Maisonnier et al. (2025) A new biogeochemical modelling framework (FLaMe-v1.0) for lake methane emissions on the regional scale: development and application to the European domain

Identification

• Journal: Earth System Dynamics
• Year: 2025
• Date: 2025-10-17
• Authors: Manon Maisonnier, Maoyuan Feng, David Bastviken, Sandra Arndt, Ronny Lauerwald, Aidin Jabbari, Goulven G. Laruelle, Murray D. MacKay, Zeli Tan, Wim Thiery, Pierre Regnier
• DOI: 10.5194/esd-16-1779-2025

Research Groups

• Department Geoscience, Environment and Society, Biogeochemistry and Modelling of the Earth System-BGEOSYS, Université Libre de Bruxelles, Brussels, Belgium
• Department of Thematic Studies – Environmental Change, Linköping University, Sweden
• iC3, Department of Geosciences, UiT The Arctic University of Norway, Tromso, Norway
• Université Paris-Saclay, INRAE, AgroParisTech, UMR Ecosys, Palaiseau, France
• Earth Sciences New Zealand, Christchurch, New Zealand
• Science and Technology Branch, Environment and Climate Change Canada, Toronto, Canada
• Pacific Northwest National Laboratory, Richland, WA, USA
• Department of Water and Climate, Vrije Universiteit Brussel, Brussels, Belgium

Short Summary

This study presents a new physical-biogeochemical modelling framework (FLaMe-v1.0) for simulating lake methane (CH4) emissions at regional scales, applying it to the European domain. The model estimates a total annual CH4 emission of 0.97 ± 0.23 Tg CH4 yr−1 from European lakes (0.1–1000 km2), highlighting strong spatio-temporal variability and the importance of carbon biogeochemical dynamics.

Objective

• Develop and test a new physical-biogeochemical modelling framework (FLaMe-v1.0) for simulating lake methane (CH4) emissions at regional scales.
• Apply FLaMe-v1.0 to the European domain to assess spatio-temporal variability and quantify total CH4 emissions from lakes.

Study Configuration

• Spatial Scale: European domain (25° W–60° E, 36–71° N), focusing on 108 407 lakes with surface areas between 0.1–1000 km2 (total area = 1.33 × 10^5 km2). The domain was divided into 2.5° × 2.5° grid cells, with lakes clustered into four size classes per cell. Model validation included two theoretical lakes, four well-surveyed real lakes (Klöntal, Erssjön, Upper Mystic, Villasjön), and 47 lakes in boreal and central European regions.
• Temporal Scale: European-scale simulations for the period 2010–2016. Validation against observed CH4 fluxes for four lakes used data from 1991–2019 (with 1991–1999 as spin-up). Regional validation against observations from late summer (August–September) during 2010–2011.

Methodology and Data

• Models used:
  • FLaMe-v1.0 (Fluxes of Lake Methane version 1.0): A new process-based physical-biogeochemical modelling framework.
  • Canadian Small Lake Model (CSLM): Used as the basis for simulating lake physical processes (temperature profile, thermocline depth, photic depth, ice cover).
  • Newly developed biogeochemical modules: Simulate transient dynamics of organic Carbon (C), Oxygen (O2), and CH4, including primary production, mineralization, oxidation, and transport.
  • Lake clustering approach: To reduce computational cost for regional-scale applications by simulating representative lakes per size class within grid cells.
  • Random Forest (RF) model: Used for uncertainty analysis of European lake CH4 emissions.
• Data sources:
  • HydroLAKES database (Messager et al., 2016): For lake areas and depths.
  • GlobalNEWS model (Mayorga et al., 2010; Lauerwald et al., 2019): For estimating lake trophic status (Total Phosphorus, TP).
  • GSWP3-W5E5 reanalysis product under ISIMIP3a (Frieler et al., 2024): For meteorological forcing data (shortwave/longwave radiation, precipitation, near-surface air temperature, specific humidity, near-surface wind velocity, atmospheric pressure).
  • In-situ measurements:
    • Monthly resolved CH4 fluxes from four well-surveyed lakes (Tan et al., 2024) for temporal pattern evaluation.
    • Diffusive and ebullitive CH4 emission rates from 17 boreal and 30 central European lakes (Rinta et al., 2017) for regional validation.
  • Empirical ranges from Wetzel (2001): For evaluating simulated primary production (FPP) across different trophic statuses.

Main Results

• FLaMe-v1.0 accurately captures contrasting physical and biogeochemical behaviors in theoretical lakes (e.g., deep oligotrophic cold vs. shallow eutrophic warm lakes) and broadly reproduces observed temporal patterns of monthly mean CH4 emissions in four well-surveyed lakes.
• Trophic level exerts the most significant control on CH4 dynamics, followed by climate and lake depth.
• For European lakes with surface areas between 0.1–1000 km2, the annual mean CH4 emission for 2010–2016 is estimated at 0.97 ± 0.23 Tg CH4 yr−1.
• Diffusive and ebullitive pathways contribute approximately 30 % and 70 %, respectively, to the total European lake CH4 emissions.
• The mean CH4 emission rate per unit lake area across Europe is 7.39 g CH4 m−2 yr−1, exhibiting a decreasing gradient from South to North.
• European lake CH4 emissions show strong seasonality, with emissions in late summer being nearly ten times higher than in winter, and episodic releases during spring and fall lake turnovers.
• Sensitivity analysis reveals that the fraction of organic matter mineralization channeled to methanogenesis (fmm) is the most sensitive parameter, followed by the maximum carbon fixation rate (Pchl,max) and the half-saturation constant of phosphorus (Ks,P).

Contributions

• Development of FLaMe-v1.0, a novel process-based physical-biogeochemical modelling framework that explicitly couples organic carbon, oxygen, and methane cycles in lakes.
• Introduction of an innovative, computationally efficient lake clustering approach, enabling regional-scale simulations across a large number of lakes (e.g., >100 000 lakes in Europe).
• First-time explicit incorporation of autochthonous primary production and its phosphorus limitation as a major driver of lake O2 and CH4 dynamics in a large-scale lake CH4 model.
• Provision of a comprehensive, spatio-temporally resolved estimate of CH4 emissions from European lakes (0.1–1000 km2) with a constrained uncertainty range (0.97 ± 0.23 Tg CH4 yr−1).
• Demonstration of the critical importance of accounting for sub-annual variability in CH4 emissions for accurate regional methane budgets.
• Establishment of a framework with potential for future embedding into Earth System Models to investigate climate warming and global lake CH4 emission feedbacks.

Funding

• Fonds National de la Recherche Scientifique of Belgium (F.R.S.–FNRS PDR T.0191.23)
• Project CLIMATE-SPACE RECCAP2: Global Land Carbon Budget and its Attribution to regional drivers
• Project ESM2025–Earth System Models for the Future (grant no. 101003536)
• European Research Council (ERC H2020; grant no. 725546)
• Swedish Research Councils VR (grant nos. 2016-04829 and 2022-03841)
• Formas (grant no. 2018-01794)
• F.R.S.–FNRS (grant no. 35266740, FIESTA)
• French state aid, managed by ANR under the “Investissements d’avenir” programme (ANR-16-CONV-0003)
• “France 2030” programme (ANR-22-PEXF-0009, PEPR Fair-CarboN – project “DEEP-C”)
• US DOE’s Earth System Modeling program through the Energy Exascale Earth System Model (E3SM) project
• Pacific Northwest National Laboratory (operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RLO1830)
• Consortium des Équipements de Calcul Intensif (CÉCI), funded by the Fonds de la Recherche Scientifique de Belgique (F.R.S.–FNRS) under grant no. 2.5020.11 and by the Walloon Region.

Citation

@article{Maisonnier2025new,
  author = {Maisonnier, Manon and Feng, Maoyuan and Bastviken, David and Arndt, Sandra and Lauerwald, Ronny and Jabbari, Aidin and Laruelle, Goulven G. and MacKay, Murray D. and Tan, Zeli and Thiery, Wim and Regnier, Pierre},
  title = {A new biogeochemical modelling framework (FLaMe-v1.0) for lake methane emissions on the regional scale: development and application to the European domain},
  journal = {Earth System Dynamics},
  year = {2025},
  doi = {10.5194/esd-16-1779-2025},
  url = {https://doi.org/10.5194/esd-16-1779-2025}
}