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Filtration Part 1

Discussion in 'Filtration / ULNS' started by TigerIssey, Sep 3, 2009.

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  1. TigerIssey

    TigerIssey Registered

    Aug 1, 2009
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    Filtration - Part 1

    I have split the filtration section into 3 parts, on researching the information that I felt needed to be included, I believe it is way too big a section to deal with in just one go if I am do justice to each method.

    Part 1

    • Biological Filtration
      Mechanical Filtration
      Chemical Filtration
      Live Rock

    Part 2

    • Filtration Styles
      Sumps / Refugia
      Protein Skimmers

    Part 3

    • Canister Filters
      Deep Sand Beds
      Ecosystem / Miracle Mud
      Algal Turf Scrubbers

    Biological Filtration

    In a marine aquarium, many living organisms provide biological filtration, which can range from bacteria to worms and microscopic crustaceans. The process by which bacteria convert Ammonia and Nitrite is called Nitrification then facultative anaerobic bacteria (bacteria that use oxygen but can live without) breakdown Nitrate to produce Nitrogen gas.

    Please see bottom for diagram of Nitrogen Cycle within the Marine Aquarium
    There is also a Graph of the test results I got whilst cycling my tank. Hopefully these will help you to compare the process as it is happening.


    Nitrification is the process by which Ammonia is converted to Nitrite and Nitrite is converted to Nitrate. The by-product of this process is H+ ions, which make water more acidic, in turn lowering the pH.

    There has been much debate over the particular organisms involved in this process and is now widely believed to be Nitrosomonas europaea to oxidise ammonia to nitrite and Nitrospira and Nitrosospira that oxidises nitrite to nitrate.

    Nitrosomonas is the first bacteria to proliferate throughout cycling; this is the reason we test for ammonia and nitrite. As ammonia levels decrease and nitrite levels increase, the Nitrosomonas are growing. Once zero ammonia is reached we see a peak in the level of Nitrite on our test kits. The emergence of sufficient Nitrospira and Nitrosospira takes longer to occur than the earlier process. We tend to see higher levels of nitrite for longer periods than we see higher levels of ammonia. It is believed that excessively high Nitrite levels can inhibit the growth of Nitrospira and Nitrosospira. There is also a belief that Nitrobacter, initially believed to perform conversion from Nitrite to Nitrate (capable of doing so at high Nitrite levels), is present to perform this conversion whilst cycling, keeping Nitrite low enough for colonies of Nitrospira and Nitrosospira to reach levels that will convert the entire amount of Nitrite to Nitrate.

    The Nitrite converting bacteria will have reached sufficient numbers when zero Nitrite is showing on test kits. At this point in the cycle, we start to see Nitrates produced and can test for them.


    Denitrification is the process of Nitrate reduction to di-nitrogen and nitrous oxide gases, in so doing OH- ions are produced which increases the alkalinity of water and in turn increases the pH. It would be prudent to mention here that this process starts much later in the cycling process than Nitrification does and therefore throughout the cycle the pH of the aquarium is often low. This can worry new marine aquarists unnecessarily as once the cycle is complete and Denitrification processes are underway, the increase in pH should return the water to the required pH for a Salt Water aquarium.

    The gases produced are either gassed off at the surface by agitation or absorbed by cyanobacteria. Due to this process occurring in the lack of oxygen (facultative anaerobe), only certain substrates are capable of supporting the process, the bottom substrate or sand, rock and inside coral heads. This is usually enough denitrification substrate to effectively keep Nitrates below 0.5ppm.

    This process is not necessarily just performed by Nitrospira and Nitrosospira, many other bacteria are capable of performing this function within the aquarium, but these however are the main organisms responsible.

    Mechanical Filtration

    Mechanical filtration is used to trap large particles in order to make the water clearer. This process uses material such as sponges, pads and floss, these can of course become colonised by bacteria, which is not necessarily required in a reef setting. If sponges and floss are used, it is advisable to swap very regularly to prevent them becoming a biological filter and hence accumulating Nitrate. Mechanical filtration of this form, is not necessarily required however, there are other methods.

    Filter Floss - A Type of Mechanical Filtration

    Aquariums that incorporate a sump will usually have a weir inside the aquarium that skims water from the surface and can be a very efficient mechanical filter for dust and particulate matter. To remove this from the system, a filter sock can be used where water enters the sump, this will again need very regular cleaning to prevent a blockage.

    An alternative to a filter sock is where the particulate matter will settle in the first chamber of the sump, being prevented from further travel by a series of baffles. Within the first chamber you then locate a Protein Skimmer (see part 2), this will remove waste by surface skimming and foam fractionation.

    Using mechanical filtration in a reef setting can remove food that would otherwise be consumed by filter feeders; therefore there are both advantages and disadvantages to these methods. Without mechanical filtration, detritus can collect and lead to algal blooms.

    You can avoid algal blooms without using mechanical filtration by using a turkey baster to periodically blow rocks off, then siphoning the detritus during a water change. The process of blowing off with the baster has been likened to a storm surge on the reef in nature.

    Chemical Filtration

    The main forms of chemical filtration in a reef aquarium are used to remove Dissolved Organic Compounds (DOC’s) for example, amino acids and fats or phosphates. DOC’s are potentially more harmful to our aquatic life than even nitrates can be. When performing water changes, we are removing Nitrates, but also removing DOC’s, which can lead to reduced growth, decreased disease resistance and metabolic stress.

    DOC’s can be converted back to ammonia by the bacteria present in the tank, this ammonia can then be utilised by plants, in the case of a reef, algae or can be oxidised by nitrification to Nitrate which then either gets processed by denitrification or accumulates in the aquarium.

    Increased Denitrification will increase the di-nitrogen and nitrous oxide gases, which will either be gassed at the surface through agitation or again consumed by cyanobacteria. DOC’s will also add a yellow tinge to the water; this impairs viewing and causes turbidity within the water, which then hampers light penetration.

    Granular Activated Carbon

    Granular Activated Carbon (GAC) can remove substances by two methods, Absorption, traps organic molecules within the pores, and Adsorption, which chemically bonds organic molecules. Carbon can be placed in various locations throughout the system depending on the design, plug and play have a chamber at the back that is suitable, sumps can hold filter bags of carbon somewhere in the system that gets flow and some protein skimmers are capable of holding chemical media where the water exits the skimmer and returns to the sump. Some aquarists choose to run an external filter for chemical media or it can even be fluidised in a reactor chamber.

    Granular Acivtated Carbon (GAC)

    Carbon has another very useful function within a reef setting, corals such as Sarcophyton release toxins into the water in a bid to out compete other corals for space, using carbon is known to remove these toxins. Aquarists that keep any invertebrate that can release toxic substances such as the purple dye released by a startled sea hare can be removed by carbon.
    Due to the large surface area of carbon, it can become a biological filter and becomes ineffective once saturated, it is therefore recommended to change the carbon regularly. When carbon reaches the end of its life, the adsorbed substances can be leached back into the water, this is again remedied by regular changes. GAC will only leach what has been collected, depending on whether levels of DOC's in the tank lowered. It's an equillibrium reaction, where by carbon keeps adsorbing/absorbing until it is either saturated or has abserbed/adsorbed to a point of equillibrium. When you lower the levels of a substance, it will leach out some of that collected substance, the levels in the tank will be fractionally lower than they were before the GAC had adsorbed/absorbed once carbon as finished leaching.


    Excessive levels of phosphate can fuel algal growth; it interferes with calcification of corals and inhibits growth of coralline algae. Hobby test kits measure orthophosphate and are not completely accurate at low levels, D-D Merck phosphate test is widely considered to be the most reliable on the market. Levels at or below 0.1 ppm orthophosphate are ok for corals but ideally less than 0.045ppm. Once lower than this level, test kits struggle to be accurate however, if levels could be kept between 0.012 and 0.02ppm this would make a huge difference to such pest algae such as Derbesia and Bryopsis.

    Beginners can be confused in to believing there phosphate level is low, despite a huge amount of algae in the display tank. Although the level is not measurable, there is phosphate available for use as there are algae growing. The reason for this is that phosphate is present within the aquarium in more than one form, not all can be measured, our hobby test kits measure inorganic phosphates as orthophosphate, when there will also be organic phosphates present.

    Phosphate Adsorption Media

    Ferric oxide / hydroxide has the highest adsorption capacity for removing phosphates in the form of orthophosphates. This media does not release phosphate into the water after the maximum adsorption level has been reached. The media can last from weeks to months depending on the phosphate levels in the aquarium. For a reef aquarium, the recommended level is <0.03ppm, which is achievable with this media.

    Phosphate Adsorption Media

    Sources of excessively high phosphates (>0.5) can include food, top-off water, GAC, and calcium reactor media. If levels are excessively high, another method of lowering phosphate levels must be used in addition. (More will be discussed in further sections, links will be added later).

    Live Rock


    Live Rock is not just rock; it is a complete ecosystem of its own. The constituents depend on the location where it is collected. The best live rock is the most porous; this aids in filtration and is also less dense. The less dense the rock is, the more rock you will get per kilo, Fuji rock is considered the most porous and therefore best for filtration and is often reflected in the price.

    Old coral Skeletons, shells, coralline algae, fused sand grains coated with coralline algae and in some areas purely fast growing coralline are constituents of live rock depending on the region collected. All live rock contains nitrifying and denitrifying bacteria with other microorganisms and many other forms of life including sponges, tunicates, small crustaceans and clams.

    The collection of live rock is monitored and each location has restrictions for collection, the collections sites are therefore varied each year. The rock that appears in the aquarium trade is loose rock collected from inshore zones or reef flats and is considered a renewable resource from these areas. The main collection areas are all now starting to produce aquacultured rock, this is usually man made as it is cheaper than importing rock and is placed in offshore reefs for approximately 8 months to seed with bacteria and other desirable organisms.

    Live rock needs to be cured after transportation from the collection sites to aquatic stores. Various organisms die off in transit and will produce ammonia as they decompose. This decomposition will kick start the nitrogen cycle and will take a few weeks, this is where buying pre-cured rock is an advantage. If your retailer has cured the rock, the cycle in your tank should take approximately a week to 2 weeks for ammonia, produced by die off, to be processed by the bacteria. If you can keep the rock wet in transportation from supplier to aquarium, this can be shortened more. At this point you will get diatoms forming on substrate, rocks and sometimes glass that will signal that nitrates are being produced. After a water change, this then is the time to add the basics of your clean up crew (CUC) however not too many, there ill not yet be enough food for the full amount.

    Before placing the rock in the aquarium it is advisable to rinse in fresh salt water and clean of any decaying algae or sponges and thoroughly clean any black areas. This will reduce the amount of ammonia produced on introduction of the rock. When cycling it is advisable to run a protein skimmer and carbon along with phosphate remover, as this will reduce considerably any algal blooms.

    • DOC's Dissolved Organic Compounds
      GAC Granular Activated Carbon
      CUC Clean Up Crew
      NH3/NH4+ Ammonia
      NO2 Nitrite
      NO3 Nitrate

    Diagram 1 - The nitrogen cycle and its contributing factors within the Marine Aquarium.

    Diagram 2 - Results from the daily testing of Ammonia, Nitrite and Nitrate throughout the process of cycling with Live Rock.

    The peak in Ammonia is ended by the production of enough bacteria to convert the die off to Nitrite, as Nitrite peaks, enough bacteria is produced to convert Nitrite to Nitrate and as Nitrate peaks, denitrification begins. Nitrate became 0 at day 28 which signified that bacteria had reached a high enough population to perform the Nitrogen Cycle within the Marine Aquarium.

    Please remember that every tank is different depending on the amount of die off on the Live Rock you have. Please do not get hung up on the figures as it is the trend you should be observing.

    [attachment=1:jgq6w5cx]Nirtogen cycle copy.jpg[/attachment:jgq6w5cx]
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