## Science Modules / Macrophyte

We approach the model by including a core state variable HALO, that is made up of above ground (AG) and below ground (BG); the former referring to the leaves, and the latter the cumulative mass of rhizomes and roots.

#### aed2_macrophyte : Mass balance and functions related to the macrophyte model

The equation for seagrass biomass in a given cell is computed as shown in the below table, assuming photosynthesis, excretion, mortality and excretion. Nutrient uptake is not included in the simulation in SCERM v1 since Hillman et al. (1995) highlight that light, salinity and temperature were the dominant drivers, with some minor correlation with phosphate levels, however the stoichiometry is known and may be included in future iterations. The effective coverage area (i.e. Leaf Area Index, HALOLAI of the meadow) can be computed based on the scaling expression in Baird et al. (2016); although this is not directly used in the photosynthesis calculation, it is useful output for comparing with field data.

Growth is calculated in response to light, but also sensitive to salinity and temperature:

Photosynthesis-irradiance relationships for Halophila have been estimated by Ralph and Burchett (1995) who found photo-inhibition occurring at modest light intensities. The Steele (1962) equation is therefore suggested as the most appropriate. Light extinction can also occur over the meadow depth, although for Halophila this is assumed to be relatively small due to the small leaf structure. The salinity effect on photosynthesis has been reported by Ralph (1998b) and Hillman et al. (1995).

Respiration, excretion and mortality are also commonly simulated with typical first-order rate coefficients for each:

The seagrass-sediment-light (SSL) feedback has been identified as a potentially important driver determining meadow persistence (Adams et al., 2016), as depicted schematically for a numerical model in Figure 8. This requires the connection between sediment resuspension and seagrass presence to be made, however, the complete feedback loop has rarely been reported in aquatic models to date. The model implemented for SCERM focuses on Halophila and accounts for the feedback by including ability to simulate the link between: a) above ground biomass (l“DYÀE) and shear stress, b) below ground biomass (l“DYFE), and c) the amount of resuspension and light.

To simulate the SSL feedback, drag is increased in proportion with the above ground biomass:

where $$C_d$$ is the base drag coefficient for a numerical cell based on its sediment material properties, and the above ground fraction is a user definable constant fraction of total biomass. The default value of $$C_{D_{bottom}}$$is stored in the hydrodynamic driver model and influences the local momentum budget; therefore the 2nd term of the RHS is passed to the host model calling AED2. The critical shear stress for resuspension is also increased based on the below ground biomass:

where $$\tau_0$$ is critical shear stress for resuspension, computed based on a minimum value (reflecting bare sediment), and linear coefficient linked to biomass. As HI increases, the concentration of SS in the local domain will reduce, thereby improving the overall light climate. Note that in the model, presence or absence of HALO in a given cell can be configured be reading in an appropriate distribution map.

#### Variable Summary & Setup Options

Variable Name Description Units Variable Type Core/Optional
MAC_{Group} macrophyte group $$mmol C\,m^{-2}$$ - core
Variable Name Description Units Variable Type Core/Optional
MAC_PAR benthic light intensity $$W\,m^{-2}$$ - -
MAC_GPP benthic plant productivity $$\,d^{-1}$$ - -
MAC_P2R macrophyte p:r ratio - - -
MAC_MAC total macrophyte biomass $$mmol C\,m^{-2}$$ - -
MAC_LAI macrophyte leaf area density $$m^{2}\,m^{-2}$$ - -
MAC_MAC_ag total above ground macrophyte biomass $$mmol C\,m^{-2}$$ - -
MAC_bg total below ground macrophyte biomass $$mmol C\,m^{-2}$$ - -
Parameter Name Description Units Parameter Type Default Typical Range Comment
num_mphy number of macrophyte groups - integer 0-5 -
the_mphy list of ID's of groups in aed_phyto_pars.nml (len=num_phyto) - integer 1 - 5 -
n_zones total number of active material zones - integer - - -
active_zones Active material Zone ID's - array - - -
dbase link to mphy database - string - - -
simStaticBiomass switch to enable static biomass simulation - boolean .false. - -
simMacFeedback switch to enable macrophyte feedback simulation - boolean .false. - -
m_name name of macrphyte group - string - - -
m0 minimum above ground density of macrophyte $$mmol C\,m^{-2}$$ float 2e-01 - -
R_growth maximum growth rate at 20C $$mmol C\,m^{-2}\,day^{-1}$$ float 2 - -
fT_Method specific temperature limitation function of growth - integer 0-1 -
theta_growth Arrenhius temperature scaling for growth function - float 1e+00 - -
T_std standard temperature deg C float 20 - -
T_opt optimum temperature deg C float 20 - -
T_max maximum temperature deg C float 20 - -
lightModel type of light response function - integer 0-1 -
I_K half saturation constant for light limitation of growth $$microE\,m^{-2}\,s^{-1}$$ float 180 - -
I_S saturation light intensity used if lightModel=1 $$microE\,m^{-2}\,s^{-1}$$ float 100 - -
KeMAC specific attenuation coefficient - float 4e-03 - -
f_pr fraction of primary production lost to exudation - float 3e-02 - -
R_resp respiration loss rate at 20C $$mmol C\,m^{-2}\,day^{-1}$$ float 2e-02 - -
theta_resp Arrhenius temperature scaling factor for respiration - float 1e+00 - -
salTol type of salinity limitation function - float - -
S_bep salinity limitation value at miximum falinity s_maxsp - float 1 - -
S_maxsp maximum salinity - float 36 - -
S_opt optimal salinity - float 1 - -
K_CD constant relating macrophyte density to drag coefficient $$mmol C\,m^{-3}\,day^{-1}$$ float - -
f_bg fraction of primary production apportioned to below-ground biomass $$mmol C\,m^{-3}\,day^{-1}$$ float - -
k_omega Omega constant relating plant density to effective area of coverage $$W\,m^{-2}$$ float - -
Xcc internal C:chla ratio of the plant leaves - float 50 - -
K_N half saturation concentration of nitrogen - float 2e+00 - -
X_ncon constant internal nitrogen concentration - float 2e-01 - -
K_P half saturation concentration of phosphorus - float 3e-01 - -
X_pcon constant internal phosphorus concentration $$kg\,m^{-3}$$ float 9e-03 - -

An example nml block for the macrophyte module is shown below. NOTE: Users must supply a valid "aed2_macrophyte_pars.nml" file.

&aed2_macrophyte num_mphy = 1 the_mphy = 3 n_zones = 4 active_zones = 2,3,4,5 simStaticBiomass = .true. simMacFeedback = .false. dbase = '../External/AED2/aed2_macrophyte_pars.nml' /

#### Examples

Under construction

#### Publications & References

To be completed ...