Biofiltration

Biological filters, Bio-filtration, or simply Biofilters, are a method of stabilizing the aquatic environment by establishing a complete organic and mineral cycle using the same basic methods God established when he created the intricate system of life on earth. In fact, we followed a similar pattern with our limited resources.
My aquarium contains no chemical filters such as activated charcoal, ammonia chips or resins, only the fiberous nylon scratch pads you find at home improvement stores for cleaning, usually made by 3M, and that in different grades of courseness to maximize flow. I start with the course materials then work to the fin materials so larger organics become trapped before the finer grades filter the smaller materials. The material in the bottom of the tanks is swimming pool filter sand. If I want the plants to grow like crazy I put mulch and soil in under the sand, the plants grow rapidly and overized. See below. The cryptocorns in the back are SUPPOSED to be 6" tall. . .

The ammonia and organic matter are broken down by bacteria found in all aquariums but are usually eliminated by replacing the filter media and deep cleaning the gravel at the bottom of most tanks and dumping chlorinated water into the tank without treating it first, or at least simultaniously. Note that these is not an overabundance of chorine in water, just sufficient to clean the water to the point of delivery, but this is enough to harm the biologic filter if it is not treated immediately and if there is more than about 5% of the tank water replaced.
There is a multitude of bacteria in the aquatic environment that break down organic waste. In fact, God created a system of bacteria to break down every single organic molecule known in order to recycle the elements for reuse. (Or, you could say "Mother Nature" and imply intelligence because it sounds so much more intelligent than saying all this complexity came by a giant cosmic accident which is, of course, against every observation humans have ever made.) This bacteria is necessary because of the limited amounts of minerals available on the earth. For instance, if iron could not be oxidized and reduced (that is, oxygenated and de-oxygenated), then all available iron would be used up and all organisms needing it for life would die.
The amount and balance of bacteria in a tank is determined by the amount of food and oxygen available to them. Bacteria counts grow or shrink based on those and other factors such as heat and light. Since bacteria need food too, in the newly created earth, the plants provided a basis for those that needed organic molecules for food.
This fits the creation model. Recall the sequence of creation in Genesis chapter 1 where God created plants first, on day 3 (verses 11-12), then he created light (day 4, verses 14-19), then the life forms in the water and birds on day 5 (verses 20-23). On the last day of creation he created land animals and man (verses 24-31). (Without going into too much cosmology here, if we are in about the center of the universe and God created mass then expandd it using a white hole, as opposed to a black hole, then the earth would have functioned at extreme rates because of the density of the universe and, gravity, being focused at centers of mass, accoding to relativity, the speed at which biology functioned during the first "days" would be millions of times faster than it currently does.)
If you think about this sequence you will see that first there were plants, then fish and water living organisms which would include bacteria. These forms are not excluded from the text and are directly implied.
The plants are needed to give a carbon based food that other things can live on. They are what captures light and enters it into the food chain. The bacteria are needed to recycle elements such as carbon, nitrogen, oxygen, sulfur, iron and other metals.
Why do organisms need these elements? All life forms need sources of minerals and organic compounds either that they form or that are taken in from the environment.

For instance, in some bacteria carbon makes up about 50% of the organic compound by weight. It gets this carbon from organic compounds or gaseous carbon such as carbon dioxide (CO2) or, in some cases, carbon monoxide (CO). Carbon is the main constituent of cellular material, where oxygen makes up about 20% of the organic structures in bacteria and is received from water (H2O) oxygen (O2) dissolved in water, organic compounds, and, again, CO2. oxygen is a constituent of their cell material and cell water; O2 is terminal electron acceptor in aerobic respiration in all aerobic living things (like humans, but, as you will see some bacteria can be either aerobic or anaerobic according to the current environmental factors).

Nitrogen is also present in bacteria, as in all life forms and makes up about 14% of the cellular weight of bacteria. It is a constituent of amino acids, used to build proteins, nucleic acids and nucleotides as well as in non-elemental co-enzymes such as vitamins and vitamers. Hydrogen makes up another 8% by weight. It is a main constituent of organic compounds and cell water. Even the much maligned phosphorus makes up 3% of the bacteria which received the phosphorous from inorganic phosphates (PO4) and is a constituent of nucleic acids (DNA and RNA), nucleotides (used for energy cycles and other things), phospholipids (such as cell walls), etc.

Sulfur makes up about 1% of the weight of bacteria. They take in sulfur from various sulfur compounds organic and inorganic and is a constituent of the amino acids (and therefore proteins made of them) cysteine, methionine, glutathione, and also several coenzyme systems. Several groups of bacteria can use sulfur as a source of energy.

Potassium is needed by bacteria. Also making up about 1% by weight of bacteria and is the primary cellular inorganic cation and cofactor for certain enzymes.

Calcium is a macro-mineral in larger organisms but is needed by bacteria as about ½% by weight used in the inorganic forms as a cellular cation and cofactor for certain enzymes.

Magnesium makes up about ½% of bacteria by weight and is an inorganic cellular cation, and is indirectly and directly a cofactor for certain enzymatic reactions.

Iron, used in larger life forms in different organic combinations is found as about 0.2% of the weight of common bacteria as a component of cytochromes and certain non-heme iron proteins and a cofactor for some enzymatic reactions.

Bacteria use these elements in their life cycle and recycle them into the environment directly and indirectly as a result.
So why don't we have a chemical filter in the tank? We do. We just use bacteria, God's filters.

How to Get Nitrogen Out of the Tank
The most common bacteria found in aquatic environments are two genera named Nitrosomonas sp. and Nitrobacter sp. Which are aerobic (needing oxygen), chemolithotrophic (living on rocks, or on the bottom, and feeding on chemicals from the water as a source of energy) autotrophic (self feeding) nitrifying (changing ammonia into nitrate or nitrate into nitrite) bacteria that multiply rapidly when the conditions are right helping the aquatic environment balance and recycle the element nitrogen.
Together they are called nitrifying bacteria because they change ammonia (NH3) into nitrates (NO2) and then nitrite (NO3), and this conversion is needed as a source of energy for these bacteria. What conditions do they need to thrive?
1) Proper range of pH.
The pH of a tank is the “potential for Hydrogen” or how much hydroxide (H₃O) is in the water (H₂O). This is measured on a scale of 0-14 with 7 being neutral. The higher the pH, the more hydroxide (alkalinity) in the water. The lower the pH, the higher the hydronium (H₃O) content of the tank. Hydronium ions are what make the water more acid since they will yield a Hydrogen ion (H+) and water (H₂O). At pH 7 there two types of atoms are balanced which means for every HO ion there is a extra H+ ion attached to water, when these are added together you get 2H₂O, which is, by itself pH 7.0, neutral. The nitrifying bacteria need hydroxide, but in the right amounts. A pH of 7.0 will support the growth of nitrifying bacteria, which prefer a pH of 6.3 to 9.0. pH. Low pH values inhibit nitrification by providing a limiting amount of bicarbonate, the preferred carbon source for nitrifying and hetrotrophic bacteria (see below). A variety of compounds, including bicarbonates, salts of weak acids, and hydroxides contribute to alkalinity. When ammonia is oxidized during nitrification, hydroxides contribute to alkalinity. When ammonia is oxidized during nitrification, hydrogen ions (H+) (producing hydronium ions H₃O) are liberated from ammonia. Alkalinity is needed to neutralize these hydrogen ions. In fact, 8.64 mg/l of alkalinity are consumed for each mg/l of ammonia that is oxidized. Without sufficient alkalinity, the pH of the system will drop, and nitrification will slow down. Nitrification works best when the pH is between 6.5 and 8.5. The process slows considerably at pH values outside this range. (This is why there is a peat bog at the bottom of Spirit Lake at Mt. Saint Helens.) The type of fish and plants in the aquarium often determine the pH range. This tank uses a high pH because of these factors. The pH is raised by adding common table salt, or baking soda, and other minerals.
2) They need to have their TAN.
In this case, TAN is Total Ammoniated Nitrogen. The nitrifying bacteria feed on ammonia. If there is none in the tank, they will die. Ammonia comes mostly from the gills of fish as a waste product of their respiration, then from decaying organic matter both from plans and animal waste. The greater the biological mass (biomass) in the tank (mainly the fish and the plants), the more ammonia is produced and the more nitrifying bacteria are needed. (This balance can be disturbed by the addition of chemicals that kill bacteria such as Methylene Blue or antibiotics, or by the sudden addition of too many fish.) Once the biological filter is working and in balance, the number of bacteria will vary according to the amount of ammonia in the tank until the total available surface area is occupied by bacteria. See how well balanced the system is? It is unusual that Ammonia ss the limiting factor, usually it is Oxygen.
3) They need their DO
Usually the limiting factor in adequate biofilters is a low dissolved oxygen (DO) level which results form either a lack of adequate oxygenation by mechanical means or lack of plant/light ratio which produces adequate oxygenation and, at the same time the plants use up nitrogen, phosphorus, potassium, sulfur, iron, magnesium, etc., etc. Since the bacteria filter uses oxygen to convert ammonia to nitrate, inadequate oxygenation is a critical factor is the establishment of a biofilter. Inadequate oxygenation also produces undesirable sulfur compounds from the deterioration of organic matter that foul the water and give off unpleasant odors (see “Plants Need Nitrogen” below). Without a bubble filter, where do we get the oxygen? This comes from the plants during photosynthesis. So, keeping the plants strong balances the tank. Healthy plants, healthy fish.
4) Temperature.
Water temperature is important for bacterial growth and propagation and therefore, for the health of the entire system. If the water is too cold, the bacteria will not reproduce fast enough to adjust to changing ammonia levels, however, this is rarely a factor in an established aquarium since the temperature is set for the needs of the tropical fish. This fish likes its water warm, about 82 degrees. Yet cooling the water also slows the production of the ammonia.
5) They need space.
They need large surface areas to live on. The question is, what will give the greatest surface area for the mass in the filter system? Small filaments, hair-like structures have the greatest surface area to mass ratio. A cheap source of this is common Fiber-Fill found in sewing and craft stores. Packed into the canister, this gives large surface area and tight passages which allow the bacteria to remove the ammonia efficiently. This is not the only substance that can be used, but it is cost and surface area efficient.
When these factors are met, then an active biological filter is slowly established.
This process is referred to as the nitrogen cycle. Ammoniafication, as listed above, starts in several places (fish and water as well as bacteria) but end up in the water where it is potentially harmful to the fish.
Again, ammonia (NH3) is oxidized by the Nitrosomonas bacteria to Nitrate (NO2)which is subsequently oxidized by Nitrobacter to Nitrite (NO3). The entire process is called nitrification. Nitrite (NO3) can be used directly by cells as a source of nitrogen (assimilatory nitrate reduction).
This entire process happens on most surface areas you can see and in the canister filter under the tank. But this is only one side of the nitrogen cycle. The other side also occurs in the tank. But where? You ask.
The Other Half of the Nitrogen Cycle
God sets up organic living systems that use everything. (This makes more sense than saying everything is balanced for no reason.) Nitrogen is used by the plants as well as by the bacteria. Certain bacteria can reduce (remove oxygen) nitrite during a process called anaerobic respiration, where nitrate is used in place of oxygen as a terminal electron acceptor for a process similar to aerobic respiration (using oxygen), in short, this is where they get their energy. This is the opposite of what id describes above. In the case of anaerobic respiration, NO3 is first reduced to NO2, which is subsequently reduced to N2 or NH3, all three of which are gasses which are soluble in water.
This process is called denitrification and it occurs in anaerobic environments where nitrates are present and oxygen is not. While this process occurs in the aquarium, it is not without merit. Even though we want most nitrogen out of the tank there are uses for it in the tank first, as above, for the nitrifying bacteria, but also for plant growth. Denitrification supplies the plants with the nitrogen needed for growth. Note that this happens in an anaerobic environment, one with little or no oxygen present. This is why we do not use an under-gravel filter. If this filter were present, then water would be drawn through the gravel making it an aerobic environment and the denitrifying bacteria would take on aerobic oxidation instead of anaerobic oxidation (yes, they can do that) starving the plants of nitrogen (in this case ammonia), which would in turn starve the plants and reducing the oxygen killing off much of the nitrifying bacteria and the entire system would fail, or parts of it would fail and need support
Hetrotrophic saprophytic bacteria break organic material down into carbon dioxide and water. The word hetrotrophic means they eat two ways. They can attach directly to organic compounds such as fish waste or dead plant materials and consume small parts by “eating” and decomposing them, or, like the autotrophs, they can absorb dissolved nutrients directly from the water. Saprophytic means they live off of decaying material. These bacteria breaking down organic matter into carbon dioxide and water. Carbon dioxide is needed by the plants to form sugars during photosynthesis. The plants release oxygen from this process, thus completing the oxygen cycle in the tank. This is one reason adequate light is needed. Light is the energy source used in photosynthesis to capture an electron that is needed to make the sugars which are used both for energy and for structures in the plant. All plant fibers are made from sugars of different types.
Facultative denitrifiers such as Bacillus licheniformis, Bacillus megaterium Bacillus subtilis, and Bacillus polymyxa produce digestive enzymes to break down organic waste of fish and plants, and, ultimately feeding the nitrifying bacteria. These are also interesting in that, when oxygen levels drop below critical levels they can burn nitrite and nitrate for energy, which, of course, returns it to ammonia.
Vibrios (curved rod-like shape similar to a comma) are common bacteria in aquatic environments like fish tanks. Pseudomonadaceae  and Vibrionaceae are families of bacteria that are facultative bacteria, that is, they facilitate the breakdown of organic materials. They have polar flagella (move by use of a tail-like appendage), and are oxidase-positive (meaning they use oxygen to oxidize sugars as an energy source). These help to break down organic matter into simpler compounds. In aquatic habitats they overlap with the in their ecology, although pseudomonads favor fresh water and vibrios prefer salt water.
Nitrogen fixation is the actual beginning of the nitrogen cycle but this is beyond the scope of this paper as it accounts for less than 1% of the nitrogen in an aquarium.
The Oxygen Cycle
As above, during plant type oxygenic photosynthesis (as opposed to bacteria type) plants take in carbon dioxide (CO2) and water with energy captured from the available light to form sugars and give off oxygen (O2). During aerobic respiration, as in fish, this cycle is reversed. The fish use the oxygen to burn sugars and convert the energy into stored energy two nucleotide molecules (ATP and GTP) giving off carbon dioxide and water.
So autotrophic bacteria and plants produce oxygen from water and carbon dioxide while heterotrophic bacteria and animals use oxygen and produce carbon dioxide and water.
The Carbon Cycle
Only organisms can reduce (remove oxygen) from carbon dioxide (CO2), so, organic chemistry is the study of organic molecules, or those molecules that have reduced carbon. Carbon forms the very basis for life. All “organic” molecules (though not necessarily all molecules in a given organism) contain carbon. Carbon dioxide can be viewed either as organic or inorganic.
Some bacteria that break down organic matter are called methanogens, or, methane generating bacteria. Methane is sometimes called swamp gas. Methanogens have an incredible type of metabolism that can use H2 as an energy source and carbon dioxide (CO2) as a carbon source for growth. (Since these are absorbed directly from the environment and not consumed pre se by the bacteria, they are also autotrophs, that is, self feeding.) In the process of making cell material from H2 and CO2, the methanogens produce methane (CH4) in a unique energy-generating process. The end product, methane gas, accumulates in their environment. When the biological filter is filly developed small amounts of methane are released from the gravel bed. When too much is being released (as evidenced by bubbles being released from the gravel bed without agitation), it is an indicator that the gravel needs to be cleaned a little more than usual to reduce the organic matter. But this takes most of the biological energy and converts it into methane. There should be some way to capture this energy and convert it into useful carbon dioxide. There is.
Methanotrophs are bacteria that can consume methane (as much as 90% of it from the tank in a well-developed biofilter) and oxygen and produce carbon dioxide and bicarbonate. This reaction can happen at any place in the aquarium but rarely in the gravel bottom which tends to be anaerobic. Bicarbonate acts as a buffer to pH and is the primary carbon source for some bacteria. These are known to contain powerful enzymes (pMMO and sMMO) that are know to attack many chlorinated organic compounds as well as many other compounds returning them to the water for use by other bacteria.
The Methylococcaceae Methylomonas methanica and Methylosinus trichosporium are two such bacteria that stay in the aerobic zone at the top of the gravel and above, including in the canister filter. In salt water Methylosphaera hansonii partially fills this niche. They oxidize formate (formic acid, from formaldehyde) and carbon monoxide to carbon dioxide. This regenerates the reducing process and is a source of energy for the microorganisms.
Interest was heightened in these bacteria after the Exxon Valdeze incident in the Prince William Sound where the areas that were left alone to deal with the oils spill recovered better after 2 years than did those areas where extensive intervention by man occurred.
As we have seen, autotrophs, such as plants, algae, photosynthetic bacteria, lithotrophs, and methanogens, use carbon dioxide as the source of carbon for growth, and therefore reduce from its gaseous form it include it into cell material. Heterotrophs require organic carbon for growth, and usually energy, then, when they deteriorate, the carbon is converted back to carbon dioxide.
This is the carbon cycle. This is why a balanced aquarium needs both autotrophic and hetrotrophic, both nitrifying and ammoniafying bacteria to balance the entire system as well as plants and fish in balance.
There are also lithotrophic bacteria that can oxidize carbon monoxide (CO) into carbon dioxide (CO2), but their significance in the aquarium is unknown and their presence in the aquarium does not seem to be of major importance at this time (but things change).
The methanogen bacteria are unique in their roll in the carbon cycle since they use carbon dioxide in two ways. About 5% is used for cellular material and 95% is used to produce methane gas (CH4), which makes them so unique. However, this is a good reason to clean the gravel periodically to reduce the food sources for them, this preserving more future carbon for making carbon dioxide which is more useful in the aquatic environment. But this brings us to the methanomorphs. Methanomorphs take up methane, methanol (oxidized methane, CH4O) or formaldehyde (CH2O) and use these as forms of energy and therefore are a part of the biodegredation in the carbon cycle as well.
This is the place most people consider bacteria during the degradation of biological components, the decomposition of, in this case, fish and plants in the aquarium. However, as we have already seen their combined efforts are needed to balance the water habitat. It is by the efforts of these bacteria that the large molecules (polymers) of an organism, either plant or animal are broken into polymer subunits (parts of the polymer) that can, by oxidation be recycled into the system as water, carbon dioxide, hydroxide, hydronium, ammonia, sulfides, and other molecules and atoms.
The Sulfur Cycle
Even though we don't normally see or smell sulfur, it is a component of most biological systems since it is a component of a number of vitamins, amino acids (cysteine and methionine, which is needed to start building proteins) and may have other uses in other organic molecules.
Anoxygenic photosynthetic bacteria (such as the various chemo-litho-autotrophic Rhodobacter or Alcaligenes species) that oxidize sulfide (H2S) sulfur and sulfur to sulfate (SO4) just like the nitrifying bacteria handle ammonia and nitrate. This is bacteria photosynthesis that differs from plant, or the oxidative form of photosynthesis. There are the purple and green sulfur bacteria that sometimes populate aquariums.
Another group are called the “colorless sulfur bacteria” such as the Riftia pachyptila endosymbiont or various Thiobacillus species which oxidize sulfide and sulfur as a source of energy. In either case, the organisms can usually mediate the complete oxidation of sulfide (H2S) to sulfate (SO4). Both are useful in plants and animals.
Usually these are seen in sulfur vents such as in Yellowstone Park, but they may also be found in the tropical aquarium but only in the anaerobic parts such as the gravel substrate at the bottom of the tank. These would be found for example in abundance at the bottom of Spirit Lake under Mount St. Helens.
Plants and Animals need Iron
The Iron cycle is like the sulfur cycle. There are bacteria that reduce (take oxygen from) iron and those that oxidize iron. Oxidation of ferrous iron causes iron to be fixed or chelated often forming red colored slime in pipes (hydrated ferric oxide), or rivers where the reducing bacteria can then use it to form black colored slimes or soil deposits.
Our friend above the Thiobacillus has relatives like Thiobacillus ferrooxidans which is an acidophile (loving acid) heterotrophs (both consuming nutrient and absorbing nutrient. They can also oxidize Magnesium.
Leptothrix discophora (and others) cause oily films on the surface of ponds and streams where they live. Is this actually oil? Yes, it is. They synthesize large amounts of fatty acids which keep them afloat where they can get more oxygen and can be used for metabolic purposes. These too oxidize both iron and magnesium.
Other iron eating bacteria include:
Leptothrix ochracea, Leptothrix sp.A, Leptothrix cholodnii, Siderocapsa cf.treubii, Siderocystis sp., Siderocystis confervarum, and Gallionella ferruginea.
Our tank uses an iron rich clay like gravel called Fluorite mixed into the bottom to introduce iron into the aquarium. That is the small red gravel at the bottom of the tank.
Other metals are handled in a similar way by these and other bacteria in oceans, rivers, ponds, and, yes, the aquarium. These are all sensitive to chlorine in tap water. This is why you need to make frequent water changes of 20%-30% and treat the water as you change it so you protect these bacteria and the others.
This is a small part of the well designed system that is the world around us.
How I Set Up the Aquarium
The previous set up included a gravel bottom and the canister filter which we had not changed for several weeks. This allowed for the build up of organic waste on the outside of the filter media can which housed activated charcoal. First I changed only the internal canister by removing the charcoal and replacing it with nylon scratch pads of differing corseness.

(Left, filter materials goin into the filter. Middle, leaves in the bottom. Right, sand over the leaves.

I had not deep cleaned my tank for several weeks allowing the detritus (debris in the bottom) in the rock to built up. When I moved plants around this detritus is pulled into the filter.
Then I planted the aquarium heavily, added some table salt and some phosphorus, potassium salts, Epsom salt, zinc, sulfur, and a few other sources of minerals to feed the bacteria and plants. I removed the defuser on the filter input to prevent the surface of the water from being agitated. This allows the carbon dioxide to accumulate in the tank for healthier plant growth, which, in turn, produces oxygen; it also allows bacteria to form at the top, which helps regulate the gasses in the tank. I moved the input away from the output pipe to create a more natural flow of water through the tank.
The minimum light requirements for a tank are about 1.5 watts per gallon of water in the tank, so, I added a second florescent light to add energy to the tank for good plant growth.
A Brief Picture of the Aquarium Biofilter
1) At the surface of the water, light and oxygen are plentiful, carbon dioxide is fixed by bacteria and oxygen is taken directly from the air into the water. At the surface bacteria take gasses from the air directly and oxidize metals for use by other organisms.
2) In the canister filter, on the sides of the tank, the plants and the top of the gravel, organic matter is captured and aerobic bacteria use plant and fish waste to produce carbon dioxide, sulfide, ammonia, nitrate and nitrite which can be used by plants.
3) In the gravel at the bottom of the tank, detritus builds up and oxygen is soon used up, then the anaerobic bacteria break down large organic particles, and produce carbon dioxide and ammonia which are use by the plants. Some methane is also produced which can act as an indicator of excessive plant material and can be used by other methane eating bacteria to produce carbon dioxide.
4) Plants take up these nutrients and create oxygen for the aerobic bacteria and fish, removing nitrogen and phosphorus from the water.
5) Light produced oxygen. Blue light which is more available at the surface produced bushier growth in the plants. Red light which is slightly more dominant at the bottom of the tank makes plants grow longer so they can reach the surface.
All together this creates a stable aquarium that has less disease, better gas regulation, and is less expensive to run than mechanical chemical filters.
Yes, this took some thought. It took intelligence and design to use the natural systems available to us in setting up this aquarium. The more complicated the system is to set up, the higher intelligence is required to create it. This is a basic rule of engineering. How much more intelligence did it take to create the life forms in the tank? One strand of DNA from one bacterium in this tank is thousands of times more complicated than this entire document you have just read. God was the writer of that blueprint.

 “And God saw every thing that he had made, and, behold, it was very good. And the evening and the morning were the sixth day.” Genesis 1:31