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8.9.3. Assimilatory Denitrification

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Author : David Bogert

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13 minutes
Difficulty : Level 7

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Nitrates in any aquarium CAN be removed via something called assimilatory denitrification but we do not recommend it.

Removing Nitrates with Assimilatory Denitrification

Bacteria, fungi, water molds,  plants and, indirectly, fish can absorb nitrates, nitrites and ammonia from the water and produce proteins. This can reduce the nitrogen compounds by something called “assimilatory denitrification”.  It is common and well documented.  This mechanism CAN be used as a filtration process to remove nitrates from aquarium water.

The most successful and easiest way to use assimilatory denitrification is to just use plants to absorb the nitrates (Mr. Hau’s aquariums and Dr. Novak’s Aquariums). We won’t cover that method here. Instead we will limit this article to assimilatory denitrification via mulm absorption.

Note this is one of many very boring and long dissertations by the author. Read on only if you are a real nerd like the author. Note that the author would simply go ahead and stock the shrimp. I’ve never seen a problem with high nitrates in any aquarium, including shrimp tanks. But some people are very uncomfortable with any nitrates.

Andinoacara pulcher Electric Blue Acara
Andinoacara pulcher Electric Blue Acara

Garbage Can Denitrification

Let us assume one has a level of 160 ppm nitrates in the tap water and one wants to use the water for a shrimp tank. Anecdotally a case can be made that shrimp do not like high nitrates. So how does one reduce the nitrates in the water using assimilatory denitrification? One CAN use “garbage can denitrification” to remove the nitrate.

To do “garbage can denitrification” one can simply set up a large garbage can full of the tap water with a filter on it like a large canister filter. Use foam, K1 or pot scrubbers as the media in the canister. Cycle the garbage can filled with the high nitrate water by any of the many cycling methods.

Then simply add sugar over a period of days till the nitrate drops to an acceptable level. Wait one week then use that low nitrate water for water changes. After taking out the water change water, simply add more nitrate rich water to the garbage can without doing anything to the filter and add more sugar.

OB Peacock
OB Peacock

Wait at least a week till the sugar is gone from the water and then use the water for another water change in the aquarium. Just keep doing this until the canister slows down in the flow. Then clean half of the media in the canister. When the flow slows again simply clean the other half of the media.

This is a way to use assimilatory denitrification to reduce nitrates. But it is tricky, to say the least. One can only use the water if sugar hasn’t been added for a week or two.

Vieja melanura Belize
Vieja melanura – Belize

Aquaponic Filtration

Note that this “garbage can” (a shallower large bin is even better) can easily be set up with a heavy duty LED grow light(s) over it.  Put an assortment of emergent plants like frogbit, water lettuce, water hyacinth, salvinia, azolla and duckweed in the water. Let them grow and simply remove handfuls of vegetation every once in a while.

Typically one of the plants will take over and grow very rapidly, absorbing nitrates. This “hydroponic” setup simply takes advantage of another type of assimilatory denitrification. Both sugar and plants can be used together.

More about using plants for nitrate removal can be found at this link:

6.6. Aquaponic Filtration

Melanotaenia boesemani, Boesemani rainbowfish
Melanotaenia boesemani – Boesemani rainbowfish

Assimilatory Denitrification in Depth

It is possible to accumulate nitrate in a nitrogen rich proteinaceous biofloc in a filter and then remove the nitrate from the aquarium by changing out the media or cleaning the media. There are a whole series of designs which can do this. But the shortcomings of this method far outweigh the benefits. Chief among the shortcomings is that it must be very carefully controlled to prevent disease breakouts in the fish.

Organisms capable of assimilatory nitrate reduction use nitrate, rather than ammonia, as a biosynthetic nitrogen source. Organisms capable of assimilatory nitrate reduction include plants, algae, bacteria and fungi. Assimilatory nitrate reduction takes place under aerobic as well as anaerobic conditions. No net removal of inorganic nitrogen is accomplished by this process, since inorganic nitrogen is converted to organic nitrogen.

Per the paper “Denitrification in Recirculating Systems: Theory and Applications” van Rijn et. al 2005:
Altolamprologus compressiceps Yellow Chaitika
Altolamprologus compressiceps Yellow Chaitika Calvus

A huge variety of organisms incorporate nitrogen compounds into their bodies as proteins as they grow. And the pathways that can accomplish this are many and VERY complex. For instance a high carbohydrate content in the food can feed a bacterial slime build up in the filter. This bacteria slime will incorporate nitrates into the bodies of the bacteria as proteins. And frequent cleaning of the filter can then remove the nitrogen in the bacterial bodies.

Another pathway is that algae can grow by absorbing nitrates from the water. Grazing microscopic worms and organisms can eat the algae. Then grazing fish eat the organisms or the algae. And the fish grow by incorporating the nitrogen compounds into protein in the muscle of their bodies. And the aquarist comes on social media and wonder why they never get any nitrates in their aquariums even though they do no water changes,

Aulonarica Phoenix Hybrid
Aulonarica Phoenix Hybrid

Carbon to Nitrogen Ratio

There is an interesting relationship which occurs in aquariums. The amount of biofloc, beneficial bacteria and nitrate produced in a filter media is dependent on the ratio of carbon to nitrogen in the food. With higher carbon to nitrogen ratios (i.e. low protein food) there is less beneficial bacteria produced, more nitrogen containing biofloc produced (more “assimilatory denitrification”) and less nitrate in the water.


Effect of Carbon to Nitrogen Ratio
Effect of Carbon to Nitrogen Ratio


It is thus desirable with assimilatory denitrification to utilize a low protein food (a high carbon to nitrogen ratio food). Nitrate is easily tied up in biofloc in a sponge filter media if the food fed has a high amount of carbohydrates in it. This absorption of nitrate via bio-accumulation is the “assimilatory denitrification” mentioned above. One can also use any carbohydrate as a carbohydrate feed which gets the carbon to nitrogen ratio up high enough to get large amounts of assimilatory denitrification. These carbohydrates include vodka (otherwise called ethanol), glycerin, sugar and vinegar.

Oranda Goldfish
Oranda Goldfish

Problems with Assimilatory Denitrification

Using high carbohydrate dosing to produce nitrate reduction by assimilatory denitrification has the following problems:

  • It encourages a high dissolved organic compound (DOCs) level in the aquarium water
    • Bacteria in the water column feed on the dissolved organic compounds and proliferate
    • The high bacterial count requires the fish devote significant portions of its immune system to fighting off this bacteria
    • Because the immune system is fish is fighting off the bacteria the fish have fewer resources to fight off diseases
    • And the fish get diseased
  • The biofloc surface has few or no “beneficial bacteria” (technically these are “nitrifying bacteria”) so ammonia spikes are common
  • Because of the water column bacteria the water will typically not be crystal clear
  • The aquarium will often smell bad
  • One needs to clean out the filter media often, which can result in more ammonia spikes and is a pain in the butt.

But it is POSSIBLE to utilize a low protein food, cellulose or carbohydrate additions (sugar, alcohol, vinegar, gluteraldehyde, starch) to remove nitrates from the water. One CAN use this process if one is absolutely dead set against water changes or has VERY high nitrate water. The author does not recommend it. Water change or plants are much better solutions. And remember, nitrate is simply not very toxic. Research says most adult fish are fine with no effects from even 440 ppm of nitrate.

Pelvicachromis taeniatus Nigeria Red
Pelvicachromis taeniatus Nigeria Red

Carbon Dosing

This process is used in a somewhat unique method where vinegar, sugar, alcohol, gluteraldehyde or other carbohydrate is added to a saltwater aquarium in what is called “carbon dosing”. The “carbon dosing” creates bacteria in the water column. The bacteria incorporate both the carbohydrates and the nitrates in the water into their bodies. Then the bacteria in the water column are removed by protein skimmers.  This can prevent nitrate buildup in saltwater. Unfortunately protein skimmers don’t work in freshwater so it doesn’t work in a freshwater aquarium.

Melanotaenia lacustris Lake Kutubu Rainbowfish
Melanotaenia lacustris Lake Kutubu Rainbowfish

Starch Media and Reactors

There are a series of products (Tetra Balance Balls, AquaMaxx Biopellets, ecoBAK PLUS, NPX BioPlastics, BRS Polyhydroxyalkanoate Biopellets) which are marketed to reduce nitrates which are balls of starch or other polymeric carbohydrates, sometimes designed to be used in special “reactors” and sometimes designed to be just added to a filter.

ALL these products say they reduce nitrates to nitrogen gas by anaerobic denitrification. This is just marketing hype. They ALL are just ways to induce assimilatory denitrification. And they have all the shortcoming of assimilatory denitrification. They work in saltwater with protein skimmers, but are very tricky. They do not work in freshwater tanks.

Melanotaenia praecox Dwarf Neon Rainbowfish
Melanotaenia praecox – Dwarf Neon Rainbowfish

Cellulose Reactor

In the 1980’s a type of farm reactor was developed where a couple tons of wood chips were buried with provisions for feeding water contaminated with nitrate fertilizers to the wood chips. “Testing” showed a sizable reduction in the nitrate level of the water coming out of the reactor and the device became all the rage of conservationists.

Then someone thought to put radioactive nitrate into the system and measure the amount of radioactivity in the gas coming out of the reactor. They found out there was little radioactive nitrogen gas in the reactor out-gassing. So the nitrate was not being reduced to nitrogen gas. Then they did isotope studies (the ratio of N15 to N14 changes with denitrification of nitrate) and found there was little or no denitrification to nitrogen gas taking place.

Cynotilapia zebroides Chilumba Maison Reef
Cynotilapia zebroides – Chilumba Maison Reef

What was happening was that bacteria, water molds and fungi were feeding on the cellulose in the wood and taking up nitrate and incorporating it into their biomass as protein. When the cellulose ran out in a few years all the nitrate accumulated was released back into the environment.

The surprising thing is that this was “invented” by a farmer as a way to prevent contamination of the environment. Any gardener will tell you that if you incorporate sawdust into the soil around a plant you will have to add a ton of nitrogen fertilizer because the sawdust will absorb the nitrogen.

Now there is some limited denitrification to nitrogen gas in such a reactor. But it is a hit or miss proposition. Some wood chip reactors will produce considerable nitrogen gas from nitrates while others will not. Conditions have to be perfect, with regions of anoxic conditions being produced in a reactor in which there has to be a good flow of well oxygenated water. This is not an easy thing to obtain.


Aquarium Cellulose Reactors

Some hobbyists have incorporated cellulose reactors into their aquariums and reported huge success with removing nitrates. This will work well if the aquarium is well aerated. When the hobbyist removes the slimy, bacteria laden decomposed cellulose they will be removing a sizable amount of nitrogen from the aquarium. It does take about three months for a reactor to begin working well and absorbing nitrate.

To build such a reactor make up an even number of mesh bags. Fill them with a mixture of 4/5 pea gravel or aquarium gravel and 1/5 wood shavings or wood chips. It is important that the gravel media have large openings that allow lots of flow through the cellulose. One cannot use sawdust as the sawdust will clog up the flow in short order.

Otopharynx Lithobates Black Orange Dorsal.
Otopharynx Lithobates – Black Orange Dorsal.

Put them in a canister or in a sump where there is a flow of well oxygenated water. Replace 50% of the cellulose filled bags on a six to twelve-month schedule. By replacing only 50% of the bags on an alternating schedule one will never be without a mature reactor.

Since this is NOT an anaerobic denitrifying reactor one does not need to worry about flow. Simply flow a goodly amount of well oxygenated water through cellulose of some sort (wood shavings or large wood chips) and let Mother Nature accumulate the proteins for you to clean out occasionally.

The biggest problem is that the cellulose (or any carbohydrate) produces something called “dissolved organic compounds” or “DOCs”. These DOCs feed bacteria in the water column. Not only does this produce cloudy water but it is very unhealthy for the fish.  This is the chief reason I do not recommend assimilatory denitrification.

Melanotaenia splendida Red Tailed Rainbowfish
Melanotaenia splendida – Red Tailed Rainbowfish

Another common problem with such a “reactor” is smell. It is extremely important to aerate the water very well before it gets to the cellulose. This will normally prevent a bad smell.

This type of cellulose assimilatory denitrification with wood chips is much easier to control as there can be a separate filter such as a second canister which does only the oxidation of ammonia to nitrate.

Also note there a million variations which can be made to this design. One can make this a slow flow reactor, where only drops of water per minute are added to the aquarium (typically one uses a dosing pump on an hourly timer). This makes this an anoxic reactor which can reduce nitrates to nitrogen gas. But this type of filter is tricky. It is difficult to avoid smells and sometimes nitrites will be released into the aquarium.

Haplachromis obliquidens
Haplachromis obliquidens

Removing Nitrates with Sugar

Nitrate can be tied up in biofloc in a sponge filter media if the food fed has a high amount of carbohydrates in it. One sets up an aquarium with three large powerhead operated sponge filters, three thick layers of 20 ppi foam in a large canister filter or three thick layers of 20 ppi foam in a sump and runs it for two months. One adds a carbohydrate such as sugar at about 10% of the level of the food added daily.

Then after two months of operation ONE of the filters is thoroughly cleaned of the nitrogen filled brown gunk in the sponge. At three months a second sponge is cleaned. And at four months a third sponge is cleaned. The process is then repeated. This means a sponge will operate for three months between cleanings.

Flowerhorn Parrot Hybrid
Flowerhorn Parrot Hybrid

This will ONLY work with a very large amount of sponge per gram of fish. If there is not a large amount of sponge the water will become filled with sugar which in turn will give lots of bacteria and a toxic environment for fish. This process is more challenging than the wood chip method as the carbohydrates are put into the water as soluble sugar.

This means any filter on the aquarium will build up biofloc and clog. So one runs the risk of losing ammonia oxidation in the aquarium. It is far better to just set this up with the sponge/foam but without the sugar. This typically will only reduce nitrate buildup. It will typically not eliminate nitrate build up. But it is a lot easier and a lot safer for the fish.

Cynotilapia aurifrons Charo
Cynotilapia aurifrons Charo