A protein skimmer is a machine that removes organic matter from the water before it has a chance to break down in your aquarium and create toxins like amonia. It is very useful in a reef or FOWLR tank because the reefs that they come from are almost completely devoid of organic matter. You may not think it makes much of a difference but wait until you see how much stuff builds up in the cup! Because of this you don't really want to skimp on your protein skimmer. You probably want to go for one that's rated for twice the size of your tank. That might seem a little extreme but I've heard from several people that that is what works best. One of the issues with protein skimmers is that they're pretty expensive. Depending on the brand and model they can range from 200-400 dollars. A really high high quality but not so expensive brand of protein skimmer is ASM. They're almost the same as Euroreef but about half the cost .
As to he bacteria I've heard of that being a problem but I'm not sure.