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 8 - System Methodology

As discussed in Chapter 1 there are many choices when it comes to aquarium goals, e.g., fish-only, reef environments, or those depicting very special habitats. Yet no matter what the visual choice certain aspects that have a pronounced affect on its longevity, such as its biological filtration processes, must be understood. And as discussed in the last chapter it helps to create a balance between them and the bulk water in the aquarium that fosters equilibrium, i.e., a balance of natural processes that result in improved water quality. And because of its importance I'll expound further on these topics in this chapter.

(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.)

Natural Filtration Techniques

There are several natural techniques or approaches utilized these days to provide the necessary 'biological' filtration processes that keep closed systems functioning whatever their visual goal. They include the Berlin live rock method, algal filtration, deep sandbeds, and of course, the Jaubert plenum method. But before these and others are discussed in length, lets look at the 'perfect' method, as it tells us something we all want to accomplish, but never do, and that is 'perfection' when energy going into the aquarium equals that leaving, or what can be referred to as the 'balanced' aquarium.

Black Box/Camelot Theorem

The word 'Camelot' brings to mind a mythical place of perfection, and aquariums can at times appear to be just that. How long that appearance of perfection lasts depends solely upon its proper use of 'energy.' Another, yet more technical label for such an enclosure where its inner workings are not fully understood or accessible would be the 'Black Box.'

Hopefully, everyone should be aware that energy cannot be created or destroyed, and can only be transformed from one form, e.g., thermal, electrical, mechanical, chemical, and/or light, to another form of energy. It's called the first law of thermodynamics, and since we can't create or destroy it, the key at least where the aquarium is concerned is to consider how its transported and transformed for an infinite number of uses.

There's no doubt we probably 'technically' understand more about what goes into and departs the Black Box than those mechanisms occurring inside it. And because of that we are held hostage to some of its internal mechanisms. Nevertheless if there is less than needed energy going into the Black Box, then decreased functions and byproducts result. Likewise, if there is greater than needed energy going into the Black Box, then increased functions and byproducts result. If either of these are not in equilibrium with the other, then storage and pollution result and the overall balance of the Black Box is negatively affected. The same is 'very' true for the aquarium!

In fact, most aquarium failures or successes can be traced back to the application of the 'Black Box' theorem where energy availability, transformations, use, and export are either in a balanced or unbalanced state, as fits the situation at hand! That simply says the overall key to a successful 'black box' focuses on 'energy.' And balance is maintained when the box or the aquarium's design parameters fit 'proportionality.' This means that if more energy, such as from animal waste, uneaten foods, poor water quality, insufficient lighting, etc., go into a system that cannot adequately utilize all those energies, then accumulation results with forms of unwanted algae occurring, and no doubt its animals exhibiting poor health, growth or even losses.

The above tells us that if the ability of the chosen filtration method is overtaxed, then it's going to incur much cost in time, effort, and money to rebalance that system, if still feasible besides the incurred frustration and stress that goes along with the overall effort. And we known where aquarium systems are involved there are 'many' opinions as to what form of biological filtration provides the best results. Honestly, whether it's the Berlin method, deep sandbed, algal filtration or other forms of biological filtration, all can provide adequate filtration 'when' the overall system stays balanced! All methods have the same biological goal, which is for its biomass to remain healthy and be able to reproduce, and there's no more important biomass than those bacteria that live in the aquarium as the health of those microbes affect overall system wellbeing!

Berlin Method

This method has more or less turned into a 'philosophy' than a very well defined technique. It came to North America from Europe in the early 90's. Peter Wilkins and a marine aquarium society in Berlin deserve credit for honing the details surrounding this more natural method of aquarium keeping. At that time it provided an alternative to trickle filtration in that it removed the wet/dry from reef aquariums and relied on four main factors; protein skimming, live rock, halogen quartz iodine lighting (HQI), and Kalkwasser. Originally it was tuned to that of keeping stony corals, such as Acropora spp., and as its popularity grew its technical aspects were also adapted for fish-only aquariums.

Its sandbed usage has varied greatly since its onset when a very shallow bed, about 1 inch (2.5 cm) consisting of very course gravel about ¼ - ½ inch was used. It was vacuumed monthly to remove collecting detritus, but as time passed fine sand, about 1 mm used at greater depths became popular with some aquarists preferring not to vacuum the sandbed so as not to disturb/harm its bacteria and/or infauna.

Foam fractionators/protein skimmers were used; often more than one per aquarium, as the thought was it was not possible to overskim the water. Aquarium water flowed via overflows or subsurface intakes to a sump, where in some cases it was prefiltered before being fed directly into the system's skimmers. In most cases it was returned directly to the aquarium. Not only did the use of skimmers help reduce the buildup of nitrate commonly associated with trickle filter use, it did a better job aerating the water.

Another advancement was its use of live rock, which was first cured then utilized in large quantities to provide biological filtration, especially nitrification. Some rock was also used in the sump for additional filtration, along with activated carbon that would only receive partial changes so as to keep the remaining portions providing some biological filtration. Live rock proved to be a far better source of biological filtration than plastic bio-balls as the nitrate produced via its bacteria laden surfaces was partly denitrified via some bacteria found deeper inside it thereby somewhat limiting nitrate buildup in aquariums.

The use of high intensity metal halide lamps was another focal point with the Berlin method, with Osram HQI lamps being frequently utilized. Often 400-watt lamps were used on systems above 500 gallons, with smaller systems using 250-watt lamps. Even though these lamps at this period in time had low Kelvin ratings, about 5100 - 5600K, there was success with corals. Additional blue spectrum lamps also saw a beginning at this time with the use of fluorescent Actinic 03 Thorn EMI Blue or Lumilux lamps. And all lamps were faithfully changed every 12 months.

Other advancements, besides the use of high intensity quality lighting and excellent protein skimming, were the used of Kalkwasser. This helped promoted coral growth and maintain the systems calcium, alkalinity, and pH levels. And trace element additions of strontium, e.g., a 10% solution of strontium chloride, and iodine, a 1% solution of potassium iodide were also used. Add to this excellent water movement with some systems switching flows to opposite directions to replicate natural tidal effects, and turnover rates between 2 – 5 times the volume of the aquarium along with 5% water changes per month and the Berlin technique became widely welcomed.

And over the past years aquarists have continued to make modifications to this technique to suit their goals. Some of these modifications have related to sandbed depth as some prefer a shallow bottom covering of about 2 inches of calcareous sand to give the aquarium a more natural appearance, while others prefer a deep sandbed of 4 inches or more thinking there is a greater presence of microorganism diversity therefore better overall biological filtration. Others have again incorporated the trickle filter, especially where the goal is a fish-only system. The use of connected refugia with large amounts of macroalgae to provide the 'assimilation' form of filtration is also another modification to the original technique. Calcium and alkalinity control has also seen numerous updates and this will be thoroughly discussed in the next Section. All-in-all this excellent technique continues to be utilized and modified, yet it has its limitations as does any technique/closed system as its only as good as its keepers knowledge in what constitutes a 'balanced' system and how to implement and maintain it!

Jaubert Plenum System

As explained in the last chapter, my interest in this technique began in 1992 when I was reviewing the book, Captive Seawater Fishes by Dr. Stephen Spotte. In fact, Tom Frakes mentioned the Jaubert plenum method in 1989 at the first MACNA in Toronto Canada and sent Julian Sprung some information on the method. Julian and Charles Delbeek then wrote about it in Freshwater Aquarium & Marine Aquariums (FAMA) in 1991. Also, Albert Thiel is said to have written about it in 1989 and 1990 in his Thiel Aqua Tech Newsletter. Nevertheless, it wasn't until early 1993 that the method began to get international attention through a series of my articles that appeared in Marine Fish Monthly titled 'Natural Nitrate Reduction (NNR).'

Further investigation showed this enhanced biological filtration process was conceived by Dr. Jean Jaubert at the University of Nice in the late 80's and that he received a French patent (03 284747) and in 1991, a U. S. patent (4,995,980) for his notable work. And since our closed systems were almost always too high in nutrients, especially nitrate, it appeared this method, primarily a more enhanced 'live sand' approach, might be useful in our closed systems. In fact, it has proved to be more microbial efficient than what's provided by any other filtration technique! Because of this, I'll need to expand on it much more than other techniques as it not only needs to be fully understood, it's a technique that's better used in an interconnected tank/sump/refugium where its maintenance can more easily be preformed.

As explained in the last chapter, the Jaubert process required a layer of sand be sandwiched between the aquariums bulk water and an open space at the aquarium bottom. Not only did the Jaubert method almost entirely eliminated nitrate naturally in my 75-gallon test aquarium, it provided a way to supplement calcium, alkalinity, and add valuable trace elements. About a year after my first series of NNR articles appeared, Tom Frakes wrote an article titled 'Red Sea Reef - Mesocosms in Monaco.' The article expounded on the founder of the process, Dr. Jaubert, and further enlightened all those who read it in SeaScope Volume 10, Fall 1993. Nevertheless, there was not any in-depth data on its microbial processes. And it wasn't until Sam Gamble contacted me because of my articles that we as a team began six years of research to find out why the Jaubert/NNR method appeared to outperform other biological methods/techniques.

In fact, many questions arose as we plowed our way through many very scientific textbooks and test systems! And during the research we occasionally contacted Dr. Jaubert to discuss our findings and at the end of our research we wrote a book tilted 'The New Wave,' to describe our findings and philosophy, to which Dr. Jaubert called – "An enormous effort to explain the complicated processes that underpin the homeostasis of an enclosed ecosystem." And Martin Moe Jr. said "Gamble and Goemans have created a fascinating journey through the structure and function of plenums and sand beds. Truly a "New Wave" in marine aquaristics."

Near the end of our research, we wanted further thoughts from others in the scientific community as to our plenum findings, and you may find the following letter quite interesting, as we did.

"Dear Bob,

I recently received an E-mail from Sam Gamble after you had sent him my address. I wanted to send you the body of my reply to him as it includes a summary of my microbiological testing on plenum systems. I thought you might find it interesting.

"Thanks for the E-mail. First I must apologize for my belated reply, I have been in Mexico for the last couple of weeks completing some planktonic bacteria testing. I was very excited to get your E-mail and to meet Bob. After reading so much about the two of you and your research, both of you have become some of my scientific heroes.

I have been working with plenum systems for the last 2 or so years and have had successes with coral culture that I have never experienced with natural systems. As a microbiologist, I have been very impressed with the firm basis for the reduction reactions in these systems. When I have had extra time and media, I have done microbiological analysis on the populations in the plenum vs. natural systems.

My specialty is the Vibrio spp. bacteria, especially those which directly infect fish or which are believed to cause toxic tank syndrome. I was amazed at the reduction in pathogenic Vibrios in plenum systems. I found that free Vibrio concentrations in the water column were 20-130 times lower in the plenum systems as compared to similar tanks with identical bioload, likely due to nutrient sequestering in the plenum, leaving little in the water for the bacteria to consume. Even more important I felt was the finding that although the total organic carbon and biochemical oxygen demand in the plenum void space was much higher than interstitial water from within "natural" sandbeds, Vibrios were almost or completely absent from this water whereas the natural water samples contained between 10,000 to 150,000 colony forming units per milliliter. I attribute this to the decreased pH in the plenum water, which allows for competitive inhibition of the Vibrios by more acid-tolerant heterotrophic bacteria. The end result I believe is a decrease in secreted toxins and increased health of the system. This system seems to naturally simulate the addition of probiotic bacteria that has become an area of great interest in the aquaculture community in the last few years.

My next experiment will be an attempt to rear clownfish larvae in a plenum equipped rearing tank. So far, the use of filtration in larval tanks has been disappointing due to the occurrence of toxic tank syndrome, so I will be interested to see if this can limit toxin secretion and whether the huge bioload of larval tanks will overwhelm the plenums filtration capacity."

I would be very interested to hear your reaction to these findings and would be happy to send you copies of the raw data if you are interested.

Best regards,

Olin Feuerbacher, Owner

Arizona Aquaculture Solutions"

To sum it up, we came away with a vast amount of 'enlightening' information, and it led to enormous requests for information on how to create plenum systems.

Grid Construction

As noted above, the plenum method involves the use of a motionless 'space' under a layer of substrate, motionless except for minute movements in its chemical processes. The plenum's entire grid-like structure is similar to that of an undergravel filter plate, however that's where any similarities end. In a plenum system, water is not mechanically flowed through the openings of the grid that separate the sandbed from its lower space, as is the process with undergravel filters. In the plenum system the lower space is a reservoir for nutrients important to the microbial processes in the above sandbed. To provide this space there needs to first be an 'elevated' grid on the aquarium bottom.

For the grid material, recommend the use of what is commonly called 'eggcrate,' a grid-like diffuser material utilized in overhead fluorescent fixtures. Inexpensive and readily available as this material is in North America some aquarists' in other locales report difficulty in locating it. Even when found its cost was sometimes three times or more its price in the United States. Finding a business that sells building supplies can sometimes solve this or visiting an office-type building that is in the process of being torn down can also help. In fact, both eggcrate and PVC pipe, i.e., the grid and its supports, can usually be found at many salvage sites since they are common building materials.

This plastic grid material, containing square .5 inch (1.25 cm) wide openings is usually white but can also be found in black, gray or a chrome-like finish. The white, black or gray varieties appear to be safe for aquarium use, but as previously discussed the chrome-colored variety remains questionable. Eggcrate is very easy to cut with a hacksaw blade and can be cemented or easily secured with plastic cable ties to PVC pipe to form the grid assembly, i.e., the grid and its supporting pieces of pipe. There are a few different grades of eggcrate, with the two most popular being a residential eggcrate material that's about a .25 inch (.6 cm) in height and a commercial grade that is sturdier, which is .5 inch in height. Either will do nicely.

Keep in mind if eggcrate grid material were to be placed directly on the bottom of the aquarium without any supporting columns, diffusion to and from the sandbed would be extremely limited to each of the tiny areas within each square of the material. This would effectively shunt horizontal diffusion throughout the entire plenum. Reports from those who have created plenums in this fashion all noted decreasing water quality parameters within the range of six months to a year. Eggcrate should only be used as the 'grid' device to separate the plenum (space) from the above sandbed. Therefore, to allow for adequate diffusion throughout the entire plenum the grid must be elevated off the bottom of the aquarium. To accomplish this, horizontal lengths or short vertical pieces of PVC pipe or other types of suitable material can be secured to the eggcrate to provide the lower vacant area.

When constructing the grid assembly its recommend the bottom space be .25 - .5 inch (.7 – 1.25 cm) for aquariums under 300 gallons (1200 liters). In larger aquariums it's recommended the plenum grid be slightly higher, i.e., 1.0 inch for systems up to a 1000 gallons. In fact, research/feedback showed there may not be a need for much over 1 - 2 inches in systems that go beyond 1000 gallons (4000 liters).

Even though eggcrate is the recommended grid material, some hobbyists have used undergravel filter plates. This has proven not to suffice in the long run as they contain a limited amount of diffusion ports/holes. However, as one aquarist noted, why can't he just drill a lot more holes in it! Go for it was the answer if what would be left were still strong enough to support the sandbed and live rock. And when constructing the grid, shape it to cover all but about .5 inch (1 cm) distant from the inside aquarium walls. The plenum space should also be kept in the dark, i.e., not open to light around the outer edge of the aquarium or from beneath it. Test results seemed to indicate that nitrate-reducing processes are slowed in lighted areas.

When elevating the grid off the bottom, sections of plastic pipe (PVC) can be used to support it. Most often pipe is laid horizontally and secured to the grid with plastic cable ties. Some hobbyists have used stainless steel wire, monofilament fishing line or various types of glue or epoxy cements. Whether laying the pipe horizontally or using short vertical pieces, holes should be drilled along their length to balance their internal fluids with surrounding plenum chemical parameters. If using short vertical pipe supports, one hole through both sides of the pipe piece would suffice. Also, don't cap the ends of horizontal lengths of pipe as that restricts the diffusion of the liquids within them.

Another possibility is forming a picture frame-like wall of PVC pipe along the circumference of the grid. Then supporting its internal span as necessary with shorter PVC pipe lengths. The outer edging of pipe could then possibly prevent some species of shrimp or large worms from burrowing underneath the grid. Whatever method is used to uphold the grid, be sure to place enough supports so as to provide a stable platform for the live rock/sand that will soon be added. Building it right the first time allows chemical parameters, which are constantly changing in the plenum area, to have sufficient and unimpeded space to carry out their functions.

As for grid screen material, common Fiberglas window screen seems to be the best choice. I have reviewed other types of screen material such as what is used on seawalls and that used to block garden weeds from sprouting. These type materials had very minute holes that would block diffusion. Nevertheless, the words 'window screen' has been another area where questions arrived from abroad in large numbers. What is window screen? In North America most window frames have an additional outside groove to hold a screen. The screen is usually made with a Fiberglas or metal mesh-like material with a mesh size just small enough to keep mosquitoes and gnats from coming in when the glass windowpanes are in the open position. This net-like material in the North America region is commonly referred to as window screen. To make a long story short, aquarists abroad were able to find something that fitted their need. In the UK it was called 'Graveltidy,' a plastic mesh used to separate layers of different size media in undergravel filters.

Furthermore, there was one reader letter where the plenum's grid screen had become coated with a fungus-like growth. The letter began by stating system parameters were cesspool-like and the reader noting the plenum system was a bad idea. It was not until the aquarium was taken apart, as noted half way through his letter that he found the screen coated with a growth that completely blocked diffusion. I mention this one letter here because it's not that it couldn't happen again and ruin a lot of hard work. Be sure the screening material is not coated with any kind of bug repellents. If it were, it should be noted on its label.

Even though common window screen is highly recommended, that has not stopped some people from using rolled cotton, mechanical filter material, felt padding, and even sheets of foam/sponge-like material! When these type materials are used they easily become clogged and either greatly limit diffusion or completely block it. This creates a situation in the sandbed that results in a very real possibility for the accumulation of hydrogen sulfide. Also, in systems where excess anaerobic conditions exist, the sand can actually generate some minor heat and can experience a methanogenisis situation as found in a swamp. Keep in mind the screen's mesh size is of great importance. A mesh size too large allows the proper size sand grains to fall into the plenum. A mesh size too small could easily clog and block diffusion. And, don't use metal screen material. Sounds logical, but you might be surprised as to what some people do!

The screen material should not only cover the top surface of the grid, but also its surrounding edges to prevent sand from slipping underneath and into the plenum area. You may find it best to first place a large piece of screen material on the work area and then place the grid assembly on top of it with its top facing downward on the material. Then simply fold enough screen material up and over the assembly as if wrapping a present. Stay with only one covering on the top of the grid, as any additional material there can lead to clogging. Additional material/folds on the bottom is not a problem.

For those wanting a custom-made plenum grid, contact


When this method was originally brought forth to aquarists the grid was placed directly on the bottom of the show tank, where its recommended aragonite-based 2 - 5 mm sand particles were placed at depth of 4 inches (10 cm). Many years and thousands of letters later there has been a tweaking of those initial recommendations. Its now recommended the grid not be placed in the show aquarium, and an interconnected aquarium or sump be used to house it. The reason for this is as time passed it was evident most aquarists were not leaving enough bed surface area open for its maintenance. In fact, Dr. Jaubert recommends at least 75% of the bed surface remain unencumbered for maintenance purposes, which includes vacuuming and monitoring for clogs as described in one of the following subjects (Plenum Bed Upkeep). There is no doubt this technique is vastly more effective when placed in an interconnected sump/refugium where its bed surface can remain nearly or totally open for maintenance. Furthermore, the plenum technique is so effective the inclusion of any live rock for biological filtration in the main system is actually unnecessary or at least can be greatly reduced.

In fact, the pictured 125 had amazing coral growth rates – e.g., the green star polyps, Briareum violacea, not only covered most of the back wall of the aquarium within a couple of years, the Yellow Leather coral, Sarcophyton elegans, began to reproduce via budding and the Turbinaria peltata also budded-off an arm-like growth besides overall doubling its original size!

Aragonite containing grains continue to be the best possible choice. And as for varying the grain size as some hobbyists have suggested, such as placing a layer of very fine sand, e.g., 1.0 mm on top of the recommended bed grain size, this is not a good idea as it interferes with proper diffusion.

Furthermore in plenum systems where falling water was directly impacting the bed surface or where major burrowing animals where housed, normal bed mechanics/diffusion were negatively affected as too much dissolved oxygen was entering the bed. In these type systems, bulk water nitrate experienced levels equal to aquarium systems having a similar bio-load with its bed directly on the aquarium bottom, as the plenum bed was then housing mostly nitrification processes.

Selecting & Placing the Sand

Once the grid is placed, some seawater should be added to at least cover the entire grid before any sand is added. This way the majority of the air trapped under the grid will easily escape. The little remaining will slowly dissipate over the coming days with no harm to the forming microbial colonies.

As for sand, if the budget cannot handle the cost associated with purchasing live sand, dry aragonite or crushed coral gravel can be used. Since it is without any live bacteria, this 'dead' sand will probably take about one month to become sufficiently colonized by bacteria, whereas those directly on aquarium bottoms take about three months to fully colonize The only drawback by starting with dead sand in any type system is that it will require more patience and planning on the part of the aquarist to bring system bio-load up to its full capacity. Nevertheless, it can occur more quickly in plenum beds.

Keep in mind a grain size of 1 mm or below cannot be used on the plenum grid, as it would either pass through the grid screening and fall into the plenum or clog its mesh openings. This would in turn limit diffusion into and/or out of the plenum. Plenum systems require a grain size of 2 - 5 mm so as to properly establish dissolved oxygen gradients/redox throughout its recommended 4-inch (10 cm) sandbed depth. To estimate the amount of properly sized sand for a 'plenum' system, multiply (in inches) the width of the aquarium by its length, then by the depth of sand (4 inches) and then multiply by 0.0579 to get pounds needed. Poundage for a courser or finer grain size would of course vary.

Whether dry or live sand is chosen, suggest it first receive a gentle 'flushing' with some freshly made seawater before going into the aquarium. Where prepackaged live sand is concerned, a gentle flushing will not overly disturb its dormant microbial colonies. Bear in mind this type sand may have at one time been dry dead sand and then made 'technically' live by flushing it with natural seawater, then allowing it to dry somewhat before packaging. By remaining somewhat moist inside the package the now dormant microbes on the sand particles can remain in that condition for many months and when becoming wet again, awaken and continue with their processes.

As for bed depth, some aquarists have questioned the need for a 4-inch sandbed and wanted to know if 3.5 inches would suffice. Others asked if 2 inches would be okay. Some wanted a sandbed deeper than 4 inches. Sam and I have found that a sand grain size between 2 – 5 mm provides the ideal oxygen/redox gradient in sandbed depths of 4 inches. A shallower sandbed than recommended would simply have less anoxic area equating to somewhat less overall system efficiency volume-wise. A much deeper bed would result in a complete change to overall sandbed redox eventually resulting in nitrogen storage/poor water conditions.

And then there were those that simply do not like the appearance of a deep plenum sandbed or were concerned about an aragonite-based sand slowly dissolving. As for aesthetics, the depth of the sandbed can always be hidden by trimming the lower few inches of the aquarium with wooden trim strips. Or do as I did and recess the aquarium into the stand by a few inches. As for concern over the dissolution of aragonite, which will occur, I've poured new sand through a 3 inch ID PVC pipe to various areas of my aquariums and then spread it out using a homemade long handle plastic rake made especially for this purpose. Of course, a more stable form of calcium carbonate such as a calcite containing crushed coral could be used for the bed.

If purchasing recently collected in the wild live sand, keep in mind there is a certain amount of die-off from its collection to your doorstep. This may cause its organic content to increase while in shipping. How much that may be depends on where collected and how long it takes to get to you. Therefore, recommend as noted above, thoroughly flush it with fresh seawater before placing it in the aquarium. Some have stated a concern because their newly purchased live sand did not contain any visible worms and crustaceans. Actually, it's the bacteria living on the sand grains that are the most valuable of the living organisms at this timeframe. Organisms such as worms and crustaceans will eventually find their way into the sandbed from live rock/corals. As they do, they will help somewhat to bring nutrients into the sandbed to fuel the now established microbial processes.

Through Flow

With most plenum systems now more properly and conveniently located in separate interconnected systems, the questions as to how quickly should water flow through these interconnected systems and how large should the plenum system be in relation to the main system. These were very good questions, and it took at least a year with feedback from both aquarists and a public aquarium to come up with a yardstick/rule-of-thumb that appears to be quite reliable.

As for physical size the plenum system 'surface area' should be about half that of the main system if feasible, as that provides a bed surface quite capable of handling systems slightly overcrowded and overfed. Depth of water/vessel height is of less importance as shallow water systems having only 6 inches of water height have proven quite successful as I have consulted on said systems in some Philippine breeding and holding facilities. When it comes to its flow rate, its something similar to that in protein skimmers as dwell time appears to have some importance, and feedback has shown flows should not exceed a turnover rate of more than the main systems capacity once per hour when sized as above. In fact, slower flow is remarkably successful as a reader noted. He had a 500-gallon fish-only system and noted that 35 ppm nitrate was flowing into his auxiliary plenum system sized at 55 gallons and 20 ppm was flowing out. I should note that water flow through his plenum system was at a rate of about 40 gallons per hour.

Plenum Bed Upkeep

When it comes to general maintenance of the various aquarium filtration methods in use today, the plenum system is without question one of the least demanding. This is not to say it doesn't require any maintenance as some aquarists have claimed. Those who have failed to meet its simple requirements have found that in the long run even its exceptional system parameters beginning to erode. Besides fielding many questions on what constitutes proper plenum maintenance, I have seen accusations that the method is a time bomb simply waiting to explode or it crashes after a period of time. What nonsense! (See Misconceptions below) Some email stated the users were told never to vacuum the substrate. The thought there was that by doing so it would kill the organisms feeding on detritus or introduce too much oxygen into the sandbed. In turn that would disturb sandbed microbial processes and lead to unwanted algae blooms. More balderdash! Some other letters focused on their plenum systems not being able to maintain natural seawater (NSW) element and compound levels as was stated in some articles authored by those who 'thought' it did/should. More misinformation.

Let's discuss those erroneous and misleading statements along with just how simple the plenum is to maintain with those thinking its sandbed should maintain NSW elements and compounds, i.e., calcium, magnesium, and/or alkalinity. In the well-managed new plenum system or in fact any type new system for that matter, there will not be a very large demand on calcium and magnesium. Nor is the new system biological load too demanding, which in turn does little to affect its alkalinity/pH. The new system can appear self-supporting when it comes to these conditions, but as it ages its bio-load increases and so does the demand on calcium and magnesium. Usage of these constituents by coralline algae, clams, and/or stony and some soft corals creates increasing demands, as does some precipitation.

When a healthy sandbed is fully established there will be some element replenishment to the bulk water especially when aragonite material is used as the substrate. Although it's very likely not enough to keep pace with the requirements of animals and calcareous algae in most aquariums, especially reef aquariums. It has always been stressed the plenum method is capable of 'supplementing' the need of certain elements — not replenishing all used by its organisms or that of precipitation caused by improper use of certain chemical additives.

Depending upon the rate of calcification; magnesium uptake by coralline algae; and the overall demand on the alkalinity base, certain additives will still be required. Although the amount required in plenum systems using suitable sand, e.g., an aragonite based particle would be less than in aquariums using calcite-based crushed coral. Nevertheless, if the aquarist wants to eliminate the need for buffers and calcium additives, especially in large complex systems, the addition of a calcium reactor should be considered.

Sandbed height is another situation that needs to be occasionally monitored as dissolution of the sand grains, especially if aragonite-based, will be noticeable. As a hobbyist noted, when he moved the contents of a perfectly functioning six-year-old plenum system to a larger system he found the lower aragonite sand grains much smaller than they were originally. Even though he occasionally added some fresh sand grains to his aquarium, he questioned what would happen if the smaller particles fell into the plenum? There's no doubt that in five to ten years lower aragonite-based sand grains will become smaller, maybe even small enough for some to fall into the plenum. Nevertheless, they would continue to dissolve to some extent and what remained would be so tiny as to not impinge on plenum mechanics. In fact, there are no doubts some new sand will be needed occasionally to maintain a recommended plenum sandbed depth if this type sand is used. Of course less soluble material, such as calcite containing crushed coral could be used if the aquarist would be more comfortable with that as that would lessen/possibly eliminate grain replenishment needs.

Not vacuuming the sandbed was another issue discussed at length many years ago when the method became quite popular, as the thought at that time was that it would damage the infauna and bacteria and thereby reduce their efficiency. Would you not dust your home, ever, was my response to this kind of thinking! Of course not! And since there's no doubt there's accumulation of detritus in all type aquarium sandbeds, and its often quite specific to certain areas due to aquarium currents, some areas need more attention than the overall sandbed surface. And yes, it's true that worms and crustaceans utilize some of the micronutrients in the detritus and in turn provide certain benefits to the sandbed microbial colonies as describe in previous discussions, but we are specifically targeting excessive detritus accumulations here. In such a circumstance it can reduce microbial efficiency and stress alkalinity and pH levels. On the average, areas of heavy detritus accumulation should receive vacuuming every one to three weeks and the entire plenum sandbed surface to about a depth of 2 inches a quarterly vacuuming. Replacing the water removed during vacuuming could be considered the only water changes the system needs.

One other maintenance factor remains, and that is surveying the bed for binding. In the past some aquarists thought this an inherent trait of plenum systems and because of it were doomed to fail. That would be something like saying automobiles are the cause of all car crashes! Not so, as the driver is the cause. And should note here that I've had plenum systems that have never developed binding, whereas others have. There are two reasons put forth as to why binding occurs.

The first is that plenum beds have far faster forming colonies of bacteria and when incoming volumes of nutrients vary greatly, the size of the colonies change to stay in balance with the level of 'food' coming their way so to speak. There is some thought that bacteria secret compounds outside their cells that cement grains of sand together forming chunks of sand particles. And furthermore, if formed by bacteria, the chunks can easily be broken up with your fingers and returned to loose sand particles.

Another reason for this occasional binding is related to precipitation 'within' the bed. As mentioned above the purpose of using aragonite, a very soft type of calcium and easily dissolved, is to supplement its content in the bulk water. However if the bulk water's calcium content is above that found in NSW, in other words out of balance with its counterparts that makeup alkalinity (explained in the next section), it cannot enter the bulk water and therefore precipitates as calcium carbonate upon adjacent sand particles securing locking them together. If resulting from this type precipitation, these chunks are far more difficult to breakup.

Have personally seen easy and hard to break up sand chunks in some past plenum systems. Experience seems to indicate that precipitation was the cause in those that experienced hard binding, as those systems all experienced high bulk water calcium levels in a hope to increase stony coral growth. In systems where 'alkalinity' was maintained in a balanced way with what appears in the wild, no binding was incurred and in fact my present plenum system as I write this is slightly over three years old and never has had any binding.

Nevertheless the plenum sandbed should receive a monthly test for binding areas and suggest occasionally using a dull knife, e.g., a butter knife (my wife still wonders where our butter knife went!) and running it through the sandbed where possible in a crisscross fashion. If any binding is found your fingers should be able to crumble them so as to restore the chemical pathways. Again, this situation only seems to manifest itself where bulk water calcium is forced above that found in the wild, e.g., far above 400 ppm.


Misinterpretation, incorrectly read or gathered data, and sometimes just running off with the mouth simply to be heard has caused this technique much undeserved poor press. Fortunately, reader interest and feedback to articles I've published over the past years have been extremely helpful in bringing to light the reasons for these misunderstandings. Let's begin with what I classify as the poorest of these misinterpretations

All Plenum Systems Fail in One Year

Probably the most ridiculous article I've ever seen, and one that appeared in a well-known US magazine, is where its writer went on to say that 'all' plenum systems fail like his did, in one year. Then went on to detail the disastrous results he experienced in his plenum system. I met the writer of this trash at a marine conference and questioned him on how he set up his plenum system. He not only 'completely' set up the system incorrectly, he overburdened a newly set up system, then incorrectly maintained it. Then wrote the article as if the technique was poor. Shameful was my words for his actions, and when I told him I knew of hobbyist plenum systems at least 12 years old and still going nicely, he refused to believe it. He also refused to comment on the success of Dr. Jaubert's public aquariums.

Plenum Systems are Cesspools

This thought trend surface back in the late 80's through the early 90's when a well-known magazine writer wrote several articles calling the plenum system a cesspool. I met this person several times and went over fact-by-fact and where he went wrong in setting up his plenum systems. He used large oyster shell and Puka shell components in his substrate along with old, heavily nutrient loaded live rock. He was polite, yet refuses to change his position or even consider indisputable evidence from one of the world leading biochemists, or from Sam Gamble (a marine biologist) and myself.

Siphon Tubes

The placing of a siphon tube into the plenum space and periodically draining its fluid came about because some people spread the word that the elements/compounds seen to accumulate in the plenum space, e.g., nitrate, would continue to do so and eventually be forced upwards into the bulk water. Nothing could be further from the truth, but the logic of the belief, of course without any evidence, caught the attention of some hobbyists who thought it sounded reasonable.

The fact of the matter is when water is siphoned out of the plenum it is replaced by water from the above substrate. This would of course change the redox value of the fluid in the plenum, negating its ability to return temporary sequestered nutrients to the above bed. To what degree it would be changed would depend on the amount siphoned, nevertheless, it would negatively upset the normal plenum processes. Keep in mind the plenum liquid remains slightly higher in charge than the sandbed particles above. The result is 'cycled' nutrients, not 'warehoused' nutrients and the sand will actually remain slightly cooler than the aquarium bulk water, which suggests endothermic reactions. Besides not needed, placing and maintaining siphon tubes is a waste of time. Those who were frightened by the temporary accumulations of nitrate in the plenum did not understand the plenum microbial processes. They then yelled wolf when there was actually none!

Mysterious Fish Deaths

There was at one time thought that a poison of some kind was being released by newly established plenums that caused the death of some fish. Even though untrue, new plenum systems 'very' quickly create huge bacteria colonies, in fact much faster than in sandbed systems directly on the aquarium bottom. In doing so, there is a huge requirement for dissolved oxygen. Microbes are rapidly expanding their colony size and utilizing oxygen to satisfy respiration needs in their metabolism cycle. Energy gained from metabolism is focused on their reproduction. Therefore additional aeration or water movement during this timeframe is advisable and may prevent mysterious fish deaths during the night when carbon dioxide levels normally become elevated.

Plenum Connected to Aquarium Bulk Water

There have also been plenums connected directly to its enclosure/aquarium bulk water by way of riser tubes, such as what is used on UGF plates. From what was understood from some of these modifications it was to increase the oxygen level in the plenum so as to hopefully keep the substrate from developing dangerous hydrogen sulfide or releasing toxic gases. Others wanted to be able to inject lactose, glucose, methanol, or ethanol into the plenum to enhance plenum and sandbed processes. There was even some thought by one person that potassium permanganate could be injected into the plenum to increase its ORP.

Actually there are no toxic gases in the plenum or its sandbed when properly established. And by having an open connection to the aquarium bulk water it would produce an 'aerobic' plenum. Therefore most of the methods denitrification processes will be negated, similar to what occurs in a reverse flow UGF. Also the introduction of any chemical into the plenum by a non-scientist is less than a good idea for the safety of all the organisms in the aquarium.

Protein Skimming Not Needed

There was at one time some opposition to the use of protein skimming in reef systems utilizing the plenum method. Thoughts were that plenum systems were already highly nutrient poor; therefore, skimmers were not needed. Others said their use should be limited to less than efficient models or used only part-time so as not to 'starve' the processes in the plenum bed!

Of course new systems may not seem to need protein skimming, as the decline in water quality is especially transparent during its first few months of operation. But concern here should be with the category of organic compounds. Some can be broken down by microbial metabolism and some cannot. That is to say some are biodegradable and some are not. Together they have been termed Dissolved Organic Carbon compounds (DOC). Their levels are difficult to judge until accumulation causes yellowing of the water or there's unwanted plant growth. In fact, colored water is actually the result of their molecules in the water changing light characteristics/refractory quality

Since carbon (C) is important and necessary for bacteria growth, increased amounts of DOC help to increase their numbers, which in turn helps cycling. But since carbon pathways and inorganic nutrient pathways are tightly linked, there is a general side affect in the accumulation of inorganic nutrients like nitrogen-laden compounds and phosphate when DOC increases. The result is poor water quality and no doubt nitrogen storage in the form on unwanted algae. Aquarists often then have to go to war with algae.

If one does limit or skips skimming, the next option is removal of DOC and excess inorganic nutrients with appropriate filters and filtering aids. Methods of adsorption are commonly used for this dilemma, with activated carbon one of the better choices besides that of skimming. Phosphate removing media, sometimes used in canister filters is another useful tool to help prevent unwanted forms of algae. Poly-Filters™ are another useful tool.

And even though there are some minor disadvantages with protein skimmer usage, the adsorption kinetics of skimmers along with other forms of chemical filtration should be considered a safety net to protect the overall system from a large nutrient flux or when sandbeds, whether in plenum systems or not, are undersized or improperly constructed and/or maintained. As for the skimmer itself, over the long run it can be considered similar to a car shock absorber by absorbing the road bumps in the life of the system or at least an aid to equilibrium because of the aquariums confined and finite volume. Therefore, highly recommend their usage and that aquarists evaluate their system conditions and use quality made protein skimmers accordingly.

Foam Plenum

There was at one time a product that simply consisted of a rigid slab of highly porous foam-like material as 'the' plenum, and in fact was advertised as such. The material was placed directly on the aquarium bottom and simply covered with a couple of inches of sand. It never became popular for several reasons. Even thought the product was highly porous, the material was composed of many tiny chambers where biomass such as detritus and bacteria could/would easily clog/impede any constituent flow into and through the material. And since it was placed directly on the aquarium bottom, would not operate any different than a sandbed directly on the aquarium bottom. It seemed obvious the entire slab of this material would quickly become anaerobic and have just the opposite result as the Jaubert plenum! In fact, one of its advertised high points was that the material would foster anaerobic denitrification, thereby reduce nitrate. Thought that kind of odd after all the evidence that minimizing such a condition was the far better approach to water quality. Short-term observations from users of this product seem to think it must have fostered anaerobic denitrification as their nitrate levels were reduced. Probably so, but ammonium production was no doubt quite high.

Bear in mind a 'true' Jaubert plenum is an open space and there is nothing in its 'space' to skew the extremely important value of its redox or interfere with its chemical processes. Nothing in this open space is needed to accommodate microbes nor should there be, as all valued microbial functions are taking place in the above sandbed.

Nitrate Conundrum

Some aquarists noted their plenum systems continued to experience 'small' amounts of nitrate, - if that could be considered a real problem! Levels experienced were anything from a few ppm to approaching 10 to 15 ppm. What was found in some instances was that some hobbyists were unaware there are two different types of nitrate test kits on the market. Some measure the 'nitrate ion' and others measure 'nitrate nitrogen.' Nitrate is a compound or combination of elements. One molecule of nitrate is composed of one nitrogen atom and three oxygen atoms (NO3). Since the atomic weight of nitrogen (N) is 14.01 and the atomic weight of one oxygen (O) atom is 16, the weight of one nitrate molecule equals 62.01, or 14.01 + 16 + 16 + 16. Therefore a test kit that reads the nitrate molecule/ion will show a reading 4.4 times higher than a test kit that reads nitrate nitrogen. It is the nitrate-nitrogen factor that is of importance. In some cases there was no nitrate level of concern. In other cases it was found some additives being used skewed test kit reagents and resulted in false high readings.

In all fairness, no one should expect plenum systems to be totally nitrate free. Some systems may not register any nitrate levels while other correctly established systems may indicate some small levels of nitrate. Aquarium systems are like people, no two are the same. The important point here is that nitrate levels are naturally and more efficiently reduced in plenum systems and bulk water levels are generally below what they would have been if the system did not have a plenum.

Heating Cable

There was at one time thought that by locating a heating cable in the plenum 'sandbed,' the heat generated would increase bacteria activity. Actually, the productive temperature range of the microbes existing in the sandbed is in the 70º F range. Two problems arise from heater cables located in the sandbed. The first is that the area nearest to the cable will be the hottest, thereby affecting the wellbeing of any microbes/microbial processes nearby. Also, the quality of the cable itself comes into play, as some are not too well regulated and/or do not dispense heat evenly. However, even more important is the fact the generated heat rises and causes rising convection currents that work against the downward flowing diffusion process. It's those downward processes in a plenum bed that are invaluable when it comes to microbial processes remaining in a 'balanced' state.

Freshwater Plenums

There continues to be much interest in using the plenum method for freshwater aquariums. In fact, have received quite a lot of mail from freshwater hobbyists that have spoken highly of their plenum-equipped freshwater systems. Here's an interesting letter from Rick Greenfield that I received many years ago:

Dear Bob:

A few individuals (including myself) have setup plenum systems for African Cichlids and the preliminary results have been very interesting. It seems as though all the benefits of the plenum in marine systems are magnified in freshwater. Especially noticeable is that the pH can be maintained in the high 8's (8.5 to 8.9) with absolutely no effort at all in the form of additional buffers. I mean this is starting from un-mineralized RO water and with a whopping amount of fish in the tank. I think that the weak ionic strength of freshwater allows the unimpeded dissolution of carbonate. We sell an unusual Cichlid gravel and advertise its buffering capability but a well documented and strictly controlled study is lacking. Since you are the one who introduced the plenum system to the United States, and championed it to the world, African Cichlids plenums may be a natural extension of your expertise. In a way, this is already your baby. Worldwide I am told the passion for African Cichlids rivals that for marine aquariums and with the rift lakes under increasing environmental pressure, captive stocks may mean the best chance for their future. The last person to setup the plenum said that he had Cichlids breeding in the first week! If you are interested in taking on a project this different, we would naturally supply you with all the substrate and rocks you need, give you what little information I have, and support you in any way we can. I hope I have piqued your interest!


Rick Greenfield

Unfortunately at that time I didn't have the time or space to take Rick up on his offer. Nevertheless I made arrangements with a Cichlid aquarium society for the tests, and Rick supplied them the substrate media free of charge for various test systems. Their tests all came back resulting in lower than expected nitrate levels and higher than expected pH levels, and healthier bioloads. In fact, I've had success stories from those with plant systems, goldfish aquariums, discus, and very general fish systems. Therefore, the door is open to those wanting to experiment with the plenum technique in freshwater systems!


We've all come a 'long' way since our plenum research completed and have concluded from our experiences that very efficient biological processes are occurring in the upper inch of live sand. Below that, in the ocean and sandbeds directly on the aquarium bottom, a less efficient form of biological filtration is occurring. Because there is such a tremendous sediment surface and volume of water in the oceans, those deficiencies found in their lower sediments are easily overcome. The same is not true in a closed system. Moreover in aquaria, the less efficient form of biological filtration can easily become prevalent because there is simply less water volume when compared to that in the wild. That is, unless the more efficient portion of the closed systems sandbed area is extended downward, possibly with the installation of a plenum!

If there are drawbacks with plenum systems they are with the alterations to its simple design or lack of proper placement or maintenance. There also continues to be some aquarists that think a plenum system guarantees success. Not so! As any farmer can tell you - you get what you sow. Nevertheless, technology is fast moving ahead and other means of controlling unwanted nutrients in the bulk water of aquariums is becoming available and they are quite easy to utilize. But for an all 'natural' approach the plenum system is without doubt, unbeatable!

Deep Sandbeds

This method simply involves the use of a very deep bed, e.g., over 4 inches used directly on the aquarium bottom. It has been said it not only provides very good biological filtration, its greater depth provides organisms that may become live food for other system inhabitants.

It's true that deep beds are ideal places to maintain sand sifting seastars (starfish), gobies that like to burrow and/or other digging type animals. It's also true there may be greater amounts of infauna than in shallow beds that in turn help to consume some detritus of which are bacteria-coated. They also consume diatoms and algae films, and move sand particles about changing its porewater thereby bringing oxygen to somewhat lower depths and helping to foster some increased nitrification in those areas. How efficiently all this happens, depends greatly on the systems bioload and the system's maintenance.

Depending upon who writes about deep bed usage, you'll see a wide range of comments from 'nothing better' to 'having drawbacks.' I'm somewhere in between, which may seem like a politically correct position. Nevertheless, as mentioned quite often in this section, any of these biological filtration techniques can have positive results, as the real deciding factor as to their success depends upon the systems 'bioload,' which in turn dictates overall maintenance! And no method/system is maintenance free.

And whether or not the deep bed is used in a refugium or the main show aquarium, keep in mind detritus monitoring is important as some users have been told not to vacuum its bed because that would damage its bacteria and infauna content. Not true, as I've seen many letters from those with older deep beds complaining of severe unwanted algae growths only to find out they have been vacuumed little or not at all. Time simply caught up with these systems, as detritus 'will' continue to accumulate, infauna or no infauna.

One other aspect to consider is the placement of live rock, as it will sink lower into the bed if not properly supported as time passes. Keep in mind the weight of the rock and possibly rocks and corals on top of those will simply push the mass downward until its bottom reaches the aquarium bottom. Therefore cave-ins and damaged corals may result depending upon how well the structures are supported.

Algal Turf Scrubbers

There has and still exists some controversy as to whether algae scrubbers are truly beneficial for closed systems. Photographs from noted aquarists and authors have showed invertebrates at well-known public aquariums utilizing algae type scrubbers in different stages of poor health. Yet others, including those who have brought their use to the forefront of our attention, spewed forth significant benefits.

When interest in Algal Turf Scrubbers first began I decided to start at ground zero with the reading of Dynamic Aquaria: Building Living Ecosystems by Adey and Loveland. They stated that in nature, dissolved inorganic nitrogen (ammonium, nitrite, and nitrate) is mostly removed/utilized (assimilated) by algae, not bacteria. And this benefits the quality of surrounding water as the algae actually use the nitrogen laden products for growth, produce oxygen and remove carbon dioxide during this process. Furthermore, excessive nitrogen can actually be removed from the closed system by simply harvesting the excess algae on a periodical basis. Whereas as in trickle filters and systems depending upon live rock, bacteria consume oxygen and produce carbon dioxide while reducing these nitrogen products to less toxic forms of nitrogen and finally discharging the nitrate algae nutrient into the surrounding waters.

Adey and Loveland were also of the opinion protein skimmers are detrimental to the closed system as they would remove plankton from the surrounding water. Their algal filter was considered a refuge for plankton, and utilization of a protein skimmer a counter-productive process. The use of activated carbon was also avoided.

Nevertheless, one has to consider the Algal Turf Scrubber method the closest possible duplication of what there is in the wild. Both the Berlin and Jaubert method are a distant second and third when thinking along those lines. Keep in mind what was just said only takes into consideration the overall looks/construction of an algal scrubber system, not its microbial balance or overall microbial efficiency!

The basis for using an Algal Turf Scrubber was to duplicate an exact slice of nature in a closed system where basic filtration was solely provided with 'algae.' However, it's not possible to take an exact slice of nature, including its substrate and water column and expect it to perform in the 'long-term' as it does in the wild. Once this slice of nature is inside an enclosed structure, aka aquarium, the same microbial balance as exists in the wild will not continue to exist in this enclosure. Nutrients will accumulate because there is not another wave or tidal effect to carry away those accumulating nutrients. Equipment designed to reduce or remove these nutrients or a process or product designed to overcome the imbalance needs to be brought into play. Therefore, even though the water in the entire system may remain nutrient poor when it comes to inorganic nitrogen and phosphate compounds, it may become rich in organic nutrients, and this was the problem when Algal Turf Scrubbers first came about.

And if used in aquaria containing corals, one must realize that a heavy growth of algae compete all too well for the same nutrients that coral zooxanthellae utilize, possibly affecting their long-term growth. Also, that algae leach organic compounds that result in yellowing of the water, and since colored water negatively affects spectrum and intensity of light this also affects coral growth to some extent. From what has transpired since their onset, their success was greatly improved when the scrubber was combined with a quality protein skimmer and/or the use of activated carbon.

Algae Scrubber systems have evolved into DIY projects and there is much to be found by searching the Internet as to helpful suggestions. Some of those I've seen contained multiple removable algae trays that could be removed, cleaned or placed in the aquarium as a food source for herbivores. Some had mirrored sides and end panels which help concentrate light for improved light intensity for algae growth. Some had turbulent water flow passing over, under and through its algae beds, yet the main environment remained quite hospitable for small organisms that inhabited them. Some hobbyist-sized algae scrubbers also seen in the far past mounted on top or above the aquarium, or even in a remotely connected sump such as with modern day 'refugium' use. Common fluorescent light fixtures were usually sufficient and in the days of store-bought systems and were included in some models as standard equipment.

During years of interfacing with those desiring this form of filtration, its been possible to developed a short list of recommendations. Some of which may be helpful if deciding to utilize this form of filtration.

  • The scrubber will need its own lighting system, which can consist of inexpensive common daylight type fluorescent lamps.
  • The scrubber should be located where its photoperiod can be opposite that of the aquarium and will not interfere light-wise with each other.
  • Having a scrubber is like having another aquarium. It requires maintenance; so make sure you have the time to maintain it.
  • Both micro and macro algae will do nicely.
  • Wave making devices or surge type equipment should be considered for use in the chamber holding the algae.
  • Additives such as iron and molybdenum may be helpful.
  • Have the water flow directly from the aquarium to the scrubber via an inside the aquarium overflow. Then through a canister filter for chemical filtration, then back to the aquarium.
  • Utilize a high quality protein skimmer, located in the flow from the scrubber.
  • Removing the oldest one-third of the algae is a good rule-of-thumb. How often depends on how fast it grows back, and when to begin harvesting depends on the physical appearance of the algae. If it looks robust, with lots of new heavy growth, allow it to accumulate until it is simply too much for the physical size of the containment area. If it begins to look frail, or starts to cellophane remove the oldest one third. Either use the harvested algae, if in good condition, as herbivore food or give it to a fellow hobbyist for his herbivores or sell it to a local aquarium shop.
  • Keep in mind, depending upon system nutrient level only a certain quantity of algae can be supported, and when the vegetation out-weighs the supply of nutrients the vegetation will die back (cellophaning is a beginning indicator). This can happen extremely fast and the final result is a major dump of nutrients back into the system from the disintegrating algae. These nutrients can spread throughout the aquarium providing the right conditions for hair algae and other unwanted algae to get a real hold on system substrates such as live rock.

Anyone interested in more information concerning this method should read the "Dynamic Aquaria: Building Living Ecosystems" by Adey and Loveland (ISBN 0-12-043790-2).

Mud Systems

This can be considered a 'hybrid' technique, as it provides both assimilation and biological filtration. The use of an iron and manganese-rich extremely fine-grained substrate, such as what has been provided by the product Miracle Mud®, and utilized in a refugium or a system called the Ecosystem Aquarium®, provides an environment especially helpful for maintaining macroalgae. It is claimed the mud contains other numerous minerals and trace elements, thereby providing an environment that behooves algae growth. And some manufacturers/suppliers of these type products recommend half the substrate be replaced after the first two years, then half every year thereafter. Systems such as these also tend to incur large growths of infauna, where 'some' may flow back to the main system providing plankton-like foodstuffs.

Keep in mind the all important destructive denitrification process in the anoxic zone of a regular sandbed, as explained above, is supplied nitrate from the above mineralization/nitrifying bacteria in the oxic zone of the bed. Mud systems, however, have practically no oxic and anoxic zones since the mud particle is so tiny. Also keep in mind the diffusion gradient in any type bed is controlled by its electrical charge (not just oxygen) and gravity. Therefore it's not possible for a bed of any size particle directly on the aquarium bottom to function in any mode except that mainly of a nutrient collection device because its redox simply becomes more negative with depth. Therefore, mud systems excel when it comes to producing nutrients that foster algae growth.

When using Caulerpa in these type systems, one should remember it's capable of absorbing nitrate from the bulk water as most alga do, which it then slowly breaks down into nitrite, then ammonium for growth. Actually, in mud systems most of its algae needed nitrogen supply is thought to come directly from the ammonification process in the bulk of the mud bed. That's because mud particles are so tiny their porewater (the space around each particle) is almost nonexistent, therefore there's no oxygen content in probably 99% of its depth unless brought there by tunneling infauna. Because of that it harbors the ammonification form of denitrification throughout most of its bed, liberating generous amounts of ammonium.

Keep in mind algae such as Caulerpa is not solely dependent upon getting nitrate from the water and wasting its energy to break it down. It would simply be supplied a readily available amount of ammonium, which is what it really needs for growth directly from the mud. And as for the iron content in these 'mud' sediments, besides a growth fostering element it also fosters a phosphate release in associated sulfur/sulfate processes that accompany chemical situations in deep beds.

There's no doubt better algae growth occurs in systems utilizing mud-like substrates, and there are now many brands selling similar fine-grained products. Yet, if wanting to try a similar, yet less expensive approach, 'very' fine sand mixed with Laterite is a possible avenue. This houseplant growth medium is high in iron and available in home improvement/household plant stores. It can be mixed into a deep bed and then topped with 1 inch of unmixed sand to cap the mixture and prevent discolored water. Just keep in mind no aquarium system can solely survive on the 'assimilation' process, therefore adequate biological and chemical filtration also needs to be provided.

Mangrove Systems

These 'plants,' i.e., Rhizophora sp., (Red Mangrove) are found in highly nutrient-rich seawater and brackish water areas near coastlines that experience intertidal flows in circumtropical and subtropical locations. They are also found in limited quantities in some freshwater areas. Their roots stay more in the aerobic/anoxic portion of the substrate, spreading its 'cable-roots' horizontally, somewhat simulating a tree with many spider-like legs.

When placed in aquaria they need an open space above the tank as their main growth is upwards and out of the water, and of course need strong light such as what is provided by metal halides. Some aquarists believe they will quickly absorb nutrients, nevertheless the truth is nutrient removal is quite slow and very limited with these terrestrial 'plants.' In fact, if the system is already high in nutrients additional lighting may encourage growths of unwanted algae.

As for planting a mangrove they do not really need a substrate, as their roots will develop in water alone. Yet for aesthetic reasons, placing the roots in sand or gravel is perfectly acceptable. Sometimes their leaves drop when first placed in the aquarium, however this is a common occurrence with budding and new leaves soon to follow. Pruning will help to keep them at a reasonable height and shape, but while fairly small should be limited to no more than removing one or two leaves per day. Roots from a healthy and well-established mangrove growing into an area where such growth in not desired can be trimmed. New plants should not have any roots trimmed until they become well established.

When mangroves, sometimes called walking trees because of their leg-like roots, become part of a seawater system they remove magnesium and if it becomes too low, their leaves and branches begin to shrivel or their leaves become yellow. Therefore its recommended magnesium levels be monitored and other elements such as potassium, iron, and manganese additions also be considered. All in all, mangroves are more a conversational item than a nutrient scrubber where aquariums are concerned.


The dictionary defines a refugium as a place of shelter - a sanctuary.

Most hobbyists think of it as a separate chamber that adds the benefits of 'natural' filtration to their system. Even though natural filtration is the basis for their existence in the hobby, the thought to be results may not always meet all expectations, as I have tried and found them to be at least interesting and in some ways beneficial, yet having limitations. In fact, much has been written about refugia and their various capabilities and accomplishments when connected to main systems.

No doubt one of the most talked and written about is their capability to reduce swings in pH when their macroalgae is lighted at opposite timeframes from the main system. That is true, and additionally it helps reduce the strain on overall system carbonate buffering (alkalinity). To what degree it's useful would depend upon the size of the refugium, the condition of its macroalgae, the quality/type lamps it's lit by and of course, the bioload in the main system.

As for refugium lighting, common daylight fluorescent lamps are the best choice when its goal is to culture macroalgae. Since algae are mostly shallow water species, they are accustomed to utilizing the more reddish spectrum for photosynthesis thereby tending to flourish when exposed to this wavelength. Nevertheless, the blue spectrum will also generate photosynthesis. Since common household lamps normally have a greater percentage of the red band wavelength because they make colors look more what 'people' think they should be, these lamps are the better choice than the much more costly high in blue spectrum reef aquarium lamps. Therefore it's not necessary to light a refugium where plant photosynthesis is its main focus with expensive high in blue spectrum lamps.

Furthermore, a refugium filled with macroalgae and lit at an opposite timeframe from the main system would act like an algal turf scrubber. As explained above, such an environment would help foster bulk water that may remain nutrient poor when it comes to inorganic nitrogen and phosphate compounds, but may become rich in alga generated organic nutrients. And it's those and others that can cause light transmissions to become refracted/negatively affected. Therefore, highly recommend such systems utilize quality skimming and the use of activated carbon to help diminished possible light transmission interferences.

And if a refugium is being added to rectify problematic pH and alkalinity conditions in the main system, it might be possible to consider such an action as 'looking for a silver bullet' to resolve the problem. I would suggest first looking for the root cause of the problems. Remember, if the main systems pH and alkalinity is 'thought' to be low, before trying different ways to raise and stabilize them, be sure there's really a need for a 'fix.' I find some hobbyists misinterpreting what are adequate ranges for these important parameters and proceeding down various avenues to rectify a situation that didn't need fixing in the first place. And because of such happenings, this is why those and other seawater parameters will be discussed at length beginning in the next Section.

Another reason for refugium popularity is that protected refugium areas often develop various plankton-like creatures that 'might' become an important food supply for the animals in the main system. When I had my refugium set up with some live rock and macroalgae, amphipods and copepods quickly multiplied. Within six months I found myself watching the refugium 'almost' more than my main system. Yet, were the amphipods and copepods finding their way into the main system? No, not unless I took the time to vacuum or siphon them into a container and then spill them into the main system. Not something I had the time or desire to keep doing, and what could be easily gathered were eaten by one fish in my main system at one serving! The remaining fish still had to be fed other type foods. And as for having some of its plankton-like creatures end up going through the refugium pump and piping to the main system, I'm sure few, if any ever made it there alive.

Another premise for installing a refugium is that it will provide for a greater overall carrying capacity since it increases overall system water volume. And the thought there is that by doing so, the main system can easily contain more animals. Nevertheless, this can lead to the downfall of the entire system when 'bioload' outstrips system microbial 'balance.' And one must use commonsense when adding a refugium to a main system, as 'small' refugia do not provide measurable water quality benefits to very large main systems. Yet, they may be a great place to hold the 'bully' that may be in the main show aquarium while you decide what to do with it. In fact, refugia can easily be isolated from the main system and serve as a temporary holding area/quarantine area for the 'new comer' to the main system.

Bottom line, whether it's a sump or partitioned area in the main show aquarium, a commercially made unit or a remotely connected small aquarium or that of a hang-on-tank unit, the use of a separate chamber, i.e., refugium, has seen a large increase in hobbyist acceptance over the past decade. Stocking it with live sand, live rock, macroalgae, possibly some invertebrates and maybe a small fish or two, along with a lighting system that has a photoperiod opposite that of the main show aquarium is probably the most accepted version. Nevertheless before going this road, I ask those considering it to ask themselves if adding another small world to their present universe is really necessary or would they be better served by improving the environment in their main show tank. That may sound somewhat negative, but that's not the case as I think refugia use can be quite helpful to many different type systems, nevertheless their need should be adequately justified before adding additional overall maintenance and cost to the main system. Could well be the main system simply needs improved alkalinity and/or phosphate control and/or its bioload adjusted to match the capacity of its microbial colonies.

Filtration Summation

When looking back over the past couple of decades much has been accomplished in the hobby, especially by those who have brought leading-edge aquarium keeping methods to the forefront. Some were gratefully received; others were torn by conjecture and misstatements. Unfortunately, where filtration was concerned, it appears to be a subject matter that has been inadequately or simplistically discussed in many aquarium books.

Nevertheless, it should now be clear that 'biological' filtration, i.e., bacteria using metabolism to 'transform' matter/elements/compounds into energy for reproduction and/or other forms of elements or compounds, are at the frontline when it comes to maintaining a healthy and 'balanced' aquarium environment. In fact, that quest for such an environment may have unknowingly begun in 1950 with the first UGF called the French Invisible Filter (Shown in Chapter 4). Then moved on in the mid 80's with the introduction of trickle filters, then later on to systems based on live rock and improved equipment. Nevertheless, and somewhat unfortunately, the understanding of the associated microbes and their pathways in aquariums did not take a big leap forward until almost the mid 90's when there was major research by Sam Gamble and myself into the anoxic sediment denitrification method conceived by Dr. Jean Jaubert. The results of which were quite amazing and set the record straight as to what biological processes were 'really' happening in several different style sandbed systems and resulted in giving the aquarist an 'informed' choice on what may better suit their desired system goals when it came to 'biological filtration!'

As to that research, it importantly showed among other things there were 'two' forms of denitrification. One occurred where .5 to 2.0 ppm of oxygen existed, the anoxic zone where facultative anaerobic heterotrophs reduced nitrate back to nitrogen gas. (Called dissimilatory denitrification.) And in a zone where less oxygen existed, more properly called the anaerobic zone, obligate anaerobic heterotrophs existed and reduced nitrate back to ammonium, no further. (Called the ammonification process.) As previously explained, in plenum-equipped beds almost the entire bed remained in a very efficient anoxic condition. But this was not the case in sandbeds placed directly on the aquarium bottom!

In those situations, as explained above, using the common grain size of between 2 – 5 mm, its first .5 inch (1.25 cm) of depth houses the aerobic autotrophs that provide the reduction of inorganic ammonia to finally that of nitrate. Just below this area/zone there's a level of facultative anaerobic heterotrophs, lets say another .5 inch (1.25 cm) in depth, reducing some of the incoming nitrate to gaseous nitrogen, which sometimes appears as bubbles rising in the sand. Below that the bed consists of obligate anaerobic heterotrophs reducing the remaining incoming nitrate to ammonium, no further. Ammonium produced in this area is either recycled backed to nitrite and nitrate, then back to ammonium, (again and again) and some of it may leach upwards into the bulk water providing exactly the nutrient needed for improved alga growth. Unfortunately, aquarists are unable to test for ammonium, but can often see its result in various forms of green algae growing on the substrate surface or elsewhere in the aquarium. And if so, some are wondering at that time what causes this growth, as possibly their bulk water nitrates may be fairly low! Keep in mind 'ammonium' is the primary alga nutrient!

Lets now reduce its grain size to something like mud. Now, aerobic autotrophs and facultative anaerobic heterotrophs only inhabit the upper 'millimeter,' with the remaining depth containing the obligate anaerobic heterotrophs. A wonderful arrangement if one's desire is to propagate algae, such as in the current mud-type refugia!

Last but not least, lets simply take a bed of very fine sugar-size sand grains. I've often seen it recommended this is the sand grain size to use because there are more grains, therefore more areas for microbes to colonize. It's true there are more microbes, but that's of no value for the closed system! Keep in mind very fine grains pack together very tightly thereby greatly reducing porewater volume. Anoxic conditions would then be restricted to an extremely shallow zone in this type sand, e.g., just below an upper shallow depth oxic area. Therefore, more valuable bacteria processes are greatly reduced because there are simply less suitable areas for them to colonize. That leaves the remainder of the bed depth for assimilatory denitrification! Basically it's more bacteria but not the right volumes of the right classes of bacteria.

Furthermore, hydrogen sulfide is a very real possibility in finer grain/mud type beds! Nevertheless, if not disturbed and allowed to enter the bulk water it generally presents no hazard to animals in the aquarium. However, in swamps/muddy environments, methane is another poisonous gas and it 'bubbles' upwards on its own. Could this happen in aquaria using a mud-like substrate? I doubt it very much, but did come by one disastrous happening that could have been its fault. (See Chapter 9 for its details)

Also in each of the above discussed beds add the situations involving the important enzyme nitrogenase and the electrical charges that accompany various substances/matter in the aquarium, and then decide for yourself what form of sandbed is right for your planned system.

In looking back I can say I've learned a lot about different style 'biological' filtration aspects, especially where aquarium sandbeds are involved. Some of it has resulted in eye-opening details. So what lessons have I learned? First and foremost, I believe aquarists can be successful with any type system if planned correctly and provided the required husbandry. Biological filtering devices e.g., UGF, trickle filters, and sponge filters to name a few, all have positive attributes if properly matched with the goals of the desired system and properly cared for. Nevertheless, it's easier said than done in this world of always thinking there's room for one more specimen! Exceed the limits of what your form of biological filtration can provide and system 'balance' is soon lost, and the struggles to regain it are extremely difficult, often quite expensive, and many times simply impossible to rectify without losses of livestock.

Now armed with the information gained over the past decades, I often look back and wonder if aquarists have miscalculated the value of some types of sandbeds and/or the use of excessive amounts of live rock, which, depending upon its porosity, basically contains the same microbial processes. In fact, those who say utilize deep beds and lots of live rocks because it will help lower nitrate accumulations are only somewhat correct. As you can see from discussions in this Section, there's much more to it as it may have a far greater impact on system health than the narrow viewpoint on 'nitrate' reduction!

And as for those expounding on the benefits of infauna and meiofauna, they are good additions to the benthic scene, however a hit or miss benefit when compared to the overall benefit provided by a large 'anoxic' zone containing energy efficient bacteria. Yes, infauna aid with the mixing and grazing of detritus, which in turn helps supply microbes some nutrients/energy. But they also expel wastes, and bacteria must process that also. And as to the value of infauna, I can calculate the zones where efficient or inefficient bacteria reside, but I can't give marching orders to infauna to carefully and evenly traverse the depths of my sandbeds (Bioturbation). However, that is not to say they provide no value at all, yet in my opinion should be considered a marginal benefit when compared to that of highly efficient bacteria.

Hopefully, the discussion on sandbed biological processes has helped some realize that if a closed system, no matter what its physical size (home or public aquarium) contained more anoxic than anaerobic areas as defined here, its bulk water may possibly contain far less nitrogen laden products. In fact, it should be evident by this time the denitrification path in an anoxic area is of far greater value than the denitrification path in anaerobic areas. And since the volume of area accomplishing 'nitrification' is usually fixed in closed systems, it's wise in my opinion to concentrate on how to enlarge the volume of anoxic zones and reduce those associated with anaerobic zones.

As an interesting side note to bed depth, I've had the opportunity to work with two aquarists in different countries where they chose to go with bare bottom reef systems using less than .5 pound of live rock per gallon. They wanted to easily stir up any settling detritus with a jet of water, thereby using some of it as a foodstuff for their corals and/or easily siphoning out collecting deposits. Both encouraged coralline algae to cover the aquarium bottom by carefully monitoring calcium, alkalinity and magnesium levels. One of the tanks, a 600-gallon system in Australia, within its first six months began developing a heavy coating of coralline algae on its bottom. As for the other smaller system in Hong Kong, it also was beginning to have some coralline developing on its bottom in only three months. (Not doubt both had hastened coralline growth because the lack of bottom sand grains/substrate somewhat initially reduced magnesium precipitation.) Both aquarists reported far less system maintenance, thriving corals and no unwanted algae growths. And I should note a past 320-gallon reef system setup in the mid 80's went that way and was very successful. But the first comment always received when people viewed it, was about the lack of bottom substrate!

And yes, esthetics do come into play where most aquarists are concerned, as they want a natural looking environment with many wanting a white sandy lagoon-looking bottom area. That's quite understandable and for those who go this road highly recommend a shallow bed directly on the bottom of the aquarium and it be limited to about 1 to 2 inches (2.5 - 5 cm) and utilize a grain size in the range of 2 - 5 mm.

Again, any of the above techniques discussed in this section can provide adequate results when associated with a bioload that does not exceed their capabilities. In fact, a while back discussed a 100 gallon aquarium having a 10 inch deep sandbed with some macroalgae, one in which the owner was very proud of and said it was established for two years and never had any problems. In fact, he felt the deep bed was totally responsible for his good water quality and healthy macroalgae. His bioload consisted of two six-inch fish that he was hoping to spawn. In such a system, with limited bioload, I had to agree. Yet, any of the above-mentioned techniques, in my opinion, would have provided the same water quality. In fact, a large sponge filter, bare-bottom tank, siphoning detritus, and water changes would have probably also sufficed with this size bioload. (Different strokes for different folks.) Bottom line - when choosing a more natural filtration method, be sure its capabilities will meet the needs of your system's planned bioload goals, and don't exceed it.

Hopefully you found the information presented here useful, and even though a plenum type system may not be desired the results of years of testing has, without a doubt broadened our overall understanding of the term 'Filtration!' What you do with the information presented here is up to you, but for sure, you can if desired move your aquarium system towards a more microbial balanced environment with the information discussed here.

Let me express here these words of wisdom:

If you attempt to stuff six pounds of waste into a five-pound bag, you'll no doubt have to resort to high tech equipment to process the excess, always far more expensive and not always successful.


Now, lets move on to Section Three – Seawater, and in Chapter 9 discuss 'Water - The Basics,'as an introduction to all aspects concerning this vital portion of marine aquarium keeping!