Biological Filtration:
Biological filtration is the conversion of toxic waste products (mainly ammonia NH3/ammonium-NH4+) in the aquarium to either less toxic or non-toxic forms. There are two main processes that occur in a bacterially based system: denitrification (conversion to non-toxic nitrogen gas-N2) or nitrification (conversion to the less toxic form NO3).
Nitrification (conversion of Ammonia to Nitrate) occurs through a two step process that is dependent on two types of bacteria. The first step involves the oxidation of NH3 to nitrite (NO2) and is facilitated by nitrosommonas bacteria. The second step occurs through the oxidation of nitrite to nitrate (NO3) and is facilitated by nitrobacter bacteria. Both of these steps require an aerobic environment (that environment which is rich in oxygen) in order to oxidize NH3 to the final less toxic NO3 form. Without bacterial denitrification or plant based ammonia fixation, nitrate will accumulate within the aquaria until it will need to be exported through water changes. Although nitrate is less toxic to inhabitants, it is still toxic and should be kept at acceptable levels.
Denitrification occurs in anaerobic environments (those areas with low or no oxygen). It involves taking nitrate (or ammonia directly) and reducing it to a completely non-toxic form-nitrogen gas. Denitrification can occur to some extent in an aerobic environment; however, an anaerobic environment must be provided for efficient denitrification to occur. Denitrifcation can be accomplished by a number of bacteria; however, Thiobacillis is one of the more common. Problems with denitrification can occur when Thiobacillis (Thio=sulfur) generates pockets of hydrogen sulfide (H2S)during the reduction processes. H2S can be identified by a rotten egg smell and black zones within sand beds. Because H2S is toxic these zones should not be disturbed as they will generally resolve themselves.
A third form of biological fixation is the plant based system in which ammonia is converted to nitrogen gas through nitrogen fixation processes. These systems have been popular in freshwater aquaria for since their inception, and have been becoming an additional facet of marine aquaria as of late. The disadvantage of this system in marine aquaria is that the more popular fish (namely tangs and other omni or herbivorous fish) can dessimate a macroalgae population rapidly unless it is kept within a refugium.
The biological systems:
While there are several choices for setting up a biological system, they are based on two basic methods: 1)a natural system of live rock and sand based substrate or 2)a medium for bacteria to proliferate on in an aerobic environment (wet-dry/biowheel/biobale/etc).
The general benifits of the natural methods (Live rock/sand) are several fold: Firstly, using live rock (aerobic and anaerobic) and a deep sand bed (anaerobic environment after the first few inches), you can provide for both nitrification and denitrification processes. Both of these processes are not simultaneously possible in the aerobic environment of wetdrys/biowheels. Therefore, in a properly established natural system, the nitrate does not accumulate as rapidly, if at all. This prevents problems of nitrate toxicity as well as algae problems associated with increased nitrate levels. Furthermore, LR in itself has anaerobic zones which permits some dentrification to occur in the absence of the deep sand bed. Second, LR/LS provides for increased diversity and environment that is similar to the natural systems. Third, LR/LS provide a chemical buffer for the aquaria, protecting against pH swings. Fourth, (my opinion) LR/LS is more aesthetically pleasing and natural.
The bacteria: Despite manufacturer's suggestions otherwise, stabalization of nitrobacter in a dormant state on LFS shelves is difficult and generally results in a significant loss of bacteria. Freeze dried nitrobacter is very difficult to keep viable-so these products should be avoided as a rapid cycle method. Nitrosomonas is more amenable to these processes; however, this only gets you half way there. Denitrification bacteria are available and are quite effective-especially if there are anaerobic zones-such as sand beds within the aquaria; however, generally these bacteria require a carbon or sulfur based food in order to carry out their processes efficiently. B/c of their diverse nature, properly maintained sand beds usually are capable of providing these necessities without further input.
Chemical Filtration:
One of the single most important components in chemical filtration is the protein skimmer. It provides the removal of dissolved organic compounds (DOC)-including proteins that can result in the direct accumulation of nitrates and phosphates. Most skimmers also provide the aquarium with a degree of particulate skimming and therefore provide some mechanical filtration benifit. There are several factors that affect protein skimming efficiency (irreguardless of the skimmer model)-1) the amount of air delivered into the reaction column; 2)the contact time of that air with a given volume of water; 3) the size of the air bubbles (the smaller the better); 4) the dissolved salt content in the water.
Activated carbon also affords some degree of DOC removal, and can be an important form of chemical filtration. Activated carbon when used intermittently will polish the water by removing yellowing compounds and DOC. It will also remove harsh and harmful chemicals/toxins quite effectively. The disadvantage to continuous use is that it is so efficient in its function, it removes important trace elements from the system that would need to be constantly replinished. Phosphate removers on the market also probably fall under chemical filtration. These are generally aluminum based and despite some manufacturers claims can not be easily regenerated in the home. Although these resins can be quite effective at binding phosphate, they are generally only good at lowering phosphate levels a few points, and therefore, other methods should be employed to get the levels down (ie. water changes, watching their introduction) prior to the use of these resins.
UV filtration is also a chemical filter that may wish to be employed intermittently after the addition of new specimens or on disease outbreak, but most likely should not be run continuously b/c it destroys benificial free swimming life, bacteria, etc.
Mechanical Filtration: Although mechanical filtration does provide a degree of effectiveness in the aquaria for removal of undesirables-IMHO continuous use does more to cause problems than it does good in a reef aquaria. Firstly, mechanical filtration traps and removes many planktonic life forms from circulation. These lifeforms are quite importnat for the maintenace of many corals and fish species. Second, accumulation of detritus within mechanical filtration if not regularly cleaned provides a significant source for the breakdown of these substances and the accumulation of nitrates.
Tim