Table of Content (alt-q)

To enhance readability, 3 sliding menus are added.

Prologue
Denitrification and Nitrate Reduction
Micro-Organisms Involved in the Denitrification Process (has menu)
Algaes
Bacteria and their Living Conditions
Simulate Wave Motion in Ocean
Denitrification Process (has menu)
Mineralization
Nitrification
Dissimilation
Careful
Biological Filteration Function of Live Rocks
Redox Potential Measurement
Finally, the Biological Filters (has menu)
BioLogical Filter (with Image Map Feature)
Denitrification Filter
Protein Skimmer
Epilogue


Prologue

We find it much easier to introduce the biological filteration process after we have delivered a proper understanding of the biochemical process that occurs in aquarium systems. So we will start off by looking into the biochemcial process and the importance of different alges and bacteria, and live rocks. Then we will come back to the biological filteration issues and introduce the basic principle of protein skimmers.

Generally speaking, decompsition in any aquarium system refers to the chemical reactions that convert organic material into inorganic material. The chemical reactions, however, do not take place automatically. The chemical reactions require different types of bacteria to break down the organics into inorganics in a step-by-step fashion. The process of the chemical breakdown, however, also produces toxic by-products. Usually these intermediate by-products will be handled by the different bacteria in the next step of the chemical reaction. But if the amount of these toxic by-products exceeds the level that your tank is able to handle, the accumulation of these by-products must be removed manually. The removal of these undesired by-products represents the biological filteration process.

Denitrification and Nitrate Reduction

The chemical organics that we want to remove from our tanks come from overfeeding, decay of dead algaes and dead corals, together with the natural metabolism of the living creatures. The major organics are Ammonia (NH3), Ammonium (NH4+), Urea, and uric acid.

Common to all these organics is the presence of the Nitrogen (N) atom, and hence, they are usually referred to as the nitrogenous organics. The breakdown of the nitrogenous organics is generally described in establishing the cycle for a new tank. The nitrogenous cycle involves three stages: Mineralization, Nitrification, and Dissimilation. These three stages occur in the order as described because the next stage cannot happen without the end products from the previous stage. If the nitrogeneous cycle is successfully established, Dinitrogen Oxide (i.e. Laughing Gas) and Nitrogen gas will be produced at the end and the process is called Denitrification.

What do we mean by "If the nitrogenous cycle is successfully established ..."? Denitrification is not necessary a-must. There is always a possibility of Nitrate Reduction. The Nitrate Reduction represents a failure in establishing the nitrogenous cycle because the end-products are Ammonia (NH3) and Ammonium (NH4+) - same as what we started with. However, same as the situation of heavy metal elements, the chance of Nitrate Reduction is very low. If you do everything correctly, Nitrate Reduction barely occurs and you should not be worrying about it.

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Micro-Organisms Involved in the Denitrification Process

Algaes

As we have mentioned above, many different types of bacteria and organisms must be present in order to set up a successful denitrification process. Therefore, we want to introduce a few terms used to describe these bacteria and their living conditions. These terms will become very useful in the following discussion of the three stages of the denitrification process: Mineralization, Nitrification, and Dissimilation. They also help you to appreciate the usefulness of live rocks (besides its aesthetic interest) later on.

Algaes are always present in your tank. Algaes are simply a type of plants that live in the water. Same as other plants, algaes are capable of doing photosynthesis. They convert inorganic material, water, and carbon dioxide molecules into sugar in the form of glucose. So we see that some algaes are desirable because in the process of supporting their own living, they eliminate some undesired inorganics, mainly nitrogen and phosphrous, from the water. This immediately fits into the goal of the bio-filteration proces.

However, as you know that not all algaes are welcomed in the tanks. This is paricularly true with the green algae. Green algae can usually be found under the bases of corals. They are bad because they weaken the skeleton of the stony corals, and hence, the bases become soft. This eventually destroys the bases and kills the corals. There is another reason for which we want to keep the growth of algaes under control. We said that algaes are capable of doing photosynthesis and they convert inorganics into organics. The problem comes in when the algaes decay. The inorganics that were stored inside the algaes' cells will be released upon the death of the algaes. For this reason, algaes are also known as the "nutrient bombs". When the "nutrient bombs" explode, they release excess amount of nitrogenous compounds into the tank. Unlike the ocean, there is comparatively much weaker current and a much smaller volume in the tanks. The biological system cannot handle the "nutrient bombs" in a tank as easily as in the ocean. This gives another good reason for you to set up a good bio-filteration system.
Bacteria and their Living Conditions

Similar to the situation of the algaes, there are numerous kinds of bacteria. However, we will only talk about four types of bacteria here. In fact, the four types represent only two groups of bacteria. The first group is aerobic and anaerobic and the second group is the heterotrophic and autotrophic bacteria. Aerobic bacteria require oygen to live; whereas anaerobic bacteria do not. On the other hand, we can also categorize bacteria according to how they generate energy to support their only living. If the bacteria gain the energy by consuming the glucose, they are heterotrophic. On the other hand, bacteria that can generate energy for their needs without consuming glucose are autotrophic. For example, nitrifying bacteria gain the energy by oxdiating inorganics (not by consuming glucose), hence they are autotrophic. Nitrifying bacteria, which is involved in the Nitrification process, is also aerobic. Bacteria involved in the Dissimilation process, however, is anaerobic. (In general, nitrifying bacteria is called chemo-autotrophic bacteria. There are other types of autorophic bacteria, but they do not clearify the discussion any further. So we omit them here.)

Wave-Making Power Bar

As you can imagine, the distribution of oxygen in the tank is closely related to the steam of the current. For a reasonably large tank, there is a need to have more than one return or power-head to pump water from the sump back to the tank. The idea is to generate a resultant steam that can eliminate the dead zone (area with a low oxygen level or anaerboic area) as much as possible. In the old days, this requires you to locate the best spots in the tank for your power-heads so that one steam is opposing to the others. This makes the distribution of oxygen in the tank more evenly.

Recently, there is a product in the market that can reduce your time to locate these spots greatly. The product is simply a power bar that has a built-in micro-controller which can provide power to a particular outlet in a pre-determined phase. By providing each outlet power at a different time, this essentially creates a cycle of the water flow in your tank. The idea is to simulate the wave motion in the ocean in your tank.

Below are two pictures of the same product: the Natural Wave Multi-Cycle Pump Timer manufactured by Aquarium Systems. The picture on the right-hand-side shows the power cycle that each outlet has. Note that this individual power bar has only 3 timer outlets. The other oulets are regular ones. On the left picture, you can see that this power bar has a knob to adjust the cycle frequency.



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Denitrification Process

As we mentioned above, denitirfication process involves three stages: Mineralization, Nitrification, and Dissimilation. These three stages require the aid of different micro-organisms. Different types of bacteria are responsible for a different stage in the whole chemical cycle.

Mineralization

In the microscopic world, a giant Protein molecule is a huge collection of well-formed segments of molecules. These segments are usually called amino-acids. In this stage, the amino-acids will be reduced by the heterotrophic bacteria into inorganics. The heterotropic bacteria make use of the carbon atoms in the organic amino-acids in the photosystheis process to support their own living. This coincides with the first step to break down the organics in your tank.

The end products are ammonia (NH3) and organic acids. Immediately, we see that these chemical products must be handled in the coming steps because none of them is desirable. Organic acids is going to drive your buffer capability, and hence, pH level down, if not properly taken care of. Your pH level will soon be low once the buffer capability is exhausted. (If needed, please refer to the MoreChemical page to clearify this point.) Although itself is not toxic, the ammonia can transform easily with water molecules into ammonium (NH4+), which is toxic in this ionic form. A certain amount of ammonia can be handled automatically in your tank by algaes. (Remember that algaes are desirable because of their capability of making use of nitrogenous molecules to produce their own food.) But the majority of these ammonia and ammonium products must be taken care of in the Nitrification stage.

Nitrification

The nitrification process is to oxidize the ammonia (NH3) and ammonium (NH4+) molecules into nitrite (NO2-) and nitrate (NO3-) respectively. Each chemical reaction involves specific bacteria and heterotrophic bacteria. It has now been widely known that heterotrophic bacteria are good for aquarium system because they can convert the amino-acids directly into nitrite and nitrate by-passing the steps of producing the toxic intermediate products. Yet again, the good algaes in your tank can take a certain amount of these nitrogenous organics in the water and convert them into harmless inorganics. Therefore, the good algaes are really sharing part of the work load for your bio-filteration system. Although we advice against keeping any excess amount of algaes (remember the "nutrient bomb" issue), a healthy portion of algaes must be present in your tank.

There are differnt test kits for you to test the nitrite and nitrate molecules. Nitrite molecules are extremely toxic. You can use the test result to estimate the Nitrification process in your tank. Although they are unwelcomed, the ammonia and ammonium levels should not be zero. They are the food for algaes in your tank. Only the excess amount of these molecules must be removed.
Dissimilation

As we mentioned in the prologue, there is a finite, but very low, possibility for the nitrogenous cycle to go wrong. That is, the result of Nitrate Reduction. If the denitrification process is succefully established (in most cases, you will), the end products of this stage are Dinitrogen Oxide (N2O) and Nitrogen (N2) gases. Because of their gaseous forms, these end-products escape by dissolving from the tank to the surounding air. (The dissolving rate depends on the surface of the tank. The larger the surface area, the better the result. This is also one of the reasons why we recommend a wide tank.)

There is one special condition required for the dissimilation process. The bacteria involved is of the anaerobic type. These bacteria live only in the environment of oxygen deficiency. This posts a very special constraint when you set up your denitrification filter. (We will come back to this point in following section in establishing denitrification filter.)

Careful

So now we have done all the introductory work and the rest of the biofilteration discussion is quite straight forward. However, we want to point out a few points that you want to be careful in setting up your nitrogneous cycle.

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Biological Filteration Function of Live Rocks

It is about time to introduce live rocks. On the MoreLighting page, we mentioned that daylight system is critical if your tank has live rocks. We also mentioned that live rocks are the biological filter in the ocean. Now, let us look at the usefulness of live rocks more closely.

It needs no introduction to how wonderful the live rocks can decorate your tank. It is the simplest and most effective way to make your tank look like the ocean scenes that you see on TV. Live rocks are erosive-looking rocks that are found in natural ocean. Live rocks are porous and usually have thousands of holes scattered throughout the entire structure. The porosity is actually an essential attribute for the live rocks to act as biological filters.

The erosive-looking surface provides a much larger surface area than a smooth surface for micro-organisms to live on. Surface area is actually very important in deciding which filter substrate to use in the denitrification filter. The idea is always to provide the largest surface area for bacteria to settle, so that the bacteria will not be washed away by the constant current entering the filter. This explains why the filter substrate should be fine and perferrably has a rough surface.

Since the holes are scattered throughout the entire structure, you can image that bacteria living inside the rock have a very different living condition than those living on the surface. For those bacteria living on the surface of the rocks, they have bright light and sufficient oxygen. For those bacteria living inside the rocks, however, there is no light and a low level of oxygen. Therefore, we have both aerobic and anaerobic bacteria living on the same piece of live rock. Live rocks are in fact an excellent bio-filter because the nitrate produced in the Nitrification stage is handled immediately in the same piece of live rock. This greatly reduces the amount of excess nitrate in the water. Our experience has also shown that using live rocks to set up the biological cycle is a lot quicker than using the other bio-filter products that you can get in the market. We strongly recommend the use of live rocks in any aquarium system.

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Redox Potential Measurement

Before we leave for the discussion of bio-filteration, we want to bring up another jargon used in aquarium system. The Redox potential is another measurement that is similar to pH in nature. They both indicate the general well-being of the tank. pH measures the acidity or basic level in your tank. Redox potential measures the ability for the chemical particles to react with each other. Redox stands for two processes: reduction and oxidation.

You may have noticed that the chemical reactions in the three stages of denitrification is really a series of transfer of electrons from one group of elements to ions. The originally neutral elements donate electrons to the ions so that the ions now become stable. On the other hand, these originally netural elements are now ionized because they have lost their electrons. The originally neutral element is called the reducing agent because it reduces the active ions to its stable form. The final stable product is called the oxidizing agent because it makes the neutral elements unstable.

Redox represents the process in which electrons are attracted and transferred to the positive charges in the water. (It is the simplest way to explain how your battery works. But we are not interested in getting into the details here.) What you want to know about the Redox potential measurement is that it has the unit of voltage. For chemical reactions to occur in the tank, there must be a certain level of Redox potential for the electrons to be transferred. Since the chemical reactions take place because of the bacteria working on the inorganics, it indicates how well the bacteria are doing their work.

Unlike, other measurements like pH, salinity, etc, there is no simple tools to measure the potential. You have to meausure the potential with a delicate electronic meter. Consult with your local pet shop with the Redox meter. However, you need to pay more attention to the Redox potenial level if you also use an ozonizer. Ozonization pumps up the Redox voltage significantly. Why use Ozone? Ozone is usually used because it breaks down organics directly without all the toxic intermediate by-products produced in the denitrification process. However, ozone has the drawback of being toxic itself. Ozonizers are generally safe to use. Again, consult with your local pet shop if you are interested.


Here is a picture of a Redox Controller. It is the same idea as using the pH controller (introduced in the MoreChemical Page) in that a controller, unlike meter, can control the Redox level.We have this particular controller in stock. Please contact us if you are interested.



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Finally, the Biological Filteration System

Biological filters serves the same purpose as mechnical filters in that they are designed to remove unwanted material from the water. Biological filters, however, use bacteria and micro-organisms to achieve that goal. We mentioned that live rocks are excellent bio-filters because they have a erosive-looking surface and thousands of holes scattered throughout the entire structure which are perfect for the bacteria to live. These gives a huge area for micro-organisms to live and a living conditions suitable for both aerobic and anaerobic bacteria needed in the denitrification process.

In this section, we want to outline the importance of three types of filteration system: bio-filters, denitrification filters and protein skimmers.

Bio-Filters (with Image Map Feature)


Bio-filters are quite easy to understand because they all serve the simple purpose: to provide the living conditions for bacteria to process the denitrification cycle. Bio-filters are to provide the living conditions for bacteria to process the nitrification stage, whereas the denitrification filters are to provide the living conditions for bacteria to process the dissimilation stage. The distinction is quite obvious when you see that constant water flow is encouraged in bio-filters, but constant water flow is discouraged in denitrification filters.

On the left, we have two bio-filters from different manufacturers.Click on each box to see what is inside the box.They are both fluidized bed bio-filters. A fluidized bed filter has a chamber filled with a fine filter media. The inlet is usually connected to a power head (with a pre-filter to block mechnical waste from entering the filter). There is an inlet for the water to flow into the bio-filter so that the water pressure will lift the fine particles up and the filterbed increases in volume. This is the fluidized bed. The filter particles remain in a constant mixing motion as long as the bio-filter is running.

The fine filter particles are where the bacteria colonized. Therefore, the finer the particles, the more surface area the total filter-bed can have in a given volume. The constant water motion within the chamber is critical because it ensures the availability of oxygen, and ammonia, or the foods for the bacteria. The rapid water motion is also good for keeping a thin bio-film formed on the inside layer of the chamber. This is because the filter particles also brush the inside layer of the chamber constantly. (Note: A thin bio-film is better than a thick bio-film since it is easier for the bacteria to exchange the organics and the inorganics with a thin bio-film. This is really the surface area argument.)

The bio-filters are very simple to use. Connect the inlet to a power head (and the pre-filter) and the outlet to another filteration unit, such as the denitrification filter, or back to the sump. The only thing that you will need to adjust is the current flowing into the bio-filter.
Although, it does not take long to install a bio-filter, it takes a much longer period for the cycle to mature. Setting up a tank with a new bio-filter can take anywhere between 3 to 6 weeks. The period is determined by the initial amount of biological load in your tank. So to speed up the cycle, you can add a small amount of detritus on startup. As we mentioned in the biological function of live rocks section, adding live rocks to your tank is always an excellent choice to set up your cycle.
Denitification Filter

Denitification Filter is designed to break down the organics in the tank that the algaes cannot handle. There are two conditions that these filters must satisify in order to function properly: the anaerobic living condtion for the dissimilating bacteria and a low current flow. The low current flow is needed to prevent the bacteria from being washed away and to provide enough time for the bacteria to work on the organics. The proper set up of such a filter requires an anaerobic area for the bacteria to live. This anaerobic area should draw your attention when you use your denitrification filter because the effluent water is low in oxygen. That is, you never connect the outlet of the denitrification filter directly back to the aquarium because of the low oxygen level in the output stream. The water flow should be deliberately limited to provide the time that the bacteria need to decompose the organics in the water.

Picture of a Denitrification Filter

Here is a denitrification filter from Aqua Media. It is all that you need for maintaining the denitrification cycle in your tank. The filter has a similar design of the Calcium reactor (also from Aqua Media) discussed on the MoreChemcial page. The bio-balls are where the bacteria live. We have this particular unit in stock. Please contact us for the details of setting up the denitrification cycle in your tank using this excellent system.


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Protein Skimmer

Protein skimmers are so critical that every saltwater aquarium must have one. The protein molecules that concern us here are the same proteins generated from dead algaes and corals, and regular metabolic behavior. The whole point of bio-filteration is to remove these protein molecules in the water. The protein can be removed by algaes through their photosynthesis and bacteria through the denitrification process. However, nitrification (the second stage of the denitrification process) usually happens in a much faster rate then the denitrification process. That is, the tank produces more than it can clean up. So, there are generally more protein in the water than these micro-organisms can handle. This introduces the need of the protein skimmer.

Pictures of a Protein Skimmer



Here we have shown an inexpensive protein skimmer from Lee's Aquarium & Pet Products just to illustrate the basic principle described in the following discussion. Please click on the left picture to see the full size of it. The terms used in the following discussion correspond to the ones shown on the full sized picture. The right picture is taken in our store. It shows the simple protein skimmer at work. The bubbles is formed in the contact chamber and the waste material is in the collection cup. The waste should be cleaned regularly.
A protein skimmer is basically a tube, called contact chamber, with a cup on the top to collect the waste which you must remove regularly. The contact chamber has an air stone sunk at the bottom and is a place where you normally see a lot of bubbles rising to the collection cup (see the right picture above.) The usually electrically charged amino- acids molecules adhere to the air bubbles, by which these charged molecules can be brought to the collection cup at the top. When the air bubbles reach the top of the foam riser tube, they come into contact with the air inside the collection cup, and hence, these bubbles form into foam.

You may notice that not all the foam formed have the protein molecules adhered. You are right. There are two types of foam here: normal and protein foam. We only want the protein foam to be collected in the collection cup and the normal foam to be returned to the aquarium. The normal foam can be quickly broken up and to be returned through the return tube. They are easily recognized as the steam of bubbles of identical size going back to the aquarium. To see the bubble stream clearly. The waste that we want to remove is a brownish protein liquid (after settled) is called adsorbate.

So what can lower your protein skimmer's ability to clean up the water? The basic principle behind the protein skimmer is that the water surface must be electrically charged. However, if the food that you feed to your corals and fishes contains fat, the left-over food in the contact chamber is going to form a layer that can break the foam easily. This lowers the probability for the protein foam to be collected. For this reason, the contact chamber should be cleaned regularly.

If you want your skimmer to work at its peak efficiency, use air stones that can generate fine air bubbles. The finer the air bubbles are, the larger the probability for the protein molecules to be stuck on the bubbles. The air stone should also be kept at the bottom because this ensures that the air bubbles have the maximum amount of time to come into contact with the protein molecules. This again increases the probability for the protein molecules to be collected.

One final note of choosing your protein skimmer is that the bigger is not necessary the better. Check the capability of the protein skimmer before you purchase. The capability is usually quoted as the number of gallon that the skimmer is good for.

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Epilogue

On this page, we have explained the bio-decomposition process in the tank, the significance of algaes and live rocks, before going into our discussion of the bio-filteration process. From our experience, we find that live rocks and a good denitrification filter, a good protein skimmer (not necessary expensive), and a sufficient water movement are three big factors that can easily give you a successful aquarium system. There is a fair amount of material on this page, we hope that you find the information useful.

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