9 Organic Matter

9.1 Contributors

Matthew R. Hipsey

9.2 Overview

Both the inorganic and organic, and dissolved and particulate forms of C, N and P are modelled in AED along the general degradation pathway of POM to DOM to dissolved inorganic matter (DIM). The OGM module simulates the organic material as a single or as multiple discrete pools. The inorganic carbon, nitrogen and phosphorus pools are reported in separate modules which are linked to from OGM.

It is well established that both autochthonous and allochthonous sources of OM have important consequences for water quality. Reactivity of OM is known to be linked with origin, varying potentially orders of magnitude, and often including a single OM pool could be a significant over-simplification. Harvey and Mannio (2001) analysed samples from several points in a US estuary according to an uncharacterisable fraction and a few major molecular classes (carbohydrates, proteins, lipids, lignins and hydrocarbons), and identified significant changes along the estuarine gradient.

Within the particulate pool, similarly there is a relatively labile POM fraction based on internal generation, and inputs from urban drains, in addition to a more refractory coarse POM pool (CPOM) that originates mainly form the forested headwaters and regions with significant intact riparian vegetation.

9.3 Model Description

A 10-pool organic matter model able to capture the variable reactivity of the OM pool and its stoichiometry is configureable within this module. 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 reservoirs, 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.


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.

Figure 9.1: 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.


The main dissolved organic matter pool balance equations are simulated as:

\[\begin{eqnarray} \frac{D}{Dt}DOC = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& \overbrace{(1-k_{ref})\:f_{hyd}^{POC}-f_{min}^{DOC}+\hat{f}_{sed}^{DOC} }^\text{aed_organic_matter} \\ \tag{9.1} &+& \color{brown}{ f_{exr}^{PHY} + f_{exr}^{ZOO} + \hat{f}_{rsp}^{MAG} + \hat{f}_{rsp}^{BIV}} \\ \nonumber \end{eqnarray}\] \[\begin{eqnarray} \frac{D}{Dt}DON = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& f_{hyd}^{PON}-f_{min}^{DON}+\hat{f}_{sed}^{DON}\\ \tag{9.2} &+& \color{brown}{ f_{exr}^{PHY} + f_{exr}^{ZOO} + \hat{f}_{rsp}^{MAG} + \hat{f}_{rsp}^{BIV}} \\ \nonumber \end{eqnarray}\] \[\begin{eqnarray} \frac{D}{Dt}DOP = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& f_{hyd}^{POP}-f_{min}^{DOP}+\hat{f}_{sed}^{DOP}\\ \tag{9.3} &+& \color{brown}{ f_{exr}^{PHY} + f_{exr}^{ZOO} + \hat{f}_{rsp}^{MAG} + \hat{f}_{rsp}^{BIV}} \\ \nonumber \end{eqnarray}\]

where \(\mathbb{M}\) and \(\mathcal{S}\) refer to water mixing and boundary source terms, respectively, and the coloured \(\color{brown}{f}\) terms reflect DOM related fluxes computed by other (optionally) linked modules such as modules of phytoplankton (\(\mathrm{PHY}\)) or zooplankton (\(\mathrm{ZOO}\)).

The main particulate organic matter pools are simulated as:

\[\begin{eqnarray} \frac{D}{Dt}POC = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& \overbrace{f_{set}^{POC}-f_{hyd}^{DOC}+\hat{f}_{res}^{POC} }^\text{aed_organic_matter} \\ \tag{9.4} &+& \color{brown}{ f_{mor}^{PHY} + f_{egs}^{ZOO} + f_{msf}^{ZOO} + \hat{f}_{mor}^{MAG} + \hat{f}_{msf}^{BIV}} \\ \nonumber \end{eqnarray}\] \[\begin{eqnarray} \frac{D}{Dt}PON = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& f_{set}^{PON}-f_{hyd}^{DON}+\hat{f}_{res}^{PON}\\ \tag{9.5} &+& \color{brown}{ f_{exr}^{PHY} + f_{exr}^{ZOO} + \hat{f}_{rsp}^{MAG} + \hat{f}_{rsp}^{BIV}} \\ \nonumber \end{eqnarray}\] \[\begin{eqnarray} \frac{D}{Dt}POP = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& f_{set}^{POP}-f_{hyd}^{DOP}+\hat{f}_{res}^{POP}\\ \tag{9.6} &+& \color{brown}{ f_{exr}^{PHY} + f_{exr}^{ZOO} + \hat{f}_{rsp}^{MAG} + \hat{f}_{rsp}^{BIV}} \\ \nonumber \end{eqnarray}\]

The OGM module optionally allows and extra 4 pools to specifically resolve the refractory (less reactive) organic matter material. In general we refer to the refractory DOM pool as \(DOM{\text -}R\), which is broken into elemental pools, plus the \(C{\text -}POM\) variables simulating coarse POM:

\[\begin{eqnarray} \frac{D}{Dt}DOC{\text -}R = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& \overbrace{k_{ref}\:f_{hyd}^{POC}-R^{DOMR}_{pm} +\hat{f}_{sed}^{DOCR} }^\text{aed_organic_matter} \\ \tag{9.7} &+& \color{brown}{ f_{exr}^{PHY} + f_{exr}^{ZOO} + \hat{f}_{rsp}^{MAG} + \hat{f}_{rsp}^{BIV}} \\ \nonumber \end{eqnarray}\] \[\begin{eqnarray} \frac{D}{Dt}DON{\text -}R = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& f_{hyd}^{PON}-f_{min}^{DON}+\hat{f}_{sed}^{DON}\\ \tag{9.8} &+& \color{brown}{ f_{exr}^{PHY} + f_{exr}^{ZOO} + \hat{f}_{rsp}^{MAG} + \hat{f}_{rsp}^{BIV}} \\ \nonumber \end{eqnarray}\] \[\begin{eqnarray} \frac{D}{Dt}DOP{\text -}R = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& f_{hyd}^{POP}-f_{min}^{DOP}+\hat{f}_{sed}^{DOP}\\ \tag{9.9} &+& \color{brown}{ f_{exr}^{PHY} + f_{exr}^{ZOO} + \hat{f}_{rsp}^{MAG} + \hat{f}_{rsp}^{BIV}} \\ \nonumber \end{eqnarray}\] \[\begin{eqnarray} \frac{D}{Dt}C{\text -}POM = \color{darkgray}{ \mathbb{M} + \mathcal{S} } \quad &+& f_{set}^{CPOM}-f_{bdn}^{CPOM}+\hat{f}_{res}^{CPOM} \\ \tag{9.10} &+& \color{brown}{ \check{f}_{lfl}^{VEG}} \\ \nonumber \end{eqnarray}\]

The details of how each flux relevant to POC and DOC is calculated, and the associated parameter settings, are described in the next sections.

9.3.1 Process Descriptions

9.3.1.1 Hydrolysis

9.3.1.2 Mineralisation

9.3.1.3 Photolysis

Ultraviolet light is known to drive photochemical breakdown of chromophoric \(DOM\), conceptually equivalent to the \(DOM{\text -}R\) pool in Figure X. This photolysis process can take shape either as photo-transformation of complex \(DOM{\text -}R\) molecules to more bioavailable molecules (ie., DOM in Figure X), or as photo-mineralisation, 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.

The rate of photolysis can be computed based on the apparent quantum yield, ø¿, which varies with wavelength, the scalar photon flux density, ¡¿, and the adsorption coefficient, α¿, by integrating across the active wavelength spectrum, √415 v ́ √49?. This can be approximated for b discrete bandwidths (e.g. UV-A, UV-B, PAR) to simplify the calculation as:

\[\begin{equation} R^{DOMR}_{pm} = \int_{\lambda_{min}}^{\lambda_{max}} \phi_{\lambda} \hat{I}_{\lambda} \alpha_{\lambda} d\lambda \: \approx \: \sum_{b=1}^3 \bar{\phi}_b \hat{I}_b \alpha_b \end{equation}\]

where \(\hat{I}_b\) is the mean bandwidth intensity (mol photons m-2 s-1) computed from the light intensity at any given depth, I, ø» is the mean bandwidth quantum yield, and \(\alpha_b\) is the mean absorbance across the window of the specific bandwidth being computed. The latter two can be approximated by substituting into the following (Vähätalo et al. 2000; Vähätalo and Zepp, 2005): \(\phi_{\lambda}=c10^{-d \lambda }\) and \(\alpha_{\lambda} = \alpha_x exp(-S[x-\lambda])\).

9.3.1.4 CPOM breakdown

Internally generated inputs of POM also include from the shedding of seagrass leaves (this happens en-mass usually associated with winds/storms) and also decomposition of macroalgae or other . These latter terms are not presently included but reserved for future development efforts.

9.3.1.5 Sediment exchange

9.3.1.6 Settling

9.3.1.7 Resuspension

9.3.3 Feedbacks to the Host Model

The organic matter can feedback conditions to the hydrodynamic model by modifying the light extinction coefficient. For each dissolved and particulate attribute a specific attenuation coefficient, \(K_e\), is required.

This total light extinction computed by the OGM model is:

\[\begin{equation} K_{d_{om}} = K_{e_{doc}} DOC + K_{e_{poc}} POC + K_{e_{cdom}}CDOM + K_{e_{cpom}}CPOM (\#eq:om_light_extc) \end{equation}\]

9.3.4 Variable Summary

The default variables created by this module, and the optionally required linked variables needed for full functionality of this module are summarised in Table 9.1. The diagnostic outputs able to be output are summarised in Table 9.2.

State variables

Table 9.1: Organic Matter - state variables
AED name Symbol Description Unit Type Typical Range Comments
aed_organic_matter
OGM_doc \[\mathbf{DOC}\] dissolved organic carbon concentration \[\small{mmol\: C/m^3}\] pelagic 0 - 5000
OGM_poc \[\mathbf{POC}\] particulate organic carbon concentration \[\small{mmol\: C/m^3}\] pelagic NA
OGM_don \[\mathbf{DON}\] dissolved organic nitrogen concentration \[\small{mmol\: N/m^3}\] pelagic NA
OGM_pon \[\mathbf{PON}\] particulate organic nitrogen concentration \[\small{mmol\: N/m^3}\] pelagic NA
OGM_dop \[\mathbf{DOP}\] dissolved organic phosphorus concentration \[\small{mmol\: P/m^3}\] pelagic NA
OGM_pop \[\mathbf{POP}\] particulate organic phosphorus concentration \[\small{mmol\: P/m^3}\] pelagic NA
OGM_docr \[\mathbf{DOC_R}\] dissolved organic carbon (refractory) concentration \[\small{mmol\: C/m^3}\] pelagic NA DOC_R activated by setting simRpools=T
OGM_donr \[\mathbf{DON_R}\] dissolved organic nitrogen (refractory) concentration \[\small{mmol\: N/m^3}\] pelagic 0 - 200 DON_R activated by setting simRpools=T
OGM_dopr \[\mathbf{DOP_R}\] dissolved organic phosphorus (refractory) concentration \[\small{mmol\: P/m^3}\] pelagic 7 - 9 DOP_R activated by setting simRpools=T
OGM_cpom \[\mathbf{CPOM}\] coarse particulate organic matter \[\small{mmol\: C/m^3}\] pelagic 0 - 500 CPOM activated by setting simRpools=T
Dependent variables
CAR_dic \[\mathbf{DIC}\] dissolved inorganic carbon concentration \[\small{mmol\: C/m^3}\] pelagic NA optionally linked
NIT_amm \[\mathbf{NH_4}\] dissolved ammonium concentration \[\small{mmol\: N/m^3}\] pelagic NA optionally linked
PHS_frp \[\mathbf{PO_4}\] dissolved phosphate concentration \[\small{mmol\: P/m^3}\] pelagic NA optionally linked
OXY_oxy \[\mathbf{O_2}\] dissolved oxygen concentration \[\small{mmol\: O_2/m^3}\] pelagic 0 - 500 optional for sediment and mineralisation reactions, via dom_miner_oxy_reactant_var
NIT_nit \[\mathbf{NO_3}\] dissolved nitrate concentration \[\small{mmol\: N/m^3}\] pelagic NA optional for advanced mineralisation reactions, via dom_miner_nit_reactant_var
NIT_no2 \[\mathbf{NO_2}\] dissolved nitrite concentration \[\small{mmol\: N/m^3}\] pelagic NA optional for advanced mineralisation reactions, via dom_miner_no2_reactant_var
NIT_n2o \[\mathbf{N_2O}\] dissolved nitrous oxide concentration \[\small{mmol\: N/m^3}\] pelagic NA optional for advanced mineralisation reactions, via dom_miner_n2o_reactant_var
GEO_fe3 \[\mathbf{FeIII}\] dissolved ferrous iron concentration \[\small{mmol\: Fe/m^3}\] pelagic NA optional for advanced mineralisation reactions, via dom_miner_fe3_reactant_var
GEO_so4 \[\mathbf{SO_4}\] dissolved sulfate concentration \[\small{mmol\: S/m^3}\] pelagic NA optional for advanced mineralisation reactions, via dom_miner_so4_reactant_var
CAR_ch4 \[\mathbf{CH_4}\] dissolved methane concentration \[\small{mmol\: C/m^3}\] pelagic NA optional for advanced mineralisation reactions, via dom_miner_ch4_reactant_var
SDF_Fsed_doc \[\mathbf{F}_{sed}^{doc}\] dissolved sediment \(DOC\) flux \[\small{mmol\: C/m^2/s}\] benthic 0 - 300 required for sediment zones; internally used as /s
SDF_Fsed_don \[\mathbf{F}_{sed}^{don}\] dissolved sediment \(DON\) flux \[\small{mmol\: C/m^2/s}\] benthic 0 - 300 required for sediment zones; internally used as /s
SDF_Fsed_dop \[\mathbf{F}_{sed}^{dop}\] dissolved sediment \(DOP\) flux \[\small{mmol\: C/m^2/s}\] benthic 0 - 300 required for sediment zones; internally used as /s
NCS_resus NA sediment resuspension rate \[\small{g/m^2/s}\] benthic 0 - 10 required for POM resuspension, set via resus_link

Diagnostics

Table 9.2: Organic Matter - diagnostic variables
AED name Symbol Description Unit Type Typical Range Comments
diag_level = 0+
OGM_CDOM \[\mathbf{CDOM}\] chromophoric dissolved organic matter \[\small{/m}\] pelagic NA
OGM_BOD5 \[\mathbf{BOD5}\] biochemical oxygen demand estimate \[\small{mg\:O_2/L}\] pelagic NA
diag_level = 1+
OGM_sed_toc NA sediment total organic carbon \[\small{mmol\: C/m^2}\] sediment NA
OGM_sed_ton NA sediment total organic nitrogen \[\small{mmol\: N/m^2}\] sediment NA
OGM_sed_top NA sediment total organic phosphorus \[\small{mmol\: P/m^2}\] sediment NA
diag_level = 2+
OGM_poc_hydrol \[\mathbf{f}_{hydrl}^{POC}\] computed \(POC\) hydrolysis/breakdown rate \[\small{mmol\: C/m^3/d}\] pelagic NA
OGM_pon_hydrol \[\mathbf{f}_{hydrl}^{PON}\] computed \(PON\) hydrolysis/breakdown rate \[\small{mmol\: N/m^3/d}\] pelagic NA
OGM_pop_hydrol \[\mathbf{f}_{hydrl}^{POP}\] computed \(POP\) hydrolysis/breakdown rate \[\small{mmol\: P/m^3/d}\] pelagic NA
OGM_doc_miner \[\mathbf{f}_{miner}^{DOC}\] computed \(DOC\) mineralisation rate \[\small{mmol\: C/m^3/d}\] pelagic NA
OGM_don_miner \[\mathbf{f}_{miner}^{DON}\] computed \(DON\) mineralisation rate \[\small{mmol\: N/m^3/d}\] pelagic NA
OGM_dop_miner \[\mathbf{f}_{miner}^{DOP}\] computed \(DOP\) mineralisation rate \[\small{mmol\: P/m^3/d}\] pelagic NA
OGM_docr_miner \[\mathbf{f}_{miner}^{DOC_R}\] computed \(DOC_R\) mineralisation rate \[\small{mmol\: C/m^3/d}\] pelagic NA
OGM_donr_miner \[\mathbf{f}_{miner}^{DON_R}\] computed \(DON_R\) mineralisation rate \[\small{mmol\: N/m^3/d}\] pelagic NA
OGM_dopr_miner \[\mathbf{f}_{miner}^{DOP_R}\] computed \(DOP_R\) mineralisation rate \[\small{mmol\: P/m^3/d}\] pelagic NA
OGM_anaerobic \[\mathbf{f}_{anaerobic}^{doc}\] rate of \(DOC\) anaerobic mineralisation \[\small{mmol\: C/m^3/d}\] pelagic NA
OGM_denit \[\mathbf{f}_{denit}^{no3}\] computed mineralisation rate due to denitrification \[\small{mmol\: C/m^3/d}\] pelagic NA
OGM_photolysis \[\mathbf{f}_{photo}^{doc}\] computed mineralisation rate due to photolysis \[\small{mmol\: C/m^3/d}\] pelagic NA requires simPhotolysis=T
OGM_pom_vvel \[\mathbf{\omega}_{pom}\] \(POM\) settling velocity \[\small{m/d}\] pelagic NA
OGM_cpom_vvel \[\mathbf{\omega}_{cpom}\] \(CPOM\) settling velocity \[\small{m/d}\] pelagic NA
OGM_Psed_poc \[\mathbf{\mathcal{F}}_{set}^{poc}\] \(POC\) sedimentation areal flux \[\small{mmol\: C/m^2/s}\] pelagic NA
OGM_Psed_pon \[\mathbf{\mathcal{F}}_{set}^{pon}\] \(PON\) sedimentation areal flux \[\small{mmol\: C/m^2/s}\] pelagic NA
OGM_Psed_pop \[\mathbf{\mathcal{F}}_{set}^{pop}\] \(POP\) sedimentation areal flux \[\small{mmol\: C/m^2/s}\] pelagic NA
OGM_Psed_cpom \[\mathbf{\mathcal{F}}_{set}^{cpom}\] \(CPOM\) sedimentation areal flux \[\small{mmol\: C/m^2/s}\] pelagic NA
OGM_swi_poc \[\mathbf{\mathcal{F}}_{resus}^{doc}\] \(POC\) resuspension flux \[\small{mmol\: C/m^2/d}\] benthic NA
OGM_swi_doc \[\mathbf{\mathcal{F}}_{dsf}^{doc}\] \(DOC\) exchange across sediment-water interface \[\small{mmol\: C/m^2/d}\] benthic NA
OGM_swi_pon \[\mathbf{\hat{f}}_{resus}^{pon}\] \(PON\) resuspension flux \[\small{mmol\: C/m^2/d}\] benthic NA
OGM_swi_don \[\mathbf{\mathcal{F}}_{dsf}^{don}\] \(DON\) exchange across sediment-water interface \[\small{mmol\: N/m^2/d}\] benthic NA
OGM_swi_pop \[\mathbf{\hat{f}}_{resus}^{pon}\] \(POP\) resuspension flux \[\small{mmol\: C/m^2/d}\] benthic NA
OGM_swi_dop \[\mathbf{\mathcal{F}}_{dsf}^{dop}\] \(DOP\) exchange across sediment-water interface \[\small{mmol\: P/m^2/d}\] benthic NA


9.3.5 Parameter Summary

The parameters and settings used by this module are summarised in Table 9.3.

Table 9.3: Organic Matter module parameters and configuration options
AED name Symbol Description Unit Type Typical Range Comments
Initialisation
poc_initial \[POC|_{t=0}\] initial \(POC\) concentration \[\small{mmol\: C/m^3}\] float 0-1000 can be overwritten by initial condition files
doc_initial \[DOC|_{t=0}\] initial \(DOC\) concentration \[\small{mmol\: C/m^3}\] float 0-1000 can be overwritten by initial condition files
pon_initial \[PON|_{t=0}\] initial \(PON\) concentration \[\small{mmol\: N/m^3}\] float 0-100 can be overwritten by initial condition files
don_initial \[DON|_{t=0}\] initial \(DON\) concentration \[\small{mmol\: N/m^3}\] float 0-100 can be overwritten by initial condition files
pop_initial \[POP|_{t=0}\] initial \(POP\) concentration \[\small{mmol\: P/m^3}\] float 0-10 can be overwritten by initial condition files
dop_initial \[DOP|_{t=0}\] initial \(DOP\) concentration \[\small{mmol\: P/m^3}\] float 0-10 can be overwritten by initial condition files
cpom_initial \[CPOM|_{t=0}\] initial \(CPOM\) concentration \[\small{mmol\: C/m^3}\] float 0-1000 can be overwritten by initial condition files
Breakdown and mineralisation
Rpoc_hydrol \[R_{hydrl}^{POC}\] reference \(POC\) hydrolysis/breakdown rate @ \(20^{\circ}C\) \[\small{/d}\] float NA
Rpon_hydrol \[R_{hydrl}^{PON}\] reference \(PON\) hydrolysis/breakdown rate @ \(20^{\circ}C\) \[\small{/d}\] float NA
Rpop_hydrol \[R_{hydrl}^{POP}\] reference \(POP\) hydrolysis/breakdown rate @ \(20^{\circ}C\) \[\small{/d}\] float NA
theta_hydrol \[\theta_{hydrl}\] Arrhenius temperature scaling coefficient for \(POC\) hydrolysis \[\small{-}\] float 1 - 1.2
Kpom_hydrol \[K_{hydrl}^{oxy}\] half-saturation \(O_2\) conc. for \(POM\) hydrolysis \[\small{mmol\: O_2/m^3}\] float NA
Rdom_minerl \[R_{minerl}^{DOM}\] reference \(DOM\) mineralisation rate @ \(20^{\circ}C\) \[\small{/d}\] float NA
theta_minerl \[\theta_{minerl}\] Arrhenius temperature scaling coefficient for \(DOM\) mineralisation \[\small{-}\] float NA
Kdom_minerl \[K_{minerl}^{oxy}\] half-saturation \(O_2\) conc. for \(DOM\) mineralisation \[\small{mmol\: O_2/m^3}\] float NA
simDenitrification \[\Theta_{nit}^{denit}\] option to select denitrification sub-model \[\small{-}\] integer 0 , 1
f_an \[f_{an}\] mineralisation scaling fraction under anaerobic conditions \[\small{-}\] float 0 - 1
K_nit \[K_{denit}^{nit}\] half-saturation \(NO_3\) conc. for denitrification \[\small{mmol\: N/m^3}\] float NA
dom_miner_oxy_reactant_var \[O_2\] state variable used to control aerobic mineralisation \[\small{-}\] string OXY_oxy optional link for oxygen consumption during mineralisation
dom_miner_nit_reactant_var \[NO_3\] state variable used to control nitrate reduction \[\small{-}\] string NIT_nit optional link for nitrate consumption during mineralisation
dom_miner_no2_reactant_var \[NO_2\] state variable used to control nitrite reduction \[\small{-}\] string NIT_no2 optional link for nitrite consumption during mineralisation
dom_miner_n2o_reactant_var \[N_2O\] state variable used to control n2o reduction \[\small{-}\] string NIT_n2o optional link for nitrous oxide consumption during mineralisation
dom_miner_fe3_reactant_var \[FeIII\] state variable used to control iron reduction \[\small{-}\] string GEO_feiii optional link for ferrous iron consumption during mineralisation
dom_miner_so4_reactant_var \[SO_4\] state variable used to control sulfate reduction \[\small{-}\] string GEO_so4 optional link for sulfate consumption during mineralisation
dom_miner_ch4_reactant_var \[CH_4\] state variable to receive methane \[\small{-}\] string CAR_ch4 optional link for methane production
doc_miner_product_variable \[DIC\] state variable to receive \(DIC\) \[\small{-}\] string CAR_dic optional link for dic production
don_miner_product_variable \[NH_4\] state variable to receive \(NH_4\) \[\small{-}\] string NIT_amm optional link for ammonium production
dop_miner_product_variable \[PO_4\] state variable to receive \(PO_4\) \[\small{-}\] string PHS_frp optional link for phosphate production
Refractory organic matter
simRPools \[\Theta_{om}^{refrac}\] option to include refractory \(OM\) pools, incl. \(DOM_R\) and \(CPOM\) \[\small{-}\] boolean T or F
Rdomr_minerl \[R_{minerl}^{DOM_R}\] reference \(DOM_R\) mineralisation rate @ \(20^{\circ}C\) \[\small{/d}\] float NA
Rcpom_bdown \[R_{bdown}^{CPOM}\] reference \(CPOM\) hydrolysis/breakdown rate @ \(20^{\circ}C\) \[\small{/d}\] float NA
X_cpom_n \[\chi_{C:N}^{cpom}\] \(CPOM\) nitrogen stoichiometry \[\small{mmol\:N/mmol\:C}\] float NA
X_cpom_p \[\chi_{C:P}^{cpom}\] \(CPOM\) phosphorus stoichiometry \[\small{mmol\:P/mmol\:C}\] float NA
Light related parameters
KeDOM \[K_e^{DOM}\] specific light attenuation coefficient for \(DOM\) \[\small{/m/(mmol\:C/m^3)}\] float NA
KePOM \[K_e^{POM}\] specific light attenuation coefficient for \(POM\) \[\small{/m/(mmol\:C/m^3)}\] float 0 - 1
KeDOMR \[K_e^{DOM_R}\] specific light attenuation coefficient for \(DOM_R\) \[\small{/m/(mmol\:C/m^3)}\] float 0.1 - 10
KeCPOM \[K_e^{CPOM}\] specific light attenuation coefficient for \(CPOM\) \[\small{/m/(mmol\:C/m^3)}\] float 1 - 1.1
simPhotolysis \[\Theta_{om}^{photo}\] option to include photo-mineralisation of \(DOM_R\) \[\small{-}\] boolean T or F
photo_c \[c_{photo}\] photolysis constant NA float 7.5
Particle settling parameters
settling \[\Theta_{set}^{pom}\] option to set the method of settling for \(POM\) and \(CPOM\) \[\small{-}\] integer 0, 1, 2, 3
w_pom \[\omega_{pom}\] sedimentation velocity of \(POM\) detrital particles \[\small{m/d}\] float NA used if \(\Theta_{set}^{pom}\) is 1 or 2
d_pom \[d_{pom}\] diameter of \(POM\) detrital particles \[\small{m}\] float NA used if \(\Theta_{set}^{pom}\) is 3
rho_pom \[\rho_{pom}\] density of \(POM\) detrital particles \[\small{kg/m^3}\] float NA used if \(\Theta_{set}^{pom}\) is 3
w_cpom \[\omega_{cpom}\] sedimentation velocity of \(CPOM\) particles \[\small{m/d}\] float NA used if \(\Theta_{set}^{pom}\) is 1 or 2
d_cpom \[d_{cpom}\] diameter of \(CPOM\) detrital particles \[\small{m}\] float NA used if \(\Theta_{set}^{pom}\) is 3
rho_cpom \[\rho_{cpom}\] density of \(CPOM\) detrital particles \[\small{kg/m^3}\] float NA used if \(\Theta_{set}^{pom}\) is 3
Resuspension
resuspension \[\Theta_{resus}^{pom}\] option to set the method of resuspension for \(POM\) and \(CPOM\) \[\small{-}\] integer 0 , 1
resus_link \[-\] diagnostic variable to link to for resuspension rate \[\small{-}\] string NCS_resus
sedimentOMfrac \[c_{om}\] fraction by weight of surficial sediment organic matter \[\small{g\:OM/g\:sediment}\] float NA
Xsc \[\chi_{OM:C}^{sed}\] stoichiometry of sedment particulate carbon \[\small{mmol\:C/g\:OM}\] float NA
Xsn \[\chi_{OM:N}^{sed}\] stoichiometry of sedment particulate nitrogen \[\small{mmol\:N/g\:OM}\] float NA
Xsp \[\chi_{OM:P}^{sed}\] stoichiometry of sedment particulate phosphorus \[\small{mmol\:P/g\:OM}\] float NA
Sediment exchange
Fsed_doc \[F_{sed}^{doc}\] reference sediment \(DOC\) flux at \(20^{\circ}C\) \[\small{mmol\: C/m^2/d}\] float 0 - 1
Fsed_don \[F_{sed}^{don}\] reference sediment \(DON\) flux at \(20^{\circ}C\) \[\small{mmol\: N/m^2/d}\] float NA
Fsed_dop \[F_{sed}^{dop}\] reference sediment \(DON\) flux at \(20^{\circ}C\) \[\small{mmol\: P/m^2/d}\] float NA
Ksed_dom \[K_{sed-dom}^{oxy}\] half-saturation oxygen conc. controlling \(DOM\) sediment flux \[\small{mmol\: O_2/m^3}\] float 20 - 100
theta_sed_dom \[\theta_{sed}^{dom}\] Arrhenius temperature multiplier for sediment \(DOM\) flux \[\small{-}\] float 1 - 1.1
Fsed_doc_variable \[\mathbf{F}_{sed}^{doc}\] variable name to link to for spatially resolved sediment zones \[\small{mmol\: C/m^2/d}\] string SDF_Fsed_doc
Fsed_don_variable \[\mathbf{F}_{sed}^{don}\] variable name to link to for spatially resolved sediment zones \[\small{mmol\: N/m^2/d}\] string SDF_Fsed_don
Fsed_dop_variable \[\mathbf{F}_{sed}^{dop}\] variable name to link to for spatially resolved sediment zones \[\small{mmol\: P/m^2/d}\] string SDF_Fsed_dop

9.4 Setup & Configuration

An example aed.nml parameter specification block for the aed_organic_matter module is shown below:

&aed_organic_matter
   !-- Initial concentrations for OM variables (mmol/m3)
     poc_initial        =  15
     doc_initial        =  15
     pon_initial        =   2
     don_initial        =   1.1
     pop_initial        =   0.1
     dop_initial        =   0.01
     docr_initial       = 150.0
     donr_initial       =   9
     dopr_initial       =   0.15
     cpom_initial       =   0
   !-- Breakdown and mineralisation (basic pool)
     Rdom_minerl        =   0.01348416
     Rpoc_hydrol        =   0.001
     Rpon_hydrol        =   0.001
     Rpop_hydrol        =   0.0001
     theta_hydrol       =   1.07
     theta_minerl       =   1.07
     Kpom_hydrol        =  33.66593
     Kdom_minerl        =  22.36079
     simDenitrification =   1
     dom_miner_oxy_reactant_var = 'OXY_oxy'
     doc_miner_product_variable = 'CAR_dic'
     don_miner_product_variable = 'NIT_amm'
     dop_miner_product_variable = 'PHS_frp'
     dom_miner_nit_reactant_var = 'NIT_nit'
     f_an               =   0.50
     K_nit              =  10.0
   !-- Refractory organic matter (optional)
     simRPools          = .true.
     Rdomr_minerl       =   0.001
   !-- Coarse particulate organic matter (optional)
     Rcpom_bdown        =   0.005
     X_cpom_n           =   0.005
     X_cpom_p           =   0.001
    !-- Light related parameters
     KeDOM              =   0.03
     KePOM              =   0.096
     KeDOMR             =   0.15
     KeCPOM             =   0.00096
     simphotolysis      = .false.
     photo_c            =   0.75
    !-- Particle settling parameters
     settling           =   1
     w_pom              =  -0.01
     d_pom              =   1e-5
     rho_pom            =   1.2e3
     w_cpom             =  -0.01
     d_cpom             =   1e-5
     rho_cpom           =   1.4e3
    !-- Sediment interaction parameters (basic model)
     resuspension       =   1
     resus_link         =  'NCS_resus'
     sedimentOMfrac     =   0.0002
     Xsc                =   0.5
     Xsn                =   0.05
     Xsp                =   0.005
     Fsed_doc           =   1.4
     Fsed_don           =   0.0
     Fsed_dop           =   0.0
     Ksed_dom           =  93.0
     theta_sed_dom      =   1.06
    !Fsed_doc_variable  = 'SDF_Fsed_doc'
    !Fsed_don_variable  = 'SDF_Fsed_don'
    !Fsed_dop_variable  = 'SDF_Fsed_dop'
     diag_level         =  10
/

Note that when users link Fsed_doc_variable then Fsed_doc is not required as this parameter will be set for each sediment zone from values input via the aed_sedflux module. The numbers reported here are for example purposes and should be reviewed before use based on the users chosen site context. The entries are optional and will be set to defaults if the user does not provide a specific value.