The Nitrogen Cycle In Aquarium – Why Is It Indispensable?

The Nitrogen Cycle in Aquarium
The Nitrogen Cycle, the Biological Cycle, the Nitrification Process, The New Tank Syndrome, Cycling Your Tank, etc., refer to the Biogeochemical Cycle in our ecosystem.
Therefore, Nitrogen Cycle is an inevitable process in any water bodies such as Oceans, Rivers, Lakes, Ponds, etc., and an aquarium tank is no exception.
It is perhaps the most vital thing that you will learn in aquarium keeping. The most significant factor in the death of fish and the failure in keeping the aquarium is the failure to understand the Nitrogen Cycle and create the right conditions for it to occur.
In this article, let us see what the Nitrogen Cycle is? How to carry out the process efficiently and effectively to maintain a healthy and conducive environment for your fish, invertebrates, and other aqua species to thrive.
What is Nitrogen Cycle?

The Nitrogen Cycle is the bio-geo-chemical cycle that converts nitrogen into multiple chemical forms through both biological and mechanical processes. 

The process involves ammonification, nitrification, denitrification, and fixation; though nitrogen forms 78% of the earth’s atmosphere, it has very little biological process use. Nitrogen is a principal element in the nucleic acid DNA and RNA, crucial to all living things, including plant and animal kingdoms.

The Nitrogen Cycle is an unending process in which nitrogen passes through the atmosphere, soil, plants, animals, water, etc. The nitrogen changes its form to pass through different elements; in the atmosphere, it exists as a gas; in the soil, nitrogen oxide, and dioxide. It also takes the forms of ammonia, nitrite, and nitrate. 

How and why Nitrogen Cycle is indispensable in an Aquarium Tank?

Clean water is fundamental for any aqua life to thrive; the Filtration in an aquarium can be mechanical, chemical, and biological. The Nitrogen Cycle deals with or processes the chemical and the biological part of aquarium water purification. In other words, the nitrogen cycle is the process that takes place in converting fish wastes from toxic to less toxic or non-toxic.

This biochemical process involves continual biodegradation from Ammonia to Nitrite to Nitrate. In this, nitrate is the least toxic nitrogenous compound; the permissible limit for nitrates in water is between 20 to 50 ppm. 

The aquarium plants control the nitrates level in the water by absorbing, and the excess nitrates are taken care of by the periodic water changes.

Fish expels ammonia through their gills; urine and feces produce ammonia while decomposing; furthermore, the leftovers and decomposing plants produce Ammonia—the nitrifying bacterium, aerobic bacteria that convert inorganic compounds into their energy source. The Nitrification process requires two different microorganisms; bacteria or enzymes that convert ammonia into nitrites, Nitrosomonas, Nitrosospira, Nitrosococcus and Nitrosolobus, and the bacteria that convert nitrites into nitrates are Nitrobacter, Nitrospina, Nitrococcus.

Ammonia is noxious to fish and invertebrates or any aqua life; it can damage the gills and cause respiratory problems; at times, it can kill your fish and invertebrates.

Without a Proper Nitrogen Cycle, an aquarium would be a pool of toxic concoctions that cannot support any fish as an aquarium is a closed-loop ecosystem.

Hence, understanding the Nitrogen Cycle in an aquarium is the prerequisite for you to benefit from the fish-keeping hobby.

Ammonia in your aquarium

The microorganisms that deal with Ammonia in the natural environment do not exist in the new tank as there is no food for them to feed on. A fishless cycle (which we will see in detail in this article) instigates developing the enzymes/bacteria; a filtration system houses these good bacterias.
A filtration system is not just to filter out solids and suspended particles from your aquarium water; it has several utilities, one of which is housing good bacterias/enzymes to digest Ammonia. All the filter media, sponge, ceramic, candle provides a home for these good bacterias; these bacterias thrive on Ammonia; develop and multiply in response to Ammonia’s presence.
Even a trace of Ammonia could burn your fish and invertebrates, which is commonly known as Ammonia Spike. Many goldfish owners wonder why my goldfish has turned black; Ammonia spike is the common cause for goldfish turning black apart from the genetics.
It can easily harm the fish’s fins and tails, especially the ones with long tails, such as fancy goldfish types, Bettas, Guppies, etc. A trace of Ammonia can kill shrimps, viz: Amano Shrimp, Bamboo Shrimp, Ghost Shrimp, Cherry Shrimp, etc., while molting.


Nitrite is the byproduct of digesting Ammonia; it is fatal to your fish and invertebrates. Nitrites fuse with blood cells that oxygen molecules are supposed to attach; hence, they prevent absorption of oxygen into the blood adequately and suffocate the fish. All the organs and tissues slow down or arrest functioning as they cannot receive adequate oxygen.
However, nitrites’ presence promotes the colony of bacterias,  Nitrospira; your aquarium filter houses them along with Nitrosomonas.
Nitrospira converts nitrites into nitrate, a less harmful compound to the fish and invertebrates unless allowed to build beyond 50 ppm.


Nitrate is the end result of nitrogenous compounds. In an aquarium, nitrates are the byproduct of the breakdown of fish excretion, dead fish, invertebrates, leftover food, and plant matters.
Freshwater aquarium fish and invertebrates are tolerant to nitrates to some extent; you would want to keep it below 50 ppm in your aquarium.

Aquarium Plants

The aquarium plants absorb nitrates ions and leftover ammonium ions to make their amino acids for synthesizing protein; thus, aquatic plants majorly keep the nitrates level in the aquarium water under control. An aquarium tank without live plants will have to do partial water change more frequently.
In summary, the Nitrogen Cycle in an aquarium breaks down organic waste, such as fish excretion, dead fish, invertebrates, leftover food, and plant matter into Ammonia into Nitrite into Nitrates; absorption of nitrates by the plants or elimination through periodic water change.

The Nitrogen Cycle – Time Line 

To establish the first cycle in a new tank, it can take anywhere between four weeks to eight weeks to complete a fishless cycle to establish a good colony of Nitrosomonas & co and Nitrospina & co. Here, patience is the virtue; it is better to arrange and adjust all the necessary parameters in a tank without your fish and invertebrates than when they are in the tank swimming around.

We have seen that the Nitrogen Cycle involves three stages:

Different form of nitrogen state

Stage 1:

Ammonia and Ionized Ammonia are introduced through the bio-waste depending on the water pH. When the pH is towards alkaline, above seven, you will have Ammonia, and when the pH is towards acidic, below seven, you will have Ammonia ions. It continues to build till the colony of Nitrosomonas, Nitrosospira, Nitrosococcus, and Nitrosolobus forms.

Once the bacterial colony is entrenched, you will notice that level of Ammonia and ionized Ammonia goes down.

Stage 2:

When the Ammonia level goes down, the nitrogen cycle enters stage 2. The nitrite level starts to rise; it continues to grow until the Nitrospina, Nitrococcus, Nitrobacter colony is ingrained in the tank enough to digest all the nitrites. You will see that the nitrite level starts to decline.

Stage 3:

When the Nitrite level starts to decline, the Nitrate level will increase in the tank water; now, the cycle enters stage 3. The live aquarium plants absorb a significant portion of nitrates in the tank to produce amino acids for protein synthesis. Also, gravel substrates, rocks, and specific decors create room for an anaerobic bacterial colony that will digest nitrates into nitrogen gas.

Nitrates are allowed to build anywhere between 20 to 50 ppm, depending on the species; the best is to keep it under 20 ppm.

Enough of science for one article; Let’s get to the practical side of it. Let us learn to cycle the fish tank.
There are two methods in practice: Cycle with fish and without fish.

The Nitrogen Cycle with fish:

Some aquarists feel it’s ok to start with some hardy fish species to supply the biowaste to set in motion to establish nitrogenous bacterial colony; usually, goldfish are used to sacrifice to inaugurate and fix the new fish tank’s nitrogen cycle. It is in practice even today, and regardless of what the hobbyists say or think, it is pretty unlikely that the fish in the tank felt good during the process.
# Some hardy fish species used during the Nitrogen Cycle: White Cloud Mountain Minnows, Zebra Danios, Banded Gouramis, X-ray Tetra, Cherry Barbs, Guppies, etc.
I would strongly recommend not to take up this method to perform the Nitrogen Cycle. You would want to know what happens to the fish during this process:
Both Ammonia and ionized Ammonia can distress respiratory organs, the fins, skin burning, internal and external bleeding, hemorrhaging of blood capillaries, white clouding/white spot disease by hyper mucus production, and continual exposer to Ammonia result in the death of the specimens.
Nitrites prevent oxygen from binding with blood cells, leading to a lack of oxygen supply to the tissues and organs; the symptoms include brown stripes in the fins and tail, tissue damage, the decline in the immune system, and contracting infections and can lead to death.
The fish will continue to suffer even after improving water parameters. Besides, a fish with a low immune system will attract parasites and making the habitat unlivable for healthy specimens.
Any day, I would recommend you to carry out a fishless Nitrogen Cycle to avoid all the unpleasantries to both you and the fish.

Fishless Nitrogen Cycle 

There are few methods to start Fishless Nitrogen Cycle; whichever method you choose, you would want to invest in your tank, a quality test kit, and a filtration system up and running.

Fish food method:

It is the simplest method to start your Nitrogen Cycle. In this way, you begin to sprinkle good quality commercial fish food or shrimps just as you feed your fish; continue to add the fish food every day. As this uneaten food starts to decay, it will produce Ammonia; Ammonia’s accumulation will promote Nitrosomonas, Nitrosospira, Nitrosococcus, Nitrosolobus bacterial growth.

Instead of sprinkling the feed directly in the water, you can tie them in a sock or cheesecloth, or stocking. The advantage of using a sock or fabric will make it easier for you to remove the leftovers when you no longer need them in the tank.

This method is just the same as it occurs naturally; only you stimulate in an enclosed environment without harming any aqua life. For the feed quantity, you would either do the trial and error method or use an Ammonia calculator

All the commercial fish feed package mentions the percentage of protein in the food; by entering daily food in grams with the tank’s volume will give you the quantity of food to feed per day. 

The fish food method is the longest as we are trying to replicate the natural process. However, you could also use this time to quarantine your fish stock.

Adding Household Ammonia:

Household Ammonia is available in any pharmacy. It usually comes diluted, mentioning the percentage on the label. You would need a calculator to know how much Ammonia you need to add to your tank. 

You can use a syringe to measure and add the required quantity of Ammonia.

I would advise you not to yield to your curiosity to sniff the content in the bottle. It can cause severe irritation of the nose, eyes, and lungs; in some cases, it can cause asphyxiation and even death.

Start adding Ammonia every day until it rises to 5 ppm or more, then measure for nitrites; just the moment the nitrites are measurable, reduce Ammonia’s dosing to 50% as soon as Ammonia and Nitrite touch zero ppm the tank has completed its Nitrogen Cycle. 

Generally, 2 to 3 ppm is good enough Ammonia to host a good colony of bacteria that will be good to deal with your fish wastes, leftovers, and plant matter decays. When you use 5ppm or more Ammonia, it is quite large enough to handle a good aquarium stock.

Using the household Ammonia method is one of the easiest, safest and fastest ways to establish an adequate bacterial colony to handle your fish wastes and plant matter. 

Ready Bio-kits for Nitrogen Cycle:

Alternate to the household Ammonia, you can find in the market a scientifically formulated mixture for the rapid maturation of bacterial colonies for completing the nitrifying process in your tank. Fundamentally, it is Ammonia in a bottle, specifically formulated for the fishless cycle.
Generally, all these kits contain a direction to use, how much to add, when to add, what else to take care of, etc.
As I’ve stated, it’s an alternate solution to using household Ammonia. It might be less dangerous to handle.

Seeding the aquarium tank:

Seeding the aquarium tank is for those who do not want to wait 4 to 8 weeks to add their stock to the fish tank. It is also a prevalent practice among aquarists. In this process, you use nitrifying bacterial colonies from an established aquarium tank. This method gives you a jump start on the Nitrogen Cycle; it only takes half the time to complete the cycle it would typically take. 

Transfering nitrifying bacteria from an established aquarium tank can be used in both the Nitrogen Cycle with the fish and fishless. 

Though traces of nitrifying bacteria reside in the water, the actual colony resides in substrates, rocks, porous material, decors, and filter media. 

If you already have an aquarium, seeding the new aquarium tank with nitrifying bacteria becomes easier. If not, you may have to obtain it from your local fish store, friends, etc. 

Transporting the seeding material should be done quickly to ensure Ammonia and Nitrite’s supply to the bacteria to keep them alive and multiplying. You can make sure of that by transporting the seeding material along with some water from the original aquarium tank. 

You would also want to transport the seeding material quickly, not to alter the water temperature significantly.

Seeding with Substrate

Substrate from a matured aquarium tank is the simplest form of using seeding your new aquarium. If your new tank substrate is a similar color, gravel size, or sand, distribute the seeding substrate evenly all over the substrate.
If the new tank substrate is different in size, color, or type, hang the seeding substrate with hosiery, socks, or even a cheesecloth in the water. You may remove the seedling sack once the initial Nitrogen Cycle is complete.

Seeding with rocks and porous decors

Using rocks or other porous elements from the original tank as seeding material is even simpler than using the substrate. Place the rock or the decor element in the new tank. Take care to transport the rock or the porous element with some water from the original tank as quickly as possible; also, ensure not to alter the water temperature too much.

Seeding with Filter Media

Filter Media is where the maximum nitrifying bacterias reside. Bonded filter pads, foam blocks, or sponge filters are some of the filter media; You can use any of these filter media.
Sponge filters are the best for nitrogenous bacterias; it provides an immense surface for the bacterias to house themselves and proliferate. A sponge filter media is inexpensive and easy to transport.
Place an extra filter media in a matured aquarium tank for a couple of weeks till the nitrogenous bacterias establish on the filter media; transfer it to the newly set up aquarium and allow the nitrogen cycle to complete. Either you can remove the media once the process is complete or leave it in the tank as an extra bed for the bacterial colony.

Pitfall in using seeding method:

Although using seeding media to jump-start the new aquarium tank with the Nitrogen Cycle can be hazardous if not properly taken care of. 

If there is even a single diseased specimen in the primary aquarium tank, you could be starting the whole new aquarium tank with disease or parasites. You wouldn’t want to have an unhealthy and troublesome aquarium tank from the start. 

Before starting the seeding, test for all the water parameters and possible diseases and parasites in the primary tank; collect your seeding material or place the filter media in the tank.

If you miss out on this point, you will not enjoy the fish-keeping hobby as you are supposed to. 

Getting ready to add an Ammonia source

Irrespective of the method you choose to go with, you need to get ready with the following:

  • An aquarium tank with dechlorinated water, Decors, Plants, a filtration system, and a heater if you live in a cold climate.
  • Test the water for pH, dGH, KH, Nitrates, and Ammonia if any trace. These parameters are bound to change during the Nitrogen Cycle; hence, you would want to know where you started to see what parameters are changing; whether the values are increasing or decreasing for you to continue with the process.
  • Maintain a notebook with all the parameters before and after you run a test every time.
  • Keep the Filtration running throughout. The dissolved oxygen level should be optimal as the nitrifying bacteria are aerobic and need oxygen to thrive. 
Once you have taken care of the above, you are ready to add your Nitrogen Source. Follow every step diligently, testing the parameters every day.
Whichever method you choose to pursue, you would want to remember that there is no magic pill that will cycle your tank. You can shrink the timeline, but performing a regular water change, testing water parameters, and maintaining are indispensable parts of a successful aquarist.
A healthy aquarium tank should never have any traceable Ammonia or Nitrite at any given time. The presence of either indicates a lack or an imbalance in nitrogenous bacterial colonies. 

Troubleshooting – The Nitrogen Cycle:

Aquarium won’t start cycling:

Ammonia should be detectable anywhere between 3 to 5 days if you can’t detect any Ammonia while testing or it has gotten to a certain point and stopped cycling. 

The reason could be that something in the tank absorbs Ammonia. 

  • It could be you have too many plants, and the pH is on the acidic side. When the pH is below 7, Ammonia converts itself into ionized Ammonia and gets absorbed by the live aquarium plants in the tank.
  • Carbonates and bicarbonates are used during the nitrifying process; it helps to stabilize pH in the aquarium.

The simple remedy to raise both the carbonates and the pH is to add bicarbonate soda from your kitchen. Please do not confuse baking powder with bicarbonate soda. You want to keep the KH level above 5 to keep the nitrification process going. 

After adding bicarbonate soda, test the pH level; you may not get the pH level rise directly proportional to the quantity of bicarbonate soda; other factors come into play as it is not directly correlated. Hence, keep checking every time you add the bicarbonate soda till the pH turns on the alkaline side.

High Nitrates level:

Many aquarists experience an unwarranted level of rising in nitrates during fishless cycles; when the nitrates go over 100 ppm, you could do two consecutive 50 to 60% water changes.

Ensure to use only dechlorinated water and keep the water temperature the same as the tank water before top-up. 

To carry out a consecutive 50% water change, you need to remove 50% of the water from the tank, refill it with fresh dechlorinated water, and repeat the same process. In this way, you throw out largely the accumulated nitrates without disturbing the nitrogenous bacterias.

Ammonia level doesn’t drop:

If the ammonia level is not dropping, causes could be 

  • either you have not dechlorinated the water
  • low pH

Using tap water directly without dechlorinating will not let the nitrifying bacteria develop; hence, you would want to ensure to dechlorinate the water every time you are topping.

When the pH level is below neutral 7, Ammonia stays ionized; the nitrifying bacterias cannot benefit.

Ammonia levels do not fall because also you could be cleaning the tank, substrate, and even the filter too often or too vigorously. As we have seen earlier in this article, these bacterias reside on the substrate, rocks, decors, filter media, etc. if you clean them too often or vigorously, there is a chance you are removing all the beneficial bacterias from the system.

Algae Bloom:

A fresh tank is an ideal setup for Algae to prosper; during the Nitrogen cycle, the pH is maintained slightly on the alkaline side; pH over 7.5 shoots up algae matter, inducing depletion of dissolved oxygen in the tank water.
Nitrogenous bacterias are aerobic hence need oxygen to thrive.
Generally, in the first week, the aquarium will look pristine clear, but, from the second week, you will start to see brown algae coatings on the surface of the glass, decors, etc., and eventually, green algae will start to take over.
The best way to combat algae is to plant the tank densely with fast-growing species such as Java Moss, Hornworts, Micro Sword, Duckweed, Anacharis, and some fast-growing red aquarium plants like Ludwigia Repens, Rotala Rotundifolia, etc.
If the algae continue to prosper, perhaps, you could inject CO2 for a short time. Beware, continuous use of CO2 during the fishless cycle might affect nitrogenous bacterial colonies.

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