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Methane Exchange (CH4)

PEPRMT_CH4.Rd

Methane production and transport module of the PEPRMT model (v1.0).

Usage

PEPRMT_CH4(
  data,
  wetland_type,
  Ea_SOM_CH4 = 14.9025078 + 67.1,
  kM_SOM_CH4 = 0.4644174 + 17,
  Ea_labile_CH4 = 16.7845002 + 71.1,
  kM_labile_CH4 = 0.4359649 + 23,
  Ea_oxi_CH4 = 15.8857612 + 75.4,
  kM_oxi_CH4 = 0.5120464 + 23,
  kI_SO4 = 486.4106939,
  kI_NO3 = 0.1020278,
  k_plant_oxi = 0.35,
  restart = F,
  prev_CH4water_store = 0,
  prev_WT_2_adj = 0,
  GPPmax = 0
)

Arguments

data

Data frame containing 18 required columns used as model inputs. See Details for expected column names.

wetland_type

Integer indicating wetland class: 1 = Freshwater peatland, 2 = Tidal wetland.

Ea_SOM_CH4

Activation energy for methane production from soil organic matter (kJ mol^-1)

kM_SOM_CH4

Half-saturation constant for SOM methane production (g C m^-3 soil)

Ea_labile_CH4

Activation energy for methane production from labile carbon (kJ mol^-1)

kM_labile_CH4

Half-saturation constant for labile methane production (g C m^-3 soil)

Ea_oxi_CH4

Activation energy for methane oxidation (kJ mol^-1)

kM_oxi_CH4

Half-saturation constant for methane oxidation (g C m^-3 soil)

kI_SO4

– Sulfate inhibition constant (mg L^-1)

kI_NO3

– Nitrate inhibition constant (mg L^-1)

k_plant_oxi

Fraction of CH4 oxidized during transport

restart

Would you like to restart the model with a known porewater CH4 pool?

prev_CH4water_store

If restart, starting concentration of porewater CH4

prev_WT_2_adj

If restart, previous water level, converted to model units ((WTD_cm / 100) + 1)

GPPmax

If restart, maximum GPP across full time series

Value

Updated dataframe containing:

CH4_mod

total methane emitted (g C CH4 m^-2 day^-1)

Plant_flux_net

net methane flux via plant-mediated transport (g C CH4 m^-2 day^-1)

Hydro_flux

net diffusive methane flux from water to atmosphere (g C CH4 m^-2 day^-1)

M1

methane pool produced from labile soil carbon (g C CH4 m^-3, top meter of soil and water)

M2

methane pool produced from soil organic carbon (g C CH4 m^-3, top meter of soil and water)

trans2

fraction of methane released via plant-mediated transport (unitless)

CH4water_store

methane pool stored in soil after emission (g C CH4 m^-3, top meter of soil and water)

Details

Runs the PEPRMT methane production and transport module for freshwater peatlands or tidal wetlands at a daily time step. Default parameter values were determined via MCMC Bayesian fitting (Oikawa et al. 2024).

The PEPRMT model was originally parameterized for restored freshwater wetlands in the Sacramento–San Joaquin River Delta, California, USA (Oikawa et al. 2017) and later updated for tidal wetlands with inhibition of methane production in response to salinity and nitrate (Oikawa et al. 2024).

Modules are intended to be run sequentially: PEPRMT_GPP, then PEPRMT_Reco, then PEPRMT_CH4.

All variables are expected at a daily time step.

All PEPRMT modules use the same input structure, although not all variables are used in every module.

Required data columns:

  1. Continuous day of year

  2. Discontinuous day of year

  3. Year

  4. Air temperature (°C)

  5. Water table depth (cm)

  6. PAR (µmol m^-2 d^-1)

  7. Leaf Area Index

  8. Greenness Index

  9. FPAR flag

  10. Wetland age (years)

  11. Salinity (ppt)

  12. NO3 (mg L^-1)

  13. Soil organic matter (g C m^-3)

  14. Site identifier

  15. Modeled GPP (g C m^-2 day^-1)

  16. Modeled Reco (g C m^-2 day^-1)

  17. Net ecosystem exchange (g C m^-2 day^-1)

References

Oikawa, P. Y., Jenerette, G. D., Knox, S. H., Sturtevant, C., Verfaillie, J., Dronova, I., Poindexter, C. M., Eichelmann, E., & Baldocchi, D. D. (2017). Evaluation of a hierarchy of models reveals importance of substrate limitation for predicting carbon dioxide and methane exchange in restored wetlands. Journal of Geophysical Research: Biogeosciences, 122(1), 145–167. https://doi.org/10.1002/2016JG003438

Oikawa, P. Y., Sihi, D., Forbrich, I., Fluet-Chouinard, E., Najarro, M., Thomas, O., Shahan, J., Arias-Ortiz, A., Russell, S., Knox, S. H., McNicol, G., Wolfe, J., Windham-Myers, L., Stuart-Haentjens, E., Bridgham, S. D., Needelman, B., Vargas, R., Schäfer, K., Ward, E. J., Megonigal, P., & Holmquist, J. (2024). A New Coupled Biogeochemical Modeling Approach Provides Accurate Predictions of Methane and Carbon Dioxide Fluxes Across Diverse Tidal Wetlands. Journal of Geophysical Research: Biogeosciences, 129(10), e2023JG007943. https://doi.org/10.1029/2023JG007943

Examples

# Example
# data(example_dataset)
# theta <- c(14.9025078, 0.4644174, 16.7845002, 0.4359649, 15.8857612, 
# 0.5120464, 486.4106939, 0.1020278)
# out <- PEPRMT_CH4(theta, example_dataset, wetland_type = 2)