By Bob Goemans
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The 'LIVING' Marine Aquarium Manual

Basic and Advanced Husbandry for the 'Modern' Marine Aquarium

by Bob Goemans

Chapter 7 Filtration Processes

Now that some system goals, equipment, materials, and products have been discussed, the next 'logical' step, especially for the neophyte, is to understand the widely varied aspects that encompass the word 'Filtration.' And it seems like almost everyone has a different idea as to what form of filtration or equipment provide the best results. Nevertheless, all agree it's essential because when animals are added to the aquarium their waste products and/or unused foods degrade and physically affect its water chemistry. This is often referred to as 'Bioload' - the total burden of metabolic activity from all life forms placed upon the aquarium's life-support/filtration system! Furthermore there are also outside influences on that aquarium water, such as contaminants from sprays of household cleaning aids or pest control, human smoking, or even that from little hands dropping unwanted matter into the aquarium water. In fact, without filtration, especially that of biological filtration, all living organisms would soon perish.

As for the word 'filtration,' which is defined as passing something through a filter, I see that meaning in the context of what protein skimmers, canister filters, and activated carbon accomplish - they collect, remove, and/or export matter from the system's bulk water (filter out matter). This, in my opinion is properly called 'mechanical or chemical filtration.' On the other hand and far more important, bacteria use metabolism to 'transform' matter, - elements and/or compounds, into energy for their own reproduction or that of producing other forms of elements or compounds, some desirable some not. This is more properly referred to as 'biological filtration' even though nothing is being filtered out/exported. Changed - yes, removed - no.

Nevertheless, it's these microbes that are Mother Nature's frontline troops in maintaining a healthy and 'balanced' environment, whether it's in the aquarium or the world around us. And since there are various microbial processes that normally inhabit the aquarium, it's important to understand their significance. In fact, it could be said 'bacteria' are the true foundation of every aquarium system. How well they function is dependent upon knowledge of their existence and requirements, as system environmental changes are usually a result of their functions.

As mentioned above, there are three forms of filtration: biological, chemical, and mechanical. Each provides a different process in which aquarium water can be cleansed. Notice I said 'cleansed,' not renewed, as the replacement or supplementation of its elements and/or compounds is a totally different subject matter, some of which was just discussed with more to be discussed in Section Three, Seawater.

Lets begin here with what could be considered the least important of the three processes, mechanical filtration.

(Please keep in mind all underlined word(s) are linkable files - just click on them and be taken to its content/photo. Also, all shown photos are clickable, which often allows a larger file to be seen.)

Mechanical Filtration

This form of filtration serves one purpose: to 'trap' large, i.e., larger than microscopic matter, free-floating particulate matter, e.g., undissolved animal wastes, uneaten food, algae, etc., in the water column. Something similar to what home dust filters accomplish that are located in the airflow entering into your heating and cooling equipment. Its efficiency depends upon the flow rate through the media, the size of its openings, and of course its overall surface area.

The early removal of this matter from the aquarium accomplishes two important functions. First, it helps prevent this type matter from clogging other biological and chemical filters. Second, it prevents the mineralization, i.e., breakdown/oxidation by bacteria, of these trapped particulates/nutrients that would eventually return to solution when being dissolved/oxidized, such as ammonium, nitrite, nitrate, and other forms of nutrients. If not cleaned often enough or replaced, the media will begin to clog, slow water flow and begin to harbor bacteria that will act somewhat as a biological filter, nevertheless, an inefficient one.

Over the past decade there has been some discussion that mechanical filtration should not be used in reef aquariums because it removes some of the matter that certain invertebrates may utilize as a food source. I agree with this to a certain extent. - When it comes to the fish-only aquarium, the use of pleated cartridges that can filter out matter down to one micron in size can certainly be used without concern. Yet, for the reef aquarium, where some corals and anemones may find some minute organisms circulating in the water a tasty and nutritional morsel, mechanical filtration should be limited. – Therefore, recommend products such as filter floss and sponge materials where minute organisms will flow through it and therefore only collect larger unwanted matter, continue to be utilized.

There are many different types of mechanical filter material, e.g., filter floss, sponge pads, pleated cartridges, fiber pads, sand, and diatomaceous earth to name some.

Filter Floss/Fiber Pads

There are many different brand products, yet most are forms of polyester or Dacron material. They are sold either in pad-form or a bag of cotton-like material. Each can be cut and sized to fit the area where it will be used. Will not spend much time on this subject except to say you may be able to find somewhat quality made similar products at a local fabric store sold by the yard or bundle, at a tenth of the prepackaged cost. Just one point when buying from a fabric store, always ask for untreated material as some manufacturers treat their materials with chemicals that could be toxic to fish and invertebrates, yet not toxic enough to be considered harmful to humans. Nevertheless, quality brand aquarium products are the safest way to go. And where quality material is used, it should be cleaned at least weekly or replaced weekly before the collected matter decomposes.

Sponge Pad Filters

As mentioned in Chapter 4, there are many different sizes and shapes for these preformed foam filters, with these being used in equipment designed to perform some kind of 'mechanical' filtering process, such as hang on tank power filters or as an aid to keep other media from clogging prematurely, such as those in canister filters. There are also bulk sponge materials available where its possible to cut the exact size filter needed. Keep in mind these 'mechanical filters' differ from the much bigger sponge filters designed for the colonization of bacteria (biological filtration), such as those described in Chapter 4 and/or used in quarantine or breeding systems.

Most sponge pad-like filters used for mechanical filtration can be cleaned and reused; while others may be so inexpensive they can be discarded frequently and replaced with new filter pads. All are very good at filtering out any discernable materials, and allowing dissolved matter to pass through. As with any type filtering media, within a few days bacteria begin to colonize the media and also provide some biological filtration. Nevertheless, the bacteria will be lost when the sponge material is cleaned, especially so if cleaned in freshwater. If sponge filters solely used for mechanical filtration are readily accessible, they should be cleaned thoroughly in running tap water once weekly, and reused or replaced as needed. Those in canister filters, cleaned when its media is replaced.

Diatomaceous Earth (DE)

This very fine media is composed of the skeleton or cell walls of single cell diatom algae and is used to coat the walls of a porous sleeve. Water from the aquarium is then pushed through this coated sleeve under pressure. The minute porous structure of these alga cell walls, which are less than one micron, effectively trap suspended matter in the incoming water providing for an extremely clear and clean water being returned to the aquarium. Some hobbyists use DE filters to reduce the number of Marine Ich parasites while treating their aquariums. Keep in mind that DE is composed of silica and since there is a slight solvency of silica above a pH of 8.0, the hobbyist may add silicate/silicic acid to their aquarium water when this product is in use. This may result in a slight growth of brown diatom algae if this product is used frequently or at any appreciable lengths of time. In fact, the DE filter is usually considered a short duration type filter, mostly used for periodical maintenance since it clogs rather quickly.

Sand Filters

Where sand based mechanical filtration is desired, those used in swimming pools are feasible for larger aquaria, yet require high-pressure water pumps to effectively pass water through the sand filled chambers. Some models are equipped with a pressure gauge that indicates back pressure from clogging sand and connections to back flush the sand, helping to keep it running for longer periods without having to open the unit. Some aquarists place phosphate-removing media in the sand and when its time to replace it, then back flush and open the unit and change out the phosphate removing media. The brand shown in the photo has unit sizes from 18 inches to 36 inches.

Sock Filters

Filter 'socks' are usually used in the sump where water from the aquarium or some form of equipment, such as a protein skimmer, flows directly into it. Particulate matter, and possibly fine bubbles from a protein skimmer are removed/captured and clear bubble-free water flows through the sock material to the sumps collection area and is then returned via the system pump to the aquarium. As the interior surface of the sock fills with matter/bacteria growth water level in the sock rises, often within a few days of use, and will overflow it's opening negating its purpose. It's always wise to have several 'socks' if this method is being used and replace the one in use as needed. The removed sock can be turned inside-out, back flushed with tap water and soaked in a pail of freshwater containing a cap full of household bleach to dispense with any bacteria that might be calling it home.

Chemical Filtration

Even though the removal of 'dissolved' matter is known as chemical filtration, which is the second most important form of filtration, it could also somewhat be thought of as mechanical filtration as it somewhat traps/filters out molecular size matter. As for dissolved matter, there are two forms, organic and inorganic. All dissolved 'organic' compounds contain carbon and are derived from the 'biological' activities of animals and plants, and are grouped under the collective term Dissolved Organic Carbon (DOC). They include amino acids, carbohydrates, carotenoids, creosols, phenols, proteins, terpenoids, vitamins, and various fats and acids. Inorganic matter is not composed of animal or vegetable matter and mainly comes from mineral sources, with few containing carbon, e.g., carbon dioxide coming from the atmosphere (inorganic carbon dioxide). Keep in mind the accumulation of inorganic and especially organic compounds can interfere with the normal growth of fish and invertebrates, therefore, it's a good reason to limit their excesses in aquaria, especially in reef systems!

There are two processes, ion-exchange, and adsorption that can effectively accomplish chemical filtration. The adsorption/polar process has already been discussed in Chapter 4 under the topic 'Protein Skimmers.' It was also discussed in Chapter 6 when discussing activated carbon.

As for the ion-exchange method, that was discussed in Chapter 3 when Deionization was discussed.

Nevertheless, you may find the discussion on 'Resins' following that of Dilutions somewhat interesting.


Even though there are various forms of chemical filtration, it does not mean water changes are not needed. If anything the use of chemical filtration by different means may lengthen the time between water changes, but it does not eliminate them. And even though water changes are not technically considered ways to chemically 'filter' water, it remains nevertheless a very useful way to limit the ever-accumulating compounds and elements that are not mineralized or result from that process, such as with nitrate. Therefore, I'm including it here, as it certainly does not fit into the other two forms of filtration, even though one could consider it more a general husbandry maintenance issue.

With that said, most aquaria in my opinion do not need water changes during their first few months of existence. But as time goes by accumulation of organic and inorganic matter do occur. To what degree depends upon the goal of the system and the skill of the aquarist. To put it into perspective for most general system goals, monthly water changes of 5% should begin at the beginning of the forth month. After another 12 months into the life of the system, accomplishing a monthly 10% water change is recommended. After that period of time, 10 - 15% monthly water changes are highly recommended. With that, you're not only ridding the system of some potentially hazard compounds and elements, you're also supplying the system with some important trace elements that have been used up by its organisms. And when compared to the costs involved in replacing chemical filtration media and/or adding certain liquid or powdered additives, the cost of salt is far less even though some specialized additives will no doubt still be needed.


Over the past couple of decades the use of resins in various products has been on the rise. Their use may seem like fairly new technology, yet, it is thought by some scholars occurrences similar to resin/ion exchange is discussed in the Bible, as explained in the activated carbon discussion in the previous chapter. In fact, naturally occurring clays and zeolite materials have continued to be utilized for water softening purposes for many decades before the existence of synthetic resins became available.

As with any subject the more you become involved the more new terminology surfaces. Even a very basic discussion on the use of resin and its use for purifying water, known as ion exchange, will require the incorporation of some new terms. It will not be necessary to remember most of these possibly strange words, yet to broaden one's knowledge even somewhat is always a step in the right direction.

To begin, when a substance dissolves in water it can disassociate or separate further into electrically charged atoms or groups of atoms. Those electrically charged atoms containing a positive charge are called 'cations' and negative charged atoms are called 'anions.' The higher its valence or number of positive or negative charges on the ion, the more strongly it is attracted to the opposite charge, which can be placed on chemically modified plastic material called 'resin.'

Even though the ion exchange process may have occurred during Biblical time it wasn't until the mid 1800's that the process was formally recognized. In fact, it wasn't until the mid 1930's the first synthetic ion exchange resin that permitted de-ionization was discovered. In the years following, many improvements came about and resins now play an important roll in not only processing water, but also many other areas such as food, sugar, waste treatment, pharmaceuticals, and wine making to mention just a few.

Improvements continue to this day and the chemistry/process of making ion exchange resins is quite interesting and complex. In the following basic discussion on how these little beads of resin are made, I've tried to keep it interesting, and stay away from overly technical aspects.

Bead Formation

If you're familiar with the fact that water and oil do not mix, you already have part of the answer as to how resin beads are made. Should you try to mix oil and water, little beads of oil will form and be suspended in the water. Once the stirring is stopped the beads will slowly join together and before long be back as oil floating on the surface. However, if while stirring a small amount of detergent were added, the little beads of oil would have stayed separated/stable for a long period after the stirring ceased. Resin beads are formed in a similar fashion.

When a monomer, i.e., a single reactive molecule capable of combining with another like itself of styrene and divinyl benzene along with a catalyst like benzoyl peroxide and a small amount of detergent is mixed/stirred in water, the result is small 'plastic' beads. Depending upon the temperature of the solution and how fast it's stirred the beads will be of various sizes. These plastic beads are further treated or reacted with various chemicals and temperatures to add specific ion exchange capabilities to the structure/frame of each bead.

Over the past ten to twenty years, manufacturers of resins have developed cost effective ways of producing copolymers, i.e., two monomers of styrene and divinyl benzene, which have resulted in chemically inert and basically insoluble material. Further improvements have followed, but the basics remain the same, - resins have an affinity or force that causes two things to combine. This makes resins a fairly simple product for removing some unwanted compounds/anions, e.g., silica, nitrate, and phosphate from the freshwater used for water changes/evaporation makeup before they can enter the aquarium.

Resin Maintenance

Technically, rechargeable resins should last indefinitely, nevertheless, in the practical sense they are somewhat limited, as their overall life span is dependant upon water flow rates, chemical attack, foulants, and maintenance practices. With fairly proper care they could easily remain useable for twenty years.

As for poor water flow through a bed of these type resins, it can lead to the upper portion of the bed clogging with the majority of unwanted ions and its lower portion remaining fairly free of unwanted ions. (The clogged/exhausted resins now have a color different from the still usable resins – color changes are the way to know when the resin needs recharging.) Poor water flow simply leads to more frequent resin maintenance and shortens their life span. As to too fast flow of water, it will not allow sufficient time for proper contact time and will result in poor utilization of the media, which generally does not affect its life span, but does result in poorly processed water. Clogged resins cause more frequent maintenance cycles, i.e., the performance of the regeneration process to remove the attracted unwanted ions.

As noted in Chapter 3, these type resins must be cleaned/rejuvenated/regenerated with acid or Sodium hydroxide (Lye). But I do want to mention here that when using hydrochloric acid such as Muriatic acid, a concrete/pool cleaner, it needs to be first reduced to the correct strength before it is used. Does this mean acid is poured into water or water is poured into acid to reach the correct strength? To most, this sounds immaterial, but it is not! It is actually safer to pour acid into water! Anyway, the point here is that safety precautions most of us would never think of come into play when resin needs to be regenerated.

And when some of these resins are regenerated with these hazardous liquids they need to be washed clean with distilled/purified water after the process is completed. The flushing contact time/flow rate is also important; as is the use of rubber gloves, eye protection and utensils that will not be damaged by acid or Lye. And again, disposal of the wastewater from the rinse also needs consideration, as dumping it down the sink is not the way to handle these hazardous waste fluids!

The ion exchange process has great valve for the marine hobbyist when it comes to processing tap water. Because of its ability to process a fairly broad range of freshwater ionic impurities it is considered a simple, efficient, and a fairly cost effective approach to producing quality water for evaporation and water changes. And with the growing number of specifically tuned resins for use in marine aquariums, such as the removal of dissolved organics, its important to accomplish some research on them and determine if your aquarium would benefit from their use, their cost, and what it takes to regenerate the product, if possible.

Biological Filtration

We often think of ourselves as 'the' key force that keeps things in our aquariums moving in the right direction. That would only be partially true, as organisms so small they can only be seen with a microscope are truly the key to why our aquariums continue to function. It's these employees (bacteria), working in a factory (the aquarium), using incoming raw compounds and elements, some of which are quite toxic, to produce more usable and sometimes safer end products that make possible the continuance of life in the aquarium.

When marine animals are added to the aquarium, their waste products, organic or more correctly called nitrogenous wastes, and food products degrade and physically change the chemistry/quality of the surrounding seawater. Without filtration, especially biological, all living organisms would soon perish. Therefore, lets begin at the very tiniest level in this subject matter and work our way upward, as understanding the bottom most basics is vital if we wish to have successful closed systems!

Cell Metabolism

This is the process by which the cell chemically seizes, distributes or transforms energy as it passes through it. It takes place via many energy-yielding reactions, all linking up and forming an intricate, interrelated network within the cell. In fact, the energy yielded by one chemical reaction drives other reactions, enabling a gradual release of work energy with minimum fatigue to the cell.

To help somewhat understand the complex actions taking place when energy is being produced or consumed, it helps to realize there are two main classes into which all cells and organisms can be grouped. Their difference stems from the mechanism, photosynthesis or respiration, used to extract energy for their own metabolism.

Where photosynthetic coral and micro or macroalgae are concerned, they have developed an ability to utilize photons, i.e., light energy, to convert inorganic substances into organic substances with a process called 'photosynthesis.' In fact, if it were not for this process and its oxygen byproduct, there might not be any life on this planet. The microorganisms that accomplish this process are labeled 'autotrophic.'

Keep in mind in the reef's surrounding water nutrient content is extremely low. To overcome this condition there is a symbiotic relationship between the autotrophic microorganisms, e.g., zooxanthellae, and some of the coral animals. These tiny zooxanthellae alga cells live in the flesh of the coral animal and actually use some of its waste products as fuel for the photosynthesis process. Portions of cell wastes, such as the basic sugar compound glucose, then flow back to the animal as a food supply where more complex molecules are made. Yet, just as important and maybe even more so, are the microorganism processes that occur in sediment.

As mentioned above, the photosynthesis process is just one of the two very important microbial processes that occur in aquariums, with the other being the 'respiration' process. It differs from the photosynthesis process, which is a producer of oxygen, because it is basically a consumer of oxygen. In this process, chemical energy inside the cell is released in very specific and coordinated steps with the help of certain oxidative enzymes that ultimately convert the incoming 'fuel/foodstuffs' into carbon dioxide and water. In fact, these heterotrophic cells obtain energy from different foodstuffs, e.g., carbohydrates, fats, and proteins that were synthesized by autotrophic organisms. The energy held by these molecules is then released mostly by oxidation with oxygen from its surroundings. The process is also called aerobic respiration. The release of water and carbon dioxide by these heterotrophic organisms completes the cycle of energy.

Furthermore, since chemical energy is exchanged in all living cells through the use of adenosine triphosphate (ATP), a compound that contains high-energy phosphate bonds, a measurement of cell energy can be had that determines how well the cell accomplishes its mission. To standardize, scientists have added measured amounts of glucose to bacteria to derive ATP figures. The higher its ATP level, the more efficient energy production and improved energy cycling.

When this is related to the world of oxygen consuming aquarium respiration processes, probably the greatest of interest to the aquarist are those microbes connected with the nitrogen cycle. Those called 'aerobic' bacterium have the greatest ATP levels, and those called anaerobic, far lower levels of ATP. But when one realizes there are two classes of anaerobic bacteria involve in the denitrification process, with one class having a far greater ATP level than the other, some forethought should be given to where these classes of bacterium exist in the aquarium. And these differences will be discussed further along in this section so it can be applied if desired, when planning a new aquarium as it has advantages in my opinion when it comes to overall water quality.

Overall, its good basics in the discussion on biological filtration to understand how important 'energy' is in microbial processes, as without it, the cell could not accomplish its primary goal – reproduction. Simply put, cell metabolism can be defined as a sum of all the chemical transformations in the cell, and includes both the breakdown and/or rebuilding processes. In regard to energy, some is used and some is liberated. This is important! Without proper cell metabolism, energy may follow undesirable routes or remain stored as an unusable form. For example, the different substances taken in by the cell as foodstuffs, e.g., glucose, amino acids, and lipids can be broken down into smaller molecules with the liberation of energy. The cell in the synthesis of new and more complex molecules in turn utilizes this energy. When not given the opportunity to be used effectively, synthesis and utilization will not happen if usable molecules are stored or removed. In fact, when it comes to closed systems, the quicker and more efficiently large amounts of nutrients are reduced to energy, the more superior its overall water quality. I should probably repeat this last sentence about 100 times, as its 'that' important, so please do not forget it!

To sum it up and without getting overly scientific, the lowest forms of life get their energy by anaerobic fermentation. Higher forms of organisms get more energy from aerobic oxidative processes, and it should suffice to say that aerobic organisms are more efficient than anaerobic organisms where aquaria is concerned.

Clearly, biological filtration is the most important form of filtration, and there are four processes that comprise biological filtration: Mineralization; Nitrification; Dissimilation; and, Assimilation.


When we feed our animals, try to feed a balanced diet of carbohydrates, fats and proteins, with fiber most of the remaining ingredient as discussed in Chapter 14. The carbohydrates and fat are converted to energy, with neither containing the element nitrogen; therefore they do not contribute to the nitrate build-up in the aquarium. But proteins are a horse or fish of another color. They contain the element nitrogen in their makeup and during a process called 'metabolism,' the nitrogen element is incorporated into a compound called ammonia. When fish waste products are introduced into the aquarium water they are basically toxic ammonia-laden compounds. We cannot do away with the foods that contain proteins as they are broken down into amino acids and used to create new tissue for growth. Yet, if the ammonia compound continued to build up in the water, it would soon rise to intolerable levels and burn fish tissues, including the sensitive gill areas thereby preventing them from acquiring life-giving oxygen. Or, if high enough, simply kill them.

If we look back at 'Chemical' filtration, we see the term DOC's discussed. But when it comes to 'Biological' filtration, its now 'Total Organic Carbon' (TOC) compounds that take on importance because a rise in the accumulation of these compounds leads to an increase in the population and/or activities of heterotrophic bacteria. And added biomass/respiration and other metabolic activities of these organisms can strain the limited resources of any closed system!

As for those bacterium responsible for this process, they are called aerobic heterotrophs, and their colonies live in oxygen-rich (oxic) areas. This would be surface areas receiving ample dissolved/free oxygen from the aquarium's bulk water, such as sand particle surfaces directly in contact with the bulk water, live rock surfaces and even on the sides of fish! Their function is to breakdown/oxidize the 'organic-laden' wastes, e.g., animal feces/wastes, excess food, and dead tissue that arrive on a daily basis in aquaria. In fact, the breakdown of these organics, especially those nitrogen-containing compounds, prevents its animals from perishing in a saturated sea of their own toxic wastes. Ultimately, the breakdown results in 'inorganic' compounds, such as ammonia, which then are utilized by another species of bacteria in what is called the 'Nitrification' process. And these bacteria naturally appear in the aquarium, therefore there is no need to especially cultivate them.


Now that the first stage in biological filtration is accomplished, its now 'inorganic' results such as ammonia, which is quite toxic even at low levels, must be reduced/oxidized to something less toxic. In shallow depth sand and possible shallow depth rock areas, where dissolved/free oxygen is less than what is present at surface areas in direct contact with the bulk water, yet still considered oxic, aerobic autotrophs colonize those areas and reduce it to less toxic substances such as nitrite, then nitrate. This process is also known as the nitrification cycle, i.e., the reduction of ammonia to nitrite, then nitrate.

In fact, there are two species of aerobic nitrifying bacteria that come to the rescue. The first has been generally termed 'Nitrosomonas' and it oxidizes ammonia (changes it) to a compound called 'Nitrite.' Even though nitrite is somewhat toxic, it is far less toxic than ammonia. Fortunately, another aerobic nitrifying bacteria often called 'Nitrobacter' convert nitrite to nitrate. Since nitrate is not as toxic as ammonia or nitrite, most fishes will be basically unaffected by its accumulation. Yet, in reef aquariums, most invertebrates are sensitive to nitrate-nitrogen levels >15 ppm.

Only three 'major' types of equipment have been designed specifically for accomplishing the nitrification cycle - the Trickle Filter, UnderGravel Filter (UGF), and Fluidized Bed Filter. All were described in Chapter 4.


This process is also referred to as denitrification, and it is basically the reverse of nitrification. There are two classes of heterotrophic bacteria involve, each colonizing areas bordering the other, yet having different oxygen requirements that do not allow either to share the others area. As the depth of a substrate deepens, there is less and less oxygen available to its colonizing classes of bacteria. Generally, any depth below the above-discussed bacteria is referred to as the 'anaerobic' area, however, that does need further clarification if one is to fully understand the importance of these two processes.

Once the area's oxygen level falls to approximately 2.0 – 0.5 ppm, facultative anaerobic heterotrophs colonize the substrates in this area/zone, and this upper area of the anaerobic area should more properly be called the 'anoxic' zone/area. The bacteria in this zone produce dissimilatory denitrification where nitrate is reduced to its basic elemental form — nitrogen gas. In an area of less oxygen content beneath the anoxic zone, more precisely called the anaerobic area, obligate anaerobic heterotrophs exist and the end result of their process, technically called assimilatory denitrification, is ammonium, as these bacteria only reduce nitrate to that of ammonium, not free nitrogen! This is generally referred to as the ammonification process for good reason! These two bacteria are quite different, even though both initially reduce nitrate, and this aspect and associated terminology for their zones, i.e., anoxic and anaerobic, will be discussed more fully further on in this section.


Generally, plants and algae are considered the main focus when this form of filtration is discussed. Even though they add dissolved solids such as vitamins and amino acids to the bulk water, they tend to assimilate or 'absorb' others, such as nitrogen and phosphate compounds, which they incorporate into their own structure. Therefore, when this process is generally discussed its usually thought of or related to what plants and algae accomplish.

In fact this is the reason why the use of refugia containing macroalgae has seen a growing use amongst many reef aquarium enthusiasts, as it provides a way out of the aquarium for nitrogen-laden compounds such as ammonium, nitrite, and nitrate that can have negative affects on some invertebrates, especially coral animals. These constituents, nitrate and nitrite, are actually reduced back to ammonium before it's incorporated into new plant cells, as this compound, ammonium, is its main food source. (Phosphate is its energy source.)

Culturing Necessary Bacteria

For those that may be starting their first marine aquarium, there are some basics that must be adhered to if it's to become successful. Probably the most important of which is culturing the proper bacteria so as to prevent the aquarium from quickly becoming a toxic waste dump. Fortunately, only those involved with 'nitrification' require some forethought, as most other types naturally occur or result from another biological process, such as those involved in denitrification. And there are three methods that have in the past or are used today to accomplish this need: the Organic Method; Inorganic Method; or the Live Rock Method, which is probably the most popular.

Organic Method

This 'was' the most common method used to establish the nitrification cycle for many decades until the Live Rock method became popular in the late 90's. In fact, I've used it to begin numerous aquariums in my younger days and in some instances today, some hobbyists (Discussed this method with hobbyists in India.) still used it even though I do not for the reasons explained below.

This method requires putting a few small fish (about 1 inch (2.5 cm) of fish per 10 gallons for startup) in the aquarium to generate waste products. These waste products soon cause a slight rise in the ammonia level. From experience, some of the best fish to use were either damsels or triggerfish. Over the next five to ten days the ammonia level will rise and at the same time Nitrosomonas bacteria will grow in number and will begin to oxidize the ammonia to nitrite. Over the next week or two, bacteria numbers will grow to millions to overcome the increased ammonia content.

Depending upon the size of the aquarium, number of fish, and how much is fed, in about three weeks there should be enough bacteria to reduce all ammonia to zero. In the future, these bacteria will downsize their numbers so as to keep pace with the newly generated amount of ammonia. During the last week of the cycle the nitrite level will begin to rise. Now that there is nitrite to feed upon, Nitrobacter will begin to be established. One to two weeks later the nitrite level will rapidly fall to zero and there will be the first reading of nitrate in the system. The Nitrification Cycle is now complete and the hobbyist is ready to safely introduce other animals into the system.

What I do not like about using this method is the fact it begins with fish that can handle high ammonia and nitrite levels, such as those mentioned above. That is a limiting factor because there are few overall choices and they may not be what you want to keep long term in the aquarium. You also cannot use too many, as they would die due to a rapid build-up of ammonia since there is not sufficient bacteria early on to oxidize it. There is also the possibility they will be so stressed by the entire process they are wide open to disease in the very near future. Yet, the most important reason is only a very small amount of ammonia and nitrite is initially produced. This limits the number of nitrifying bacteria, thereby limiting the early bio-load carrying capacity of the newly setup system. This means the aquarist must be careful when adding to the bio-load and not add too much, too fast as the additional waste products will generate ammonia in a system where there are still insufficient bacteria to handle the new incoming load. If handled correctly and with patience, the organic method is a tried and proven method to start the Nitrification Cycle in new aquariums. But, in my opinion, there are better ways.

Inorganic Method

WHAT IF----the Nitrification Cycle could be completed without adding any starter fish and have a greater abundance of bacteria in the aquarium when finished with the cycle! In the Organic Method mentioned above, it's begun with only a few small fish. The fish are fed, they eat and digest their food and excrete their waste products. These ammonia-laded products became an ammonium chloride compound that will be converted into nitrite by Nitrosomonas bacteria. - Why not simply buy some ammonium chloride compound and add it directly to the aquarium. This bypasses the adding fish and feeding portion of the process. Ammonium chloride is a very inexpensive compound and can be found at some pharmacies, chemical supply houses or even some aquarium shops.

Therefore, the use of ammonium chloride precludes the possibility of stressing the fish and possibly introducing a disease into a newly setup aquarium. Also, by using enough of this compound it creates a large initial ammonia presence that would be more than any fish(s) could normally survive and which will lead to a greater amount of bacteria in the initial system.

I've tried to come up with a comparison to show why the Inorganic Method provides more bacteria and hope the following sounds sensible. ...With the Organic Method there is a very small amount of ammonium chloride produced because there is a very small amount of fish waste. It is like putting 'five grains' of sugar on the ground and watching five ants carrying them away. When employing the Inorganic Method you're using a large amount of ammonium chloride compared to what would be ultimately generated by a few small fish, and it's like putting 'five pounds' of sugar on the ground and watching one heck of a bunch of ants carting it off! Not only have you completed the Nitrification Cycle disease free, but now have much larger colonies of useful bacteria in the system. The system is now ready to handle a large initial load and do so disease free.

How much ammonium chloride to add is something no two people have yet to decided on. So let me simply tell you how I accomplished it in the past. The first time this method was used I followed the instructions in The Marine Aquarium Handbook, by Martin Moe, Jr. It required 2 to 3 grams of ammonium chloride for every 20 gallons of water and then simply sitting back and waiting until nitrite dropped to zero. It proved to be very successful. Yet, as more information surfaced on this method I increased the amount of ammonium chloride in the hope to increase the initial amount of bacteria. With the last aquarium started using this method I used 2 to 3 grams of ammonium chloride for each 10 gallons of water on the first day and placed a cup full of healthy substrate from another aquarium in the system. The substrate introduced a large quantity of live bacteria and shortened the entire cycle. Then, on the fifth day I added another half dose of ammonium chloride. The entire process took about two weeks to complete.

And since this method starts off with a much larger amount of ammonia, the end result of nitrate is also much higher. Therefore suggest checking the nitrate level before adding any animals and if necessary, accomplishing a major water change before stocking the system.

Live Rock Method

Before going any further, keep in mind the methods described above have been basically used for starting fish-only systems prior to this method becoming popular. With the advent of 'reef' systems in the mid 80's, it was eventually realized that rock coming from the ocean already contained varying amounts of bacteria, including nitrifying bacteria. And by using various amounts of so-called 'live' rock, the aquarist could overnight, go from a newly setup aquarium to one that could safely maintain some live animals. The key word here is 'some,' as the amount and condition of the live rocks are the principal factors as to how much organic waste material can safely be processed. Yet if handled properly with slow increases to the bioload, this method, whether used for fish-only or reef aquariums, has become the method of choice with most hobbyists as it allows for a much faster way to accomplish one's aquarium goals.

Although a variety of healthy bacteria are important to a successful aquarium, overall system environment must be properly maintained. Not only must the biological aspects of the system be balanced properly, its chemical and physical attributes are major contributing factors.

Life without interconnecting support systems is short lived!

The Natural Approach

To do this topic justice, lets go back to what is thought as the first natural 'balanced' aquarium, which occurred in the mid 1800's. It was perceived as such because it contained visible substances in proportions that would equal those found in nature. These substances — sand, rock, plants, and animals could then represent for all 'visible' possibilities the local conditions where its animals originated. It's still a method utilized in many of today's aquariums, both in private homes and public aquaria. And in such environments, those aspects actually contributed certain 'biological' processes that for all practical aspects could be termed 'filtration' in today's way of thinking.

In fact, in 1858 Henry D. Butler's book "The Family Aquarium" depicted a four-sided glass aquarium containing small pebbles, a few rocks, plants, and some fishes. It was referred to as 'The Balanced Freshwater Aquarium.' Yet, during those early years of aquarium keeping, animal waste products were very limiting factors and many attempts at natural systems failed due to insufficient attention to the overall balance of natural forces or what is more often today referred to as 'equilibrium,' i.e., a state of balance between interacting or opposing forces of energy.

Even though Henry D. Butler's freshwater aquarium with no support equipment may have been the very beginning of what can be called the 'Balanced Natural Aquarium,' most marine aquarists today credit Lee Chin Eng with the first natural system or what Eng called 'nature's system.' Mr. Eng was a businessman and hobbyist who lived in Indonesia during the late 1950's and early 1960's. He used sunlight, and local unfiltered seawater, ocean sand, live rock, invertebrates, plants, and fishes in his system. The only water circulation came from the development of currents caused by rising air bubbles escaping from airstones and open-ended air hoses.

Its 'biological' filtration depended on live rock and live sand collected from local waters, with the live rock first being cleaned of sponges and any animal or plant growths that could not be sustained in his simple, yet all-natural system. Those who personally knew him say he took much pride in his natural system. And that he carefully controlled its bio-load so import of nutrients would not exceed the system's natural export of waste products, or what aquarists now generally refer to as 'balance,' i.e., equilibrium! Of course, this is still of importance today, however, many only initially concentrate on the appearance of their aquaria, not the microbial processes that help provide equilibrium/balance.

Except for Mr. Eng, not many people recognized the inherent potential in his technique. Unfortunately Mr. Eng passed away in the early 80's and probably never realized how important his contribution was to the hobby. Because his system did not have visible filtering equipment it was considered too chancy by most people that viewed it. As for those that did try the Eng system, most failed because they used improperly prepared live rock or simply exceeded the system's natural biological carrying capacity (equilibrium/balance).

In fact, it's this successful use of energy and energy shared between microbes/cells along with maximizing energy conversion to sustain their equilibrium that allows substrates such as live sand to out-perform other biological filtration methods. To put it simply, equilibria begets balance - set the forces of equilibria into action and balance will follow! You may want to return to 'Cell Metabolism' and review 'energies' importance.


And when one thinks of 'balance' a mental picture of an equal amount of something on either side of a dividing line comes to mind. Lately, the words 'microbial balance' are being tied to biodiversity, as the thought there is the closed system's environment needs to be in sync with what is found in the wild. Actually, aquarium environmental balance has nothing to do with equal sums or the vast diversity of organisms found in the wild. But it does, whether freshwater or marine, need to contain the correct 'proportions/volumes' of certain microbial processes that adequately use the incoming energy/nutrients so accumulation does not occur! That's fact, not fiction!

Now think about that for a moment. What goes into the system in the way of energy, which includes food, water and light, should result in the total utilization of that energy so no leftovers from all the various processes tend to accumulate in the bulk water or substrate. In other words, what goes in is properly used up to maintain system environment. When that happens, true balance is achieved. In all honesty that is easier to say than achieve, and doubt most closed systems ever attain that goal for one reason or another. Yet we aquarists should at least be aware of some thoughts on how to move in that direction, as the longevity of your selected system's goal depends upon it!

An area of major difficulty with setting up an aquarium, especially the more natural aquarium, is the tendency to confuse the result desired with the techniques that may be required to accomplish it! That simply says the wagon is often placed in front of the horse instead of the other way around. Often, colorful fishes and/or invertebrates attract those new to the marine hobby. And even though many aquarists are more informed these days, there's still a tendency to focus on filtration 'equipment' and the basic nitrification cycle. In fact, in the later 80's I stopped using the UGF and switched to the trickle filter, sometimes building my own versions. But still found my aquariums growing more nutritionally rich. And even though I thought my fairly deep sandbeds and live rock should negate that situation, that was not occurring except in the most underfed and under stocked systems.

As the 90's came about, there was an increase in discussions centering on sandbed depth and the use of live rock. Even though most of what was read sounded quite reasonable, I was not seeing those talked about results in some of my aquariums even though I felt sure my general husbandry procedures were quite adequate. So where was I making the wrong decisions, or was there more to live rock and sandbed processes that I did not understand? I decided it was necessary for me to go back and revisit my current knowledge of water quality and biological processes.

The aspects centering on seawater, i.e., the correct levels of various elements and compounds was fairly straightforward, and did not entail any major changes in my husbandry methods. But the biological aspects occurring in sand of different physical size grains and depths seemed to be far more complicated than I ever thought! And in those days, it entailed numerous trips to the local public library or the university's library. But it wasn't until 1992 when I was reviewing the book Captive Seawater Fishes by Dr. Stephen Spotte that a door was opened for me that finally brought about much enlightenment, along with the friendship and tutorage of some very special scientists. What followed gave me a clear understanding as to what biological processes were really occurring in different grain size and depth beds, and it made me realize I was interpreting some aspects of the microbial processes in sand incorrectly or inadequately and why nutrient accumulation and unwanted forms of algae were occurring in my tanks where even 'nitrate' accumulations were quite low!


As for that 'door,' it was a short description in that book of what was called 'anoxic sediment denitrification.' It pertained to an enhanced biological filtration process conceived by Dr. Jean Jaubert at the University of Nice in the late 80's. Since closed systems were almost always too high in nutrients, especially nitrate, it appeared this different live sand approach might be quite useful in aquariums.

The description of the process called for a sand layer to be separated from the bottom of the aquarium by a water-filled space called a 'plenum.' It went on to say: "Solutes presumably diffuse into the different layers of sediment and are transformed by resident microorganisms; reaction products diffuse outward to the stagnant water or bulk seawater of the aquarium. (Stephen Spotte quotes Jaubert (1989)) How right Dr. Spotte was, however, there was no further discussion on these microbes or how they functioned.

A sketch in the book showed a sand layer separated from the lower water area by a 'grid.' Armed with this small amount of information I setup a 75-gallon aquarium using eggcrate (plastic diffuser material utilized in overhead fluorescent lights) as the grid material. I then separated what was termed the 'Oxidation' sediment layer from the lower 'Reduction' sediment layer using a piece of common window screening that is generally available throughout North America. I thought by separating the sand layers it would prevent digging animals from disturbing the 'hoped-for' reduction processes in the lower sand layer, but that additional screening proved mostly unnecessary in future versions.

The results of my experiment with the Jaubert method almost eliminated all traces of nitrate naturally. A few months after my first series of articles in early 1993 on 'Natural Nitrate Reduction (NNR),' a phrase I coined to fit closed systems using the Jaubert plenum method, Julian Sprung and Tom Frakes came to my home to view the first NNR aquarium in North America. Since then my articles on this subject received worldwide recognition.

It was not until early 1994 when Sam Gamble, Aquarium Biologist at the John Pennekamp Coral Reef State Park in Key Largo Florida contacted me that interest in plenum processes really heightened. He noted the reduced amount of nutrients, including nitrate, in all the exhibit aquariums equipped with common undergravel filters during a lengthy power-outage (6 days) caused by Hurricane Andrew and began to question why. As a scientist and devoted aquarium biologist, Sam was particularly interested in my NNR articles and its connection to the exhibits aquariums during the power outage! The search for what we called the Holy Grail of biological filtration began.

We both agreed that in recent years there had been an increased hobbyist desire to maintain what was loosely being called 'natural marine aquariums' at that time where methods used to maintain them are more inline with the natural processes that occur in the wild than what high tech equipment could provide. Nevertheless that was a challenge in many cases because the desire to have one more pretty specimen in the aquarium often tipped the scales in favor of a pending disaster, or, that not enough is yet known about Mother Nature's energy pathways in aquaria. And without additional 'equipment' in those so-called natural systems it was difficult to maintain them without increases in unwanted algae growth. We realized there was little we could do about rectifying overcrowding, except to say it's a commonsense issue. But where energy paths were concerned, we needed to delve into the word 'balance,' and that did not mean X-amount of fish per gallon! Nor did it mean other visible substances such as specific coral types and fish that would depict an area in the wild. In our opinions it related to an intricate network of physical, biological and chemical energy processes that finally enable creatures so tiny they can only be seen with a microscope, i.e., bacteria, to accomplish processes that 'enhance' our ability to keep these 'natural' systems functioning efficiently.

And furthermore, that the success of bacteria hinge on the efficient usage of energy, whether that is light or chemical energy, which depends upon the quality and quantity of that energy and the pathways it must travel. In fact, we thought of these pathways as the streets and roads that transport the 'energy' that link the entire maze of metabolic and chemical functions that are occurring in aquariums. And all aspects of that journey are important and interconnected because fundamentally they finally affect bacteria health and their ability to function and reproduce. It's they who actually control the wellbeing of the system!

I was happy to have the level of Sam's expertise and his interest in the 'Jaubert' process, as we were both stumped as to why my aquarium and those at the Pennekamp responded as they did! In fact, Sam's comment at the beginning of the plenum testing procedures continues to stick in my mind. I think you may find it not only somewhat humorous, but also quite true. He said: "The plenum is much like our basements. A lot of things end up down there in the dark to be eventually recycled. What goes on in the living area above will determine how much is thrown down the stairs. Without the basement we have a tendency to accumulate the junk upstairs. How things get up and down the stairs and what goes on in the dark, are still guesswork."

One of our first resolutions was to mutually understand certain aspects and the terminology used to describe various situations/processes. Then began a six-year endeavor where we studied sandbeds of different depths and grain sizes, both in the wild and in aquaria so we could find out why the Jaubert plenum appeared to outperform other type sandbed methods and how its functions could possibly benefit other style systems. Its results were quite informative and it helped not only decipher the plenum method, but also illustrated why other forms of natural filtration such as the Berlin method or those using deep sandbeds may have somewhat different filtration results

Natures Pathways

Lets begin this topic with an understanding of the energy pathways associated with 'biological' filtration and first discuss light, then water, and finally the pathways in the substrate/sandbed, as they all are the main highways that lead to a 'healthy and well-balanced' aquarium environment, and then the results of the testing which were quite remarkable!


Keep in mind that light (energy) is an electromagnetic force and therefore its passage through water can affect the orientation and structure of its dissolved constituents or itself changed to less effective wavelengths/spectrum. In freshwater the passage of light past its trivial amount of elements and compounds when compared to that of seawater is a fairly easy task, yet not so in seawater. The seemingly endless array of elements and compounds in seawater, often increasing their quantities/complexity as aquarists apply different additives or allow it to accumulate different compounds, elements, and/or nutrients, makes the efficient passage of light through this medium sometimes extremely difficult. It should suffice to say there must also be adequate quantity (intensity) and quality (spectrum) of light energy to traverse the difficult path before it, i.e., pass through seawater and adequately reach the targeted organisms

Nevertheless, one would think all of light's energy/spectrums would easily penetrate the aquariums shallow depth. That would be correct if there were a constant flow of natural seawater and light energy from aquarium lamps approached that of natural sunlight. But there is far less light energy from aquarium lamps 'and' it may be skewed by excessive mineral content in aquarium water. In fact, water does not have to be 'yellow' looking to inhibit light transmission, as clear water also contains dissolved nutrients such as nitrate, which in closed systems almost always exceeds what is found in the wild. And it's these nutrients 'and' the over usage of certain mineral additives that can create transmission problems for light energy. Therefore quality water and adequate lighting are essential factors in the road towards success.


As for water, it's a solvent and transport medium, and these functions are vital to biological processes. Also, the direction of its movement along with its flow rate should coincide with the areas where desired species originate. One should keep in mind some species spend much of their lifetime in turbulent areas or quiet backwater areas. Others may live in areas such as seagrass beds that daily experience strong tidal flows that occur in opposite directions.

In fact, there are three forms of water movement: Surge; Turbulence: and, Laminar. Back and forth movement caused by wave action and ocean swells cause organisms living in areas experiencing such surge movement to sway back and forth as water moves past them in one direction, then in the opposite direction. Such movement is healthy for stationary organisms, e.g., sea fans, as their polyps are exposed to nutrients coming from both directions. Turbulence, such as what is experienced where waves crash over reef crests help facilitate the exchange of oxygen and carbon dioxide at its surface, and in bringing nutrients to or carrying wastes away from animals in those affected areas. Laminar flow is more a one-direction flow, such as that from an aquarium pump, and/or is found in very deep areas in the wild. All will be further defined and related to individual species in Section 5, Animal Husbandry.


Substrate is usually regarded as the bed of material/sediment that covers the aquarium bottom. Nevertheless, rock can also be considered substrate. In fact, anything bacteria grow on or where infauna exists can be considered substrate, which is thought to be the aquariums primary filtration medium.

Lets again say that as for the word 'filtration,' that process is what protein skimmers and activated carbon provide. They 'remove' or 'export' elements and compounds from the water. On the other hand, bacteria use a process called 'metabolism' to accomplish environmental changes by transforming elements and compounds into something different. And without a doubt, various microbial processes are the foundation of every aquarium system. Furthermore, healthy longevity of which is based upon how well they (bacteria) function. How well they function is in turn dependent upon your knowledge of their existence, their requirements and the results one can expect from them! In my opinion, they are the heart and soul of the system.

Nevertheless, infauna also need to be taken into consideration, as they and bacteria are part of every sandbed, and the only difference between them is the percentage of each that encompasses that quantity of substrate. And to better understand them, there are several terms that need defining, e.g., diffusion, bioturbation, porewater and oxygen, which are useful when it comes to establishing a sandbed in the so-called 'natural aquarium.'


This is the all-encompassing way nature moves molecules from one place to another. It could also be said it's the movement of a fluid down a gradient from an area of higher concentration to an area of lower concentration, and it can be considered 'Natures' fundamental transport process. It exists in the majority of aquarium sandbeds where it's responsible for most nutrient transport and encompasses how molecules collide and react, how food molecules approach cells, and how wastes leave local environments. It's a very dynamic process that facilitates many biological functions.


This is the disturbing and/or altering of a surface or substrate by the physical activity of organisms such as worms/crustaceans (infauna). In the wild it generally occurs in fine sand and mud-like substrates and in deeper portions of deep beds where diffusion is no longer possible and/or where infauna is present. It would be fair to say that relatively simple alterations to this type bioactivity transport structure can result in dramatic changes. Whether these are good or not for the equilibrium/balance of closed systems depend on many factors. For example, infauna tunneling may release ammonium or cause increased nitrification rather than nitrate reduction because of elevated oxygen levels. Orthophosphate may also be released.

It should also be said that many models of bioturbation have shown both advantages and disadvantages resulting from a best-fit application, i.e., each model is appropriate for particular circumstances, particular use, and/or explanation of basic phenomena. Therefore the interactions between reactions, organic matter decomposition pathways, transport regime, pore-filling secretions, and the complex structures formed by individual burrows or burrow groupings in the wild remain a largely unexplored area of both modern sedimentary bio-geochemistry and the study of the evolution of biogeochemical cycles. Therefore, those individual model results shouldn't be over generalized for the purpose of answering questions relating to the majority of aquarium sandbeds. Our closed systems are just that, a world by itself where the aquarist is God-like, and who needs to understand 'its' parameters and limitations!


This refers to the minute water-filled area around each sand particle. It's an active region of diffusion for all elemental components of energy flow and nutrient cycling. And, the smaller the sediment particles, the closer each particle is to each other thereby reducing the amount of space/water between them. This relates to the word 'permeability' which in turn defines the physical shape and distribution of the sediment (sand). Fine-grained sediments have low permeability, thus restricting porewater flow (B. Bourdreau, 2002). Courser sediments, i.e., above .5 mm, have more useful permeability and diffusion is usually the main form of transportation for foodstuffs to microbial colonies. In finer sand/mud, infauna may provide for the mixing and distribution of foodstuffs. They also consume some of the nutrients and also generate similar nutrients.


Another word that sometimes causes confusion is the word 'oxygen.' It's sometimes written as dissolved oxygen or molecular oxygen, and sometimes simply as oxygen. Oxygen exists either in the gaseous form (molecular oxygen (O2)) or in water as dissolved oxygen, also as O2. As for bacteria, those at the upper most segment of the sediment are about the only users of oxygen dissolved in the water (dissolved oxygen). It's also what's measured when one takes a water sample from the aquarium for the purpose of testing its oxygen level. As for its presence in the upper most portion of the sediment, even that is a varying subject because of the interaction between autotrophs and heterotrophs and diurnal cycles (oxygen used versus oxygen produced at what time of day). As you travel downward into the sediment, the word 'oxygen' is mostly associated with the complex reactions taking place. And when it comes to our sandbeds, the element oxygen (O) is tied to all kinds of things; however, the real issue is oxygen flux from the bed's surface/bulk water interface area on down to the anaerobic zone.

In fact, one of the more interesting statements our early research unearthed was the following; "As in any environment, oxygen is not only responsible for the direct mineralization of organic matter, but also for the reoxidation of the reduced electron acceptors from anaerobic respiration processes. Therefore, the relative position of the oxic-anoxic interface causes a layering of microbial processes, which directly or indirectly depend on oxygen, and the basic principle controlling the flow of electrons from organic matter to oxygen is molecular diffusion! (Brune A., Frenzel P., & Cypionka H. 2000)"

Microbial Biomass

After these pathways and logistic aspects were clarified it was necessary to setup several plenum style systems of different sizes and bioload. Each had a standard plenum grid elevated off the bottom of the aquarium, some by .5 inch (1 cm), and others to about 1 inch (2.5 cm). (Plenum setup will be fully discussed in the next chapter) All systems in the beginning had a sandbed depth of 4 inches (10 cm), which is optimum depth when using 2 - 5 mm grain sand particles. Deeper beds with and without plenums as were shallower beds were also experimented with. Also, different size grain sand was used in various systems. Keep in mind these tests went on for six years, so the testing aspects ranged over a very long time and a wide variety of systems.

Probably the first and biggest shocker that was found in the plenum sandbeds was there were 'different' chemical results occurring in sand areas that contained little oxygen and those in areas that contained basically no oxygen! Therefore, the term 'anaerobic,' i.e., an area containing little or no oxygen and one that aquarists had always associated with nitrate reduction to nitrogen gas was actually not totally true! You may want to reread this last sentence, as its entirely correct!

Testing showed that bacteria, obligate anaerobic heterotrophs, living in a zone containing less than .5 ppm oxygen reduced nitrate back to ammonium, no further! That is a process called ammonification or assimilatory denitrification (reassembly of ammonium, i.e., ammonification) and should be considered the 'anaerobic' area. Therefore, a nitrogen-based product (ammonium), which is of greater value to algae than nitrate, is returned to most of the bed area or may leach upward through the bed into the bulk water! However, in a zone where oxygen is between .5 to 2.0 ppm, and what should be called the 'anoxic' zone, another class of bacteria, facultative anaerobic heterotrophs, reduce nitrate back to gaseous elemental forms and this process is termed dissimilatory denitrification. See the attached photo below showing the circled bubbles of nitrogen rising in one of my plenum beds! And note, neither class of bacterium can live in the other's zone (an important fact.)!

Let me clarify here our decision to use the terms 'anoxic' and 'anaerobic' to describe these particular areas as there was much discussion before this decision was made, even personal correspondence with Dr. Jaubert who thought, depending upon the field of expertise of the researcher, what we preliminarily called the anoxic area could be called either hypoxic or anoxic. After sifting through various 'opinions' and that from Bo Barker Jorgensen and Bernard P. Boudreau, who used the terms oxic, oxic-anoxic, anoxic, and anaerobic to describe the decreasing availability of oxygen in their scientific writings, e.g., The Benthic Boundary Layer: Transport Processes and Biogeochemistry, the decision was made to use the term 'anaerobic,' to describe the area having little or no oxygen to fit the area where obligate anaerobic heterotrophs exist as its term was far more recognized by aquarists.

As for the facultative anaerobic heterotrophs living in a defined, yet small range of oxygen, oxic-anoxic was a term not at all recognized in the aquarium world, and further complicating the matter, anoxic and hypoxic were also terms seen by many as identical, meaning no oxygen. It seemed that whomever we chatted with, had different ideas as to how to label this other area. Ultimately we chose to use 'anoxic' over that of hypoxic and others, as our research showed aquarists somewhat better recognized it, even though quite misunderstood when it came to exactly what it meant, and especially so after our findings. And so, we marched on with our use of these key words, anaerobic and anoxic, and made sure we defined their use upfront so readers of our work were onboard with our findings. In fact, its absolutely necessary to define certain terms to prevent broadcasting misinformation!

Furthermore, both aerobic autotrophs (found in the top portion of the bed) and facultative anaerobic heterotrophs produce adenosine triphosphate (ATP) during their respiration process. However, obligate anaerobic heterotrophs (in the anaerobic zone) are inefficient, as they produce none. Bear in mind ATP production equates to efficient energy production and improved energy cycling! This would mean that those producing ATP are by far more efficient in reducing large amounts of nutrients, and that fluxes in system nutrients can be quickly utilized/better controlled by these bacteria.

As to actual oxygen penetrations of the sandbed, it of course depends upon grain size, but for all practical purposes we chose a grain size between 2 - 5 mm for testing purposes. In plenum systems, the 'majority' of the sand below the first .5 inch (1.25 cm) where aerobic autotrophs thrive and reduce inorganic ammonia to nitrate contained enough oxygen to keep it in an 'anoxic' state! In other words, 3.5 inches (8.75 cm) of the total bed depth of 4 inches (10 cm) was anoxic where nitrate was reduced to nitrogen gas. That was exactly 'opposite' that in beds directly on the aquarium bottom or similar sediment areas in the wild where the top .5 inch (1.25 cm) contained aerobic autotrophs, the following .5 inch (1.25 cm) contained an anoxic area, and the remaining depth was anaerobic!

It was found the reason for the difference was that the water retained in the plenum area contained varying oxygen levels, with the far greater percentage of samples having an oxygen presence of between .5 to .8 ppm. A few showed more, and one that I know of showed zero oxygen. Nevertheless, almost all test results had enough dissolved oxygen to keep the above bed in an anoxic state! We now understood why the plenum bed, when compared to those directly on the aquarium bottom, was so much more efficient!

But the answer as to how oxygen gets to the plenum area eluded us for a long time, and while those tests were going on, it was found the plenum area (bottom water filled area) was showing accumulations of different elements and compounds as the systems aged. And furthermore, those accumulations actually fluctuated, sometimes rising, then falling as time passed with none becoming a threat to the system itself. Why was there oxygen below a 4 inch (10 cm) deep sandbed, and why did these concentrations fluctuate were questions we could not resolve and therefore we turned to Dr. Craig Jones (Terra Kinetics, L.L.C.) who is in our opinion one of the worlds leading scientists when it comes to 'water.' He offered his thoughts on its fluctuating chemical levels, which was the electrical charge that accompanies various substances/matter in the aquarium and also his thoughts as to why oxygen tends to accumulate in the plenum. (Sketch Credits: Sam Gamble)

As for the electrical charge, which is measured in millivolts (mV) with an ORP meter, most aquarists are already familiar with it as its why protein skimmers work as they do, e.g., the positive charge on nutrients is attracted to the negative charge of its air bubbles, hence collecting/binding them together and removing them in the collected foam.

Now keep in mind any type sandbed is a chemical sink where the diffusion of nutrients to and through it is also a function of an electrical charge. In fact, the water's surface and the air above it is a negative mV. (That is the reason why supplying water from near the aquarium surface to a skimmer is far more effective than from deeper levels, as those nutrients are naturally closer to the water's surface to satisfy their charges!) In the bulk water there is many charged molecules with much of it a positive mV. So is most of the living biomass, e.g., corals and fishes. Substrate surfaces (the interface between bulk water and the sandbed) are largely a negative mV. The overall sandbed itself is negative with increasing magnitude with depth. The deeper the sand, the more negative it becomes and the more nutrients are attracted to lower depths. And the bottoms of beds directly on the aquarium bottom are a dead end for nutrients because that is where the greatest negative charge occurs.

Nevertheless, even though plenum 'bed' charges become more negative with depth, the fluid in the plenum area has a less negative charge than the sand above it because of its oxygen content! Therefore, those element and compound accumulations seen in the plenum (some seen to correspond with overfeeding, etc.) are consistently being 'attracted back' to the bacteria living on the sand particles above (because there's a higher negative charge there), or what could be called a natural supply and demand process! It seems like the space (plenum) acts like a temporary reservoir and helps prevent buildup of nutrients in the bulk water from possible overfeeding or other temporary mishaps. How much accumulates in the plenum seems to depend upon system bioload, and moreover, we know of no leaching of these excesses back into the bulk water. An amazing process and only found in plenum-equipped sandbeds!

As to oxygen in the plenum, Dr. Jones put forth three possibilities;

1 Oxygen penetration is less and less with depth. It decreases for two reasons - Microbial metabolism and subsequent biogeochemical processes. Diffusion is a very effective process over short distances, however it has its limitations. Yet, the presence of oxygen in the plenum suggests that oxygen does diffuse as far as the space under the sandbed. Concomitantly, biogeochemical processes may produce or retain some oxygen.

2 Differential Pressure existing across gradients. - Ion displacement (Differential Pressure) exists when there is a relationship with carbon dioxide removal. If there is a substrate producing some carbon dioxide, it then becomes a factor in creating an anoxic condition. The addition of an anion producer such as microbial or aggregate or both needs to produce enough oxygen to engage or attract the carbon dioxide and that will then move the cations, releasing the oxygen and consequently going more aerobic.

3 Silica. There is an inactive and active side to silica. The active side is where the plenum is probably gaining some oxygen. The active acids are Monosilicic acid and Polysilicic acid. These acids hold 6 - 8 elements of oxygen. Dissolved silica can easily deliver the amount of oxygen that has been recorded.

Our conclusion was that dissolved silica could easily deliver the amount of oxygen that had been recorded. Further testing appeared to show slight dissolved oxygen increases that corresponded to decreases in accumulating plenum silica levels. However, that was more conjecture on our part as we were unable to fully quantify that portion of the research. Nevertheless, we felt that silica, the earth's most common element, 'may' be the real reason for oxygen accumulation in the plenum. Throughout the years plenums were tested, silica swung up and down and oxygen levels fluctuated. In fact, Charles Delbeek also noticed silica swings on the plenum he tested, however unfortunately he did not record plenum oxygen levels.

You may find interesting the results of hourly/daily graphs that were maintained by Sam Gamble on pH, dissolved oxygen, and nitrate in a plenum system:

Dissolved oxygen - while being at the saturated level (7.0 ppm) in the aquarium bulk water, the lower sand level oxygen was 0.5 ppm. And the plenum contained a slightly 'higher' level at 0.6 ppm.

Nitrate - level of nitrate in the upper sand level was less than that in the aquarium bulk water. Nitrate level in the lower sand level was slightly lower than the upper sand level. And the plenum area remained slightly 'higher' than the aquarium bulk water, which indicated it was cycling nitrate, not accumulating nitrate.

pH - aquarium bulk water was 8.2. Yet, pH was 0.6 lower in both sand levels and plenum.

Another interesting research fact, one with deep and shallow beds directly on the aquarium bottom, was they are apt to counter a certain process/chemical compound (enzyme) that is advantageous to the efficient use of available energy. In fact, nitrogen fixation - the utilization and production of energy, can be thought of as hinging upon the production of the enzyme 'Nitrogenase,' and oxygen controls several important aspects of the nitrogenase activity.

In sandbeds without a plenum, especially in fine grain beds, oxygen decreases rapidly with depth. In this type environment microbial metabolism uses most of the oxygen within a few millimeters of the sediment-bulk water interface. This condition can also be compounded by the result of microbial activity under raised nutrient loads (dirty sandbeds), which significantly decrease oxygen further. In either situation decreased oxygen quickly falls below the anoxic level needed for the more energy efficient destructive denitrification process. This less efficient shift, now into an anaerobic condition, can cause storage of nutrients via assimilatory denitrification (reassembly of ammonium, i.e., ammonification). In view of the fact that nitrogenase is extremely oxygen sensitive it does best in fully aerobic and anoxic zones. To limit these areas or their overall area volume would logically reduce nitrogenase production. In such a case there would be decreased dissimilatory denitrification and possibly increased nutrient storage (nitrogen compounds - which by the way can be considered green colored - algae!).

Ammonium also effects nitrogenase production and not for the better. Experiments have shown ammonium additions cause a rapid reduction of its activity. Therefore it appears there is a need for a barrier or distance between the mineralization/nitrification zone and that of the destructive denitrification zone. To increase the depth of the oxic-anoxic layer or zone, as with the plenum method, is very beneficial to efficient denitrification by further separating the negative influence of ammonium on nitrogenase.

And since ammonium inhibits nitrogenase production it can also be surmised that nitrogenase inhibition by ammonium is a likely nucleus for unwanted plant growth. Think about that for a moment! In deep beds directly on the aquarium bottom most of its volume is anaerobic where ammonium is a nitrogen-based product continuing to be recycled over and over! It may fit a situation where persistent algal growth in some aquariums continues in spite of low nutrients (including nitrate) in the bulk water. Keep in mind algal growth is a form of nitrogen storage (incorporation).

Ironically, algal mats, e.g., slime algae - cyanobacteria and hair algae can develop and build the same or similar conditions. In fact when an algal mat develops its surface coating/mat-like base facilitates a similar mechanism for ammonification. Therefore when a sandbed becomes structured to favor a lesser efficient form of denitrification such as using nitrate to build ammonium (not breaking it down into lesser ions), it's logical that algal mats will follow by ecological succession. They seem to propagate their own environment by nitrogenase inhibition. In short, nutrient pathways shift toward propagation of plant cells or storage for that goal. This distracts greatly from energy cycling and the balance of the system as a whole.

Keep in mind it could technically be said that no matter what the type or size sand grains or their bed depth, the microbial population in the sand will be in equilibrium/balance with its supply of foodstuffs. But that is somewhat misleading because in the closed system it's the 'overall' efficiency of the bed in relation to the systems incoming foodstuffs that really counts, not that the microbes themselves in the bed are living with each other in a balanced state. Once the bulk water nutrient load exceeds the balanced state in the sandbed (and that degree of balance depends upon what class and number of microbes are existing in the bed), further nutrients result both in the bed and the bulk water. Therefore, choose the sandbed grain size and depth carefully, as your sandbed will be your systems most important biological filter. Understand its capabilities and limitations!

And as to phosphate, most hobbyists know it comes about mainly from the foods fed and/or the quality of tap water used for evaporation makeup or water changes and that excessive amounts, e.g. >0.02 ppm, interferes with coral growth and encourages algae growth. Therefore phosphate-removing media/reactors are important in closed systems. But beyond that, it's been said anaerobic areas where obligate anaerobic heterotrophs reside, accumulate phosphate. Actually, the word 'accumulate' is somewhat incorrect. Yes these bacteria are inefficient and produce copious amounts of phosphate. However, the anaerobic area with its lower pH and redox is a fairly efficient user of the oxygen electrons tied to the phosphorous element. This results in the phosphate being reduced back to phosphorus.

That's a good point for deep beds on the aquarium bottom as most of its substrate is in a truly 'anaerobic' condition (<.5 ppm oxygen). It could also then be said phosphate accumulates in the bed in the more aerobic/anoxic zones, however, that's also not 100% accurate! In those areas it's mostly bound to calcium where it's quite stable because it's very easy in those zones to maintain its 'electrical charge' balance because of the surrounding diffusion of oxygen. Therefore, phosphate is usually not available for uptake in substrates unless directly associated with reducing conditions.

Of course the above relates to the bacteria that inhabit the bed. But in all fairness, there is also another aspect to consider and that would be the impact of infauna on those various microbial processes. Whether worms or crustaceans, they depend on oxygen to live and have to link with the bulk water interface/boundary, whereas microbes do not. Therefore, their tunneling effect can have positive and negative affects on the efficiency of various microbial processes. And if phosphate is liberated to the bulk water, its in the form of orthophosphate, something not registered on aquarium phosphate test kits and which can easily cause algae blooms if in excess.

As to what size and type-tunneling creature would add or subtract benefits from the microbial processes is something not quantifiable in aquaria. Therefore, they are a wild card as no one can say how many of what type infauna species is needed (or actually supply them) and that they would behave as hoped for and create a more balanced condition. Keep in mind infauna also ingest sources of phosphate and produce phosphate-laden wastes. Nevertheless, they are more movers of the compound than users. In my opinion, bacteria are predictable, infauna are not!


Lets now move to Chapter 8 and look at 'System Methodology' and some natural filtration techniques to complete Section Two!