Heterotrophic Bacteria and Their Practical Application in a Freshwater Aquarium

Written by Kmuda. Posted in All About the Water

Aquarium Bacteria and Filtration Manifesto, Part 2

In part 1, we discussed the "good guys", the autotrophic nitrifying bacteria. Now let's turn our attention to the dark side and discuss Heterotrophic bacteria. These can be considered the “bad guys”. While Heterotrophic bacteria perform a necessary role in our aquariums, it’s a role we need to manage. Otherwise, these bacteria can limit, or even eliminate, the effectiveness of autotrophic nitrifying bacteria.

Heterotrophic bacteria in our tanks are generally from the genera Bacillus and Pseudomonas. It is important to note that some species of Pseudomonas bacteria are believed to be the cause of some bacterial ulcerations in our fish.

Heterotrophic Bacteria

Heterotrophic bacteria are the organic sludge degraders in an aquarium, deriving energy from breaking down organic compounds they take in from the environment. In our aquariums, the principle-limiting factor affecting populations of heterotrophic bacteria is the availability of organic carbon, with the primary organic carbon source being provided by the fish and by the aquarist, in the form of fish poo and excess food.

The other role that heterotrophic bacteria play in our tanks is as the denitrifiers (convert nitrate into nitrogen gas). In this instance, they are the good guys. But, as we will discuss later, these good guys can easily turn bad.

Heterotrophic Bacteria: Prerequisites

Unlike autotrophic bacteria, there are no prerequisites to supporting heterotrophic bacteria, excluding the denitrifying bacteria, which we will discuss later. Where there is an organic food source, there will be heterotrophic bacteria. They will exist in a high oxygen environment and they will exist in a low oxygen environment. In addition, there are many species of heterotrophic bacteria that are facultative anaerobes, which means they can function with or without oxygen, filling completely different roles depending on the level of dissolved oxygen. Some of these facultative anaerobes are denitrifiers.

Heterotrophic Bacteria: Impact on Autotrophic Nitrifying Bacteria

Heterotrophic bacteria can divide every 20 minutes, compared to every 12-20 hours for autotrophic bacteria. This indicates that, provided a sufficient food source is available, Heterotrophic bacteria can out-populate autotrophic nitrifying bacteria in our tanks by an astromical factor of 4,722,366,482,869,645,213,696 to 11 over a 24 hour period.

As has been mentioned, heterotrophic bacteria directly compete with autotrophic nitrifying bacteria for both oxygen and surface area. In fact, they hold the upper hand in this regard. Research has identified that even in environments low in organic carbon, heterotrophic bacteria occupy 50% of the available surface area of an aquarium. The only factor limiting their population, preventing them from over running the tank, consuming the oxygen and surface area required by the autotrophic nitrifying bacteria, is the amount of organics the tank contains.

Unlike autotrophic nitrifying bacteria, many species of heterotrophic bacteria can survive being dried out. If you allow your filter media to dry out and then place it back into the tank, the heterotrophic bacteria will quickly come to life and populate the media, making it that much more difficult for the media to be populated by nitrifying bacteria. For this reason, amongst others, I recommend any media that has been dried out be sterilized (by boiling) prior to reuse. The sterilization process will kill off any heterotrophic bacteria remaining on the media, leveling the playing field once the media is reintroduced to the tank. Since autotrophic nitrifying bacteria do not survive being dried out, there is no benefit to not sterilizing the media. There is a benefit in doing so.

Organic Carbon

Please do not confuse “organic carbon” with “activated carbon”. Organic carbon is organic matter of biological origins that is capable of decay or is the product of decay. Examples of organic carbon in our tanks are fish poo, uneaten food, plants, dead fish, etc… Activate carbon is a chemical filtration media.

Cloudy Water

Whenever you hear reference to a “bacteria bloom” resulting in cloudy water, it is the heterotrophic bacteria that are causing this bloom, not the nitrifying bacteria. Autotrophic nitrifying bacteria reproduce too slowly to cause cloudy water. Therefore, cloudy water from a bacterial bloom is not necessarily an indication of a cycling tank, a common reference that could only be correct if it is an indication that all bacteria in the tank has been wiped out (a result of medications, chlorination, etc…) or if it is a new tank void of heterotrophic bacteria. Regardless, in most cases associated with an established tank, cloudy water is an indication of excess organics, not a tank cycle.

While a tank cycle is not the cause of cloudy water, cloudy water could, however, result in tank mini-cycle. A bacterial bloom resulting in cloudy water is an indication of excess dissolved organics existing in the water column. A subsequent explosion of heterotrophic bacteria will occur to consume these organics, eventually converting them into ammonia. If the existing colonies of nitrifying bacteria are insufficient to deal with the sudden (but temporary) increase in ammonia, spikes will occur. In addition, since heterotrophic bacteria compete with autotrophic bacteria for oxygen and surface area, such an explosion of heterotrophic bacteria may reduce oxygen levels available to the autotrophic nitrifying bacteria, potentially making them less efficient and less able to compete. With the excess food source available to the heterotrophs, along with the reduction in oxygen, combined with the ability of heterotrophs to out-populate the autotrophs by a factor of 4,722,366,482,869,645,213,696 to 11 , the heterotrophs can quickly take over the available surface area. The potential end result, the heterotrophs over run the autotrophs, resulting in subsequent spikes in ammonia and/or nitrite, until the excess organics are consumed (or removed), at which point the autotrophs can start to regain ground.

As has been mentioned several times, you prevent this potential issue by providing an environment conducive to autotrophic nitrifying bacteria. With sufficient (excess) surface area, sufficient (excess) flow rates, sufficient (excess) oxygen levels, and an optimal temperature, an explosion of heterotrophic bacteria can occur without impacting the autotrophic bacteria. The heterotrophic bacteria population will expand, but with sufficient surface area and oxygen, they will not overrun the autotrophs and the colonies of nitrifying bacteria will be able to expand (provided an optimal temperature is maintained) to deal with the additional ammonia.

Should you face a bacterial bloom, one of the first actions that should be taken is to increase aeration by whatever means necessary. This should be done as much to protect your fish as it should be done to protect the autotrophic nitrifying bacteria. In sufficient quantities, heterotrophic bacteria can quickly consume all of the available oxygen, leaving none for the fish or the autotrophs. A bacterial bloom sufficient to cause cloudy water suggests that your tank is at risk of becoming depleted in oxygen.

Managing Heterotrophic Bacteria Populations

Managing populations of heterotrophic bacteria basically involves a single goal. Limit their food source. This is accomplished via two methods, standard aquarium maintenance and use of chemical filtration.

Food sources (sources of organic carbon) for heterotrophic bacteria in our tanks are fish poo, uneaten food, dying plants, dying plant leaves, dead fish, and even dead bacteria. In a nutshell, there is no shortage of food for heterotrophic bacteria in an aquarium.

Standard tank maintenance removes much of the organics from the aquarium before the heterotrophic bacteria can consume them. Necessary maintenance includes:

  1. Perform regular gravel vacs. Gravel vacs remove fish poo and uneaten food from the substrate, eliminating it as a food source for heterotrophic bacteria.
  2. Clean/Replace mechanical filter media often (weekly). The purpose of mechanical filter media is to capture all of the poo, gunk, and organic matter that heterotrophic bacteria feed on. If you do not regularly clean/replace this media, it performs no function other than to serve as an all you can eat buffet for the heterotrophs.
  3. Rinse biomedia often (monthly). This washes off the organic matter that makes it through the mechanical filtration as well as removing dead bacteria. By removing these organics from the media, you limit the amount of heterotrophic bacteria that media will contain. You want this surface area to be available to autotrophic nitrifying bacteria. In addition, whenever heterotrophic bacteria consume organics, they leave behind a “slime” coating (this is the white slime that accumulates on the front of your tank). If this slime coating is allowed to accumulate on your biomedia, it will fill in the pores, drastically reducing available surface area. Washing the media removes this slime, further protecting your biomedia, which, in turn, protects your nitrifying bacteria.
  4. Water changes, water changes, water changes. Of course, water changes do much more good than just reducing organics, but for the purpose of this discussion, we will focus on the removal of dissolved organics from the water. These dissolved organics, which you cannot see (unless they are causing cloudy water), are a significant food source for heterotrophic bacteria (and are generally the cause of a bacterial bloom). By limiting the amount of dissolved organics in the water column, you also help protect your bio-media. Think of dissolved organics in the water column as the equivalence of ammonia in that bacteria will consume it as it passes through the filter media. By restricting these levels, you limit the amount of heterotrophic bacteria that populate the biomedia, as there is limited food available to heterotrophic bacteria populating that media (after all, your cleaning the bio-media as well).
  5. Don't increase heterotrophic bacteria populations by using products labeled as “sludge reducers”. These products simply are not required as heterotrophic bacteria do not need a “boost”. If you carefully read the instructions on these products, they usually identify that their use may result in temporary ammonia/nitrite spikes. After reading this document, you should understand the potential causes.

The other method of controlling heterotrophic bacteria is the use of chemical filtration, with the primary chemical media for this purpose being activated carbon. The most important potential benefit (in my opinion) of using activated carbon (and other chemical medias that perform the same function) is that it (they) will adsorb dissolved organics, removing them as a food source for heterotrophic bacteria. To retain this benefit, carbon must be replaced frequently (at least every two weeks). If allowed to remain in the tank, once it looses its effectiveness, it becomes another all you can eat buffet for the heterotrophic bacteria.

Denitrifying Heterotrophic Bacteria

When discussing Autotrophic Nitrifying Bacteria in Part 1 of this article, mention was made of the Nitrogen Cycle. What is missing in that prior discussion, and what is often left out of the discussion, are the final components of the nitrogen cycle, “denitification”, the conversion of nitrate into harmless nitrogen gas. This conversion is the true completion of the nitrogen cycle.

Diagram of completed nitrogen cycle

While it is the autotrophic nitrifying bacteria that convert ammonia to nitrite and nitrite to nitrate, the elimination of nitrate (denitrification) is a function of heterotrophic bacteria.

Unlike nitrification, which requires an abundance of oxygen, denitrification only occurs with little (or no) oxygen. Technically, this is an inaccurate statement, as there are actually heterotrophic bacteria that will perform both nitrification and denitrification in aerobic conditions, but they only do so in the absence of organics. While feasible in a lab, this is not feasible in our tanks. In addition, there are sulfur fixing heterotrophic bacteria that will perform denitrification in aerobic conditions but this type of denitrification is unacceptable in freshwater tanks as the outflow is extremely acidic with a major by product of sulfate (nitrates are converted to sulfate).

Of the heterotrophic bacteria, the one type we would like to cultivate is denitrifying bacteria, but doing so is much more complicated than cultivating autotrophic nitrifying bacteria. Denitrifying heterotrophic bacteria only exist in environments where oxygen is limited. In an aquarium, this type of environment is difficult and potentially dangerous to establish. It can be established via a deep sand/gravel bed (in excess of 2”) or it can be established via a special external filter under very low flow rates (as in drips per minute). However, there are dangers associated with these setups, with the viability of risk being associated with the second requirement of denitrifying bacteria, dissolved organic carbon. Denitrifying bacteria are heterotrophic bacteria, which means they require organic carbons. While our tanks are generally laden with organics, a decently maintained tank will not contain enough organic carbon to support effective denitrification. So they have to be supplemented, generally in the form of sugars such as acetate, methanol, or ethanol (many people use cheap vodka). The problem is that there are many variables and the necessary concentration of organic carbon to support denitrification fluctuates by the moment. Without extensive and expensive equipment it is not really possible to determine how much supplementation of organic carbon is required. If an insufficient quantity of organic carbon exist in a low oxygen environment, the result is incomplete denitrification, which results in the conversion of nitrate back into nitrite or ammonia, both of which are more toxic to the fish than is nitrate. If an excessive supply of organic carbon exists in a low oxygen environment, you run the risk that hydrogen sulfide will be generated, which is more hazardous to fish than is ammonia, nitrite, or nitrate. So, if you decide the attempt to achieve substantial denitrification is worth the risk, in the absence of cost prohibitive monitoring equipment, you are left with testing the water to determine the effectiveness of denitrification and its potentially lethal side effects. If using a deep sand or gravel bed, this testing would involve daily monitoring of the water for ammonia and nitrite levels while using your nose in an attempt to detect hydrogen sulfide (rotten egg smell). However, if you smell it, it’s probably too late. If using an external denitrification filter, you test the outflow for ammonia and nitrite, as well as your nose to detect hydrogen sulfide. In either circumstance, if you are getting a reading for ammonia and/or nitrite, you should increase the quantity of organic dosing. If you detect hydrogen sulfide, you should decrease the amount of organic dosing (assuming your fish are still alive).

It should be mentioned that the act of “organic dosing” is against all concepts associated with maintaining healthy populations of autotrophic nitrifying bacteria. By dosing with organic carbons, you are providing a food source for all heterotrophic bacteria, not just the denitrifying bacteria. This creates a risk of establishing an environment where heterotrophic bacteria can easily out compete autotrophic nitrifying bacteria, inhabiting all available surface area and over consuming oxygen, subsequently limiting the colonies of autotrophic nitrifying bacteria. But that may be the least of your concerns. If you overdose with organic carbon, the heterotrophic bacteria can consume all available oxygen, suffocating your fish. At a minimum, if you overdose with organic carbon, or dose in a method where the organic carbon is consumed by aerobic heterotrophic bacteria in the main tank, the results will be cloudy water and slime coatings on the glass of the aquarium, the substrate, and all tank decorations.

Deep Sand Beds

Long used in saltwater setups, deep substrates have been used less often in freshwater tanks, primarily due to fears associated with the possible creation of hydrogen sulfide pockets within oxygen-depleted areas of the bed. This is more likely to occur in freshwater tanks than saltwater tanks because freshwater tanks will be absent the animals that make up “live sand” that exist in saltwater tanks. These animals (worms, copepods, etc…) act to slowly stir up the sand preventing these pockets of hydrogen sulfide from developing. In a freshwater tank, housing animals that serve the same purpose are not feasible. Plants, however, are, and their root structures can serve much the same function, provide the sand bed does not extend substantially below the root structure of the plants.

As mentioned, any sand or gravel bed in excess of 2” will develop anaerobic conditions and it is only in these oxygen-depleted areas that denitrification or putrification (which creates the hydrogen sulfide) can exist. As freshwater aquarists, if we manually “stir up” the sand bed, or gravel vac a gravel bed, we will introduce oxygen into the lower levels of the bed, eliminating the denitrification capacity of the bed. By stirring sand, or performing gravel vacs, we also run the risk of releasing hydrogen sulfide directly into the water column. In reality, an undisturbed sand or gravel bed carries little risk of leaching hydrogen sulfide into the water column. Hydrogen sulfide will only be created in areas that are entirely oxygen-free. This usually only occurs in beds that are in excess of 4” in depth and is more likely with a sand bed than a gravel bed.

What occurs is the top layer of substrate (the initial 1”-2”) becomes inhabited by aerobic autotrophic and heterotrophic bacteria that consume oxygen as a component of their biological processes. The next few inches of substrate (if left undisturbed) will contain denitrification bacteria, which strip the oxygen from nitrate and nitrite. Below these 4 inches a zone will exist in which there is no oxygen, nitrate, or nitrite remaining to support continued bacterial process. What will exist, however, is sulfate. So sulfate becomes the next-best electron receptor for anaerobic bacteria. The waste product resulting from the biological process of these sulfur-fixing bacteria is hydrogen sulfide. The production of hydrogen sulfide is of little concern provided the bed is left undisturbed. In an undisturbed bed, additional aerobic sulfur-oxidizing bacteria will exist in the upper layers of the substrate (where oxygen is available) ready to scavenge available hydrogen sulfide as it rises through the substrate, returning it to sulfate. Risk of hydrogen sulfide poisoning only exists if the bed is disturbed, which can result in hydrogen sulfide being directly released into the water. This risk is not restricted to the well-intentioned actions of an aquarist performing maintenance. Many of our fish, especially Oscars and other cichlids, are diggers. If a deep substrate (in excess of 4”) is attempted in a tank containing fish with a propensity for digging, the chances of the fish digging up undisturbed pockets of hydrogen sulfide is very real.


At issue are not only the risks, but also the effectiveness of using a deep substrate in controlling nitrates. All aquariums, which utilize a substrate of 2” or more, possess some level of denitrification capacity. But with the larger fish, such as Oscars, chances are that nitrate production will far exceed nitrate consumption by denitrifying bacteria in such a substrate. It’s also important to understand the biology/chemistry to minimize risk as the biology/chemistry determines how deep the bed should be to minimize hydrogen sulfide concerns. As mentioned, as long as nitrate (or nitrite) exists in the water, bacteria within the substrate will strip oxygen from these compounds before switching to sulfate. So, for every tank, there is a “magic” depth to the bed (and livestock stocking level) that could, in theory, virtually eliminate nitrates without the concern of hydrogen sulfide production. I have no idea what that “magic” depth is. Nor, if I discovered what it was in my tank, could I tell you what that depth would be in your tank. There are too many variables. Chief amongst them are stocking levels, the amount of food fed, and the contents of the food. To achieve a nitrate creep of zero, you would need a tremendously under stocked tank with a very large (and deep) substrate. An added concern when trying to consider these factors is that in such a deep bed, you run the risk that not enough aerobic surface area exists to support aerobic sulfur-oxidizing bacteria to convert the hydrogen sulfide potentially filtering up from the deepest layers of the bed. So you have to consider bed width as well as depth.

It is also necessary to mention that the depths I’ve mentioned are generalizations, not “fixed” definitions. There are many variables. In some tanks, a functional denitrifying sand (or gravel) bed may be 4”. In other tanks, it may require 9”. What is important to understand is as long as oxygen exists in the water, bacteria will utilize it as an electron receptor and denitrification will not occur. When there is no oxygen, but there is nitrate or nitrite, bacteria will become established that use these substances as electron receptors. It is only when these substances (oxygen, nitrate, and nitrite) do not exist that bacteria within the substrate will begin oxidizing sulfate, producing hydrogen sulfide. To these hydrogen sulfide producing bacteria, oxygen is a toxin. The slightest hint of oxygen will kill them.

I’ve experimented with the practical application of these concepts by utilizing an imitation deep sand bed in my sump, using sponges. I selected the use a sump because I house oscars and convicts, both notorious diggers. As has been mentioned, in order for a deep sand/gravel bed to be effective and safe, it cannot be disturbed below the 1st inch. Since I am also a firm believer in managing the amount of available organics, in an effort to level the battlefield between autotrophic nitrifying bacteria and heterotrophic bacteria while eliminating a nitrate source, I clean my substrate thoroughly each week, well beyond the 1st inch, to remove uneaten food (of which there is little) and fish poo(of which there is a lot). In a properly pre-filtered sump, there will be no need to clean these substances from the substrate. In my sump, I have created what is basically a 9” bed, using sponges (sponges made for hanging wall-paper, bought at Home Depot). Each sponge is 3” thick and I’ve stacked them three high. Sponges were selected for two reasons, the first being cost (they are cheap). The second reason is that there is no chance of ditrius, that may have made it through the pre-filters leading into the sump, becoming embedded in the center of a dense sponge, contributing to nitrate creep or hydrogen sulfide production. Since this concept is just one of several I use in an attempt to manage nitrates, I cannot quantify results. I simply do not know how much nitrate creep is reduced via this method. But the science is sound and I believe it has had some impact. One of the limiting factors in my configuration is I only have a 20 gallon sump with only ½ of the sump utilized in this fashion. With a larger sump, and more area covered by the sponges, the potential for dramatic results does exist. However, I do not currently dose with an external organic carbon source, relying only upon my fish to supply organic carbon to the denitrification process. This is another limiting factor.

A photo of my imitation deep sand bed (using sponges). In addition to the two rows of sponges seen in the front, there is another row behind them:


I am in the process of converting to a larger tank (125 gallons), which will have a 125-gallon sump. I intend to fully explore use of a deep sand bed (using pool filter sand) in the sump. The bed will be based with a 6” layer of sponges covering the entire bottom of the 125 gallon sump, with a 1” gap between the individual stacks of sponges. These 1” gaps will be filled with course gravel, all covered with an UGF filter plate, with another 2” of pool filter sand on top of the UGF plate. The only limiting factor in this configuration will be the availability of organic carbon and I will experiment with that component as well, attempting to develop a method to evenly introduce (and distribute) the carbon source into the deep layers of the bed, where it can be consumed by denitrifying bacteria before it becomes available to aerobic heterotrophic bacteria, eliminating that point of concern (competition between heterotrophic and autotrophic denitrifying bacteria). As an supplemental carbon source, I will likely use a product called MicroCg, which is a non-hazardous, non-toxic organic carbon source specifically made for this purpose (on a larger scale, for water treatment plants), utilizing an automatic medicine doser to add the carbon at a predetermined rate (with that rate yet to be determined).

Some examples of “Remote Deep Sand Beds” (sand beds that are external to the main tank) are included below. This is the only type of configuration that should be attempted with fish such as Oscars (that like to dig).

Remote Sand Bed Example

Remote Sand Bed Example

Remote Sand Bed Example

Remote Sand Bed Example

Anaerobic Denitrification Filters

Standard denitrification filters consist of an external canister containing biological media through which water is passed very slowly (as in drips per minute). Under such a slow flow rate, the water within the canister will become oxygen depleted, allowing for the existence of nitrate oxidizing heterotrophic bacteria. Some denitrification filters contain a specific type of media (denimar balls) that serve as both the biomedia and the source of “organic carbon” necessary for denitrification. These types of denitrification filters do not require additional carbon dosing and run little risk of contributing to excessive populations of heterotrophic bacteria. With filters that use “deni-balls”, the media should be replaced yearly. Other denitrification filters require external organic carbon supplementation, such as cheap vodka or packages specially formulated for that specific filter. Organic carbon is usually introduced via a “feeding tube” through which the carbon source is pored or injected. Care must be taken not to introduce oxygen in the feeding process. With these types of filters, the possibility of overdosing with organic carbon, resulting in over population of aerobic heterotrophic bacteria within the main tank, and a subsequent potential decline in autotrophic nitrifying bacteria, is a concern.

Regardless of the type of denitrification filter used, the risks associated with them are the same as with a deep substrate, incomplete denitrification (conversion of nitrate into nitrite or ammonia) and hydrogen sulfide. But not only do you have to be concerned with the levels of organic carbon. You have to be concerned with flow rate. If the flow rate is too high, the oxygen content of the water within the filter will be too high to support denitrification. The filter will just be a standard nitrifying filter. It is also possible to achieve a flow rate where just enough oxygen exists in the water that incomplete denitrification occurs. Under these conditions, the outflow will contain nitrite. If the flow rate is too low, nitrate may be exhausted and the bacteria will start consuming sulfate. Under these conditions the outflow will contain hydrogen sulfide. So, as with any denitrification method, it is essential you monitor the outflow of the denitrification filter to ensure it does not contain nitrite, ammonia, or hydrogen sulfide, as well as to measure the effectiveness of denitrification by measuring the nitrate concentration of the outflow vs. the main tank. This requires constant adjustments, both in how much organic carbon is used and in the flow rate. An important point to remember is that it is better for the flow rate to be too high as opposed to too low.

Another important consideration is that the outflow from a denitrification filter will contain very little oxygen. It is recommended that this water be aerated as it is released back into the tank. This can be accomplished by having the outflow trickle into an HOB filter, or released directly in front of a power head or canister outflow. My recommendation is that some type of configuration be employed where the water is exposed to the atmosphere and allowed to flow down into the tank. This serves two functions, first it will re-oxygenate the water. Secondly, if hydrogen sulfide does exist in the outflow, it can escape into the atmosphere before the water is returned to the tank. Your house might stink, but the fish will remain alive.

Safe Denitrification

This is a term I coined myself and it is a method I am currently utilizing that results in limited denitrification. There are numerous types of filter media on the market capable of supporting anaerobic conditions deep within the interior of the media. While the external sections of the media are exposed to oxygen rich conditions, aerobic bacteria that inhabit these sections of the media remove the oxygen so that water reaching the interior sections of the media has sufficiently low oxygen content to support denitrification (nitrate-oxidizing bacteria). Hagen BioMax (no longer manufactured) was such a brand of media. Another product, which remains available, is Cell-Pore media (now known as RefresH2O Biomedia). But the media most often marketed for this purpose is SeaChem DeNitrate. Examples of biomedia that contain internal pore structures capable of supporting limited “Safe Denitrification” are included below:


I am of the opinion that with the proper selection of media, some levels of denitrification will occur in almost any filter. However, the higher the flow rate of the filter, the less efficient the denitrification will be. So while some measure of denitrification will occur using these medias in our standard canister filters, it will not be substantial.

To improve the effectiveness of these media in performing denitrification it is necessary to reduce flow rates to below 50gph. I am currently utilizing a DIY filter that consists of a 7' of 4” PVC pipe, filled with a combination of (mostly) SeaChem DeNitrate and Eheim Ehfilav. Using a Quite One 4000 pump (with restricted flow), I am able to maintain a flow rate of about 30gph. If you attempt this setup, do not underestimate the pump requirements. It takes a lot of pump to push water through 7’ of 4” PVC tubing.


Since the introduction of this filter, I have subsequently achieved a nitrate creep rate of zero (eliminated nitrates), with a 20 micron prefilter leading into the denitrate tower. It does so safely, as I am not creating anaerobic conditions within the filter itself and I am not dosing with organic carbon, hence, the term “safe denitrification”. For details, as well as the work that led to these results, please reference the following thread.

The same thread also details use of SeaChem Matrix Biomedia in canisters to provide some level of denitrification.

Clarification on “Available Surface Area”

With all of the references made within this document to “available surface area”, I felt it important to clarify that I cannot quantify how much surface area is enough, or how much “excess” is suggested. I know of no way to calculate such an equation. It is entirely possible that my ideal of “enough” is extremely excessive. I can only make judgments based on my personal experiences and those experiences indicate success in a wide range of applications whenever use of biomedia (which provide the surface area) is “over the top”.

As an example, biomedia on my 120 gallon Oscar tank (spread amongst multiple filters) consists of:

  • 4 boxes of Eheim Ehflilav
  • 4 boxes of Hagen Biomax
  • 1 Box of Fluval Biomax
  • 1 Liter of SeaChem Matrix
  • 2 Liters of Cell-Pore BioSpheres,
  • Three Biowheels (one of which is a Biowheel Pro 30).

And this does not account for the substrate, sponge filters, pre-filters, sponges, etc… that exist elsewhere in the filtration system, as well as the 15 (or so) liters of SeaChem Denitrate in my “safe denitrification” filter.

For more information on surface are and my opinions of impacts to beneficial bacteria populations, please reveiw Nitrifying Bacteria Populations - A Benefit of Over Filtration.


While not necessarily in strict compliance with the subject of this article, this topic is worthy of mention as it will become a significant component of an aquarist’s tool kit in the future. Already, we are seeing “Probiotic” products being offered on the market. An example of this is Hikari Bio-Gold Plus, which utilizes a specific strain of Bacillus bacteria to aid in digestion and the break down of fish waste. Commercial shrimp and fish farms are currently experimenting with probiotic formulations that protect their product from bacterial or viral ailments. This involves adding one type of microbe that is harmless to livestock, to defeat/prevent another type of microbe, such as harmful bacteria. It is only a matter of time before these experiments result in products available to aquarist.


Hopefully this article provided you with some information you may not have been aware of and which you may use to improve the longevity and health of your fish. What is important to understand is that that the bacteria in our tanks plays a vital role in supporting our fish and it needs to be treated as such.

Being aware of the requirements of beneficial bacteria allows us to maintain conditions optimal for the growth of the proper types of bacteria while limiting the growth of less desirable, or even harmful, bacteria. In doing so, we improve the lives and health of our fish. This should include being aware of the “safety factors”. Having “just enough” filtration and surface area is not acceptable in my book, as it does not provide a “safety backup”. The more abundant the use of filtration and biomedia, the higher the “safety factor” associated with your aquarium. It’s all about available (excess) oxygen, available (excess) surface area, and sufficient (excess) flow rates, of which all are provided by (excess) filtration.