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Old 07-16-2012, 10:32 AM   #1 (permalink)
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Default Biological Filtration (translated from the Dutch)

Biological Filtration, Part 1

This post will be more like an article but is meant to discuss filtration in dept. It is a (shortened) translation of a couple articles on a Dutch website, not written by myself but by Adriaan Briene, a passionate aquarian, who died a few years back in an unfortunate attempt to rescue a Thai tourist.

Filtration can be divided in three ways:
- Mechanical
- Chemical
- Biological

Mechanical filtration is just the collection of particles without a chemical or biological effect. With chemical filtration the particles are chemically bound to the filtration substrate. Biological filtration is the binding of substances by bacteria in a filter (or substrate). This article will mostly cover biological filtration, to start with where bacteria live, the biofilm.

This will be boring for a lot of people, so if you don’t like it, just stop reading and don’t comment, but if you get through there will be some interesting conclusions!

There are bacteria everywhere on this planet and everywhere in your aquarium. Not only in your filter, but on the glass, in the substrate, in the water, on plants everywhere!

Bacteria are there right from the start of an aquarium. They’re looking for places to attach and this can be anything in the beginning, even the water surface, also known as a scum layer (first thing you learned from this article, scum layer are live bacteria looking for something to attach to, isn’t this an exciting article?!) The bacteria use the surface tension to hold on to and this is the first visible sign of a biofilm. The same layer will form at your glass, substrate, filter inlet and outlet, etc… if the circumstances are right for the bacteria (bad for you) than they even attach to your fish!

How does this layer form?
- Starting phase: bacteria are mostly in your water and if there are enough nutrients in the water, they colonize the water, this shows up as milky water and is basically a bacteria bloom. Just wait till all nutrients are used up or refresh your water with water with less nutrients.
- Migration phase: Bacteria migrate to a desirable substrate to live on. This will be your filter and substrate but also plants and fish can be subject to the bacteria. (Another reason not to put fish in straight away besides nitrites).
- Colonization phase: Bacteria start to divide and form colonies of bacteria. These bacteria secrete substances which will be noticed by other bacteria (‘Quorum Sensing) and if a concentration of a certain substance is high enough, bacteria start to secrete exopolysaccharides.
- Biofilm formation phase: Epopolysaccharide is a gel like substance (also known as ‘glycocalyx’) with lots of canals. This is the biofilm where bacteria live in to receive nutrients and move around. It protects them from bacteria eating phagocytes, disinfectia (like excel), antibiotics (this is partly why anti BGA antibiotics don’t kill your entire filter bacteria colony) and also serves as reservoir for nutrients.

Here you can see ‘langzaam groeiende cel’ slow growing cell and ‘snel groeiende cel’ fast growing cell (starting to learn Dutch yet?). Nitrifying bacteria are slow growing and heterotrophic bacteria are fast growing. You’ll read the consequences of this later on…

This 3D structure has another consequence; the way bacteria receive there nutrients. Most people think this is controlled by the flow of the filter, but water is almost stagnant inside this 3D structure and depends mostly on diffusion (back to your high school physics book or friend: google). The flow of water through a filter doesn’t add much to the nutrient supply of a filter as seen in the picture below. First conclusion: don’t increase the flow of your filter but increase the surface (more substrate or substrate with a bigger surface)

B is a magnification of A. The biofilm starts at 200Ám. ‘Midden stromingsprofiel’ means middle of the measured tube.

So as you can see, closer to the edges, the flow is always less, but inside the biofilm (first 200 Ám) flowrate doesn’t affect the flow much (4 lines come closer together). This means that your bacteria are almost independent of flowrate, but more dependent on diffusionrate. Diffusion is a quite slow progress, but fortunate for us, small molecules and ions diffuse quite well through the biofilm. Nontheless, diffusion is a quite slow progress as seen in the figure below, and concentrations of different substances/ions can vary a lot inside a biofilm.

This figure is an example of a denitrifying biofilm. Oxygen concentrations are already declining before the biofilm surface is reached (depth=0). Clearly visible is the increase in nitrite in the top layer and the decrease in the deeper levels of the biofilm as a result of the decreasing oxygen levels. In the deepest layers you see the formation of H2S as a result of the lack of oxygen.

In this figure you see a nitrifying biofilm. Oxygen levels are depleting even before the biofilm is reached and inside it is anaerobe after 0,1mm and nitrite increases fast. Faster than most people expect. This means a thick biofilm are not very good and it is better to clean your filter a little more often!

From Adriaan Brienes own experiences; after cleaning his filter, he was able to increase his nitrate concentration from 2,5 to 7,5 mg/L. If you have constant problems with BGA, cleaning your filter might also help because it increases your nitrate concentrations, shifting the N:P ratio (Redfield Ratio) towards N (nitrogen) and making the environment less suitable for BGA.

Also the C:N ratio is very important in the nitrification process. When there is a high C:N ratio (lots of carbon and low nitrogen) the nitrification process stops! This is due to the fact that heterotrophic bacteria outcompete nitrifying bacteria when there is a lot of organic carbon. This makes sense because they grow faster, and if the circumstances for these heterotrophic bacteria are suited, they easily outcompete the nitrifying bacteria.
Feeding with food with a low C:N ratio keeps heterotrophic bacteria count low, the biofilm keeps thinner and your substrate will keep cleaner.

The last graph to make this clear. ‘Koolstof’ is carbon and the rest is almost English I guess.

Adding organic carbon in this case as glucose or ‘suiker esdoorn’ maple tree sugar. This effect is also notable when you add peat or tea (both high C:N ratio) to you water/filter. It slows down the nitrification process!

The positive effect of peat on your plants is besides the fact that it lowers pH, also that it slows down nitrification. Less nitrification means there will be more NH4+ in the water and this is easier for plants to absorb. (Be careful, not good for fish!)

This is only the first part of a serie of articles. If people like this I’ll also translate the next part of this article, where Adriaan Briene covers the question: do we need a filter?

A short summary of this part for the people who didn’t find the motivation to read this all (I think this only becomes interesting if you learned the basics and have a little chemical background so read it again in a few months/years if you like):

- A biofilm is a 3D structure with the nitrifying bacteria in the deepest layer.

- Waterflow is very low in a biofilm and diffusion is the main transportation method for nutrients. In real life this means: don’t increase flow but increase surface of the substrate in the filter.

- Oxygen decreases fast with a thicker biofilm and denitrification starts.

- A high C:N ratio is bad because heterotrophic bacteria take over.

- Peat and tea are negative for the nitrification process (and for your fish) but positive for plant growth.
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Old 07-16-2012, 11:02 AM   #2 (permalink)
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Default re: Biological Filtration (translated from the Dutch)

Oh boy! Haven't had time to read yet, but this evening I will!
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Old 07-16-2012, 11:56 AM   #3 (permalink)
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Default re: Biological Filtration (translated from the Dutch)

Thank you so much for taking the time to translate this!!! It is much easier to read than what the translator online gave me. Yes, please continue...subscribed...
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Old 07-16-2012, 03:49 PM   #4 (permalink)
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Default re: Biological Filtration (translated from the Dutch)

Nice! I can't be happier and some of you know why.

Now brace up because if Yo-han here continues translating you are about to literally go through a college level course in planted tanks. There will be no more of this "But why I have algae when I dose ferts by the book?". There is much more information to come from that Dutch site and it will blow your brains. Guaranteed.

Best part about Adrian's site is that it is READABLE. Anybody can read it and make sense why this or that information is presented.

And, of course, there is more:
After that Dutch site gets enough attention, if things are good, we may look into another similar amazing piece of work: About 670 pages of information specifically about the inner workings of a planted tank. Everything planted tank you can think of and more, much more. All of it objective information, without any fluff. Look at what you just read above and multiply by 670.

How many people here find this to be an exciting time?

I do.
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Old 07-16-2012, 05:02 PM   #5 (permalink)
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Default re: Biological Filtration (translated from the Dutch)

Great stuff, please keep going!

Diana Walstad gives a similar description of the biofilm in her book, but doesn't relate the information directly to aquarium filtration practices. This really puts the pieces together for me. It also explains the inportance of "contact time" in the operation of a biofilter.

Johan, I really appreciate your explanatory comments, and yes, I am begining to read a little Dutch, LOL. Could you put them in parenthesis or italicize them to make it easier to distinguish them from the rest of the translation?
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Old 07-16-2012, 06:19 PM   #6 (permalink)
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Default re: Biological Filtration (translated from the Dutch)

This is great info.

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Old 07-17-2012, 04:39 AM   #7 (permalink)
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Default Biological filtration (part II)

Biological Filtration, Part 2

This second part of this article is about: what is the best filter? A sump, a Hamburger mattenfilter (HMF), a small canister filter, something else or maybe even no filter at all…

For everyone who hoped for a short answer, I’m sorry! But after reading this you’ll hopefully understand the function of your filter better and should be able to determine the best filter and substrate for your aquarium, keep reading!

Why do we use a filter?
- Removing small particles out of the water
- To remove fish produced ammonia and convert it to nitrate
- To convert organic waste (for example food left overs) to substances like phosphate and nitrate.
- To provide flow inside the aquarium (distribution of nutrients)

So the filter has 3 basic functions:
- Flow
- Mechanical function (collecting small floating particles)
- Biological function (converting organic substances to inorganic or simple organic substances)


This is not really a basic function of a filter because you can use a streamer for this as well, but to get water through to filter we need to have a water flow. A filter can be driven by air, the canister pump or a circulation pump in case of a sump. By creating flow through a filter, we no longer rely on diffusion (which is a quite slow process as you read in part I) and we increase the effectiveness of the filter by increasing the amount of water in contact with our filter media. By having more flow, there will be more floating particles collected in the mechanical part but there is a maximum in increasing flow for the biological part. Besides that it is energetic unfavorable because resistance increases quadratic by increasing flow, you don’t want to turn your aquarium into a whirlpool.

Another advantage of flow through a filter is that the longer the water stays in the filter, the less oxygen there is left. Flow provides constant oxygen rich water into the filter and prevents the filter from becoming anaerobic.

Second advantage of flow is the distribution of water through the entire aquarium. The advantages are:
- Heat gets distributed, no warm or cold zones
- Nutrients created in the filter or added by you, are mixed homogeneous and distributed to all corners of the aquarium.
- Reduction of stagnant water layer around aquatic leaves, so they never face a deficiency although a nutrient is available (happens more often than expected)
- Movement of the water surface for gas exchange. In a planted tank this should not be too much, but for an African cichlid aquarium this is perfect to reduce CO2 in the water and raise pH and add oxygen.

You can calculate the influence of the flow on the efficiency of your filter here (this page will be translated later on but shows some illustrations about laminar water flow and the real flow of a filter):

In short, multiple outlets is much better, especially in big aquaria. The location of the filter inlet is not very critical, but a surface skimmer is a nice inlet to reduce a scum layer. the rest of this article will be translated later on.

Mechanical filter function

When you put obstructions in a water flow, objects bigger than the space between them will get stuck. The smaller the obstructions and the space between them the smaller the particles that will get stuck are. This is how a mechanical filter works. A fine sponge will trap smaller particles than a coarse sponge. If you use a diatom filter or diatom earth in your filter, you even filter out the smallest visible particles. In practice we mostly use white foam for the finest particles.

The effects happening in a mechanical filter are:
- Interception/sedimentation: particles crash into an object because of their mass. The faster the flow, the higher the change on a crash.
- Diffusion effect: by its molecular movement (Brown’s movement) small particles take up a bigger space than their own diameter and crash into an object as well.
- Sieve/sifter (zeef in Dutch) effect: like said before, an object bigger than the space between an obstruction gets stuck. Most people think this is the most important function of a mechanical filter, this is not! Only with very small diameter filters or when filters get clogged up, this is the case.
- Sinking/coagulation effect: particles heavier than water and particles that coagulate will sink down in the slower flowing parts of a filter.
- Electrostatic and polar (adsorption) effects: charged particles will attach to objects with an opposite charge, like activated carbon.

Nice all these effects, but in practice most people just put sponges and foam in there filters and they’re done. Yes, this works but you’ll only notice how clear your water can get when you start using diatom filters!
And what happens if we even leave out the foam and sponges… you’ll probably won’t even notice the difference! The rest of the substrate functions enough as a mechanical filter but will clog a little faster.
In the aquarium itself sinking and adsorption happens as well, so even without a filter you’ve this effect and still a clear aquarium.

Small conclusion on the mechanical part: For a mechanical filter, a high flow is better! But it doesn’t contribute a lot to the overall clearness unless you use something as fine as a diatom filter.

Biological filter function

This is basically the most important part of the filter. We already read about the biofilm, but most aquarians think the only function of a filter is converting fish produced ammonia via nitrite to nitrate, also known as nitrification. But there happens a lot more in your filter, and this is only a small part of a filter function! (More can be read in the book: “Water management in Closed Systems” by S. Spotte.) This researcher examined a sand bed filter after 134 days and found the bacteria cultures below:

The phrase on top (aantal bacterien per gram filterzand) means number of bacteria per gram of filter sand, and it is a logarithmic scale. The words before are easily translated to the English word that looks most like it

Only 0.02% of all bacteria are nitrifying!!!

Second remarkable fact is that there are a lot of anaerobic bacteria. Not as many as aerobic but still. Most people think their filter runs purely on aerobic bacteria and some even setup a anaerobic filter but in every filter, almost half of the bacteria is anaerobic!

So there are not many nitrifying bacteria, even less than denitrifying bacteria, who would’ve expected that!
Than how is it possible we still got nitrate in our aquarium? The answer is metabolism…
- When converting ammonia to nitrite, this releases 66 kcal per mol.
- When converting nitrite to nitrate, this releases 18 kcal per mol.
- When denitrifying nitrate to nitrite, this releases 460 kcal per mol.
So this is why nitrite is almost never measurable in our aquaria, converting nitrite to nitrate releases very little energy and these bacteria remain always hungry for more nitrite to satisfy their energy needs.

Also denitrifying bacteria work much slower than nitrifying bacteria so there will be always more nitrate made than used. It also takes months before a filter is colonized by denitrifying bacteria because of this slowness.
But although these nitrifying bacteria are present in low numbers, they’re very important for our aquarium because of their capability of converting ammonia into nitrate.

We’ve seen nitrifying bacteria grow faster than denitrifying bacteria, but heterotrophic bacteria are even way faster. Nitrifying bacteria need 12 hour to double in number. Heterotrophic bacteria can do this in 20 minutes. It is almost a miracle that nitrifying bacteria survive in our filters. And yes, this is true! When there are a lot of organics present nitrifying bacteria are completely outcompeted. De biofilm gets too thick (like seen in the last article) by the heterotrophic bacteria and an anaerobic layer starts to form where denitrifying bacteria start multiplying. So a high organic load leads to a drop in nitrate. This is the opposite of most people think! More fish, means more ammonia (and food) means more nitrate, but this is not true, because there will be more denitrification and thus less nitrate!

It may be clear; the optimal filter depends on the organic load…

Last edited by Yo-han; 07-17-2012 at 04:48 AM..
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Old 07-17-2012, 04:46 AM   #8 (permalink)
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Default Re: Biological filtration (part II)

Biological Filtration, Part 2 (continued)

The article was too long, so here's the rest!

Organic load

What is organic load? Organic load are those molecules made by living organisms containing mostly hydrocarbons. For example, sugars, enzymes, proteins etc.

By feeding a lot, you insert a lot of organics into your aquarium. The more carbon the food contains, the higher the organic load. And this brings us back to the C:N ratio from the first article. Food with a high C:N ratio has a high organic load on the aquarium/filter, will cause a thick biofilm and your filter will promote denitrifying bacteria in your filter, reducing your nitrate.
In other words, the C:N ratio of the food determines which bacteria proliferate in your filter and also affects your nitrate concentration. (Now all to your local lfs and ask for low/high C:N food, I think I’m one of few people working in a lfs knowing what you mean!)

Here is a list of live food sorted by N:P ratio, which also shows C:N.

Nitrate concentrations appear to be influenced by food, filter and of course plant growth.

So what is the best choice for my filter?
If you’ve constant high nitrates, what you want is food rich in carbon, a fine filter substrate and don’t clean your filter too often. A Hamburger mattenfilter would be a good and cheap way to start, low flow and excellent clogging capability. When you experience a lot of BGA and use this or something similar, take it out!
On the other hand if you experience low nitrates, feed low carbon food (for example daphia, cyclops or mysis), low mechanical filtration and clean your filter regular (not too clean off course). Or don’t put anything in your filter at all! With few fish this is a very good option, there are enough nitrifying bacteria in your aquarium to convert ammonia to nitrate and this way denitrification is kept to a minimum. Don’t do this in a heavily stocked tank with few plants!
Also adding peat to your filter (or below your substrate) will add organics and thus lower nitrates.

The use of a sand bed filter is would be a tool as well to keep your biofilm thin because of the sand grains rubbing against each other. This way you also keep denitrification low and nitrates high. Strangely, these filters are mostly used on aquaria with big fish where due to heavy feeding nitrate is usual already high!

Image of an empty sand bed filter integrated into a sump.

Last edited by Yo-han; 07-17-2012 at 04:51 AM.. Reason: Corrected weird font
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Old 07-17-2012, 05:58 AM   #9 (permalink)
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Default re: Biological Filtration (translated from the Dutch)

Johan, I have merged your threads because this is important information, and I am afraid the different parts will become separated if they are in different threads.

I have also added headings on your posts to indicate which part it is, and changed the title of the thread.

Thanks for allowing me to meddle!
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Old 07-17-2012, 06:34 AM   #10 (permalink)
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No problem! Looks good!
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