The Importance Of Nitrifying Bacteria In An Aquaponic System.



You probably have heard that if you use chlorinated tapwater in your aquaponic system you risk killing all your fish. That’s true, but there are other creatures you will also certainly kill. You can’t see them, but they are there, in your media bed and/or your solids removal and filtration system. These invisible creatures are called nitrifying bacteria.

Yukkk! You are probably thinking that bacteria are all bad, bad, bad. Not so.

You would not be here if it were not for all sorts of friendly bacteria. These are Nature’s cleaning crew. They eat up poisons and waste products and churn out substances that we can use as food, drink, or air.  Nitrifying bacteria are important friendly bacteria.

In the case of nitrifying bacteria living in the filtration parts of aquaponic systems, what they do is eat up ammonia and nitrite and churn out AMMONIUM NITRATE which is what plants need to eat to GROW.

If you kill all these nitrifying bacteria, by putting chlorine, chloramine, or antibiotics in your aquaponic system, you risk KILLING EVERYTHING ELSE IN YOUR AQUAPONIC SYSTEM.

There will be undigested ammonia going around your system, and no nitrate for the plants to eat.

Ammonia, which fish sweat, pee and poo, straight into the water, is toxic in tiny amounts to fish.  If the nitrifying bacteria, which eat it, are gone, it will build up and kill your fish very fast.

There are TWO KINDS of nitrifying bacteria, nitrosomonas and nitrobacter.  Each of these performs a different task in getting that ammonia to turn into nitrate. However, the whole process of turning ammonia into ammonium nitrate fertilizer with bacteria is called NITRIFICATION.


The biological conversion of ammonia to nitrate fertilizer is called nitrification. Nitrification is a two-step process. Bacteria known as Nitrosomonas convert ammonia and ammonium (a different version of ammonia in the water) to ammonium nitrite. Next, bacteria called Nitrobacter finishthe conversion of nitrite to nitrate. The reactions are generally coupled and proceed rapidly to the ammonium nitrate form; therefore, ammonium nitrite levels at any given time should usually be low.

However, if the levels of nitrobacter are low, and nitrosomonas levels still remain high, you may get excess amounts of ammonium nitrite in your system.  This can happen due to overfeeding your fish, and a buildup of ammonia and ammonium due to having undigested rotting feed hanging around in your system. Excess ammonium nitrite causes fish to go down with brown blood disease which can kill all your fish in half an hour.  Therefore test daily for excess ammonia and ammonium nitrite. 

Another indicator of this excess ammonium nitrite situation is if you see your fish refusing to feed and congregating near the surface, gasping for air. Do a 50% water change of the whole system immediately with dechlorinated dechloramined water, and make sure no undigested food and fish mulm is hanging around in the filtration units and grow beds/hydroponic raceways.

These bacteria known as ‘nitrifiers’are strict ‘aerobes,’ meaning they must have free dissolved oxygen (lots of air bubbling through the water in practical terms) to perform their work. Nitrification occurs only under ‘aerobic’ conditions (with lots of air dissolved in the water) at dissolved oxygen levels of 1.0 mg/L or more.At dissolved oxygen (DO for short) concentrations less than 0.5 mg/L, the growth rate of nitrifying bacteria is minimal. Nitrification requires a long fluid retention time, a low food to microorganism ratio (F:M for short), a high mean cell residence time (measured as MCRT), and adequate buffering (alkalinity). 

In other words, the water should not flow too fast through your system to allow the bacteria to hang on to the orchard net, sponge or media you are using as your filter and happily sit there digesting ammonia and ammonium nitrite.  Your aquaponic system should be designed to achieve this in its filtration section and/or media based grow beds. Temperature, as discussed below, is also important, but not really.

The nitrification process produces acid.This acid formation lowers the pH of the biological population in the filtration tank or grow bed and can cause a reduction of the growth rate of your nitrifying bacteria. Since these can take up to four weeks to repopulate your aquaponic system if they are lost due to inattention or other malfunctions, pH maintenance in your aquaponic system is vital. 

The optimum pH for Nitrosomonas and Nitrobacter is between 7.5 and 8.5; most aquaponic systems’ circulating water is adjusted with tiny amounts of lime and potash to stay at a neutral pH of 7.0.   Nitrification stops at a pH below 6.0.The nitrification reaction (that is, the conversion of ammonia to nitrate) consumes 7.1 mg/L of alkalinity, so the pH of the water in your aquaponic system should be tested daily and the levels adjusted when necessary back to a neutral pH of 7.0.

Water temperature also affects the rate of nitrification. Nitrification reaches a maximum rate at temperatures between 30 and 35 degrees C (86oF and 95oF). At temperatures of 40oC (104oF) and higher, nitrification rates fall to near zero. At temperatures below 20 degrees C, nitrification proceeds at a slower rate, but will continue at temperatures of 10 degrees C and less. However, if nitrification is lost, it will not resume until the temperature increases to well over 10 oC.  So watch your water temperature and also make sure it is the right temperature for the species of fish you are raising!

 Some of the most toxic compounds to nitrifiying bacteria include cyanide, thiourea, phenol and heavy metals such as silver, mercury, nickel, chromium, copper and zinc. Nitrifying bacteria can also be inhibited by nitrous acid and free ammonia.  As I said, the chlorine and chloramine used as antiseptics in your ordinary domestic water supply will also kill them.

Water quality in your aquaponic system depends on the partnership between these two kinds of nitrifying bacteria, your plant population, and YOU.

It’s up to you to check and test daily and at every feeding time to make sure that conditions in your aquaponic system are right for all its inhabitants, including the all-important nitrifying bacteria.

Look after these little creatures, and they will look after you, and your plants and fish.

However, if you are in an emergency situation, it is always useful to have these (below) to restart your nitrifying bacteria population WITHOUT a four-week wait-instant nitrifyng bacteria:

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Over 30 long chapters of aquaponics advice, how-to articles, and journalism.Aquaponics Global Anthology 1 [paiddownloads id=”1″]



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4 thoughts on “The Importance Of Nitrifying Bacteria In An Aquaponic System.

  1. Pingback: Aquaponic System Rules Of Thumb. | Aquaponics Global

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  3. With havin so much written content do you ever run into any
    problems of plagorism or copyright violation? My blog has a lot of exclusive content I’ve either created myself or outsourced
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    • The whole idea is to spread the news about aquaponics. And to sell a few authoritative books about it, and make sure people can buy equipment they can actually use. If people copy the content, if they leave a link back to the site, that is good netiquette.

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