Before a discussion of biological filtration can happen, we need to discuss the nitrogen cycle. In very basic terms, the nitrogen cycle is the biological method of getting fish pee out of the pool before anyone becomes sick.
Whether eaten or not, natural process render most food into ammonia, which can be toxic in concentration. Bacterial processes in the tank will convert this toxic ammonia into equally toxic nitrite. Wow, what a deal. Now other beneficial bacteria convert the toxic nitrite to nontoxic nitrate. Actually, in significant concentrations of nitrate can be toxic, or at best have a negative impact on water quality. This "cycle" is the process that must take place in a marine tank, or your gonna have a bunch o' dead stuff.
Now, every new tank must be "cycled." This cycle is closely related to the nitrogen cycle discussed above. But in this case, we are referring to establishing significant concentrations of beneficial bacteria in order to support the aforementioned nitrogen cycle.
This is how the cycle is achieved: After setting up the tank, some hardy species such as the much-maligned damsels are added to the tank and fed regularly (you can actually use only live rock if you wish, as dying matter in the rock produces the necessary ammonia source). In a few short days the concentration of ammonia climbs steadily due to an inadequate concentration of the right types of bacteria. The fish are a little tense by now; clamped fins and rapid breathing. Over time, several more days, the beneficial bacteria gain a foothold and the ammonia concentration starts to drop. Now here comes the equally toxic nitrite. Since the necessary bacteria for nitrite conversion still don't exist in concentration, nitrite quickly ramps up to toxic levels. The little fishes are stressing out by now; clamped fins, and pumping gills, and hiding in the corner. Finally, the appropriate bacteria levels are present and nitrite starts to decline, leaving nitrate in its wake. This is a good thing. Once ammonia and nitrite have dropped to 0 and nitrate starts to rise, the tank is cycled. Now you can start adding livestockůslowly. See the animation below for a visual representation of the "cycle."
Now, back to biological filtration. The beneficial bacteria necessary to support the nitrogen cycle need someplace to grow. Traditionally this has been accomplished using an undergravel filter and crushed coral. By pulling water through the undergravel filter, using an airstone or powerhead, bacterial colonization is encouraged in the huge amounts of surface area available in the crushed coral. This was the best idea for a long time, but it had a couple of drawbacks.
Pulling water through this crushed coral also pulls detritus and junk into the filter bed eventually clogging it and reducing its effectiveness. Also, due to the endless supply of oxygenated water, aerobic bacteria was abundant, yet anaerobic bacteria, that which converts nitrate to harmless free nitrogen, was not. Therefore, nitrates had to be controlled with water changes. Overtime, the use of undergravel filters fell out of favor. (So did wet/dry filters due to their propensity to become "nitrate factories.")
What allowed undergravel filters to be shunned was the widespread use of live rock. Now the rock isn't really live. Maybe some things on it are, but the rock is rock. Actually, it is usually coral rubble retrieved from the reef. Highly porous, this limestone material makes the perfect realistic aquarium decoration and an excellent habitat for aerobic bacteria. But what about the nitrate?
Well, now that there is no longer an undergravel filter on the bottom of the tank, what can that area do for us now?. It just so happens that a ~4" deep mixture of crushed coral in varying sizes and oolitic sand makes and excellent tank floor covering and it helps reduce nitrate. Since no longer are we pulling oxygen-rich water through the sand bed, the aerobic bacteria is not so prevalent, and the anaerobic bacteria takes over. It is this anaerobic bacteria that converts the nitrate to free nitrogen, and it is released to the atmosphere. Now the nitrogen cycle is really complete, and the goal of biological filtration is fulfilled.
A quick note about the use of live sand as a tank bottom. Live sand is no more alive than live rock is. What are alive are all the things in the sand; bristle worms, mini starfish, and all kinds of thingies. You can purchase live sand at a couple of bucks a pound, or in a sense you can grow your own. A 4" bed of live sand for a 40-gallon breeder would require ~90lbs, or more than $180. That's a lot of dough for sand. I use 80lbs of the mixture of small crushed coral (called reef sand) and oolitic sand mentioned above, and another 10lbs of commercially bought live sand spread on top to seed the bed. Also, each time I visit a new aquarium store, I buy an additional pound of live sand and add it back to the existing bed. I feel that this greatly increases the bio-diversity of the sand bed, but I could be wrong. (See The Why's and How's of Sand Beds, with Ron Shimek at reefs.org.)
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