Science Modules / Oxygen

Dissolved Oxygen (DO) dynamics respond to processes of atmospheric exchange, sediment oxygen demand, microbial use during organic matter mineralisation and nitrification, photosynthetic oxygen production and respiratory oxygen consumption, chemical oxygen demand, and respiration by other biotic components such as seagrass and bivalves (see table below).

Other processes impacting the oxygen concentration include the breakdown of DOC by aerobic heterotrophic bacteria to CO2, whereby a stoichiometrically equivalent amount of oxygen is removed. Chemical oxidation, for example processes such as nitrification or sulfide oxidation, also consume oxygen dependent on the relevant stoichiometric factor. Photosynthetic oxygen production and respiratory oxygen consumption by pelagic phytoplankton is also included and is summed over the number of simulated phytoplankton groups. Seagrass interaction with the oxygen cycle is configurable within the model.

aed2_oxygen : oxygen solubility & atmospheric exchange

Atmospheric exchange is typically modelled based on Wanninkhof (1992) and the flux equation of Riley and Skirrow (1974) for the open water, and on Ho et al. (2011) for estuarine environment.

\begin{equation} F_{O_2} = k_{O_2} \left(C_{air} - C_{water}\right) \end{equation}

where \(k_{O_2} (ms^{-1})\) is the oxygen transfer coefficient, \(C_{water} (gm^{-3})\) is the oxygen concentration in the surface waters near the interface and \(C_{air} (gm^{-3})\) is the concentration of oxygen in the air phase near the interface. A positive flux represents input of oxygen from the atmosphere to the water. \(C_{air}\) is dependent on temperature, T, salinity, S and atmospheric pressure, p, as given by \cite{Rile74}:

\begin{eqnarray} C_{air}\left(T,S,p \right) &=& 1.42763\: f\left(p\right) \exp \left\{ -173.4292+249.6339 \left[\frac{100}{\theta_k}\right] + 143.3483 \ln \left[ \frac{\theta_k}{100}\right] \right. \nonumber \\ &-& \left. 21.8492 \left[\frac{\theta_k}{100}\right] + S\left(-0.033096 +0.014259 \left[\frac{\theta_k}{100}\right] -0.0017 \left[\frac{\theta_k}{100}\right]^2 \right) \right\} \end{eqnarray} where \(\theta_k\) is temperature in degrees Kelvin, salinity is expressed as parts per thousand and atmospheric pressure is in kPa. The pressure correction function, f(p) varies between one and zero for the surface and high altitudes respectively: \begin{equation} f\left(p\right)=\frac{p_H}{p_{SL}}\left[1-\frac{p_{vap}}{p_H}\right]/\left[1-\frac{p_{vap}}{p_{SL}}\right]. \end{equation}

aed2_oxygen : sediment oxygen demand

Modelling sediment oxygen demand can take a variety of forms. The simplest form in AED2 is the SOD varies as a function of the overlying water temperature and dissolved oxygen levels.

\begin{equation} f_{O_2}^{DSF}(T,DO)= S_{SOD}\:f_{SED}^{T2}(T)\:f_{SOD}^{DO1}(DO) \end{equation} where \(S_{SOD}\) is a fixed oxygen flux across the sediment-water interface and \(K_{DO_{SOD}}\) is a half-saturation constant for the sediment oxygen demand.

other oxygen sources/sinks (optional)

  • Oxygen consumption during baterial mineralisation of DOC is done in the bacteria module - aed2_bacteria;
  • Oxygen consumption during nitrification is done in the nitrogen module - aed2_nitrogen;
  • Oxygen production/consumption by phytoplankton phtosynthesis/respiration is done in the phytoplankton module - aed2_phytoplankton;
  • Oxygen consumption due to zooplankton respiration is done in the zooplankton module - aed2_zooplankton;
  • Oxygen production/consumption by seagrass phtosynthesis/respiration is done in the bateria module - aed2_seagrass;
  • Oxygen consumption due to bivalve respiration is done in the benthic module - aed2_benthic;

  • Variable Summary & Setup Options

    The following state variables are core or optional STATE variables within aed2_oxygen

    Variable Name Description Units Variable Type Core/Optional
    OXY_oxy dissolved oxygen concentration mmol m^{-3} pelagic core

    The following state variables are core or optional DIAGNOSTIC variables within aed2_oxygen

    Variable Name Description Units Variable Type Core/Optional
    OXY_oxysat dissolved oxygen saturation % pelagic diagnostic core

    The following parameters and configuration variables are available to be set via the nml module block:

    Parameter Name Description Units Parameter Type Default Typical Range Comment
    oxy_initial initial dissolved oxygen (DO) concentration $$mmol\,m^{-3}$$ float 0.0 0-400 Note: will be overwritten by GLM or TFV IC
    Fsed_oxy sediment oxygen demand (SOD) $$mmol\,m^{-2}\,day^{-1}$$ float 0.0 -100-0 Note: unused if Fsed_oxy_variable is activated via aed2_sedflux
    Ksed_oxy half-saturation concentration of oxygen sediment flux $$mmol\,m^{-3}$$ float 50 10-100 Changes the sensitivity of the oxygen flux to the overlying oxygen concentration
    theta_sed_oxy Arrhenius temperature multiplier for sediment oxygen flux - float 1.08 1.04 - 1.12 Changes the sensitivity of the oxygen flux to the overlying temperature
    Fsed_oxy_variable oxygen sediment flux variable link - string '' e.g.: SDF_Fsed_oxy will use the value supplied by the aed2_sedflux model for Fsed_oxy; use this option to allow for spatial or temperal variation
    oxy_min minimum dissolved oxygen (DO) concentration $$mmol\,m^{-3}$$ float 0.0 0 Optional variable to enforce negative number clipping
    oxy_max maxmium dissolved oxygen (DO) concentration $$mmol\,m^{-3}$$ float - 1000 Optional variable to enforce high number clipping

    An example nml block for the oxygen module is shown below:

    &aed2_oxygen oxy_initial = 225.0 Fsed_oxy = -18.75 Ksed_oxy = 15.625 theta_sed_oxy = 1.05 ! Fsed_oxy_variable = 'SDF_Fsed_oxy' oxy_min = 0 oxy_max = 500 /

    AED2 v2.x introduced ...


    Example 1: Cross-section plots comparing modelled and field salinity (psu, left) and oxygen (mg/L, right) for Sep-Dec 2008 at Swan River. The field plots are based on a contouring around 20 profile data locations.
    Example 2: The total area of anoxia (<2 mg O2 / L) and hypoxia (<4 mg O2 / L) within the estuary for 2008 and 2010, comparing the model (black line) and spatially interpolated weekly profile data (shaded region).

    Publications & References

    Wanninkhof, R.. 1992. Relationship between windspeed and gas exchange over the ocean. J. Geophys. Res. (Oceans) 97(C5): 7373– 7382.

    Riley, J.P. & Skirrow, G.. 1974. Chemical Oceanography Academic Press, London.

    Ho, D.T., Schlosser P., & Orton, P.M., 2011. On factors controlling air-water gas exchange in a large tidal river. Estuaries and Coasts. 34:1103-1116.

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