What does a Bio filter and a Denitrification filter do?

Generally speaking, bio filters are more well known than denitrification filters to us. Usually people only remember that there is a bio filter that goes with a mechanical filter in the system, but forget that there is another filter, denitrification filter that is also needed in the tank. This is unfortunate since a single bio filter only completes half of the biological decomposition by itself. The other half of the biological decomposition is only completed by a denitrification filter.

While the objective of a mechanical filter is obvious - it removes physical wastes from the water, the objective of a biological filter may not be so obvious. In a broad sense, a bio filter removes the "biological wastes" from your water. But this simple definition does not help much because at the minimum, you need to understand what you want to remove and how you remove the "biological wastes". What a bio filter really does is to provide a suitable condition for Nitrifying bacteria in your water to decompose ammonia (NH3) and ammonium (NH4+) molecules into nitrite (NO2-) and nitrate (NO3-) respectively. This deviates from any mechanical filters. Instead of actually participating in the removal of the wastes, it only provides a room for bacteria to remove the wastes.

For some reason, denitrification filters are less well known than bio filters. It is quite often for poeple to confuse bio filters with denitrification filters. In fact, some people believe that denitrification filters are unnecessary. By describing the part that each of the filters does in cleaning up the biological wastes in your tank, we hope to show you that the two are not the same and because they really serve two different purposes - one is equally important as the other.

Living Conditions for Nitrifying and Dissimilating Bacteria

To fully understand why the bio and denitrification filters are different, it is unavoidable to learn a bit of how the biological cycle works. (Since this topic has been dealt with on the More Bio Filteration page, you can find more specific information on the page if needed.) It turns out that to understand just what a bio filter and a denitrification filter does, we only need to remember a few things.

1. There are 3 stages in a normal biological cycle.

• Mineralization - The first step in the chemical decomposition. The end products are ammonia (NH₃) and organic acids.
• Nitrification - To oxidize the ammonia (NH₃) and ammonium (NH₄+) molecules into nitrite (NO₂-) and nitrate (NO₃-) respectively. Note that none of these chemicals are desired in your tank. If your nitrification process is not working, you will end up with nothing but Nitrate Reduction.
• Dissimilation - The end products of this stage are Dinitrogen Oxide (N₂O) and Nitrogen (N₂) gases. These two gases escape from your tank through the water surface. This is one of the reasons for the large volume tanks to have a wide surface, rather than a deep tank.

2. Different types of bacteria are responsible for different stages.

• Nitrifying bacteria, which is involved in the Nitrification process, is aerobic, which means that Nitrifying bacteria need oxygen to live.
• Dissimilating Bacteria, which is involved in the Dissimilation process, however, is anaerobic, which means that Dissimilating bacteria do not need oxygen to live.

3. Different living conditions for different types of bacteria.

• Bio-filters are used so that they provide the necessary living conditions for bacteria to process the nitrification stage.
• Denitrification filters are used so that they provide the living conditions for bacteria to process the dissimilation stage.
• The distinction of the two is quite obvious: Constant water flow is encouraged in bio-filters, but discouraged in denitrification filters. The reason for this is that whenever there is a strong current flow, there is oxygen. Hence, it is necessary for bio filters to have a constant current flow to provide oxygen the nitrification bacteria to live. (When we discuss the Reef 500 system later on, you see one of the advantages of the Reef 500 is that it gives a very good current flow plus a good oxygen level for its biological filter.)

Potential Flaw with Trickle Filters

So far, we see that for a biological filter, current flow and oxygen is enouraged, but for a denitrification filter, current flow and oxygen is discouraged. In fact, with this simple understanding, you may see why many trickle filters fail to do their jobs. A Trickle filter is a wet-dry filter that is supposed to perform as a bio and denitrification filter. In other words, it tries to duplicate what a piece of live rock can do for you. Immediately, you see that the living conditions that your trickle filter needs to provide for the two stages are totally different. In fact, the living conditions for the two types of bacteria are opposite to each other. The critical questions that you must ask are how does the filter take care of the current flow and how does it provide a totally different oxygen requirement for the two types of bacteria. It is quite obvious to see that if either one of these are not taken into account properly, there is a serious problem with your tank - there is no biological filteration going on in your tank. This is the point that we made earlier on that the objective of a biological filter may not be obvious. There is certainly water running in the trickle filter. But is it doing what it is supposed to do?

Please do not mis-understand what we just said. We are not saying that trickle filters are bad. The idea is very good. But a trickle filter only works if enough research has been done before the filter is built. How strong is the current going into the bio filter? How slow is the current going into the denitrification filter? What is the optimal dimension of the trickle filter? If you decide to use a home-made trickle filter, please be aware of these issues. If the power head pumps a current that is too strong , this does not allow a good contact time for the bacteria to work on the ammonia and ammonium chemcials. If the power head is too weak, there will be dead zones (places with no oxygen) in the filter. How strong (or weak) the power head is depends on the dimension of the trickle filter. If the trickle filter is bigger than what the power head is capable of supplying, the power head is "too weak". Also, some power heads are designed for circulation use only, while some are heavy duty power heads; so the type of power head used in your trickle filter really matters also.

Bio Filteration with Live Rocks

Having said that, you may appreciate what your live rocks can do for your tank. A single piece of live rock has the capability of handling both of the nitrification and denitrification process. The surface of the live rock provides the perfect living condition for nitrificating bacteria because there is a strong current flow and a good oxygen level. As the water moves into the interior of the live rock through the many tiny holes scattered throughout the entire piece of live rock, the live rock provides a weak current flow and a much lower oxygen level, which is what the disissimilating bacteria need. For this reason, it is quite common to put live rocks in the tank to provide a good bio and deni' filter, besides the decorative purpose. (This means that the following set ups are only one of the many choices you can use in setting up your biological cycle handling mechanism.)

What does the Redox measurement mean?

Whenever we are talking about the efficiency of a biological filter, a denitrification filter, and a protein skimmer, it is necessary to mention briefly about the redox measurement. Redox, which stands for reduction and oxidation process, is a general measurement that is equally important as salinity, and pH. Here we would like to briefy highlight what redox measurement means when it is referred to different devices.

• Biological and denitrification filters: Redox measurement is basically an index that measures how rapidly the electrons are transferred from the donors to the acceptors, or vice versa. Since the biological cycle is really about charges moving from one type of chemicals to another, the redox measurement refers to how well the bacteria works in the decomposition process. (Note: when charges are transfered from one element to another, the one that just lost the charges is called the donor and the one that just received the extra charges is called acceptor.) Of course, the bacteria can only work at the peak efficiency only when the living conidtions are suitable, the other way to say this is that the redox measurement indicates whether the living conditions are suitable for the bacteria in your tank. (The bacteria that we have been constantly referring to is the bacteria that we need to kick off the cycle in the tank.)

• Protein skimmers: When we explain how a protein skimmer works, we say that the air bubbles produced by your air stone or your venturi pump, can pick up the charged protein (and other) molecules. There is, in fact, a critical assumption that we have made in the statement - the molecules are charged. In pure water where the pH is around 7.0, there are equal amount of positive charges as well as negative charges. So the assumption is generally not valid with pure water. But in the natural sea water and so the water in our tanks, where the pH is around 8.2 to 8.4, the assumption is generally true. In the context of determining the efficiency of a protein skimmer, we say that the redox measurement is a measure of how much of the charged molecules is available for the air bubbles to pick up. As you can imagine, there is really no mechanism for the protein skimmer to pick up only the protein molecules, but not the others. This means that your protein skimmer also removes some beneficial molecules from your tank. Therefore, you need to add a certain amount of chemicals such as iodine, trace elements, etc. regularly to your tank. For what exactly you need to add to your tank, please consult with your dealer.

• Ozoniers and Protein Skimmers: Quite often an ozonier is used with a protein skimmer to maximize the protein skimmer's performance. The ozonier is connected to the air intake of the protein skimmer to pump ozone (O₃) into the air and water mixture inside the reaction chamber of the protein skimmer. Ozone is used because it rapidly breaks down the huge protein molecules from the first stage of biological cycle, the mineralization, directly to the last stage of the biological cycle, the dissimlation. The benefit of doing this is that it completely skips the nitrification process, and hence the tank will be troubled by the ammonia, ammonium, nitrite, and nitrate problems. However, since ozone is toxic and no ozone should be injected into your tank at any time, usage of ozone must be very closely monitored. The way to measure the ozone level inside the reaction chamber is to hook up a redox controller to the ozonizer. First you set the ozonizer to detect a maximum and a minimum level. The range bounded by these two levels is what you think is the safe ozone level. If the ozone level is beyond the maixmum level, the controller then turns off the ozonizer and the ozone level will drop because the ozone will be used up inside the reaction chamber to break down the protein molecules. Once the ozonizer has detected that the ozone level is below the lower limit, the redox controller turns the ozonier on and the ozone level will rise again. By constantly switching the ozonizer on and off, the redox controller ensures that there is no extra ozone anywhere in your tank. Therefore, it is absolutely necessary to use a redox controller accompany with an ozonizer.

Note: Since the redox meausrement has been dealt with on the More Bio Filteration page, please go back to that page for more information. The principle of the redox controller to control the level of ozone is very similar to the pH controller, the Calcium Reactor, and the Carbon Dioxide Regulator described on More Chemicals page.

General Introduction to Bio Filters

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 this 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 give a huge area for micro-organisms to live and a living conditions suitable for both aerobic and anaerobic bacteria needed in the denitrification process.

Having said that, it is quite easy to understand that bio filters represent half of your live rocks: to provide the living conditions for bacteria to process the denitrification cycle. (Unfortunately, the term "denitrification cycle" actually refers to the entire process of the chemcial decomposition of the biological wastes in the tank, which may have confused people of thinking a denitrification tower takes care of the whole denitrification cycle.)

The bio filters that we are going to talk about are Quicksand and MERLIN filter, which are 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 filter bed 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, 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.)

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. In general, it takes a shorter period for live rocks to set up a biological cycle.

Fluidized Bed Bio Filter -Merlin

On the left is a picture of the MERLIN (Fluidized Bed) bio filter that is working in our invertebrate tanks. We have also introduced this product in More Bio Filteration. Let us take a closer look at it here.

With the MERLIN product, the water-flow to the chamber can be adjusted mechanically by varying the Flow Regulator. The Flow Regulator has a Regulator Pin connected at the bottom. Turning the Pin in different directions can raise or lower the Inlet Tube, thereby varying the opening between the Flow Nozzle and the Deflection Plate. The larger the opening between the Flow Nozzle and the Deflection Plate, the larger the flow rate and the higher the level of fluidization. The appropritate level is anywhere between the marked levels shown on the bio-filter

As you can see the bio-filter is quite easy to install. All you need to do is to connect the inlet (the middle and higher blue hose) to a power head. In our case, there is also a pre-filter connected to the power head in order to keep any mechanical waste from entering the power head and destroying it. Water enters the bio-filter by first going through the middle plastic pipe, which directs the water to flow to the bottom of the chamber first. The water then enters the chamber that actually contains the filter media. Once the water has entered the chamber, the filter media is lift up by the water pressure and the fluidized bed is formed. Outside of the chamber, there is a sticker showing the water levels that your fluidized bed should be. It is better to adjust the level to be within the range. Just under the inlet blue hose, you can see the knobs that you can do the adjustment with The adjustment can be made by turning the bigger knob and then the smaller knob (for fine adjustment).

Maintaining your MERLIN bio-filter is also straight forward. The filter media should be added once a while since running the filter constantly can have some of the (really) fine filter media getting away from the chamber and entering your tank. However, this is not the main concern in maintaining this filter. Besides the problem of losing the filter media over time into the tank, there is really no need to change the filter media. This is one of the big advantage of the fluidized bed filters compared to the traditional filters in which you need to change the activated carbon, and others regularly. (Extensive use of activated carbon, as we mentioned before on More Lighting page, is going to cause bleaching and other problems too.)

What is more important is that as time goes by, there will be algaes formed on the surface of the chamber. This calls for the need of maintainance. You need to shut off the filter first and clean the chamber. (Please read the following Quicksand section for a problem with shutting down this bio filter.) If you think it is needed, you can add the filter media at the same time. In fact, the filter that you see here was just cleaned before the photo was taken. But you can still see the algae attached near the bottom of the chamber (the little red suraface area).

To ensure that your filter is working at its peak efficiency, there are two other external factors that you need to check also. Do you need to clean the pre-filter? Is your power head providing enough power for the filter? To answer these two questions, you ask yourself: Are you having a hard time for the fluidized bed to stay at a level that you have set a few days ago? Are you having a hard time to adjust the level to the minimum recommended level? Do you need to keep the inlet open to its maximum level at all times in order to reach the minimum level? If one or more of this answers is yes, then your power head is not strong enough for the filter and you may consider getting a one-level up power head to optimize the filter's performance.

In fact, choosing the right power head for this and other similar bio-filter is critical to the fluidizied bio-filter. This is because we always want a constant water flow into the chamber. Recall that a bio-filter provides the living conditions for the bacteria needed in the 2nd step of the bio chemical decomposition process. This type of bacteria is aerobic in nature. They need oxygen and food. The constant water flow can ensure the availability of the oxygen and food to the bacteria. In other words, if you have purchased this or a similar fluidized bed filter, but forget to get a power head that can support the water flow required, you are wasting your filter. All you need to do is to get a power head that is strong enough to do the job, so there is no need to get a really expensive one. But do remember this point if you are using or thinking of getting a bio-filter

Fluidized Bed Bio Filter - Quicksand

The bio-filters are very simple to use. Connect the inlet to a power head (and a 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.

The QuickSand Filter has a flow restrictor which must be inserted into the filter's outlet hose before set-up. When you are ready to plug the QuickSand bio-filter in your system, place your finger over the outlet hose opening. Fill the chamber with water and let go of your finger once the chamber is purged of air. Let the water running for an hour and turn the adjusting bolt (next to the blue inlet) to adjust the water flow. The fluidized bed should be wihin several inches of the top of a vertical filter. However, in daily usage of the Quicksand, it is recommended to tile the bio filter a bit, so that the bio filter is not actually vertical to the gound. This prevents the filter medic from leaving the bio filter easily and gives extra control of the current flow.

The Quicksand product is really not much different from the Merlin. However, it is generally easier to maintain the Quicksand then the Merlin. The reason is that there is a built-in valve, which is nothing but a metal ball, inside the Merlin reaction chamber. This is a very good idea in case of the power is cut off, or when you shut down the filter for maintainance, or whatever reason. The valve prevents the water from flowing back to your tank. The trouble is that if you don't have a pre-filter, or if you have algaes grown near the valve, there is a very big change that the filter will not be able to start again the next time when you fire it up. The valve is jammed. To fix this, you need to shake the filter hard enough so that the metal ball can move again. Although it may be annoying to do this every time, this problem is not a big deal in general, since you don't need to wash the bio filter very often.

Denitification Filters

As we have said, a denitrification filter is designed to break down the organics in the tank that the algaes cannot handle. We have also mentioned that there are generally two conditions that a denitrification filter must provide, namely, a weak current flow and the anaerobic living condtion in order to function properly.

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 living condition should draw your attention because the effluent water is low in oxygen. That is, you never connect the outlet of a denitrification filter directly back to the aquarium because of the low oxygen level in the output stream.

Here is a denitrification filter from Aqua Media. The denitrification filter certainly looks different from those fluidized bed bio filters. Instead of having the filter medic constantly brushing against the chamber, the bio balls are not moving inside the tower. The bio balls that you see inside the tower is where the bacteria live.

The purpose of having the bio balls is to limit the water flow: they make sure that a strong current directly from the top to the bottom of the tower is avoided. Also water can only come out from the top of the tower, which has a circulation pump installed to pump water from the bottom of the tower back to the sump. By now, we hope that you are convinced that bio filters and denitrification filters are indeed two totally separate equipments and that the potential flaw of the home-made trickle filters is more than merely possible.

With the features of bio and denitrification filters, the living conditions of the different bacteria clearly understood, and the knowledge of the turboflotor 1000 protein skimmer, we are ready to see why the REEF 500 is such a popular system.

REEF 500

To the left is a picture of the REEF 500 system. It consists of a pre-filter (the leftmost), the Ammonia tower (the middle section), and the turboflotor 1000 protein skimmer.

In this system, water first goes to the mechanical filter, then to the protein skimmer, and then to the Ammonia tower. (For some reason, the manufacturer likes to connect the components in a different order than the actual water flow sequence.) It is important to remember the actual water flow sequence since if you connect this system in the order such that water first goes to the Ammonia tower, then to the skimmer, the whole system will become totally useless. If you look at the schematics of the REEF 500, you will see that the water enters the protein skimmer through the bottom section of the Ammonia tower and returns back to the Ammonia tower from the outlet of the protein skimmer, near the top of the tower.

The Ammonia tower has the same set up as a denitrification filter mentioned above. But it is a bio filter, not a denitrification filter. The trick of this system is that the outcoming water of the protein skimmer is rich of oxygen. Since the skimmer has its outlets connected to the Ammonia tower, the water entering the Ammonia tower is rich in oxygen. The water flow can be adjusted by the "adjust knobs" of the skimmer mentioned on Protein Skimmers page.

If you remember that a strong water flow and aerobic living condition of the Nitrifying bacteria, then you see that the REEF 500 unit is generally prefrerred. This is because the system provides an adjustable current and a very good oxygen level needed for the Nitrifying bacteria in the Ammonia tower. However, the system does not include a Denitrification filter, but it is easy to include one if you choose to do so.

The additional advantage of this system is that it can be easily extended to include Calcium tower and other technologies if needed. Calcium tower is a technology that can supply Calcium (chemical needed for corals to build their skeletons) easily to the tank. It is a very important piece of equipment for advance users. If you haven't gone through the More Chemical page, the reason of introducing Calcium tower is that Calcium, although crucial to the growth of corals, does not dissolve into water easily. Then there is the issue of injecting Carbon Dioxide into a Calcium tower to speed up the dissolving process. But the higher the Carbon Dioxide level, the lower the pH, etc. There is an interesting discussion on how to set up a system using a Calcium Reactor, a Carbon Dioxide Regulator, and a pH Controller on More Chemicals. Please go to the page for more details.