The Nitrogen cycle

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By: Tony Gai

18 August 2011


Whether it be setup of freshwater, brackish, marine, or a pond, the most important effect to understand is the Nitrogen Cycle. Just as humans release ammonia through urination, fish secrete ammonia through their gills. Ammonia is severely toxic to fish and in even small concentrations can prove to be lethal. Billions of years of evolution and growth has solved this issue with the smallest organisms, bacteria. Special bacteria consume ammonia and dispenses Nitrite as an end-product. Nitrite is not as lethal as ammonia but can still cause issues even in small concentrations. Again, bacteria come to the rescue and consume the nitrite. This time the bacteria produces Nitrate. This is the end of the nitrogen cycle. Nitrate is harmless in small concentrations.


Plants can remove nitrate from the system by using it as fertilizers. Also, nitrate can (and should) be removed by waterchanges. I try to keep a strict water change schedule and change 15-25% of the water in my tanks weekly. Different tanks require different care. A cichlid tank or discus tank could even require waterchanges more than 50% twice a week!


A poorly drawn image depicting the Nitrogen Cycle


The nitrifying bacteria live on decoration, the substrate, and in your filter media. Proper water circulation through your tank or pond will ensure that all the water is treated with the Nitrogen cycle.


How to:


The bacteria required to keep your aquarium running can be grown using a couple of methods. Morals will always vary between hobbyiests. Fish health should be the NUMBER ONE priority ALWAYS!


Method 1: Seeding Media

Materials: Filter and media, access to an established aquarium with similar parameters (freshwater, saltwater, pH, etc.), Master Test Kit


My personal favorite method to cycle an aquarium is to use old filter media. The bacteria required to complete the nitrogen cycle will be present in a fully established tank. The bacteria can then be "seeded" or transplanted into a new tank by running the filter with media on an established tank for about a week (can be done while preparing the rest of a new tank). All the bacteria in the system of the established tank will then grow onto the new area.


After about a week the filter will be fully established with bacteria and can be moved to a new aquarium. You can immediately add fish (and should be added to feed the bacteria). The number of fish will depend on the size of the tank, the amount of seeded filter media, and the type of fish determine how many fish can be added.


Similarly, old filter media from an established tank can be placed in a filter to immediately add the bacteria to a system. Once again,the number of fish will depend on the size of the tank, the amount of seeded filter media, and the type of fish will determine how many fish should be added.


Always monitor the Ammonia, Nitrite, and Nitrate levels. If any of the levels get too high do a partial water change to lower these levels.


Method 2: Fishless Cycling

Materials: Master Test Kit, Ammonia (purchased at supermarket), aquarium heater (for speed)


Ammonia can be added directly into a system to begin the cycling process. Ammonia can be purchased at a supermarket for less than a couple of USD. Be sure to purchase pure ammonia or a ammonia and water mixture. Check the ingredients list to make sure there are no additives such as phosphates and soaps. These extra chemicals will be hazardous to fish when you add them after the cycle.


A master test kit will be necessary to monitor the progress of a cycle. Monitor ammonia levels in the tank and add ammonia to keep the level at around 1-2 ppm. Also, bump up the aquarium temperature to around 86 degrees Fahrenheit. The greater temperature is more idea for bacteria growth and will speed up your cycling process.


Monitor Ammonia, Nitrite, and  Nitrate levels. First you will notice a spike in ammonia. After a few days you'll notice a drop in ammonia and a spike in Nitrite. Keep adding ammonia to keep ammonia levels between 1-2 ppm. This will ensure bacteria on all parts of the cycle will remain fed. After a few more days you will see an increase in Nitrate. once this occurs your cycle is nearly complete. Wait a few more days and your aquarium will be ready for fish. Be sure ammonia levels and nitrite levels are at 0 before adding fish. To achieve 0's you can either wait (don't wait too long or the bacteria will starve) or conduct partial water changes.


Add fish and once again monitor ammonia, nitrite, and nitrate levels to monitor the cycle's progress.



Method 3: Live Fish Cycle

Materials: *MASTER TEST KIT*, set up aquarium with filter, few  hardy fish


I must first start out by saying that this method is morally unethical for some people. I am not here to force morals on anyone, only to describe the method some people use. Exposing fish, even hardy fish, to any levels of ammonia and nitrite (other than 0), can cause unnecessary stress. A master test kit is strongly recommended to protect the health of the fish.


Begin by setting up your aquarium with chlorinated water, filter, and heater. Be sure tank parameters are stable meaning pH does not fluctuate significantly throughout the day (a difference between 6.5 and 7.0 or 7.0 and 7.5 is not as bad as 7.5-8.0.


Purchase a few hardy fish and acclimate them to your tank. Fish people use often are zebra danios or glofish. The fish will produce ammonia to feed the bacteria. Ammonia, nitrite, and nitrate levels must be monitored to protect the fish. If ammonia levels rise about 2.0 ppm a partial water change MUST be performed.


This method will take up to a month and a half to complete. A spike in Nitrite will happen after a week or two. Ammonia will then drop. Another week or two later Nitrite will drop and nitrate will spike. Durations will vary depending on water parameters. Once both ammonia and nitrite levels are at 0 the tank will be cycled. Additional fish can then be added to the aquarium in small batches. If large amounts of fish are added a spike in ammonia and nitrite could occur which can be fatal to a system.




Notes: When conducting water changes using tap water be sure to fully chlorinate the new water. Chlorine can kill the nitrifying bacteria. If this occurs your cycle will restart and will severely disrupt your system.


Special Thanks:



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Awesome Writeup! Thanks (Thumbs Up)

"The bacteria can then be "seeded" or transplanted into a new tank by running the filter with media on an established tank for about a week (can be done while preparing the rest of a new tank)."


There is nothing to feed off on and bacterial will die. You can add new fish in right away without harm.

I may  need to reword that. What I was hoping to say was run your filter on an established tank. this will allow the bacteria to grow in your filter media. You can then transplant the seeded filter into your new tank and add fish right away.


How could I reword it so that message comes across more clearly?

Great Article. I have found threw my own trial and error along with research that ponds go threw this cycle and will go clear to green a few times.
This sure helps me.  I am about to get started on my first planted aquarium.  So should I have the same type filter as the one that I am going to be borrowing from a friend?  It has to fit on my filter, right?  Sorry, I am new to all this.  If I use a filter from an established tank, it must be the same type, right?

you should get the type of filter that would be best for your tank. You can place the filter media on the output of the filter just hanging there (it's not too scientific) if the used media is coming from a larger filter. If it's coming from a smaller filter (like how I cycled my Aqueon 55/75 with my filters from my 5g and 10g) you can place the media inside the chamber along with the new media. This will let the bacteria move onto the new and properly sized cartridge.


Sorry if that's confusing. I'm having trouble explaining.

Thanks Tony.  That helps.
Thanks Vin

A couple of thoughts:

1) For the bio-seed, the article does not embrace using some substrate to seed a new tank (either dispersed or bagged). The fact is that the substrate in an established tank actually has as much or more biology than filter media.

2) The article states that once nitrites are converted to nitrates, the nitrogen cycle is ended. Not so, weedhopper. The nitrates that are not absorbed by plants or flushed in a water change may be further processed by other (anaerobic) bacteria into harmless N2 - nitrogen gas - now we can say the N2 cycle is complete.


Excellent point about the substrate. That is another method. However, I prefer using filter media because the water flow through the filter media is much higher than through the substrate. It doesn't take much bacteria to seed an aquarium so putting a little amount in a high flow area works well.

As for the nitrogen cycle addition, yes, plants remove the organics. However, if you don't have plants, that's where the cycle ends. Many people don't jump into plants when starting a new aquarium and therefore the most umbrella summary is stated above.




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