The protein skimmer or foam fractionator as it sometimes called, originated in the waste water treatment industry many years ago, as did trickle filters. It has been arranged differently over the years, and eventually eliminated, but it was mainly used to reduce the organic load before the water reached the Activated sludge reactors, Trickling filters, or other bacterial filters. Since its removal from these systems, it has been employed in aquaculture on both salt and fresh water systems, with varied degrees of efficiency. There have been many different designs since the first three tubed version, in this article, I hope to touch on these and explain them a little better.
The protein skimmer in its most basic form, air is injected into a tube filled with water that has a high level of dissolved organic compounds, or DOCs, with the intent of removing them as foam, otherwise known as adsorbant.
The skimmer has at least three parts:
1) The skimmer body, where most of the contact between the DOCs and water takes place,
2) the foam separation neck or riser tube, where the protein laden foam is separated from the water and dried,
3) and the collection cup where the foam spills from the riser tube and is then prevented from re-entering the water column and is drained away.
The skimmer body can be almost any diameter, on hobbiest skimmers it is usually between 4 and 8 inches in diameter, corresponding to the amount of air being injected. In any skimmer the body must be at least 24 inches tall to remove DOC's efficiently, but there are ways around this. If you slow down the flow and inject more air, like with the EuroReef (H&S) skimmer, you will find that it will prove just as efficient. In Downdraft skimmers it depends on how much air is being introduced, as most of the contact takes place in the bioball column. Some venturi skimmer manufacturers have found ways around the 24" minimum. A few examples of short skimmers having long contact chamber equivalents are:
1) the Tunze rotation skimmers , which are about 10" high, but have 1.2 meters equiv. contact time because of their tangential contact chamber,
2) the Biozone Live Sand Skimmer uses compression piping to achieve a very long contact time,
3) the Red Sea Berlin skimmer uses a tangential contact chamber and a triple pass counter current chamber, but needs a really large pump, like the Live Sand Skimmer.
Below on the left is the Tunze rotation skimmer (Rotationsabschäumer), as produced by Tunze Aquarientechnik GMBH, Germany. Below on the right is the Red Sea berlin skimmer as produced by Red Sea fish Pharm.

Dissolved Organic Compounds (DOC's)
DOCs are Bipolar molecules, aka, surfactants, meaning that they are molecules that have one or more atoms attracted to air, and one or more atoms attracted to water, and so are attracted to air/water interfaces, i.e., bubbles. The longer that the DOCs are in contact with the bubbles, the more that will attach, the more that will be removed. To increase air/water contact, some skimmers make the water inside the skimmer body swirl via tangential injection of water- or air and water, some provide a counter current flow of water; meaning that it is moving against the main flow of water, and some skimmers recirculate water within themselves and only have a very slow flow through of water. These are the most important ways of increasing contact time-most of what is left are just modifications to the original three methods. As you can see from this (now animated) clip from a Top Fathom Ltd. brochure, the venturi injects an air/water mixture into the skimmer body so that it rotates all the way up the body of the skimmer.
I must say, at this point, that DOC's may not only be that which is removed, things removed may be; VOC's (volitile organic compounds), Trace elements, Bacteria, macro and micro Plankton, coral eggs and sperm and other similar compounds. Look for an article on this soon.
Foam/Adsorbant
Foam is what is produced when one passes a gas through a liquid that contains high levels of surfactants.
There are two main types of foam, and they are:
1) white, wet foam that is made any time you inject air into sea water
2) protein foam that consists of differently sized bubbles that are usually darker in color.
The type of foam that we want is the dark protein variety-as that contains what we want to remove from our aquariums, the wetter foam contains more plankton and trace elements which are desirable to have. The darker the foam is the better, but you must balance that with how much your skimmer removes, or you will not have your water as clean as it could be. There are a few ways to get darker drier foam;
1) use a foam support grid ( LifeReef, Amiracle, ATK)
2) use a larger foam riser
3) inject less air
4) inject more air and increase foam riser size
5) lower the water level
Of course, 1, 2 and 4 are the better choices as you can have more air, more flow and more contact time as well, therefore making the skimmer more efficient. You can also combine methods which will work satisfactorily. Good quality foam should be thick and paste-like in consistency(Fossa/Nilsen, The Modern Coral Reef Aquarium Vol. 1).
Below is the general VS2 36-72 design as produced by LifeReef, which use a foam support grid and tangential venturi injector, this skimmer is counter current as well.
One note on the testing of how good a skimmer is:
One skimmer shutting down another is not a good way to tell which one is better, as the one that was shut down, I have found in some cases, can get the water much cleaner than the one that kept running. Also there are strange things that go on when you use two skimmers on a system, that are not fully understood as of yet. And therefore I and others believe that the shutdown method is highly inaccurate and should not be used to as an indicator of skimmer efficiency.
But most skimmers are indeed tested this way , and given that methods inaccuracy you must decide for yourself as to which is better. An example of this would be when my DIY air driven skimmer "shut down" one of my venturi skimmers and my Down Draft skimmer as well.
Judge your skimmers efficiency on how high your ORP is and your rH2 and T*Factor levels as well as NO3, PO4 and just general water conditions before and after you added your skimmer, as well as how good your tank looks. For more information on T*Factor and rH2, see Advanced Reefkeeping by Albert Thiel.
Down Draft skimmers
The Down draft skimmer is quite different from all other skimmer designs, it uses a 1/4" jet of water aimed at 1.5" bio balls in a 3" diameter column to create its bubbles instead of a regular venturi or air wood as most skimmers now do. After the bubbles that come from this "stack" of the DD skimmer enter the sump box they are deflected upwards to the foam collection riser, or "neck" of the skimmer. Here, unlike in venturi skimmers, the water level is kept at about 2-6" because of the amount of air going through the skimmer. A very dark, smelly foam is produced rather quickly and in mass quantities as well with this design. The only drawbacks to this skimmer are its cost, the cost of the pump to run it with, and the amount of plankton and vital trace elements it removes. Most of the contact time in this skimmer, as I already said, takes place in the bio-ball column. Because of the very high efficiency of this skimmer, it is not recommended ,IME ,to use it on a soft coral tank,(unless you know what you're doing) and it is recommended to increase the dosage of trace elements to a higher degree than normal. Below, is the ETS Gemini 800.

In the Down draft skimmer the water goes first to "a", the injector system, where the water is narrowed into a 1/4" jet and propelled over "b", the bioballs, which break air into the water to make the bubbles in the mixing area "c". Next, the bubbles go out of "d", the hole in the stack, then, the bubbles are deflected upwards by a deflector "e" upwards toward "f" the skimmer body which sends the foam into "g", the foam riser which lets the foam spill into "h", the collection cup to be drained away.
The most recent type of skimmer to hit the market is new type of downdraft that I will be reporting more on soon, only one company makes it, MTC ,and the skimmer is the HSA.
This skimmer does not use the typical jet of water and bioballs used in regular down draft skimmers, which is very inefficient and uses a lot of energy, it uses a Pond pump foam generating head located on the lid of the skimmer. You can produce lots of foam of air driven skimmer quality by adjusting the valve located on top. This skimmer is very efficient and, IME, blows the ETS away. It is $650 and uses a GenX or Little giant MDQ4. Below is a Raytrace rendered 3d image of the HSA injector, done by me. It is not done, and is not completely accurate, as I have just now opened one of these injectors and looked inside. I will post the correct picture soon
Venturi skimmers
The venturi skimmer uses a venturi injector to create its bubbles. A venturi injector forces water through a small hole that leads into a wider tube that creates a under pressure and sucks air through a hole near the small tubes outlet. The most efficient form of venturi injectors are the Mazzei injectors.Venturi skimmers need large, high pressure pumps to work correctly. Below to the left are venturi skimmers by LifeReef.To the right is a very large venturi protein skimmer. Below that is a venturi injector scanline rendered 3d image done by me. It is not done. I will post a new picture when it is.

There is a new type of venturi skimmer that uses the very large venturi injectors, in the 1" to 1.5" range, it is called the EVS and it is made by Lumar Technology, it is like a ETS but sucks in more air, up to 240 cubic feet per hour. It is designed like the ETS, but in place of the stacks it uses the venturi.
Air driven Counter Current skimmers
Air driven skimmers use Air woods and a real strong air pump to produce their bubbles and can be every bit as efficient as venturi skimmers, but at a higher price. There is also a difference in the foam consistency of the air driven skimmers as opposed to the Venturi and DD skimmers, it contains more particulate matter and is of much higher quality than Venturi skimmers as it tends to be more dense and drier as well. The Air driven CC skimmers should have 2 to 3 air woods for every 4" of skimmer width, so a 6" diameter skimmer should have 4 to 6 air woods and so on. But, not many air driven skimmers are built to handle this much air, which is very unfortunate for us indeed. In fact, most mass produced Air driven skimmers only use 1 to 2 airwoods for every 6" of diameter, making them very inefficient. There is one, however, it is made by Knop Aquarientechnik of Germany that uses a very large amount of air woods, but it is not cheap. The foam neck of a good air driven skimmer can be just like the venturi skimmer necks as they can make just as much foam. To the top left, you can see the Knop Mega series air driven protein skimmers and Kalkreaktors, as produced by Knop Aquarientechnik GMBH of Germany.
It has been IME that the above chart is correct as to the number of air woods needed to make an air driven skimmer work correctly, notice that I have not included the smaller skimmers in this chart--that is because you need at least 24" of height for CC skimmers to work with any degree of efficacy. This is based on my opinions and personal testing.
This chart illustrates on the vertical the number of air woods in a skimmer and on the horizontal the width of the foam riser column , and in the body of the chart is how high the foam riser should be with X diameter and Y air woods. As you may have noticed, not many skimmers fit this description, so what are you to do? Either buy a skimmer that allows you to drop the water level about 4-6" below where the foam riser begins, or build your own. This is in my opinion, and my personal testing, that I have found this arrangement to work effectively.
I will be writing an article on how to build your own skimmer relatively soon.
Aspirating Impeller skimmers
As for this new twist to the old venturi concept, I must say that I am impressed. They are cheap, efficient, and quiet. The Turboflotor 1000, CPR SR series and BakPak, and EuroReef (H&S) are all Aspirating skimmers, they are quite efficient and like air driven skimmers do not remove as much plankton as Venturi or Down draft skimmers do. Which is quite helpful with getting filter feeders to survive. They make bubbles by directing air into either the regular impeller or a specialized needle wheel, or pegged wheel that chops up the air into very fine bubbles like those found in an air driven skimmer. I am curious to see where these skimmers go in the next few years. Below, to the left, are the Klaes skimmers as produced by Aqua rien Technik Klaes GMBH, to the right, is the Turboflotor 1000 as produced by Aqua medic, both of Germany.

a= needle wheel impella
b= air intake fitting
c= air/water outlet
d= magnetic induction coil
To recapitulate;
Down draft skimmers are very efficient, however, they also cost a lot to buy and operate, and their pumps cost a lot as well. Because of down draft skimmers efficiency, they remove greater proportions of vital trace elements, and so those trace elements must be replenished
often with complete additives, and replenished to a higher degree than would have to be with any other skimmer as well. Down Draft skimmers also remove a lower degree of particulates and a higher degree of plankton as well. Removing plankton should not be done to such a degree without some way to replenish the supply, i.e., a refugium, which I will cover soon.
Down draft skimmers, due to their efficiency, in most cases should not be used for soft coral tanks or clam tanks, except for the skimmers in their smaller versions.
Venturi skimmers rival DD skimmers in efficiency, and in some cases exceed them, but have to be larger to do this. Venturi skimmers remove less plankton and about as much particulates and diatoms as DD skimmers.High quality venturi skimmers can cost as much to run and use as a down draft skimmer. Venturi skimmers are preferable soft coral tanks as well as clam tanks.
Air driven skimmers remove very little plankton, a very large amount of particulates and diatoms and very little trace elements as opposed to either venturi or DD skimmers.
A GOOD air driven skimmer, one that can rival verturi or DD skimmers, cost about as much to buy and operate as a large down draft skimmer.
Aspirating impeller skimmers are relatively inexpensive to run, buy and operate compared to venturi, a good air driven, or a down draft skimmer. Aspirating impeller skimmers remove very little trace elements, diatoms or plankton when compared to other skimmer designs. This skimmer is most preferred on clam ,carnation coral or soft coral tanks, or on any other tank that is either dominated by, or has filter feeders in it.
I hope to eventually expand this "article" with more detailed info, or answers to anyones questions.
Fwiw,
Ian McDonald