Image: The Kent Marine Bio Reef Aquarium by Interpet
The Kent Marine Bio Reef Aquarium by Interpet

Aquarium filtration has traditionally been divided into three types: biological, chemical, and mechanical. While in some recent systems the boundaries are less clear, this is still a good place to start. In the article, we’ll take a look at biological filtration. Mechanical and chemical filtration will be discussed in next articles.

Biological Filtration

Biological filtration is the process of using living organisms, usually bacteria (although algae-based systems can be used), to remove waste products, particularly nitrogenous compounds. Aquatic animals excrete nitrogenous wastes as ammonia, which is highly toxic. The classic biological filtration process converts ammonia, via nitrite, to nitrate, which is much less toxic (a process called nitrification). An additional step is the conversion of nitrate to nitrogen gas (denitrification), which, in effect, completely removes the nitrogenous wastes from the system.

The nitrification process is what classic biological filters are designed to do. They pump oxygen-rich aquarium water over substrates on which nitrifying bacteria can grow. This is the principle behind artificial biofilters ranging from simple sponge filters and under gravels, to biological media in canister filters and trickle filters, to fluidized sand beds. Such filters need to be cycled, or matured, prior to stocking the aquarium because the bacterial population needs to be large enough to handle the waste output of the first inhabitants.

This is usually done by adding a source of ammonia to the aquarium water and either waiting for bacteria in the environment to colonize the filter or adding a starter culture. Ammonia and nitrite levels are then monitored. First ammonia levels drop and nitrite levels rise (as the bacterial population that converts ammonia to nitrite becomes established), then the nitrite level drops as another population of bacteria flourishes and converts the nitrite to nitrate. At the point where both ammonia and nitrite levels are zero, biofiltration is established and the process of stocking the aquarium can begin.

Denitrification is trickier to achieve. It can be performed by bacteria growing in water with low oxygen levels, for which specific filters are used. These fillers utilize slow water flow and microporous media with low-oxygen zones within. A similar principle underlies the use of deep sand beds. Filters filled with sulfur beads to encourage specific types of bacteria can also be used to try to control nitrate levels.

Because using bacteria-based filters to reduce nitrate levels can be problematic, a range of other methods have been developed, including growing either macroalgae or mangrove plants in the system or using nitrate-adsorbent materials, such as zeolite. Partial water changes are a more traditional method.

More recently, methods for reducing levels of nitrates and other nutrients to extremely low levels (to create so-called ultra-low-nutrient systems, or ULNS) have been developed. These techniques are based on stimulating the growth of bacteria that assimilate a range of waste products (these methods claim to reduce levels of dissolved organic compounds and phosphates as well as nitrates) and then using skimming to remove the bacteria from the system.

Bacterial growth is encouraged by dosing with a variety of different probiotic compounds (including carbon sources such as ethanol, usually in the form of vodka, although various commercial products arc available) or by using fluidized reactors containing pelleted media that fulfill the same role. Some systems, particularly various commercial ones, also utilize specific types of chemical filtration (using special adsorbent media, such as zeolite and phosphate-binding media) as an adjunct to stimulating bacterial growth. These systems have found favor with hobbyists trying to grow corals that prefer very low nutrient levels, and to enhance coloration in such corals, but ULNS methods remain the subject of considerable debate among advanced reef hobbyists.

Marine aquarium hobbyists arc fortunate to have access to a ready-made combination of biological filtration and tank decor in the form of live rock. Live rock can handle the whole nitrogen cycle with very little effort on the hobbyist’s part. All that's needed is enough live rock and/or live sand in the system, together with some water flow, and the basics of filtration are in place. As a result, almost all modern marine aquariums use live substrates as the heart of their biological filtration. Other measures to further increase water quality, such as the use of chemical media, carbon source dosing, and skimming, among others, are used as add-ons to live rock. You don’t have to use any of these extra things, however. Just put some live rock in your aquarium, and you’ll have a good biofiltration system.

Image: Fish excrete nitrogenous wastes in an aquarium and bacteria detoxify those wastes by converting them from ammonia to nitrite and then nitrate
Fish excrete nitrogenous wastes in an aquarium, and bacteria detoxify those wastes by converting them from ammonia to nitrite and then nitrate.

Image: Live rock can serve as a biological filter as well as a form of decoration
Live rock can serve as a biological filter as well as a form of decoration.

What Is Live Rock?

Live rock is rock collected from tropical seas. In most cases, the rock is essentially rubble resulting from the breakdown of reefs by erosion and storms, collected in shallow water. Live rock is generally made up of coral skeletons and the remains of dead coralline algae. In some cases, where the rock is relatively new, coral skeletons may be readily identifiable as such, whereas material that has been subjected to a longer period of erosion looks more like rock. In addition to natural coral rubble of this type, live rock can be aquacultured by leaving suitable terrestrial rocks, or artificial rock made using concrete, in a shallow marine environment close to a reef area for a period of time. In clue course, this material becomes colonized by a variety of marine organisms and is then ready for collection and aquarium use.

Image: Live rock is collected in the shallow waters of tropical seas
Live rock is collected in the shallow waters of tropical seas.

Good live rock is highly porous, which gives it a huge surface area for bacterial colonization and a combination of aerobic and anaerobic zones that allow both nitrification and denitrification within the same material. Apart from bacteria, the range of other organisms in the rock varies tremendously depending on where the rock was collected (in terms of both the broad geographic location and specific local conditions, for example depth, exposure to water flow and light, nutrient levels, etc.). Most live rock supports a wide variety of organisms, including micro- and macroalgae and usually a lot of worms and small crustaceans. Other organisms that may be present include sponges, bryozoans, sea squirts, small starfishes, corals and anemones, and mollusks, including both snails and bivalves.

Live rock doesn't just act as a bacteria-driven biological filter the way a traditional biofilter does. In addition, algal growth on the rock (which may not be very obvious in a well-run tank that houses herbivorous fishes or invertebrates) helps to remove dissolved nutrients. Also, live rock helps create an ecosystem in which nutrients, rather than being dissolved in the water, are locked up in the tissues of algae and myriad small creatures (much like the situation on a coral reef)

There are many different types of live rock, varying in their origins, shapes (largely determined by the types of dead coral that make up the rock), and the range of organisms likely to be present. All live rock will work as a biological filter, so the choice of which rock to use is generally more a question of aesthetics than filtration efficiency, although it is worth noting that extremely dense and minimally porous rock is likely to be less effective than more lightweight, highly porous rock.

Image: Quality live rock will have plenty of marine life growing on it
Quality live rock will have plenty of marine life growing on it.

How Much Rock?

A few years ago, it was common practice to recommend the use of a certain quantity of live rock per volume of water, typically 1 pound per gallon. This rule, however, doesn't take into account the varying density of live rock. If very light and porous material is used, the lank can end up being almost full of rock—which used to be a common look in reef aquariums. In fact, it’s very hard to be precise about how much rock to use, but a better guide might be to use enough rock to visually fill about one-fourth to one-third of the tank volume with the rock loosely stacked. Remember that too much rock can limit your options with respect to tank layout.

Image: You can use live rock to cycle an aquarium since some of the organisms on it will die off acting as a source of ammonia
You can use live rock to cycle an aquarium, since some of the organisms on it will die off, acting as a source of ammonia.

Cycling with Live Rock

As described previously, artificial biofilters require cycling in order to establish populations of bacteria before the aquarium can be stocked. Given that live rock comes fully colonized with a range of bacteria and other organisms, the traditional cycling process is not required.

This doesn’t mean, however, that you can always simply place some live rock in a new aquarium and immediately stock the tank with fish. The process of collecting and shipping the rock can lead to the death of some of the organisms living on or in it. If rock in this state is added to an aquarium, the result will be a high ammonia concentration, not to mention some pretty nasty smells, as the dead creatures decay.

To avoid this, most of the live rock that you’re likely to buy is seeded, or cured. Basically, this involves importers or wholesalers holding the rock in large tanks until any dead organisms have completely decayed. By the time the rock arrives in your home aquarium, this process should be complete and the rock should have a healthy population of the required bacteria (which would build up during the seeding process) together with a host of microfauna and a variety of algae. The microfauna and algae may not be very obvious at the point of purchasing the rock, but its always amazing to see the range of marine life that appears on the rock and in the tank within a few weeks or months.

Image: If live rock smells bad you can assume it needs more time to cure
If live rock smells bad, you can assume it needs more time to cure.

Image: Live rock is likely not appropriate for a hospital aquarium since the medication may kill off the invertebrates so other forms of biological filtration should be used
Live rock is likely not appropriate for a hospital aquarium since the medication may kill off the invertebrates, so other forms of biological filtration should be used.

If you are in any doubt that the rock you are offered is ready to use, there is one easy test: Use your sense of smell. Properly seeded live rock does not have an offensive smell—perhaps a hint of fresh seafood, or of seaweed, but nothing stronger than that. If you sniff and get even a hint of decaying marine life (pretty unpleasant), the rock isn’t ready yet.

Having got your sweet-smelling rock into your aquarium, it is still best not to assume that the tank is ready to stock. Instead, wait a few days and test for ammonia and nitrite every day or two. If readings for both have been zero for a week or so, the tank should be safe to stock. If you do get an ammonia or nitrite reading higher than zero, all you need to do is wait and keep testing. Eventually the rock will gel there.

Living Without Rock

Given the advantages of using live rock as a primary biofilter, why, or under what circumstances, would one use any other type of biological filler in a marine aquarium? Cost may be one reason to avoid using live rock. Typically it will be more expensive to use live rock rather than, for example, a fluidized sand filter and inert tank decor. However, in most aquariums, the cost of the live rock, while a significant proportion of the total cost of the system, is not prohibitive.

A more sensible reason to use an artificial biofilter is having aquarium conditions that would be deleterious to live rock. An example of this would be in a hospital tank where copper treatments (or other remedies likely to kill small invertebrates) are being used. In this situation, while the bacterial population of the rock would remain functional, the death of numerous invertebrates on and in the rock would likely create a spike in the ammonia level. Quarantine tanks represent a similar situation, as it is always possible that medication will be needed in these systems. Another situation in which artificial filters may be preferred is in tanks used by breeders for rearing fry. In these tanks, live rock might be bad news, as small predatory organisms might be present on the rock.

Which Filter to Use?

In situations where live rock would be unsuitable as a biofilter, there are various options. If the appearance of the tank is not important and the bioload is likely to be relatively low (quarantine and hospital tanks, for example), internal power filters with synthetic foam as a biological medium are a good choice. They are inexpensive, simple to setup, easy to maintain, and available in sizes to suit most tanks. Where more filtration capacity is needed (where larger fishes are being treated or quarantined, for example), external canister filters with ceramic or sintered-glass biomedia are a good choice, as are fluidized sand fillers. None of these filters are particularly good for breeders’ grow-out tanks, as they arc likely to trap fry, but simple air-driven sponge filters can he used for that application.

Author: Philip Hunt