Lets understand biological filtration. First off, in the nature of keeping captive, biological organisms in closed containers (aquariums) problems arise due to the discharge of metabolic waste by-products of living things, by digestion and respiration. They eat and breath, consume food and oxygen, and discharge solid waste and CO�. The first consideration in the establishment of an aquarium is the need for Oxygen, absorbed at the water's surface, through surface agitation. The greater the surface area and the agitation, the greater the absorption, and the greater the depletion of waste gasses (CO�). Digestive waste products (fecal matter) breaks down, from complex compounds into complex molecules, (simpler forms), by the dissolutional powers of water, into primarily nitrogenous compounds (ammonia).
Ammonia is quite toxic to marine life and is probably the leading cause of early deaths in newly set-up tanks, plus, is probably responsible for additional ailments due to its powers to 'stress', even if its not detectible by popular hobbyist's type test kits. Its best to get the best test kits!
Fortunately, for us, there are several species of bacteria, which seem to 'spontaneously' appear to consume nitrogenous wastes, collectively known as nitrifyers. One species, Nitrosomonas, consumes ammonia and converts it into nitrite. Not as toxic as ammonia, but still considered undesirable. A second group of bacteria develop, stimulated by the presence of nitrite, Nitrobacter sp, which further reduces nitrite into nitrate. This entire process is known as aerobically based biological filtration. Aerobic, meaning being in the presence of oxygen.
Its very important not to 'short cut' the process time, for maturation of biological filters, even when no detectible levels of ammonia are observed. How often has it been said, "my tank has 'cycled' in two weeks, and upon introduction of some fish (mosly damsels or clowns) they died the next (hour, day, week)". It takes approximately 6 to 8 weeks for nitrifying bacteria to firmly establish themselves, to the point where one can be confident in introducing animal life. I would advise at least 8 weeks!
To put the picture in perspective, oxygenated water flows in, thru, and around materials where nitrogenous consuming bacteria develop, reside, and multiply. This material can be in the form of silicate or calcerous sands, rocks, ceramics, or highly porous plastics. These bacteria have a way of growing and multiplying (gratefully, because without which, it would make it virtually impossible to keep fish in aquariums, for the most part, unless you had a constant supply of fresh natural water) and settling on and in the material that is highly porous, the greater the area, and porosity, the greater the bacterial population, given proper and adequate oxygen levels, and a food source (nitrogenous wastes). These bacteria are not only in your filters, but in and on your substrate, rockwork and even on glass surfaces.
The very first biological filters for SW aquaria came from fresh water aquarias, which came from large scale reclamation filters, known as sand filters. This was quickly adapted for FW applications in the form of an under gravel filter or UGF. Well, guess what, the most efficient, simplest and inexpensive device for culturing nitrifying bacteria is the UGF. Since it entirely covers the bottom of your tank, and can be made having sufficient depths, and, given proper and adequate water flow, has the greatest potential for establishing nitrifying bacteria, because it offers the greatest areas for nitrifying bacteria to proliferate. The problem with a UGF is that fact that it unfortunately becomes a mechanical filter, as well as biological, because it traps wastes, which then clogs the substrate, with the need for periodic cleaning, which disrupts biological processes. Still, utilizing adjunctive devices for mechanical filtration can delay the need for cleaning. One additional benefit exists with a UGF, utilizing calcium carbonate based substrate materials, is the constant percolating of oxygenated water circulating via the UGF, which increases the buffering of your water and aids in maintaining the stability of the water's constituents.
Unfortunately, with the advent of wet/dry systems the UGF has fallen into disuse, although many 'old-timers' including yours truly, still employs a UGF, power pump driven, in a FO system, for over 12 years. Until one has acquired the experience and expertise of water management, and desires a less costly introduction into SW, especially if one is only interested in fish, the UGF should not be overlooked. If one establishes a SW tank with an eye towards the future, and desires a 'Reef' or keeping invertebrates, then a UGF would not be where to start, because its dismantling will create many more problems. The phenomenon of nitrification via sand beds, is utilized by large commercial and public water reclamation industries for purifying and recycling our tap water supplies, and has been employed longer then the (modern) aquarium hobby has existed!
Every system that promotes aerobic nitrification, utilizes the same principles, oxygen rich water flowing through, in and around porous materials where bacteria reside that consume waste products. It matters not about the construction of the device, just its size and efficiency, whether its in the tank (UGF), outside the tank, in the form of a fluidized filter bed, a so called wet/dry, or canister, the principles remain the same. In the presence of oxygen (aerobic) waste (ammonia) is converted to nitrate.
NITRATE Now lets discuss nitrate. Nitrate is the final stage of aerobic nitrification. In nature, its absorbed by dentrifying organisms and utilized by plant life (algaes) and bacteria. In our aquariums it builds up unless appropriate action is taken to establish denitrification, which is done by designing conditions that promotes bacterial action that consume nitrate under anaerobic conditions in a DSB (deep sand bed), plus the introduction of denitrifying processing, as in LiveRock, and filters that utilize algaes.
Whereas nitrification is the biological process where ammonia is reduced to nitrate, denitrification is the complete processing of nitrate into harmless constituents. Why the need for nitrate reduction or elimination? First off, nitrate is toxic to many life forms. Because free nitrate in the ocean's water is almost non-existent, most invertebrates have little, if any tolerance for nitrate. Fish on the other hand, are able through some adaptive mechanism, to tolerate otherwise lethal levels of nitrate, when nitrate levels are gradually increased at the rates tolerated by the varying fish species.
Many fish classifications based on different levels of 'hardiness' are determined by their ability to tolerate increasing levels of nitrate. Individual differences do exist even amongst nitrate tolerant (hardier) species. Nitrate is not desirable, but sometimes a necessary evil, when keeping fish. The most efficient method of nitrate control, is simply, that regular, frequent, partial water change! Another adjunctive and simpler method, is the deliberate cultivation of algaes.