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Presented by Charles & Linda Raabe
Mactan Island, The Philippines
© 2008 All Rights Reserved

This is yet another area which would be worthy of writing a book about, but I will refrain from doing that here and just stick to providing my own few thoughts on this subject along with what I feel are relevant links to great articles.

Since equipment is a major part of filtration this area will only deal with methods and set ups of filtration methods

My point of view when it comes to filtration is to not rely upon just one method or type of filtration. Throwing a few methods at a tank ensures that at least one of them will become effective or dominant.

Filtration methods can be divided into specific categories depending on how they achieve filtration or in what they provide.

When one thinks of any type of filtration, they all deal with nutrients in one form or another. Keep in mind, that what ever is put into the tank, whether it is food or livestock, will generate nutrients, or more correctly termed, DOCs, dissolved organic compounds. It is these compounds that all filtration trys to control or remove.

    This is the backbone of any aquarium. If you are familiar with the term "cycle" you are already aware of the nitrogen cycle that various bacterial strains perform within our tanks. Often over looked is the denitrification process that anaerobic/anoxic bacteria also perform in the low oxygen areas within our tanks . As such, Any piece of equipment that is labeled a biological filter is somewhat misleading to most, the equipment does not do any of the actual filtering, but is simply providing a "home" for the bacteria to live upon, which do the actual filtering. These homes can come in a variety of forms, anything as simple as just rocks up to elaborate drip (wet/dry) systems. Keep in mind that these bacteria will grow upon all surfaces within the water and can be felt as a slimy coating, which is more correctly termed, a bio-film. A good example of a bacterial bio film is that slimy feeling you have on your teeth when you wake up in the morning, yes, thats all bacteria. The key to a good bacterial bed (filter) is in keeping it cleaned, allowing detritus to become trapped or settled upon it just allows that matter to rot into eventually becoming more nutrients. As such, when picking your method or "home" for the bacteria, its ease of cleaning should be a big factor in your choice.

    This form of filtration is pretty cut and dry, all such devices use some method to trap matter and hold it for removal. This can be done by skimmers and all the various models that use a trapping material such as floss pads or sponges. A skimmer is in its own class though and one that I feel every tank may have occasional use of..  The other types that trap larger particles may do a good job for what they were designed to do, as long as they are kept clean, the longer that trapped material is allowed to remain in the water, the more of it will break down into nutrients, thus defeating the whole purpose of such filters. I personally do not use any of the filter pad/sponge type filters since I prefer to allow any and all micro life to remain in the tank to help keep the diversity of life and to act as a live food source. I also believe that the trapping of particulates is very counter productive and removes a very important food source for a great number of reef animals that we strive to keep. Please see this article on Detritus.  One other type of filtration that I suppose could be considered mechanical is the use of live plants to absorb nutrients, the most commonly used plants for this purpose are the macro algae' and mangrove trees, with the use of macro algae, as the plant grows, it absorbs nutrients and thus competes with the pest type algae' for food, when the macro algae is trimmed and thrown away, you are in effect, throwing away its absorbed nutrients also.

    The use of any "chemical filter" such as phosphate binders, or oxidizers should only be used in an emergency situation to clean up excessive nutrients when more traditional methods have not matured yet or have been overloaded and failed to keep up. Each of the chemical methods has their own dangers involved with their use, its the old to much of a good thing. Unless you can test for the elements you are targeting for removal, I would not use any of the above methods. It is very possible to remove to much of a given nutrient/element and your livestock can suffer for it. I feel all these methods are "band aides" only, in that they should never be relied upon as a constant use item. If you are having to do so to maintain water quality, then your tank's filtration is ineffective or inadequate and needs to be examined to increase its effectiveness. 

     I am not too sure if the word "filter" is an appropriate term for what should be correctly called a Food Chain or Food Web. But since we as aquarium hobbyists think in terms of "dirty" water containing organic compounds such as the infamous nitrates, we expect to have biological actions "filter" out those compounds. Since it is a good place to start, lets start at the beginning of the biological "filter". 

The Sources of organic compounds (waste?) - But first, we should know what is an organic compound. In the most simplest of terms,  An organic compound is any compound that contains both carbon and hydrogen atoms. They can contain other atoms, but must still contain carbon and hydrogen. The most obvious sources are all the life forms that we keep in our aquarium and our feeding of organic compounds to them (food). Further, even more organic compounds are created or released when digestion takes place, but lets focus on the actual events that occur with biological "filtration" For more reading on organic compounds, please take the time to read : Organic Compounds in the Reef Aquarium.
  As you can see in the above graphic, organic compounds will quickly attach or adhere to any surface area that we place into the aquarium, be it sand, rocks, plastic tubing and even the aquariums glass walls, as well as there being many compounds still floating about within the water. All it takes to get the proverbial ball rolling when establishing a new aquarium is a source of organic compounds, be it a piece of shrimp or fish meat, or simply just a few drops of ammonia.
  These compounds then become the basis or start of the food web. Without any need to introduce them ourselves, a great many bacterial strains will arrive either already on a piece of fish/shrimp flesh, or by parachuting in out of the air. As is the case every where on this planet, including our aquariums, life could not be possible without bacteria. So lets take a look at bacteria and introduce ourselves.

The Bacteria -  Since the multitudes of bacterial strains present within our systems would take volumes to discuss, lets just focus on a few that are found in the marine environment and play important roles within our aquariums.

 Marine Bacteria : From ecology to molecular genetics  -  An extremely in depth study.

  The Sulfur Bacteria - This group is thought to account for the anaerobic oxidation of more than 50% of the organic matter in sediments. A good argument for the use of live deep sand beds if I have ever heard one. For a bacteria to be considered a part of this group, they must either be aerobic (need oxygen to live) or anaerobic (killed by oxygen), as well as being either autotrophic (use carbon dioxide as food) or heterotrophic (use organic matter for food). The sulfur bacteria do a vital job for our aquariums by either reducing sulphates using organic matter for their carbon and energy sources, or by oxidizing the reduced sulfur compounds for their energy sources. As you can see, this group can work hand in hand at keeping sulphide levels under control within our aquariums.
  While on the subject of sulphides, I think it is important to point out a common concern with the use of deep sand beds. Quite often, deep sand beds are blamed for killing an aquarium due to the amount of sulphide gas produced. For one, it is not the sand bed that is to be blamed, it is the hobbyist fault by not understanding a sand beds ecology and setting up the sand bed properly and maintaining it. When there is a great abundance of organic matter, which would be or fault to begin with, the sulfur bacteria will multiply to their available sources of energy and thus increase production of hydrogen sulphide, a gas. A deep sand bed, with all of its microscopic life forms, which include worms, ciliates, protozoa, and multitudes of other sand dwelling species will consume a good deal of the organics thus keeping the sulfur bacteria populations in balance as well. For more information on setting up a deep sand bed. Please see Dr. Ron Shimek's Deep Sand Bed Article. , Also see my Live Rock & Live Sand Web page as well.

  The Bacterial Decomposers - This bacterial group are extremely important in the overall functioning of a marine aquarium. The process of decomposition is an important one as it is the main mechanism whereby inorganic nutrients, such as nitrogen and phosphorus, can be released to be used by yet more organisms. For a bacteria to be considered a member of this group, they have to be able to feed on organic matter, and can be either aerobic (need oxygen to live) or anaerobic (inhibited or killed by oxygen). Bacterial decomposers can be found everywhere there is dead organic matter. They live in the sediments of the sea bed, in the guts of marine animals, and as part of the plankton community feeding on dissolved organic compounds or attached to particulate material. Bacterial decomposers consume dissolved organic compounds that have been released from other organisms such as microscopic algae, seaweeds and animals. They feed on the dead bodies of all other organisms and decompose fecal and other organic waste material. They also help breakdown food material in the intestinal tracts of marine animals.

  The CyanoBacteria -  They are are microscopic unicellular organisms which also grow in filamentous form up to a few millimeters. The filaments can grow up into large masses reaching 10-20 centimeters in diameter and appear reddish, blue or dark brown. They make their own food using photosynthesis and nutrients dissolved in the water. Most notably, phosphates.
  There are of course a great many other groups of bacteria that can be found in our aquariums, some are not so nice, such as the pathogenic bacteria that cause diseases. They of course live, eat and reproduce much like their helpful cousins do. Which is why it is important to control carbon and organic compound sources, (nutrients, waste matter). As with all things alive, an over abundance of energy and food sources can easily lead to a population explosion putting your pets at risk.

  The Nitrogen Cycle -  This is of course, what makes our keeping of an aquarium possible, and all thanks to the multitudes of bacteria that show up and establish themselves in our aquariums with absolutely no help from us. The following are excerpts taken from the link provided.

  This cycle has a large gaseous phase. Nitrogen is essential for life - it is a component of amino acids which are the building blocks of proteins, nucleic acids which form the genetic material of the cell and enzymes which regulate cell metabolism. It is found in a variety of valence states from -3 in NH3 to +5 in NO3- and the energy released by changes in the redox potential of the element is harnessed by organisms to maintain life.  Please see the article linked to for a greater understanding of the processes that occur within our aquarium systems.

 The Fungi  - Along with bacteria, fungi breakdown organic materials, so they will be found wherever dead and dying plants and animals are found. Fungi can also cause disease. By invading hosts such as algae, fishes, corals or crabs, they cause distress and sometimes death. The fungi form huge numbers of small spores which disperse in the water. Only a few spores establish colonies. Accidental contact between the spore and a potential host surface then leads to growth and development of the fungus. Fungi gain their energy by absorbing energy rich compounds from the environment after they have digested them outside of their bodys. While fungus also perform a vital role within the ecosystem of our aquariums, they can also become a problem in nutrient rich aquarium, allowing fungal diseases to become a problem in animals stressed by any number of reasons. 

 The Protists - Surprisingly, this classification now includes the algae, diatoms, dinoflagellates, silicoflagellates, and ciliates, to name but a few.  The most obvious to us are the algae and the dinos, seen as either a green or brown film. Which of course, are part of the biofilm, but only as "late comers", being able to establish themselves after the bacteria have paved the way. They use photosynthesis as their energy source while consuming organic compounds that the bacteria have broken down from inorganic compounds, such as some of the iodides, and is why I refuse to dose my aquarium with iodine. Within this group, the protozoa are also included, some protozoa are of help, while others are parasitic, such as cyrptocaryon irritans, better known as marine ich, feeding directly from fish for their organic needs.

  There are of course other organisms that continue the building up of a biofilm, including the sponges, the larger algae species, and all the way up to corals.

Bacterial Diversity Study Guide - A list of bacterial Nitrospira.

Marine Microbes  -  A very interesting read.

Another way to look at nutrients is found in the terms "import","recycle" and "export"

    As the word implies, anything that we put into the tank, all life forms and their food. Limit what is put into the tank, and you limit what has to be removed. Over stocking livestock and over feeding are the two biggest offenders. Limiting the types of food is also a good control method also. Dry prepared foods such as flakes and pellets are extremely high in nutrients (phosphates), The frozen foods are more ideal as they can be rinsed of any nutrient laden water/juices. 

    This is when what nutrients are present are used by "something" and then later released back into the system again. A good example would be the clean up crew, algae absorbs nutrients to grow, thus locking it up within it, a snail comes along and eats the algae, removes some of the nutrients for its own biological needs and then poops, which then rots back into nutrients, while not as much nutrients as the algae first encountered, there is still some of the original nutrients being recycled back into the tank as the snail's waste breaks down.

    This is where all the above mentioned filters come into play by either physically removing the nutrients both before and after they have broken down, or by locking them up within other plants which can be trimmed and thrown away, or by something so simple as just doing a water change or something more complicated as chemically attracting them (binding) or even by destroying them with oxidizers.

All of the filtration methods are discussed / linked to in further detail with my site's info link area under "equipment", the below drop down menu also has many good articles linked to.

My Method : Since I do not have access to all those wonderful gizmos that we call equipment,  I have been forced to allow my system to be run in a much more natural method, in that the live rock and live sand with its multitudes of life forms has the task of cleaning house. My only "chores" are to perform water changes to replenish lost elements and to dilute out unwanted organic byproducts, the organics though can be dealt with by simply using a good grade of carbon. Besides having nature do all the dirty work for me, the diversity of life makes for a much more realistic reef and a more interesting aquarium to watch.

( Tri Based Pelletized Carbon )
   While I am a proponent of running an aquarium system as naturally as possible, I fully understand that the needs and wants of other hobbyists systems may not allow running an aquarium without some additional help in providing biofiltration and organic byproduct removal. Even systems such as mine will greatly benefit from the use of carbon and I do not run it simply because it is not available to me here and instead, have to rely on massive water changes, something not everyone wants to do, nor can afford to do. As such, I strongly recommend, no matter what your aquarium is or how it is set up, that you consider installing what has been proven ( See this Article ) to be a highly effective method of ensuring your aquarium system is at its best.  I believe this additional filtration method  if used, will make a great difference on any aquarium. A special thanks to Stan Hauter of for his efforts and research in this area.

  Do it yourself Carbon Tube Filter  -  All the information you will need to make your own carbon based filter.


Reef Aquaria as EcoSystems  -  " we let the organisms do most of the dirty work, whilst we aquarists sit back and enjoy the fruits of their labors. "

Eutrophication effect in Coral Reefs  -  " Elevated nutrient concentrations are bad news for corals. On the level of primary producers (plants) the competition between corals and macro-algae is influenced by nutrient concentrations. "

Ultra Violet Units  -  " while they may not be of great use on an established tank, they can be of use in a quarantine / hospital tank set up. Given that most newly acquired fish are weakened by stress, any reduction of a pathogen, how ever slight, by a UV unit is still a benefit "

Air Stone Bubble Trap  -  If you have a nano tank, or not able to use a sump, this method provides a great way to provide aeration without having the bubbles being blown around inside the aquarium nor making a mess of your lights.

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This mirror is being hosted with the permissions of the original content creator for preservation and educational purposes.