Essentially, for beginners, substrate is purely esthetic. The filtration purposes attained from a deep sand bed or whatever rocks used as a substrate isn't something imperative for the well being of most aquariums. Even more, usually beginners will not be dealing with animals or plants that are dependent on a specific kind of substrate.
As for more advanced keepers, or keepers with organisms that are substrate dependent, then missing a substrate can lead to the downfall of an aquatic ecosystem. Some animals are especially dependent on sand burrowing and their well being may depend on this habit. The number one thing that tells you whether the organism is dependent on the substrate is if it has evolved in some way in order to sustain itself with the substrate in a propitious way. Some organisms may simply take advantage of a substrate in it's environment, but that does not mean all of this species needs the substrate, as it may vary in different geographic locations this species has spread to. Substrate can alter the water chemistry, softening, or hardening the water, and affecting the pH. Though the substrate can have a discernable contribution to the biological filtration, this can be made up for in the filter itself. Also, substrate may be important for hibernation, many animals such as frogs and turtles wil dig in the substrate underwater and hibernate if temperatures are very cold. Owners of outdoor ponds in countries with cold winters should provide their pond inhabitants with a substrate appropriate for their hibernation needs.
Essentially, you'll only need to be specific when it comes to the substrate when your tank inhabitants are reliant on it. It is worth noting though that even organisms not reliant on a substrate may prefer a substrate.