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Biological filtration (biofiltration) involves heterotrophic and autotrophic bacteria. In some cases, archaea may also be involved or even dominate the process, especially in freshwater systems (Sauder et al. 2011). Many species of heterotrophic bacteria use available organic compounds as energy sources, degrading them into simpler and simpler compounds until they are reduced to inorganic minerals (termed mineralization). However, many of these same bacteria can also feed on living organisms including other bacteria, invertebrates, and fish, crossing over from being beneficial to detrimental. For example, many Aeromonas and Vibrio spp. can behave like this. Autotrophic bacteria use carbon from an inorganic source, such as carbonate, so they are not associated with biodegradation or pathology.

Aquatic animals release nitrogenous organic waste from the breakdown of proteins, and other metabolic waste in the form of ammonia, urea, or uric acid. Nitrification is an aerobic two‐step process in which specific genera of primarily autotrophic nitrifying bacteria convert ammonia (NH₃ and NH₄⁺) to nitrate (NO₃−). Billions of aerobic bacteria on substrate and surfaces exposed to ammonia‐rich water use ammonia for energy and transform it to nitrite during this process (nitrification step 1) NH₄⁺ + 1.5O₂ →NO₂⁻ + H₂O + 2H⁺. Billions of other aerobic bacteria, living on the same surfaces, use toxic nitrite for energy, transforming it into the relatively nontoxic nitrate (nitrification step 2) NO₂⁻ + 0.5O₂ → NO₃⁻.

The actual species that become established in a system will vary based on the environmental conditions and the species' competitive edge. They all require sufficient oxygen. Necessary nutrients are primarily carbon (as carbonate and bicarbonate), nitrogen (as ammonia and nitrite), phosphorus (as phosphates), and sulfur. Other critical elements include calcium, iron, manganese, and molybdenum. These are primarily supplied by the solids in the water, so animal feeding and waste have direct effects on the bacterial population. It is important to note that the bacteria require complex organic foods, but only use simple sugars and small amounts of amino acids and micronutrients. Very little of the nitrogen, phosphorus, and sulfur in animal feeds or waste is used by the bacteria. The leftover dissolved organic wastes accumulate in a closed‐system aquarium and can reach levels that are harmful to aquatic organisms. That is why rapid uptake of solid wastes using high flow rates through efficient mechanical filtration is so important in closed‐system aquariums.

While biofiltration bacteria are on all surfaces, filters have been designed to specifically support them:

 Sand filters (Figure A3.4a): These filters are often a preferred location for these bacteria if the source water is rich in oxygen and nitrogen‐rich organic waste. The substrate provides abundant surface area. A secondary benefit is that the biofilm aids in the filtration of organic particulates, heavy metals, and pathogenic bacteria.

 Undergravel filters (Figure A3.8): These consist of a perforated plate covering the bottom of the environment with an appropriate medium, ranging from fine sand to coarse gravel, on top of the plate. Air‐driven uplift tubes draw the water from the space below the plate to near the surface. As a result, water is pulled downward through the media where the nitrifying bacteria exist, thus performing mechanical and biological filtration simultaneously.

 Reverse flow undergravel filters: In these, mechanically filtered water is introduced underneath the filter plate, making them dedicated biological filters.

 Foam/sponge filters (Figure A3.9): Water is drawn through a block of open‐celled polyurethane foam or sponge (serving as the biological medium) by an air‐driven uplift tube. These combine mechanical and biological filtration. These are particularly good for quarantine and hospital systems, since they can be easily replaced.

 Trickle filters/biotowers (Figure A3.10): These use a container above the water line filled with biological medium (e.g. bioballs). Prefiltered water is evenly distributed across the top of the medium via a spray bar or a perforated diffuser plate. Water then drips evenly down through the exposed medium, mixing with the air, and eventually collecting in a sump below to be pumped back into the system. These provide biological filtration and gas exchange.

 Biowheel filters or rotating biological contactors (RBC) (Figure A3.11a): These consist of discs or cylinders of rigid biofilter medium positioned half in and half out of the water. They rotate slowly, exposing all surfaces intermittently to water and air. These provide biological filtration and gas exchange.

 Fluidized beds or fluidized sand bed filters (Figure A3.11b): These consist of a tube through which the system water flows from the bottom upward through a suitable biological medium, usually a fine quartz silica sand. The upwelling water expands the sand bed as it passes through it, allowing any particulate waste to pass through and preventing plugging of the bed, and then exits out the top to return to the system. These provide highly efficient biological filtration.

The process of bacterial selection and growth within these filters can be slow, often taking several weeks. With immature filters, animal additions to the system should be very slow, allowing the biological filtration to catch up prior to further animal additions. The process may be accelerated by feeding or seeding immature filters. Filters may be fed with ammonium chloride, ammonium sulfate, or urea to allow for some bacterial selection, prior to adding fish or invertebrates. Alternatively or in combination, filters can be artificially seeded with nitrifying bacteria. These may be purchased commercially, but the contents of the mixtures are unregulated. Alternatively, bacterial media from systems with similar environmental parameters may be transferred over to accelerate colonization of the biological filters. It seems very likely that this could also transmit pathogenic bacteria, viruses, and parasites from the source system. The risk of disease transfer should be assessed. A great option for immature biological filters, and a safeguard in case of filter damage, is to manage a “biofarm” of filter media, fed artificially (without any animals), which can be used to seed systems as needed.

Biological filtration does have its challenges as well. Aquarium environments create unnaturally large populations of relatively few species of nitrifying bacteria. Any limiting factor (e.g. low dissolved oxygen, low alkalinity, low phosphate, reduced feed amounts) or any environmental change (e.g. temperature, pH, salinity, antibacterials) can have dramatic effects on these bacteria. This can destroy their ability to oxidize toxic ammonia and nitrite. The bacterial biofilm can also foul the mechanical filtration (clogging). Also, biofiltration bacteria produce by‐products such as nitrate, phosphate, carbon dioxide, silicate, and biologically inert organic compounds which can lead to excess algae growth and yellowing of aquarium water. They also compete with the fish and invertebrates for dissolved oxygen and trace elements. And if deprived of oxygen (e.g. due to poor water flow, deep substrate, or pump failure), they can create toxic hydrogen sulfide within the system.

Figure A3.8 Undergravel filter showing the direction of water flow (blue arrows) and air flow (orange arrows). Some gravel has been removed to show the filter plate.

Source: Image courtesy of Nicholas Reback, copyright reserved.