Soil model configuration#

The Soil model configuration is used to provide:

Trait data on the microbial groups required for the soil model. The soil model requires a defined set of these groups, currently: saprotrophic_fungi, ectomycorrhiza, arbuscular_mycorrhiza, bacteria.

These are currently configured directly in the TOML file using the soil.microbial_group_definition configuration option but this may move to loading from a CSV file using the soil.microbial_group_definition_path setting.
Enzyme kinetics data for the enzymes produced by the taxonomic groups. Data is required for each pair of the higher taxonomic groups of microbes (fungi or bacteria) and the enzyme substrates targeted in the model (particulate organic matter or mineral associated organic matter): (‘fungi’, ‘pom’), (‘bacteria’, ‘maom’), (‘bacteria’, ‘pom’), (‘fungi’, ‘maom’)

These are currently configured directly in the TOML file using the soil.enzyme_class_definition configuration option but this may move to loading from a CSV file using the soil.enzyme_class_definition_path setting.
A set of soil model constants using the soil.constants configuration.

Soil microbial groups#

The soil microbial groups are defined as a set of traits associated with each of the required groups.

[soil.microbial_group_definition]
name = "bacteria"
taxonomic_group = "bacteria"
max_uptake_rate_labile_C = 0.04
activation_energy_uptake_rate = 47000.0
half_sat_labile_C_uptake = 0.364
activation_energy_uptake_saturation = 30000.0
max_uptake_rate_ammonium = 0.005
half_sat_ammonium_uptake = 0.02275
max_uptake_rate_nitrate = 0.0005
half_sat_nitrate_uptake = 0.02275
max_uptake_rate_labile_p = 0.0025
half_sat_labile_p_uptake = 0.02275
turnover_rate = 0.005
activation_energy_turnover = 20000.0
reference_temperature = 12.0
c_n_ratio = 5.2
c_p_ratio = 16.0
reproductive_allocation = 0.0
symbiote_nitrogen_uptake_fraction = 0.0
symbiote_phosphorus_uptake_fraction = 0.0

[soil.microbial_group_definition.enzyme_production]
pom = 0.005
maom = 0.005

soil.microbial_group_definition.name: The name of the microbial group functional type. Default = bacteria
soil.microbial_group_definition.taxonomic_group: The high level taxonomic group that the microbial group belongs to. Default = bacteria
soil.microbial_group_definition.max_uptake_rate_labile_C: Maximum rate at the reference temperature of labile carbon uptake [day^-1]. Default = 0.04
soil.microbial_group_definition.activation_energy_uptake_rate: Activation energy for nutrient uptake [J Kelvin^-1]. Default = 47000
soil.microbial_group_definition.half_sat_labile_C_uptake: Half saturation constant for uptake of labile carbon (LMWC) [kg{C} m^-3]. Default = 0.364
soil.microbial_group_definition.activation_energy_uptake_saturation: Activation energy for nutrient uptake saturation constants [J Kelvin^-1]. Default = 30000
soil.microbial_group_definition.max_uptake_rate_ammonium: Maximum possible rate for ammonium uptake [day^-1]. Default = 0.005
soil.microbial_group_definition.half_sat_ammonium_uptake: Half saturation constant for uptake of ammonium [kg{N} m^-3]. Default = 0.02275
soil.microbial_group_definition.max_uptake_rate_nitrate: Maximum possible rate for nitrate uptake [day^-1]. Default = 0.0005
soil.microbial_group_definition.half_sat_nitrate_uptake: Half saturation constant for uptake of nitrate [kg{N} m^-3]. Default = 0.02275
soil.microbial_group_definition.max_uptake_rate_labile_p: Maximum possible rate for labile inorganic phosphorus uptake [day^-1]. Default = 0.0025
soil.microbial_group_definition.half_sat_labile_p_uptake: Half saturation constant for uptake of labile inorganic phosphorus [kg{P} m^-3]. Default = 0.02275
soil.microbial_group_definition.turnover_rate: Microbial maintenance turnover rate at reference temperature [day^-1]. Default = 0.005
soil.microbial_group_definition.activation_energy_turnover: Activation energy for microbial maintenance turnover rate [J Kelvin^-1]. Default = 20000
soil.microbial_group_definition.reference_temperature: The temperature that turnover and uptake rates were measured at [Celsius]. Default = 12.0
soil.microbial_group_definition.c_n_ratio: Ratio of carbon to nitrogen in biomass [unitless]. Default = 5.2
soil.microbial_group_definition.c_p_ratio: Ratio of carbon to phosphorus in biomass [unitless]. Default = 16
soil.microbial_group_definition.enzyme_production: Details of the enzymes produced by the microbial group. The keys are the substrates for which enzymes are produced, and the values are the allocation to enzyme production. This allocation is expressed as a fraction of the (gross) cellular biomass growth. Default = {‘pom’: 0.005, ‘maom’: 0.005}
soil.microbial_group_definition.reproductive_allocation: Reproductive allocation as fraction of (gross) cellular biomass growth [unitless] Only fungi generate separate reproductive bodies, so this value must be set to zero for bacterial functional groups. Providing a non-zero value for a bacterial functional group will prevent the soil model from configuring. Default = 0.0
soil.microbial_group_definition.symbiote_nitrogen_uptake_fraction: Fraction of nitrogen uptake that is supplied to symbiotic (plant) partners. [unitless]. This should only have a non-zero value for mycorrhizal fungi. Default = 0.0
soil.microbial_group_definition.symbiote_phosphorus_uptake_fraction: Fraction of nitrogen uptake that is supplied to symbiotic (plant) partners. [unitless]. This should only have a non-zero value for mycorrhizal fungi. Default = 0.0

Soil enzyme classes#

The soil enzyme classes are defined as a set of traits associated with each pair of higher taxon and substrate

[soil.enzyme_class_definition]
source = "bacteria"
substrate = "pom"
maximum_rate = 60.0
half_saturation_constant = 70.0
activation_energy_rate = 37000.0
activation_energy_saturation = 30000.0
reference_temperature = 12.0
turnover_rate = 0.024
c_n_ratio = 5.2
c_p_ratio = 16.0

soil.enzyme_class_definition.source: The higher microbial group which produces the enzyme. Default = bacteria
soil.enzyme_class_definition.substrate: The substrate which the enzyme acts upon. Default = pom
soil.enzyme_class_definition.maximum_rate: The maximum rate of the enzyme at the reference temperature [day^-1]. Default = 60.0
soil.enzyme_class_definition.half_saturation_constant: The half saturation constant for the enzyme at the reference temperature. Units of [kg{C} m^-3]. Default = 70.0
soil.enzyme_class_definition.activation_energy_rate: Activation energy for enzyme rate with temperature [J Kelvin^-1]. Default = 37000
soil.enzyme_class_definition.activation_energy_saturation: Activation energy for enzyme saturation with temperature [J Kelvin^-1]. Default = 30000
soil.enzyme_class_definition.reference_temperature: The temperature that enzyme rate and saturation were measured at [Celsius]. Default = 12.0
soil.enzyme_class_definition.turnover_rate: The turnover rate of the enzyme [day^-1]. Default = 0.024
soil.enzyme_class_definition.c_n_ratio: Ratio of carbon to nitrogen for the enzyme [unitless]. Default = 5.2
soil.enzyme_class_definition.c_p_ratio: Ratio of carbon to phosphorus for the enzyme [unitless]. Default = 16

Soil constants#

[soil.constants]
reference_cue_logit = 0.094
cue_reference_temp = 20.0
logit_cue_with_temperature = -0.039
soil_microbe_water_potential_optimum = -3.0
soil_microbe_water_potential_halt = -15800.0
microbial_water_response_curvature = 1.47
min_pH_microbes = 2.5
lowest_optimal_pH_microbes = 4.5
highest_optimal_pH_microbes = 7.5
max_pH_microbes = 11.0
base_soil_protection = 0.694
soil_protection_with_clay = 1.36
solubility_coefficient_lmwc = 0.05
solubility_coefficient_ammonium = 0.05
solubility_coefficient_nitrate = 1.0
solubility_coefficient_labile_p = 0.005
necromass_decay_rate = 0.23104906018664842
maom_desorption_rate = 1e-05
lmwc_sorption_rate = 0.001
necromass_sorption_rate = 0.6931471805599453
litter_leaching_fraction_carbon = 0.0015
litter_leaching_fraction_nitrogen = 0.0015
litter_leaching_fraction_phosphorus = 0.0001
organic_proportion_litter_nitrogen_leaching = 1.0
organic_proportion_litter_phosphorus_leaching = 1.0
ammonium_mineralisation_proportion = 0.9
tectonic_uplift_rate_phosphorus = 0.0
ammonia_volatilisation_rate_constant = 8.64e-05
nitrification_rate_constant = 0.08639999999999999
denitrification_rate_constant = 0.21600000000000003
nitrification_optimum_temperature = 311.15
nitrification_maximum_temperature = 343.15
nitrification_thermal_sensitivity = 12
denitrification_infinite_temperature_factor = 93.34598
denitrification_minimum_temperature = 227.12999999999997
denitrification_thermal_sensitivity = 308.56
nitrogen_fixation_cost_zero_celcius = 59.19651970522086
nitrogen_fixation_cost_infinite_temp_offset = -0.8034802947791453
nitrogen_fixation_cost_thermal_sensitivity = 0.27
nitrogen_fixation_cost_equality_temperature = 50.28
free_living_N_fixation_reference_rate = 4.106776180698152e-06
free_living_N_fixation_reference_temp = 293.15
free_living_N_fixation_q10_coefficent = 3.0
primary_phosphorus_breakdown_rate = 2.2831050228310502e-07
secondary_phosphorus_breakdown_rate = 7.407407407407407e-05
labile_phosphorus_sorption_rate = 0.0016666666666666668
ammonium_deposition_rate = 4.1067761806981517e-07
phosphorus_deposition_rate = 1.3689253935660508e-08
nitrogen_fixer_supply_fraction = 0.3
ectomycorrhiza_supply_fraction = 0.25

soil.constants.reference_cue_logit: Logit of carbon use efficiency of microbial community at reference temperature [unitless]. Parameter estimated from a beta-logit GLMM using the data from Qiao et al. (2019). Default = 0.094
soil.constants.cue_reference_temp: Reference temperature for carbon use efficiency [Celsius]. Default value taken from Qiao et al. (2019). Default = 20.0
soil.constants.logit_cue_with_temperature: Change in the logit of carbon use efficiency with unit increase in temperature [Celsius^-1]. Parameter estimated from a beta-logit GLMM using the data from Qiao et al. (2019). Default = -0.039
soil.constants.soil_microbe_water_potential_optimum: The water potential at which soil microbial rates are maximised [kPa]. Value is taken from Moyano et al. (2013). Default = -3.0
soil.constants.soil_microbe_water_potential_halt: The water potential at which soil microbial activity stops entirely [kPa]. Value is taken from Moyano et al. (2013). Default = -15800.0
soil.constants.microbial_water_response_curvature: Curvature of function for response of soil microbial rates to water potential [unitless]. Value is taken from Moyano et al. (2013). Default = 1.47
soil.constants.min_pH_microbes: Soil pH below which microbial activity is completely inhibited [unitless]. This value cannot be larger than SoilConstants.lowest_optimal_pH_microbes. The default value was obtained by averaging the fungi and bacteria specific values given in Orwin et al. (2011). Default = 2.5
soil.constants.lowest_optimal_pH_microbes: Soil pH above which microbial activity is not inhibited at all [unitless]. This value cannot be smaller than SoilConstants.min_pH_microbes or larger than SoilConstants.highest_optimal_pH_microbes. The default value was obtained by averaging the fungi and bacteria specific values given in Orwin et al. (2011). Default = 4.5
soil.constants.highest_optimal_pH_microbes: Soil pH below which microbial activity is not inhibited at all [unitless]. This value cannot be smaller than SoilConstants.lowest_optimal_pH_microbes or larger than SoilConstants.max_pH_microbes. The default value was obtained by averaging the fungi and bacteria specific values given in Orwin et al. (2011). Default = 7.5
soil.constants.max_pH_microbes: Soil pH above which microbial activity is completely inhibited [unitless]. This value cannot be smaller than SoilConstants.highest_optimal_pH_microbes. The default value was obtained by averaging the fungi and bacteria specific values given in Orwin et al. (2011). Default = 11.0
soil.constants.base_soil_protection: Basal change in saturation constants due to soil structure [unitless]. This value is multiplicative and is taken from Fatichi et al. (2019). Default = 0.694
soil.constants.soil_protection_with_clay: Rate at which soil protection of carbon increases with clay content [unitless]. This protection contributes multiplicatively to the effective saturation constant. The value of this constant is taken from Fatichi et al. (2019). Default = 1.36
soil.constants.solubility_coefficient_lmwc: Solubility coefficient for low molecular weight organic carbon [unitless]. Value taken from Fatichi et al. (2019), where it is estimated in quite a loose manner. Default = 0.05
soil.constants.solubility_coefficient_ammonium: Solubility coefficient for ammonium in soil [unitless]. Value taken from Fatichi et al. (2019), where it is estimated in quite a loose manner. Default = 0.05
soil.constants.solubility_coefficient_nitrate: Solubility coefficient for nitrate in soil [unitless]. Value taken from Fatichi et al. (2019), where it is estimated in quite a loose manner. Default = 1.0
soil.constants.solubility_coefficient_labile_p: Solubility coefficient for labile inorganic phosphorus [unitless]. Value taken from Fatichi et al. (2019), where it is estimated in quite a loose manner. Default = 0.005
soil.constants.necromass_decay_rate: Rate at which microbial necromass decays to low molecular weight carbon [day^-1]. I have not been able to track down any data on this, so for now choosing a rate that corresponds to halving every three days. This parameter is a key target for tracking down data for and for sensitivity analysis. Default = 0.23104906018664842
soil.constants.maom_desorption_rate: Rate constant for mineral associated organic matter desorption [day^-1]. The default value of this rate is not based on data. It was instead chosen to be small relative to the rate at which microbes breakdown LMWC. This is another key target for sensitivity analysis. Default = 1e-05
soil.constants.lmwc_sorption_rate: Rate constant for low molecular weight carbon sorption to minerals [day^-1]. The default value of this rate is not based on data. It was instead chosen so that the ratio of :term:LMWC to :term:MAOM would tend to 1/100, in the absence of microbes. This is another key target for sensitivity analysis. Default = 0.001
soil.constants.necromass_sorption_rate: Rate constant for necromass sorption to minerals [day^-1]. The default value was chosen to be three times the value of SoilConstants.necromass_decay_rate, this means that 75% of necromass becomes MAOM with the remainder becoming LMWC. Replacing this with a function that depends on environmental conditions is a post release goal. Default = 0.6931471805599453
soil.constants.litter_leaching_fraction_carbon: Fraction of carbon mineralisation from litter that occurs by leaching [unitless]. The remainder of the mineralisation consists of particulates. Value is an order of magnitude estimate taken from Fatichi et al. (2019). Default = 0.0015
soil.constants.litter_leaching_fraction_nitrogen: Fraction of nitrogen mineralisation from litter that occurs by leaching. [unitless]. The remainder of the mineralisation consists of particulates. Value is an order of magnitude estimate taken from Fatichi et al. (2019). Default = 0.0015
soil.constants.litter_leaching_fraction_phosphorus: Fraction of phosphorus mineralisation from litter that occurs by leaching. [unitless]. The remainder of the mineralisation consists of particulates. Value is an order of magnitude estimate taken from Fatichi et al. (2019). Default = 0.0001
soil.constants.organic_proportion_litter_nitrogen_leaching: Fraction of leached nitrogen from litter mineralisation that is organic form. [unitless]. The remainder of the leaching consists of ammonium. Value is taken from Fatichi et al. (2019), where it is assumed that nitrogen leaches from litter solely in organic form. Default = 1.0
soil.constants.organic_proportion_litter_phosphorus_leaching: Fraction of leached phosphorus from litter mineralisation that is organic form. [unitless]. The remainder of the leaching consists of inorganic phosphorus. Value is taken from Fatichi et al. (2019), where it is assumed that phosphorus leaches from litter solely in organic form. Default = 1.0
soil.constants.ammonium_mineralisation_proportion: Proportion of microbially mineralised nitrogen that takes the form of ammonium. [unitless]. The remainder gets mineralised as nitrate. Estimate taken from Fatichi et al. (2019), but the way it was obtained wasn’t made particularly clear. Default = 0.9
soil.constants.tectonic_uplift_rate_phosphorus: Rate at which tectonic uplift exposes new primary phosphorus [kg{P} m^-3 day^-1]. This rate is essentially zero for decadal simulations. We have only included to give the flexibility to run longer term test scenarios. Default = 0.0
soil.constants.ammonia_volatilisation_rate_constant: Rate constant for ammonia volatilisation from ammonium [day^-1]. Following Dickinson et al. (2002), linear kinetics are assumed. We also take our default value from there. Default = 8.64e-05
soil.constants.nitrification_rate_constant: Rate constant for nitrification from ammonium [day^-1]. Following Dickinson et al. (2002), linear kinetics are assumed. We also take our default value from there. Default = 0.08639999999999999
soil.constants.denitrification_rate_constant: Rate constant for denitrification from nitrate [day^-1]. Following Dickinson et al. (2002), linear kinetics are assumed. We also take our default value from there. Default = 0.21600000000000003
soil.constants.nitrification_optimum_temperature: Soil temperature at which nitrification is maximised [Kelvin]. Value taken from Xu-Ri and Prentice (2008). This value should not be varied independently of SoilConstants.nitrification_maximum_temperature and SoilConstants.nitrification_thermal_sensitivity! Default = 311.15
soil.constants.nitrification_maximum_temperature: Temperature at which our empirical nitrification model stops working [Kelvin]. This is well outside field values so this should be too much of a problem. Value taken from Xu-Ri and Prentice (2008). This value should not be varied independently of SoilConstants.nitrification_optimum_temperature and SoilConstants.nitrification_thermal_sensitivity! Default = 343.15
soil.constants.nitrification_thermal_sensitivity: Sensitivity of nitrification rate to changes in temperature [unitless]. Value taken from Xu-Ri and Prentice (2008). This value should not be varied independently of SoilConstants.nitrification_optimum_temperature and SoilConstants.nitrification_maximum_temperature! Default = 12
soil.constants.denitrification_infinite_temperature_factor: Denitrification temperature factor at infinite temperature [unitless]. Value is obtained from Xu-Ri and Prentice (2008), by taking the exponential of the constant part of the expression. This value should not be varied independently of SoilConstants.denitrification_minimum_temperature and SoilConstants.denitrification_thermal_sensitivity! Default = 93.34598
soil.constants.denitrification_minimum_temperature: Temperature at which denitrification stops entirely [Kelvin]. Value is obtained from Xu-Ri and Prentice (2008), and converted to Kelvin. The expression we are using does not function below this temperature, but this is not a major problem as it is a very low temperature. This value should not be varied independently of SoilConstants.denitrification_infinite_temperature_factor and SoilConstants.denitrification_thermal_sensitivity! Default = 227.12999999999997
soil.constants.denitrification_thermal_sensitivity: Sensitivity of denitrification rate to changes in temperature [Kelvin]. Value is obtained from Xu-Ri and Prentice (2008). This value should not be varied independently of SoilConstants.denitrification_infinite_temperature_factor and SoilConstants.denitrification_minimum_temperature! Default = 308.56
soil.constants.nitrogen_fixation_cost_zero_celcius: Cost (in carbon) that plants pay to their symbiotic partners at zero Celsius [kg{C} kg{N}^-1]. This is cost per unit of nitrogen received, and will be higher than the symbiotic partners actually spend to fix the nitrogen. Value is obtained from Brzostek et al. (2014). Default = 59.19651970522086
soil.constants.nitrogen_fixation_cost_infinite_temp_offset: Difference in nitrogen fixation cost between zero Celsius and infinite limit. Units of [kg{C} kg{N}^-1]. This limit of infinite temperature is not biologically meaningful and is instead just a way of characterising the form of the empirical function. A negative value means that the cost in the infinite temperature limit is higher than at zero Celsius. Value is obtained from Brzostek et al. (2014). Default = -0.8034802947791453
soil.constants.nitrogen_fixation_cost_thermal_sensitivity: Sensitivity of symbiotic nitrogen fixation cost to changes in temperature [Celsius^-1]. Value is obtained from Brzostek et al. (2014). Default = 0.27
soil.constants.nitrogen_fixation_cost_equality_temperature: Positive temperature at which nitrogen fixation cost is the same at zero Celsius. [Celsius]. Value is obtained from Brzostek et al. (2014). Default = 50.28
soil.constants.free_living_N_fixation_reference_rate: Rate at which free living microbes fix nitrogen (at the reference temperature). Units of [kg{N} m^-2 day^-1]. Value specific to tropical forests, and is taken from Lin et al. (2000) (with the units adjusted). Should not be changed independently from SoilConstants.free_living_N_fixation_reference_temp. Default = 4.106776180698152e-06
soil.constants.free_living_N_fixation_reference_temp: Temperature reference rate of free-living nitrogen fixation was measured at [Kelvin]. Value taken from Lin et al. (2000). Should not be changed independently from SoilConstants.free_living_N_fixation_reference_rate. Default = 293.15
soil.constants.free_living_N_fixation_q10_coefficent: Q10 coefficient for free-living fixation of nitrogen [unitless]. Value taken from Lin et al. (2000). Default = 3.0
soil.constants.primary_phosphorus_breakdown_rate: Rate constant for breakdown of primary phosphorus to labile phosphorus [day^-1]. Default value taken from Parton et al. (1988). Default = 2.2831050228310502e-07
soil.constants.secondary_phosphorus_breakdown_rate: Rate constant for breakdown of secondary mineral to labile phosphorus [day^-1]. Default value taken from Parton et al. (1988). Default = 7.407407407407407e-05
soil.constants.labile_phosphorus_sorption_rate: Rate constant for sorption of labile phosphorus to secondary mineral phosphorus [day^-1]. Default value taken from Parton et al. (1988). Default = 0.0016666666666666668
soil.constants.ammonium_deposition_rate: Rate at which ammonium is deposited into the system [kg{N} m^-2 day^-1]. We are assuming that deposition rates won’t vary substantially over the area the simulation encompasses. Value taken from Vet et al. (2014). Default = 4.1067761806981517e-07
soil.constants.phosphorus_deposition_rate: Rate at which phosphorus is deposited into the system [kg{P} m^-2 day^-1]. We are assuming that deposition rates won’t vary substantially over the area the simulation encompasses. Value taken from Mahowald et al. (2008). Default = 1.3689253935660508e-08
soil.constants.nitrogen_fixer_supply_fraction: Fraction of carbon supplied by plants to symbiotes that goes to nitrogen fixers. [unitless]. The remainder goes to mycorrhizal fungi. Default = 0.3
soil.constants.ectomycorrhiza_supply_fraction: Fraction of plant carbon supply to mycorrhizal fungi that goes to ectomycorrhiza. [unitless]. The remainder goes to arbuscular mycorrhizal fungi. Default = 0.25