It is important to remember when adding live rock to an aquarium that, unless the rock has been cured, there can be substantial die off. Scavengers are an integral part of the reef aquarium, but use caution, some species such as this hermit crab (Dardanus megistos), can grow up to 5” and be predatory toward small fish, and will definitely eat corals. However, there are many smaller hermit crabs that are well suited to a reef tank and are excellent scavengers (Paguristes cadenati, Clibanarius digueti and C. tricolor, Calcinus laevimanus).

Another means of biological filtration that does not involve bacteria is the use of algae to metabolize nitrogenous compounds.  This includes, not only the symbiotic algae that grow in corals, but micro and macro species as well. Many reef aquarists are incorporating a small area in their systems to grow various algal species.  These areas, often referred to as algae scrubbers, are located in a separate tank that is in some way connected to the main system.  The algae are grown in a protected area for two reasons.  First, many beneficial herbivorous species, such as Tangs or Angelfish will usually wipe out any cuttings that are initially introduced.  Second, many aquarists have found that these types of algae, once established, grow very rapidly, eventually overtaking the slower growing corals.  With the use of these scrubbers, aquarists can easily harvest the excess algae for use as fish food or to simply export nutrients from the aquarium.  An added bonus to this sort of system is the ability to protect and “farm” various invertebrate species that, like the algae, would normally be consumed by the various fish in the main reef.  When live sand (and/or live rock) is placed in these protected areas, they become a refugium for all sorts of livestock that could not be maintained in the main reef tank.     The next type of filtration is mechanical filtration.  This is the process in which undissolved particles are removed from the water column.  This helps to maintain the water clarity and allows for the removal of organic matter from the aquarium before it has a chance to break down. In fish only systems, this type of filtration can be very important by protecting various pumps and preventing the fouling of the biological filter. Mechanical filters can take many forms, from the simple floss pad inserts in a typical powerfilter to enormous rapid sand filters at Sea World.  They all have the same purpose, to catch stuff that is floating around in the tank.  Today more and more aquarists are finding that mechanical filters are unnecessary in the reef aquarium.  This is mainly due to the fact that the surfaces in the aquarium where detritus settles is constantly being picked over by an enormous clean-up crew consisting of fish, crabs, shrimps, snails, polychaete worms, etc. all the way down to the bacteria. In fact, some aquarists believe that the absence of a mechanical filter is preferable because the free-floating debris helps to feed various filter feeding organisms.

There are times, however, when filter pads can be helpful.  For instance, a filter pad or sponge may help remove tiny air bubbles that accumulate in the aquarium from the discharge of a protein skimmer or to help quiet the splash of water into a sump.

So, if you do choose to use some sort of mechanical filter in your reef, there are a few things to keep in mind. 

• It is important to make sure the filter is easy to access and clean.  In my experience, the more difficult something is to keep clean, the less likely you are to keep up with it.  

• Try to buy or build a filter that will allow you to use a “cut your own” type of filter pad.  It can be costly to continually replace the pads, and frequent rinsing will pull the fibers of the pads apart and greatly reduce their effectiveness.  Sponges can be used for some applications, but be warned, they can hold a LOT of debris so you will spend longer rinsing them out. 

• Try to clean or replace the filters frequently to prevent the buildup of materials that can act as a sink for nutrients. These nutrient build-ups can contribute to various algae problems.    

An unexpected bonus that can arise from using some sort of prefilter sponge or pad in a reef is that often the filter becomes a breeding ground for various beneficial organisms such as copepods, amphipods, bristle worms etc.  So, before you wash or toss that old filter pad out, look it over for anything that you can toss back into your tank as fish food. 

If you choose not to use any sort of mechanical filtration on your reef, there are a few things that you can do to prevent the same nutrient build-ups from occurring. 

It is essential that you have an effective “clean up crew.”  Many companies sell packages that include various snails, crabs, brittle stars etc. that you can add to your reef to keep all of the undisolved debris from accumulating.  There are even companies that can sell you starter (or recharger) kits that contain tiny animals (polychaete worms, copepods etc.) that can help you maintain an active sand bed.

Another method, usually used in conjunction with the animals, is to siphon off the live rock when you do water changes.  This is especially helpful on newer set-ups.

Then as the tank matures, and the number of scavengers increases, you can use a small powerhead (or even a turkey baster) to blow the debris out of any holes and crevasses.  This sort of man-made storm can help to prevent nutrient buildup on the rocks and corals themselves.

Another important type of filtration is chemical filtration.  This is the non-biological removal of dissolved substances from the aquarium.  Typically, most people think of this process as being accomplished by absorption, adsorption or ion exchange. There are however other methods such as foam fractioning (or protein skimming), ozonation and ultraviolet sterilization that should be added to this category as well.  There are many methods of chemical filtration available to the marine reef aquarist, and although none of them is absolutely necessary for success, all of them can be very helpful in the export of unwanted organic material from your reef.

All of the animals, algae, and bacteria in your aquarium release organic compounds as they go about their life processes.  These compounds (proteins, carbohydrates, phenols etc.) are collectively referred to as dissolved organic compounds (DOC).  Because these compounds are dissolved in the aquarium water, mechanical filtration alone cannot remove them. As these compounds accumulate in the aquarium, they cause the water to take on a yellowish tinge.  Although there are tests for DOC, one easy way to check the level in your aquarium is to view the tank from end to end.  If the water looks greenish/yellow then you may benefit from some sort of chemical filtration.

Probably the most common method of chemical filtration is the use of activated carbon.   “Activated” carbon, is bituminous coal that it has been subjected to very high temperatures and pressures which drives out all of the impurities.  This process opens up billions of tiny pores that can either physically trap various organic molecules (absorption) or they can be held to the carbon by chemical bonds (adsorption). 

Many types of carbon are washed with phosphoric acid during their processing, and can leach phosphate back into the aquarium.  Since excessive phosphates can encourage algal growth and retard or stop calcification by calcifying animals, it is important to use a carbon that is designed for aquariums and releases very little (if any) phosphates.

When adding carbon to your system it is best to place it in an area of at least moderate flow.  The use of mesh bags, and baskets is very commonly used for this purpose. Unfortunately, there are no hard and fast rules as to the amount of carbon that should be used.  The amount of DOC, as well as the quality of the carbon you are using, will greatly affect how long it will last. In my experience, it is best to use carbon on an as needed basis. For many tanks, this means around 8oz (around 1 cup) per 50 gallons every month. Many aquarists will remove the carbon after one month for fear of having the material that have been bound up in the carbon re-released back into the aquarium. 

There are other products available that act like carbon, but are actually synthetic adsorbents.  Some of these products have certain advantages over carbon in that they can target various substances, such as phosphate, and can be regenerated.

In my opinion these types of products should only be used as “safety nets” and should not be used as the sole means of nutrient export.

One word of caution, if your reef has become very yellow and you wish to use some form of chemical filtration to clear it up, you may want to do so over the course of several days.  The rapid clearing of the water can expose your corals to light levels that they are not used to.

One piece of equipment that many aquarists use as their main source of nutrient export is the protein skimmer (aka foam fractionator).  Most people probably don’t think of a protein skimmer as chemical filter, but technically they are removing materials that are dissolved in the aquarium water.  Generally speaking, the process of skimming is very straightforward.