These days, it seems as though a pretty solid majority of reef aquarium systems include a refugium. The growing popularity of refugia has been more a glorious resurgence than a successively rising trend. Indeed, they were quite commonly used in the hobby in the early 1990s. Unlike the refugia we’ve been seeing today, however, the set-ups of yesteryear much more often featured a deep, soft substrate as well as a lush bed of macroalgae (typically Caulerpa spp.). It seems that refugia went away, substrate and all, with the plummeting popularity of Caulerpa later in that decade (no other macroalgae were widely available to aquarists at that time).

Improved lighting technology and increased availability of non-caulerpoid macroalgae (e.g. Chaetomorpha) have, at least in part, spurred the presently renewed interest in planted refugia. Given the significant improvements to refugium design and methodology, they appear poised to stay. As we look ahead to possibilities for future innovations, we should perhaps also look back and ask ourselves, “What about refugium substrate?”

Another big change since the early 90s is the prominence of SPS corals. Among other things, this has led to a reliance on much higher water flow rates. The use of stronger water movement has caused a lot of frustration with aquarists who find that the brisk currents tend to blow sand all over tank (including over corals, clams, etc.). Interestingly, these issues have helped to restore the popularity of another oldschool reefkeeping MO: bare bottoms.

Bare bottoms actually make a lot of sense for reef tanks, especially those dominated by SPS species. Natural coral reefs get pounded and ripped by powerful waves and currents, yet they hold firm because they are, well, reefs–big, solid, rocky structures. Our reef tanks should reflect this.

Yet, in the wild, soft-bottom habitats are never far from reefs. Not only are they physically close, but they also are tightly interconnected ecologically. So, how can we incorporate that element into aquarium systems that feature bare-bottomed display tanks? With refugia that feature deep sand or mud beds!

Sorting out refugium substrates

Stronger water currents transport larger particles. Therefore, median grain diameter of your refugium substrate increases where there is higher current velocity, as erosion transports finer sediments to other, calmer areas. In highly turbulent waters, all that may be left behind is solid reef base or rubble. This separation of sediments according to size class is referred to as sorting. Sediments may be thoroughly sorted where current strength is steady.

These same processes tend to deposit particulate organic matter in areas of lesser water movement. As these deposits accumulate, they form the silty, mucky bottoms that are typical in estuaries, lagoons and sheltered bays. These sinks of organic material often support huge, rich communities of deposit-feeding bacteria, protists and animals. Most of these are infaunal (i.e. spend most of the time with most of their bodies beneath the substrate surface). If you dig into a natural soft-bottom environment, you’ll see that colors and even odors change with depth.

There are typically several layers (referred to as microzones) present. At the top is a more-or-less “clean” surface layer. In addition to receiving ever fresh deposits, the surface grains are constantly disturbed by waves and/or animal activity. Thus, it is well-oxygenated. Diverse animals, protists and aerobic microbes (especially cyanobacteria, nitrifying bacteria and various aerobic heterotrophic bacteria) live here. Oxygen could diffuse deeper into the refugium substrate but nevertheless doesn’t make it very far. That is because it is rapidly consumed (i.e. respired) by aerobic organisms that dwell in the surface layer.

The boundary between the upper, oxygenated zone and the lower, anoxic zone is known as the redox potential discontinuity (RPD). The RPD might be greyish in color. Below this, the substrate takes on a black color. This (and an unmistakable rotten egg smell) is due to an abundance of hydrogen sulfide. Particularly in well-established, minimally disturbed deposits, the space beneath the RPD may be divided several distinct microzones.

Photoheterotrophs such as purple non-sulfur bacteria (PNSB) may reside in or just below the grey region; these tolerate microaerobic conditions. They get first grabs at fresh organic material that seeps below the RPD from above and additionally benefit from the wee bit of light that peeks through the surface. Just below them are purple and/or green sulfur bacteria (PSB/GSB). While not at all tolerant of oxygen, these are even more efficient than PNSB at harvesting light. They also are more tolerant of the toxic hydrogen sulfide (in fact they utilize it metabolically) that seeps upward from the sulfate reducing bacteria in your refugium below them. Many obligately anaerobic “fermenters” such as denitrifying bacteria also inhabit this zone. Any organic materials that make their way down past the sulfate reducers are consumed by methanogenic bacteria; methanogens produce methane as a waste product, which is evidenced by an unmistakably poopy odor.

You would think that animals cannot live below the RPD–but they do. Some are surprisingly adapted to “holding their breath” and even withstanding exposure to sulfides; many construct well-irrigated burrows that exchange waters from far above.

Together as one

Traditionally, deep aquarium substrates have been aimed at supporting large populations of denitrifying bacteria–controlling nitrate concentrations. But they can do way, way more than that! Consider them complete recycling centers for particulate organic waste; the refugium itself is a sediment settling basin, the substrate is a biomedium and the critters therein are agents of degradation/mineralization.

A scheme such as this allows the keeper to scrap mechanical filter media, which correspondingly decreases zooplankton (e.g. pod) mortality. The increase of zooplankton abundance intensifies detritivory, leading to better nutrient cycling and a cleaner tank!

Pretty much all of the commonly used refugium macroalgae can be cultivated over a soft bottom. Drifting forms such as Chaetomorpha and Ulva (including the former Enteromorpha) are most appropriate here. Deeper substrates additionally permit plantings of some really cool ornamental types such as shaving brush and mermaid’s fan.

The tiniest infaunal organisms live interstitially, moving on or between grains of sand. Larger organisms must displace sediment grains in bulk (i.e. burrow). Some such animals (e.g. bristle worms) are mobile, constantly moving around below the surface in search of food; others are sedentary (tube anemones), usually poking out from the substrate surface to catch food particles as they drift by.

And that’s just the beginning of a long list of possible inhabitants. A large refugium with a sufficiently deep refugium substrate can house everything from sludge-eating nematodes to larger animals such as tube worms, burrowing shrimp, deposit-feeding sea cucumbers, etc. With or without the stunning coloration of your SPSs, your soft-bottom refugium might be just as fun and interesting to keep as your “main” tank!