Science Modules / Organic Matter

An 8-pool organic matter module is outlined in the figure below, able to capture the variable reactivity of the OM pool and its stoichiometry. Under this conceptual model the decomposition of particulate detrital material is broken down through a process of enzymatic hydrolysis that slowly converts POM to labile DOM. A small fraction, f_ref, of this material is diverted to the DOM-R pool. The bioavailable DOM material enters the bacterial terminal metabolism pathways. These are active depending on the ambient oxygen concentrations and presence of electron acceptors, and of most relevance to the SCE, these pathways aerobic breakdown, denitrification, sulfate reduction, and methanogenesis. In most model approaches it is assumed these communities vary in response to temperature, and are mediated using a simple oxygen dependence or limitation factor. Ultimately, extending the mineralization rates to be computed from thermodynamic arguments is possible and has been discussed recently by Paraska et al. (2014), with the potential for advances in this area as analytical tools for NOM characterization are applied within the SCE system. Reoxidation of reduced by-products is also included to account the role of nitrifiers, sulfate oxidising bacteria (SOB) and methane oxidising bacteria (MOB).

Figure 1: Schematic overview of organic matter (OM) pools and their interactions. Grey dashed line indicates optional process pathway. Different tributaries to the model must be prescribed OM pool boundary concentrations based on land-use specific ratios of POM and DOM reactivity.

Ultraviolet light is also known to drive photochemical breakdown of chromophoric DOM, conceptually equivalent to the DOM-R pool in Figure 2. This photolysis process can take shape either as phototransformation of complex DOM-R molecules to more bioavailable molecules (ie., DOM in Figure 2), or as photomineralisation, where by components of the DOM-R molecule are mineralised. This is modelled based on a known intensity of UV photons, which drives a stoichiometrically equivalent loss of DOM-R via the photolysis reaction, and f_(photo) is introduced as an empirically defined fraction that indicates the extent to which the process transforms the DOM-R molecules to bioavailable molecules or completely mineralises them.

Filterable reactive phosphorus also is known to adsorb onto suspended solids (SS), however, the rate is often site specific (Froelich, 1988). In particular the adsorbed fraction varies considerably within estuaries depending on the nature of the particle origin and their size distribution, and both Langmuir and Freundlich isotherm models have been demonstrated to capture the adsorption process well (Zhang et al., 2009).

Filterable reactive phosphorus also is known to adsorb onto suspended solids (SS), however, the rate is often site specific (Froelich, 1988). In particular the adsorbed fraction varies considerably within estuaries depending on the nature of the particle origin and their size distribution, and both Langmuir and Freundlich isotherm models have been demonstrated to capture the adsorption process well (Zhang et al., 2009).

The above descrioption is summarized in the equation tables in the right 'Equations' tab and in the 'Inorganic nutrient' module in the form of balance equations.

aed2_organic_matter: Mass balance and functions related to the organic matter model

  • Note: Equations of C/N/P/Si breakdown from organic matter to inorganic nutrients can be found in the 'Inorganic Nutrient' Module. This section contains only equations relative to organic C/N/P and the generic parameterization of organic matter process.
  • ---------------Dissolved and partical organic carbon --------------------

    ---------------Dissolved and partical organic nitrogen --------------------

    ---------------Dissolved and partical organic phosphorus --------------------

    ---------------Generic parameterization --------------------

    ---------------Parameters --------------------



    Variable Summary & Setup Options

    Variable Name Description Units Variable Type Core/Optional
    OGM_don Dissolved Organic Nirtogen (DON) $$mmol\,m^{-3}$$ Pelagic Core
    OGM_dop Dissolved Organic Phosphorus (DOP) $$mmol\,m^{-3}$$ Pelagic Core
    OGM_pon Particulate Organic Nitrogen (PON) $$mmol\,m^{-3}$$ Pelagic Core
    OGM_pop Particulate Organic Phorsphorus (POP) $$mmol\,m^{-3}$$ Pelagic Core
    OGM_poc Particulate Organic Carbon (POC) $$mmol\,m^{-3}$$ Pelagic Core
    OGM_doc Dissolved Organic Carbon (DOC) $$mmol\,m^{-3}$$ Pelagic Core
    OGM_donr Refractory DON $$mmol\,m^{-3}$$ Pelagic Optional : simRpools = .true.
    OGM_dopr Refractory DOP $$mmol\,m^{-3}$$ Pelagic Optional : simRpools = .true.
    OGM_docr Refractory DOC $$mmol\,m^{-3}$$ Pelagic Optional : simRpools = .true.
    OGM_cpom Coarse Particulate Organic Matter (CPOM) $$mmol\,m^{-3}$$ Pelagic Optional : simRpools = .true.
    Variable Name Description Units Variable Type Core/Optional
    OGM_cdom Chromophoric Dissolved Organic Matter $$mmol\,m^{-3}$$ - -
    OGM_pon_miner PON mineralisation $$mmol\,m^{-3}\,day^{-1}$$ - -
    OGM_don_miner DON mineralisation $$mmol\,m^{-3}\,day^{-1}$$ - -
    OGM_sed_pon PON sediment flux $$mmol\,m^{-2}\,day^{-1}$$ - -
    OGM_sed_don DON sediment flux $$mmol\,m^{-2}\,day^{-1}$$ - -
    OGM_pop_miner POP mineralisation $$mmol\,m^{-3}\,day^{-1}$$ - -
    OGM_dop_miner DOP mineralisation $$mmol\,m^{-3}\,day^{-1}$$ - -
    OGM_sed_pop POP sediment flux $$mmol\,m^{-2}\,day^{-1}$$ - -
    OGM_sed_dop DOP sediment flux $$mmol\,m^{-2}\,day^{-1}$$ - -
    OGM_poc_miner POC mineralisation $$mmol\,m^{-3}\,day^{-1}$$ - -
    OGM_doc_miner DOC mineralisation $$mmol\,m^{-3}\,day^{-1}$$ - -
    OGM_sed_poc POC sediment flux $$mmol\,m^{-2}\,day^{-1}$$ - -
    OGM_sed_doc DOC sediment flux $$mmol\,m^{-2}\,day^{-1}$$ - -
    OGM_psed_poc POC sedimentation $$mmol\,m^{-2}\,s^{-1}$$ - -
    OGM_psed_pon PON sedimentation $$mmol\,m^{-2}\,s^{-1}$$ - -
    OGM_psed_pop POC sedimentation $$mmol\,m^{-2}\,s^{-1}$$ - -
    Parameter Name Description Units Parameter Type Default Typical Range Comment
    poc_initial initial POC conc $$mmol\,m^{-3}$$ float 100 - -
    doc_initial initial DOC conc $$mmol\,m^{-3}$$ float 100 - -
    pon_initial initial PON conc $$mmol\,m^{-3}$$ float 16 - -
    don_initial initial DON conc $$mmol\,m^{-3}$$ float 16 - -
    pop_initial initial POP conc $$mmol\,m^{-3}$$ float 1 - -
    dop_initial initial DOP conc $$mmol\,m^{-3}$$ float 1 - -
    docr_initial initial DOCR conc $$mmol\,m^{-3}$$ float - Only required if simRPools == .true.
    donr_initial initial DONR conc $$mmol\,m^{-3}$$ float - Only required if simRPools == .true.
    dopr_initial initial DOPR conc $$mmol\,m^{-3}$$ float - Only required if simRPools == .true.
    cpom_initial initial CPOM conc $$mmol\,m^{-3}$$ float - Only required if simRPools == .true.
    Rpoc_hydrol Maximum rate of decomposition of POC at 20C $$day^{-1}$$ float 5e-01 0.01-0.08 -
    Rdoc_minerl Maximum rate of aerobic mineralisation of labile DOC at 20C $$day^{-1}$$ float 5e-01 0.01-0.08 -
    Rpon_hydrol Maximum rate of decomposition of PON at 20C $$day^{-1}$$ float 5e-01 0.01-0.08 -
    Rdon_minerl Maximum rate of aerobic mineralisation of labile DON at 20C $$day^{-1}$$ float 5e-01 0.01-0.08 -
    Rpop_hydrol Maximum rate of decomposition of POP at 20C $$day^{-1}$$ float 5e-01 0.01-0.08 -
    Rdop_minerl Maximum rate of aerobic mineralisation of labile DOP at 20C $$day^{-1}$$ float 5e-01 0.01-0.08 -
    theta_hydrol temperature multiplier for temperature dependence of particulate decomposition rate - float 1e+00 1e+00 -
    theta_minerl temperature multiplier for temperature dependence of mineralisationrate - float 1e+00 1e+00 -
    Kpom_hydrol half saturation constant for oxygen dependence on particulate decomposition rate $$mmol O2\,m^{-3}$$ float 3e+01 47-78 -
    Kdom_minerl half saturation constant for oxygen dependence on aerobic mineralisation rate $$mmol O2\,m^{-3}$$ float 3e+01 47-78 -
    doc_miner_reactant_variable state variable to be linked to rate of DOC mineralisation - string - - -
    doc_miner_product_variable state variable to be product of DOC mineralisation - string - - -
    don_miner_product_variable state variable to be product of DON mineralisation - string - - -
    dop_miner_product_variable state variable to be product of DOP mineralisation - string - - -
    simRPools switch to enable refractory organic matter pools - boolean .false. - -
    Rdocr_miner Maximum rate of aerobic mineralisation of labile DOCR at 20C $$day^{-1}$$ float 1e-02 - -
    Rdonr_miner Maximum rate of aerobic mineralisation of labile DONR at 20C $$day^{-1}$$ float 1e-02 - -
    Rdopr_miner Maximum rate of aerobic mineralisation of labile DOPR at 20C $$day^{-1}$$ float 1e-02 - -
    Rcpom_bdown Maximum rate of CPOM breakdown at 20C $$day^{-1}$$ float 1e-02 - -
    X_cpom_n C:N stoichiometry of CPOM - float  106:16 - -
    X_cpom_p C:P stoichiometry of CPOM - float 106:1 - -
    KeDOM light extinction coefficient due to DOM contribution - float 1e-04 - -
    KePOM light extinction coefficient due to POM contribution - float 1e-04 - -
    KeDOMR light extinction coefficient due to DOMR contribution - float 1e-04 - -
    KeCPOM light extinction coefficient due to CPOM contribution - float 1e-04 10% per year -
    simphotolysis switch to enable light related organic matter processes - boolean .false. - -
    photo_c quantum yield coefficient - float 8e-01 - -
    settling option of settling velocity calculation method - integer - -
    w_pom settling rate of POM $$m\,day^{-1}$$ float - -
    d_pom diameter of POM m float - -
    rho_pom POM density $$kg\,m^{-3}$$ float - -
    w_cpom settling rate of POM $$m\,day^{-1}$$ float - -
    d_cpom diameter of POM m float - -
    rho_cpom POM density $$kg\,m^{-3}$$ float - -
    resuspension switch to enable sediment resuspension calculation - integer - -
    resus_link resuspension-linked variable - string - - -
    sedimentOMfrac Organic matter fraction in sediment - float 5e-01 - -
    Xsc C fraction in sediment OM - float 5e-01 - -
    Xsn N fraction in sediment OM - float 5e-02 - -
    Xsp P fraction in sediment OM - float 5e-03 - -
    Fsed_doc sediment DOC flux $$mmol\,m^{-2}\,day^{-1}$$ float - -
    Fsed_don sediment DON flux $$mmol\,m^{-2}\,day^{-1}$$ float - -
    Fsed_dop sediment DOP flux $$mmol\,m^{-2}\,day^{-1}$$ float - -
    Ksed_dom sediment DOM flux $$mmol\,m^{-2}\,day^{-1}$$ float - -
    theta_sed_dom temperature multiplier for temperature dependence of sediment DOM decomposition rate - float 1e+00 - -
    extra_diag switch to store net sediment fluxes as diagnostic variables .false. boolean - -

    An example nml block for the organic matter module is shown below:

    &aed2_organic_matter !-- Initial concentrations for OM variables (mmol/m3) poc_initial = 78.5 doc_initial = 39.9 pon_initial = 8.3 don_initial = 1.3 pop_initial = 8.3 dop_initial = 1.5 docr_initial = 350.00 donr_initial = 13.0 dopr_initial = 3.0 cpom_initial = 100.00 !-- Breakdown and mineralisation (basic pool) Rpoc_hydrol = 0.05 Rdoc_minerl = 0.001 Rpon_hydrol = 0.05 Rdon_minerl = 0.005 Rpop_hydrol = 0.05 Rdop_minerl = 0.001 theta_hydrol = 1.08 theta_minerl = 1.08 Kpom_hydrol = 31.25 Kdom_minerl = 31.25 doc_miner_reactant_variable='OXY_oxy' doc_miner_product_variable='' don_miner_product_variable='NIT_amm' dop_miner_product_variable='PHS_frp' !-- Refractory organic matter (optional) simRPools = .false. Rdocr_miner = 0.0001 Rdonr_miner = 0.0001 Rdopr_miner = 0.0001 Rcpom_bdown = 0.0001 X_cpom_n = 0.0005 X_cpom_p = 0.0001 !-- Light related parameters KeDOM = 0.000005 KePOM = 0.00096 KeDOMR = 0.10000 ! = 1 (assuming KeDOMR is applied to CDOM in /m) KeCPOM = 0.00096 ! = 0.08 (/m)/(mg/L) /83.3 (mmol/m3)/(mg/L) simphotolysis = .false. !.true. !photo_fmin photo_c = 0.75 !-- Particle settling parameters settling = 3 w_pom = -0.06 d_pom = 2e-6 rho_pom = 1.12e3 w_cpom = -0.01 d_cpom = 1e-5 rho_cpom = 1.3e3 !-- Sediment interaction parameters (basic model) resuspension = 1 resus_link = 'TRC_resus' sedimentOMfrac = 0.5 Xsc = 0.5 Xsn = 0.05 Xsp = 0.005 Fsed_doc = 2.0 Fsed_don = 1.0 Fsed_dop = 0.020 !Fsed_doc_variable, !Fsed_dop_variable, !Fsed_don_variable, Ksed_dom = 4.5 theta_sed_dom = 1.08 !-- Other options extra_diag = .false. !.true. !poc_min, poc_max, doc_min, doc_max !pon_min, pon_max, don_min, don_max !pop_min, pop_max, dop_min, dop_max /



    Examples

    Example: Simulated vs. measured DON concentration at site of RIV and RON of Swan River.


    Publications & References

    Paraska, D.W., Hipsey, M.R., and Salmon, S.U. 2014. Sediment diagenesis models: review of approaches, challenges and opportunities. Environmental Modelling and Software 61, 297-325.

    Zhang, W., et al, 2009. Evaluation of two Langmuir models for phosphorus sorption of phosphorus-enriched soils in New York for environmental applications. Soil Science 174, 523-530.

    Froelich, P.N. 1988. Kinetic control of dissolved phosphate in natural rivers and estuaries: a primer on the phosphate buffer mechanism. Limnology and Oceanography 33, 649-668.

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