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Soil Organic Parameters

This section documents the SoilOrganicModuleParameters JSON object used by MONICA.

The parameters control:

  • soil organic matter (SOM) turnover
  • soil microbial biomass (SMB) turnover
  • added organic matter (AOM) decomposition
  • nitrogen mineralisation and immobilisation
  • urea hydrolysis and ammonia volatilisation
  • nitrification, denitrification, and N2O production
  • optional STICS-based nitrogen transformations

JSON conventions

  • Most numeric parameters may be supplied either as a plain number:

    "QTenFactor": 2.9

    or as a value-unit array:

    "QTenFactor": [2.9, ""]

    MONICA ignores the unit string when reading the parameter. Its serializer generally emits the array form.

List of soil organic parameters

Parameter Name Type Unit Description Example
QTenFactor Float Empirical sensitivity and shape parameter in MONICA's soil temperature response for decomposition "QTenFactor": 2.95
TempDecOptimal Float °C Temperature parameter defining the optimum region of the empirical decomposition temperature response "TempDecOptimal": 38.2
MoistureDecOptimal Float fraction of saturation Water-filled pore space (WFPS) fraction at which the decomposition moisture response is maximal. A value of 0.45 means 45% of saturation. "MoistureDecOptimal": 0.45
AOM_FastMaxC_to_N Float ratio Maximum C:N ratio assigned to the fast AOM pool "AOM_FastMaxC_to_N": 1000
AOM_FastUtilizationEfficiency Float fraction Fraction of decomposed fast AOM carbon incorporated into fast microbial biomass "AOM_FastUtilizationEfficiency": 0.1
AOM_SlowUtilizationEfficiency Float fraction Fraction of decomposed slow AOM carbon incorporated into microbial biomass "AOM_SlowUtilizationEfficiency": 0.4
ActivationEnergy Float J mol-1 Activation energy used in the Arrhenius temperature response for urea hydrolysis "ActivationEnergy": 41000
AmmoniaOxidationRateCoeffStandard Float d-1 Standard rate coefficient for oxidation of ammonium to nitrite in the standard nitrification model "AmmoniaOxidationRateCoeffStandard": 0.1
AtmosphericResistance Float s m-1 Compatibility parameter historically associated with NH3 volatilisation. It is loaded and serialized but is not used by the current soil organic calculations. "AtmosphericResistance": 0.0025
CN_Ratio_SMB Float ratio C:N ratio of the soil microbial biomass "CN_Ratio_SMB": 6.7
Denit1 Float fraction Moisture-response value at the upper intermediate breakpoint of the standard denitrification response. With the default settings, the response reaches 0.2 at a WFPS of 0.9. "Denit1": 0.2
Denit2 Float fraction Nominal lower WFPS breakpoint used by the standard denitrification moisture-response interpolation "Denit2": 0.8
Denit3 Float fraction Nominal upper intermediate WFPS breakpoint used by the standard denitrification moisture-response interpolation "Denit3": 0.9
HydrolysisKM Float Michaelis-Menten half-saturation constant for urea hydrolysis "HydrolysisKM": 0.00334
HydrolysisP1 Float First empirical coefficient used to derive the maximum urea hydrolysis rate from soil organic matter "HydrolysisP1": 4.259e-12
HydrolysisP2 Float Second empirical coefficient used to derive the maximum urea hydrolysis rate from soil organic matter "HydrolysisP2": 1.408e-12
ImmobilisationRateCoeffNH4 Float d-1 Maximum fraction of soil ammonium available for microbial immobilisation per day "ImmobilisationRateCoeffNH4": 0.5
ImmobilisationRateCoeffNO3 Float d-1 Maximum fraction of soil nitrate available for microbial immobilisation per day "ImmobilisationRateCoeffNO3": 0.5
Inhibitor_NH3 Float kg N m-3 Half-saturation-style coefficient in the NH3 inhibition factor applied to nitrite oxidation "Inhibitor_NH3": 1
LimitClayEffect Float fraction Parameter controlling the clay modifier applied to microbial maintenance. With the default decomposition response, it acts as the lower/asymptotic value of the clay response. "LimitClayEffect": 0.25
MaxMineralisationDepth Float m Target maximum soil depth included in organic matter turnover and mineralisation. Whole model layers are included until their cumulative depth reaches or exceeds this value. "MaxMineralisationDepth": 0.4
N2OProductionRate Float d-1 Rate coefficient applied to the nitrite pool in the standard N2O production calculation, together with temperature and pH response factors. "N2OProductionRate": 0.015
NitriteOxidationRateCoeffStandard Float d-1 Standard rate coefficient for oxidation of nitrite to nitrate in the standard nitrification model "NitriteOxidationRateCoeffStandard": 0.2
PartSMB_Fast_to_SOM_Fast Float fraction Fraction of dead fast microbial biomass transferred to the fast SOM pool "PartSMB_Fast_to_SOM_Fast": 0.6
PartSMB_Slow_to_SOM_Fast Float fraction Fraction of dead slow microbial biomass transferred to the fast SOM pool "PartSMB_Slow_to_SOM_Fast": 0.6
PartSOM_Fast_to_SOM_Slow Float fraction Fraction of decomposed fast SOM transferred to the slow SOM pool "PartSOM_Fast_to_SOM_Slow": 0.3
PartSOM_to_SMB_Fast Float fraction Fraction of initial soil organic carbon assigned to the fast microbial biomass pool during pool initialization "PartSOM_to_SMB_Fast": 0.0002
PartSOM_to_SMB_Slow Float fraction Fraction of initial soil organic carbon assigned to the slow microbial biomass pool during pool initialization "PartSOM_to_SMB_Slow": 0.015
SMB_FastDeathRateStandard Float d-1 Standard death rate coefficient of the fast microbial biomass pool "SMB_FastDeathRateStandard": 0.01
SMB_FastMaintRateStandard Float d-1 Standard maintenance respiration rate of the fast microbial biomass pool "SMB_FastMaintRateStandard": 0.01
SMB_SlowDeathRateStandard Float d-1 Standard death rate coefficient of the slow microbial biomass pool "SMB_SlowDeathRateStandard": 0.001
SMB_SlowMaintRateStandard Float d-1 Standard maintenance respiration rate of the slow microbial biomass pool "SMB_SlowMaintRateStandard": 0.001
SMB_UtilizationEfficiency Float fraction Fraction of eligible carbon from dead microbial biomass that is incorporated into the fast SMB pool. The remainder contributes to respiration. "SMB_UtilizationEfficiency": 0
SOM_FastDecCoeffStandard Float d-1 Standard decomposition rate coefficient for the fast SOM pool. Temperature and moisture response factors are applied during simulation. "SOM_FastDecCoeffStandard": 0.00014
SOM_FastUtilizationEfficiency Float fraction Fraction of the decomposed fast SOM carbon not transfered to slow SOM that is incorporated into slow microbial biomass "SOM_FastUtilizationEfficiency": 0.5
SOM_SlowDecCoeffStandard Float d-1 Standard decomposition rate coefficient for the slow SOM pool. Temperature and moisture response factors are applied during simulation. "SOM_SlowDecCoeffStandard": 0.000043
SOM_SlowUtilizationEfficiency Float fraction Fraction of decomposed slow SOM carbon incorporated into slow microbial biomass "SOM_SlowUtilizationEfficiency": 0.4
SpecAnaerobDenitrification Float g gas-N (g CO2-C)-1 Potential anaerobic denitrification relative to microbial CO2-C production "SpecAnaerobDenitrification": 0.1
TransportRateCoeff Float d-1 Maximum fraction of the nitrate pool that can be consumed by denitrification per day in the standard denitrification model. Despite its name, it does not transport dissolved organic matter between soil layers. "TransportRateCoeff": 0.1
type String Serialization metadata identifying the object as soil organic parameters "type": "UserSoilOrganicParameters"

Decomposition-response compatibility switches

MONICA also accepts the following internal compatibility switches:

Parameter Name Type Description Example
__enable_kaiteew_TempOnDecompostion__ Boolean Enables the current empirical temperature response. If false, the legacy temperature response is used. "__enable_kaiteew_TempOnDecompostion__": true
__enable_kaiteew_MoistureOnDecompostion__ Boolean Enables the current water-filled pore space decomposition response. If false, the legacy pF-based moisture response is used. "__enable_kaiteew_MoistureOnDecompostion__": true
__enable_kaiteew_ClayOnDecompostion__ Boolean Enables the current sigmoid clay response. If false, the legacy threshold response is used. "__enable_kaiteew_ClayOnDecompostion__": true

Optional STICS nitrogen parameters

The optional stics object configures alternative nitrification, denitrification, and N2O calculations.

The three processes are selected independently:

  • use_nit selects STICS nitrification
  • use_denit selects STICS denitrification
  • use_n2o selects STICS N2O calculation

When a switch is false, MONICA uses its standard implementation for that process.

Process switches and option codes

Parameter Name Type Description Example
use_n2o Boolean Enables the STICS calculation of N2O from nitrificaiton and denitrification "use_n2o": false
use_nit Boolean Enables the STICS nitrification "use_nit": false
use_denit Boolean Enables the STICS denitrification "use_denit": false
code_vnit Integer Selects the potential nitrification formulation: 1 = linear fraction using fnx; 2 = Michaelis-Menten using vnitmax and Kamm. "code_vnit": 1
code_tnit Integer Selects the nitrification temperature response: 1 = piecewise linear; 2 = Gaussian "code_tnit": 2
code_rationit Integer Selects the nitrification N2O ratio: 1 = constant rationit; 2 = WFPS-dependent ratio "code_rationit": 2
code_hourly_wfps_nit Integer Compatibility option for hourly nitrification WFPS handling. Currently parsed but not used by the active calculation. "code_hourly_wfps_nit": 2
code_pdenit Integer Selects potential denitrification: 1 = constant vpotdenit; 2 = soil organic carbon response. "code_pdenit": 1
code_ratiodenit Integer Selects the denitrification N2O ratio: 1 = constant ratiodenit; 2 = pH-, WFPS-, and nitrate-dependent ratio. "code_ratiodenit": 2
code_hourly_wfps_denit Integer Compatibility option for hourly denitrification WFPS handling. Currently parsed but not used by the active calculation. "code_hourly_wfps_denit": 2

STICS nitrification parameters

Parameter Name Type Unit Description Example
hminn Float fraction Multiplier of field capacity used to construct the lower WFPS threshold for nitrification "hminn": 0.3
hoptn Float fraction Multiplier of field capacity used to construct the beginning of the optimal WFPS range. The response remains optimal up to field capacity and decreases toward saturation. "hoptn": 0.9
pHminnit Float pH pH at or below which the nitrification pH response is zero "pHminnit": 4.0
pHmaxnit Float pH pH at or above which the nitrification pH response reaches one "pHmaxnit": 7.2
nh4_min Float mg NH4-N kg-1 soil Residual ammonium content excluded from nitrification "nh4_min": 1.0
fnx Float d-1 Fraction of ammonium above nh4_min nitrified per day when code_vnit = 1 "fnx": 0.8
vnitmax Float mg NH4-N kg-1 soil d-1 Maximum nitrification rate when code_vnit = 2 "vnitmax": 27.3
Kamm Float mg NH4-N L-1 soil water Ammonium half-saturation constant when code_vnit = 2 "Kamm": 24
tnitmin Float °C Lower temperature boundary of the piecewise-linear response used when code_tnit = 1 "tnitmin": 5.0
tnitopt Float °C Beginning of the optimal-temperature plateau when code_tnit = 1 "tnitopt": 30.0
tnitop2 Float °C End of the optimal-temperature plateau when code_tnit = 1 "tnitop2": 35.0
tnitmax Float °C Upper temperature boundary above which the piecewise-linear response is zero "tnitmax": 58.0
tnitopt_gauss Float °C Optimum temperature of the Gaussian nitrification response used when code_tnit = 2 "tnitopt_gauss": 32.5
scale_tnitopt Float °C Width parameter of the Gaussian nitrification temperature response "scale_tnitopt": 16.0
rationit Float fraction Constant fraction of nitrified N emitted as N₂O when code_rationit = 1 "rationit": 0.0016

STICS denitrification parameters

Parameter Name Type Unit Description Example
wfpsc Float fraction WFPS threshold at or below which the denitrification moisture response is zero "wfpsc": 0.62
tdenitopt_gauss Float °C Optimum temperature of the Gaussian denitrification response "tdenitopt_gauss": 47.0
scale_tdenitopt Float °C Width parameter of the Gaussian denitrification temperature response "scale_tdenitopt": 25.0
Kd Float mg NO3-N L-1 soil water Nitrate half-saturation constant in the denitrification response "Kd": 148.0
k_desat Float d-1 Compatibility parameter associated with desaturation. It is parsed but is not used by the current calculation. "k_desat": 3.0
cmin_pdenit Float % soil organic C Soil organic carbon value corresponding to min_pdenit when code_pdenit = 2. "cmin_pdenit": 1.0
cmax_pdenit Float % soil organic C Soil organic carbon value corresponding to max_pdenit when code_pdenit = 2. "cmax_pdenit": 6.0
min_pdenit Float mg N kg-1 soil d-1 Lower potential-denitrification rate used by the organic-carbon response. "min_pdenit": 1.0
max_pdenit Float mg N kg-1 soil d-1 Upper potential-denitrification rate used by the organic-carbon response. "max_pdenit": 20.0
vpotdenit Float kg N ha-1 d-1 Constant potential-denitrification parameter selected when code_pdenit = 1 "vpotdenit": 2.0
profdenit Float cm Configured denitrification depth. It is parsed but is not currently used to restrict the active denitrification calculation. "profdenit": 20.0
pHminden Float pH Lower pH breakpoint of the STICS denitrification N2O-fraction response used when code_ratiodenit = 2 "pHminden": 5.6
pHmaxden Float pH Upper pH breakpoint at which the pH contribution to the denitrification N2O fraction reaches zero "pHmaxden": 9.2
ratiodenit Float fraction Constant fraction of denitrified N emitted as N2O when code_ratiodenit = 1 "ratiodenit": 0.2

Example: soilorganic.json

{
    "QTenFactor": [2.95, ""],
    "TempDecOptimal": [38.2, "C"],
    "MoistureDecOptimal": [0.45, "%"],
    "AOM_FastMaxC_to_N": [1000, ""],
    "AOM_FastUtilizationEfficiency": [0.1, ""],
    "AOM_SlowUtilizationEfficiency": [0.4, ""],
    "ActivationEnergy": [41000, ""],
    "AmmoniaOxidationRateCoeffStandard": [0.1, "d-1"],
    "AtmosphericResistance": [0.0025, "s m-1"],
    "CN_Ratio_SMB": [6.7, ""],
    "Denit1": [0.2, ""],
    "Denit2": [0.8, ""],
    "Denit3": [0.9, ""],
    "HydrolysisKM": [0.00334, ""],
    "HydrolysisP1": [4.259e-12, ""],
    "HydrolysisP2": [1.408e-12, ""],
    "ImmobilisationRateCoeffNH4": [0.5, "d-1"],
    "ImmobilisationRateCoeffNO3": [0.5, "d-1"],
    "Inhibitor_NH3": [1, "kg N m-3"],
    "LimitClayEffect": [0.25, "kg kg-1"],
    "MaxMineralisationDepth": 0.4,
    "N2OProductionRate": [0.015, "d-1"],
    "NitriteOxidationRateCoeffStandard": [0.2, "d-1"],
    "PartSMB_Fast_to_SOM_Fast": [0.6, ""],
    "PartSMB_Slow_to_SOM_Fast": [0.6, ""],
    "PartSOM_Fast_to_SOM_Slow": [0.3, ""],
    "PartSOM_to_SMB_Fast": [0.0002, ""],
    "PartSOM_to_SMB_Slow": [0.015, ""],
    "SMB_FastDeathRateStandard": [0.01, "d-1"],
    "SMB_FastMaintRateStandard": [0.01, "d-1"],
    "SMB_SlowDeathRateStandard": [0.001, "d-1"],
    "SMB_SlowMaintRateStandard": [0.001, "d-1"],
    "SMB_UtilizationEfficiency": [0, "d-1"],
    "SOM_FastDecCoeffStandard": [0.00014, "d-1"],
    "SOM_FastUtilizationEfficiency": [0.5, ""],
    "SOM_SlowDecCoeffStandard": [0.000043, "d-1"],
    "SOM_SlowUtilizationEfficiency": [0.4, ""],
    "SpecAnaerobDenitrification": [0.1, "g gas-N g CO2-C-1"],
    "TransportRateCoeff": [0.1, "d-1"],
    "type": "UserSoilOrganicParameters"
}