A protein skimmer removes
some organic compounds. A good portion of these compounds are food for bacteria and larger invertebrates. (One man's trash is another man's treasure

)
- The advantage of using a skimmer is that the biofiltration then does not have to deal with some organic compounds removed by the skimmer.
- The disadvantage of using a skimmer is that organisms would grow better if some organic compounds were not removed.
While in general the hobby seems to believe that a skimmer is a necessary piece of equipment for a healthy reef aquarium, that is just not true. A skimmer is an invaluable piece of equipment in the aquarium maintenance industry, where the owner knows nothing of husbandry and a problem, like overfeeding could quickly destroy the tank. A skimmer is a personal choice determined by the individual hobbyist and the needs of the tank. Though I have set up and run hundreds of skimmers, many with Ozone, neither of those units are needed as can be seen from the pics here.
http://www.utahreefs.com/forum/forum_posts.asp?TID=37523The story of why I stopped using a skimmer and what I did instead is here in this old SeaStar Newsletter tiltled "RDP Filtration/Nightime pH control".
http://utahreefs.com/SeaStar/wmasSeaStar02Feb.pdfTwo weeks ago I added a skimmer to my large coral farm system. The reason has to do with removing some nasty organic compounds in the tank brought in by some LS that were not being removed fast enough nor economically by other methods, namely Activated Carbon, Macroalgae, Poly Filter, water changes. and PO4 remover.
Whether a person chooses to use a skimmer or not, one necessity for all reef aquariums is Activated Carbon (AC). AC removes some organic compounds that neither skimming nor algae can remove.
This is just the beginning of a long discussion we could have about protein skimming, but hopefully will be the beginning basis for the answer to your question. It's a very good question, btw.
Edited by Mark Peterson - May 23 2011 at 10:19am