The problem with most aquariums is that they accumulate nitrate from the nitrogen cycle process. We may change the water to rid nitrates from the water column, yet denitrification is a good addition to help this problem. The process of taking nitrate and turning it into nitrogen and nitrous oxide gas, is denitrification. In a closed system, this is not the case because nitrification is an aerobic process, and denitrification is an anaerobic process. In conventional closed systems, the two areas are not close enough together to diffuse well.

Biological- Usually incorporating a trickle filters, this method uses Bio-media to grow the nitrobacteria to break down toxins. I recommend this method for fish only tanks, as this is the easiest and in my opinion best method to grow the beneficial bacteria for a fish only aquarium.

Berlin Method- This method includes 4 basic concepts.
1. Good lighting
2. Protein Skimming (Don't skimp on this one!)
3. Live Rock
4. Excellent water column movement
The Berlin System provides for some denitrification in the pores and crevices of the rock, which get very little water flow (anaerobic) and are stagnant. Here, the denitrifying bacteria can do their thing. Since they are close to the nitrifying bacteria, the accumulation of nitrate is reduced.

Modern Berlin System- A deep layer of live sand is used for both biological functions, the denitrifying on the bottom and the nitrification on the top. This is the same theory but it keeps both, closer together. I have used this method with success.

Jaubert Method- This method was thought up by a marine biologist, Dr. Jaubert, who took the Berlin method, and improved upon it. A plenum is covered by substrate. Within the plenum, water will provide an area for denitrification. This has a low O2 content.
In the substrate, I recommend surface feeding and burrowing animals, which will work the organic material into the substrate. Eventually, organic material will diffuse to the plenum region.
Oxygen, being low at the bottom and high at the top, osmosis occurs, pulling with it ammonia. Gas tends to find equilibrium. This process of moving towards equilibrium is called diffusion. Once the ammonia moves down, nitrification takes place, resulting in nitrate. Oxygen is then depleted, and denitrification continues to occur. Nitrogen and nitrous oxide are produced from denitrification, which then diffuse upwards and eventually leaving the water.

Put an under gravel filter on the bottom and an egg crate next. On top of this, use two layers of screen so that nothing will fall through. This should give you 1.5' of water at the bottom. Next lay your first layer of sand, 1' deep. I use crushed coral. Then, another layer of screening and a final layer of sand 2' in depth. Lay your rockwork on top of all this.

A final note. Use GAC (granular activated carbon), which keeps the water from yellowing over time. It also takes out many chemicals that may be present.