A refugium is typically the middle part of a sump that is used as a denitrifying area. Normally it includes some or all of the following ; rocks and or rubble (just like in the tank), a deep sand bed and plants or macro algea.
Each of the 3 contribute to a healthy tank albeit somewhat differently.
Rock and/or rubble serve the same purpose as in the tank. Bacteria will breakdown ammonia to nitrates. As well, a pod population will grow which can end up in the main tank as long as there is no filter between the refugium and return sections. I keep my rocks right to the surface of the water on the fuge to help prevent macro algae from sneaking past into the return.
A deep sand bed (DSB
) has a completely different type of bacteria in the non-oxygen layer that will actually consume nitrates and expel nitrogen gas. Unfortunately hydrogen sulphate may also be produced in very small quantities. this gas is a nerve toxin and smells like rotten eggs when it gets released. If the DSB
is disturbed thru vacuuming it can cause a massive die off in the tank (worst case scenario). I don't use one because there is a much easier and safer way to get rid of nitrates.
Putting plants and/or a macro algae like cheato will consume both nitrates and phosphates. A cheap cfl fixture with a normal cfl bulb is all it takes to grow algae and consume nitrates. Periodic trimming then removes those proteins from the tank. Mine only has cheato but many others have much more exotic plants in theirs.
Hopefully that helped