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Nitrifying bacteria produce nitrate. Even though nitrate is not known to be directly toxic to fish, it does act as a stressor, has endocrine‐disrupting activity, and leads to algal and bacterial blooms.

Nitrates are most simply removed through water changes. They are also used by plants in the system. Where water changes are not feasible or nitrates cannot be reduced to target levels, biological denitrification is required. This is the process of turning nitrates into nitrogen through anaerobic microbial action. This involves heterotrophic, autotrophic, and/or anammox (autotrophic anaerobic ammonium oxidizing) bacteria.

Denitrification filters are technically challenging, labor‐intensive, and often costly. They can also produce toxic elements that can be released into the main water system. For these reasons, denitrification should not be attempted without experienced staff.

Figure A3.9 Foam/sponge filter showing the direction of water flow (blue arrows) and air flow (orange arrows) along with the position of the air stone. Inserts show how cracking of the sponge leads to channeling of the water, bypassing the filter media.

Source: Image courtesy of Nicholas Reback, copyright reserved.

Denitrification filters use a carbon source and anaerobic conditions to grow bacteria that can convert nitrate to nitrogen (or in some cases, nitrite). They are done on a side‐stream off the main system LSS. Historically, a heterotrophic process using a variety of bacteria and a constant input of an organic food source (often methanol, CH₃OH) has been common. For safety, the concentration of methanol at all points in the process requires daily analyses, constant adjustment, and many fail‐safes to assure that methanol residual does not build up in the water, as this can trigger a bacterial bloom resulting in rapidly falling dissolved oxygen. Bacterial blooms and reduced activity can result if the system is taken off‐line for any reason; this can take days to recover from.

In recent years, a sulfur‐oxidizing autotrophic process has become popular (Figure A3.12). In this case, the bacteria live and derive their food from a sulfur media. This is much less labor‐intensive, requiring monitoring of outside inputs (e.g. flow rate, temperature, and organic debris), regular back‐washing, and the addition of more sulfur every 6–12 months. Thiobacillus denitrificans was believed to be the primary bacteria in this process, but recent research has demonstrated that it is a diverse community of anaerobes that typically carry out the process (Burns et al. 2018). This denitrification process works best in tropical water (>24°C, 75°F), and the bacteria tend to establish very rapidly upon startup (e.g. two to three days at 25°C, 77°F), even with new sulfur media and no bacterial seeding. The top of the bed is established with the aerobic heterotrophic bacteria necessary to remove oxygen for the anaerobic denitrification process deeper in the bed. A buffering reactor filled with calcareous material such as scallop shell or magnesium oxide/calcite media should follow the acidifying denitrification process. Additional buffer may be needed to manage the system pH, such as a sodium carbonate, sodium bicarbonate, or sodium hydroxide. Heavy back‐washing of the media is required at regular intervals to prevent biofouling. Possible nitrite and hydrogen sulfide in the return stream must be monitored for safety. Fouled filters must be taken off‐line for maintenance.

Figure A3.10 Biotower showing the direction of water flow (blue arrows) and air (orange arrows). The top insert shows one type of bioball.

Source: Image courtesy of Nicholas Reback, copyright reserved.

Deep sand bed filtration is used in some marine aquariums, typically within the main enclosure. A deep sand bed is designed to cultivate anaerobic bacteria in bottom layers of sand, converting nitrate to nitrogen. The filter usually consists of a bed of fine sand (0.05–1 mm grain size) with a minimum depth of 10–15 cm; this ensures that a portion of the sand at the bottom will not be exposed to water circulation. Eventually, the bed becomes established with bacteria, algae, and other marine organisms such as worms, crabs, snails, and sea stars. The animals burrow and overturn the top 5–7 cm of sand in search of food, which causes water to circulate deeper in the sand than it would if the animals were not present. This helps prevent the production of anoxic substances that would be toxic to the fish, and provides a naturally balanced microecology.

Anammox‐related microorganisms were identified in both marine and freshwater aquaculture recirculating systems by Tal et al. (2003, 2004). Bacteria of the order Planctomycetales were shown to eliminate nitrogen by combining ammonia and nitrite to produce nitrogen gas, thereby providing an alternative approach to denitrification (van de Graaf et al. 1995). Its application has the potential to provide significant oxygen and energy savings due the oxidation of only half of the ammonia produced in the system. It is possible that the “passive denitrification” or nitrogen loss observed in recirculating systems is the result of this anammox activity. Processes to promote this special type of autotrophic bacteria (currently being tested in industry) could result in simpler and safer denitrification methods than using methanol or sulfur.

Figure A3.11 Biowheel filter (a) and fluidized bed (b).

Source: Image (a) courtesy of Chris Limcaco, Algaewheel Technologies, LLC, and (b) courtesy of Catherine Hadfield, National Aquarium.