The Jaubert method is much more difficult to explain than it is to set up. Basically, a plate, not unlike an undergravel filter plate, is placed on the bottom of the tank, on top of which a thick layer of live sand is spread. Live rock is place on top of this thick sand layer so that not more than 20 percent of the sand is covered.
Over time, the lower layers of the sand will contain less oxygen and eventually become low in oxygen (anoxic), but not totally without oxygen (anaerobic) * the sand will still contain about 1 part per million (ppm) oxygen. In this low oxygen environment, certain bacteria that can only survive in this type of environment will develop. They are capable of converting nitrate into nitrogen gas, which will then bubble out of the system.
In order for all of this to occur, natural microfauna need to be present to keep the sand stirred up. Similarly, the system also needs to contain large sand-sifting organisms, like hermit crabs and gobies, to reduce the likelihood of the sand compacting and becoming anaerobic.
While this system is rather simple and easy to set up, many aquarists who have tried it have not followed the guidelines devised by Dr. Jaubert precisely and have run into problems. Only when the guidelines are strictly adhered to can any success be achieved.
One of the biggest problems is getting the "right" live sand. The live sand typically available is too fine, and, more importantly, it rarely contains any of the valuable burrowing organisms that are necessary to make the system work. As a result, nutrients accumulate in the sand that eventually cause microalgae to overgrow everything.
Another factor limiting the success of this system is that when it is set up no more than 20 to 25 percent of the tank's bottom should be covered by live rock. Otherwise, too much of the live sand will be compacted under the rock and burrowing orangisms will not be able to keep the sand clean. This will also result in algae overgrowth.