Many aquarists prefer not to have a substrate at all. This choice allows for close regulation of nutrient levels in the aquarium through use of high flow, strong skimming, and manual and mechanical removal of detritus (waste, leftover food, etc). No money need be spent on sand, or animals for the sand. Startup costs are thus very low, excepting a suitable protein skimmer. Systems set up this way are often called "bare-bottom tanks".
This approach is an update of the "Berlin system", using better skimmer and water flow technology. The goal is to prevent the breakdown of leftover food and waste by removing such detritus before bacteria can begin to consume it. The water can be kept very low in dissolved nutrients with diligent effort. Proponents argue that this method is useful in controlling nutrient levels, such as phosphate content.
This is a common choice of stony coral tanks, often Acropora-dominated, where the strong focus on nutrient levels is thought to aid growth and color. As with any system, some livestock may not be compatible with this method. For example, sea cucumbers and various conchs that feed on sand are not appropriate in such systems.
Many aquarists recommend an extended "curing" of the rock for BB systems. For this process, the rock is kept in the dark in containers heated to reef temperatures with good flow and frequent water changes. Any detritus sloughed off the rock is removed as well. This treatment removes nutrients from the rock. Often called "cooking", this
process usually requires 1-2 months.