PEPRMT-DAMM (Peatland Ecosystem Photosynthesis, Respiration, and Methane Transport – Dual Arrhenius Michaelis-Menten)

Criterion	Explanation
General Description	Hierarchal biogeochemical model for CO₂ and CH₄ exchange in restored managed wetlands through simulation of carbon pools.
Model Domain	Sacramento-San Joaquin Bay-Delta
Developer	Patricia Y. Oikawa. Department of Earth and Environmental Sciences, California State University, East Bay, Hayward, CA. patty.oikawa@gmail.com
Hardware computing requirements	Not specified.
Code language	MATLAB
Original application	Originally developed for predicting CO₂ and CH₂ exchange in mature and restored freshwater wetlands in the Sacramento-San Joaquin Delta, CA, USA.
Public/proprietary and cost	Public, no known cost for usage.
Physically or empirically based	Process based model, simulates carbon pools to estimate ecosystem CO₂ and CH₄ production. Some empirical relationship derived from Delta specific wetland restoration cases are also used.
Mathematical methods used	The model consists of a hierarchy of biogeochemical models designed to estimate CO₂ and CH₄ exchange in wetlands by simulating substrate limited ecosystem respiration and methanogenesis using three carbon pools (labile carbon, biomass carbon and recalcitrant soil organic carbon). Emission from the top meter of soil is simulate using initial soil carbon content, with consideration to water table height to distinguish between saturated and unsaturated soil layers. Gross primary productivity was simulated using a Light Use Efficiency (LUE) model and Beer-Lambert law, with an embedded temperature function that assumes exponential increase in photosynthesis with temperature until an optimal temperature after which photosynthesis is inhibited. Total ecosystem respiration rate and methanogenesis simulated using modified Dual Arrhenius Michaelis-Menten (DAMM) models based on enzyme kinetics. Respiration is modeled as a function of temperature, available substrate, and water table height; CO₂ is mostly conserved. CH₄ can be oxidized and therefore not all CH₄ produced within the soil is released to the atmosphere. CH₄ concentrations in the soil and water column are modeled quantities that respond to changes in water table. Plant mediated flux simulated using concentration gradient between soil/water/air, plant transport efficiency and plant activity. Hydrodynamic flux simulated using a gas transfer velocity model. Net ecosystem exchange estimates using simulated gross primary productivity, ecosystem respiration, methanogenesis, plant mediated transport and hydrodynamic flux.
Input data requirements	Air temperature, photosynthetically active radiation, leaf area index (LAI), water table height, initial soil organic carbon, time since restoration. Meteorological data can be obtained through various public databases. Water table height and LAI are not available online and easy to obtain. LAI can be derived from satellite images and a site-specific calibration.
Outputs	Net ecosystem exchange of CO₂ (g C m^-2) at half-hour timestep and CH₄ (mg C m^-2) at daily timestep.
Pre-processing and post-processing tools	Scripts to build model are provided at https://github.com/pattyoikawa/PEPRMT.
Representation of uncertainty	No uncertainty representation built into model framework. Uncertainty in model predictions were assessed using a model-data fusion method accounting for uncertainty in data, model parameters and model structure (Oikawa et al., 2017).
Prevalence	Limited: model relatively new, not yet widely applied. Current applications are limited to individual modelers in academic institutes and some government entities. Model mainly used for scientific publication. The use of the model is allowed in the methodology for the carbon market "Restoration of California Deltaic and Coastal Wetlands," adopted by the American Carbon Registry in 2017. The model has been used to simulate conditions in rice and wetlands in the Delta.
Ease of use for public entities	Easy to moderate: model available via internet, model is simple and easy to use.
Ease of obtaining information and availability of technical support	No commercial help desk available, no web-based support forums found, no user guide available. Information availability and support constrained to contact with individual modelers or developer. A description of the model is available in Oikawa et al. (2017).
Model and Source code availability	Model publicly available at https://github.com/pattyoikawa/PEPRMT. Source code available upon request from developer.
Status of model development	Model developed and available. Future developments include refining and expanding for modeling rice systems and tidal wetlands in the Bay-Delta and Suisun regions.
Challenges for integration	Model currently limited to mature and restored freshwater wetland simulations, integration with models requiring emission estimates from other land practices (aside from rice and tidal wetlands inclusion and refinement in the near future) would not be applicable.
Model limitations	Limitations for use in the Delta The model has been used for a limited number of situations in rice and wetlands.

References

American Carbon Registry, 2017. Methodology for the quantification, monitoring, reporting and verification of greenhouse gas emissions reductions and removals from the restoration of California Deltaic and Costal Wetlands. Version 1.1. Available at https://americancarbonregistry.org/carbon-accounting/standards-methodologies/restoration-of-california-deltaic-and-coastal-wetlands/ca-wetland-methodology-v1.1-November-2017.pdf (accessed 26 October 2018).

Oikawa, P.Y., Jenerette, G.D., Knox, S.H., Sturtevant, C., Verfaillie, J., Dronova, I., Poindexter, C.M., Eichelmann, E. and 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), pp.145-167.

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