With the popularization of Reef Aquarias and the greater availability of invertebrates, comes the need for clarification of which biological filtration methodologies to use. In order to keep and maintain invertebrates, it is essential to keep free nitrate levels in the water to a minimum, by the total processing of ammonia. Because, unfortunately invertebrates have little if any tolerance for free nitrate in the water, although there is some utilization by some filter feeders, as clams, and also algaes.

Fish, on the other hand, depending upon the individual species, can and do develop some tolerance for nitrate in the water, as long as acclimation processes are gradual, and nitrate levels build up slowly. Nitrate is still not highly desireable, and its reduction and control is the prime focus in the establishment of denitrification processes in SW aquarias.

There is much confusion about the utilization of biological processes that, either lead to nitrification or denitrification. In both processes, one that leads to nitrification, the production of nitrate, you have two types of bacteria, aerobic nitrifyers, (nitrosomonas and nitrobacter sp.) that in the presence of oxygen, process ammonia, which is then converted into nitrite, and then, nitrate. In addition, carbon dioxide is also being produced. These bacteria form and live on any surface that will hold them, being within the aquarium, or any external device that contains porous material where they can lodge. The greater the porosity of the material, the more concentrated they become, and the greater the flow of oxygenated water, the more efficient the process is. This is now considered as an incomplete form of biological filtration, still acceptable in some situations, usually with Fish Only aquariums.

For further clarificatrion and those not familiar with certain terms, aerobes or aerobic refers to organisms that must have oxygen in order to survive and proliferate, and process nutrients. The term anaerobic means 'in the absence of oxygen' also known as anoxic, which specifically denotes a condition where little if any oxygen exists.

The process of nitrification is fully matured when no detectible levels of either ammonia or nitrite are measureable. Actually that's not true, its that our test equipment generally does not extend itself to the levels where its measureable. Ammonia and nitrite are in the water, but levels generally less then .005ppm. In other words, in a fully matured aerobically based biological filter, bacterial colonies are so concentrated and prolific, that the processing of ammonia occurs almost immediately as its being produced! Nitrite is an intermediate stage in the nitrification process, and is also quickly ingested by aerobic bacteria. The final product of the enzymatic action of these bacteria is nitrate and carbon dioxide.

This comes to the second system, denitrification, the further reduction of nitrate into harmless constituents, that, in addition to utilizing nitrifyers, also includes another group of bacteria, known as facultative anaerobes. These bacteria, unlike nitrifyers that are aerobes, live in conditions with or without oxygen (the meaning of facultative). Not only do they process nitrate, but also nitrite, but only when certain conditions exist for them to do so. Their discovery was made in the investigation of how natural processes in the ocean consume nitrogenous wastes, first in the anaerobic conditions found to exist in the interior of porous rocks, and also what occurs in the deeper anoxic layers of the ocean floor.

In the ocean, naturally occuring populations of nitrosomonas and nitrobacter sp. bacteria (nitrifyers), reside on the porous surfaces of the rocks, and in the oxygenated upper layers of sand beds, where nitrogenous wastes are being produced by the benthic life forms residing in and on the ocean's floor. As one goes down deeper in the layers that makes up the oceans floor, conditions become favorable for the establishment of denitrifying bacteria, facultative anaerobes, where in the absence of oxygen (anaerobic or anoxic conditions) and the availability of nitrate and carbon dioxide, denitrification occurs. Nitrite/Nitrate and carbon dioxide migrates directly from the area where its being produced thru a barrier, so to speak, where oxygen stops traveling, generally because little if any water flow takes place, and the existing oxygen is being consumed by the aerobic bacteria. In this condition, nitrite/nitrate is being 'fixed' with carbon dioxide, and is not released into the water. Whatever free nitrate and carbon dioxide is being produced, its quickly ingested by organisms that require it, as algaes, bacteria, and some filter feeders. The difference is that where nitrifying bacteria seem to appear spontaneously in aquariums, denitrifyers have to be introduced through some media, as in LiveRock and/or innoculating the sand beds with LiveSand cultures. For denitrification to take place, there must be direct flow of nutrients, (nitrite/nitrate fixed with carbon dioxide) and a lack of oxygen (anoxia) to these bacteria. These bacteria also exist in the presence of oxygen (facultative), but do not process nitrate unless oxygen levels reach a certain (anoxic) stage. The key, in order for facultative anaerobes to process nitrate, is an anoxic state and carbon dioxide. Carbon dioxide, CO� is another by-product of aerobic nitrification.

Aerobically based externally produced nitrification, as in outside filtering devices, also produces nitrate and carbon dioxide. Initially, there is an attachment between nitrate and carbon dioxide, but this bond is very weak, and carbon dioxide molecularily easily attaches itself to other ions in SW or becomes liberated by the turbulance of the water. Since denitrification also requires the presence of carbon dioxide, attached, if you will, to nitrite or nitrate, free nitrate in the water cannot be processed by denitrifying bacteria. This is a very important point. One has to make a distinction between free nitrate in the water and nitrite/nitrate fixed with carbon dioxide under anaerobic conditions, being available to denitrifying bacteria. That is why, if one establishes denitrification in their aquarium, by the introduction of LiveRock, and constructs a deep sand bed with LiveSand, designed for denitrification, (a DSB) to completely process ammonia in the water, and in addition, also has an aerobically based external biological filter, (basically any porous media where oxygenated water is flowing, i.e. a UGF, canister, wet/dry with bio-balls, fluidized filter bed, etc), along with nitrogenous wastes (ammonia) where nitrifying bacteria can form, then free nitrate is also being produced, which defeats the whole purpose of having denitrification processes in the aquarium. The free nitrate cannot be utilized by the facultative anaerobes, only nitrite/nitrate fixed with carbon dioxide can.

Since nitrifying bacteria form in direct proportion to the level of oxygen and ammonia, and the greater the rate of oxygenation, the greater their concentration, thus free nitrate will be produced by the far more efficient external biological filters, as less ammonia is available to nitrifyers living in the LiveRock and LiveSand sand beds. By removing the external media where nitrifyers reside, a greater shift of nitrifying bacterial populations will develop on the surface of the LiveRock and in the Livesand sand bed, which in turn, promotes an increase in the population of facultative anaerobes, and when external processes are eliminated, little if any free nitrate will be produced. Since nitrifyers also reside on other surfaces within the aquarium system, its not always possible to completely eliminate external nitrification. However, having a low level of nitrate (<5 ppm) is also essential for coraline algaes, as well as some filter feeders, so zero nitrate levels are not always desirable.

One caution when removing external aerobic media, (filter floss, bio-balls, ceramic pipes, etc.) is to remove only a small percentage at a time, because one has to allow the gradual shift of bacterial populations and activity, from external to internal, at some appropriate pace, and total removal at one time, might overwhelm the internal processes, and possibly lethal levels of ammonia might occur, before the internal aerobic processes can catch up. Since bacterial populations take some time to grow, the recommended removal rate is 1/4 weekly, over a 4 week period.

A lot of the mythinformation concerning biological filtration comes from FW, where the primary concern is in establishing nitrification, the elimination of ammonia, by bacterial processing, to a relatively less harmful constituent, nitrate. This information and technology was carried over to SW aquaria, where, the main concern was and still is, the reduction of free ammonia. The 'new' discoveries now make it possible for the complete breakdown of ammonia into harmless components, by duplicating 'natural' biological processes as occuring in the oceans, whose principles can now be utilized in home aquaria, thanks to the investigative efforts of some marine biologists and professional aquarists working in the public and private sectors, who have generously given, freely, this vital information.

In the battle to reduce free nitrate in the water, especially when it came to invertebrates and prior to the discovery of denitrifyers, the emphasis was, and still is, concentrated on removal of suspended organic nitrogenous wastes before nitrifying processes begin. The oldest known device, which has had a tremendous resurgence, especially with the advent of the Reef system, is foam fractionization (the technical term), using devices commonly known as Protein Skimmers, first improved with the use of ozone, and generally discarded (ozone) because of problems with its use, and largely due to the development of pump driven venturi type Protein Skimmers, with their greater efficiency of water turnover, and waste removal. One of the problems with having a too efficient waste removal system, is the starvation of some organisms that require waste material in order to facilitate denitrification, as well as organisms that actually require some levels of nitrate, like coraline algae, clams and other filter feeders. Many advanced Reef aquarists have been removing skimmers from their systems, utilizing better water management techniques and more judicious feeding practices.

One also has to address the type of system one has, and the types of life forms one chooses to keep. You cannot universally apply Reef systems in every situation, as there are limits to the biological processing capabilities of marine aquariums. Just the inclusion of LiveRock to a heavily loaded aquarium will do little good, if one is not aware of its limitations, and the ability of the volume of water to support and promote marine life.

You must also be aware that the establishment of denitrification, will greatly limit one's ability to treat one's tank with medication, if fish are or become ill. By and large, the most successful treatment regimens for eradication of parasites or disease, destroys either nitrification or denitrification processes, notwithstanding claims to the contrary, besides endangering invertebrates in your tank. Many problems occur because one fails to understand the limitations of their aquariums, for its system, inhabitants, or its size. �

I must also mention the fact that there are also other anaerobic processes occuring under anoxic conditions. One such process is the formation of hydrogen sulfide, a highly noxious and poisonous gas, produced by sulfur ingesting bacteria, known as Thisbacilles anaerobes, that form where there is decaying foods and wastes, in the absence of nitrification processes. To insure that this does not occur, its very necessary to have a rich and diverse number of livesand creatures, that ingest uneaten foods and wastes, and convert them to ammonia, which then feeds the bacteria that ultimately leads to denitrification. Before the principles of the operations of DSB's were discovered, the first successful method to incorporate denitrification became known as the Berlin system, which only utilizd LiveRock and Protein Skimming, along with current flow, without a substrate. This was the first Marine system where corals and anemones, and other invertebrates could be successfully kept, in closed aquarium systems.

Because of the danger of putrification in substrates, in which uneaten foods and wastes could reside, and the formation of sulfur ingesting bacteria, under anaerobic conditions, with the resultant discharge of hydrogen sulfide, a highly noxious and poisonous gas, substrates in marine aquariums was discouraged, especially in Berlin systems.

With the need for greater denitrification as greater degrees of bio-loading was taking place in Berlin systems, and with the discoveries of the function of livesand benthic organisms by pioneers such as Dr. Jean Jaubert, did investigations into successful NNR systems (natural nitrate reduction) take place, first using a Plenum, then followed by the subsequent development of DSB's (deep sand bed)