Seawater around natural coral reefs is extremely nutrient-poor. A protein skimmer is a piece of equipment used in saltwater aquaria to help reproduce this condition by removing dissolved organic compounds (DOCs) before they can be broken down into poisonous ammonia and nutrients. Protein skimmers capitalize on the fact that DOCs - mainly proteins and lipids - are hydrophobic and like to gravitate towards air by creating many fine bubbles in the water column. DOCs stick to the air-water interface surrounding the bubbles, which rise to the top of the skimmer and foam over into a collection cup. The skimmate is discarded, and voila - nutrient-free water. The unappealing brown foam that one sees occasionally on a beach is the product of the same process.
The principle underlying all skimmers is the same, but there are different methods of creating the bubbles and keeping them suspended in the water column for as long as possible, which is necessary for the skimmer to work efficiently. Most protein skimmers fall into one of the following three categories:
Airstone: This type uses an air pump to force air through a porous "airstone," which produces a flood of tiny bubbles. A separate water pump pushes aquarium water through the skimmer and returns it to the tank. Airstones clog and must be replaced fairly frequently, and the air pump adds another point of failure as well as additional noise; thus, airstone-driven skimmers are not much used anymore.
Venturi: A venturi-driven skimmer injects a mixed stream of air and water into the skimmer cylinder through a venturi valve, which produces the requisite fine bubbles. The water flow is relatively powerful compared to that of an airstone-driven model, and is directed into the cylinder at an angle so as to produce a strong circular current. This results in a vortex effect that keeps the bubbles in the water column for as long as possible, and looks pretty neat.
Downdraft: Downdraft skimmers work by forcing very powerful streams of water down at an angle through bioballs or some other medium that disrupts the water flow. The turbulence thus created induces bubbles, which are forced further down through the inclined skimmer body by the strong water flow. A vertical tube at the bottom end of the media chamber allows the bubbles to rise at last and form a foam/skimmate, while the water is returned to the tank. Downdraft skimmers are perhaps the most efficient type, but their minimum size and power-hungry nature make them inefficient for anything but very large tanks.
The Berlin Method of reefkeeping relies entirely on live rock, live sand, and a good protein skimmer, and discards mechanical filtration entirely.