3.3 Simulation Class: Organics
3.3.1 Overview
The intent of this simulation class is that it provide a relatively advanced water quality modelling tool. There are many applications for this class. For example it might be used to examine detailed reservoir phytoplankton dynamics or the response of an estuary to both inorganic and organic pollutant loading.
This simulation class includes the oxygen, silicate, inorganic nitrogen, inorganic phosphorus, organic matter, phytoplankton and (optionally) pathogen model classes.
Figure 3.13: Simulation Class: Organics (as an estuarine example)
3.3.2 Model Class: Oxygen
This constituent model class is the same as that described in Section 3.1.2
3.3.3 Model Class: Silicate
This constituent model class is the same as that described in Section 3.2.3
3.3.4 Model Class: Inorganic nitrogen
This constituent model class is the same as that described in Section 3.2.4
3.3.5 Model Class: Inorganic phosphorus
This constituent model class is the same as that described in Section 3.2.5
3.3.6 Model Class: Organic matter
The following constituent models are available to select from within the organic matter model class. The differentiator between constituent models is the exclusion or inclusion of refractory organic matter.
3.3.6.1 Constituent Model: Labile
This organic matter constituent model considers only labile particulate and dissolved organic matter. The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.14 and Table 3.13. Both the Figure and Table (and Table 3.14) make reference to dissolved inorganic carbon (DIC). This is for completeness only because the WQ Module does not currently support simulation of DIC. Doing so is not required in order to deploy either the labile or refractory organic matter constituent model within the WQ Module.
Figure 3.14: Constituent model: Labile
| Computed Variables | Units | Processes | Interacting Quantities |
|---|---|---|---|
| Labile Particulate Organic Carbon | mg C/L or mmol C/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Settling model | ||
| Labile Particulate Organic Nitrogen | mg N/L or mmol N/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Settling model | ||
| Labile Particulate Organic Phosphorus | mg P/L or mmol P/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Settling model | ||
| Labile Dissolved Organic Carbon | mg C/L or mmol C/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Sediment properties |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) POC |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
||
| Labile Dissolved Organic Nitrogen | mg N/L or mmol N/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Sediment properties |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) PON |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
||
| Labile Dissolved Organic Phosphorus | mg P/L or mmol P/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Sediment properties |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) POP |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
The four processes that govern (labile) organic matter behaviour in this constituent model are:
- Sediment flux
- Hydrolysis (the conversion of particulate organics to dissolved organics)
- Mineralisation (the conversion of dissolved organics to inorganics), and
- Settling, of only particulate organics
A range of rate constants can be specified to control these processes, or the defaults used. By design, the library default rates are set to zero so as to render all processes initially inactive. Specification of non-zero rates activates these processes.
Simulation of labile organic dynamics in the organics simulation class directly modifies the concentrations of other computed variables. These are listed in Table 3.14.
| Computed Variables | Units | Processes | Interacting Quantities |
|---|---|---|---|
| Dissolved Oxygen | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) DOP |
| Nitrate | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate \(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) DOP |
| Ammonium | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate \(\cdot\quad\) DON |
| FRP | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate \(\cdot\quad\) DOP |
| DIC | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate \(\cdot\quad\) DOC |
3.3.6.2 Constituent Model: Refractory
This organic matter constituent model considers both labile and refractory particulate and dissolved organic matter. The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.15 and Table 3.15. Both the Figure and Table (and Table 3.16) make reference to dissolved inorganic carbon (DIC). This is for completeness only because the WQ Module does not currently support simulation of DIC. Doing so is not required in order to deploy either the labile or refractory organic matter constituent model within the WQ Module.
Figure 3.15: Constituent model: Refractory
| Computed Variables | Units | Processes | Interacting Quantities |
|---|---|---|---|
| Labile Particulate Organic Carbon | mg C/L or mmol C/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Settling model | ||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) RPOM |
||
| Labile Particulate Organic Nitrogen | mg N/L or mmol N/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Settling model | ||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) RPOM |
||
| Labile Particulate Organic Phosphorus | mg P/L or mmol P/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Settling model | ||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) RPOM |
||
| Labile Dissolved Organic Carbon | mg C/L or mmol C/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Sediment properties |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) POC |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) RDOC |
||
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) RDOC |
||
| Labile Dissolved Organic Nitrogen | mg N/L or mmol N/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Sediment properties |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) PON |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) RDON |
||
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) RDON |
||
| Labile Dissolved Organic Phosphorus | mg P/L or mmol P/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Sediment properties |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) POP |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) RDOP |
||
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) RDOP |
||
| Refractory Particulate Organic Carbon | mg C/L or mmol C/m\(^3\) |
|
\(\cdot\quad\) Settling model |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
||
| Refractory Dissolved Organic Carbon | mg C/L or mmol C/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) RDOC |
||
| Refractory Dissolved Organic Nitrogen | mg N/L or mmol N/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) RDOC \(\cdot\quad\) RDON |
||
| Refractory Dissolved Organic Phosphorus | mg N/L or mmol N/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) DOC \(\cdot\quad\) RDOC \(\cdot\quad\) RDOP |
The processes that govern (labile and refractory) organic matter behaviour in this constituent model are:
- Sediment flux
- Hydrolysis (the conversion of particulate organics to dissolved organics)
- Mineralisation (the conversion of dissolved organics to inorganics)
- Breakdown (the conversion of refractory particulate organic matter to labile particulate organic matter)
- Photolysis (the conversion of refractory dissolved organic matter to labile dissolved organic matter and corresponding inorganics)
- Activation (the conversion of refractory dissolved to labile dissolved organic matter)
- Settling, of only particulate organics
A range of rate constants can be specified to control these processes, or the defaults used. By design, the library default rates are set to zero so as to render all processes initially inactive. Specification of non-zero rates activates these processes.
Simulation of labile and refractory organic dynamics in the organics simulation class directly modifies the concentrations of other computed variables. These are listed in Table 3.16.
| Computed Variables | Units | Processes | Interacting Quantities |
|---|---|---|---|
| Dissolved Oxygen | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen |
| Nitrate | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
| Ammonium | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) RDON |
||
| FRP | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) RDOP |
||
| DIC |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Nitrate |
|
|
|
\(\cdot\quad\) Radiation \(\cdot\quad\) RDOC |
3.3.7 Model Class: Phytoplankton
This constituent model class is the same as that described in Section 3.2.6, except that in the current constituent model class, phytoplanktonic losses are to labile organic computed variables rather than inorganic nutrients. These processes and interactions are described below.
3.3.7.1 Constituent Model: Basic
As per Section 3.2.6.1, this phytoplankton constituent model assumes that the ratios of both internal nitrogen and phosphorus concentrations to internal chlorophyll a (or carbon) concentration are fixed. These internal nutrients are not simulated explicitly, but increase and decrease proportionately with increasing and decreasing carbonaceous biomass, according to the specified (or default) nitrogen-chlorophyll a and phosphorus-chlorophyll a (or their carbon equivalents) ratios. Carbonaceous biomass is simulated dynamically and is the measure of phytoplankton concentration. Internal nutrient concentrations are not required to be specified as initial or boundary conditions, and are not treated as computed variables.
The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.16 and Table 3.17. Silicate interactions only apply if phytoplankton is set to uptake silicate via specification of silicate limitation function parameters (section 4.7.3.5.1). The configuration for phytoplankton simulation presented below applies only to the organics simulation class. A different, and simpler, configuration applies when phytoplankton is simulated using this basic constituent model in the inorganics simulation class. That simplified configuration is described in section 3.2.6.1.
Figure 3.16: Constituent model: Basic
| Computed Variables | Units | Processes | Interacting Quantities |
|---|---|---|---|
| Phytoplankton | \(\mu\)g Chl a/L or mmol C/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Ammonium \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Silicate (if activated) |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Dissolved oxygen |
||
|
|
\(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) DOP \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) POC \(\cdot\quad\) PON \(\cdot\quad\) POP \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) Settling model \(\cdot\quad\) Cell density |
The three processes that govern phytoplankton behaviour are:
- Primary productivity (the photosynthetic conversion of light and carbon to stored energy and oxygen, also referred to as growth)
- Respiration (the expenditure of stored energy and oxygen), and
- Settling
A range of light, temperature, salinity, nitrogen, phosphorus and silicate limitation functions can be parameterised and applied in various combinations to the first two processes above, and a range of settling models are available to tailor the third. By design, the associated library default rates are set to zero so as to render all processes initially inactive. Specification of non-zero rates activates these processes.
The distinguishing property of this phytoplankton constituent model is that internal (phytoplankton cell) nutrient concentrations are considered to be fixed proportions of cell chlorophyll a (or carbon) concentrations. They are therefore not treated as computed variables, but rather as multiples of phytoplankton chlorophyll a (or carbon) (which is treated as a computed variable). The key implication of this is the method of calculation of the nitrogen and phosphorus uptake and limitation functions applied to primary productivity. These calculations depend only on ambient (i.e. external to a phytoplankton cell) water column nitrogen and phosphorus concentrations.
Simulation of phytoplankton dynamics in the organics simulation class directly modifies the concentrations of a range of other computed variables. These are listed in Table 3.18. Silicate interactions only apply if phytoplankton is set to uptake silicate.
| Computed Variables | Units | Processes | Interacting Quantities |
|---|---|---|---|
| Dissolved Oxygen | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Ammonium \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Silicate (if activated) |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light |
||
| Ammonium | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Silicate (if activated) |
| Nitrate | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Ammonium \(\cdot\quad\) FRP \(\cdot\quad\) Silicate (if activated) |
| FRP | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Nitrate \(\cdot\quad\) Ammonium \(\cdot\quad\) Silicate (if activated) |
| Silicate (if activated) | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Nitrate \(\cdot\quad\) Ammonium \(\cdot\quad\) FRP |
|
|
\(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) DOP |
||
|
|
\(\cdot\quad\) POC \(\cdot\quad\) PON \(\cdot\quad\) POP |
||
| Labile Particulate Organic Carbon | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) PON \(\cdot\quad\) POP \(\cdot\quad\) Silicate (if activated) |
| Labile Particulate Organic Nitrogen | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) POC \(\cdot\quad\) POP \(\cdot\quad\) Silicate (if activated) |
| Labile Particulate Organic Phosphorus | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) POC \(\cdot\quad\) PON \(\cdot\quad\) Silicate (if activated) |
| Labile Dissolved Organic Carbon | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) DON \(\cdot\quad\) DOP \(\cdot\quad\) Silicate (if activated) |
| Labile Dissolved Organic Nitrogen | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) DOC \(\cdot\quad\) DOP \(\cdot\quad\) Silicate (if activated) |
| Labile Dissolved Organic Phosphorus | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) Silicate (if activated) |
3.3.7.2 Constituent Model: Advanced
As per Section 3.2.6.2, this phytoplankton constituent model directly simulates internal (phytoplankton cell) nitrogen and phosphorus concentrations. These are allowed to vary between upper and lower limits, expressed as ratios to chlorophyll a (or carbon) concentrations. Internal nutrient concentrations (not as ratios) are required to be specified as initial and boundary conditions, and are treated as computed variables.
The constituent model code and associated variables, processes and potentially interacting simulated quantities are provided in Figure 3.17 and Table 3.19. Silicate interactions only apply if phytoplankton is set to uptake silicate. The configuration for phytoplankton simulation presented below applies only to the organics simulation class. A different, and simplified, configuration applies when phytoplankton is simulated using this advanced constituent model in the inorganics simulation class. That configuration is described in section 3.2.6.2.
Figure 3.17: Constituent model: Advanced
| Computed Variables | Units | Processes | Interacting Quantities |
|---|---|---|---|
| Phytoplankton | \(\mu\)g Chl a/L or mmol C/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Ammonium \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus |
||
|
|
\(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) DOP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) POC \(\cdot\quad\) PON \(\cdot\quad\) POP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) Settling model \(\cdot\quad\) Cell density \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus |
||
| Internal Nitrogen | mg N/L or mmol N/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Ammonium \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Ammonium \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Internal phosphorus |
||
|
|
\(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) DOP \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) POC \(\cdot\quad\) PON \(\cdot\quad\) POP \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) Settling model \(\cdot\quad\) Cell density \(\cdot\quad\) Internal phosphorus |
||
| Internal Phosphorus | mg P/L or mmol P/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Ammonium \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Silicate (if activated) |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Ammonium \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Dissolved oxygen \(\cdot\quad\) Internal nitrogen |
||
|
|
\(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) DOP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) POC \(\cdot\quad\) PON \(\cdot\quad\) POP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Silicate (if activated) |
||
|
|
\(\cdot\quad\) Settling model \(\cdot\quad\) Cell density \(\cdot\quad\) Internal nitrogen |
The three processes that govern phytoplankton behaviour are:
- Primary productivity (the photosynthetic conversion of light and carbon to stored energy and oxygen, also referred to as growth)
- Respiration (the expenditure of stored energy and oxygen), and
- Settling
A range of light, temperature, salinity, nitrogen, phosphorus and silicate limitation functions can be parameterised and applied in various combinations to the first two processes above, and a range of settling models are available to tailor the third. By design, the associated library default rates are set to zero so as to render all processes initially inactive. Specification of non-zero rates activates these processes.
The distinguishing property of this phytoplankton constituent model is that internal (phytoplankton cell) nutrient concentrations are simulated directly. They are therefore treated as computed variables. The key implication of this is the method of calculation of the nitrogen and phosphorus uptake and limitation functions applied to primary productivity. These calculations depend on both internal nutrient stores and ambient (i.e. external to a phytoplankton cell) water column nitrogen and phosphorus concentrations.
Simulation of phytoplankton dynamics in the organics simulation class directly modifies the concentrations of a range of other computed variables. These are listed in Table 3.20. Silicate interactions only apply if phytoplankton is set to uptake silicate.
| Computed Variables | Units | Processes | Interacting Quantities |
|---|---|---|---|
| Dissolved Oxygen | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Ammonium \(\cdot\quad\) Nitrate \(\cdot\quad\) FRP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
|
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light |
||
| Ammonium | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Nitrate \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) FRP \(\cdot\quad\) Silicate (if activated) |
| Nitrate | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Ammonium \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) FRP \(\cdot\quad\) Silicate (if activated) |
| FRP | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Nitrate \(\cdot\quad\) Ammonium \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
| Silicate (if activated) | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) Water temperature \(\cdot\quad\) Salinity \(\cdot\quad\) Light \(\cdot\quad\) Nitrate \(\cdot\quad\) Ammonium \(\cdot\quad\) FRP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus |
|
|
\(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) DOP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus |
||
|
|
\(\cdot\quad\) POC \(\cdot\quad\) PON \(\cdot\quad\) POP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus |
||
| Labile Particulate Organic Carbon | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) PON \(\cdot\quad\) POP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
| Labile Particulate Organic Nitrogen | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) POC \(\cdot\quad\) POP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
| Labile Particulate Organic Phosphorus | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) POC \(\cdot\quad\) PON \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
| Labile Dissolved Organic Carbon | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) DON \(\cdot\quad\) DOP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
| Labile Dissolved Organic Nitrogen | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) DOC \(\cdot\quad\) DOP \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
| Labile Dissolved Organic Phosphorus | mg/L or mmol/m\(^3\) |
|
\(\cdot\quad\) DOC \(\cdot\quad\) DON \(\cdot\quad\) Internal nitrogen \(\cdot\quad\) Internal phosphorus \(\cdot\quad\) Silicate (if activated) |
3.3.8 Model Class: Pathogens (optional)
This model class is the same as that described in Section 3.1.3.
3.3.9 Computed variables
The relationships between all available computed variables and processes is this simulation class are presented in Figure 3.18. Depending on the constituent model classes deployed, not all of the computed variables and processes shown in the figure will necessarily be active. All network link labels have been removed (other than denoting the relevant phytoplankton model), and optional non-interacting model classes (e.g. pathogens) omitted, for clarity.
Figure 3.18: Simulation class: Organics
