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By Charles & Linda Raabe
Mactan Island, The Philippines
© 2011 All Rights Reserved

  Having observed the fringing reefs found near my home on Mactan island since 2004, I have become much more aware of not only how the various habitats work in conjunction with each other, but also what threatens the balance that each of them brings to the reef equation. By taking apart that equation, I hope to show how we can recreate the reef's solutions and apply them to reef aquariums, thus creating a more realistic, and functional coral reef within the glass boxes that we like to call our reef aquariums.  This series of articles will examine a Philippine fringing reef's habitats and how we can apply each of those habitats to our reef aquarium systems with the intention of creating a functional ecosystem that provides multiple habitats, each with their own unique populations that in combination will provide the means to further the hobby towards the meaning of the word "reef".

Part One: Land meets Ocean

What is a fringing reef?  They are those reefs that develop in shallow waters along the coast of tropical islands or continents.  Fringing reefs are generally narrow platforms a short distance from shore and do not contain substantial lagoons. Given suitable substrates and no algal competition, the corals would grow right up to the shoreline. But with the constant influx of sediments, having those sediments moved about through tidal and wave actions, and with high dissolved nutrient levels near shore, corals are restricted to those areas that lack sediment and nutrient-fueled algae.

   What is a reef aquarium?  Note that I did not ask what is a coral reef aquarium.  I purposely left out the word coral simply because a reef is so much more than just a few coral species growing on top of some rocks. With the vast diversity of life found on a reef, we should strive to obtain and maintain as much of that diversity as possible in order to be able to use the word "reef" when describing our aquariums. In order to do so, we must provide not only the habitat for the corals to thrive in, we must also provide the various other habitats that, in turn, make a fringing coral reef possible. It is my hope that through this series of articles you and I will both get a sense of the much bigger picture that the word "reef" should invoke.

  So what do fringing reefs have in common with our reef aquariums? As it turns out, a great deal with the answer found in one word; nutrients. Just as our aquariums struggle with the daily input of nutrients, so do most of the fringing reefs of the world. With shore-based nutrients and sediment run-off into the oceans, fringing reefs have developed a number of habitats that in combination allows coral reef development to exist in areas that normally would not be favorable to coral growth. It is notable that I describe fringing reefs in a current historical context since many of the inputs to fringing reefs are anthropogenic in origin and have not always impacted coastal areas as they do today.

  We will, of course, not be able to contain the various fringing reef habitats all in one aquarium for a number of reasons. Space for the habitats is the main issue, but we also have to ensure that each habitat is given functional separation from the inhabitants of the others. Keeping predators, prey and grazers apart from each other will ensure a greater diversity is possible. Such refuge can only be obtained by having a number of aquariums, each being their own habitat, while able to share the entire system's water volume thus creating a functional ecosystem. 

   With ever increasing human populations, the land is subjected to more and more development that is putting increasingly greater amounts of terrestrial based nutrients and sediments into the ocean (Gorgula 2004), especially when heavy rains wash the land and flush it into the oceans. The first line of defense that the coral reefs have against such pollutants can be found right at the shoreline.

Filamentous algae that form turf mats on near shore substrates.

  All along the coast, from the shore line to approximately fifty yards into the shallow ocean, a great deal of filamentous algae can be found. These fast growing algae form both a turf mat on the shoreline boulders as well as suspended strands and clumps in slightly deeper water. The shoreline turfs are comprised of numerous species of tightly packed erect filaments that are generally 3 to 5-mm high and accumulate a great deal of sediments. These algal turfs are permanent occupants on the available nearshore substrates while the suspended mats tend to be transient in nature with their appearance being dependent upon the availability of nutrient loaded run off from terrestrial sources.

    The suspended mats appear to be generally monospecific. After periods of heavy rainfall, the speed at which these algae grow can be quite rapid, indicating the amounts of nutrients that are being washed into the ocean as well as suggesting that such algae species respond to and utilize those nutrients for rapid growth.
   In a recent study (McClanahan 2007) it was shown that the turf algae were responsible for the greatest amount of nitrogen and phosphorous uptake when subjected to field tests. In the study, the growth of algae on coral skeletons were examined while subjected to four treatments; an untreated control, a pure phosphate fertilizer, a pure nitrogen fertilizer, and an equal mix of the two fertilizers. Turf algae cover was the only algae to respond significantly to fertilization. The encrusting corallines and frondose algal cover showed either a marked decline or complete loss when subjected to fertilization. Algae turf cover was three times higher in treatments with added nitrogen when compared with the pure phosphorus treatment, making the turf algae limited by either too much of one, or not enough of the other.
   Since nitrogen and phosphorous compounds are the most abundant nutrients within a typical reef aquarium, it would be wise to understand the basics of how varying levels of those compounds can either limit or encourage the growth and diversity of algae and cyanobacteria.
   A high phosphate and low nitrogen content appears to enhance the abundance of nitrogen-fixing cyanobacteria while at the same time reducing the diversity of algae cover, most notably the large (macro) frondose algae species.
   High nitrogen and low phosphate is also effective in influencing algae species composition, increasing the cover of various small turf-forming green algae and cyanobacteria. In the study, high nitrogen did not increase the abundance of other algae groups. Within the hobby it is generally accepted that phosphates will fuel the rapid growth of cyanobacteria. This is supported in the study, but not in the sense that the cyanobacteria are acting on phosphate levels alone. With phosphates being a limiting factor on the macro algae, such limitation would make more nitrogen compounds available for the cyanobacteria resulting in decreased algae diversity and increased cyanobacteria. Furthermore, Thacker has shown in several publications (Thacker et al.2001) the strongest negative correlation for common mat-forming cyanobacteria (i.e.Lyngbya spp.) to be water flow and not a lack of nutrients.
  Under a normal feeding and maintenance regimen of a typical reef aquarium, it is likely there will be somewhat of a balance between phosphorous and nitrogen compounds since most organisms used for food contain relatively balanced C:P ratios. The level of the balanced nutrient load will still be a factor in what species of algae will be favored in a given aquarium. A properly fed reef aquarium (Borneman 2002), which is one that provides the daily nutritional requirements in the correct quantity, quality and particle size for all of the aquariums inhabitants will normally have a slightly higher balanced level than found near coral reefs due to the constraints of an enclosed, relatively minute volume of water that aquariums are.
   The use of filamentous algae with their apparent ability to quickly reduce excessive phosphates and nitrates will keep the nutrient levels low enough to where the larger and less nutrient-requiring macro algae species, that are usually kept within an algae refugium or sump section, can thrive. These species further  reduce nutrients while adding diversity, all to the well-being of the entire aquarium system. Should the nutrient levels rise rapidly, the macroalgae, instead of growing faster will be limited while the turf algae species will respond to the increase and quickly bring nutrient levels back into reef tolerances, while at the same time denying cyanobacteria the phosphate-rich conditions that favor it from becoming dominant.
     At first glance the shoreline turf algae does not appear to be much to look at, but upon closer examination with a microscope I was quite surprised by the diversity of life forms that use these algae mats as a habitat in which to live. A single square inch scraping yielded many microscopic animals that I normally associate with macroalgae covered rocks in deeper water. Note the amount of sediment held within a small sampling.

    Within the above sample, I counted at least eight different species of filamentous algae, and the apparent monospecificity by appearance is clearly deceptive. They are all intertwined creating a living net that captures and holds both abiotic sediments and detritus. Not only do these living nets give the algae more substrate on which to anchor and expand their growth, they in turn provide both habitat and food for a multitude of microscopic animals, which are then preyed upon by microscopic predators. A microcosm that has a complete food chain starting with the filamentous algae being sought after by a number of herbivores who then become food for slightly larger predators, all performing the much needed nutrient extraction and production from the surrounding waters.

  Below are just a few examples of the many life forms found within the sample, which also included numerous protozoans and other animals too small for me to photograph properly.


In the 1970s, Dr. Walter Adey, Curator of coralline algae and Director of the Marine Systems Laboratory at the Smithsonian Institution in Washington DC (USA), was studying corals and soon realized that nutrient levels within his aquariums had to be managed. Dr. Adey looked to natural processes for the solution which led to the development of a more suitable habitat that had most of the natural reef components necessary to support a tropical coral reef.

  By providing for the same conditions as are found on a natural reef shoreline, Dr. Adey surmised that it could be possible to use filamentous algae as a filter to remove nutrients from an enclosed aquarium system. By simply incorporating plastic mesh screens into a surge device, Dr. Adey was able to recreate the conditions that favored the filament algae species and thus the Algae Turf Scrubber® was born.

  Within all ecosystems, photosynthesis by plants, bacteria and algae forms the basis of all food chains with some exceptions; perhaps most notably those of deep ocean hydrothermal vents. Algae, like other plants, must absorb nitrogen and other nutrients for growth and reproduction. The development of the Algae Turf Scrubber® simply simulates the processes that occur in nature on any shoreline; a device that provides sufficient water movement over semi-submerged substrates and high light intensity. In these areas of turbulent mixing, a zone of short, dense algae will develop.

Photo copyright:
Photo Courtesy by Morgan Lidster of  Inland Aquatics
  The above photo illustrates a 225 gallon custom reef system after about 30 months with ATScrubbing as the only means of nutrient export.  The ATShuttle Model 250 (algal screen measures 9.5" x 24") is scraped once a week.  BioTrace and Restore (B-Ionic analog) are added weekly and frozen foods are fed weekly.  All other maintenance is handled by the ATS and the automatic feeder, with the exception of the two 24 gallon water changes during that time frame.

Photo provided by Morgan Lister   Photo provided by Morgan Lister
                                Mini (Hang On) ATScrubber on 75 gallon reef          View of the screen on the Mini ATScrubber

  Inland Aquatics has been so kind as to provide the photographs of various ATScrubber models, all of which are available for purchase for those of us not inclined towards do it yourself projects.  For more information please contact Morgan at  

Photo provided by Morgan Lister   Photo provided by Morgan Lister
                                                A 325 gallon ATS prototype display                                         ATScrubber model 225

  The Algae Turf Scrubber® has been around now for quite a number of years and at one time, was used by many hobbyists, yet lately it seems to have fallen by the way side within the hobby and never really became widely utilized. With a great many aquariums that combat filamentous algae growth, it is understandable that such algae species are looked upon with scorn and not thought of as being able to work for our aquariums instead of against them.  The only problem with having such algae species is simply a matter of location.  Just as the reefs in the ocean cannot have such turf algae growth, neither can our coral aquariums as the turfs would quickly smother our corals.  This is not to say that we cannot use such algae, but we have to force limitations upon it.

  Having noticed in my own aquarium that such filamentous algae only grew within the interiors of my overflow boxes, I soon realized that I had unintentionally forced the algae to seek its own refuge. Not only were the overflow boxes providing the high water flow and light intensity that turf algae require, but it was also providing a safe haven from the larger algae grazers of my system; most notably the ringed cowry (Cypraea annulus) and a brown tang (Zebrasoma scopas).

   Not wanting to miss out on the nutrient uptake potential of these fast growing algae species as I see in the nearshore areas of my local reef, and not having the space to install a dedicated turf algae habitat, I allowed the last baffle of my sump to provide the same conditions as found in my overflow boxes. Simply lowering the water level of the sump's last compartment to expose more glass to the "waterfall" effect and providing sufficient light intensity soon had a simple turf algae scrubber in action.
   Once a week I simply take a single edged razor blade and clean alternating stripes down the length of the glass, leaving a razor blade's width of untouched algae between the cleaned stripes so that by the next week, it will have grown back onto the cleaned areas, giving me another crop to harvest the following week.  This can, of course, be expanded to include more glass panels to get the same "waterfall" effect on multiple panes as part of a sump or as a dedicated turf algae habitat, which has many possible designs, one of which is bound to serve your needs.

  As of May 2009 my main display aquarium has been running as a single tank system with one important feature installed.  A compartment section that provides the surface area for an ATS as well as the important surface skimming as the water overflows into the compartment.  For those of you with limited space this is by far one of the best methods I have ever employed in maintaining proper dissolved nutrient levels while at the same time providing yet another habitat that creates a great deal of zooplankton.

Photo by Charles Raabe   Photo by Charles Raabe

  By placing a matting material onto the glass, it gives the filamentous algae a rougher surface in which to hang onto and speeds it growth, which in turn speeds the nutrient reduction.  Once a week I simply scape off the algae and discard, thus exporting a good amount of nutrients along with it.  I chose to use a side compartment as I do not have easy access to the back of the aquarium, but for those that do, you could run such a compartment along the back of the aquarium making it virtualy invisible.  Proper bracing of the compartment's glass is very important.

Photo by Charles Raabe   Photo by Charles Raabe

  Generally, most of us only think in terms of either how to be rid of algae, or how it can be used to remove nutrients from our aquarium's water. What is often over looked is that even the filamentous algae provide yet another habitat within our aquarium's system and is home to a great many different animals. I was pleasantly surprised to discover that the wild algae mats and my aquarium mats are almost indistinguishable, both containing several filamentous algae species and nearly the same microscopic life forms which contribute to the diversity and functionality of a natural reef and my reef aquarium.

   Within this one sampling of filament algae taken from my sump's mini turf scrubber, I was able to find a great many species of microscopic life forms. Some we are all familiar with and some were quite a surprise.
    There appears to be two or more species of filamentous algae taking advantage of the conditions that I provided for them. All of which trap a good amount of detritus which in turn feeds the microscopic life found living amongst the red and green branches of this miniature aquatic forest.  These algae species are often known as "nuisance algae" and "undesirable" which could be said of any algae if they are able to grow unchecked either out on the coral reef or within our coral display aquariums where such algae can easily outcompete the corals. Such algae is however highly desirable as part of the reef aquarium's nutrient exporting and live food production mechanisms.
   When found to be growing where they are not wanted, many hobbyists will wage an all out war upon these algae species determined to eradicate them entirely through a great many methods ranging from nutrient starvation, turning off lights to the aquarium for extended periods of time, adjusting basic water parameters to unnatural levels, or adding subtropical herbivorous animals that will consume the algae while they slowly die from being in tropical temperatures. The eradication method most often suggested is to reduce nutrient levels to starve out the algae. What is not often thought of is that by starving out the algae, you are in effect also starving your corals and fish in a direct and an indirect manner by denying them a ready supply of live food that such a habitat can produce, a habitat that in itself is reducing nutrient levels at the same time they are providing your larger species with nutrition. Below are but a few examples of the life forms that were found in a small sampling of filament algae. 


  The most abundant of the infauna appears to be microscopic worms that feed upon the detritus that the algae traps out of the water, with copepods and amphipods being the next most numerous members of the algae infauna. Other infauna does not appear to be feeding upon either the algae or the detritus that it traps but instead simply use the algae as a substrate in which they gain shelter from predators while they gather passing food particles such as phytoplankton and bacteria.
  Having such an abundance of microscopic animals not only provides nutrient processing but they also contribute to the feeding of the larger members of our aquariums, thus reducing the need to add additional nutrients in the form of prepared foods while providing highly nutritious live food in the form of both adult infauna and their spawn. Additionally, such live food is of the correct size for many of the coral species we wish to maintain.

The remains of an algae filament after having had its cells consumed.

  The amphipod species living within the filamentous algae feeds directly upon the algae by piercing a filament and withdrawing the algae cells as it feeds, leaving behind the transparent algae membrane. It has been argued (Hay et al. 1987) that amphipods could be ecologically similar to terrestrial insects by having evolved a tolerance to secondary compounds that deter other herbivores, thus allowing them to feed upon algae species that other herbivores are unable to eat while gaining protection from predators within the confines of the algae. Such grazing, while evident in the algae samples I have examined, is not enough to control the algae or limit its spread. It does, however, appear that such grazing stimulates algae growth as the amphipods reduce the mature filaments exposing the vigorous pioneer stages of the algal population.

 Aside from gaining a natural method of reducing nutrients and providing more biodiversity, there are a number of other benefits one can realize from employing a "pest algae"  If run on an alternate light cycle, the photosynthesis that will take place during the night will keep the aquarium system's oxygen level and pH much more stabilized during the night's normally lowered oxygen and pH levels.
 Many other hobbyists have noted other "side" benefits of using filamentous algae within their systems, most notably an overall healthy environment that others have used as a "hospital" tank to allow weakened, stressed fish and corals to recover. To me, that is a very obvious indication that naturally run aquariums do provide a much better environment for our pets than other traditional methods that work so hard at removing any and all nutrients, particulate matter, algae, and of course, any microscopic animals that could have been feeding the aquarium's inhabitants.
  Providing the filamentous algae a place within your aquarium system will also reduce or eliminate the need to run a protein skimmer or any other mechanical filtration. In fact I would discourage the use of such equipment as they are intended to remove the very benefits of what the algae habitat is providing. It would make no sense to have numerous microscopic animals being produced only to filter and eliminate them, thus denying your pets a good source of live nutrition.

  Of course now one must ask how such algae can be kept restricted to one specific area and not allowed to over grow the coral display aquarium.  The answer is simply to provide enough suitable grazers as mentioned previously. A brown scopas tang along with any number of herbivore snails will keep filamentous turfs as well as most other palatable algae species in check. The turf algae species shown above seems to restrict itself by requiring high rates of water flow while growing within the boundary between water and air, just as it does on turbulent shorelines and in my overflow boxes.  If enough space is given, it will also nutrient-limit itself.
  I am of the opinion that if this hobby is going to progress past simply keeping corals alive and continue to use the words "reef" and "aquarium" within the same sentence, then we are going to have to learn of the reef's ecosystems and apply them in our attempts to contain a reef within our homes. Please take the time and effort to look beyond your coral specimens and wonder at the diversity and beauty of function that in nature, takes care of these corals.

  For more details and a discussion about this type of algae filter, please see this Marine Depot Thread.

Related Reading :

  A Philippine Fringing Reef & The Reef Aquarium  Part Two

  A Philippine Fringing Reef & The Reef Aquarium  Part Three

  A Philippine Fringing Reef & The Reef Aquarium Part Four

An Online Philippine Reef Tour

  The Reef Aquarium Clean Up Crew

Acknowledgments :  I would like to thank my wife Linda for her loving support and understanding of my interests in all things marine. A special thanks also goes out to Eric Borneman for his generosity in providing assistance with this article and in helping me to make sense of tropical reefs. To Dr. Ron Shimek and Leslie Harris, thank you for the many identifications made as well as teaching me a great deal about marine biology.


Adey W. (1982), The Microcosm: A New Tool for Reef Research. Coral Reefs (1983) 1:193 201

Bell S. (1991), Amphipods as Insect Equivalents? An Alternative View Ecology, Vol. 72, No. 1 (Feb., 1991), pp. 350-354

Borneman E. (2002),  Reef Food,

Gorgula S. et al. (2004), Expansive covers of turf-forming algae on human-dominated coast: the relative effects of increasing nutrient and sediment loads. Marine Biology (2004) 145: 613–619

McClanahan, T.R. et al. (2007), Effect of nitrogen, phosphorous, and their interaction on coral reef algae succession, Mar. Pollut. Bull. (2007), doi:10.1016/j.marpolbul.2007.09.023

Thacker, R.W., Ginsburg, D.W., Paul, V.J., 2001. Effects of herbivore exclusion and nutrient enrichment on coral reef macroalgae and cyanobacteria. Coral Reefs 19, 318–329.

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