Reefkeeping 101 -
Natural Filtration - Part 3
The Final Chapter

Sand Worms

Last month I was talking mainly about deep sand beds (DSB). During that discussion, I pointed out that a good DSB:

is nearly 4” deep
Has sugar-sized sand (ranging in .05-2 mm size)
Contains numerous, tiny sand shifting organisms that circulate the sand bed
Should not be unduly disturbed by the aquarist or overly active, large sand-digging critters.
If base sand is used it must be seeded with true live sand
From time to time new live sand (LS) must be added to the bed to maintain diversity
Aragonite sand is best as it is light, provides buffering and the smooth texture allows it to “flow” as the sand is gently stirred by sand shifters. If you can find aragonite, silica or other non-carbonate sands can be used

First off, there are just a couple of other things upon which I would like to expound. After a sand bed is added to the tank, one should see tracks in the bed. These tracks are the marks of sand shifters moving about in the sand. Seeing these tracks below the sand bed against the glass is a very good sign, as it shows the inhabitants are tunneling into the bed. After dark, using a flashlight with a red lens, the nighttime critters that dwell in the bed can often be seen scurrying about. Within a couple of hours after the lights go off, there is an explosion of active life. Copepods and other nocturnal sand dwellers come out to play, because during the daytime when the lights are on, they would be easy prey for many marine fish. Under the cover of darkness, they forage the tank’s sand avoiding any predators. After a couple of months, there is usually some darkening of an aragonite bed. This usually indicates that zones are being formed with the darker sand denoting the anoxic layers with algae growing against the glass. It is usually only against the glass area as there is not enough light in the bed to sustain anything but the lowest light alga. In some beds, with burrowing snails, the alga never takes hold as it is eaten by the snails.

A little word of caution: once the rock is cured and the tank set up, the first thing people add is the so-called “clean-up crew.” Usually, this consists of mainly snails and hermit crabs. Most snails are fine as they tend to be herbivores. Hermits are more carnivore than herbivore, but if fresh meat is available, that “meat” is usually all those valuable sand shifters so vital to the bed will go after. Almost every aquarist finds out that hermits eat snails, sometimes to get their shells, but more commonly just to eat. They can make pretty short work of the sand bed population. If you must have some, limit it to only a couple. Some conches will also feast on the bed’s inhabitants and large sea cucumbers are sure to clean out the bed. People say “cukes” (sea cucumbers) clean and renew the sand. That may be true when it comes to bacteria, but the other small creatures (like pods) cannot breed fast enough and can become non-existent in due time.

Filling the Void

It so happens that just before deep sand beds were catching on, there was another substrate-based method making the rounds. Jean Jaubert, who worked at the Monaco aquarium, had developed a method very similar in nature to the modern deep sand bed. It first reached America thanks to Tom Frakes, and was patented in 1991 by Jaubert. In the U.S. it became known as the Natural Nitrate Reduction (NNR) method. The unique part of it was the void area under the bed, created by use of a plenum. A plenum is just a porous box placed at the bottom of the bed. It is then covered with gravel. The plenum itself can be as low as a half inch to as high as two inches. It is then covered with at least 4”inches of additional gravel. Jaubert contended that his system allowed zones to be created, just like in a deep sand bed, but the plenum limited the total area as it allowed partly oxygenated water to exist in the plenums void. It worked very well in Monaco but did not fair too well when placed in the hands of the home aquarist. It was not entirely Jaubert’s fault, as many did not follow his design. Live sand was used instead of gravel. This restricted flow so much that the plenum void soon became completely anaerobic. People were not too fond of having a quarter of their tank dedicated to substrate so they cut way back on the gravels covering the plenum. This allowed too much oxygenated water to enter the void and denitrification was never established. Pumps were used to circulate water into the void with the same result. Today it is rare to see a plenum system as it was found that a deep sand bed did just as well at denitrification.

Bed in a Bucket

Anthony Calfo gets credit for this method. Although he himself calls it a “Sand Bed in a Bucket,” it is more properly termed a remote deep sand bed (RDSB). It is just a deep sand bed that, instead of being located in the tank, is in another container, be it a large bucket, sump, or refugium. Anthony claims that this allows the bed to be kept in the dark, thus eliminating algae outbreaks that sometimes occur in the brightly illuminated aquarium. He also uses higher flows than most tanks. Lastly, and a very good point, is that it is much easier to take it off-line than it is to clean out an in-tank deep sand bed if something goes wrong.

I have only two strikes against this method. First is that some of these beds are very deep and even at the high flow rates suggested they run the risk of going totally anaerobic. The second is they have very limited surface area compared to that of an in-tank bed. This means they can handle less loading. Reefers using them often report good results but nitrate levels hovering around 5 ppm. While not too bad, some species kept in the aquaria cannot take that high a level for long periods. The usual deep sand bed will usually keep nitrate levels near detection limits if it is well set-up and maintained. Anthony does know his stuff and says his method is simpler than having a tank-based deep sand bed. With refugiums becoming so much more common in home aquariums even compared to a few years ago, there are many benefits to this method.

It’s a Miracle

Another highly touted bed method is the use of Ecosystem’s Miracle Mud. Unlike a deep sand bed, mud is used in a reactor, similar to most refugiums. It is claimed that the mud eliminates nitrate, lowers phosphates, and provides a controlled release of “essential” elements into the water column. All these benefit occurring at a cost 4-6 times less than having a deep sand bed. Truly, it is a miracle by any known standard. The Mud is a true mud (particle size less than 0.05 mm and mainly of silica based clays and silt). It is also supplemented with 68 “Minerals and trace elements” that pretty much covers most of the periodic table of elements. These trace mineral dissolve over time and replenish the lost trace elements in the marine tank. I have yet to find any reference to the need for praseodymium for biological health but knowing it is there, ready to replenish the biological uptake of this “important” element in one’s tank, must create warm fuzzies for any reefkeepers that use the product. I do cringe that it lists silver as one of the added elements. Copper is a potent biocide but it pales in comparison to silver. I trust that most of the elements listed are at very, very low levels or one would need to have an EPA hazardous waste permit to get rid of the mud laced with antimony, barium, cadmium, chromium and a host of other EPA-regulated metals.

It requires only a 1” bed in the reactor, about a forth of that used in a true deep sand bed. Although it is thin, it probably has anoxic zones close to the upper portion of the bed. It is very hard for water to circulate in a sand bed much less a bed of mud. That alone would mean low oxygen levels in the Miracle Mud system.

The mechanism of phosphate removal is not that well explained. The possible key to that is that the reactor’s bed is planted with Caulerpa sp., a macro algae of dubious benefits. I suppose the minimal root structure of Caulerpa sp. maintains the integrity of the bed and serves as the major export agent for phosphorus removal; actively growing algae are very good at that.

The Mud is partly replaced after a two-year period, 50% each year. Although that is not a great deal, it costs twice as much as true live sand and with live sand, you only add about 5-10% per year. I guess you figured out that I am not a major proponent of this system. Still, it has a large following. But I sure wish they would publish a paper on the long term (>3 years) results of using this method.

Anyway, here is mud in your eye.

Algal-Based Filtration

There are many other sand bed-type filters described in the literature but those listed above are the most common. Predating the bed filters was a natural filtration method designed for the Smithsonian Institution in the early 1980’s by Walter Adey. Termed an “Algae Turf Scrubber,” it consisted of large trays near the tank with intermittent water flow over the tray material (plastic screening). It was illuminated and brown or green turf algae were encouraged to grow on the screens. This algae would uptake both nitrate and phosphorus as it grew. From time to time, the screen would be gently scraped and some algae removed. This still left a film of active algae to continue the process. In some designs, two sets of trays are used with trays being cleaned in an alternating sequence.

I’ve never been sure why intermittent flow is used on the trays. Adey used dump buckets to provide surges in flow that he said simulated wave action. Why that would be important I do not know, but I speculate that perhaps bacteria are also present on the trays. Periodic exposure to the atmosphere would then supply the bacteria with oxygen without placing a demand on the water column itself; somewhat like a trickling filter (wet/dry).

The main drawback of the design is that it has periodic release of algae from the screen mats. This often creates “green water” in the aquarium and a canister filter is needed to clear things up following such an event. The filter also was fairly large, hard to hide and fairly noisy when the bucket dumps, so it lost favor over time. Some people employ it as a natural filtration method today and the method does work.

Macro Algae

Currently the trend is to use macro algae to do the same job as Adey’s turf filters. A benefit here is that macro algae does not require any elaborate dosing system and no “green water” outbreaks occur, well almost none. It probably helps keep the sand bed in place and possibly helps move the bed as its root system grows. Caulerpa sp. grows very rapidly and can be heavily harvested in the tank. A major drawback is its weed-like nature and reproduction by spore production. From time to time it goes “sexual” and one ends up with algae all over the place. It is very invasive, in fact, so invasive that it is a problem on our Pacific coast and using it in California is banned.

One of the hidden dangers of an algae going into sporification is the flood of unfertilized spores can decay soon after they are released. This can cause a serious drop in the tank’s dissolved oxygen content that can result in injury or the death of the tank’s occupants. Not only Caulerpa sp., but also the attractive cactus algae Halimeda sp. can have these sexual reproductive stages with the resulting problems.

There are better options available to Caulerpa sp. and the most used macro today is Chaetomorpha, known as spaghetti algae. This rapidly growing, floating algae is nearly as good as Caulerpa sp. at removing nutrients by export. All algae uptake nitrogen and phosphorus; what one needs is an algae that grows fast. Fast growth equates to faster uptake. After enough growth is obtained, the algae is merely pruned and the excess thrown away (much to the wrath of the California authorities in the case of Caulerpa). “Chaeto” is easy to obtain and is a better choice than Caulerpa sp.

The Refugium - A Place of Refuge

As the title of this section suggests a refugium is a safe haven. It is not a natural filter per say, but is often stocked with good growths of macro algae thereby making it part of a natural filter. Refugiums, aka “fuges,” are sometimes part of the sump but also can be stand-alone. The stand-alone is just a tank that is illuminated and usually has a lower flow rate going through it from the main tank or the sump. Often is has a DSB and may have live rock (LR). Macro algae is used in most but not necessarily required. Some people run high flow rates through the fuge and that is usually better if the fuge is also used as a remote DSB. The fuge is free of livestock - this allows the tiny creatures that dwell in the fuge a safe place to grow and reproduce. It is good for macro alga in that herbivorous fish tend to eat macro in the display. The problem with that type of algae trimming is that nothing is really exported from the tank and most of the nutrients in the algae are returned to the water column by excretion. In the safety of the fuge, it can be harvested and nutrients exported by rigorous pruning. Very often planted fuges have what is known as a reverse photoperiod. That is where the refugium is illuminated when the main tank is dark. This allows the macro algae in the fuge to produce oxygen at night. Doing so helps control the low pH swings and the reduced dissolved oxygen levels that usually occur in the display at night.

Things like worms and copepods, so important to a DSB, do not last long in the display tank as carnivorous fish and invertebrates relish them. Again, they are fruitful and multiply in a simple refugium. Many fuges today are quite large so there is far larger surface area for a sand bed than there was in the small fuges used in the past. Setting one up is so easy that any serious reefkeeper should look into having one. Editor’s Note: Check out this month’s Reefslides: “Refugiums, naturally!”

Denitrifiers -An Older Method Getting New Life

Now we get to the WaterKeeper Method of denitrification, the biomechanical removal of nitrogen from the tank. Well, actually nobody ever called it the WaterKeeper Method, as I never made my own designs public. In my fish-only days in the early 1980’s, it was widely proclaimed that nitrates were toxic to marine fish if they exceeded 40 ppm. That level was interesting as it was also the EPA limit for nitrate in drinking water, which may not have been sheer coincidence. Anyway, it just so happened I was working on the development of package denitrification plants for a pharmaceutical manufacturing plant. Naturally, I built a prototype but used it on my own marine tank rather than processing the hog intestines used to culture medicines. It was a wet/dry, so popular at that time, with added modules that produced added anoxic conditions following the wet/dry. The first module was a de-oxygenator where nitrogen gas was bubbled through the effluent from the wet/dry to de-aerate it. A small dosing pump then added corn syrup, later changed to ethanol as the corn syrup clogged up the pump, providing a carbon source. It then has a module where nitrogen purges an under gravel filter to convert nitrate to nitrogen gas by bacteria action. From there it passed over another aerated undergravel section where air was re-introduced back into the water column. The final stage was a micron-polishing filter. By George, it worked. It did have a drawback in that it was over twice the size of the 55 gallon tank it served and cost over $500 to build. You also needed a source of cheap nitrogen. As I knew, no reef keeper would ever in their right mind pay over $500 for equipment; it was a one of a kind model. Of course, if I had paid better attention in economics classes, I’d be selling them today.

Today, you can still purchase units that operate similar to the one I built back then, however without needing the very large nitrogen tanks used in my design. Currently, one of the more popular designs is what is known as a coil denitrifier. This is just a tube or hose wrapped into a long coil. A low flow is then sent through the tube and bacteria colonize the inner surface. In some designs, a carbon source (such as sugar) is added at the head of the coil. As the tube is so long, at least 50’, oxygen is depleted as the water passes down the length of the tube. Carbon is provided by wastes from bacterial metabolism upstream of the anoxic zones in the tube. Usually that alone is sufficient to reduce nitrate. A final aeration stage strips the nitrogen gas from the effluent. Sometimes it is passed through a skimmer to accomplish the reoxygenation. Small units use standard airline tubing. Larger units are made with garden hose and the hose coil submerged in a heated container. Flow through the small units is about a half liter per hour. Larger units can handle twice that amount, sometimes more.

Another version is the block denitrifiers. Here a sheet of lexan, like that used for fluorescent light panels, is the denitrifying device. These sheets have a tube like structure where the bacteria grow. Their function is just like the coil denitrifiers in most units.

The major drawback of these systems is the very low flow through the coils. Nitrate production is continuous in a reef tank and, as these reactors only process 5-10% of the water on a daily basis, it invites the slow buildup of nitrates in the display. Most units only claim to reduce nitrate to the area of 5 ppm, which is not enough to satisfy the more sensitive organisms’ needs. You can lengthen the tube but that presents another problem. Eventually you reach a length were the latter stages of the system are completely anaerobic. Then, with the large amounts of sulfates in salt water, it too is reduced to toxic hydrogen sulfide. The re-aeration section of these denitrifiers will air-strip the vast amount of sulfide from the effluent. Nonetheless, if the effluent stinks of rotten eggs then shortening the coil length is needed. Do those in small amounts until sulfides become non-detectable. If one supplements with iron, this too will bind with hydrogen sulfide and render it insoluble. Many designs for denitrifiers are available on the Reef Central Do It Yourself forum so building your own is not that hard.

Keep Your Hands Off Those Remotes

One of the poorer “Help Me” replies I see is when someone asks, “I have a wet/dry and use bioballs. Should I replace the bioballs as I have high nitrates?” The “helper” then tells the person they should replace the bioballs with live rock rubble (small broken up pieces of LR). The bad part is, that doesn’t fix a thing and even may worsen the problem.

Remember when we talked about denitrification, we said that anoxic conditions must be present. In fully submerged live rock, located in the display or sump, the pore structure does provide a limited area for anoxic conditions to form. Now place that same rock in air and just splash oxygenated water over it hour after hour. Anoxic conditions my eye; there is not a low oxygen zone on the rock. Using rubble to replace synthetic media in a wet/dry doesn’t solve a nitrate problem. It may, in fact, make it worse as often cyanobacter will grow on the rubble. Cyano has the ability to “fix” nitrogen, that is, convert nitrogen gas to ammonia or directly to nitrate. With cyano getting all the nitrogen gas it can use with atmospheric exposure, it may well add nitrates into the tank on top of what the tank produces itself.

Another dubious filter is the canister loaded with rock rubble. Now we have the rock fully submerged but sitting in the dark. Coralline covering the surface gets no light and stops oxygen production. Soon it dies off and, after awhile, only the bacteria slime remains on the rock. It may reduce nitrates a trifle but it is also an oxygen sponge. If the bioload (livestock) becomes excessive, it may reduce dissolved oxygen levels in system to dangerous or even fatal levels. Canisters are for mechanical or chemical filtration. Never use one as a bio-filter in the marine tank. Save that rubble and use it in the fuge if you wish.

Water Wheels

As you are now probably aware, older filtration methods such as under gravel filters (UGF), wet/dries and bio-wheels are not considered proper filters for the marine tank. They do work well in the fish only tank where higher nitrate levels can be tolerated but should be avoided in the reef tank.

The humble bio-wheel is somewhat of an exception. In the past, I had a 20-gallon hospital tank set up with a UGF and let it run all the time in case it was needed. I think it was Steven Pro that suggested a better method. Steve only sets up a hospital tank when it is required. I asked about how he kept it cycled, as it is a nearly sterile environment when newly set-up. Steven said he runs a small hang-on bio-wheel on the sump and if the H-tank is needed just moves it to that tank. Great idea; so I got a little Whisper bio-wheel filter and it sits on the sump. It is small, about 100 gallons per hour and only runs the bio-wheel, no media, it really does not do much to increase nitrate. When the hospital tank is needed, I just fill it with water from the main tank and move the bio-wheel filter to that tank. Instant hospital tank and it saves having to make up for evaporation and the other routine duties needed to keep a full-time hospital tank set-up

There are all sorts of mechanically assisted biological filters available on the market. New ones come out every day. As the old adage states, “It is hard to improve on Mother Nature.” If one uses a good DSB and has at least a pound of live rock for each gallon of tank capacity then the only mechanical assistance needed is a pump to provide flow thought the display. Be warned – if you want to use a remote DSB or a coil type denitrifier, they will probably help, but they may not reduce nitrate levels far enough for very sensitive invertebrates.

Next month we will talk briefly about a couple more things that one should consider before stocking the display. See you right after the 4th of July.

Additional Reading:

The Sand bed in a Bucket Thread - It's long, folks
DIY Coil Denitrifier
Marc's Sump & Refugium Page

If you have any questions or comments about this article, please visit this thread in the New to the Hobby forum on Reef Central.