Bare bottom tanks have never been uncommon in fish stores. Often, it’s much easier for someone selling marine fish to maintain a bare bottom tank, simply because decorations can easily be pulled out if someone buys a fish. These systems are normally based off multiple holding tanks which are filtered by a central sump which is full of live rock and sand. This refuge was a place for aerobic and anaerobic bacteria to flourish, creating the backbone of biological filtration. Bare bottom tanks weren’t common in private aquariums and I still wouldn’t refer to them as common. They are growing in popularity though and embracing a bare bottom tank is still a new trend for reef aquarists. Aesthetics aside, is running a bare bottom tank of any benefit? Those who have given up on substrate claim it prevents old tank syndrome and reduces the risk to coral health posed by sedimentation. Are any of these claims true? Substrate’s role in the aquarium:
It could be argued that substrate is entirely aesthetic, based on the personal preference of each aquarist. That wouldn’t be entirely accurate. Live rock in many ways is a form of substrate. It’s a key puzzle piece to creating an interface for biological filtration and can jump start tank cycling. Some aquarists claim an aquarium can be instantly cycled by cramming it full of cycled live rock. In my experience this practice reduces the intensity and duration of the cycle, but doesn’t prevent it altogether. Sand plays a similar role, geared more toward the anaerobic bacteria that breaks down nitrate. Since anaerobic bacteria prefers oxygen depleted environments, the nooks and crannies of the sand bed serve it well. Sand also plays a critical role for various fish, such as jawfish and invertebrates like sand sifting sea stars. For a long time deep sand beds were considered a necessity in reef aquariums and more recently shallow sand beds became popular. There are still outlets that sell crushed coral substrate but I know of very few aquarists that use it. It’s without a doubt that substrate plays an important role in our aquariums. 
So why abandon sand altogether? While it serves as a home for anaerobic bacteria, it also serves as a debris trap. Uneaten food, fish waste, detritus – all become lodged in the sand bed. Here they decay and are hopefully broken down into harmless compounds by bacteria.… More:
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