Articles | Volume 15, issue 19
https://doi.org/10.5194/gmd-15-7325-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-15-7325-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
04 Oct 2022
Model description paper |
| 04 Oct 2022
| 04 Oct 2022
FESDIA (v1.0): exploring temporal variations of sediment biogeochemistry under the influence of flood events using numerical modelling
Stanley I. Nmor
CORRESPONDING AUTHOR
Laboratoire des Sciences du Climat et de l'Environnement,
LSCE/IPSL,CEA-CNRS-UVSQ-Université Paris Saclay, 91198 Gif sur Yvette,
France
Eric Viollier
Laboratoire des Sciences du Climat et de l'Environnement,
LSCE/IPSL,CEA-CNRS-UVSQ-Université Paris Saclay, 91198 Gif sur Yvette,
France
Institut de Physique Du Globe de Paris, 1 Rue Jussieu, Université Paris Cité, 75238, Paris CEDEX 05, France
Lucie Pastor
Laboratoire Environnement Profond, Ifremer – Centre de Bretagne,
29280 Plouzané, France
Bruno Lansard
Laboratoire des Sciences du Climat et de l'Environnement,
LSCE/IPSL,CEA-CNRS-UVSQ-Université Paris Saclay, 91198 Gif sur Yvette,
France
Christophe Rabouille
Laboratoire des Sciences du Climat et de l'Environnement,
LSCE/IPSL,CEA-CNRS-UVSQ-Université Paris Saclay, 91198 Gif sur Yvette,
France
Karline Soetaert
Royal Netherlands Institute of Sea Research (NIOZ), Department of
Estuarine and Delta Systems, Korringaweg 7, P.O. Box 140, 4401 NT Yerseke,
the Netherlands
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V. Sanial, P. van Beek, B. Lansard, M. Souhaut, E. Kestenare, F. d'Ovidio, M. Zhou, and S. Blain
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We investigated the origin and mechanisms of the natural iron fertilization that sustains a phytoplankton bloom downstream of the Kerguelen Islands. We used radium isotopes to trace the fate of shelf waters that may transport iron and other micronutrients towards offshore waters. We show that shelf waters are rapidly transferred offshore and may be transported across the polar front (PF). The PF may thus not be a strong physical barrier for chemical elements released by the shelf sediments.
K.-K. Liu, C.-K. Kang, T. Kobari, H. Liu, C. Rabouille, and K. Fennel
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Biogeosciences, 9, 5341–5352, https://doi.org/10.5194/bg-9-5341-2012, https://doi.org/10.5194/bg-9-5341-2012, 2012
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Observation-based sowing dates and cultivars significantly affect yield and irrigation for some crops in the Community Land Model (CLM5)
The statistical emulators of GGCMI phase 2: responses of year-to-year variation of crop yield to CO2, temperature, water, and nitrogen perturbations
A novel Eulerian model based on central moments to simulate age and reactivity continua interacting with mixing processes
AdaScape 1.0: a coupled modelling tool to investigate the links between tectonics, climate, and biodiversity
An along-track Biogeochemical Argo modelling framework: a case study of model improvements for the Nordic seas
Peatland-VU-NUCOM (PVN 1.0): using dynamic plant functional types to model peatland vegetation, CH4, and CO2 emissions
Quantification of hydraulic trait control on plant hydrodynamics and risk of hydraulic failure within a demographic structured vegetation model in a tropical forest (FATES–HYDRO V1.0)
SedTrace 1.0: a Julia-based framework for generating and running reactive-transport models of marine sediment diagenesis specializing in trace elements and isotopes
A high-resolution marine mercury model MITgcm-ECCO2-Hg with online biogeochemistry
Improving nitrogen cycling in a land surface model (CLM5) to quantify soil N2O, NO, and NH3 emissions from enhanced rock weathering with croplands
Ocean biogeochemistry in the coupled ocean–sea ice–biogeochemistry model FESOM2.1–REcoM3
Forcing the Global Fire Emissions Database burned-area dataset into the Community Land Model version 5.0: impacts on carbon and water fluxes at high latitudes
Modeling of non-structural carbohydrate dynamics by the spatially explicit individual-based dynamic global vegetation model SEIB-DGVM (SEIB-DGVM-NSC version 1.0)
Simulating Bark Beetle Outbreak Dynamics and their Influence on Carbon Balance Estimates with ORCHIDEE r7791
MEDFATE 2.9.3: a trait-enabled model to simulate Mediterranean forest function and dynamics at regional scales
Modelling the role of livestock grazing in C and N cycling in grasslands with LPJmL5.0-grazing
Implementation of trait-based ozone plant sensitivity in the Yale Interactive terrestrial Biosphere model v1.0 to assess global vegetation damage
The Permafrost and Organic LayEr module for Forest Models (POLE-FM) 1.0
CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics
Validation of a new spatially explicit process-based model (HETEROFOR) to simulate structurally and compositionally complex forest stands in eastern North America
Guohua Liu, Mirco Migliavacca, Christian Reimers, Basil Kraft, Markus Reichstein, Andrew D. Richardson, Lisa Wingate, Nicolas Delpierre, Hui Yang, and Alexander J. Winkler
Geosci. Model Dev., 17, 6683–6701, https://doi.org/10.5194/gmd-17-6683-2024, https://doi.org/10.5194/gmd-17-6683-2024, 2024
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Our study employs long short-term memory (LSTM) networks to model canopy greenness and phenology, integrating meteorological memory effects. The LSTM model outperforms traditional methods, enhancing accuracy in predicting greenness dynamics and phenological transitions across plant functional types. Highlighting the importance of multi-variate meteorological memory effects, our research pioneers unlock the secrets of vegetation phenology responses to climate change with deep learning techniques.
Thi Lan Anh Dinh, Daniel Goll, Philippe Ciais, and Ronny Lauerwald
Geosci. Model Dev., 17, 6725–6744, https://doi.org/10.5194/gmd-17-6725-2024, https://doi.org/10.5194/gmd-17-6725-2024, 2024
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The study assesses the performance of the dynamic global vegetation model (DGVM) ORCHIDEE in capturing the impact of land-use change on carbon stocks across Europe. Comparisons with observations reveal that the model accurately represents carbon fluxes and stocks. Despite the underestimations in certain land-use conversions, the model describes general trends in soil carbon response to land-use change, aligning with the site observations.
Nathaelle Bouttes, Lester Kwiatkowski, Manon Berger, Victor Brovkin, and Guy Munhoven
Geosci. Model Dev., 17, 6513–6528, https://doi.org/10.5194/gmd-17-6513-2024, https://doi.org/10.5194/gmd-17-6513-2024, 2024
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Coral reefs are crucial for biodiversity, but they also play a role in the carbon cycle on long time scales of a few thousand years. To better simulate the future and past evolution of coral reefs and their effect on the global carbon cycle, hence on atmospheric CO2 concentration, it is necessary to include coral reefs within a climate model. Here we describe the inclusion of coral reef carbonate production in a carbon–climate model and its validation in comparison to existing modern data.
Huajie Zhu, Mousong Wu, Fei Jiang, Michael Vossbeck, Thomas Kaminski, Xiuli Xing, Jun Wang, Weimin Ju, and Jing M. Chen
Geosci. Model Dev., 17, 6337–6363, https://doi.org/10.5194/gmd-17-6337-2024, https://doi.org/10.5194/gmd-17-6337-2024, 2024
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In this work, we developed the Nanjing University Carbon Assimilation System (NUCAS v1.0). Data assimilation experiments were conducted to demonstrate the robustness and investigate the feasibility and applicability of NUCAS. The assimilation of ecosystem carbonyl sulfide (COS) fluxes improved the model performance in gross primary productivity, evapotranspiration, and sensible heat, showing that COS provides constraints on parameters relevant to carbon-, water-, and energy-related processes.
Fang Li, Zhimin Zhou, Samuel Levis, Stephen Sitch, Felicity Hayes, Zhaozhong Feng, Peter B. Reich, Zhiyi Zhao, and Yanqing Zhou
Geosci. Model Dev., 17, 6173–6193, https://doi.org/10.5194/gmd-17-6173-2024, https://doi.org/10.5194/gmd-17-6173-2024, 2024
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A new scheme is developed to model the surface ozone damage to vegetation in regional and global process-based models. Based on 4210 data points from ozone experiments, it accurately reproduces statistically significant linear or nonlinear photosynthetic and stomatal responses to ozone in observations for all vegetation types. It also enables models to implicitly capture the variability in plant ozone tolerance and the shift among species within a vegetation type.
Alexander S. Brunmayr, Frank Hagedorn, Margaux Moreno Duborgel, Luisa I. Minich, and Heather D. Graven
Geosci. Model Dev., 17, 5961–5985, https://doi.org/10.5194/gmd-17-5961-2024, https://doi.org/10.5194/gmd-17-5961-2024, 2024
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A new generation of soil models promises to more accurately predict the carbon cycle in soils under climate change. However, measurements of 14C (the radioactive carbon isotope) in soils reveal that the new soil models face similar problems to the traditional models: they underestimate the residence time of carbon in soils and may therefore overestimate the net uptake of CO2 by the land ecosystem. Proposed solutions include restructuring the models and calibrating model parameters with 14C data.
Nina Raoult, Simon Beylat, James M. Salter, Frédéric Hourdin, Vladislav Bastrikov, Catherine Ottlé, and Philippe Peylin
Geosci. Model Dev., 17, 5779–5801, https://doi.org/10.5194/gmd-17-5779-2024, https://doi.org/10.5194/gmd-17-5779-2024, 2024
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We use computer models to predict how the land surface will respond to climate change. However, these complex models do not always simulate what we observe in real life, limiting their effectiveness. To improve their accuracy, we use sophisticated statistical and computational techniques. We test a technique called history matching against more common approaches. This method adapts well to these models, helping us better understand how they work and therefore how to make them more realistic.
Jorn Bruggeman, Karsten Bolding, Lars Nerger, Anna Teruzzi, Simone Spada, Jozef Skákala, and Stefano Ciavatta
Geosci. Model Dev., 17, 5619–5639, https://doi.org/10.5194/gmd-17-5619-2024, https://doi.org/10.5194/gmd-17-5619-2024, 2024
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To understand and predict the ocean’s capacity for carbon sequestration, its ability to supply food, and its response to climate change, we need the best possible estimate of its physical and biogeochemical properties. This is obtained through data assimilation which blends numerical models and observations. We present the Ensemble and Assimilation Tool (EAT), a flexible and efficient test bed that allows any scientist to explore and further develop the state of the art in data assimilation.
Dongyu Zheng, Andrew S. Merdith, Yves Goddéris, Yannick Donnadieu, Khushboo Gurung, and Benjamin J. W. Mills
Geosci. Model Dev., 17, 5413–5429, https://doi.org/10.5194/gmd-17-5413-2024, https://doi.org/10.5194/gmd-17-5413-2024, 2024
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This study uses a deep learning method to upscale the time resolution of paleoclimate simulations to 1 million years. This improved resolution allows a climate-biogeochemical model to more accurately predict climate shifts. The method may be critical in developing new fully continuous methods that are able to be applied over a moving continental surface in deep time with high resolution at reasonable computational expense.
Boris Ťupek, Aleksi Lehtonen, Alla Yurova, Rose Abramoff, Bertrand Guenet, Elisa Bruni, Samuli Launiainen, Mikko Peltoniemi, Shoji Hashimoto, Xianglin Tian, Juha Heikkinen, Kari Minkkinen, and Raisa Mäkipää
Geosci. Model Dev., 17, 5349–5367, https://doi.org/10.5194/gmd-17-5349-2024, https://doi.org/10.5194/gmd-17-5349-2024, 2024
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Updating the Yasso07 soil C model's dependency on decomposition with a hump-shaped Ricker moisture function improved modelled soil organic C (SOC) stocks in a catena of mineral and organic soils in boreal forest. The Ricker function, set to peak at a rate of 1 and calibrated against SOC and CO2 data using a Bayesian approach, showed a maximum in well-drained soils. Using SOC and CO2 data together with the moisture only from the topsoil humus was crucial for accurate model estimates.
Jacquelyn K. Shuman, Rosie A. Fisher, Charles Koven, Ryan Knox, Lara Kueppers, and Chonggang Xu
Geosci. Model Dev., 17, 4643–4671, https://doi.org/10.5194/gmd-17-4643-2024, https://doi.org/10.5194/gmd-17-4643-2024, 2024
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We adapt a fire behavior and effects module for use in a size-structured vegetation demographic model to test how climate, fire regime, and fire-tolerance plant traits interact to determine the distribution of tropical forests and grasslands. Our model captures the connection between fire disturbance and plant fire-tolerance strategies in determining plant distribution and provides a useful tool for understanding the vulnerability of these areas under changing conditions across the tropics.
Yoshiki Kanzaki, Isabella Chiaravalloti, Shuang Zhang, Noah J. Planavsky, and Christopher T. Reinhard
Geosci. Model Dev., 17, 4515–4532, https://doi.org/10.5194/gmd-17-4515-2024, https://doi.org/10.5194/gmd-17-4515-2024, 2024
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Soil pH is one of the most commonly measured agronomical and biogeochemical indices, mostly reflecting exchangeable acidity. Explicit simulation of both porewater and bulk soil pH is thus crucial to the accurate evaluation of alkalinity required to counteract soil acidification and the resulting capture of anthropogenic carbon dioxide through the enhanced weathering technique. This has been enabled by the updated reactive–transport SCEPTER code and newly developed framework to simulate soil pH.
David Sandoval, Iain Colin Prentice, and Rodolfo L. B. Nóbrega
Geosci. Model Dev., 17, 4229–4309, https://doi.org/10.5194/gmd-17-4229-2024, https://doi.org/10.5194/gmd-17-4229-2024, 2024
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Numerous estimates of water and energy balances depend on empirical equations requiring site-specific calibration, posing risks of "the right answers for the wrong reasons". We introduce novel first-principles formulations to calculate key quantities without requiring local calibration, matching predictions from complex land surface models.
Oliver Perkins, Matthew Kasoar, Apostolos Voulgarakis, Cathy Smith, Jay Mistry, and James D. A. Millington
Geosci. Model Dev., 17, 3993–4016, https://doi.org/10.5194/gmd-17-3993-2024, https://doi.org/10.5194/gmd-17-3993-2024, 2024
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Wildfire is often presented in the media as a danger to human life. Yet globally, millions of people’s livelihoods depend on using fire as a tool. So, patterns of fire emerge from interactions between humans, land use, and climate. This complexity means scientists cannot yet reliably say how fire will be impacted by climate change. So, we developed a new model that represents globally how people use and manage fire. The model reveals the extent and diversity of how humans live with and use fire.
Amos P. K. Tai, David H. Y. Yung, and Timothy Lam
Geosci. Model Dev., 17, 3733–3764, https://doi.org/10.5194/gmd-17-3733-2024, https://doi.org/10.5194/gmd-17-3733-2024, 2024
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We have developed the Terrestrial Ecosystem Model in R (TEMIR), which simulates plant carbon and pollutant uptake and predicts their response to varying atmospheric conditions. This model is designed to couple with an atmospheric chemistry model so that questions related to plant–atmosphere interactions, such as the effects of climate change, rising CO2, and ozone pollution on forest carbon uptake, can be addressed. The model has been well validated with both ground and satellite observations.
Jerome Guiet, Daniele Bianchi, Kim J. N. Scherrer, Ryan F. Heneghan, and Eric D. Galbraith
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-26, https://doi.org/10.5194/gmd-2024-26, 2024
Revised manuscript accepted for GMD
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Numerical models that capture key features of the global dynamics of fish communities play a crucial role in addressing the impacts of climate change and industrial fishing on ecosystems and societies. Here, we detail an update of the BiOeconomic marine Trophic Size-spectrum model that corrects the model representation of the dynamic of fisheries in the High Seas. This update also allows a better representation of biodiversity to improve future global and regional fisheries studies.
Fabian Stenzel, Johanna Braun, Jannes Breier, Karlheinz Erb, Dieter Gerten, Jens Heinke, Sarah Matej, Sebastian Ostberg, Sibyll Schaphoff, and Wolfgang Lucht
Geosci. Model Dev., 17, 3235–3258, https://doi.org/10.5194/gmd-17-3235-2024, https://doi.org/10.5194/gmd-17-3235-2024, 2024
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We provide an R package to compute two biosphere integrity metrics that can be applied to simulations of vegetation growth from the dynamic global vegetation model LPJmL. The pressure metric BioCol indicates that we humans modify and extract > 20 % of the potential preindustrial natural biomass production. The ecosystems state metric EcoRisk shows a high risk of ecosystem destabilization in many regions as a result of climate change and land, water, and fertilizer use.
Elin Ristorp Aas, Heleen A. de Wit, and Terje K. Berntsen
Geosci. Model Dev., 17, 2929–2959, https://doi.org/10.5194/gmd-17-2929-2024, https://doi.org/10.5194/gmd-17-2929-2024, 2024
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By including microbial processes in soil models, we learn how the soil system interacts with its environment and responds to climate change. We present a soil process model, MIMICS+, which is able to reproduce carbon stocks found in boreal forest soils better than a conventional land model. With the model we also find that when adding nitrogen, the relationship between soil microbes changes notably. Coupling the model to a vegetation model will allow for further study of these mechanisms.
Katarína Merganičová, Ján Merganič, Laura Dobor, Roland Hollós, Zoltán Barcza, Dóra Hidy, Zuzana Sitková, Pavel Pavlenda, Hrvoje Marjanovic, Daniel Kurjak, Michal Bošeľa, Doroteja Bitunjac, Masa Zorana Ostrogovic Sever, Jiří Novák, Peter Fleischer, and Tomáš Hlásny
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-45, https://doi.org/10.5194/gmd-2024-45, 2024
Revised manuscript accepted for GMD
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We developed a multi-objective calibration approach leading to robust parameter values, aiming to strike a balance between their local precision and broad applicability. Using Biome-BGCMuSo model, we tested the calibrated parameter sets for simulating European beech forest dynamics across large environmental gradients. Leveraging data from 87 plots and five European countries, the results demonstrated reasonable local accuracy and plausible large-scale productivity responses.
Thomas Wutzler, Christian Reimers, Bernhard Ahrens, and Marion Schrumpf
Geosci. Model Dev., 17, 2705–2725, https://doi.org/10.5194/gmd-17-2705-2024, https://doi.org/10.5194/gmd-17-2705-2024, 2024
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Soil microbes provide a strong link for elemental fluxes in the earth system. The SESAM model applies an optimality assumption to model those linkages and their adaptation. We found that a previous heuristic description was a special case of a newly developed more rigorous description. The finding of new behaviour at low microbial biomass led us to formulate the constrained enzyme hypothesis. We now can better describe how microbially mediated linkages of elemental fluxes adapt across decades.
Salvatore R. Curasi, Joe R. Melton, Elyn R. Humphreys, Txomin Hermosilla, and Michael A. Wulder
Geosci. Model Dev., 17, 2683–2704, https://doi.org/10.5194/gmd-17-2683-2024, https://doi.org/10.5194/gmd-17-2683-2024, 2024
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Canadian forests are responding to fire, harvest, and climate change. Models need to quantify these processes and their carbon and energy cycling impacts. We develop a scheme that, based on satellite records, represents fire, harvest, and the sparsely vegetated areas that these processes generate. We evaluate model performance and demonstrate the impacts of disturbance on carbon and energy cycling. This work has implications for land surface modeling and assessing Canada’s terrestrial C cycle.
Yannek Käber, Florian Hartig, and Harald Bugmann
Geosci. Model Dev., 17, 2727–2753, https://doi.org/10.5194/gmd-17-2727-2024, https://doi.org/10.5194/gmd-17-2727-2024, 2024
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Many forest models include detailed mechanisms of forest growth and mortality, but regeneration is often simplified. Testing and improving forest regeneration models is challenging. We address this issue by exploring how forest inventories from unmanaged European forests can be used to improve such models. We find that competition for light among trees is captured by the model, unknown model components can be informed by forest inventory data, and climatic effects are challenging to capture.
Jalisha T. Kallingal, Johan Lindström, Paul A. Miller, Janne Rinne, Maarit Raivonen, and Marko Scholze
Geosci. Model Dev., 17, 2299–2324, https://doi.org/10.5194/gmd-17-2299-2024, https://doi.org/10.5194/gmd-17-2299-2024, 2024
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By unlocking the mysteries of CH4 emissions from wetlands, our work improved the accuracy of the LPJ-GUESS vegetation model using Bayesian statistics. Via assimilation of long-term real data from a wetland, we significantly enhanced CH4 emission predictions. This advancement helps us better understand wetland contributions to atmospheric CH4, which are crucial for addressing climate change. Our method offers a promising tool for refining global climate models and guiding conservation efforts
Stephen Björn Wirth, Johanna Braun, Jens Heinke, Sebastian Ostberg, Susanne Rolinski, Sibyll Schaphoff, Fabian Stenzel, Werner von Bloh, and Christoph Müller
EGUsphere, https://doi.org/10.5194/egusphere-2023-2946, https://doi.org/10.5194/egusphere-2023-2946, 2024
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We present a new approach to model biological nitrogen fixation (BNF) in the Lund Potsdam Jena managed Land dynamic global vegetation model. While in the original approach BNF depended on actual evapotranspiration, the new approach considers soil water content and temperature, the nitrogen (N) deficit and carbon (C) costs. The new approach improved global sums and spatial patterns of BNF compared to the scientific literature and the models’ ability to project future C and N cycle dynamics.
Benjamin Post, Esteban Acevedo-Trejos, Andrew D. Barton, and Agostino Merico
Geosci. Model Dev., 17, 1175–1195, https://doi.org/10.5194/gmd-17-1175-2024, https://doi.org/10.5194/gmd-17-1175-2024, 2024
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Creating computational models of how phytoplankton grows in the ocean is a technical challenge. We developed a new tool set (Xarray-simlab-ODE) for building such models using the programming language Python. We demonstrate the tool set in a library of plankton models (Phydra). Our goal was to allow scientists to develop models quickly, while also allowing the model structures to be changed easily. This allows us to test many different structures of our models to find the most appropriate one.
Taeken Wijmer, Ahmad Al Bitar, Ludovic Arnaud, Remy Fieuzal, and Eric Ceschia
Geosci. Model Dev., 17, 997–1021, https://doi.org/10.5194/gmd-17-997-2024, https://doi.org/10.5194/gmd-17-997-2024, 2024
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Quantification of carbon fluxes of crops is an essential building block for the construction of a monitoring, reporting, and verification approach. We developed an end-to-end platform (AgriCarbon-EO) that assimilates, through a Bayesian approach, high-resolution (10 m) optical remote sensing data into radiative transfer and crop modelling at regional scale (100 x 100 km). Large-scale estimates of carbon flux are validated against in situ flux towers and yield maps and analysed at regional scale.
Moritz Laub, Sergey Blagodatsky, Marijn Van de Broek, Samuel Schlichenmaier, Benjapon Kunlanit, Johan Six, Patma Vityakon, and Georg Cadisch
Geosci. Model Dev., 17, 931–956, https://doi.org/10.5194/gmd-17-931-2024, https://doi.org/10.5194/gmd-17-931-2024, 2024
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To manage soil organic matter (SOM) sustainably, we need a better understanding of the role that soil microbes play in aggregate protection. Here, we propose the SAMM model, which connects soil aggregate formation to microbial growth. We tested it against data from a tropical long-term experiment and show that SAMM effectively represents the microbial growth, SOM, and aggregate dynamics and that it can be used to explore the importance of aggregate formation in SOM stabilization.
Jianhong Lin, Daniel Berveiller, Christophe François, Heikki Hänninen, Alexandre Morfin, Gaëlle Vincent, Rui Zhang, Cyrille Rathgeber, and Nicolas Delpierre
Geosci. Model Dev., 17, 865–879, https://doi.org/10.5194/gmd-17-865-2024, https://doi.org/10.5194/gmd-17-865-2024, 2024
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Currently, the high variability of budburst between individual trees is overlooked. The consequences of this neglect when projecting the dynamics and functioning of tree communities are unknown. Here we develop the first process-oriented model to describe the difference in budburst dates between individual trees in plant populations. Beyond budburst, the model framework provides a basis for studying the dynamics of phenological traits under climate change, from the individual to the community.
Skyler Kern, Mary E. McGuinn, Katherine M. Smith, Nadia Pinardi, Kyle E. Niemeyer, Nicole S. Lovenduski, and Peter E. Hamlington
Geosci. Model Dev., 17, 621–649, https://doi.org/10.5194/gmd-17-621-2024, https://doi.org/10.5194/gmd-17-621-2024, 2024
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Computational models are used to simulate the behavior of marine ecosystems. The models often have unknown parameters that need to be calibrated to accurately represent observational data. Here, we propose a novel approach to simultaneously determine a large set of parameters for a one-dimensional model of a marine ecosystem in the surface ocean at two contrasting sites. By utilizing global and local optimization techniques, we estimate many parameters in a computationally efficient manner.
Shuaitao Wang, Vincent Thieu, Gilles Billen, Josette Garnier, Marie Silvestre, Audrey Marescaux, Xingcheng Yan, and Nicolas Flipo
Geosci. Model Dev., 17, 449–476, https://doi.org/10.5194/gmd-17-449-2024, https://doi.org/10.5194/gmd-17-449-2024, 2024
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This paper presents unified RIVE v1.0, a unified version of the freshwater biogeochemistry model RIVE. It harmonizes different RIVE implementations, providing the referenced formalisms for microorganism activities to describe full biogeochemical cycles in the water column (e.g., carbon, nutrients, oxygen). Implemented as open-source projects in Python 3 (pyRIVE 1.0) and ANSI C (C-RIVE 0.32), unified RIVE v1.0 promotes and enhances collaboration among research teams and public services.
Sam S. Rabin, William J. Sacks, Danica L. Lombardozzi, Lili Xia, and Alan Robock
Geosci. Model Dev., 16, 7253–7273, https://doi.org/10.5194/gmd-16-7253-2023, https://doi.org/10.5194/gmd-16-7253-2023, 2023
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Climate models can help us simulate how the agricultural system will be affected by and respond to environmental change, but to be trustworthy they must realistically reproduce historical patterns. When farmers plant their crops and what varieties they choose will be important aspects of future adaptation. Here, we improve the crop component of a global model to better simulate observed growing seasons and examine the impacts on simulated crop yields and irrigation demand.
Weihang Liu, Tao Ye, Christoph Müller, Jonas Jägermeyr, James A. Franke, Haynes Stephens, and Shuo Chen
Geosci. Model Dev., 16, 7203–7221, https://doi.org/10.5194/gmd-16-7203-2023, https://doi.org/10.5194/gmd-16-7203-2023, 2023
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We develop a machine-learning-based crop model emulator with the inputs and outputs of multiple global gridded crop model ensemble simulations to capture the year-to-year variation of crop yield under future climate change. The emulator can reproduce the year-to-year variation of simulated yield given by the crop models under CO2, temperature, water, and nitrogen perturbations. Developing this emulator can provide a tool to project future climate change impact in a simple way.
Jurjen Rooze, Heewon Jung, and Hagen Radtke
Geosci. Model Dev., 16, 7107–7121, https://doi.org/10.5194/gmd-16-7107-2023, https://doi.org/10.5194/gmd-16-7107-2023, 2023
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Chemical particles in nature have properties such as age or reactivity. Distributions can describe the properties of chemical concentrations. In nature, they are affected by mixing processes, such as chemical diffusion, burrowing animals, and bottom trawling. We derive equations for simulating the effect of mixing on central moments that describe the distributions. We then demonstrate applications in which these equations are used to model continua in disturbed natural environments.
Esteban Acevedo-Trejos, Jean Braun, Katherine Kravitz, N. Alexia Raharinirina, and Benoît Bovy
Geosci. Model Dev., 16, 6921–6941, https://doi.org/10.5194/gmd-16-6921-2023, https://doi.org/10.5194/gmd-16-6921-2023, 2023
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The interplay of tectonics and climate influences the evolution of life and the patterns of biodiversity we observe on earth's surface. Here we present an adaptive speciation component coupled with a landscape evolution model that captures the essential earth-surface, ecological, and evolutionary processes that lead to the diversification of taxa. We can illustrate with our tool how life and landforms co-evolve to produce distinct biodiversity patterns on geological timescales.
Veli Çağlar Yumruktepe, Erik Askov Mousing, Jerry Tjiputra, and Annette Samuelsen
Geosci. Model Dev., 16, 6875–6897, https://doi.org/10.5194/gmd-16-6875-2023, https://doi.org/10.5194/gmd-16-6875-2023, 2023
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We present an along BGC-Argo track 1D modelling framework. The model physics is constrained by the BGC-Argo temperature and salinity profiles to reduce the uncertainties related to mixed layer dynamics, allowing the evaluation of the biogeochemical formulation and parameterization. We objectively analyse the model with BGC-Argo and satellite data and improve the model biogeochemical dynamics. We present the framework, example cases and routines for model improvement and implementations.
Tanya J. R. Lippmann, Ype van der Velde, Monique M. P. D. Heijmans, Han Dolman, Dimmie M. D. Hendriks, and Ko van Huissteden
Geosci. Model Dev., 16, 6773–6804, https://doi.org/10.5194/gmd-16-6773-2023, https://doi.org/10.5194/gmd-16-6773-2023, 2023
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Vegetation is a critical component of carbon storage in peatlands but an often-overlooked concept in many peatland models. We developed a new model capable of simulating the response of vegetation to changing environments and management regimes. We evaluated the model against observed chamber data collected at two peatland sites. We found that daily air temperature, water level, harvest frequency and height, and vegetation composition drive methane and carbon dioxide emissions.
Chonggang Xu, Bradley Christoffersen, Zachary Robbins, Ryan Knox, Rosie A. Fisher, Rutuja Chitra-Tarak, Martijn Slot, Kurt Solander, Lara Kueppers, Charles Koven, and Nate McDowell
Geosci. Model Dev., 16, 6267–6283, https://doi.org/10.5194/gmd-16-6267-2023, https://doi.org/10.5194/gmd-16-6267-2023, 2023
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We introduce a plant hydrodynamic model for the U.S. Department of Energy (DOE)-sponsored model, the Functionally Assembled Terrestrial Ecosystem Simulator (FATES). To better understand this new model system and its functionality in tropical forest ecosystems, we conducted a global parameter sensitivity analysis at Barro Colorado Island, Panama. We identified the key parameters that affect the simulated plant hydrodynamics to guide both modeling and field campaign studies.
Jianghui Du
Geosci. Model Dev., 16, 5865–5894, https://doi.org/10.5194/gmd-16-5865-2023, https://doi.org/10.5194/gmd-16-5865-2023, 2023
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Trace elements and isotopes (TEIs) are important tools to study the changes in the ocean environment both today and in the past. However, the behaviors of TEIs in marine sediments are poorly known, limiting our ability to use them in oceanography. Here we present a modeling framework that can be used to generate and run models of the sedimentary cycling of TEIs assisted with advanced numerical tools in the Julia language, lowering the coding barrier for the general user to study marine TEIs.
Siyu Zhu, Peipei Wu, Siyi Zhang, Oliver Jahn, Shu Li, and Yanxu Zhang
Geosci. Model Dev., 16, 5915–5929, https://doi.org/10.5194/gmd-16-5915-2023, https://doi.org/10.5194/gmd-16-5915-2023, 2023
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In this study, we estimate the global biogeochemical cycling of Hg in a state-of-the-art physical-ecosystem ocean model (high-resolution-MITgcm/Hg), providing a more accurate portrayal of surface Hg concentrations in estuarine and coastal areas, strong western boundary flow and upwelling areas, and concentration diffusion as vortex shapes. The high-resolution model can help us better predict the transport and fate of Hg in the ocean and its impact on the global Hg cycle.
Maria Val Martin, Elena Blanc-Betes, Ka Ming Fung, Euripides P. Kantzas, Ilsa B. Kantola, Isabella Chiaravalloti, Lyla L. Taylor, Louisa K. Emmons, William R. Wieder, Noah J. Planavsky, Michael D. Masters, Evan H. DeLucia, Amos P. K. Tai, and David J. Beerling
Geosci. Model Dev., 16, 5783–5801, https://doi.org/10.5194/gmd-16-5783-2023, https://doi.org/10.5194/gmd-16-5783-2023, 2023
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Enhanced rock weathering (ERW) is a CO2 removal strategy that involves applying crushed rocks (e.g., basalt) to agricultural soils. However, unintended processes within the N cycle due to soil pH changes may affect the climate benefits of C sequestration. ERW could drive changes in soil emissions of non-CO2 GHGs (N2O) and trace gases (NO and NH3) that may affect air quality. We present a new improved N cycling scheme for the land model (CLM5) to evaluate ERW effects on soil gas N emissions.
Özgür Gürses, Laurent Oziel, Onur Karakuş, Dmitry Sidorenko, Christoph Völker, Ying Ye, Moritz Zeising, Martin Butzin, and Judith Hauck
Geosci. Model Dev., 16, 4883–4936, https://doi.org/10.5194/gmd-16-4883-2023, https://doi.org/10.5194/gmd-16-4883-2023, 2023
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This paper assesses the biogeochemical model REcoM3 coupled to the ocean–sea ice model FESOM2.1. The model can be used to simulate the carbon uptake or release of the ocean on timescales of several hundred years. A detailed analysis of the nutrients, ocean productivity, and ecosystem is followed by the carbon cycle. The main conclusion is that the model performs well when simulating the observed mean biogeochemical state and variability and is comparable to other ocean–biogeochemical models.
Hocheol Seo and Yeonjoo Kim
Geosci. Model Dev., 16, 4699–4713, https://doi.org/10.5194/gmd-16-4699-2023, https://doi.org/10.5194/gmd-16-4699-2023, 2023
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Wildfire is a crucial factor in carbon and water fluxes on the Earth system. About 2.1 Pg of carbon is released into the atmosphere by wildfires annually. Because the fire processes are still limitedly represented in land surface models, we forced the daily GFED4 burned area into the land surface model over Alaska and Siberia. The results with the GFED4 burned area significantly improved the simulated carbon emissions and net ecosystem exchange compared to the default simulation.
Hideki Ninomiya, Tomomichi Kato, Lea Végh, and Lan Wu
Geosci. Model Dev., 16, 4155–4170, https://doi.org/10.5194/gmd-16-4155-2023, https://doi.org/10.5194/gmd-16-4155-2023, 2023
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Non-structural carbohydrates (NSCs) play a crucial role in plants to counteract the effects of climate change. We added a new NSC module into the SEIB-DGVM, an individual-based ecosystem model. The simulated NSC levels and their seasonal patterns show a strong agreement with observed NSC data at both point and global scales. The model can be used to simulate the biotic effects resulting from insufficient NSCs, which are otherwise difficult to measure in terrestrial ecosystems globally.
Guillaume Marie, Jina Jeong, Hervé Jactel, Gunnar Petter, Maxime Cailleret, Matthew McGrath, Vladislav Bastrikov, Josefine Ghattas, Bertrand Guenet, Anne-Sofie Lansø, Kim Naudts, Aude Valade, Chao Yue, and Sebastiaan Luyssaert
EGUsphere, https://doi.org/10.5194/egusphere-2023-1216, https://doi.org/10.5194/egusphere-2023-1216, 2023
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This research looks at how climate change influences forests, particularly how altered wind and insect activities could make forests emit, instead of absorb, carbon. We've updated a land surface model called ORCHIDEE to better examine the effect of bark beetles on forest health. Our findings suggest that sudden events, like insect outbreaks, can dramatically affect carbon storage, offering crucial insights for tackling climate change.
Miquel De Cáceres, Roberto Molowny-Horas, Antoine Cabon, Jordi Martínez-Vilalta, Maurizio Mencuccini, Raúl García-Valdés, Daniel Nadal-Sala, Santiago Sabaté, Nicolas Martin-StPaul, Xavier Morin, Francesco D'Adamo, Enric Batllori, and Aitor Améztegui
Geosci. Model Dev., 16, 3165–3201, https://doi.org/10.5194/gmd-16-3165-2023, https://doi.org/10.5194/gmd-16-3165-2023, 2023
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Regional-level applications of dynamic vegetation models are challenging because they need to accommodate the variation in plant functional diversity. This can be done by estimating parameters from available plant trait databases while adopting alternative solutions for missing data. Here we present the design, parameterization and evaluation of MEDFATE (version 2.9.3), a novel model of forest dynamics for its application over a region in the western Mediterranean Basin.
Jens Heinke, Susanne Rolinski, and Christoph Müller
Geosci. Model Dev., 16, 2455–2475, https://doi.org/10.5194/gmd-16-2455-2023, https://doi.org/10.5194/gmd-16-2455-2023, 2023
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We develop a livestock module for the global vegetation model LPJmL5.0 to simulate the impact of grazing dairy cattle on carbon and nitrogen cycles in grasslands. A novelty of the approach is that it accounts for the effect of feed quality on feed uptake and feed utilization by animals. The portioning of dietary nitrogen into milk, feces, and urine shows very good agreement with estimates obtained from animal trials.
Yimian Ma, Xu Yue, Stephen Sitch, Nadine Unger, Johan Uddling, Lina M. Mercado, Cheng Gong, Zhaozhong Feng, Huiyi Yang, Hao Zhou, Chenguang Tian, Yang Cao, Yadong Lei, Alexander W. Cheesman, Yansen Xu, and Maria Carolina Duran Rojas
Geosci. Model Dev., 16, 2261–2276, https://doi.org/10.5194/gmd-16-2261-2023, https://doi.org/10.5194/gmd-16-2261-2023, 2023
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Plants have been found to respond differently to O3, but the variations in the sensitivities have rarely been explained nor fully implemented in large-scale assessment. This study proposes a new O3 damage scheme with leaf mass per area to unify varied sensitivities for all plant species. Our assessment reveals an O3-induced reduction of 4.8 % in global GPP, with the highest reduction of >10 % for cropland, suggesting an emerging risk of crop yield loss under the threat of O3 pollution.
Winslow D. Hansen, Adrianna Foster, Benjamin Gaglioti, Rupert Seidl, and Werner Rammer
Geosci. Model Dev., 16, 2011–2036, https://doi.org/10.5194/gmd-16-2011-2023, https://doi.org/10.5194/gmd-16-2011-2023, 2023
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Permafrost and the thick soil-surface organic layers that insulate permafrost are important controls of boreal forest dynamics and carbon cycling. However, both are rarely included in process-based vegetation models used to simulate future ecosystem trajectories. To address this challenge, we developed a computationally efficient permafrost and soil organic layer module that operates at fine spatial (1 ha) and temporal (daily) resolutions.
Heewon Jung, Hyun-Seob Song, and Christof Meile
Geosci. Model Dev., 16, 1683–1696, https://doi.org/10.5194/gmd-16-1683-2023, https://doi.org/10.5194/gmd-16-1683-2023, 2023
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Microbial activity responsible for many chemical transformations depends on environmental conditions. These can vary locally, e.g., between poorly connected pores in porous media. We present a modeling framework that resolves such small spatial scales explicitly, accounts for feedback between transport and biogeochemical conditions, and can integrate state-of-the-art representations of microbes in a computationally efficient way, making it broadly applicable in science and engineering use cases.
Arthur Guignabert, Quentin Ponette, Frédéric André, Christian Messier, Philippe Nolet, and Mathieu Jonard
Geosci. Model Dev., 16, 1661–1682, https://doi.org/10.5194/gmd-16-1661-2023, https://doi.org/10.5194/gmd-16-1661-2023, 2023
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Spatially explicit and process-based models are useful to test innovative forestry practices under changing and uncertain conditions. However, their larger use is often limited by the restricted range of species and stand structures they can reliably account for. We therefore calibrated and evaluated such a model, HETEROFOR, for 23 species across southern Québec. Our results showed that the model is robust and can predict accurately both individual tree growth and stand dynamics in this region.
Cited articles
Ait Ballagh, F. E., Rabouille, C., Andrieux-Loyer, F., Soetaert, K.,
Lansard, B., Bombled, B., Monvoisin, G., Elkalay, K., and Khalil, K.:
Spatial variability of organic matter and phosphorus cycling in rhône
river prodelta sediments (NW mediterranean sea, france): A model-data
approach, Estuaries Coasts, 44, 1765–1789, 2021.
Aller, R. C.: Mobile deltaic and continental shelf muds as suboxic,
fluidized bed reactors, Marine Chem., 61, 143–155, 1998.
Aller, R. C.: Conceptual models of early diagenetic processes: The muddy
seafloor as an unsteady, batch reactor, J. Marine Res., 62,
815–835, 2004.
Aller, R. C. and Aller, J. Y.: Meiofauna and solute transport in marine
muds, Limnol. Oceanogr., 37, 1018–1033, 1992.
Anschutz, P., Jorissen, F., Chaillou, G., Abu-Zied, R., and Fontanier, C.:
Recent turbidite deposition in the eastern Atlantic: early diagenesis and
biotic recovery, J. Marine Res., 60, 835–854, 2002.
Antonelli, C., Eyrolle, F., Rolland, B., Provansal, M., and Sabatier,F.: Suspended sediment and 137Cs fluxes during the exceptional December
2003 flood in the Rhône River, southeast France, Geomorphology, 95,
350–360, 2008.
Archer, D., Morford, J., and Emerson, S.: A model of suboxic sedimentary
diagenesis suitable for automatic tuning and gridded global domains, Global
Biogeochem. Cycles, 16, 17-1–17-21, 2002.
Arndt, S., Jørgensen, B. B., LaRowe, D. E., Middelburg, J., Pancost, R.,
and Regnier, P.: Quantifying the degradation of organic matter in marine
sediments: a review and synthesis, Earth-Sci. Rev., 123, 53–86, 2013.
Bauer, J. E., Cai, W.-J., Raymond, P. A., Bianchi, T. S., Hopkinson, C. S.,
and Regnier, P. A.: The changing carbon cycle of the coastal ocean, Nature,
504, 61–70, 2013.
Berg, P., Rysgaard, S., and Thamdrup, B.: Dynamic modeling of early
diagenesis and nutrient cycling. A case study in an artic marine sediment,
Am. J. Sci., 303, 905–955, 2003.
Berner, R. A.: Early Diagenesis: A Theoretical Approach, Princeton
University Press, https://doi.org/10.1515/9780691209401, 1980.
Bissett, A., Burke, C., Cook, P. L., and Bowman, J. P.: Bacterial community
shifts in organically perturbed sediments, Environ. Microbiol., 9,
46–60, 2007.
Boudet, L., Sabatier, F., and Radakovitch, O.: Modelling of sediment
transport pattern in the mouth of the Rhône delta: Role of storm and
flood events, Estuarine, Coast. Shelf Sci., 198, 568–582,
https://doi.org/10.1016/j.ecss.2016.10.004, 2017.
Boudreau, B. P.: Is burial velocity a master parameter for bioturbation?, Geochim. Cosmochim. Ac., 58, 1243–1249, 1994.
Boudreau, B. P.: A method-of-lines code for carbon and nutrient diagenesis
in aquatic sediments, Comput. Geosci., 22, 479–496, 1996.
Boudreau, B. P.: Diagenetic models and their implementation, vol. 410,
Springer, Berlin, https://doi.org/10.1007/97S-3-642-60421-S, 1997.
Boudreau, B. P. and Jorgensen, B. B.: The benthic boundary layer: Transport
processes and biogeochemistry, Oxford University Press, ISBN 0-19-511881-2, 2001.
Bourgeois, S., Pruski, A. M., Sun, M.-Y., Buscail, R., Lantoine, F., Kerhervé, P., Vétion, G., Rivière, B., and Charles, F.: Distribution and lability of land-derived organic matter in the surface sediments of the Rhône prodelta and the adjacent shelf (Mediterranean Sea, France): a multi proxy study, Biogeosciences, 8, 3107–3125, https://doi.org/10.5194/bg-8-3107-2011, 2011.
Burdige, D. J.: The kinetics of organic matter mineralization in anoxic
marine sediments, J. Marine Res., 49, 727–761, 1991.
Burdige, D. J.: Burial of terrestrial organic matter in marine sediments: A
re-assessment, Global Biogeochem. Cycles, 19, GB4011, https://doi.org/10.1029/2004GB002368, 2005.
Burdige, D. J. and Komada, T.: Anaerobic oxidation of methane and the stoichiometry of remineralization processes in continental margin sediments, Limnol. Oceanogr., 56, 1781–1796, 2011.
Cai, W.-J.: Estuarine and coastal ocean carbon paradox: CO2 sinks or sites
of terrestrial carbon incineration?, Annu. Rev. Marine Sci., 3,
123–145, 2011.
Cathalot, C., Rabouille, C., Pastor, L., Deflandre, B., Viollier, E., Buscail, R., Grémare, A., Treignier, C., and Pruski, A.: Temporal variability of carbon recycling in coastal sediments influenced by rivers: assessing the impact of flood inputs in the Rhône River prodelta, Biogeosciences, 7, 1187–1205, https://doi.org/10.5194/bg-7-1187-2010, 2010.
Cathalot, C., Rabouille, C., Tisnérat-Laborde, N., Toussaint, F.,
Kerhervé, P., Buscail, R., Loftis, K., Sun, M.-Y., Tronczynski, J.,
Azoury, S., and Lansard, B.: The fate of river organic carbon in coastal areas: A
study in the Rhône River delta using multiple isotopic (δ13C,
Δ14C) and organic tracers, Geochim. Cosmochim. Ac., 118,
33–55, 2013.
Chaillou, G., Anschutz, P., Dubrulle, C., and Lecroart, P.: Transient states
in diagenesis following the deposition of a gravity layer: dynamics of O 2,
Mn, Fe and N-species in experimental units, Aquatic Geochem., 13,
157–172, 2007.
Couture, R.-M., Shafei, B., Van Cappellen, P., Tessier, A., and Gobeil, C.:
Non-steady state modeling of arsenic diagenesis in lake sediments,
Environ. Sci. Technol., 44, 197–203, 2010.
De Borger, E., Tiano, J., Braeckman, U., Rijnsdorp, A. D., and Soetaert, K.: Impact of bottom trawling on sediment biogeochemistry: a modelling approach, Biogeosciences, 18, 2539–2557, https://doi.org/10.5194/bg-18-2539-2021, 2021.
Deflandre, B., Mucci, A., Gagné, J.-P., Guignard, C., and Jørn
Sundby, B.: Early diagenetic processes in coastal marine sediments disturbed
by a catastrophic sedimentation event, Geochim. Cosmochim. Ac., 66,
2547–2558, 2002.
Dezzeo, N., Herrera, R., Escalante, G., and Chacón, N.: Deposition of
sediments during a flood event on seasonally flooded forests of the lower
Orinoco River and two of its black-water tributaries, Venezuela,
Biogeochemistry, 49, 241–257, 2000.
Dumoulin, J., Pozzato, L., Rassman, J., Toussaint, F., Fontugne, M.,
Tisnérat-Laborde, N., Beck, L., Caffy, I., Delqué-Koli, C. E.,
Moreau, C., and Rabouille, C.: Isotopic Signature (δ13C,14C) of DIC in Sediment
Pore Waters: An Example from the Rhône River Delta, Radiocarbon, 60,
1465–1481, 2018.
Efron, B.: Bootstrap methods: another look at the jackknife, in:
Breakthroughs in statistics, Springer, 569–593, https://doi.org/10.1007/978-1-4612-4380-9_41, 1992.
Fiadeiro, M. E. and Veronis, G.: On weighted-mean schemes for the finite-difference approximation to the advection-diffusion equation, Tellus, 29, 512–522, 1977.
Froelich, P., Klinkhammer, G., Bender, M. L., Luedtke, N., Heath, G. R.,
Cullen, D., Dauphin, P., Hammond, D., Hartman, B., and Maynard, V.: Early
oxidation of organic matter in pelagic sediments of the eastern equatorial
Atlantic: suboxic diagenesis, Geochim. Cosmochim. Ac., 43,
1075–1090, 1979.
Ghil, M.: A century of nonlinearity in the geosciences, Earth Space
Sci., 6, 1007–1042, 2019.
Gooday, A. J.: Biological responses to seasonally varying fluxes of organic
matter to the ocean floor: a review, J. Oceanogr., 58, 305–332,
2002.
Grenz, C., Denis, L., Boucher, G., Chauvaud, L., Clavier, J., Fichez, R.,
and Pringault, O.: Spatial variability in sediment oxygen consumption under
winter conditions in a lagoonal system in new caledonia (south pacific), Elsevier,
285, 33–47, 2003.
Gruber, N.: Carbon at the coastal interface, Nature, 517, 148–149, 2015.
Hensel, P. F., Day, J. W., Pont, D., and Day, J. N.: Short-Term
Sedimentation Dynamics in the Rhône River Delta, France: The Importance
of Riverine Pulsing, Estuaries, 21, 52, https://doi.org/10.2307/1352546,
1998.
Hindmarsh, A. C.: ODEPACK: A systemized collection of ODE solvers, 55–64,
1983.
Jørgensen, B. B. and Revsbech, N. P.: Diffusive boundary layers and the
oxygen uptake of sediments and detritus 1, Limnol. Oceanogr., 30,
111–122, 1985.
Jørgensen, B. B., Findlay, A. J., and Pellerin, A.: The biogeochemical
sulfur cycle of marine sediments, Front. Microbiol., 10, 849, https://doi.org/10.3389/fmicb.2019.00849, 2019.
Katsev, S., Sundby, B., and Mucci, A.: Modeling vertical excursions of the
redox boundary in sediments: Application to deep basins of the Arctic Ocean,
Limnol. Oceanogr., 51, 1581–1593,
https://doi.org/10.4319/lo.2006.51.4.1581, 2006.
Kittel, T., Heitzig, J., Webster, K., and Kurths, J.: Timing of transients:
quantifying reaching times and transient behavior in complex systems, New
Journal of Physics, 19, 083005, https://doi.org/10.1088/1367-2630/aa7b61, 2017.
Krumins, V., Gehlen, M., Arndt, S., Van Cappellen, P., and Regnier, P.: Dissolved inorganic carbon and alkalinity fluxes from coastal marine sediments: model estimates for different shelf environments and sensitivity to global change, Biogeosciences, 10, 371–398, https://doi.org/10.5194/bg-10-371-2013, 2013.
Lansard, B., Rabouille, C., Denis, L., and Grenz, C.: In situ oxygen uptake
rates by coastal sediments under the influence of the Rhône River (NW
Mediterranean Sea), Cont. Shelf Res., 28, 1501–1510,
https://doi.org/10.1016/j.csr.2007.10.010, 2008.
Lansard, B., Rabouille, C., Denis, L., and Grenz, C.: Benthic
remineralization at the land–ocean interface: A case study of the Rhône
River (NW Mediterranean Sea), Estuarine, Coast. Shelf Sci., 81,
544–554, 2009.
Lasaga, A. and Holland, H.: Mathematical aspects of non-steady-state
diagenesis, Geochim. Cosmochim. Ac., 40, 257–266, 1976.
Lorenz, E. N.: Deterministic nonperiodic flow, J. Atmos.
Sci., 20, 130–141, 1963.
Mayer, L. M.: Surface area control of organic carbon accumulation in
continental shelf sediments, Geochim. Cosmochim. Ac., 58,
1271–1284, 1994.
McKee, B. A., Aller, R., Allison, M., Bianchi, T., and Kineke, G.: Transport
and transformation of dissolved and particulate materials on continental
margins influenced by major rivers: benthic boundary layer and seabed
processes, Cont. Shelf Res., 24, 899–926, 2004.
Mermex Group, T. M., de Madron, X. D., Guieu, C., Sempéré, R.,
Conan, P., Cossa, D., D'Ortenzio, F., Estournel, C., Gazeau, F., Rabouille,
C., and Stemmann, L.: Marine ecosystems' responses to climatic and anthropogenic
forcings in the Mediterranean, Prog. Oceanogr., 91, 97–166, 2011.
Meybeck, M., Dürr, H., Roussennac, S., and Ludwig, W.: Regional seas and
their interception of riverine fluxes to oceans, Marine Chem., 106,
301–325, 2007.
Middelburg, J. J.: A simple rate model for organic matter decomposition in
marine sediments, Geochim. Cosmochim. Ac., 53, 1577–1581, 1989.
Middelburg, J. J., Vlug, T., Jaco, F., and Van der Nat, W.: Organic matter
mineralization in marine systems, Global Planet. Change, 8, 47–58,
1993.
Middelburg, J. J., Soetaert, K., and Herman, P. M.: Empirical relationships
for use in global diagenetic models, Deep-Sea Res. Pt. I, 44, 327–344, 1997.
Miralles, J., Radakovitch, O., and Aloisi, J.-C.: 210Pb sedimentation rates
from the Northwestern Mediterranean margin, Marine Geol., 216, 155–167,
https://doi.org/10.1016/j.margeo.2005.02.020, 2005.
Mucci, A. and Edenborn, H. M.: Influence of an organic-poor landslide
deposit on the early diagenesis of iron and manganese in a coastal marine
sediment, Geochim. Cosmochim. Ac., 56, 3909–3921, 1992.
Munhoven, G.: Model of Early Diagenesis in the Upper Sediment with Adaptable complexity – MEDUSA (v. 2): a time-dependent biogeochemical sediment module for Earth system models, process analysis and teaching, Geosci. Model Dev., 14, 3603–3631, https://doi.org/10.5194/gmd-14-3603-2021, 2021.
Nmor, S. and Soetaert, K.: FESDIA: An early diagenesis model including Iron (Fe), Sulfur (S) and Methane (CH4) dynamics, Zenodo [code], https://doi.org/10.5281/zenodo.6369288, 2022.
Pastor, L., Cathalot, C., Deflandre, B., Viollier, E., Soetaert, K., Meysman, F. J. R., Ulses, C., Metzger, E., and Rabouille, C.: Modeling biogeochemical processes in sediments from the Rhône River prodelta area (NW Mediterranean Sea), Biogeosciences, 8, 1351–1366, https://doi.org/10.5194/bg-8-1351-2011, 2011.
Pastor, L., Rabouille, C., Metzger, E., Thibault de Chanvalon, A., Viollier, E., and Deflandre, B.: Transient
early diagenetic processes in Rhône prodelta sediments revealed in
contrasting flood events, Cont. Shelf Res., 166, 65–76,
https://doi.org/10.1016/j.csr.2018.07.005, 2018.
Pont, D., Day, J. W., and Ibáñez, C.: The impact of two large floods
(1993–1994) on sediment deposition in the Rhône delta: Implications for
sustainable management, Sci. Total Environ., 609, 251–262,
https://doi.org/10.1016/j.scitotenv.2017.07.155, 2017.
Pozzato, L., Rassmann, J., Lansard, B., Dumoulin, J.-P., Breugel, P. van, and Rabouille, C.: Origin of remineralized organic matter in sediments from the rhone river prodelta (NW mediterranean) traced by Δ14C and δ13C signatures of pore water DIC, Prog. Oceanogr., 163, 112–122, 2018.
Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T.: Numeric recipes in c: The art of scientific computing, Cambridge university press, 3rd edn., 1992.
Pusceddu, A., Dell'Anno, A., Fabiano, M., and Danovaro, R.: Quantity and
bioavailability of sediment organic matter as signatures of benthic trophic
status, Marine Ecol. Prog. Ser., 375, 41–52, 2009.
Rabouille, C. and Gaillard, J.-F.: The validity of steady-state flux
calculations in early diagenesis: a computer simulation of deep-sea silica
diagenesis, Deep-Sea Res. Pt. A, 37,
625–646, 1990.
Rabouille, C. and Gaillard, J.-F.: Towards the EDGE: Early diagenetic global
explanation. A model depicting the early diagenesis of organic matter, O2,
NO3, Mn, and PO4, Geochim. Cosmochim. Ac., 55, 2511–2525, 1991.
Rabouille, C., Mackenzie, F. T., and Ver, L. M.: Influence of the human
perturbation on carbon, nitrogen, and oxygen biogeochemical cycles in the
global coastal ocean, Geochim. Cosmochim. Ac., 65, 3615–3641,
2001a.
Rabouille, C., Witbaard, R., and Duineveld, G.: Annual and interannual
variability of sedimentary recycling studied with a non-steady-state model:
application to the North Atlantic Ocean (BENGAL site), Prog.
Oceanogr., 50, 147–170, 2001b.
Radakovitch, O., Charmasson, S., Arnaud, M., and Bouisset, P.: 210Pb and
Caesium Accumulation in the Rhône Delta Sediments, Estuarine, Coast. Shelf Sci., 48, 77–92, https://doi.org/10.1006/ecss.1998.0405, 1999.
Rassmann, J., Lansard, B., Pozzato, L., and Rabouille, C.: Carbonate chemistry in sediment porewaters of the Rhône River delta driven by early diagenesis (northwestern Mediterranean), Biogeosciences, 13, 5379–5394, https://doi.org/10.5194/bg-13-5379-2016, 2016.
Rassmann, J., Eitel, E. M., Lansard, B., Cathalot, C., Brandily, C., Taillefert, M., and Rabouille, C.: Benthic alkalinity and dissolved inorganic carbon fluxes in the Rhône River prodelta generated by decoupled aerobic and anaerobic processes, Biogeosciences, 17, 13–33, https://doi.org/10.5194/bg-17-13-2020, 2020.
R Core Team: R: A Language and Environment for Statistical Computing, R
Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (last access: 2 August 2022), 2021.
Regnier, P., Friedlingstein, P., Ciais, P., Mackenzie, F. T., Gruber, N.,
Janssens, I. A., Laruelle, G. G., Lauerwald, R., Luyssaert, S., Andersson,
A. J., and Arndt, S.: Anthropogenic perturbation of the carbon fluxes from land to
ocean, Nat. Geosci., 6, 597–607, 2013.
Sciberras, M., Hiddink, J. G., Jennings, S., Szostek, C. L., Hughes, K. M., Kneafsey, B., Clarke, L. J., Ellis, N., Rijnsdorp, A. D., McConnaughey, R. A., et al.: Response of benthic fauna to experimental bottom fishing: A global meta-analysis, Fish Fish., 19, 698–715, 2018.
Sempéré, R., Charrière, B., Van Wambeke, F., and Cauwet, G.:
Carbon inputs of the Rhône River to the Mediterranean Sea:
Biogeochemical implications, Global Biogeochem. Cycles, 14, 669–681,
https://doi.org/10.1029/1999GB900069, 2000.
Smith, K. L., Ruhl, H. A., Huffard, C. L., Messié, M., and Kahru, M.:
Episodic organic carbon fluxes from surface ocean to abyssal depths during
long-term monitoring in NE Pacific, P. Natl. Acad.
Sci. USA, 115, 12235–12240, 2018.
Soetaert, K.: Package rootSolve: roots, gradients and steady-states in R,
Google Scholar [code], https://cran.r-project.org/web/packages/rootSolve/index.html (last access: 2 August 2022), 2014.
Soetaert, K. and Herman, P. M.: A practical guide to ecological modelling:
Using r as a simulation platform, Springer, https://doi.org/10.1007/978-1-4020-8624-3, ISBN 978-1-4020-8623-6, 2009.
Soetaert, K. and Meysman, F.: Reactive transport in aquatic ecosystems:
Rapid model prototyping in the open source software R, Environ.
Model. Softw., 32, 49–60, 2012.
Soetaert, K. and Petzoldt, T.: marelac: Tools for Aquatic Sciences,
https://CRAN.R-project.org/package=marelac (last access: 2 August 2022), r package version 2.1.10,
2020.
Soetaert, K., Herman, P. M., and Middelburg, J. J.: A model of early
diagenetic processes from the shelf to abyssal depths, Geochim. Cosmochim.
Ac., 60, 1019–1040, 1996a.
Soetaert, K., Herman, P. M., and Middelburg, J. J.: Dynamic response of
deep-sea sediments to seasonal variations: A model, Limnol.
Oceanogr., 41, 1651–1668, 1996b.
Soetaert, K., Petzoldt, T., and Meysman, F.: Marelac: Tools for aquatic
sciences, [code], https://cran.r-project.org/web/packages/marelac/index.html (last access: 2 August 2022), 2010a.
Soetaert, K., Petzoldt, T., and Setzer, R. W.: Solving Differential
Equations in R: Package deSolve, J. Statist. Softw., 33, 1–25,
https://doi.org/10.18637/jss.v033.i09, 2010b.
Strogatz, S. H.: Nonlinear dynamics and chaos: with applications to physics,
biology, chemistry, and engineering, CRC press, ISBN 13 978-0-8133-4910-7, 2018.
Stumm, W. and Morgan, J. J.: Aquatic chemistry: chemical equilibria and
rates in natural waters, John Wiley & Sons, 126, ISBN 0-471-51184-6, 2012.
Sulpis, O., Humphreys, M. P., Wilhelmus, M. M., Carroll, D., Berelson, W. M., Menemenlis, D., Middelburg, J. J., and Adkins, J. F.: RADIv1: a non-steady-state early diagenetic model for ocean sediments in Julia and MATLAB/GNU Octave, Geosci. Model Dev., 15, 2105–2131, https://doi.org/10.5194/gmd-15-2105-2022, 2022.
Sundby, B.: Transient state diagenesis in continental margin muds, Marine
Chem., 102, 2–12, 2006.
Tesi, T., Langone, L., Goñi, M., Wheatcroft, R., Miserocchi, S., and
Bertotti, L.: Early diagenesis of recently deposited organic matter: A 9-yr
time-series study of a flood deposit, Geochim. Cosmochim. Ac., 83,
19–36, 2012.
Toussaint, F., Tisnérat-Laborde, N., Cathalot, C., Buscail, R.,
Kerhervé, P., and Rabouille, C.: Depositional processes of organic
matter in the Rhône River Delta (Gulf of Lions, France) traced by
density fractionation coupled with Δ14C and δ13C,
Radiocarbon, 55, 920–931, 2013.
van de Velde, S., Van Lancker, V., Hidalgo-Martinez, S., Berelson, W. M.,
and Meysman, F. J. R.: Anthropogenic disturbance keeps the coastal seafloor
biogeochemistry in a transient state, Sci. Rep.-UK, 8, 5582,
https://doi.org/10.1038/s41598-018-23925-y, 2018.
Wang, Y. and Van Cappellen, P.: A multicomponent reactive transport model of
early diagenesis: Application to redox cycling in coastal marine sediments,
Geochim. Cosmochim. Ac., 60, 2993–3014, 1996.
Westrich, J. T. and Berner, R. A.: The role of sedimentary organic matter in
bacterial sulfate reduction: The G model tested 1, Limnol.
Oceanogr., 29, 236–249, 1984.
Wheatcroft, R. A.: Preservation potential of sedimentary event layers,
Geology, 18, 843–845, 1990.
Wollast, R.: Interactions of carbon and nitrogen cycles in the coastal zone,
in: Interactions of C, N, P and S biogeochemical cycles and global change, Springer,
195–210, https://doi.org/10.1007/978-3-642-76064-8, 1993.
Yakushev, E. V., Protsenko, E. A., Bruggeman, J., Wallhead, P., Pakhomova, S. V., Yakubov, S. Kh., Bellerby, R. G. J., and Couture, R.-M.: Bottom RedOx Model (BROM v.1.1): a coupled benthic–pelagic model for simulation of water and sediment biogeochemistry, Geosci. Model Dev., 10, 453–482, https://doi.org/10.5194/gmd-10-453-2017, 2017.
Zebracki, M., Eyrolle-Boyer, F., Evrard, O., Claval, D., Mourier, B.,
Gairoard, S., Cagnat, X., and Antonelli, C.: Tracing the origin of suspended
sediment in a large Mediterranean river by combining continuous river
monitoring and measurement of artificial and natural radionuclides, Sci. Total Environ., 502, 122–132, 2015.
Zindorf, M., Rooze, J., Meile, C., März, C., Jouet, G., Newton, R.,
Brandily, C., and Pastor, L.: The evolution of early diagenetic processes at
the Mozambique margin during the last glacial-interglacial transition,
Geochim. Cosmochim. Ac., 300, 79–94, 2021.
Short summary
The coastal marine environment serves as a transition zone in the land–ocean continuum and is susceptible to episodic phenomena such as flash floods, which cause massive organic matter deposition. Here, we present a model of sediment early diagenesis that explicitly describes this type of deposition while also incorporating unique flood deposit characteristics. This model can be used to investigate the temporal evolution of marine sediments following abrupt changes in environmental conditions.
The coastal marine environment serves as a transition zone in the land–ocean continuum and is...
