They aren't really harmful, just DOC
's, which come from food, waste, etc. They are the major fuel for algae as well. The way a protien skimmer works, is by making bubbles contact the water, which in turn "lift" the DOC
's out of the water. The only problem I'd see with them being in there is having the fuel for algae, and maybe blocking out some light for corals, though it'd be minimal. If you are having algae issues, adding a skimmer might be a big help.
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