Baseline estimates for microbial functional group and enzyme class parameters

We provide baseline estimates for each of the soil microbial groups and each of the enzyme classes as part of the example data. These values are displayed below, with comments indicating the source that we obtained each parameter from:

# N.B. Values taken from Wang et al. often have to be transformed from the (mg C/g soil)
# units used in that paper into the (kg C/m^3) units we use, by multiplying by an
# estimated bulk density of 1400.0 kg/m^3
[[soil.microbial_group_definition]]
name = "bacteria"
taxonomic_group = "bacteria"
max_uptake_rate_labile_C = 0.04 # Fatichi et al. Global Biogeochemical Cycles (2019)
activation_energy_uptake_rate = 47000 # Mean value from Wang et al. Ecological Applications (2013)
half_sat_labile_C_uptake = 0.364 # Fatichi et al. Global Biogeochemical Cycles (2019)
activation_energy_uptake_saturation = 30000 # Mean value from Wang et al. Ecological Applications (2013)
max_uptake_rate_ammonium = 5e-3 # Complete guess
half_sat_ammonium_uptake = 0.02275 # Complete guess
max_uptake_rate_nitrate = 5e-4 # Complete guess
half_sat_nitrate_uptake = 0.02275 # Complete guess
max_uptake_rate_labile_p = 0.0025 # Complete guess
half_sat_labile_p_uptake = 0.02275 # Complete guess
turnover_rate = 0.005 # Fatichi et al. Global Biogeochemical Cycles (2019)
activation_energy_turnover = 20000 # Mean value from Wang et al. Ecological Applications (2013)
reference_temperature = 12.0
c_n_ratio = 5.2 # Fatichi et al. Global Biogeochemical Cycles (2019)
c_p_ratio = 16 # Fatichi et al. Global Biogeochemical Cycles (2019)
enzyme_production.pom = 0.005 # Complete guess
enzyme_production.maom = 0.005 # Complete guess
reproductive_allocation = 0.0 # Has to be zero by definition
symbiote_nitrogen_uptake_fraction = 0.0 # Has to be zero by definition
symbiote_phosphorus_uptake_fraction = 0.0 # Has to be zero by definition

[[soil.microbial_group_definition]]
name = "saprotrophic_fungi"
taxonomic_group = "fungi"
max_uptake_rate_labile_C = 0.02 # Fatichi et al. Global Biogeochemical Cycles (2019)
activation_energy_uptake_rate = 47000 # Assumed same as bacteria (bad assumption)
half_sat_labile_C_uptake = 0.364 # Assumed same as bacteria (terrible assumption)
activation_energy_uptake_saturation = 30000 # Assumed same as bacteria (terrible assumption)
max_uptake_rate_ammonium = 5e-3 # Assumed same as bacteria (terrible assumption)
half_sat_ammonium_uptake = 0.02275 # Assumed same as bacteria (terrible assumption)
max_uptake_rate_nitrate = 5e-4 # Assumed same as bacteria (terrible assumption)
half_sat_nitrate_uptake = 0.02275 # Assumed same as bacteria (terrible assumption)
max_uptake_rate_labile_p = 0.0025 # Assumed same as bacteria (terrible assumption)
half_sat_labile_p_uptake = 0.0227 # Assumed same as bacteria (terrible assumption)
turnover_rate = 0.002 # Fatichi et al. Global Biogeochemical Cycles (2019)
activation_energy_turnover = 20000 # Assumed same as bacteria (bad assumption)
reference_temperature = 12.0
c_n_ratio = 6.5 # Fatichi et al. Global Biogeochemical Cycles (2019)
c_p_ratio = 40.0 # Fatichi et al. Global Biogeochemical Cycles (2019)
enzyme_production.pom = 0.005 # Complete guess
enzyme_production.maom = 0.005 # Complete guess
reproductive_allocation = 0.1 # Complete guess
symbiote_nitrogen_uptake_fraction = 0.0 # Has to be zero by definition
symbiote_phosphorus_uptake_fraction = 0.0 # Has to be zero by definition

[[soil.microbial_group_definition]]
name = "arbuscular_mycorrhiza"
taxonomic_group = "fungi"
max_uptake_rate_labile_C = 0.02 # Assumed same across fungi
activation_energy_uptake_rate = 47000 # Assumed same as bacteria (bad assumption)
half_sat_labile_C_uptake = 0.364 # Assumed same as bacteria (terrible assumption)
activation_energy_uptake_saturation = 30000 # Assumed same as bacteria (terrible assumption)
max_uptake_rate_ammonium = 5e-3 # Assumed same as bacteria (terrible assumption)
half_sat_ammonium_uptake = 0.02275 # Assumed same as bacteria (terrible assumption)
max_uptake_rate_nitrate = 5e-4 # Assumed same as bacteria (terrible assumption)
half_sat_nitrate_uptake = 0.02275 # Assumed same as bacteria (terrible assumption)
max_uptake_rate_labile_p = 0.0025 # Assumed same as bacteria (terrible assumption)
half_sat_labile_p_uptake = 0.02275 # Assumed same as bacteria (terrible assumption)
turnover_rate = 0.0012 # Fatichi et al. Global Biogeochemical Cycles (2019)
activation_energy_turnover = 20000 # Assumed same as bacteria (bad assumption)
reference_temperature = 12.0
c_n_ratio = 18.0 # Fatichi et al. Global Biogeochemical Cycles (2019)
c_p_ratio = 120.0 # Fatichi et al. Global Biogeochemical Cycles (2019)
enzyme_production.pom = 0.0 # Assume that AMF do no produce enzymes at all (needs to be double checked)
enzyme_production.maom = 0.0 # Assume that AMF do no produce enzymes at all (needs to be double checked)
reproductive_allocation = 0.1 # Complete guess
symbiote_nitrogen_uptake_fraction = 0.2 # Complete guess
symbiote_phosphorus_uptake_fraction = 0.2 # Complete guess

[[soil.microbial_group_definition]]
name = "ectomycorrhiza"
taxonomic_group = "fungi"
max_uptake_rate_labile_C = 0.02 # Assumed same across fungi
activation_energy_uptake_rate = 47000 # Assumed same as bacteria (bad assumption)
half_sat_labile_C_uptake = 0.364 # Assumed same as bacteria (terrible assumption)
activation_energy_uptake_saturation = 30000 # Assumed same as bacteria (bad assumption)
max_uptake_rate_ammonium = 5e-3 # Assumed same as bacteria (terrible assumption)
half_sat_ammonium_uptake = 0.02275 # Assumed same as bacteria (terrible assumption)
max_uptake_rate_nitrate = 5e-4 # Assumed same as bacteria (terrible assumption)
half_sat_nitrate_uptake = 0.02275 # Assumed same as bacteria (terrible assumption)
max_uptake_rate_labile_p = 0.0025 # Assumed same as bacteria (terrible assumption)
half_sat_labile_p_uptake = 0.02275 # Assumed same as bacteria (terrible assumption)
turnover_rate = 0.0012 # Fatichi et al. Global Biogeochemical Cycles (2019)
activation_energy_turnover = 20000 # Assumed same as bacteria (bad assumption)
reference_temperature = 12.0
c_n_ratio = 18.0 # Fatichi et al. Global Biogeochemical Cycles (2019)
c_p_ratio = 120.0 # Fatichi et al. Global Biogeochemical Cycles (2019)
enzyme_production.pom = 0.02 # Complete guess
enzyme_production.maom = 0.02 # Complete guess
reproductive_allocation = 0.1 # Complete guess
symbiote_nitrogen_uptake_fraction = 0.2 # Complete guess
symbiote_phosphorus_uptake_fraction = 0.2 # Complete guess

[[soil.enzyme_class_definition]]
source = "bacteria"
substrate = "pom"
maximum_rate = 60.0 # Mean value (for cellulose) from Wang et al. Ecological Applications (2013)
half_saturation_constant = 70.0  # Mean value from Wang et al. Ecological Applications (2013)
activation_energy_rate = 37000 # Mean value from Wang et al. Ecological Applications (2013)
activation_energy_saturation = 30000 # Mean value from Wang et al. Ecological Applications (2013)
reference_temperature = 12.0
turnover_rate = 2.4e-2 # Mean value from Wang et al. Ecological Applications (2013)
c_n_ratio = 5.2 # Chosen to match the stoichiometry of bacteria
c_p_ratio = 16 # Chosen to match the stoichiometry of bacteria

[[soil.enzyme_class_definition]]
source = "bacteria"
substrate = "maom"
maximum_rate = 24.0 # Mean value from Wang et al. Ecological Applications (2013)
half_saturation_constant = 350.0 # Mean value from Wang et al. Ecological Applications (2013)
activation_energy_rate = 47000 # Mean value from Wang et al. Ecological Applications (2013)
activation_energy_saturation = 30000 # Mean value from Wang et al. Ecological Applications (2013)
reference_temperature = 12.0
turnover_rate = 2.4e-2 # Mean value from Wang et al. Ecological Applications (2013)
c_n_ratio = 5.2 # Chosen to match the stoichiometry of bacteria
c_p_ratio = 16 # Chosen to match the stoichiometry of bacteria

[[soil.enzyme_class_definition]]
source = "fungi"
substrate = "pom"
maximum_rate = 120.0 # Double bacteria case (so that fungal enzymes are "better")
half_saturation_constant = 35.0 # half bacteria case (so that fungal enzymes are "better")
activation_energy_rate = 37000 # Assumed thermal responses are the same as for bacterial enzymes (shaky assumption)
activation_energy_saturation = 30000 # Assumed thermal responses are the same as for bacterial enzymes (shaky assumption)
reference_temperature = 12.0
turnover_rate = 2.4e-2 # Assumed all enzymes have the same turnover rate regardless of source (dubious)
c_n_ratio = 6.5 # Chosen to match the stoichiometry of saprotrophic fungi
c_p_ratio = 40.0 # Chosen to match the stoichiometry of saprotrophic fungi

[[soil.enzyme_class_definition]]
source = "fungi"
substrate = "maom"
maximum_rate = 48.0 # Double bacteria case (so that fungal enzymes are "better")
half_saturation_constant = 175.0 # half bacteria case (so that fungal enzymes are "better")
activation_energy_rate = 47000 # Assumed thermal responses are the same as for bacterial enzymes (shaky assumption)
activation_energy_saturation = 30000 # Assumed thermal responses are the same as for bacterial enzymes (shaky assumption)
reference_temperature = 12.0
turnover_rate = 2.4e-2 # Assumed all enzymes have the same turnover rate regardless of source (dubious)
c_n_ratio = 6.5 # Chosen to match the stoichiometry of saprotrophic fungi
c_p_ratio = 40.0 # Chosen to match the stoichiometry of saprotrophic fungi