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Understanding Biological Filtration - Jody Karlin

In nature, fish & turtles have an unlimited supply of water to frolic in.  Oceans, lakes, rivers, streams, ponds etc. and rainfall all contribute to this continual clean, fresh, water supply.  However, in captivity we offer our aquatic friends a closed system with a limited amount of water available.  Therefore, all the food and subsequent waste produced by fish and decaying plant material slowly pollute the water. What does it pollute the water with, you might ask ?  The answer is many things, but for the sake of simplicity all we will be concerned with in this article is the very toxic contaminant ammonia (NH3).

Before we can understand how ammonia gets into our fish tanks and how we get rid of it, one must learn that "humans may rule the world, but bacteria run it" (author unknown). Any animal or plant material that dies is broken down, or more technically called mineralized, by the action of bacteria living in the aquarium. These bacteria have a specific name, they are called heterotrophic bacteria. After these microscopic little guys get finished with their afternoon snack, they don't leave over candy wrappers or empty pizza boxes, they throw away ammonia (NH3). Now, these heterotrophic bacteria are always hungry so they are always eating something. As they do, harmful ammonia is continually released into the aquariums water and since new water is not constantly entering the system NH3 levels build up and can eventually cause the death of your aquatic friends.

Don't fret yet, because nature has come to the rescue and gives us another form of bacteria that live in the aquarium called Nitrosomonas, not getting any easier I know. Nitrosomonas bacteria consume ammonia. Unfortunately, they leave over a second fish killing substance called Nitrite (N02). Fortunately, nature
comes to the rescue once again and provides the aquarium with a third form of bacteria called Nitrobacter, which love to eat Nitrite. What Nitrobacter bacteria have left over after their meal is, for our intents and purposes, harmless. Are you all still with me? Don't get discouraged,  I have met many people who have kept a number of aquariums on and off over a 10 year span that could not describe the process by which fish and plant waste are broken down within an aquarium.

The process of getting rid of toxic ammonia in closed aquatic systems is called Biological Filtration and is specifically termed the Nitrogen Cycle and occurs in both freshwater and saltwater aquariums, ponds and our aquatic turtle displays. Just remember "Bio" means living and refers to the different forms of bacteria that filter the harmful ammonia and subsequent nitrite from the aquarium's water.




Now that everyone understands biological filtration is the action of bacteria on ammonia to produce nitrite to nitrate and they need a place to live inside our filters, on any inert substance, let us move to the second form of filtration called mechanical filtration.

This one is going to be the topic of conversation with us turtle people. Extracting the solid waste before it is broken down to ammonia.

Mechanical filtration is simply the removal of any suspended debris in the aquarium's water. Getting out the large stuff!  As water flows through your filter the first stage should be a bonded filter pad, wad of floss or micron cartridge, which will catch pieces of fish,  turtle  and plant waste floating in the water. If you learn nothing else, PLEASE LEARN THIS, mechanical filters must be cleaned as often as humanely possible. Just because the waste is caught in a mechanical filter pad somewhere, out of sight inside your expensive filter, does not mean it is not harming your water quality. If the waste filled pad is not removed from the direct flow of water the decay bacteria (heterotrophic bacteria) will still act upon the waste placing all the toxic by-products of mineralization into the aquarium's water. And if you think waste breaks down quick sitting on the bottom in the corner of your tank, then just get it into a filter where the water is directly flowing over it 200 gph plus!!

We now can see the problems with some filter systems.  If the ease of cleaning your mechanical filter is restricted you will not get the harmful uneaten food and wastes out before it overwhelms your system.

This is the major drawback of undergravel filters. Both biological and mechanical filtration operate together causing the unwanted debris from being properly removed.  Now with fish only  aquariums, undergravel filters work because fish are no where near the waste producers of our aquatic friends, Mr. & Or Mrs. Turtle. They are however, still a pain in the butt and if you don't syphon and clean the gravel regularly, the solid waste will clog the gravel where you also want your bacteria to live.

Therefore, it is the fish mans recommendation to always, and I mean always, separate your mechanical and biological filtration material.

The Nitrosomonas and Nitrobacter bacteria that use ammonia and nitrite for energy need two criteria to survive, a place to live and oxygen. These bacteria are surface dwellers and will live on most any material you place in your filter, plastic media, filter pads, floss, gravel, etc. As the water from your aquarium is pulled through your particular filter, whether it is a hang-on-the-back power filter, undergravel filter, canister filter or wet-dry filter, the bacteria living on the material in your filter receive a constant supply of fresh oxygen. This is a very important point to understand. High water flow rates through a filter are necessary to supply the bacteria within with essential oxygen.

To illustrate, let us use for an example the ubiquitous undergravel filter. As air is blown into the stacks of an undergravel filter, through an air pump or those motorized powerheads,  it rises bringing the water with it to the surface of the aquarium where it is replenished with oxygen. To complete the natural flow, water from the aquarium must be drawn through the gravel to feed the water loss in the stacks. The Nitrosomonas and Nitrobacter bacteria live on the surface of the gravel covering the undergravel plate and extract the ammonia, nitrite and oxygen that they need to survive from the water that is constantly passing over them. Unfortunately, you must clean your gravel with a gravel washer periodically because as water is pulled into your gravel bed left over food and fish waste also enters the gravel layers.

Now, this brings us to the place where the fish people and turtle people may need to reevaluate things to their particular situation Fish produce considerably less waste than our other aquatic friends, so an undergravel filter will pull the waste into the gravel bed and decompose it there, where the bacteria live. But with the amount of waste that turtles produce, may you not be better off siphoning off the food off of a bare bottom every other day for 10 minutes than having to remove and clean 2-3 inches of gravel sitting on top of a gravel plate that has just become overwhelmed by the amount of large solid waste turtles
produce, (like every 2 weeks??). This will bring us to possibly look at a different type of system, open, external wet-dry filtration  where we can get to the solid waste easily before it is broken down to cloudy the tank, and which offers a much more efficient oxygenation system for the water. Remember, 02 is a highly oxidizing molecule, which if is maximized within any system by using a high flow rate of water, will keep the water cleaner without any ancillary filter system.


The third form of filtration performed inside filters is called chemical filtrationChemical filtration is the use of material such as activated carbon and / or resins, i.e. poly-filters (polymeric absorbent), which remove toxic substances other than ammonia and nitrite from the water.  Without getting complicated, certain polluting molecules, i.e.. yellowing compounds, stick like glue to the surface of these substances thus removing them from the aquarium's water.  In essence, chemical filtration is actually mechanical filtration at a molecular level.

Remember, as with mechanical filter material, chemical filter material must be changed regularly. Usually monthly for activated carbon unless specified differently on the package. For most turtle situations, chemical filtration would be an expensive endeavor. A large amount would need to be used and it would get saturated quickly. Really good mechanical filtration coupled with an efficient biological filter will do the trick nicely in our reptile situation.

There you have it, Biological, Mechanical and Chemical filtration. All filters are designed to perform one or a combination of all three functions. Armed with the knowledge of Why Filters Work, you can decide for yourself the two most important factors when setting up an aquarium.  How to keep the water sparkling clean, thus the animals healthy, and how to do this while keeping maintenance of the aquarium to a minimum.


We have discussed biological filtration, the bacterial breakdown of ammonia to nitrite to nitrate, mechanical filtration, the removal of solid waste, and chemical filtration, the absorption & adsorption of harmful molecules into carbon or a resin substance.

Now, let us discuss a state-of-the-art piece of equipment used by the saltwater aquarium snobs, I mean hobbyists. If you are one of those fortunate individuals to be keeping Diamondback Terrapins, no, not to consume, to raise,  (No personal preference being display here, uh uh!), and you want to keep these salty, marsh &  mango loving creatures really happy,  learn about the protein skimmer, foam fractionator or just plain, "what the heck does that thing do", device.

Ever been on a beach and watch the the wave recede and leave behind a half moon of foamy stuff ? That's natures protein skimming at work.

Now that stuff you walk barefoot right through is filled with extracted fish waste and all sorts of other nasty molecular substances, enjoy!  ( I know,  weird sense of humor,  that's why I am still single, so let's get off  it, alright!

As fine air bubbles enter water, with the density of saltwater, (sorry folks, won't work in freshwater, without a very, very, very elaborate system) waste molecules with hydrophilic (water loving) and hydrophobic (water hating) ends attach themselves to the air-water interface on the air bubbles and rise to the surface as an easily removable foam scum. These molecules include proteins, carbohydrates, scatoles, phenols, albumen and all sorts of other things that enter water from organic sources be it food, plant or waste product.

Now, here is where it gets tricky. If we mechanically extract these substances from the water before they breakdown further into ammonia, don't we in essence, circumvent the decay process and intervene before our aquatic friends are subjected to ammonia laden water. Follow me now, this takes a lot of pressure off your biological and/or chemical filters and helps the particular  system maintain a better balance.

Oh boy, now I went and said it "balance" , the cat is out of that brown thing! When we take aquatic friends out of their natural environment with a seemingly unlimited water supply, and place them in small, closed water systems, we are messing with, "Balance", and all forms of filtration is nothing more than our attempt to rekindle that word.


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