogen source, and that is limitations on growth. Should an organism be limited by other chemicals needed for growth, then ammonia cannot be further consumed as a nitrogen source.
Consumption of ammonia by microorganisms as a nitrogen source can also result in 'bacterial blooms', or 'microbial blooms' to be more precise. After all, the organisms have to grow and reproduce to be able to consume ever more ammonia. Because of this, a lot more oxygen can be depleted compared to consumption of ammonia as an energy source.
Comparing ammonia consumption as an energy versus nitrogen source
Given the above information, there can be concerns with relying on non-nitrifiers to remove ammonia in our aquariums. Bacterial blooms can rapidly deplete oxygen, and has been linked to suffocation of fish. Reliant on plants or algae means relying on them not dying.
In contrast, there seems to be a link between a robust nitrification capacity results in nitrogen limitation and suppression of growth of non-nitrifying microorganisms, i.e. from my experience cycling to ensure a large amount of nitrifiers are enriched seems to suppress bacterial blooms in the future. No matter how much food I add to my aquariums, I personally do not see bacterial blooms. However, this is not extensively studied with potential confounding factors removed, so while it is an interesting observation, further investigations are necessary.
Hopefully these considerations can help you better decide what method is preferable for you, and explain some of what you see in your aquariums too.