Aquaculture Magazine

December/ January 2016

Carbonate Chemistry Games for Aquaculture:The Basics

By Dallas Weaver

Almost four decades ago, I got an interesting introduction to carbon dioxide in aquaculture from a presentation by Dr. John Colt who explained in great detail how, “if you put fish in a closed bag with pure oxygen, the fish will not die of ammonia toxicity, but from CO2 toxicity”.

By Dallas Weaver, Ph.D., P.E. Scientific Hatcheries

What happens is that the fish excrete both ammonia and CO2 as waste products of metabolism, and the ammonia increases the pH in the bag while the CO2 decreases the pH. There is a lot more CO2 produced, on a molar basis, than ammonia, and the pH drops fast enough to keep shifting the un-ionized ammonia (the toxic version) to lower concentration and toxicity. Meanwhile, the CO2 partial pressure keeps increasing over time to the point of becoming toxic.

This is why when we ship fish and other aquaculture organisms in sealed bags, the bags arrive at their destinations with low pH water, even when they started with very high pH water, like seawater at pH of 8.1. If you just open up that low pH bag and add an air stone, the CO2 will leave the water and the pH will go up and the un-ionized ammonia will kill the fish. If you just take the fish out of the water in the bag and put it into high/normal pH water, you will pH shock and possibly kill the fish. However, if you replace the low pH and high ammonia shipping water with low pH but ammonia free water then slowly introduce the receiving water to increase the pH, everything will be fine. These phenomena are all parts of the “Carbonate Chemistry Game”.

Understanding carbonate chemistry and how it interacts with alkalinity, carbonate alkalinity, pH, calcite and aragonite (shell building CaCO3 components), organic acids and the kinetics of this chemistry is critical to successful aquaculture. Most of this chemistry is very well known and well described in Books like “Aquatic Chemistry” by Stumm and Morgan. Detailed knowledge about the behavior of CO2 in liquids goes back about a century, as the oil industry dealt with natural gas and other gases containing CO2 that needed removal.

If you start with pure CO2 gas and add it to water, some of the gas dissolves as a gas in the liquid, much as oxygen and nitrogen dissolve in water. If you have ever used a Soda Stream to make sparkling water, you are just dissolving CO2 into the water. However, this CO2 (g) dissolved in the water then reacts with H2O forming H2CO3 (carbonic acid). This chemical hydration is kinetically slow and takes about 15 seconds to occur in pure water.

The carbonic acid then decomposes, according to the pH, into bicarbonate and carbonate forms. Each one of these steps has a thermodynamic constant that will allow calculation of the ratios of the ions involved.  When the pH related to the negative log[H+] increases, it will cause equation 1 to shift to the right as the pH increases, with the amount of carbonate increasing relative to the amount of free CO2 (g).


1) CO2 (g) ⇔ CO2 (aq) + H2O ⇔ H2CO3 ⇔ H+ + HCO3- ⇔ 2H+ + CO32-



From a health standpoint, the total of all these forms of inorganic carbon is reasonably irrelevant, and only the free CO2 dissolved in the water counts. This is related to the CO2 partial pressure (ppmv) that would exist in air in equilibrium with the water. Most discussions of CO2 in water specify a maximum of about 20 mg/l as free CO2, which translates to about 1.5% CO2 in the air.  At this level in air, humans are seeing measurable impacts such as drowsiness and so are fish.

As mentioned above, the kinetics of hydration and dehydration between dissolved CO2 (aq) and water to form H2CO3 is slow. All the other reactions between carbonic acid to bicarbonate to carbonate are almost instantaneous. As CO2 is a major chemical of life as both a waste product and a nutrient source for carbon fixation like photosynthesis, this potential slow step in mass transport is critical.

Nature has handled this problem by making enzymes such a carbonic anhydrases to speed up this reaction. Because CO2 is somewhat soluble in the lipids that make up cell walls, while bicarbonate is insoluble in lipids, nature can take CO2 in the form of bicarbonate on one side of a membrane, convert it to free CO2, diffuse it across the cell wall and convert it back into bicarbonate. It is the slowness of this reaction that prevents a soda or beer with very high levels of total inorganic carbon from literally exploding in our faces when opened, while the carbonic anhydrases in our mouths allow the CO2 to rapidly come out of solution and provide the mouth the feeling of bubbles.

The lack of carbonic anhydrases in clean water to speed up the equilibrium of this hydration reaction is what dramatically decreases the ability to either add or remove CO2 from aquaculture water at high rates and low cost. The only reason we can get CO2 out of our lungs fast enough to not die from CO2 toxicity is the carbonic anhydrases in our lungs. The slowness of this reaction impacts everything from the ability of the oceans to adsorb CO2 from the atmosphere to the ability to easily strip CO2 from water in a packed column.

An example of this kinetic issue is seen in a recycle system using a fluidized bed followed by a packed column for re-aeration. In the fluidized bed, we convert organic carbon waste into CO2 and water, while using oxygen. In the packed column we add back the oxygen and remove some of the CO2. However, since it only takes a second or so for the water to go through the column, only the dissolved free CO2 can be stripped from the water and all the carbonic acid, bicarbonate and carbonate remains the same. This is easily demonstrated by putting a pH meter in the water directly coming from the bottom of the column and measuring the pH and you will find the pH is the same as at the top of the column.

However, with the removal of CO2 the pH should increase. If you sample that same water collected in a cup after about 15 seconds the pH will increase indicating the sample came back to equilibrium as the CO2 (aq) came to equilibrium with the carbonates and carbonic acid in the water. If this equilibrium were fast, a short column could bring the water to equilibrium with the air flowing through the column in one pass in less than a second as can be done with oxygen and other gases without this slow kinetic step such as SO2.

If we bring water into equilibrium with outside air, which has 400 ppmv of CO2 partial pressure (putting an air stone into a sample of the water), we now have a defined CO2 partial pressure. Determining the pH at this defined equilibrium point can tell you a lot about your water and water chemistry. This pH value is then related to the Carbonate Alkalinity and the TIC of your water. This Alkalinity subject will be covered in the next column where we will go into the details of how the relationships between Alkalinity, Carbonate Alkalinity, CO2 and pH are related, such that when two of these values are known, the third is determined.


Dallas Weaver, PhD, started designing and building closed aquaculture systems in 1973 and worked for several engineering/consulting companies in the fields of air pollution, liquid wastes, and solid wastes until 1980. Today, he’s the Owner/President of Scientific Hatcheries.

e-mail: deweaver@mac.com


Dallas  Weaver

Dallas Weaver

Dallas E. Weaver has a Ph.D. in Applied Science from the University of California at Davis. He also has a Professional Engineer Licence.

After graduation, Dr. Weaver began working for several engineering/consulting companies in the fields of air pollution, liquid wastes, and solid wastes until 1980, when aquaculture became his main interest. Since 1973, Dr. Weaver began designing and building closed aquaculture systems with the intent of creating the technology necessary to build a business that could compete with existing Asian tropical fish producers. As part of this business plan, he began conducting research on water treatment systems for aquaculture and was able to explore a number of different possible approaches, thus creating several innovations such as fine media fluidized bed biofilters for both waste treatment and aquaculture, the application of packed column re-aeration, the use of pure oxygen systems with feedback control, the design, development and use of automated feeding systems and the use of low cost lime-based pH feedback control systems, among many others. Today Dallas is semi-retired; he’s the Owner/President of Scientific Hatcheries. He works as an aquaculture consultant, especially in the aquatic environments, aquatic chemistry, water treatment, hazardous waste biological destruction systems and similar topics. He is part of many organizations such as the Marine Conservation Research Institute (Board), the Aquaculture Engineering Society, the Editorial Board for Aquaculture Engineering Journal, and the World Aquaculture Society through the American Fisheries Society.


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