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      Decreases in calcification rates affect coral reefs, planktonic microalgae, coccolithophores, phytoplankton, and all shellfish. Coral reef growth has been shown to decline due to the decrease of calcification, with a predicted decrease of 21–40% over the period of 1880–2065 (Turley et al., 2006). This decline is also dependent on the temperature of the water and other available nutrients. Oysters and abalone have been the focus of many studies in regards to acidification. These organisms have been shown to have a decreased rate of survival at the larval stage due to lack of calcification of the shell and decreased ability to ingest nutrients. The shell of mollusks is produced throughout all its life stages. During the larval stages, the shell is made from deposition of amorphous calcium carbonate, which then forms into a crystalline aragonite. Both these stages of shell development are more soluble in a low pH. Studies have shown that certain levels of pH will cause holes to form in the shells (Wessel et al., 2018).

      Acidification of our oceans has a great effect on the ecosystem of the ocean. It is leading to changes in the phytoplankton that are available for ingestion by fish and cultivation. It is predicted to decrease the available fish population of our reefs, which will damage the animal protein consumption of many developing nations. The high fluctuations of pH in the estuaries and coastal areas have the potential to greatly affect fisheries. Mitigation of these fluctuations should include consistent monitoring of the water to enable fisheries to add buffering if necessary (Clements and Chopin, 2017). Options for buffering may include:

      Further mitigation strategies should include breeding plants and animals that have a high tolerance for low pH. Integration of a multitrophic aquaculture system can help to mitigate pH fluctuations and other stress caused by run‐off and increased population. An integrated system should include three levels of nutrient absorption (Clements and Chopin, 2017):

      While acidification of natural aquasystems can only be mitigated by global reduction of atmospheric carbon dioxide, further research is necessary to fully understand the impacts of global climate change and the acidification of our oceans.

      1.3.2.14 Ammonia, Nitrite and Nitrate

      Ammonia is a colorless, odorless substance which can accumulate in aquasystems and cause direct mortality, a decrease in production and increased incidence of many diseases. In water, ammonia occurs in two forms, which together are called the total ammonia nitrogen. Ammonia gas is usually released from the gills or from decomposing organics dissolved in the water. Some reacts with the water to produce ammonia ions. The remainder is present as un‐ionized, which is acutely toxic to aquatic life. Chemically, these two forms are represented as NH₄⁺ and NH₃. NH₄⁺ is called ionized ammonia because it has a positive electrical charge, and NH₃ is called un‐ionized ammonia (UIA), since it has no charge. This is important to know, since NH₃, UIA is the form that is toxic to fish. The percentage of UIA in solution depends on the pH and temperature of the water; as both go higher, so does the toxicity.

      A typical aquasystem has bacteria, which in the presence of dissolved oxygen converts (oxidizes) ammonia to the intermediate form of nitrite and then to nitrate. Ammonia is converted into nitrite (NO₂^–) due to the influence of Nitrosomonas bacteria. Nitrite (NO₂^–) is converted into nitrate (NO₃^–) due to the influence of Nitrobacter bacteria. Most test kits measure total ammonia nitrogen, so the aquarist must determine what percentage of the total is toxic.

      Nitrite is an intermediate in the oxidation of ammonium to nitrate. Nitrite is less toxic to fish than ammonia. An elevated ambient nitrite concentration is a potential problem for freshwater fish since nitrite is actively taken up across the gills in competition with chloride. Nitrite is a well‐known toxicant for fish, as well as a disrupter of multiple physiological functions including ion regulatory, respiratory, cardiovascular, endocrine and excretory processes. One critical consequence of nitrite accumulation is the oxidation of hemoglobin to methemoglobin, compromising blood oxygen transport (Kroupova et al., 2005). Nitrite toxicity to fish varies considerably and depends on many external and internal factors. Among the most important ones are water quality (e.g. pH, temperature, cation, anion and oxygen concentration), length of exposure, fish species, fish size and age, and individual fish susceptibility.

      Nitrate is relatively non‐toxic; however, high concentrations reduce animal growth and can decrease survival. For example, concentrations over about 400 mg NO₃^–N/l have been shown to depress the growth rate and survival of marine shrimp (Litopenaeus vannamei). In intensive biofloc aquaculture systems used for shrimp culture, concentrations of 400 mg NO₃^–N/l have been observed after using water for roughly three culture cycles. Salinity influences the toxicity of nitrate, as it does with ammonia and nitrite. At higher salinities, these compounds are less toxic to aquatic animals. Several options exist for dealing with nitrate, including water exchange, phytoremediation, denitrification, and heterotrophic assimilation (Svobodova and Kolarova, 2004; Svobodova et al., 2005; Tepper, 2000).

      It is recommended that un‐ionized ammonia should be less than 0.02 ppm to prevent stress and reduced growth. Ammonia has been reported to be lethal to catfish at about 0.4 ppm (Jensen, 2003). Ammonia, nitrite and nitrate are labile ions and must be analyzed rapidly or samples frozen as soon as possible after filtration. Samples that cannot be submitted within a few hours should be filtered (0.45 mm) then frozen to reduce the loss of ammonia and changes in nitrite/nitrate concentrations. Plain blood collection tubes are suitable containers for freezing. Two 10‐ml tubes will provide enough samples for all three tests. Do not fill completely; leave space for expansion during freezing.

      1.3.2.15 The Nitrogen Cycle

In aquaculture, the nitrogen cycle eliminates ammonia from the water column by bioconversion to nitrite and then nitrate. Nitrate is used by plants, including algae, as a nutrient. This constant change from ammonia to nitrite to nitrate is called the nitrogen cycle (Figure 1.1). In ponds, this process takes place in the surface layers of the mud, but in tanks or aquaria, a special place is provided for the bacteria to live and flourish. This is called a biological filter, or biofilter. One important point to mention about the nitrogen cycle is that both groups of nitrifying bacteria need oxygen to function. If oxygen levels are insufficient, the process can slow down and the levels of ammonia and nitrite will rise in the system.