Total alkalinity, PH and aragonite saturation state (GBR4 BGC v3.1 baseline)

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    Carbon chemistry background

    Coral reefs are constructed from calcium carbonate (CaCO3) produced by hard corals and other calcifying organisms. Coral polyps form this calcium carbonate by combining calcium (Ca2+) and carbonate (CO32-) ions in the seawater. This is achieved by the corals trapping small amounts of seawater, containing calcium ions (Ca2+), in small vesicles (small capsules) at the surface of the coral tissue. These vesicles slowly migrate through the coral tissue to its skeleton. On the way carbonate ions (CO32-) are then injected into these vesicles from the coral tissue, raising its concentration above surrounding seawater levels, helping to accelerate the carbonate precipitation (solid crystal formation). The biological process used to pump in the carbonate ions is not yet well understood. In the vesicles an amorphous (unstructured) calcium carbonate forms. Once the vesicles reach the surface of the skeleton the amorphous calcium carbonate particles attach to the skeleton and slowly transform into aragonite, which is the crystal structure of calcium carbonate that makes up the bulk of the coral skeleton (Mass et al., 2017).

    The total Dissolved Inorganic Carbon (DIC) in seawater is made up from the sum of dissolved carbon dioxide (CO2(aq)), bicarbonate ions (HCO3-) and carbonate ions (CO32-). The distribution of these carbon molecule species varies with the seawater pH. At a typical seawater pH of 8.1, bicarbonate dominates, representing around 90% of DIC. Carbonate ions (CO32-) are the next most abundant species (~10% of DIC), while carbon dioxide CO2(aq) represents less than 1% (Barker and Ridgwell, 2012). Increases in atmospheric CO2 results in more dissolved CO2 combining with water (H2O) to form carbonic acid (H2CO3). This lowers the pH of the water as the carbonic acid molecule splits into hydrogen ions (H+) and bicarbonate ions (HCO3-). It is the free hydrogen ions (H+) that make it acidic. The existing carbonate ions (CO32-) in the water buffer the pH by combining with the extra hydrogen ions (H+) to form bicarbonate (HCO3-). As a result, increasing CO2 levels lowers the seawater pH, which in turn lowers the amount of carbonate in the seawater, which can impede calcification. While the CSIRO eReefs BioGeoChemical (BCG) model assumes a constant atmospheric CO2 level (and as such doesn't model increasing CO2 levels) understanding this causal change is useful to understanding how pH and total alkalinity (HCO3-+CO32-) are related.

    Surface seawater is generally supersaturated with respect to calcium carbonate minerals, meaning that the concentration of calcium and carbonate ions is higher than the concentration needed for precipitation to occur. The aragonite saturation state is commonly used to track ocean acidification because it is a measure of carbonate ion concentration. Aragonite is one of the more soluble forms of calcium carbonate (CaCO3) and is widely used by marine calcifiers to build their skeletons and shells. Corals and other calcifiers are more likely to survive and reproduce when the saturation state is greater than three. When aragonite saturation state falls below 3, these organisms become stressed, and when saturation state is less than 1, shells and other aragonite structures begin to dissolve (NOAA, n.d.).

    What do these visualisations show?

    These maps show estimates, based on the eReefs BioGeoChemical model, of key variables that relate to ocean acidity and a metric (aragonite saturation state) that measures how easy it is for calcium carbonate (which makes up shells and coral skeletons) to precipitate (solidify) or dissolve.

    In these visualisations we can see that the pH goes through a seasonal cycle with a lower pH in summer due to higher temperatures. The pH and aragonite saturation state is often lower near the coast. This is most likely due to plankton growth, which removes DIC from the water as it is converted to biological forms of carbon. This lowers the DIC, which in turn lowers the aragonite saturation state and pH.


    The version of the BGC model here assumes a constant value for atmospheric CO2 of 396.4 ppm, see page 101 of Baird (2019). It is therefore not suitable for looking at trends in changes due to ocean acidification.

    Model variables

    Total alkalinity

    Concentration of ions that can be converted to uncharged species by a strong acid. The model assumes total alkalinity is the sum of the bicarbonate and carbonate ions (AT =[HCO3-] + [CO32-]), often referred to as carbonate alkalinity. Alkalinity and DIC together quantify the equilibrium state of the seawater carbon chemistry.


    pH based on [H+] calculated from carbon chemistry equilibra at water column values of temperature (T), salinity (S), dissolved inorganic carbon (DIC) and total alkalinity (AT).

    Aragonite saturation state

    The aragonite saturation state of seawater is the product of the concentrations of dissolved calcium and carbonate ions in seawater divided by their product at equilibrium: ( [Ca2+] × [CO32-] ) / [CaCO3], where dissolved calcium [Ca2+] is the seawater concentration of dissolved calcium ions, [CO32-] is the seawater concentration of carbonate ions and [CaCO3] is the solubility of aragonite in seawater. When the aragonite saturation state is 1, the seawater is exactly in equilibrium or saturation with respect to aragonite and as a result aragonite does not dissolve or precipitate.

    In the BGC model coral growth is halted for aragonite saturation state values less than 2. The aragonite saturation state value determines the coral calcification rate in the model, where calcification is proportional to the amount that the aragonite saturation state value is above 1 and the carbon reserves of the coral.


    Baird, M. E., Wild-Allen, K. A., Parslow, J., Mongin, M., Robson, B., Skerratt, J., Rizwi, F., Soja-Woznaik, M., Jones, E., Herzfeld, M., Margvelashvili, N., Andrewartha, J., Langlais, C., Adams, M. P., Cherukuru, N., Gustafsson, M., Hadley, S., Ralph, P. J., Rosebrock, U., Schroeder, T., Laiolo, L., Harrison, D., Steven, A. D. L. (2019) CSIRO Environmental Modelling Suite (EMS): Scientific description of the optical and biogeochemical models (vB3p0). Geosci. Model Dev. Discuss.

    Barker, S. & Ridgwell, A. (2012) Ocean Acidification. Nature Education Knowledge 3(10):21,

    Mass, T., Giuffre, A.J., Sun, Stifler, C.A., Frazier M.J., Neder, M., Tamura, N., Stan, C.V., Marcus, M.A., Gilbert, P.U.P.A. (2017) Growing coral crystals attach particles, not ions. Proceedings of the National Academy of Sciences Sep 2017, 114 (37) E7670-E7678; DOI: 10.1073/pnas.1707890114

    NOAA, (n.d.) Ocean Acidification: Saturation State. Retrieved: September, 17, 2020, from

    Zheng, M. & Cao, L. (2015) Simulation of global ocean acidification and chemical habitats of shallow- and cold-water coral reefs,

    Source data

    The videos/images on this page are based on the 4km eReefs BioGeoChemical model (v3.1) (GBR4_H2p0_B3p1_Cq3b_Dhnd) run with SOURCE Catchments using Baseline catchment conditions. Detailed information about the model can be found in the paper: CSIRO Environmental Modelling Suite (EMS): Scientific description of the optical and biogeochemical models (vB3p0). The raw model data is available from the NCI THREDDS server (daily, in curvilinear NetCDF format) and the aggregate data from the AIMS eReefs THREDDS server (daily, monthly, yearly, in in regular rectangular grid NetCDF format).

    Data span

    These results are based on a fixed time period (Dec 2010 - Apr 2019) hind-cast analysis developed for comparing changes in land practices. The river run off used to drive the BGC model were provided by the SOURCE Catchments modelling.