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The Nitrogen Cycle and Conditioning Period in New Aquariums


A thorough understanding of how water quality affects animal life is essential if one is to be a successful aquarist.  This is sometimes a bit difficult for beginners to accept, but please remember that it is a serious mistake to spend time learning about the habits and dietary needs of aquatic creatures while ignoring the “less glamorous” aspects of the hobby.  Once you understand water chemistry basics, your appreciation of how fishes and invertebrates survive in their environments will be heightened. 


The Nitrogen Cycle

The nitrogen cycle is a critical factor in the establishment of a crystal clear, well-balanced aquarium.  Poor functioning of the nitrogen cycle is undoubtedly the most common reason behind new aquarium failures.


Basically, the nitrogen cycle is a process by which nitrogen is converted to other organic compounds that are then utilized by plants and animals as food.  Nitrogen enters the aquarium via dead animals and plants, uneaten food, and the waste products of fish and invertebrates.  The most toxic nitrogenous compound that is added to aquariums in this manner is ammonia.  Ammonia occurs in two forms, ionized and un-ionized, with the un-ionized type being extremely toxic to aquatic organisms.  The proportion of the total ammonia that is un-ionized rises as the water’s temperature and alkalinity increases.


Bacteria and the Nitrogen Cycle

Two types of bacteria control the functioning of the nitrogen cycle.  These bacteria are aerobic, which means that they require oxygen in order to survive.  Bacteria populations develop and thrive on substrates that are exposed to oxygenated water, such as gravel and the filter pads and carbon within filters.


The process by which aerobic bacteria convert ammonia to less harmful compounds occurs in two phases. Nitrosomas bacteria convert ammonia to compounds known as nitrites. Nitrites, while dangerous to aquatic organisms, are less toxic than is ammonia.  In the second stage of the process, bacteria of the genus Nitrobacter utilize these nitrites as food, and in doing so convert the nitrites to nitrates.  Nitrates are the end product of the nitrogen cycle, and are the least toxic of the compounds involved.


Nitrogenous bacteria (the name given to the various species of bacteria that feed upon ammonia-based compounds) exist in huge populations in natural water bodies and in healthy aquariums.  Until such are established in your aquarium, its levels of nitrogen-based compounds will be toxic to nearly all fishes and invertebrates.


The time it takes for healthy populations of nitrogenous bacteria to become established in an aquarium is often referred to as the “conditioning period”. Its actual timetable varies greatly depending upon the unique characteristics of each aquarium and of the animals therein, but usually falls in the range of 1-6 weeks.


Please bear in mind that water clarity is not an indicator of the functioning of the nitrogen cycle.  The only sure way to monitor the cycle is via frequent testing of the water to determine the levels of ammonia, nitrates, and nitrites (please see below).


Altering the Nitrogen Cycle

Your aquarium’s conditioning period may be shortened by the addition live aerobic bacteria.  I have had good experience with Biozyme Freshwater and Biozyme Saltwater, and strongly urge you to use either with all new aquariums.  Products such as Coral Vital LSB Pro, which accelerates the growth and reproduction of bacteria in marine aquariums, should also be considered.


You can also help the process along by adding filter material from a well- conditioned, parasite-free tank into the filter of your new aquarium.  Natural materials such as “live rock and “live sand” also host beneficial bacteria and offer another option.


In the past, it was standard practice to use hardy fish, such as domino damselfish in marine aquariums or guppies in freshwater aquariums, to hasten the conditioning period (their waste products started the process and provided food for bacteria).  However, additives such as those mentioned above are more effective and infinitely kinder, as many of the fish subjected to this process did not survive.


When cleaning your filters, always retain a bit of old filter medium (carbon, floss) and add this to the clean filtering material.  In this way, you will introduce aerobic bacteria into the newly-cleaned filter.  These will reproduce rapidly and greatly increase filtration effectiveness.


Please be aware that the addition of packaged bacteria does not eliminate the need for a proper conditioning period. Water quality must still be monitored carefully, and animals should be introduced to the aquarium in small numbers. 


Measuring the Levels of Nitrogenous Compounds

The frequent use of test kits is essential during the aquarium’s conditioning period, and on a regular basis thereafter.


Ammonia should be tested daily until you notice a sudden decrease in its level.  This decrease signals the presence of Nitrosomas bacteria.  Nitrate levels will then follow the same pattern, as the Nitrobacter bacteria become established.


The conditioning period may be considered at an end once the nitrate levels drop substantially.  You may now begin to introduce fish and invertebrates into their new home.  Be sure to add animals in small quantities, so as not to overwhelm the nitrifying potential of the bacteria present, and observe them carefully for signs of stress.


The pH level should be checked often as well, since the water may become acidic during the conditioning period.


I am very interested to hear about your successes and challenges in establishing new aquariums, and will be sure to pass along your information to my readers in future articles.  Thanks, until next time, Frank.


An interesting technical article on the role of nitrogenous bacteria in natural marine habitats is posted at:


Canister Filters for Saltwater

A customer recently asked me a question about using a canister filter on their saltwater aquarium. The customer had read on Reef Central that you should not use a canister filter on a saltwater aquarium, especially on a reef aquarium. That they do not work well, and will cause high nitrates.

This is a topic that you will see differing opinions on. The problem with canister filters is not that they don’t work on saltwater or reef aquariums, they work very well. Any biological filter is going to produce nitrate on a closed aquarium system, it is the natural end product of the nitrogen cycle.

This is why many reef tank owners will remove the bio balls from their wet dry filters, or run their systems on a sump only set up, in an effort to reduce nitrate production. This is why some people are of the opinion that canister filters should not be used on a reef tank. You can get away with this approach if you have a sufficient amount of live rock and substrate in your aquarium to act as your biological filter. In fact, live rock is an excellent source of nitrifying bacteria, and will function as a very efficient biological filter in an aquarium with enough rock. Most reef set ups will work well without a dedicated biological filter, so long as the biological load is not too high, and you are using a good protein skimmer. This method is often referred to as a “Berlin” style aquarium (lots of live rock, good water movement, heavy protein skimming, and no biological filter). Canister filters can still be used on reef tanks, they can be used as additional biological filters in heavily stocked tanks, and can easily be used for whatever chemical filtration media you may want to use.

Saltwater fish only tanks are a different story; in most cases you will need a biological filter to handle the fish waste and biological load, even if your tank has live rock in it. You will also want to have a mechanical filter on a saltwater fish tank, especially if you have large fish in your tank. Most canister filters give you the ability to operate them in different ways. You can use them for biological, mechanical or chemical filtration as needed.

Nitrate is going to be produced in any set up, some more than others. My best advice is to use as much filtration as your aquarium demands. Ammonia and Nitrite should be near zero in an established aquarium, if you are detecting either, chances are your aquariums biological filter is insufficient. Nitrate levels will creep up slowly over time in any system, so whatever filtration method you employ, you still need to monitor your water chemistry. Water changes will remove nitrate from your aquarium, so as long as you are testing your water, and performing regular water changes, nitrates should not be a problem.

Speaking canister filters, here’s a video my staff created to help aquarists set up a canister filter on their aquarium. Canister Filter Video