The Nitrogen Cycle & New Aquarium Syndrome

aquarium nitrogen cycle

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I brought home my first aquarium when I was just in second grade, probably in my seventh year in existence. To say that that project didn’t exactly go smoothly is likely a bit of an understatement.

I procured some long-tailed zebra Danios to feature in my 10-gallong aquarium, newly acquired as a hand-me-down from my older brother.

The setup was simple enough, under-gravel filter powered by a small air pump. The heater hung off the back of the tank. The tank was topped by a plastic cover replete with an incandescent “strip light” with two 25w incandescent bulbs to illuminate the tank. All of this paid for with savings from my allowance, and the few bucks I’d made mowing the lawn of the elderly neighbor who lived across the street.

It was a Friday evening when I filled the tank, started the air-pump, and plugged in the heater. Despite the prudent advice of my father, I moved all five of my Danios from a jar on my bookshelf into the newly minted tropical aquarium.

Unfortunately, by the time the weekend was over, I’d started losing fish. What I’d failed to grasp was what we call “new tank syndrome.”

In essence, because I’d failed to properly cycle my aquarium, the aquarium system was little more than a fish-bowl…especially over that first weekend. What ensued was a response of overt panic, emergency water changes, and ultimately the replacement of my danios.

In the decades since, this story has been re-told to me in a myriad of similar circumstances by various customers and clients. It remains the most common of circumstances that seem to trouble a fair number of novice aquarists, as well as the most fundamental bits of chemistry you’ll need to understand in order to  maintain your aquarium properly.

The “nitrogen cycle” is actually an ecological concept and applies to gardens and forests, as well as lakes and closed aquarium systems as well. Follow along for the details pertinent to your aquarium system in this rudimentary overview of the nitrogen cycle.


nitrogen cycle

Fish Create Waste

The process starts of course as fish create waste in the form of ammonia expressed by the chemical formula NH3. Contrary to popular belief, much of that nitrogen is excreted from the fish’s gills as a chemical called ammonium (NH4), that ammonium is converted into the toxic ammonia in a system with a neutral or alkaline pH.

In addition to the ammonium excreted across gill membranes, additional ammonia is produced by the decomposition of excess food in the tank, as well as decaying plant and animal matter (including feces).

In a very short period of time, ammonia will accumulate in a closed system to levels lethal to fish.


aquarium nitrogen cycle

Bacteria Utilize Ammonia

Very shortly after ammonia is introduced to the system bacteria called Nitrosomonas begin to colonize your aquarium. These bacteria utilize ammonia and/or ammonium in their metabolism, thereby imbibing themselves with the ammonia and removing it from the aquarium water.

These bacteria are “aerobic”, meaning that their metabolism requires oxygen, just like animals. Thus the aeration you provide for your aquarium is necessary to biologically process your ammonia, just as it is necessary to keep your fishes alive.


Conveyor Belt of Chemistry

Just as the fish have a waste product, the Nitrosomonas bacteria have waste products as well. After absorbing the ammonia in the water, they will release another nitrogenous compound called nitrite (NO2) into the water column as their waste.

This is important because nitrite (NO2) can be dangerous for fish, especially in higher concentrations like ammonia, it too can be lethal.

In a similar fashion as with the toxic ammonia, the nitrite in your aquarium is consumed by a type of bacteria called Nitrospira. These bacteria in turn produce a chemical called Nitrate (NO3) as a waste product.

Nitrate is significantly less toxic to the fish than either of the two precursor chemicals, and for most intents and purposes this is the “end” of the nitrogen cycle. It should be noted that plants and algae will utilize this nitrate as a fertilizer, thus elevated levels of nitrate will make it likely that nuisance algaes can take hold. In a literal sense, these compounds are “nutrients” for algae and are referred to in that way by most seasoned aquarists.

Waste Products

It is worth noting that in addition to the waste products mentioned above, the bacteria will also release carbon dioxide into the water as well. Thus you will need to provide ample aeration to facilitate adequate gas exchange to keep your fish vertical and your beneficial bacteria active as well.

In addition, if you start to get technical about the “stoichiometry” or the balance of chemicals in these biological functions, you’ll see that the nitrogen cycle itself produces a small amount of acid, represented in the image above by the excess hydrogen atoms produced at each step. This indicates that in a closed aquarium system, the pH is trending down simply due to the chemistry of the nitrogen cycle.

As part of normal aquarium maintenance, it is necessary to remove some water from your aquarium and replace it with clean water free of algae-causing “nutrients”. If you’d like to see a discussion about how much water you should change, check this blog for a mathematical discussion about aquarium maintenance and how it impacts chemistry.

In a TLDR scenario, you’ll want to shoot for a regular schedule for water changes. Whether your schedule is monthly, bi-weekly, or perhaps more often, the goal should be to keep nutrients low and pH stable.

New Tank Syndrome

What I failed to grasp during my first aquarium setup was that there is a bit of a time-delay in the development of bacteria in your aquarium system…or really, that it was the bacteria that made the tank stable in the first place.

Now I understand that the first weeks of an aquarium set-up can be very “bumpy” with ammonia or nitrite spikes that can definitely cause harm to your aquarium inhabitants. Traditional advice has been to “go slowly” over the first month or two of your aquarium’s setup. During this time the beneficial bacteria will begin to colonize your system and begin neutralizing the toxic nitrogenous compounds in your system.

If you can navigate this initial period, ammonia and nitrite will drop to zero provided adequate husbandry practices are maintained. This includes adequate filtration, pH monitoring and maintenance, regular water changes, not over-feeding or over-stocking your aquarium, et cetera.

For those with a bit more confidence or experience with aquariums, fish-less cycling of new aquarium systems is a great way to stabilize the system without endangering the lives of any aquarium inhabitants. The process involves adding the chemicals noted above in ionic form, and potentially adding a bacterial seeding product to speed up the cycling process. Done correctly, it can reduce cycling times by several weeks.

You can also move filtration materials, driftwood, or even a small amount of gravel from an healthy established system. You can add a small amount of substrate in a reusable media bag, or an old pair of nylons works as well. This process will speed any cycling method, including the “slow-as-you-go” method employed nearly universally in the aquarium hobby.

Geeky Sidenotes

If you’ve made it this far, you’re prepared for a couple additional points that will improve your understanding of the nitrogen cycle.

First, a neutral or alkaline pH is vital to the speedy conversion of ammonia. At slightly acidic pH (e.g. 6.5), the biological cycle is impeded, and proceeds more slowly. At pH’s of 6.0 or below, the nitrification process whereby ammonium is converted into nitrite basically slows to a halt. This implies that if you allow the pH in your aquarium to drop to this level, you’ll have to be vigilant about ammonia monitoring and mitigation. Thus, it is advisable to maintain a pH level above a pH of 7.0, and no lower than 6.5 in most circumstances.

Additionally, the toxicity of ammonia actually increases as the pH increases. In basic chemical terms, the ratio of ammonia (NH3) versus ammonium (NH4) in the water depends on the number of free hydrogen atoms, a figure we call pH. In low pH environments, free hydrogen atoms abound, and ammonia (NH3) is rapidly converted to ammonium (NH4). Again, without getting too complicated, NH3 is much more lethal than is NH4.

Closed aquarium systems are said to “crash” when pH levels drop to a point where nitrification is impeded and ammonia/ammonium build up in the system.

The only solution to a crashed aquarium is a large-volume water change, as simply addressing pH will push any ammonium present in the aquarium into the more toxic form.

It is for this very important reason that proper aquarium maintenance includes pH management and the regular export of nutrients via water changes.


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