A protein skimmer is in place to remove unwanted protein and organic waste from your water before it is in a state where it can be consumed by unwanted algae and other organisms in your tank. It does this by building up a froth of bubbles through pumped water. The bubbles are collected in a cup that then settles to produce a tea like liquid. This is then discarded. The liquid contains the unwanted protein and organic matter.
This cleans the water and improves the quality giving your tank a much more healthy environment.
Keep in mind that the use of a skimmer can also remove trace elements from the water that some animals depend on. Microscopic elements like phytoplankton and copeopods that may feed some fish and corals. These should be replenished through a dosing schedule or other feeding.
have a look at this Wikipedia article.
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