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Anoxic Filtration   (Anoxic Filtration)


I wrote the following articles for Koi Carp Magazine.
Therefore they own the copyright but the Editor has given permission for them to be republished here.
Thank you, Karen.

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Anoxic Filtration - Part 2

Nitrifying bugs are everywhere
Nitrifying bugs, (nitrogen cycle bugs), are abundant in nature.  They don’t just grow and thrive in a biological filter. In fact, they will grow everywhere in a pond environment. In a natural pond, lake or river, they grow on every available surface.  This includes the pond bottom, rocks and plants. In an ornamental pond they will also grow on all available surfaces, not just within the filter.

The purpose of a biological filter is to make a “bacteria friendly” environment that will concentrate the bulk of the population in one easy to manage area where the main nitrogen cycle will occur.  But that does not mean that this is the only place where ammonia is being nitrified (turned into nitrate).

Ammonia is also being nitrified throughout the whole pond. All that is necessary for this to occur is a wet surface and a supply of ammonia, oxygen and carbon.  Taking all the biological media out of the filtration system, therefore, won’t stop the production of nitrate altogether, it will still be produced elsewhere.

It may not be immediately obvious but there are also ample opportunities for the nitrogen cycle to take place actually within the biocenosis baskets themselves. The baskets are underwater and so, stating the obvious, all surfaces of the clay particles are wet.  The water that is just inside the baskets will also be rich in oxygen and carbonate, so we have an ideal place for nitrifying bugs to set up home and to convert ammonia to nitrate.

So, if nitrate is actually produced within a basket that is designed to eliminate nitrate, does this mean that these baskets are a failure?  Not in the least, as will be described later.

The scientific bit
The science panel below shows two equations that I light heartedly refer to as; “what nitrosomonas and nitrobacter eat for lunch”. They are included for those that may be interested.  It isn’t necessary for the purposes of this article to try to understand them, but they are how a biochemist would make sense of the nitrogen cycle. The description following them that explains what they mean has been simplified as far as is possible with all the nasty chemistry taken out.  You may need to read it a couple of times to understand it, or if you prefer, you may safely skip the panel entirely.

What nitrosomonas eat for lunch:-
55NH4+ + 76O2 + 109HCO3- = C5H7O2N + 54NO2- + 57H2O + 104H2CO3

What nitrobacter eat for lunch:-
400NO2- + NH4+ + 4H2CO3 + HCO3- + 195O2 = C5H7O2N + 3H2O + 400NO3-

What the equations tell us
You can either count atoms and molecules, or you can take my word for it, that these equations could very roughly be described as saying:- One molecule of ammonia + four molecules of oxygen + seven molecules of carbonate becomes one molecule of nitrate + a bit of bug tissue (that is what C5H7O2N means in these equations, a molecule of “bug”).  In other words, the bacteria can be thought of as “eating” ammonia, oxygen and carbonate and getting slightly bigger.  (Eventually when they have consumed enough, each bug will divide into two separate bugs, but that is beyond the scope of this article).

If we ignore the carbonate and also ignore the fact that, in this process, the bugs are getting bigger in the process and we just concern ourselves with what happens to the ammonia, it gets even simpler.

One ammonia + four oxygen eventually equals one nitrate. Let us now apply this to what is going on inside a biocenosis basket, and follow the ammonia molecules as they are drawn by into the baskets to their doom.

Beginner biocenosis basket (grey 203,203,230) 360 px
Figure 1.  For clarity, zones A and B have not been drawn to scale.  In practice these two zones are only a few millimetres thick before all the oxygen has been exhausted

Zone A
Negative charges in the baskets start to attract ammonia molecules towards its centre.  As these molecules pass through zone A, nitrifying bacteria, (nitrogen cycle bugs), will grab one ammonia molecule and four oxygen molecules; they will then excrete one nitrate molecule.

The ammonia level in zone A will have dropped a little, the nitrate level will have risen by roughly the same amount but the oxygen will have dropped considerably, (four times as much).  Although there is now far less oxygen, there will still be enough of it for the nitrogen cycle to continue.  We will continue to journey with the ammonia molecules into zone B.

Zone B
As more and more ammonia is converted to nitrate, the ammonia level drops even more and the nitrate level rises. So much oxygen has been used in the process that this area can no longer be called truly aerobic, (oxygen rich), but there is still a little oxygen left to sustain some nitrifying bacteria so we will follow the remaining ammonia as it journeys into zone C.

Zone C
The biochemistry in this zone is the stuff of nightmares and almost defies simplification, but I will try. The ammonia is still being pulled remorselessly toward the centre of the basket but almost all oxygen in the water has already been used. The nitrogen cycle, as we know it, ceases. Nitrification cannot occur if dissolved oxygen levels fall too far below about 2 mg/L, and it will be lower than that in zone C. In this zone, facultative anaerobic heterotrophic bacteria live.

The first thing to understand about this zone is; what on Earth is a facultative anaerobic heterotrophic bug anyway? Roughly speaking, facultative anaerobic, means that it has the facility (or ability) to live anaerobically, (where there is very little oxygen), provided it can steal some.  Heterotrophic bacteria is simply a description of their “eating” habits; they like to “eat” organic molecules. So a facultative anaerobic heterotroph is simply a bug that can live where there is very little oxygen and likes to “eat” organic molecules.  That wasn’t so hard was it?

Where it can steal its supply of oxygen from is not hard to understand either. Remember the nitrate that was produced by the nitrogen cycle bugs? The chemical symbol for nitrate is NO3, (one atom of nitrogen, joined to three atoms of oxygen).  For a facultative anaerobic heterotroph, this is a feast.  It can easily take the three oxygen atoms and leave the nitrogen.

Bugs don’t actually eat!
Although it is convenient to refer to bugs “eating” ammonia or nitrate and breathing oxygen, in reality, they don’t have little mouths nor, indeed, do they have lungs. Ammonia, nitrate and oxygen are simply absorbed directly through their cell walls, just as if we were able to eat by placing food onto our stomachs or breathe by absorbing oxygen through our chests.  When oxygen is taken from nitrate in this way, the atoms of oxygen enter the bug and the nitrogen is left behind. This nitrogen is still dissolved in the pond water but it will be pleased to leave the water behind and go back into the atmosphere at the first opportunity. In this way, although there are nitrogen cycle bugs living in the biocenosis baskets and they will be busy putting nitrate into the water, other bugs in that same basket are just as busy disposing of it.  The overall effect of a basket is to totally remove ammonia with no by product chemicals remaining in the water.

There’s more
If that was all a biocenosis basket achieved, it would be pretty marvelous, but there is even more science going on. We haven’t even considered the full extent of what is going on deep in the baskets yet, other than to say that “electrical charges” attract ammonia molecules toward the centre of the basket. How does it do this, and what happens to the ammonia when it gets there?

Molecules are not little magnets, but for a basic understanding of how molecules work, it is convenient to imagine that they behave just like little magnets.  When we played with magnets as children, we discovered that two similar magnetic poles repel each other but opposite poles attract and will stick together.  Molecules behave just like that, but the forces are electrical charges, similar to static electricity, not magnetism.

The charge on an ammonia molecule (NH4+) is positive, and the charges in the basket are negative. The strength of these charges increases towards the centre of the basket.  Opposite charges attract and the greater the opposite charge, the greater will be the strength of the attraction and so ammonia molecules will be pulled inside through zones A, B and into zone C as described above.

Although some of the ammonia will have been totally disposed of along the way, much will still remain, and once it is there, it cannot escape.  The way ammonia is taken up by plants roots is a complex relationship involving yet more molecular charges and it isn’t necessary to understand this mechanism in order to understand how biocenosis baskets work. It’s sufficient to say that the charges attract ammonia right up to the plant roots and hold it there. When the plant is good and ready, (dependent on more biochemistry), its roots will simply absorb the ammonia and the plant will produce luxuriant growth.  In this way yet more ammonia has been permanently removed from the pond ecology.

What happens in unplanted baskets? More bugs, I’m afraid. For those biocenosis baskets that don’t contain plants, the facultative anaerobic bacteria that inhabit zone C will perform a second clever trick. Earlier, we discovered that these bacteria preferred to take oxygen directly from the pond water, but when there was little or no oxygen available, as in zone C, their first trick was to obtain some by taking the atoms of oxygen from any nitrate that had been produced by the nitrifying bacteria, (nitrosomonas and nitrobacter).  What happens when they have used up all that nitrate? They simply switch to directly metabolising ammonia to provide their energy needs!  The expression “clever as a sack of monkeys” should be changed to “clever as a basket of bugs”. Whether or not the biocenosis baskets contain plants, the ammonia that is drawn into a basket has no escape. If plants don’t get it, the bugs will.

Not every pond keeper wants to have a pond full of aquatic plants behind their koi pond, or they may not have the space to do so.  The fact that the biocenosis baskets don’t have to contain plants to mop up ammonia because a colony of bugs will soon develop and will take the opportunity of a free ammonia lunch, enables anoxic filtration to be sited indoors or disguised under decking.

Building the system
Fortunately, building an anoxic pond is far easier than understanding how it works.  In Kevin Novak’s original pump-fed design, (figure 2), water is pumped from the main pond into the anoxic pond. In order to prevent the flow of water from disturbing the baskets, it enters through a simple diffuser.  Figure 4 shows Kevin’s suggested diffuser but any other design could be used if preferred. The water then returns back to the main pond by gravity. The anoxic pond should be about 24 inches (600 mm) deep and it can be any convenient shape that is large enough to allow approximately one basket per adult fish.  For clarity, only three baskets are shown, in practice there should be approximately one basket per adult fish.

Anoxic filtration - pump fed

It’s possible to modify the design to a gravity fed system for those who don’t like pump fed systems or who want to modify an existing gravity fed system (see figure 3).  As in the pump fed system, the water should be diffused as it enters the anoxic pond. One way to achieve this would be to extend the 4” bottom drain pipe above water level and to drill around 100 x ¼” (6 mm) holes in it.

Anoxic filtration - gravity fed

Are there any drawbacks?
There are no drawbacks but one point is worth careful consideration. Settlement will occur in the anoxic pond and it will eventually need to be emptied or flushed to waste just as any other settlement chamber. In order to keep the drawings as simple as possible, I have left out details of pre-filtration and a drain to make emptying easier. A sieve is a suitable pre-filter for the gravity system and a simple way to close off the main pond when a gravity fed anoxic pond is being emptied would be to make the perforated section of pipe removable and have a suitable length of un-perforated 4” pipe that can replace it whilst emptying.

And the advantages?
Apart from the reduction in nitrate levels, and the fact that the system can be built so inexpensively, it is ubiquitous.  It will fit anywhere because it can be built to fit whatever space is available; the only constraint is that there should be about one basket per full size fish.  But even in this, there is flexibility. If ever you need more baskets and space is limited, simply stack an extra layer of baskets on top of the bottom layer, taking care that they are spaced so that the bottom of one basket doesn’t rest directly on the surface of the one below so that water can still flow past all surfaces of all baskets.

[Update 2015]

This article was published in the UK in Koi Carp magazine in 2009 and, since then, many hobbyists in the UK and elsewhere have built an anoxic system.  Naturally, there has been a great deal of feedback via this website, via personal email to me and also in long-running forum threads.
For anyone who wishes to build an anoxic system I have written a more detailed article that addresses all the questions that have been asked and issues that have arisen during that time.
The article is much more detailed but all the complicated science has been confined to science panels that can be read by those who want to know these details but which can safely be ignored, without losing any important detail, by those who don’t.
There is also a detailed step by step by step build and details of substitute materials for hobbyists in countries or areas where Kevin’s originally recommended materials aren’t available.
(click here)

The future

The anoxic system has been developed in America over the past 20 years. It has gained considerable respect over there, from those who have tried it and found that it provides nitrate reduction even below that of the incoming tap-water, leading to crystal clear pond water. In the UK it is becoming a much talked-about subject and I believe that none who have tried it so far have been disappointed.

The anoxic filtration system was design by Dr. Kevin Novak PhD. Full details have been published in his CD book which is now available as a free download on iTunes:

Kevin also has FAQs and gives other useful information on his blog on this link:


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