Theoretically, a refugium can be set up like any kind of aquarium system. Thus, if it is large enough, you could put virtually any aquarium species in it. Of course, you might have to make some special,
additional accommodations; for example, if housing an eel, a refugium would need a tight-fitting lid.
But, as their name implies, refugia serve one big purpose:
To separate and provide a refuge for flora and fauna that would not survive (e.g. get eaten) in the main tank. By convention, this mainly includes, but is not necessarily restricted to, pods and macro.
But, hey, if you have that entire “extra” tank running “empty,” it’ll be too tempting not to put some fun stuff in it, right? In addition to the pods and macro, there are a few items you could add.
Regarding flora, some aquarists have done cool things with seagrasses and/or mangroves. There aren’t a lot of fishes that work well here… most fish species are too big/active or eat all the pods/macro! However, there are a handful of notable exceptions (Sargassum anglers, for example). There are a lot more inverts that are suitable for refugia, so long as they are not herbivorous. Things that can’t be kept in the main tank (i.e. not reef safe) come to mind… mantis shrimp, chocolate chip stars, etc. Though this method of filtration remains fairly arcane to date, some aquarists are experimenting with sponge-dominated refugia (i.e. cryptic zone filtration methods) to strip excess plankton and particulate organic matter from the water column.
It will be interesting to see what sorts of critters aquarists attempt to keep in refugia--and what the results will be. To be sure, it is best to err on the side of caution when thinking about introducing any sort of animal to a fuge; remember always that there can be unintended consequences to this, and that the priority of most refugia is to support the health of pods and macro!
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