3.1 BIOLOGICAL FILTRATION:

Biological filtration is probably the one type of filtration that most hobbyists are familiar with, and have used in some form or fashion if they have kept aquariums before. It is also the one that all hobbyists pay the most attention to, often to the detriment of the other types of filtration mentioned earlier. Such is a dangerous mistake.

Store owners too, tend to put great emphasis on biological filtration, at times perhaps too much. The latter may explain why it has taken on such an important position in the mind of the novice and experienced hobbyist alike. Do not misunderstand me, biological filtration is an important form of filtration. But it can, and should, not be the only one that gets attention, or most of the attention. Especially not in reef tanks. Others types are of as much importance, if not of a greater one in many cases.

To put it simply, biological filtration deals with the removal of nitrogen breakdown by-products from the water. These nitrogen compounds appear in the tank as a result of the animal life that is placed in the aquarium. The food that is added to the tank, the algae that die off, and the respiration and metabolism of the fish and invertebrates, all contribute to the eventual appearance of ammonia/ammonium ion.

There are, basically, three types of bacteria that break down, or decompose, organic matter (de Graaf 1976) in our aquariums: bacterium coli, proteus and subtilis. Decomposition is a multiple stage process, and far more complicated than we usually imagine. Organic matter, for example protein, first breaks down into peptides and subsequently into amino acids, but the process also includes many intermediate stage chemical compounds such as amines and nitrosamines, some of which can be very toxic.

It has even been suggested that in filters that do not run properly, these intermediate products may be the cause of the dreaded "wipe-out" syndrome (Thiel, 1988), especially when in addition to such pollutants a sudden increase in organic waste occurs, for example as a result of a fish or other animal that died. The chemistry of protein and organic matter breakdown is very complex. I attempted to explain some basics of it in the first edition of this book, published in 1988, but my comments did not meet the expected response. Hobbyists found the explanations too complicated and unnecessary. As a result, I have left them out of this 7^th printing and 2^nd edition of THE MARINE FISH AND INVERT REEF AQUARIUM.

Unfortunately, even though the water quality is usually excellent when an aquarium is first started up, as soon as animals are added, that same water quality starts deteriorating quickly. The purpose of all filtration is, therefore, to counteract these negative effects and remove whatever noxious compounds may have been added to the water as a result of populating the tank, feeding the animals, biochemical activity taking place, etc.

Biological filtration deals with the removal of nitrogen breakdown products which, as indicated earlier, involve, in a first stage, ammonia or ammonium ion, or both. The first and very important goal that we are trying to achieve with proper biological filtration, is ensuring that the breakdown of protein and organic material follows its normal course, and is not interrupted at some intermediate stage. The latter can cause major water quality problems, as some of the intermediate compounds can be extremely toxic.

The second and third very important goals of biological filtration, is ensuring that all ammonia gets converted to nitrite, that all nitrite gets converted to nitrate, and that some of the nitrate gets eliminated from the system, through the presence in the filter, pipes, and generally throughout the aquarium, of bacteria that are referred to as facultatively aerobic-anaerobic, which can reduce nitrates through assimilation, also called nitrate respiration.

Our goal, therefore, must be to build up a very potent and large colony of the bacteria that eliminate ammonia and nitrite on one hand, and also not to interfere with their process under any circumstances, on the other. This is the main reason why I am strongly opposed to the addition of medication, and have said so for the longest of times. Medicine can, in certain cases, interrupt the normal course of the chemical and biological breakdown of organic matter, and can result in the build up of the kind of compounds that can be harmful to all lifeforms we keep in reef tanks, especially to the more delicate invertebrates. It is much better when medication needs to be used, to treat the fish in a separate tank, usually called a hospital tank. We will discuss this in one of the later chapters.

Ammonia present in the water is broken down to nitrite by a form of bacteria called Nitrosomonas. These bacteria appear spontaneously, or their proliferation can be sped up by the addition of a batch of seeded gravel or rock from another tank. Seeded gravel is gravel, or rock, that comes from an aquarium that has been running for a while, and already has a great deal of bacterial life. Transferring some of the gravel (rock, coral pieces) also transfers bacteria.

Alternatively you can add one of the many commercial filter starter products, e.g. Super Zyme from my own company, Cycle, Biozyme, Nitro-Quick, and a few others. They will speed up the cycling of the aquarium, and reduce the stress created on the fish and invertebrates as a result. Such is positive insomuch as it also reduces the risk of parasitic infestations during the first couple of weeks your aquarium is set up.

Ammonia can be present in the aquarium as ammonia gas or as ammonium ion. Whether ammonia gas is present at all, and in what proportion, depends on the pH of the water. For this reason ammonia becomes a more important problem in salt water tanks than it is in freshwater aquariums. More ammonia is formed at higher pH's than at lower ones, and because it mixes so readily with the water, it is extremely dangerous. Ammonia tests should, therefore, always show zero mg/l, or ppm. Even small amounts are unacceptable in reef systems, as they will definitely harm fish and invertebrates alike. Ensuring you do not have residual ammonia in your tank's water, is the same as saying that you must ensure that your biological filter is potent enough to deal with whatever amount of organic material may need to be broken down.

Conversely one can also say that reducing the amount of organic material added to the tank, will create less of a demand on the filters. In simple language this translates to, for instance, do not overfeed.

The biochemical conversion process that ammonia goes through results in the creation of nitrite, a closely related compound, just as noxious to the animals as ammonia gas is when it mixes with water.

Nitrite must also be removed at all costs. Fortunately for the hobbyist, another type of bacterium, Nitrobacter species, appears spontaneously as well, and converts the nitrite to nitrate, a compound that is far less noxious, providing it is present only in small amounts. Nitrobacter species bacteria are present in our biological filters but in numbers far smaller than Nitrosomonas. Nevertheless, a well seeded filter that is not subjected to interference from medications such as antibiotics, or heavy metals such as copper and zinc, will harbor a sufficient amount of these beneficial bacteria to cope efficiently with the nitrite that is formed in the tank.

Should tests of the aquarium water show the presence of merely low amounts of nitrite, such still is an indication that somewhere in the aquarium, or in the filters, the natural breakdown cycle has been, or is being, interfered with. The hobbyist should immediately determine where this interference is coming from and remedy the situation. This may entail cleaning all mechanical filters, ensuring that the gravel or substrate is clean and does not harbor trapped detritus and other organic matter, removing dead or dying algae, checking the cleanliness of corner overflow boxes and/or surface skimming siphons, etc.

It may also suggest that, perhaps, the hobbyist is feeding too much, or in the worst of all cases, that the tank is overloaded to such a degree that the filters can no longer deal efficiently with that biological load. This should prompt the hobbyist to remove lifeforms (unlikely to happen in my experience), or to increase the filter capacity by adding additional biological filtration (more likely to happen). We will discuss how this can be done in a later section.

Nitrates are another problem altogether. Traditionally nitrate, NO3 has been regarded as a compound that is not harmful. Such may be the case in fish-only tanks, the ones we were used to keeping before the advent of reef tanks, but it is not so in today's living reef aquariums. Nitrate is definitely a pollutant, and it does affect the well being and appearance of corals and other invertebrates. I have been able to verify that levels as high as 8 ppm of NO3 result in both Catalaphylia jardinei and Discosoma species corals not opening as much as they do at lower levels, respectively not lifting themselves as far off the rocks to which they are attached, and not stretching out as much as usual.

The differences were even more obvious, and significant, as the nitrate levels were increased to 15 ppm of NO3 in the same aquarium. These tests were conducted on a 150 gallon aquarium running at generally accepted levels of pH and specific gravity, temperature, redox, etc. and lasted a total of 9 weeks. Objective opinions were obtained from outside parties, who were not aware of the changes made in nitrates, but were merely asked for their opinion as to the appearance of the aquarium's lifeforms. Two such outsiders are George Bepko and Scott Jerome. Because these were blind tests neither even knew why their opinion was being asked so often.

To confuse the picture somewhat more, many tests available to the hobbyist measure nitrate as nitrogen nitrate, or N-NO3, and not the total nitrate. This is unfortunate because many hobbyists do not realize what a large difference exists between the two. For example, 10 ppm of N-NO3 is equivalent to +/- 44 ppm of NO3. And such a level is much too high for a reef tank. Because of the lack of knowledge about the differences between these differences, hobbyists assume that their tank is in good shape, and nitrates are low. After all, is their reasoning, 10 ppm "is" low.

Unfortunately those 10 ppm are not low at all, because they are ppm's of N-NO3, which is really equivalent to +/- 44 ppm of nitrate. As you can well imagine, nitrogen breakdown product removal and conversion from one type of compound to the next one, is a much more complex matter than is usually imagined. Because the process is, for the most part, spontaneous, little attention is paid to the process as such. All the hobbyist does, is provide an appropriate area for these bacteria to grow, colonize in large numbers, and do their "thing". The quality of that environment - the area where the bacteria actually grow - is what differentiates excellent and good filters from mediocre ones.

Making that environment not only adequate, but as close to ideal as possible is, therefore, an important part of maximizing the water quality, and running a successful aquarium.

Besides ammonia, nitrite and nitrate, phosphate can also occur in your tank, sometimes in significant quantities, and pollute the aquarium water. Phosphates have different origins: they result from the mineralization of organic compounds (breakdown) such as food, micro and macro algae, the metabolism of fish and invertebrates; they can be introduced in the tank because they are present in the water you use (whether tap or well), and they can be a part of the salt that you add to make up new salt water.

Phosphates are not removed biologically, but through other means, and will therefore be covered in another chapter. Phosphates can, however, create lots of problems for the hobbyist because they often give rise to large amounts of micro-algae on one hand, and can interfere with coral survival and growth on the other. Indeed, text books report that phosphate interferes with the calcium carbonate uptake, and can, as a result, lead to corals coming loose from their hard exoskeletons.

Then again, Thiel (1989) reports that such can also occur as a result of a lack of strontium and molybdenum in the water, two elements normally present in traces only, but rapidly removed from the water as a result of ozonization and protein skimming, as well as through the normal metabolism of all animals present in the aquarium.

We touched briefly on the presence of bacteria in our filters already. Beneficial bacteria that is. Two species already mentioned are the ones that assist in the conversion of ammonia to nitrite, and nitrite to nitrate: Nitrosomonas and Nitrobacter species. Besides those two species of bacteria, many other varieties are always present in the tank, whether we want it or not. Most of them are harmless, and thus are not a concern. There is, however, another type that can cause a great deal of problems if it occurs in the filters and tank: Shigella species (deGraaf 1976). These bacteria, which by the way also cause food poisoning, could be one cause of the so called wipe-out syndrome that occurs in fish-only tanks that are not well cared for, when these Shigella bacteria are liberated from the filters and end up in the water. One sure way to prevent their presence is to clean all filters on a regular basis and ensure that no areas occur in those filters where water does not travel freely through whatever material is used inside the filter itself.

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