Other than the biological filter, there are basically 2 theory on filtration on a Salt Water tank to remove organic waste within an aquarium. That's the Refugrium or the Protein Skimmer. In this article I will cover the basics of what I know about skimmers to help shine some light on the theory of skimmers and reduce confusion.
Protein skimming is the only form of filtration that physically removes organic compounds before they begin to decompose. It lessens the load that the biological filter has to work, increases the oxygen in the water column, allows one to have a much larger bioload within an aquarium, and is known to lower phosphates when used in conjunction with a kalk reactor drip. This is why I personally endorse them as the BACKBONE of any successful reef aquarium.
How does it work?
Protein skimmers are basic in theory. Basically it's a chamber where all the aquarium water eventually passes while being highly aireated with a large amount of tiny bubbles. Generally the smaller the bubbles, the longer the contact time with water and bubbles, and the more generous amount of bubbles, the more efficient the skimmer. The theory is that as the water is aireated and a froth builds, protein, amino acids, and waste will stick to these tiny bubbles and rise into a collection cup where it is seperated from the aquarium water and collected for disposal. If you've ever taken a bubble bath you've probably experienced this. Yes, it's the soap scum build up along the surface of the tub water during a bubble bath. This process in a SW tank is highly efficient at taking out waste before it creates havoc. Remember, reef tanks in general require strong lighting, and any means of reducing waste in the tank is highly recommended.
General types of skimmers.
There are a many types of skimmers out there that cause major confusion to hobbiest so I will try to explain a few types, their theory and their advantage, and their disadvantage.
Air stone skimmers
These were the first types of skimmers to have ever been used in SW tanks.
This type of skimmer gets the air from an air pump and typically has a water pump supplying the chamber with aquarium water. The advantage to this skimmer is that it's relative inexpensive, however this type of skimmer is generally not too efficient. Not enough water can be passed through the chamber and not enough air can be fed into the skimmer unless the skimmer is built to a rather large scale. This kind of skimmer generally would be used on a smaller aquarium with a light Bio load.
Down draft skimmers.
Downdraft skimmers uses a powerful pump to "ram" water down into the chamber causing bubbles to gentrate, froth builds and floats back up into the chamber towards the collection cup for removal. Think of it like a can of soda pop. If you shake the can violently it creates many bubbles and overflows through the opening. This is similar in theory to the downdraft. The advantage to this skimmer is that it's very efficient in generating bubbles, can filter large amounts of water and generally is a good skimmer. However the big disadvantage is that it requires a rather powerful pump that consumes alot of electricity and you can't control the size of the bubbles being generated.