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Originally Posted by chshwong
I read that protein skimmer removes the organisms which could go into the nitrogen cycle.
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Nope. It removes organics, not necessarily organisms. I.e. it can remove nutrients from water that fuel nuisance algae growth, as well as things that will rot and become ammonia (... then nitrite... then nitrate...), and it can even remove certain forms of chemical warfare between critters. It can also remove some algae. Furthermore, it helps keep a high level of oxygen and lowers CO2 from artificially high levels caused by livestock by aerating the water. The organisms that go into the nitrogen are aerobic bacteria, and tend to mostly stick to solid surfaces such as substrate, live rock, bioballs, etc etc. The amount that goes through your skimmer and gets pulled out of the water is negligible.
Quote:
Originally Posted by chshwong
So to me, that means protein skimmer could largely reduce ammonia, nitrites and nitrates. Am I correct?
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Yes - it will not lower ammonia, nitrite, or nitrate but it will remove some of the things that turn into ammonia->nitrite->nitrate before they ever have a chance to break down. Skimmers are not 100% efficient though, they cannot remove 100% of any nutrients from the water.
Quote:
Originally Posted by chshwong
In this case, the beneficial bacteria would also be reduced as well, as there are now less food for them (less ammonia and less nitrites).
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Again, yes and no. It doesn't remove ammonia, but it does remove some of the organics and nutrients that will break down into ammonia.
Quote:
Originally Posted by chshwong
So does that mean the sudden removal of the protein skimmer could cause Ammonia to spike? And then Nitrite to Spike?
Thanks! 
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Absolutely. If you are still adding things that will break down into ammonia, not having a skimmer will mean there will be a surge of these things. It will not help speed a cycle if your using liquid ammonia though (skimmers remove what breaks down to ammonia, not ammonia itself) and skimmers remove more then just what turns into ammonia. I'd strongly recommend just running the skimmer.