Articles | Volume 14, issue 10
https://doi.org/10.5194/gmd-14-5999-2021
© Author(s) 2021. 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-14-5999-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
07 Oct 2021
Model description paper |
| 07 Oct 2021
| 07 Oct 2021
A model for marine sedimentary carbonate diagenesis and paleoclimate proxy signal tracking: IMP v1.0
Department of Earth and Planetary Sciences, University of California – Riverside, Riverside, CA 92521, USA
currently at: School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Dominik Hülse
Department of Earth and Planetary Sciences, University of California – Riverside, Riverside, CA 92521, USA
Sandra Kirtland Turner
Department of Earth and Planetary Sciences, University of California – Riverside, Riverside, CA 92521, USA
Andy Ridgwell
Department of Earth and Planetary Sciences, University of California – Riverside, Riverside, CA 92521, USA
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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 pH and bulk soil pH is thus crucial to accurate evaluation of alkalinity required to counteract soil acidification and resulting capture of anthropogenic carbon dioxide through the Enhanced Rock Weathering technique. This has been enabled by the updated reactive-transport SCEPTER code and newly developed framework to simulate soil pH.
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Dominik Hülse, Sandra Arndt, Stuart Daines, Pierre Regnier, and Andy Ridgwell
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Biogeosciences, 15, 1367–1393, https://doi.org/10.5194/bg-15-1367-2018, https://doi.org/10.5194/bg-15-1367-2018, 2018
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We conclude that different initial states for an ocean model result in different capacities for ocean carbon storage due to differences in the ocean circulation state and the origin of the carbon in the initial ocean carbon reservoir. This could explain why it is difficult to achieve comparable responses of the ocean carbon system in model inter-comparison studies in which the initial states vary between models. We show that this effect of the initial state is quantifiable.
Natalie S. Lord, Michel Crucifix, Dan J. Lunt, Mike C. Thorne, Nabila Bounceur, Harry Dowsett, Charlotte L. O'Brien, and Andy Ridgwell
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In this paper we describe the experimental design for a set of simulations which will be carried out by a range of climate models, all investigating the climate of the Eocene, about 50 million years ago. The intercomparison of model results is called 'DeepMIP', and we anticipate that we will contribute to the next IPCC report through an analysis of these simulations and the geological data to which we will compare them.
J. D. Wilson, A. Ridgwell, and S. Barker
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N. S. Jones, A. Ridgwell, and E. J. Hendy
Biogeosciences, 12, 1339–1356, https://doi.org/10.5194/bg-12-1339-2015, https://doi.org/10.5194/bg-12-1339-2015, 2015
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R. Death, J. L. Wadham, F. Monteiro, A. M. Le Brocq, M. Tranter, A. Ridgwell, S. Dutkiewicz, and R. Raiswell
Biogeosciences, 11, 2635–2643, https://doi.org/10.5194/bg-11-2635-2014, https://doi.org/10.5194/bg-11-2635-2014, 2014
G. Colbourn, A. Ridgwell, and T. M. Lenton
Geosci. Model Dev., 6, 1543–1573, https://doi.org/10.5194/gmd-6-1543-2013, https://doi.org/10.5194/gmd-6-1543-2013, 2013
M. Eby, A. J. Weaver, K. Alexander, K. Zickfeld, A. Abe-Ouchi, A. A. Cimatoribus, E. Crespin, S. S. Drijfhout, N. R. Edwards, A. V. Eliseev, G. Feulner, T. Fichefet, C. E. Forest, H. Goosse, P. B. Holden, F. Joos, M. Kawamiya, D. Kicklighter, H. Kienert, K. Matsumoto, I. I. Mokhov, E. Monier, S. M. Olsen, J. O. P. Pedersen, M. Perrette, G. Philippon-Berthier, A. Ridgwell, A. Schlosser, T. Schneider von Deimling, G. Shaffer, R. S. Smith, R. Spahni, A. P. Sokolov, M. Steinacher, K. Tachiiri, K. Tokos, M. Yoshimori, N. Zeng, and F. Zhao
Clim. Past, 9, 1111–1140, https://doi.org/10.5194/cp-9-1111-2013, https://doi.org/10.5194/cp-9-1111-2013, 2013
P. B. Holden, N. R. Edwards, S. A. Müller, K. I. C. Oliver, R. M. Death, and A. Ridgwell
Biogeosciences, 10, 1815–1833, https://doi.org/10.5194/bg-10-1815-2013, https://doi.org/10.5194/bg-10-1815-2013, 2013
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FABM-NflexPD 2.0: testing an instantaneous acclimation approach for modeling the implications of phytoplankton eco-physiology for the carbon and nutrient cycles
Evaluating the vegetation–atmosphere coupling strength of ORCHIDEE land surface model (v7266)
Non-Redfieldian carbon model for the Baltic Sea (ERGOM version 1.2) – implementation and budget estimates
Implementation of a new crop phenology and irrigation scheme in the ISBA land surface model using SURFEX_v8.1
Simulating long-term responses of soil organic matter turnover to substrate stoichiometry by abstracting fast and small-scale microbial processes: the Soil Enzyme Steady Allocation Model (SESAM; v3.0)
Modeling demographic-driven vegetation dynamics and ecosystem biogeochemical cycling in NASA GISS's Earth system model (ModelE-BiomeE v.1.0)
Forest fluxes and mortality response to drought: model description (ORCHIDEE-CAN-NHA r7236) and evaluation at the Caxiuanã drought experiment
Matrix representation of lateral soil movements: scaling and calibrating CE-DYNAM (v2) at a continental level
CANOPS-GRB v1.0: a new Earth system model for simulating the evolution of ocean–atmosphere chemistry over geologic timescales
Low sensitivity of three terrestrial biosphere models to soil texture over the South American tropics
FESDIA (v1.0): exploring temporal variations of sediment biogeochemistry under the influence of flood events using numerical modelling
Impact of changes in climate and CO2 on the carbon storage potential of vegetation under limited water availability using SEIB-DGVM version 3.02
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.
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
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.
Jacquelyn K. Shuman, Rosie A. Fisher, Charles D. Koven, Ryan G. Knox, Lara M. Kueppers, and Chonggang Xu
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2023-191, https://doi.org/10.5194/gmd-2023-191, 2023
Revised manuscript accepted for GMD
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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.
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.
Oliver Perkins, Matthew Kasoar, Apostolos Voulgarakis, Cathy Smith, Jay Mistry, and James Millington
EGUsphere, https://doi.org/10.5194/egusphere-2023-2162, https://doi.org/10.5194/egusphere-2023-2162, 2023
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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.
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.
David Sandoval, Iain Colin Prentice, and Rodolfo L. B. Nóbrega
EGUsphere, https://doi.org/10.5194/egusphere-2023-1626, https://doi.org/10.5194/egusphere-2023-1626, 2023
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Numerous estimations of water and energy balances heavily depend on empirical equations that necessitate site-specific calibration. This equifinality poses the risk of obtaining 'right answers for wrong reasons.' In this paper, we introduce novel formulations based on first-principles to calculate calibration-free quantities, such as net radiation, evapotranspiration, condensation, soil water content, surface runoff, subsurface lateral flow, and snow-water equivalent.
Fabian Stenzel, Johanna Braun, Jannes Breier, Karlheinz Erb, Dieter Gerten, Jens Heinke, Sarah Matej, Sebastian Ostberg, Sibyll Schaphoff, and Wolfgang Lucht
EGUsphere, https://doi.org/10.5194/egusphere-2023-2503, https://doi.org/10.5194/egusphere-2023-2503, 2023
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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 >25 % of the potential pre-industrial natural biomass production. The ecosystems state metric EcoRisk shows a high risk of ecosystem destabilization in many regions as a result of land, water, and fertilizer use, as well as climate change.
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.
Yoshiki Kanzaki, Isabella Chiaravalloti, Shuang Zhang, Noah J. Planavsky, and Christopher T. Reinhard
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2023-137, https://doi.org/10.5194/gmd-2023-137, 2023
Revised manuscript accepted for GMD
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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 pH and bulk soil pH is thus crucial to accurate evaluation of alkalinity required to counteract soil acidification and resulting capture of anthropogenic carbon dioxide through the Enhanced Rock Weathering technique. This has been enabled by the updated reactive-transport SCEPTER code and newly developed framework to simulate soil pH.
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.
Amos P. K. Tai, David H. Y. Yung, and Timothy Lam
EGUsphere, https://doi.org/10.5194/egusphere-2023-1287, https://doi.org/10.5194/egusphere-2023-1287, 2023
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We have developed the Terrestrial Ecosystem Model in R (TEMIR), which simulates plant carbon and pollutant uptake and predict their response to varying atmospheric conditions. This model is designed to couple with an atmospheric chemistry model so that important questions related to plant-atmosphere interactions can be addressed, such as the effects of rising CO2 and ozone pollution on carbon uptake of the biosphere. The model has been well validated with both ground and satellite observations.
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.
Maureen Beaudor, Nicolas Vuichard, Juliette Lathière, Nikolaos Evangeliou, Martin Van Damme, Lieven Clarisse, and Didier Hauglustaine
Geosci. Model Dev., 16, 1053–1081, https://doi.org/10.5194/gmd-16-1053-2023, https://doi.org/10.5194/gmd-16-1053-2023, 2023
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Ammonia mainly comes from the agricultural sector, and its volatilization relies on environmental variables. Our approach aims at benefiting from an Earth system model framework to estimate it. By doing so, we represent a consistent spatial distribution of the emissions' response to environmental changes.
We greatly improved the seasonal cycle of emissions compared with previous work. In addition, our model includes natural soil emissions (that are rarely represented in modeling approaches).
Rui Ying, Fanny M. Monteiro, Jamie D. Wilson, and Daniela N. Schmidt
Geosci. Model Dev., 16, 813–832, https://doi.org/10.5194/gmd-16-813-2023, https://doi.org/10.5194/gmd-16-813-2023, 2023
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Planktic foraminifera are marine-calcifying zooplankton; their shells are widely used to measure past temperature and productivity. We developed ForamEcoGEnIE 2.0 to simulate the four subgroups of this organism. We found that the relative abundance distribution agrees with marine sediment core-top data and that carbon export and biomass are close to sediment trap and plankton net observations respectively. This model provides the opportunity to study foraminiferal ecology in any geological era.
Onur Kerimoglu, Markus Pahlow, Prima Anugerahanti, and Sherwood Lan Smith
Geosci. Model Dev., 16, 95–108, https://doi.org/10.5194/gmd-16-95-2023, https://doi.org/10.5194/gmd-16-95-2023, 2023
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In classical models that track the changes in the elemental composition of phytoplankton, additional state variables are required for each element resolved. In this study, we show how the behavior of such an explicit model can be approximated using an
instantaneous acclimationapproach, in which the elemental composition of the phytoplankton is assumed to adjust to an optimal value instantaneously. Through rigorous tests, we evaluate the consistency of this scheme.
Yuan Zhang, Devaraju Narayanappa, Philippe Ciais, Wei Li, Daniel Goll, Nicolas Vuichard, Martin G. De Kauwe, Laurent Li, and Fabienne Maignan
Geosci. Model Dev., 15, 9111–9125, https://doi.org/10.5194/gmd-15-9111-2022, https://doi.org/10.5194/gmd-15-9111-2022, 2022
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There are a few studies to examine if current models correctly represented the complex processes of transpiration. Here, we use a coefficient Ω, which indicates if transpiration is mainly controlled by vegetation processes or by turbulence, to evaluate the ORCHIDEE model. We found a good performance of ORCHIDEE, but due to compensation of biases in different processes, we also identified how different factors control Ω and where the model is wrong. Our method is generic to evaluate other models.
Thomas Neumann, Hagen Radtke, Bronwyn Cahill, Martin Schmidt, and Gregor Rehder
Geosci. Model Dev., 15, 8473–8540, https://doi.org/10.5194/gmd-15-8473-2022, https://doi.org/10.5194/gmd-15-8473-2022, 2022
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Marine ecosystem models are usually constrained by the elements nitrogen and phosphorus and consider carbon in organic matter in a fixed ratio. Recent observations show a substantial deviation from the simulated carbon cycle variables. In this study, we present a marine ecosystem model for the Baltic Sea which allows for a flexible uptake ratio for carbon, nitrogen, and phosphorus. With this extension, the model reflects much more reasonable variables of the marine carbon cycle.
Arsène Druel, Simon Munier, Anthony Mucia, Clément Albergel, and Jean-Christophe Calvet
Geosci. Model Dev., 15, 8453–8471, https://doi.org/10.5194/gmd-15-8453-2022, https://doi.org/10.5194/gmd-15-8453-2022, 2022
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Crop phenology and irrigation is implemented into a land surface model able to work at a global scale. A case study is presented over Nebraska (USA). Simulations with and without the new scheme are compared to different satellite-based observations. The model is able to produce a realistic yearly irrigation water amount. The irrigation scheme improves the simulated leaf area index, gross primary productivity, evapotransipiration, and land surface temperature.
Thomas Wutzler, Lin Yu, Marion Schrumpf, and Sönke Zaehle
Geosci. Model Dev., 15, 8377–8393, https://doi.org/10.5194/gmd-15-8377-2022, https://doi.org/10.5194/gmd-15-8377-2022, 2022
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Soil microbes process soil organic matter and affect carbon storage and plant nutrition at the ecosystem scale. We hypothesized that decadal dynamics is constrained by the ratios of elements in litter inputs, microbes, and matter and that microbial community optimizes growth. This allowed the SESAM model to descibe decadal-term carbon sequestration in soils and other biogeochemical processes explicitly accounting for microbial processes but without its problematic fine-scale parameterization.
Ensheng Weng, Igor Aleinov, Ram Singh, Michael J. Puma, Sonali S. McDermid, Nancy Y. Kiang, Maxwell Kelley, Kevin Wilcox, Ray Dybzinski, Caroline E. Farrior, Stephen W. Pacala, and Benjamin I. Cook
Geosci. Model Dev., 15, 8153–8180, https://doi.org/10.5194/gmd-15-8153-2022, https://doi.org/10.5194/gmd-15-8153-2022, 2022
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We develop a demographic vegetation model to improve the representation of terrestrial vegetation dynamics and ecosystem biogeochemical cycles in the Goddard Institute for Space Studies ModelE. The individual-based competition for light and soil resources makes the modeling of eco-evolutionary optimality possible. This model will enable ModelE to simulate long-term biogeophysical and biogeochemical feedbacks between the climate system and land ecosystems at decadal to centurial temporal scales.
Yitong Yao, Emilie Joetzjer, Philippe Ciais, Nicolas Viovy, Fabio Cresto Aleina, Jerome Chave, Lawren Sack, Megan Bartlett, Patrick Meir, Rosie Fisher, and Sebastiaan Luyssaert
Geosci. Model Dev., 15, 7809–7833, https://doi.org/10.5194/gmd-15-7809-2022, https://doi.org/10.5194/gmd-15-7809-2022, 2022
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To facilitate more mechanistic modeling of drought effects on forest dynamics, our study implements a hydraulic module to simulate the vertical water flow, change in water storage and percentage loss of stem conductance (PLC). With the relationship between PLC and tree mortality, our model can successfully reproduce the large biomass drop observed under throughfall exclusion. Our hydraulic module provides promising avenues benefiting the prediction for mortality under future drought events.
Arthur Nicolaus Fendrich, Philippe Ciais, Emanuele Lugato, Marco Carozzi, Bertrand Guenet, Pasquale Borrelli, Victoria Naipal, Matthew McGrath, Philippe Martin, and Panos Panagos
Geosci. Model Dev., 15, 7835–7857, https://doi.org/10.5194/gmd-15-7835-2022, https://doi.org/10.5194/gmd-15-7835-2022, 2022
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Currently, spatially explicit models for soil carbon stock can simulate the impacts of several changes. However, they do not incorporate the erosion, lateral transport, and deposition (ETD) of soil material. The present work developed ETD formulation, illustrated model calibration and validation for Europe, and presented the results for a depositional site. We expect that our work advances ETD models' description and facilitates their reproduction and incorporation in land surface models.
Kazumi Ozaki, Devon B. Cole, Christopher T. Reinhard, and Eiichi Tajika
Geosci. Model Dev., 15, 7593–7639, https://doi.org/10.5194/gmd-15-7593-2022, https://doi.org/10.5194/gmd-15-7593-2022, 2022
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A new biogeochemical model (CANOPS-GRB v1.0) for assessing the redox stability and dynamics of the ocean–atmosphere system on geologic timescales has been developed. In this paper, we present a full description of the model and its performance. CANOPS-GRB is a useful tool for understanding the factors regulating atmospheric O2 level and has the potential to greatly refine our current understanding of Earth's oxygenation history.
Félicien Meunier, Wim Verbruggen, Hans Verbeeck, and Marc Peaucelle
Geosci. Model Dev., 15, 7573–7591, https://doi.org/10.5194/gmd-15-7573-2022, https://doi.org/10.5194/gmd-15-7573-2022, 2022
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Drought stress occurs in plants when water supply (i.e. root water uptake) is lower than the water demand (i.e. atmospheric demand). It is strongly related to soil properties and expected to increase in intensity and frequency in the tropics due to climate change. In this study, we show that contrary to the expectations, state-of-the-art terrestrial biosphere models are mostly insensitive to soil texture and hence probably inadequate to reproduce in silico the plant water status in drying soils.
Stanley I. Nmor, Eric Viollier, Lucie Pastor, Bruno Lansard, Christophe Rabouille, and Karline Soetaert
Geosci. Model Dev., 15, 7325–7351, https://doi.org/10.5194/gmd-15-7325-2022, https://doi.org/10.5194/gmd-15-7325-2022, 2022
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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.
Shanlin Tong, Weiguang Wang, Jie Chen, Chong-Yu Xu, Hisashi Sato, and Guoqing Wang
Geosci. Model Dev., 15, 7075–7098, https://doi.org/10.5194/gmd-15-7075-2022, https://doi.org/10.5194/gmd-15-7075-2022, 2022
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Plant carbon storage potential is central to moderate atmospheric CO2 concentration buildup and mitigation of climate change. There is an ongoing debate about the main driver of carbon storage. To reconcile this discrepancy, we use SEIB-DGVM to investigate the trend and response mechanism of carbon stock fractions among water limitation regions. Results show that the impact of CO2 and temperature on carbon stock depends on water limitation, offering a new perspective on carbon–water coupling.
Cited articles
Aloisi, G., Wallmann, K., Haese, R. R., and Saliège, J. F.: Chemical, biological and hydrological controls on the 14C content of cold seep carbonate crust: numerical modeling and implications for convection at cold seeps, Chem. Geol., 213, 359–383, https://doi.org/10.1016/j.chemgeo.2004.07.008, 2004. a
Archer, D. and Maier-Reimer, E.: Effect of deep-sea sedimentary calcite preservation on atmospheric CO2 concentration, Nature, 367, 260–263, https://doi.org/10.1038/367260a0, 1994. a
Archer, D., Kheshgi, H., and Maier-Reimer, E.: Multiple timescales for neutralization of fossil fuel CO2, Geophys. Res. Lett., 24, 405–408, https://doi.org/10.1029/97GL00168, 1997. a
Archer, D., Kheshgi, H., and Maier-Reimer, E.: Dynamics of fossil fuel CO2 neutralization by marine CaCO3, Global Biogeochem. Cy., 12, 259–276, https://doi.org/10.1029/98GB00744, 1998. a, b
Archer, D. E.: An atlas of the distribution of calcium carbonate in sediments of the deep sea, Global Biogeochem. Cy., 10, 159–174, https://doi.org/10.1029/95GB03016, 1996. a
Archer, D. E., Morford, J. L., and Emerson, S. R.: A model of suboxic sedimentary diagenesis suitable for automatic tuning and gridded global domains, Global Biogeochem. Cy., 16, 17–1, https://doi.org/10.1029/2000GB001288, 2002. a, b
Bard, E.: Paleoceanographic implications of the difference in deep-sea sediment mixing between large and fine particles, Paleoceanography, 16, 235–239, https://doi.org/10.1029/2000PA000537, 2001. a, b, c, d
Bard, E., Arnold, M., Duprat, J., Moyes, J., and Duplessy, J. C.: Reconstruction of the last deglaciation: Deconvolved records of δ18O profiles, micropaleontological variations and accelerator mass spectrometric14C dating, Clim. Dynam., 1, 101–112, https://doi.org/10.1007/BF01054479, 1987. a, b
Barker, S., Broecker, W., Clark, E., and Hajdas, I.: Radiocarbon age offsets of foraminifera resulting from differential dissolution and fragmentation within the sedimentary bioturbated zone, Paleoceanography, 22, PA2205, https://doi.org/10.1029/2006PA001354, 2007. a, b, c
Berger, W. H., Johnson, R., and Killingley, J.: “Unmixing” of the deep-sea record and the deglacial meltwater spike, Nature, 269, 661–663, https://doi.org/10.1038/269661a0, 1977. a
Berner, R. A.: Early Diagenesis: A Theoretical Approach, Princeton University Press, Princeton, NJ, 1980. a
Berner, R. A., Lasaga, A. C., and Garrels, R. M.: The carbonate-silicate geochemical cycle and its effect on atmospheric carbon dioxide over the past 100 million years, Am. J. Sci., 283, 641–683, https://doi.org/10.2475/ajs.283.7.641, 1983. a
Boudreau, B. P.: A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments, Comput. Geosci., 22, 479–496, https://doi.org/10.1016/0098-3004(95)00115-8, 1996. a
Boudreau, B. P. and Imboden, D. M.: Mathematics of tracer mixing in sediments; III, The theory of nonlocal mixing within sediments, Am. J. Sci., 287, 693–719, https://doi.org/10.2475/ajs.287.7.693, 1987. a
Boudreau, B. P., Middelburg, J. J., Hofmann, A. F., and Meysman, F. J.: Ongoing transients in carbonate compensation, Global Biogeochem. Cy., 24, GB4010, https://doi.org/10.1029/2009GB003654, 2010. a
Broecker, W. S. and Takahashi, T.: Neutralization of fossil fuel CO2 by marine calcium carbonate, in: The Fate of Fossil Fuel CO2 in the Oceans, edited by: Andersen, N. R. and Malahoff, A., 213–248, Plenum, New York, 1977. a
Choi, J., Francois-Carcaillet, F., and Boudreau, B. P.: Lattice-automaton bioturbation simulator (LABS): implementation for small deposit feeders, Comput. Geosci., 28, 213–222, https://doi.org/10.1016/S0098-3004(01)00064-4, 2002. a, b, c, d
Dunkley Jones, T., Lunt, D. J., Schmidt, D. N., Ridgwell, A., Sluijs, A., Valdes, P. J., and Maslin, M.: Climate model and proxy data constraints on ocean warming across the Paleocene–Eocene Thermal Maximum, Earth-Sci. Rev., 125, 123–145, https://doi.org/10.1016/j.earscirev.2013.07.004, 2013. a
Emerson, S.: Organic carbon preservation in marine sediments, in: The Carbon Cycle and Atmospheric CO2: Natural Variations Archean to Present, edited by Sundquist, E. and Broecker, W., 78–87, American Geophysical Union, Washington, DC, https://doi.org/10.1029/GM032p0078, 1985. a, b, c
Emerson, S. and Archer, D.: Calcium carbonate preservation in the ocean, Philos. T. R. Soc. A, 331, 29–40, https://doi.org/10.1098/rsta.1990.0054, 1990. a
Goldberg, E. D. and Koide, M.: Geochronological studies of deep sea sediments by the ionium/thorium method, Geochim. Cosmochim. Ac., 26, 417–450, https://doi.org/10.1016/0016-7037(62)90112-6, 1962. a
Greene, S., Ridgwell, A., Kirtland Turner, S., Schmidt, D. N., Pälike, H., Thomas, E., Greene, L., and Hoogakker, B.: Early Cenozoic decoupling of climate and carbonate compensation depth trends, Paleoceanography and Paleoclimatology, 34, 930–945, https://doi.org/10.1029/2019PA003601, 2019. a
Gutjahr, M., Ridgwell, A., Sexton, P. F., Anagnostou, E., Pearson, P. N., Pälike, H., Norris, R. D., Thomas, E., and Foster, G. L.: Very large release of mostly volcanic carbon during the Palaeocene–Eocene Thermal Maximum, Nature, 548, 573–577, https://doi.org/10.1038/nature23646, 2017. a
Hönisch, B., Ridgwell, A., Schmidt, D. N., Thomas, E., Gibbs, S. J., Sluijs, A., Zeebe, R., Kump, L., Martindale, R. C., Greene, S. E., Kiessling, W., Ries, J., Zachos, J. C., Royer, D. L., Barker, S., Marchitto, Jr., T. M., Moyer, R., Pelejero, C., Ziveri, P., Foster, G. L., and Williams, B.: The geological record of ocean acidification, Science, 335, 1058–1063, https://doi.org/10.1126/science.1208277, 2012. a
Hull, P. M., Franks, P. J., and Norris, R. D.: Mechanisms and models of iridium anomaly shape across the Cretaceous–Paleogene boundary, Earth Planet. Sci. Lett., 301, 98–106, https://doi.org/10.1016/j.epsl.2010.10.031, 2011. a
Hülse, D., Arndt, S., Daines, S., Regnier, P., and Ridgwell, A.: OMEN-SED 1.0: a novel, numerically efficient organic matter sediment diagenesis module for coupling to Earth system models, Geosci. Model Dev., 11, 2649–2689, https://doi.org/10.5194/gmd-11-2649-2018, 2018. a
Humphreys, M. P., Gregor, L., Pierrot, D., van Heuven, S. M. A. C., Lewis, E. R., and Wallace, D. W. R.: PyCO2SYS: marine carbonate system calculations in Python, Zenodo, https://doi.org/10.5281/zenodo.3744275, 2020. a
Jennions, S., Thomas, E., Schmidt, D., Lunt, D., and Ridgwell, A.: Changes in benthic ecosystems and ocean circulation in the Southeast Atlantic across Eocene Thermal Maximum 2, Paleoceanography, 30, 1059–1077, https://doi.org/10.1002/2015PA002821, 2015. a, b, c, d
Kanzaki, Y. and Hülse, D.: imuds/iMP: Revised for GMD (v1.0), Zenodo [code], https://doi.org/10.5281/zenodo.5213875, 2021. a
Keir, R. S.: The dissolution kinetics of biogenic calcium carbonates in seawater, Geochim. Cosmochim. Ac., 44, 241–252, https://doi.org/10.1016/0016-7037(80)90135-0, 1980. a, b, c, d
Kirtland Turner, S. and Ridgwell, A.: Recovering the true size of an Eocene hyperthermal from the marine sedimentary record, Paleoceanography, 28, 700–712, https://doi.org/10.1002/2013PA002541, 2013. a
Kirtland Turner, S., Hull, P. M., Kump, L. R., and Ridgwell, A.: A probabilistic assessment of the rapidity of PETM onset, Nat. Commun., 8, 1–10, https://doi.org/10.1038/s41467-017-00292-2, 2017. a, b
Kristensen, E., Penha-Lopes, G., Delefosse, M., Valdemarsen, T., Quintana, C. O., and Banta, G. T.: What is bioturbation? The need for a precise definition for fauna in aquatic sciences, Mar. Ecol. Prog. Ser., 446, 285–302, https://doi.org/10.3354/meps09506, 2012. a
Kump, L. R. and Arthur, M. A.: Interpreting carbon-isotope excursions: carbonates and organic matter, Chem. Geol., 161, 181–198, https://doi.org/10.1016/S0009-2541(99)00086-8, 1999. a
Kump, L. R., Bralower, T. J., and Ridgwell, A.: Ocean acidification in deep time, Oceanography, 22, 94–107, https://doi.org/10.5670/oceanog.2009.100, 2009. a
Lewis, E. and Wallace, D. W. R.: Program Developed for CO2 System Calculations, ORNL/CDIAC-105, Environmental System Science Data Infrastructure for a Virtual Ecosystem, 1998. a
Lord, N. S., Ridgwell, A., Thorne, M., and Lunt, D.: An impulse response function for the “long tail” of excess atmospheric CO2 in an Earth system model, Global Biogeochem. Cy., 30, 2–17, https://doi.org/10.1002/2014GB005074, 2016. a
Lu, W., Ridgwell, A., Thomas, E., Hardisty, D. S., Luo, G., Algeo, T. J., Saltzman, M. R., Gill, B. C., Shen, Y., Ling, H.-F., Edwards, C. T., Whalen, M. T., Zhou, X., Gutchess, K. M., Jin, L., Rickaby, R. E. M., Jenkyns, H. C., Lyons, T. W., Lenton, T. M., Kump, L. R., and Lu, Z.: Late inception of a resiliently oxygenated upper ocean, Science, 361, 174–177, https://doi.org/10.1126/science.aar5372, 2018. a
Mayer, L. M., Schick, L. L., Hardy, K. R., Wagai, R., and McCarthy, J.: Organic matter in small mesopores in sediments and soils, Geochim. Cosmochim. Ac., 68, 3863–3872, https://doi.org/10.1016/j.gca.2004.03.019, 2004. a
McInerney, F. A. and Wing, S. L.: The Paleocene-Eocene Thermal Maximum: a perturbation of carbon cycle, climate, and biosphere with implications for the future, Annu. Rev. Earth Pl. Sc., 39, 489–516, https://doi.org/10.1146/annurev-earth-040610-133431, 2011. a
Meyers, S. R.: Production and preservation of organic matter: The significance of iron, Paleoceanography, 22, PA4211, https://doi.org/10.1029/2006PA001332, 2007. a
Meysman, F. J., Middelburg, J. J., and Heip, C. H.: Bioturbation: a fresh look at Darwin's last idea, Trends Ecol. Evol., 21, 688–695, https://doi.org/10.1016/j.tree.2006.08.002, 2006. a
Meysman, F. J. R., Boudreau, B. P., and Middelburg, J. J.: Modeling reactive transport in sediments subject to bioturbation and compaction, Geochim. Cosmochim. Ac., 69, 3601–3617, 2005. a
Millero, F. J.: Thermodynamics of the carbon dioxide system in the oceans, Geochim. Cosmochim. Ac., 59, 661–677, https://doi.org/10.1016/0016-7037(94)00354-O, 1995. a, b
Millero, F. J., Graham, T. B., Huang, F., Bustos-Serrano, H., and Pierrot, D.: Thermodynamics of the carbon dioxide system in the oceans, Mar. Chem., 100, 80–94, https://doi.org/10.1016/j.marchem.2005.12.001, 2006. a
Mucci, A.: The solubility of calcite and aragonite in seawater at various salinities, temperatures, and one atmosphere total pressure, Am. J. Sci., 283, 780–799, https://doi.org/10.2475/ajs.283.7.780, 1983. a
Munhoven, G.: Glacial–interglacial rain ratio changes: Implications for atmospheric CO2 and ocean–sediment interaction, Deep-Sea Res. Pt. II, 54, 722–746, 2007. a
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. a, b
Orr, J. C. and Epitalon, J.-M.: Improved routines to model the ocean carbonate system: mocsy 2.0, Geosci. Model Dev., 8, 485–499, https://doi.org/10.5194/gmd-8-485-2015, 2015. a
Oxburgh, R.: The Holocene preservation history of equatorial Pacific sediments, Paleoceanography, 13, 50–62, https://doi.org/10.1029/97PA02607, 1998. a, b
Oxburgh, R. and Broecker, W. S.: Pacific carbonate dissolution revisited, Palaeogeogr Palaeocl, 103, 31–40, https://doi.org/10.1016/0031-0182(93)90049-O, 1993. a, b, c
Panchuk, K., Ridgwell, A., and Kump, L. R.: Sedimentary response to Paleocene-Eocene Thermal Maximum carbon release: A model-data comparison, Geology, 34, 315–318, https://doi.org/10.1130/G24474A.1, 2008. a
Penman, D. E., Kirtland Turner, S., Sexton, P. F., Norris, R. D., Dickson, A. J., Boulila, S., Ridgwell, A., Zeebe, R. E., Zachos, J. C., Cameron, A., Westerhold, T., and Röhl, U.: An abyssal carbonate compensation depth overshoot in the aftermath of the Palaeocene–Eocene Thermal Maximum, Nat. Geosci., 9, 575–580, https://doi.org/10.1038/NGEO2757, 2016. a
Reed, D., Boudreau, B. P., and Huang, K.: Transient tracer dynamics in a lattice-automaton model of bioturbation, J. Mar. Res., 65, 813–833, https://doi.org/10.1357/002224007784219039, 2007. a
Ridgwell, A.: Application of sediment core modelling to interpreting the glacial-interglacial record of Southern Ocean silica cycling, Clim. Past, 3, 387–396, https://doi.org/10.5194/cp-3-387-2007, 2007a. a
Ridgwell, A. and Hargreaves, J.: Regulation of atmospheric CO2 by deep-sea sediments in an Earth system model, Global Biogeochem. Cy., 21, GB2008, https://doi.org/10.1029/2006GB002764, 2007. a
Ridgwell, A. and Zeebe, R. E.: The role of the global carbonate cycle in the regulation and evolution of the Earth system, Earth Planet. Sci. Lett., 234, 299–315, https://doi.org/10.1016/j.epsl.2005.03.006, 2005. a, b, c
Ridgwell, A. J., Watson, A. J., and Archer, D. E.: Modeling the response of the oceanic Si inventory to perturbation, and consequences for atmospheric CO2, Global Biogeochem. Cy., 16, https://doi.org/10.1029/2002GB001877, 2002. a
Ridgwell, A. J., Kennedy, M. J., and Caldeira, K.: Carbonate deposition, climate stability, and Neoproterozoic ice ages, Science, 302, 859–862, https://doi.org/10.1126/science.1088342, 2003. a
Robie, R. A. and Hemingway, B. S.: Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 bar (105 Pascals) Pressure and at Higher Temperatures, 2131, US Government Printing Office, Washington, DC, 1995. a
Saunders, P. M. and Fofonoff, N.: Conversion of pressure to depth in the ocean, Deep Sea Research and Oceanographic Abstracts, 23, 109–111, https://doi.org/10.1016/0011-7471(76)90813-5, 1976. a
Schmidt, D. N., Renaud, S., Bollmann, J., Schiebel, R., and Thierstein, H. R.: Size distribution of Holocene planktic foraminifer assemblages: biogeography, ecology and adaptation, Mar. Micropaleontol., 50, 319–338, https://doi.org/10.1016/S0377-8398(03)00098-7, 2004. a, b
Shull, D. H.: Transition-matrix model of bioturbation and radionuclide diagenesis, Limnol. Oceanogr., 46, 905–916, https://doi.org/10.4319/lo.2001.46.4.0905, 2001. a, b, c
Sluijs, A., Bowen, G. J., Brinkhuis, H., Lourens, L. J., and Thomas, E.: The Palaeocene–Eocene Thermal Maximum super greenhouse: biotic and geochemical signatures, age models and mechanisms of global change, in: Deep-Time Perspectives on Climate Change: Marrying the Signal from Computer Models and Biological Proxies, edited by: Williams, M., Haywood, A. M., Gregory, F. J., and Schmidt, D. N., 323–349, The Geological Society, London, https://doi.org/10.1144/TMS002.15, 2007. a
Steefel, C. I. and Lasaga, A. C.: A coupled model for transport of multiple chemical species and kinetic precipitation/dissolution reactions with application to reactive flow in single phase hydrothermal systems, Am. J. Sci., 294, 529–592, https://doi.org/10.2475/ajs.294.5.529, 1994. a, b, c
Steiner, Z., Lazar, B., Levi, S., Tsroya, S., Pelled, O., Bookman, R., and Erez, J.: The effect of bioturbation in pelagic sediments: lessons from radioactive tracers and planktonic foraminifera in the Gulf of Aqaba, Red Sea, Geochim. Cosmochim. Ac., 194, 139–152, https://doi.org/10.1016/j.gca.2016.08.037, 2016. a, b
Thullner, M., Dale, A. W., and Regnier, P.: Global-scale quantification of mineralization pathways in marine sediments: A reaction-transport modeling approach, Geochem. Geophy. Geosy., 10, Q10012, https://doi.org/10.1029/2009GC002484, 2009. a
Trauth, M. H.: TURBO: A dynamic-probabilistic simulation to study the effects of bioturbation on paleoceanographic time series, Comput. Geosci., 24, 433–441, https://doi.org/10.1016/S0098-3004(98)00019-3, 1998. a, b, c
Trauth, M. H.: TURBO2: A MATLAB simulation to study the effects of bioturbation on paleoceanographic time series, Comput. Geosci., 61, 1–10, https://doi.org/10.1016/j.cageo.2013.05.003, 2013. a, b, c, d
Ullman, W. J. and Aller, R. C.: Diffusion coefficients in nearshore marine sediments, Limnol. Oceanogr., 27, 552–556, https://doi.org/10.4319/lo.1982.27.3.0552, 1982. a, b
van Heuven, S., Pierrot, D., Rae, J., Lewis, E., and Wallace, D.: MATLAB Program Developed for CO2 System Calculations, ORNL/CDIAC-105b, Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, https://cdiac.ess-dive.lbl.gov/ftp/co2sys/CO2SYS_calc_MATLAB_v1.1 (last access: 26 September 2021), 1998. a
Walter, L. M. and Morse, J. W.: Magnesian calcite stabilities: A reevaluation, Geochim. Cosmochim. Ac., 48, 1059–1069, https://doi.org/10.1016/0016-7037(84)90196-0, 1984. a, b
Walter, L. M. and Morse, J. W.: The dissolution kinetics of shallow marine carbonates in seawater: A laboratory study, Geochim. Cosmochim. Ac., 49, 1503–1513, https://doi.org/10.1016/0016-7037(85)90255-8, 1985. a, b
Zachos, J., Pagani, M., Sloan, L., Thomas, E., and Billups, K.: Trends, rhythms, and aberrations in global climate 65 Ma to present, Science, 292, 686–693, https://doi.org/10.1126/science.1059412, 2001. a
Zachos, J. C., Röhl, U., Schellenberg, S. A., Sluijs, A., Hodell, D. A., Kelly, D. C., Thomas, E., Nicolo, M., Raffi, I., Lourens, L. J., McCarren, H., and Kroon, D.: Rapid acidification of the ocean during the Paleocene-Eocene Thermal Maximum, Science, 308, 1611–1615, https://doi.org/10.1126/science.1109004, 2005. a, b
Zeebe, R. E. and Zachos, J. C.: Reversed deep-sea carbonate ion basin gradient during Paleocene-Eocene thermal maximum, Paleoceanography, 22, PA3201, https://doi.org/10.1029/2006PA001395, 2007. a
Short summary
Sedimentary carbonate plays a central role in regulating Earth’s carbon cycle and climate, and also serves as an archive of paleoenvironments, hosting various trace elements/isotopes. To help obtain
trueenvironmental changes from carbonate records over diagenetic distortion, IMP has been newly developed and has the capability to simulate the diagenesis of multiple carbonate particles and implement different styles of particle mixing by benthos using an adapted transition matrix method.
Sedimentary carbonate plays a central role in regulating Earth’s carbon cycle and climate, and...
