Articles | Volume 17, issue 14
https://doi.org/10.5194/gmd-17-5619-2024
© Author(s) 2024. 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-17-5619-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
25 Jul 2024
Model description paper |
| 25 Jul 2024
| 25 Jul 2024
EAT v1.0.0: a 1D test bed for physical–biogeochemical data assimilation in natural waters
Jorn Bruggeman
CORRESPONDING AUTHOR
Bolding & Bruggeman ApS, 5466 Asperup, Denmark
Karsten Bolding
Bolding & Bruggeman ApS, 5466 Asperup, Denmark
Lars Nerger
Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany
Anna Teruzzi
National Institute of Oceanography and Applied Geophysics – OGS, 34010 Trieste, Italy
Simone Spada
National Institute of Oceanography and Applied Geophysics – OGS, 34010 Trieste, Italy
Jozef Skákala
Plymouth Marine Laboratory, Plymouth, PL1 3DH, UK
National Centre for Earth Observation, Plymouth, PL1 3DH, UK
Stefano Ciavatta
Mercator Ocean International, 31400 Toulouse, France
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Eva Álvarez, Gianpiero Cossarini, Anna Teruzzi, Jorn Bruggeman, Karsten Bolding, Stefano Ciavatta, Vincenzo Vellucci, Fabrizio D'Ortenzio, David Antoine, and Paolo Lazzari
Biogeosciences, 20, 4591–4624, https://doi.org/10.5194/bg-20-4591-2023, https://doi.org/10.5194/bg-20-4591-2023, 2023
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Chromophoric dissolved organic matter (CDOM) interacts with the ambient light and gives the waters of the Mediterranean Sea their colour. We propose a novel parameterization of the CDOM cycle, whose parameter values have been optimized by using the data of the monitoring site BOUSSOLE. Nutrient and light limitations for locally produced CDOM caused aCDOM(λ) to covary with chlorophyll, while the above-average CDOM concentrations observed at this site were maintained by allochthonous sources.
Qing Li, Jorn Bruggeman, Hans Burchard, Knut Klingbeil, Lars Umlauf, and Karsten Bolding
Geosci. Model Dev., 14, 4261–4282, https://doi.org/10.5194/gmd-14-4261-2021, https://doi.org/10.5194/gmd-14-4261-2021, 2021
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Different ocean vertical mixing schemes are usually developed in different modeling framework, making the comparison across such schemes difficult. Here, we develop a consistent framework for testing, comparing, and applying different ocean mixing schemes by integrating CVMix into GOTM, which also extends the capability of GOTM towards including the effects of ocean surface waves. A suite of test cases and toolsets for developing and evaluating ocean mixing schemes is also described.
Ieuan Higgs, Ross Bannister, Jozef Skákala, Alberto Carrassi, and Stefano Ciavatta
EGUsphere, https://doi.org/10.48550/arXiv.2504.05218, https://doi.org/10.48550/arXiv.2504.05218, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
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We explored how machine learning can improve computer models that simulate ocean ecosystems. These models help us understand how the ocean works, but they often struggle due to limited observations and complex processes. Our approach uses machine learning to better connect the parts of the system we can observe with those we cannot. This leads to more accurate and efficient predictions, offering a promising way to improve future ocean monitoring and forecasting tools.
Gabriela Martinez-Balbontin, Julien Jouanno, Rachid Benshila, Julien Lamouroux, Coralie Perruche, and Stefano Ciavatta
EGUsphere, https://doi.org/10.5194/egusphere-2025-1246, https://doi.org/10.5194/egusphere-2025-1246, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
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This study uses machine learning to predict chlorophyll-a levels, which are important for monitoring marine ecosystems and the carbon cycle. By using forecasts of sea surface temperature, salinity, height, and mixed layer depth, we can make global predictions up to six months ahead in just minutes. Our approach is as accurate or better than traditional methods, while being faster and more resource-efficient.
Frauke Bunsen, Judith Hauck, Sinhué Torres-Valdés, and Lars Nerger
Ocean Sci., 21, 437–471, https://doi.org/10.5194/os-21-437-2025, https://doi.org/10.5194/os-21-437-2025, 2025
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Computer models are often used to estimate the ocean's CO2 uptake due to a lack of direct observations. Because such idealized models do not match precisely with the real world, we combine real-world observations of ocean temperature and salinity with a model and study the effect on the modeled air–sea CO2 flux (2010–2020). The corrections of temperature and salinity have their largest effect on regional CO2 fluxes in the Southern Ocean in winter and a small effect on the global CO2 uptake.
Hongyi Li, Ting Yang, Lars Nerger, Dawei Zhang, Di Zhang, Guigang Tang, Haibo Wang, Yele Sun, Pingqing Fu, Hang Su, and Zifa Wang
Geosci. Model Dev., 17, 8495–8519, https://doi.org/10.5194/gmd-17-8495-2024, https://doi.org/10.5194/gmd-17-8495-2024, 2024
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To accurately characterize the spatiotemporal distribution of particulate matter <2.5 µm chemical components, we developed the Nested Air Quality Prediction Model System with the Parallel Data Assimilation Framework (NAQPMS-PDAF) v2.0 for chemical components with non-Gaussian and nonlinear properties. NAQPMS-PDAF v2.0 has better computing efficiency, excels when used with a small ensemble size, and can significantly improve the simulation performance of chemical components.
Anna Teruzzi, Ali Aydogdu, Carolina Amadio, Emanuela Clementi, Simone Colella, Valeria Di Biagio, Massimiliano Drudi, Claudia Fanelli, Laura Feudale, Alessandro Grandi, Pietro Miraglio, Andrea Pisano, Jenny Pistoia, Marco Reale, Stefano Salon, Gianluca Volpe, and Gianpiero Cossarini
State Planet, 4-osr8, 15, https://doi.org/10.5194/sp-4-osr8-15-2024, https://doi.org/10.5194/sp-4-osr8-15-2024, 2024
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A noticeable cold spell occurred in Eastern Europe at the beginning of 2022 and was the main driver of intense deep-water formation and the associated transport of nutrients to the surface. Southeast of Crete, the availability of both light and nutrients in the surface layer stimulated an anomalous phytoplankton bloom. In the area, chlorophyll concentration (a proxy for bloom intensity) and primary production were considerably higher than usual, suggesting possible impacts on fishery catches.
Gianpiero Cossarini, Andy Moore, Stefano Ciavatta, and Katja Fennel
State Planet Discuss., https://doi.org/10.5194/sp-2024-8, https://doi.org/10.5194/sp-2024-8, 2024
Revised manuscript accepted for SP
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Marine biogeochemistry refers to the cycling of chemical elements resulting from physical transport, chemical reaction, uptake, and processing by living organisms. Biogeochemical models can have a wide range of complexity, from single parameterizations of processes to fully explicit representations of several nutrients, trophic levels, and functional groups. Uncertainty sources are the lack of knowledge about the parameterizations, initial and boundary conditions and the lack of observations
Jozef Skakala, David Ford, Keith Haines, Amos Lawless, Matthew Martin, Philip Browne, Marcin Chrust, Stefano Ciavatta, Alison Fowler, Daniel Lea, Matthew Palmer, Andrea Rochner, Jennifer Waters, Hao Zuo, Mike Bell, Davi Carneiro, Yumeng Chen, Susan Kay, Dale Partridge, Martin Price, Richard Renshaw, Georgy Shapiro, and James While
EGUsphere, https://doi.org/10.5194/egusphere-2024-1737, https://doi.org/10.5194/egusphere-2024-1737, 2024
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In this paper we review marine data assimilation (MDA) in the UK, its stakeholders, needs, past and present developments in different areas of UK MDA, and offer a vision for their longer future. The specific areas covered are ocean physics and sea ice, marine biogeochemistry, coupled MDA, MDA informing observing network design and MDA theory. We also discuss future vision for MDA resources: observations, software, hardware and people skills.
Deep S. Banerjee and Jozef Skakala
EGUsphere, https://doi.org/10.22541/essoar.171405637.76928549/v1, https://doi.org/10.22541/essoar.171405637.76928549/v1, 2024
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Nitrate is a crucial nutrient in oceans. Excess nutrients can trigger uncontrolled algae growth (eutrophication), damaging marine ecosystems. We used a machine learning tool to generate a skilled, gap-free, bi-decadal surface nitrate dataset from sparse observations. This dataset reveals areas on the North West European Shelf at risk of eutrophication, bi-decadal trends in coastal nitrate, and an impact of winter nitrate on spring phytoplankton blooms.
Yumeng Chen, Lars Nerger, and Amos S. Lawless
EGUsphere, https://doi.org/10.5194/egusphere-2024-1078, https://doi.org/10.5194/egusphere-2024-1078, 2024
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In this paper, we present pyPDAF, a Python interface to the parallel data assimilation framework (PDAF) allowing for coupling with Python-based models. We demonstrate the capability and efficiency of pyPDAF under a coupled data assimilation setup.
Changliang Shao and Lars Nerger
Geosci. Model Dev., 17, 4433–4445, https://doi.org/10.5194/gmd-17-4433-2024, https://doi.org/10.5194/gmd-17-4433-2024, 2024
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This paper introduces and evaluates WRF-PDAF, a fully online-coupled ensemble data assimilation (DA) system. A key advantage of the WRF-PDAF configuration is its ability to concurrently integrate all ensemble states, eliminating the need for time-consuming distribution and collection of ensembles during the coupling communication. The extra time required for DA amounts to only 20.6 % per cycle. Twin experiment results underscore the effectiveness of the WRF-PDAF system.
Carolina Amadio, Anna Teruzzi, Gloria Pietropolli, Luca Manzoni, Gianluca Coidessa, and Gianpiero Cossarini
Ocean Sci., 20, 689–710, https://doi.org/10.5194/os-20-689-2024, https://doi.org/10.5194/os-20-689-2024, 2024
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Forecasting of marine biogeochemistry can be improved via the assimilation of observations. Floating buoys provide multivariate information about the status of the ocean interior. Information on the ocean interior can be expanded/augmented by machine learning. In this work, we show the enhanced impact of assimilating new in situ variables (oxygen) and reconstructed variables (nitrate) in the operational forecast system (MedBFM) model of the Mediterranean Sea.
Qi Tang, Hugo Delottier, Wolfgang Kurtz, Lars Nerger, Oliver S. Schilling, and Philip Brunner
Geosci. Model Dev., 17, 3559–3578, https://doi.org/10.5194/gmd-17-3559-2024, https://doi.org/10.5194/gmd-17-3559-2024, 2024
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We have developed a new data assimilation framework by coupling an integrated hydrological model HydroGeoSphere with the data assimilation software PDAF. Compared to existing hydrological data assimilation systems, the advantage of our newly developed framework lies in its consideration of the physically based model; its large selection of different assimilation algorithms; and its modularity with respect to the combination of different types of observations, states and parameters.
Ieuan Higgs, Jozef Skákala, Ross Bannister, Alberto Carrassi, and Stefano Ciavatta
Biogeosciences, 21, 731–746, https://doi.org/10.5194/bg-21-731-2024, https://doi.org/10.5194/bg-21-731-2024, 2024
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A complex network is a way of representing which parts of a system are connected to other parts. We have constructed a complex network based on an ecosystem–ocean model. From this, we can identify patterns in the structure and areas of similar behaviour. This can help to understand how natural, or human-made, changes will affect the shelf sea ecosystem, and it can be used in multiple future applications such as improving modelling, data assimilation, or machine learning.
Eva Álvarez, Gianpiero Cossarini, Anna Teruzzi, Jorn Bruggeman, Karsten Bolding, Stefano Ciavatta, Vincenzo Vellucci, Fabrizio D'Ortenzio, David Antoine, and Paolo Lazzari
Biogeosciences, 20, 4591–4624, https://doi.org/10.5194/bg-20-4591-2023, https://doi.org/10.5194/bg-20-4591-2023, 2023
Short summary
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Chromophoric dissolved organic matter (CDOM) interacts with the ambient light and gives the waters of the Mediterranean Sea their colour. We propose a novel parameterization of the CDOM cycle, whose parameter values have been optimized by using the data of the monitoring site BOUSSOLE. Nutrient and light limitations for locally produced CDOM caused aCDOM(λ) to covary with chlorophyll, while the above-average CDOM concentrations observed at this site were maintained by allochthonous sources.
Simone Spada, Anna Teruzzi, Stefano Maset, Stefano Salon, Cosimo Solidoro, and Gianpiero Cossarini
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2023-170, https://doi.org/10.5194/gmd-2023-170, 2023
Revised manuscript under review for GMD
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In geosciences, data assimilation (DA) combines modeled dynamics and observations to reduce simulation uncertainties. Uncertainties can be dynamically and effectively estimated in ensemble DA methods. With respect to current techniques, the novel GHOSH ensemble DA scheme is designed to improve accuracy by reaching a higher approximation order, without increasing computational costs, as demonstrated in idealized Lorenz96 tests and in realistic simulations of the Mediterranean Sea biogeochemistry
Giovanni Coppini, Emanuela Clementi, Gianpiero Cossarini, Stefano Salon, Gerasimos Korres, Michalis Ravdas, Rita Lecci, Jenny Pistoia, Anna Chiara Goglio, Massimiliano Drudi, Alessandro Grandi, Ali Aydogdu, Romain Escudier, Andrea Cipollone, Vladyslav Lyubartsev, Antonio Mariani, Sergio Cretì, Francesco Palermo, Matteo Scuro, Simona Masina, Nadia Pinardi, Antonio Navarra, Damiano Delrosso, Anna Teruzzi, Valeria Di Biagio, Giorgio Bolzon, Laura Feudale, Gianluca Coidessa, Carolina Amadio, Alberto Brosich, Arnau Miró, Eva Alvarez, Paolo Lazzari, Cosimo Solidoro, Charikleia Oikonomou, and Anna Zacharioudaki
Ocean Sci., 19, 1483–1516, https://doi.org/10.5194/os-19-1483-2023, https://doi.org/10.5194/os-19-1483-2023, 2023
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The paper presents the Mediterranean Forecasting System evolution and performance developed in the framework of the Copernicus Marine Service.
Valeria Di Biagio, Riccardo Martellucci, Milena Menna, Anna Teruzzi, Carolina Amadio, Elena Mauri, and Gianpiero Cossarini
State Planet, 1-osr7, 10, https://doi.org/10.5194/sp-1-osr7-10-2023, https://doi.org/10.5194/sp-1-osr7-10-2023, 2023
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Oxygen is essential to all aerobic organisms, and its content in the marine environment is continuously under assessment. By integrating observations with a model, we describe the dissolved oxygen variability in a sensitive Mediterranean area in the period 1999–2021 and ascribe it to multiple acting physical and biological drivers. Moreover, the reduction recognized in 2021, apparently also due to other mechanisms, requires further monitoring in light of its possible impacts.
Stefania A. Ciliberti, Enrique Alvarez Fanjul, Jay Pearlman, Kirsten Wilmer-Becker, Pierre Bahurel, Fabrice Ardhuin, Alain Arnaud, Mike Bell, Segolene Berthou, Laurent Bertino, Arthur Capet, Eric Chassignet, Stefano Ciavatta, Mauro Cirano, Emanuela Clementi, Gianpiero Cossarini, Gianpaolo Coro, Stuart Corney, Fraser Davidson, Marie Drevillon, Yann Drillet, Renaud Dussurget, Ghada El Serafy, Katja Fennel, Marcos Garcia Sotillo, Patrick Heimbach, Fabrice Hernandez, Patrick Hogan, Ibrahim Hoteit, Sudheer Joseph, Simon Josey, Pierre-Yves Le Traon, Simone Libralato, Marco Mancini, Pascal Matte, Angelique Melet, Yasumasa Miyazawa, Andrew M. Moore, Antonio Novellino, Andrew Porter, Heather Regan, Laia Romero, Andreas Schiller, John Siddorn, Joanna Staneva, Cecile Thomas-Courcoux, Marina Tonani, Jose Maria Garcia-Valdecasas, Jennifer Veitch, Karina von Schuckmann, Liying Wan, John Wilkin, and Romane Zufic
State Planet, 1-osr7, 2, https://doi.org/10.5194/sp-1-osr7-2-2023, https://doi.org/10.5194/sp-1-osr7-2-2023, 2023
Nicholas Williams, Nicholas Byrne, Daniel Feltham, Peter Jan Van Leeuwen, Ross Bannister, David Schroeder, Andrew Ridout, and Lars Nerger
The Cryosphere, 17, 2509–2532, https://doi.org/10.5194/tc-17-2509-2023, https://doi.org/10.5194/tc-17-2509-2023, 2023
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Observations show that the Arctic sea ice cover has reduced over the last 40 years. This study uses ensemble-based data assimilation in a stand-alone sea ice model to investigate the impacts of assimilating three different kinds of sea ice observation, including the novel assimilation of sea ice thickness distribution. We show that assimilating ice thickness distribution has a positive impact on thickness and volume estimates within the ice pack, especially for very thick ice.
Alexandre Mignot, Hervé Claustre, Gianpiero Cossarini, Fabrizio D'Ortenzio, Elodie Gutknecht, Julien Lamouroux, Paolo Lazzari, Coralie Perruche, Stefano Salon, Raphaëlle Sauzède, Vincent Taillandier, and Anna Teruzzi
Biogeosciences, 20, 1405–1422, https://doi.org/10.5194/bg-20-1405-2023, https://doi.org/10.5194/bg-20-1405-2023, 2023
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Numerical models of ocean biogeochemistry are becoming a major tool to detect and predict the impact of climate change on marine resources and monitor ocean health. Here, we demonstrate the use of the global array of BGC-Argo floats for the assessment of biogeochemical models. We first detail the handling of the BGC-Argo data set for model assessment purposes. We then present 23 assessment metrics to quantify the consistency of BGC model simulations with respect to BGC-Argo data.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
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In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
Hao-Cheng Yu, Yinglong Joseph Zhang, Lars Nerger, Carsten Lemmen, Jason C. S. Yu, Tzu-Yin Chou, Chi-Hao Chu, and Chuen-Teyr Terng
EGUsphere, https://doi.org/10.5194/egusphere-2022-114, https://doi.org/10.5194/egusphere-2022-114, 2022
Preprint archived
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We develop a new data assimilative approach by combining two parallel frameworks: PDAF and ESMF. This allows maximum flexibility and easy implementation of data assimilation for fully coupled earth system model applications. It is also validated by using a simple benchmark and applied to a realistic case simulation around Taiwan. The real case test shows significant improvement for temperature, velocity and surface elevation before, during and after typhoon events.
Anna Teruzzi, Giorgio Bolzon, Laura Feudale, and Gianpiero Cossarini
Biogeosciences, 18, 6147–6166, https://doi.org/10.5194/bg-18-6147-2021, https://doi.org/10.5194/bg-18-6147-2021, 2021
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During summer, maxima of phytoplankton chlorophyll concentration (DCM) occur in the subsurface of the Mediterranean Sea and can play a relevant role in carbon sequestration into the ocean interior. A numerical model based on in situ and satellite observations provides insights into the range of DCM conditions across the relatively small Mediterranean Sea and shows a western DCM that is 25 % shallower and with a higher phytoplankton chlorophyll concentration than in the eastern Mediterranean.
Qing Li, Jorn Bruggeman, Hans Burchard, Knut Klingbeil, Lars Umlauf, and Karsten Bolding
Geosci. Model Dev., 14, 4261–4282, https://doi.org/10.5194/gmd-14-4261-2021, https://doi.org/10.5194/gmd-14-4261-2021, 2021
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Different ocean vertical mixing schemes are usually developed in different modeling framework, making the comparison across such schemes difficult. Here, we develop a consistent framework for testing, comparing, and applying different ocean mixing schemes by integrating CVMix into GOTM, which also extends the capability of GOTM towards including the effects of ocean surface waves. A suite of test cases and toolsets for developing and evaluating ocean mixing schemes is also described.
Lars Nerger, Qi Tang, and Longjiang Mu
Geosci. Model Dev., 13, 4305–4321, https://doi.org/10.5194/gmd-13-4305-2020, https://doi.org/10.5194/gmd-13-4305-2020, 2020
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Data assimilation combines observations with numerical models to get an improved estimate of the model state. This work discusses the technical aspects of how a coupled model that simulates the ocean and the atmosphere can be augmented by data assimilation functionality provided in generic form by the open-source software PDAF (Parallel Data Assimilation Framework). A very efficient program is obtained that can be executed on high-performance computers.
Stefano Salon, Gianpiero Cossarini, Giorgio Bolzon, Laura Feudale, Paolo Lazzari, Anna Teruzzi, Cosimo Solidoro, and Alessandro Crise
Ocean Sci., 15, 997–1022, https://doi.org/10.5194/os-15-997-2019, https://doi.org/10.5194/os-15-997-2019, 2019
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After 10 years of research and development, validated analysis and forecasts of the main parameters of the Mediterranean Sea biogeochemistry (e.g. phytoplankton, nutrients, oxygen, pH, carbon fluxes) at high spatial and temporal resolution are provided in the frame of the EU Copernicus Marine Environment Monitoring Service. Along with a traditional skill performance assessment, novel metrics exploiting the Biogeochemical Argo floats data are designed to estimate the forecasts uncertainty.
Qinghua Yang, Martin Losch, Svetlana N. Losa, Thomas Jung, Lars Nerger, and Thomas Lavergne
The Cryosphere, 10, 761–774, https://doi.org/10.5194/tc-10-761-2016, https://doi.org/10.5194/tc-10-761-2016, 2016
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We assimilate the summer SICCI sea ice concentration data with an ensemble-based Kalman Filter. Comparing with the approach using a constant data uncertainty, the sea ice concentration estimates are further improved when the SICCI-provided uncertainty are taken into account, but the sea ice thickness cannot be improved. We find the data assimilation system cannot give a reasonable ensemble spread of sea ice concentration and thickness if the provided uncertainty are directly used.
Momme Butenschön, James Clark, John N. Aldridge, Julian Icarus Allen, Yuri Artioli, Jeremy Blackford, Jorn Bruggeman, Pierre Cazenave, Stefano Ciavatta, Susan Kay, Gennadi Lessin, Sonja van Leeuwen, Johan van der Molen, Lee de Mora, Luca Polimene, Sevrine Sailley, Nicholas Stephens, and Ricardo Torres
Geosci. Model Dev., 9, 1293–1339, https://doi.org/10.5194/gmd-9-1293-2016, https://doi.org/10.5194/gmd-9-1293-2016, 2016
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ERSEM 15.06 is a model for marine biogeochemistry and the lower trophic levels of the marine food web. It comprises a pelagic and benthic sub-model including the microbial food web and the major biogeochemical cycles of carbon, nitrogen, phosphorus, silicate, and iron using dynamic stochiometry. Further features include modules for the carbonate system and calcification. We present full mathematical descriptions of all elements along with examples at various scales up to 3-D applications.
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Optimising CH4 simulations from the LPJ-GUESS model v4.1 using an adaptive Markov chain Monte Carlo algorithm
The XSO framework (v0.1) and Phydra library (v0.1) for a flexible, reproducible, and integrated plankton community modeling environment in Python
AgriCarbon-EO v1.0.1: large-scale and high-resolution simulation of carbon fluxes by assimilation of Sentinel-2 and Landsat-8 reflectances using a Bayesian approach
SAMM version 1.0: a numerical model for microbial- mediated soil aggregate formation
A model of the within-population variability of budburst in forest trees
Computationally efficient parameter estimation for high-dimensional ocean biogeochemical models
Tatsuya Miyauchi, Makoto Saito, Hibiki M. Noda, Akihiko Ito, Tomomichi Kato, and Tsuneo Matsunaga
Geosci. Model Dev., 18, 2329–2347, https://doi.org/10.5194/gmd-18-2329-2025, https://doi.org/10.5194/gmd-18-2329-2025, 2025
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Solar-induced chlorophyll fluorescence (SIF) is an effective indicator for monitoring photosynthetic activity. This paper introduces VISIT-SIF, a biogeochemical model developed based on the Vegetation Integrative Simulator for Trace gases (VISIT) to represent satellite-observed SIF. Our simulations reproduced the global distribution and seasonal variations in observed SIF. VISIT-SIF helps to improve photosynthetic processes through a combination of biogeochemical modeling and observed SIF.
Mateus Dantas de Paula, Matthew Forrest, David Warlind, João Paulo Darela Filho, Katrin Fleischer, Anja Rammig, and Thomas Hickler
Geosci. Model Dev., 18, 2249–2274, https://doi.org/10.5194/gmd-18-2249-2025, https://doi.org/10.5194/gmd-18-2249-2025, 2025
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Our study maps global nitrogen (N) and phosphorus (P) availability and how they changed from 1901 to 2018. We find that tropical regions are mostly P-limited, while temperate and boreal areas face N limitations. Over time, P limitation increased, especially in the tropics, while N limitation decreased. These shifts are key to understanding global plant growth and carbon storage, highlighting the importance of including P dynamics in ecosystem models.
Wolfgang Knorr, Matthew Williams, Tea Thum, Thomas Kaminski, Michael Voßbeck, Marko Scholze, Tristan Quaife, T. Luke Smallman, Susan C. Steele-Dunne, Mariette Vreugdenhil, Tim Green, Sönke Zaehle, Mika Aurela, Alexandre Bouvet, Emanuel Bueechi, Wouter Dorigo, Tarek S. El-Madany, Mirco Migliavacca, Marika Honkanen, Yann H. Kerr, Anna Kontu, Juha Lemmetyinen, Hannakaisa Lindqvist, Arnaud Mialon, Tuuli Miinalainen, Gaétan Pique, Amanda Ojasalo, Shaun Quegan, Peter J. Rayner, Pablo Reyes-Muñoz, Nemesio Rodríguez-Fernández, Mike Schwank, Jochem Verrelst, Songyan Zhu, Dirk Schüttemeyer, and Matthias Drusch
Geosci. Model Dev., 18, 2137–2159, https://doi.org/10.5194/gmd-18-2137-2025, https://doi.org/10.5194/gmd-18-2137-2025, 2025
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When it comes to climate change, the land surface is where the vast majority of impacts happen. The task of monitoring those impacts across the globe is formidable and must necessarily rely on satellites – at a significant cost: the measurements are only indirect and require comprehensive physical understanding. We have created a comprehensive modelling system that we offer to the research community to explore how satellite data can be better exploited to help us capture the changes that happen on our lands.
Luke Oberhagemann, Maik Billing, Werner von Bloh, Markus Drüke, Matthew Forrest, Simon P. K. Bowring, Jessica Hetzer, Jaime Ribalaygua Batalla, and Kirsten Thonicke
Geosci. Model Dev., 18, 2021–2050, https://doi.org/10.5194/gmd-18-2021-2025, https://doi.org/10.5194/gmd-18-2021-2025, 2025
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Under climate change, the conditions necessary for wildfires to form are occurring more frequently in many parts of the world. To help predict how wildfires will change in future, global fire models are being developed. We analyze and further develop one such model, SPITFIRE. Our work identifies and corrects sources of substantial bias in the model that are important to the global fire modelling field. With this analysis and these developments, we help to provide a basis for future improvements.
Trine Frisbæk Hansen, Donald Eugene Canfield, Ken Haste Andersen, and Christian Jannik Bjerrum
Geosci. Model Dev., 18, 1895–1916, https://doi.org/10.5194/gmd-18-1895-2025, https://doi.org/10.5194/gmd-18-1895-2025, 2025
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We describe and test the size-based Nutrient-Unicellular-Multicellular model, which defines unicellular plankton using a single set of parameters, on a eutrophic and oligotrophic ecosystem. The results demonstrate that both sites can be modeled with similar parameters and robust performance over a wide range of parameters. The study shows that the model is useful for non-experts and applicable for modeling ecosystems with limited data. It holds promise for evolutionary and deep-time climate models.
Ying Ye, Guy Munhoven, Peter Köhler, Martin Butzin, Judith Hauck, Özgür Gürses, and Christoph Völker
Geosci. Model Dev., 18, 977–1000, https://doi.org/10.5194/gmd-18-977-2025, https://doi.org/10.5194/gmd-18-977-2025, 2025
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Many biogeochemistry models assume all material reaching the seafloor is remineralized and returned to solution, which is sufficient for studies on short-term climate change. Under long-term climate change, the carbon storage in sediments slows down carbon cycling and influences feedbacks in the atmosphere–ocean–sediment system. This paper describes the coupling of a sediment model to an ocean biogeochemistry model and presents results under the pre-industrial climate and under CO2 perturbation.
Juliette Bernard, Elodie Salmon, Marielle Saunois, Shushi Peng, Penélope Serrano-Ortiz, Antoine Berchet, Palingamoorthy Gnanamoorthy, Joachim Jansen, and Philippe Ciais
Geosci. Model Dev., 18, 863–883, https://doi.org/10.5194/gmd-18-863-2025, https://doi.org/10.5194/gmd-18-863-2025, 2025
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Despite their importance, uncertainties remain in the evaluation of the drivers of temporal variability of methane emissions from wetlands on a global scale. Here, a simplified global model is developed, taking advantage of advances in remote-sensing data and in situ observations. The model reproduces the large spatial and temporal patterns of emissions, albeit with limitations in the tropics due to data scarcity. This model, while simple, can provide valuable insights into sensitivity analyses.
Christian Poppe Terán, Bibi S. Naz, Harry Vereecken, Roland Baatz, Rosie A. Fisher, and Harrie-Jan Hendricks Franssen
Geosci. Model Dev., 18, 287–317, https://doi.org/10.5194/gmd-18-287-2025, https://doi.org/10.5194/gmd-18-287-2025, 2025
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Carbon and water exchanges between the atmosphere and the land surface contribute to water resource availability and climate change mitigation. Land surface models, like the Community Land Model version 5 (CLM5), simulate these. This study finds that CLM5 and other data sets underestimate the magnitudes of and variability in carbon and water exchanges for the most abundant plant functional types compared to observations. It provides essential insights for further research into these processes.
Jianyong Ma, Almut Arneth, Benjamin Smith, Peter Anthoni, Xu-Ri, Peter Eliasson, David Wårlind, Martin Wittenbrink, and Stefan Olin
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-223, https://doi.org/10.5194/gmd-2024-223, 2024
Revised manuscript accepted for GMD
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Nitrous oxide (N2O) is a powerful greenhouse gas mainly released from natural and agricultural soils. This study examines how global soil N2O emissions have changed from 1961 to 2020 and identifies key factors driving these changes using an ecological model. The findings highlight croplands as the largest source, with factors like fertilizer use and climate change enhancing emissions. Rising CO2 levels, however, can partially mitigate N2O emissions through increased plant nitrogen uptake.
Katherine A. Muller, Peishi Jiang, Glenn Hammond, Tasneem Ahmadullah, Hyun-Seob Song, Ravi Kukkadapu, Nicholas Ward, Madison Bowe, Rosalie K. Chu, Qian Zhao, Vanessa A. Garayburu-Caruso, Alan Roebuck, and Xingyuan Chen
Geosci. Model Dev., 17, 8955–8968, https://doi.org/10.5194/gmd-17-8955-2024, https://doi.org/10.5194/gmd-17-8955-2024, 2024
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The new Lambda-PFLOTRAN workflow incorporates organic matter chemistry into reaction networks to simulate aerobic respiration and biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow in a Jupyter notebook interface that digests raw organic matter chemistry data via Fourier transform ion cyclotron resonance mass spectrometry, develops a representative reaction network, and completes a biogeochemical simulation with the open-source, parallel-reactive-flow, and transport code PFLOTRAN.
Ling Li, Peipei Wu, Peng Zhang, Shaojian Huang, and Yanxu Zhang
Geosci. Model Dev., 17, 8683–8695, https://doi.org/10.5194/gmd-17-8683-2024, https://doi.org/10.5194/gmd-17-8683-2024, 2024
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In this study, we incorporate sea surfactants and wave-breaking processes into MITgcm-ECCOv4-Hg. The updated model shows increased fluxes in high-wind-speed and high-wave regions and vice versa, enhancing spatial heterogeneity. It shows that elemental mercury (Hg0) transfer velocity is more sensitive to wind speed. These findings may elucidate the discrepancies in previous estimations and offer insights into global Hg cycling.
Jerome Guiet, Daniele Bianchi, Kim J. N. Scherrer, Ryan F. Heneghan, and Eric D. Galbraith
Geosci. Model Dev., 17, 8421–8454, https://doi.org/10.5194/gmd-17-8421-2024, https://doi.org/10.5194/gmd-17-8421-2024, 2024
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The BiOeconomic mArine Trophic Size-spectrum (BOATSv2) model dynamically simulates global commercial fish populations and their coupling with fishing activity, as emerging from environmental and economic drivers. New features, including separate pelagic and demersal populations, iron limitation, and spatial variation of fishing costs and management, improve the accuracy of high seas fisheries. The updated model code is available to simulate both historical and future scenarios.
Jize Jiang, David S. Stevenson, and Mark A. Sutton
Geosci. Model Dev., 17, 8181–8222, https://doi.org/10.5194/gmd-17-8181-2024, https://doi.org/10.5194/gmd-17-8181-2024, 2024
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A special model called AMmonia–CLIMate (AMCLIM) has been developed to understand and calculate NH3 emissions from fertilizer use and also taking into account how the environment influences these NH3 emissions. It is estimated that about 17 % of applied N in fertilizers was lost due to NH3 emissions. Hot and dry conditions and regions with high-pH soils can expect higher NH3 emissions.
Guillaume Marie, Jina Jeong, Hervé Jactel, Gunnar Petter, Maxime Cailleret, Matthew J. McGrath, Vladislav Bastrikov, Josefine Ghattas, Bertrand Guenet, Anne Sofie Lansø, Kim Naudts, Aude Valade, Chao Yue, and Sebastiaan Luyssaert
Geosci. Model Dev., 17, 8023–8047, https://doi.org/10.5194/gmd-17-8023-2024, https://doi.org/10.5194/gmd-17-8023-2024, 2024
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This research looks at how climate change influences forests, and particularly how altered wind and insect activities could make forests emit instead of absorb carbon. We have updated a land surface model called ORCHIDEE to better examine the effect of bark beetles on forest health. Our findings suggest that sudden events, such as insect outbreaks, can dramatically affect carbon storage, offering crucial insights into tackling climate change.
Stephen Björn Wirth, Johanna Braun, Jens Heinke, Sebastian Ostberg, Susanne Rolinski, Sibyll Schaphoff, Fabian Stenzel, Werner von Bloh, Friedhelm Taube, and Christoph Müller
Geosci. Model Dev., 17, 7889–7914, https://doi.org/10.5194/gmd-17-7889-2024, https://doi.org/10.5194/gmd-17-7889-2024, 2024
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We present a new approach to modelling 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, vertical root distribution, the nitrogen (N) deficit and carbon (C) costs. The new approach improved simulated BNF compared to the scientific literature and the model ability to project future C and N cycle dynamics.
Saeed Harati-Asl, Liliana Perez, and Roberto Molowny-Horas
Geosci. Model Dev., 17, 7423–7443, https://doi.org/10.5194/gmd-17-7423-2024, https://doi.org/10.5194/gmd-17-7423-2024, 2024
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Social–ecological systems are the subject of many sustainability problems. Because of the complexity of these systems, we must be careful when intervening in them; otherwise we may cause irreversible damage. Using computer models, we can gain insight about these complex systems without harming them. In this paper we describe how we connected an ecological model of forest insect infestation with a social model of cooperation and simulated an intervention measure to save a forest from infestation.
Katarína Merganičová, Ján Merganič, Laura Dobor, Roland Hollós, Zoltán Barcza, Dóra Hidy, Zuzana Sitková, Pavel Pavlenda, Hrvoje Marjanovic, Daniel Kurjak, Michal Bošel'a, Doroteja Bitunjac, Maša Zorana Ostrogović Sever, Jiří Novák, Peter Fleischer, and Tomáš Hlásny
Geosci. Model Dev., 17, 7317–7346, https://doi.org/10.5194/gmd-17-7317-2024, https://doi.org/10.5194/gmd-17-7317-2024, 2024
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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 the 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.
Hoa T. T. Nguyen, Ute Daewel, Neil Banas, and Corinna Schrum
EGUsphere, https://doi.org/10.5194/egusphere-2024-2710, https://doi.org/10.5194/egusphere-2024-2710, 2024
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Parameterisation is key in modeling to reproduce observations well but is often done manually. This study presents a Particle Swarm Optimizer-based toolbox for marine ecosystem models, compatible with the Framework for Aquatic Biogeochemical Models, thus enhancing its reusability. Applied to the Sylt ecosystem, the toolbox effectively (1) identified multiple parameter sets that matched observations well, thus providing different insights into ecosystem dynamics, (2) optimized model complexity.
Sylvain Schmitt, Fabian Fischer, James Ball, Nicolas Barbier, Marion Boisseaux, Damien Bonal, Benoit Burban, Xiuzhi Chen, Géraldine Derroire, Jeremy Lichstein, Daniela Nemetschek, Natalia Restrepo-Coupe, Scott Saleska, Giacomo Sellan, Philippe Verley, Grégoire Vincent, Camille Ziegler, Jérôme Chave, and Isabelle Maréchaux
EGUsphere, https://doi.org/10.5194/egusphere-2024-3106, https://doi.org/10.5194/egusphere-2024-3106, 2024
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We evaluate the capability of TROLL 4.0, a simulator of forest dynamics, to represent tropical forest structure, diversity and functioning in two Amazonian forests. Evaluation data include forest inventories, carbon and water fluxes between the forest and the atmosphere, and leaf area and canopy height from remote-sensing products. The model realistically predicts the structure and composition, and the seasonality of carbon and water fluxes at both sites.
Zhengyang Lin, Ling Huang, Hanqin Tian, Anping Chen, and Xuhui Wang
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-170, https://doi.org/10.5194/gmd-2024-170, 2024
Revised manuscript accepted for GMD
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Wildfires release large amounts of greenhouse gases, contributing to global warming. We developed a new model that provides near-real-time estimates of wildfire emissions in China. Our model improves the accuracy of burned area measurements and incorporates advanced data in fuel loads and emission factors. We found that most emissions come from agricultural fires, while emissions from forests and grasslands are decreasing. This model will help reduce the environmental impacts of wildfires.
Elchin E. Jafarov, Helene Genet, Velimir V. Vesselinov, Valeria Briones, Aiza Kabeer, Andrew L. Mullen, Benjamin Maglio, Tobey Carman, Ruth Rutter, Joy Clein, Chu-Chun Chang, Dogukan Teber, Trevor Smith, Joshua M. Rady, Christina Schädel, Jennifer D. Watts, Brendan M. Rogers, and Susan M. Natali
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-158, https://doi.org/10.5194/gmd-2024-158, 2024
Revised manuscript accepted for GMD
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Thawing permafrost could greatly impact global climate. Our study improves modeling of carbon cycling in Arctic ecosystems. We developed an automated method to fine-tune a model that simulates carbon and nitrogen flows, using computer-generated data. Using computer-generated data, we tested our method and found it enhances accuracy and reduces the time needed for calibration. This work helps make climate predictions more reliable in sensitive permafrost regions.
Zavud Baghirov, Martin Jung, Markus Reichstein, Marco Körner, and Basil Kraft
EGUsphere, https://doi.org/10.5194/egusphere-2024-2044, https://doi.org/10.5194/egusphere-2024-2044, 2024
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We use an innovative approach to study the Earth's water cycle by blending advanced computer learning techniques with a traditional water cycle model. We developed a model that learns from meteorological data, with a special focus on understanding how vegetation influences water movement. Our model closely aligns with real-world observations, yet there are areas that need improvement. This study opens up new possibilities to better understand the water cycle and its interactions with vegetation.
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.
Ye Liu, Huilin Huang, Sing-Chun Wang, Tao Zhang, Donghui Xu, and Yang Chen
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-151, https://doi.org/10.5194/gmd-2024-151, 2024
Revised manuscript accepted for GMD
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This study integrates machine learning with a land surface model to improve wildfire predictions in North America. Traditional models struggle with accurately simulating burned areas due to simplified processes. By combining the predictive power of machine learning with a land model, our hybrid framework better captures fire dynamics. This approach enhances our understanding of wildfire behavior and aids in developing more effective climate and fire management strategies.
Sergi Molins, Benjamin Andre, Jeffrey Johnson, Glenn Hammond, Benjamin Sulman, Konstantin Lipnikov, Marcus Day, James Beisman, Daniil Svyatsky, Hang Deng, Peter Lichtner, Carl Steefel, and David Moulton
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-108, https://doi.org/10.5194/gmd-2024-108, 2024
Revised manuscript accepted for GMD
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Developing scientific software and making sure it functions properly requires a significant effort. As we advance our understanding of natural systems, however, there is the need to develop yet more complex models and codes. In this work, we present a piece of software that facilitates this work, specifically with regard to reactive processes. Existing tried-and-true codes are made available via this new interface, freeing up resources to focus on the new aspects of the problems at hand.
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.
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.
Naveenkumar Parameswaran, Everardo González, Ewa Burwicz-Galerne, Malte Braack, and Klaus Wallmann
EGUsphere, https://doi.org/10.5194/egusphere-2024-1360, https://doi.org/10.5194/egusphere-2024-1360, 2024
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Our research uses deep learning to predict organic carbon stocks in ocean sediments, crucial for understanding their role in the global carbon cycle. By analyzing over 22,000 samples and various seafloor characteristics, our model gives more accurate results than traditional methods. We estimate the top 10 cm of ocean sediments hold about 171 petagrams of carbon. This work enhances carbon stock estimates and helps plan future sampling strategies to better understand oceanic carbon burial.
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.
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.
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.
Cited articles
Allen, J. I., Eknes, M., and Evensen, G.: An Ensemble Kalman Filter with a complex marine ecosystem model: hindcasting phytoplankton in the Cretan Sea, Ann. Geophys., 21, 399–411, https://doi.org/10.5194/angeo-21-399-2003, 2003.
Andersen, T. K., Bolding, K., Nielsen, A., Bruggeman, J., Jeppesen, E., and Trolle, D.: How morphology shapes the parameter sensitivity of lake ecosystem models, Environ. Model. Softw., 136, 104945, https://doi.org/10.1016/j.envsoft.2020.104945, 2021.
Aumont, O., Ethé, C., Tagliabue, A., Bopp, L., and Gehlen, M.: PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies, Geosci. Model Dev., 8, 2465–2513, https://doi.org/10.5194/gmd-8-2465-2015, 2015.
Bagniewski, W., Fennel, K., Perry, M. J., and D'Asaro, E. A.: Optimizing models of the North Atlantic spring bloom using physical, chemical and bio-optical observations from a Lagrangian float, Biogeosciences, 8, 1291–1307, https://doi.org/10.5194/bg-8-1291-2011, 2011.
Bannister, R. N.: A review of operational methods of variational and ensemble-variational data assimilation, Q. J. Roy. Meteor. Soc., 143, 607–633, https://doi.org/10.1002/qj.2982, 2017.
Bertino, L., Evensen, G., and Wackernagel, H.: Sequential Data Assimilation Techniques in Oceanography, Int. Stat. Rev., 71, 223–241, https://doi.org/10.1111/j.1751-5823.2003.tb00194.x, 2003.
Brankart, J.-M., Testut, C.-E., Béal, D., Doron, M., Fontana, C., Meinvielle, M., Brasseur, P., and Verron, J.: Towards an improved description of ocean uncertainties: effect of local anamorphic transformations on spatial correlations, Ocean Sci., 8, 121–142, https://doi.org/10.5194/os-8-121-2012, 2012.
Brasseur, P., Gruber, N., Barciela, R., Brander, K., Doron, M., El Moussaoui, A., Hobday, A., Huret, M., Kremeur, A.-S., Lehodey, P., Matear, R., Moulin, C., Murtugudde, R., Senina, I., and Svendsen, E.: Integrating Biogeochemistry and Ecology Into Ocean Data Assimilation Systems, Oceanography, 22, 206–215, https://doi.org/10.5670/oceanog.2009.80, 2009.
Brewin, R. J. W., Ciavatta, S., Sathyendranath, S., Jackson, T., Tilstone, G., Curran, K., Airs, R. L., Cummings, D., Brotas, V., Organelli, E., Dall'Olmo, G., and Raitsos, D. E.: Uncertainty in Ocean-Color Estimates of Chlorophyll for Phytoplankton Groups, Front. Mar. Sci., 4, 104, https://doi.org/10.3389/fmars.2017.00104, 2017.
Brewin, R. J. W., Sathyendranath, S., Platt, T., Bouman, H., Ciavatta, S., Dall'Olmo, G., Dingle, J., Groom, S., Jönsson, B., Kostadinov, T. S., Kulk, G., Laine, M., Martínez-Vicente, V., Psarra, S., Raitsos, D. E., Richardson, K., Rio, M.-H., Rousseaux, C. S., Salisbury, J., Shutler, J. D., and Walker, P.: Sensing the ocean biological carbon pump from space: A review of capabilities, concepts, research gaps and future developments, Earth. Sci. Rev., 217, 103604, https://doi.org/10.1016/j.earscirev.2021.103604, 2021.
Bruggeman, J. and Bolding, K.: A general framework for aquatic biogeochemical models, Environ. Model. Softw., 61, 249–265, https://doi.org/10.1016/j.envsoft.2014.04.002, 2014.
Bruggeman, J., Bolding, K., and Nerger, L.: EAT: Ensemble and Assimilation Tool (v1.0.0), Zenodo [code], https://doi.org/10.5281/zenodo.11111437, 2024a.
Bruggeman, J., Teruzzi, A., Spada, S., and Skákala, J.: EAT example applications (v2.3), Zenodo [data set], https://doi.org/10.5281/zenodo.11111361, 2024b.
Brüning, T., Li, X., Schwichtenberg, F., and Lorkowski, I.: An operational, assimilative model system for hydrodynamic and biogeochemical applications for German coastal waters, Hydrographische Nachrichten, 118, 6–15, https://doi.org/10.23784/HN118-01, 2021.
Burchard, H., Bolding, K., and Ruiz Villarreal, M.: GOTM – a General Ocean Turbulence Model. Theory, applications and test cases., Tech. Rep. EUR 18745 EN, European Commission, 1999.
Burchard, H., Bolding, K., Kühn, W., Meister, A., Neumann, T., and Umlauf, L.: Description of a flexible and extendable physical-biogeochemical model system for the water column, J. Marine Syst., 61, 180–211, https://doi.org/10.1016/j.jmarsys.2005.04.011, 2006.
Butenschön, M., Clark, J., Aldridge, J. N., Allen, J. I., Artioli, Y., Blackford, J., Bruggeman, J., Cazenave, P., Ciavatta, S., Kay, S., Lessin, G., van Leeuwen, S., van der Molen, J., de Mora, L., Polimene, L., Sailley, S., Stephens, N., and Torres, R.: ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels, Geosci. Model Dev., 9, 1293–1339, https://doi.org/10.5194/gmd-9-1293-2016, 2016.
Campbell, J. W.: The lognormal distribution as a model for bio-optical variability in the sea, J. Geophys. Res.-Oceans, 100, 13237–13254, https://doi.org/10.1029/95JC00458, 1995.
Carrassi, A., Bocquet, M., Bertino, L., and Evensen, G.: Data assimilation in the geosciences: An overview of methods, issues, and perspectives, WIREs Climate Change, 9, e535, https://doi.org/10.1002/wcc.535, 2018.
Ciavatta, S., Lazzari, P., Alvarez, E., Bruggeman, J., Capet, A., Cossarini, G., Daryabor, F., Nerger, L., Skakala, J., Teruzzi, A., Wakamatsu, T., and Yumruktepe, C.: D3.2 Observability of the target indicators and parameter sensitivity in the 1D CMEMS sites. Deliverable report of project H2020 SEAMLESS (grant 101004032), Zenodo [data set], https://doi.org/10.5281/zenodo.6580236, 2022.
Daewel, U. and Schrum, C.: Simulating long-term dynamics of the coupled North Sea and Baltic Sea ecosystem with ECOSMO II: Model description and validation, J. Marine Syst., 119–120, 30–49, https://doi.org/10.1016/j.jmarsys.2013.03.008, 2013.
Doron, M., Brasseur, P., Brankart, J.-M., Losa, S. N., and Melet, A.: Stochastic estimation of biogeochemical parameters from Globcolour ocean colour satellite data in a North Atlantic 3D ocean coupled physical–biogeochemical model, J. Marine Syst., 117–118, 81–95, https://doi.org/10.1016/j.jmarsys.2013.02.007, 2013.
Egbert, G. D. and Erofeeva, S. Y.: Efficient Inverse Modeling of Barotropic Ocean Tides, J. Atmos. Ocean. Tech., 19, 183–204, https://doi.org/10.1175/1520-0426(2002)019<0183:EIMOBO>2.0.CO;2, 2002.
Eknes, M. and Evensen, G.: An Ensemble Kalman filter with a 1-D marine ecosystem model, J. Marine Syst., 36, 75–100, https://doi.org/10.1016/S0924-7963(02)00134-3, 2002.
E.U. Copernicus Marine Service Information (CMEMS): Atlantic-European North West Shelf-Ocean Biogeochemistry Reanalysis, Marine Data Store (MDS), https://doi.org/10.48670/moi-00058, last access: 19 July 2024.
Evensen, G.: The Ensemble Kalman Filter: theoretical formulation and practical implementation, Ocean Dynam., 53, 343–367, https://doi.org/10.1007/s10236-003-0036-9, 2003.
Ford, D.: Assimilating synthetic Biogeochemical-Argo and ocean colour observations into a global ocean model to inform observing system design, Biogeosciences, 18, 509–534, https://doi.org/10.5194/bg-18-509-2021, 2021.
Fournier, A., Nerger, L., and Aubert, J.: An ensemble Kalman filter for the time-dependent analysis of the geomagnetic field, Geochem. Geophys. Geosyst., 14, 4035–4043, https://doi.org/10.1002/ggge.20252, 2013.
Gharamti, M. E., Samuelsen, A., Bertino, L., Simon, E., Korosov, A., and Daewel, U.: Online tuning of ocean biogeochemical model parameters using ensemble estimation techniques: Application to a one-dimensional model in the North Atlantic, J. Marine Syst., 168, 1–16, https://doi.org/10.1016/j.jmarsys.2016.12.003, 2017a.
Gharamti, M. E., Tjiputra, J., Bethke, I., Samuelsen, A., Skjelvan, I., Bentsen, M., and Bertino, L.: Ensemble data assimilation for ocean biogeochemical state and parameter estimation at different sites, Ocean Model. (Oxf), 112, 65–89, https://doi.org/10.1016/j.ocemod.2017.02.006, 2017b.
Goodliff, M., Bruening, T., Schwichtenberg, F., Li, X., Lindenthal, A., Lorkowski, I., and Nerger, L.: Temperature assimilation into a coastal ocean-biogeochemical model: assessment of weakly and strongly coupled data assimilation, Ocean. Dynam., 69, 1217–1237, https://doi.org/10.1007/s10236-019-01299-7, 2019.
Gordon, H. R. and McCluney, W. R.: Estimation of the Depth of Sunlight Penetration in the Sea for Remote Sensing, Appl. Optics, 14, 413–416, https://doi.org/10.1364/ao.14.000413, 1975.
Gropp, W., Lusk, E., and Skjellum, A.: Using MPI: Portable Parallel Programming with the Message-Passing Interface, MIT Press, Cambridge, MA, 1994.
Harris, R.: The L4 time-series: the first 20 years, J. Plankton Res., 32, 577–583, https://doi.org/10.1093/plankt/fbq021, 2010.
Hersbach, H., Bell, B., Berrisford, P., Biavati, G., Horányi, A., Muñoz Sabater, J., Nicolas, J., Peubey, C., Radu, R., Rozum, I., Schepers, D., Simmons, A., Soci, C., Dee, D., and Thépaut, J.-N.: ERA5 hourly data on single levels from 1940 to present, Copernicus Climate Change Service (C3S) Climate Data Store (CDS) [data set], https://doi.org/10.24381/cds.adbb2d47, 2023.
Hoteit, I., Triantafyllou, G., Petihakis, G., and Allen, J. I.: A singular evolutive extended Kalman filter to assimilate real in situ data in a 1-D marine ecosystem model, Ann. Geophys., 21, 389–397, https://doi.org/10.5194/angeo-21-389-2003, 2003.
Kurtz, W., He, G., Kollet, S. J., Maxwell, R. M., Vereecken, H., and Hendricks Franssen, H.-J.: TerrSysMP–PDAF (version 1.0): a modular high-performance data assimilation framework for an integrated land surface–subsurface model, Geosci. Model Dev., 9, 1341–1360, https://doi.org/10.5194/gmd-9-1341-2016, 2016.
Leibniz Institute for Baltic Sea Research: ERGOM: Ecological ReGional Ocean Model, https://ergom.net/ (last access: 19 July 2024), 2015.
Lenartz, F., Raick, C., Soetaert, K., and Grégoire, M.: Application of an Ensemble Kalman filter to a 1-D coupled hydrodynamic-ecosystem model of the Ligurian Sea, J. Marine Syst., 68, 327–348, https://doi.org/10.1016/j.jmarsys.2006.12.001, 2007.
Li, Q., Bruggeman, J., Burchard, H., Klingbeil, K., Umlauf, L., and Bolding, K.: Integrating CVMix into GOTM (v6.0): a consistent framework for testing, comparing, and applying ocean mixing schemes, Geosci. Model Dev., 14, 4261–4282, https://doi.org/10.5194/gmd-14-4261-2021, 2021.
Mamnun, N., Völker, C., Vrekoussis, M., and Nerger, L.: Uncertainties in ocean biogeochemical simulations: Application of ensemble data assimilation to a one-dimensional model, Front. Mar Sci., 9, 984236, https://doi.org/10.3389/fmars.2022.984236, 2022.
Mattern, J. P., Dowd, M., and Fennel, K.: Sequential data assimilation applied to a physical–biological model for the Bermuda Atlantic time series station, J. Marine Syst., 79, 144–156, https://doi.org/10.1016/j.jmarsys.2009.08.004, 2010.
Moore, A. M., Martin, M. J., Akella, S., Arango, H. G., Balmaseda, M., Bertino, L., Ciavatta, S., Cornuelle, B., Cummings, J., Frolov, S., Lermusiaux, P., Oddo, P., Oke, P. R., Storto, A., Teruzzi, A., Vidard, A., and Weaver, A. T.: Synthesis of Ocean Observations Using Data Assimilation for Operational, Real-Time and Reanalysis Systems: A More Complete Picture of the State of the Ocean, Front. Mar Sci., 6, 90, https://doi.org/10.3389/fmars.2019.00090, 2019.
Mu, L., Liang, X., Yang, Q., Liu, J., and Zheng, F.: Arctic Ice Ocean Prediction System: evaluating sea-ice forecasts during Xuelong's first trans-Arctic Passage in summer 2017, J. Glaciol., 65, 813–821, https://doi.org/10.1017/jog.2019.55, 2019.
Nerger, L. and Hiller, W.: Software for ensemble-based data assimilation systems – Implementation strategies and scalability, Comput. Geosci., 55, 110–118, https://doi.org/10.1016/j.cageo.2012.03.026, 2013.
Nerger, L., Hiller, W., and Schröter, J.: The Parallel Data Assimilation Framework: Experiences with Kalman filtering, in: Use of High Performance Computing in Meteorology, in: Use of High Performance Computing in Meteorology, World Scientific, 63–83, https://doi.org/10.1142/9789812701831_0006, 2005.
Nerger, L., Janjić, T., Schröter, J., and Hiller, W.: A Unification of Ensemble Square Root Kalman Filters, Mon. Weather Rev., 140, 2335–2345, https://doi.org/10.1175/MWR-D-11-00102.1, 2012.
Nerger, L., Tang, Q., and Mu, L.: Efficient ensemble data assimilation for coupled models with the Parallel Data Assimilation Framework: example of AWI-CM (AWI-CM-PDAF 1.0), Geosci. Model Dev., 13, 4305–4321, https://doi.org/10.5194/gmd-13-4305-2020, 2020.
Pardini, F., Corradini, S., Costa, A., Esposti Ongaro, T., Merucci, L., Neri, A., Stelitano, D., and de' Michieli Vitturi, M.: Ensemble-Based Data Assimilation of Volcanic Ash Clouds from Satellite Observations: Application to the 24 December 2018 Mt. Etna Explosive Eruption, Atmosphere (Basel), 11, 359, https://doi.org/10.3390/atmos11040359, 2020.
Park, J.-Y., Stock, C. A., Yang, X., Dunne, J. P., Rosati, A., John, J., and Zhang, S.: Modeling Global Ocean Biogeochemistry With Physical Data Assimilation: A Pragmatic Solution to the Equatorial Instability, J. Adv. Model. Earth Sy., 10, 891–906, https://doi.org/10.1002/2017MS001223, 2018.
Pelc, J. S., Simon, E., Bertino, L., El Serafy, G., and Heemink, A. W.: Application of model reduced 4D-Var to a 1D ecosystem model, Ocean Model. (Oxf), 57–58, 43–58, https://doi.org/10.1016/j.ocemod.2012.09.003, 2012.
Penny, S. G., Akella, S., Alves, O., Bishop, C., Buehner, M., Chevallier, M., Counillon, F., Draper, C., Frolov, S., Fujii, Y., Karspeck, A., Kumar, A., Laloyaux, P., Mahfouf, J.-F., Martin, M., Peña, M., de Rosnay, P., Subramanian, A., Tardif, R., Wang, Y., and Wu, X.: Coupled Data Assimilation for Integrated Earth System Analysis and Prediction: Goals, Challenges and Recommendations, WWRP 2017-3, World Meteorological Organization, https://library.wmo.int/idurl/4/57666 (last access: 19 July 2024), 2017.
Pingree, R. D. and Griffiths, D. K.: Tidal fronts on the shelf seas around the British Isles, J. Geophys. Res., 83, 4615, https://doi.org/10.1029/JC083iC09p04615, 1978.
Pradhan, H. K., Völker, C., Losa, S. N., Bracher, A., and Nerger, L.: Assimilation of Global Total Chlorophyll OC-CCI Data and Its Impact on Individual Phytoplankton Fields, J. Geophys. Res.-Oceans, 124, 470–490, https://doi.org/10.1029/2018JC014329, 2019.
Pradhan, H. K., Völker, C., Losa, S. N., Bracher, A., and Nerger, L.: Global Assimilation of Ocean-Color Data of Phytoplankton Functional Types: Impact of Different Data Sets, J. Geophys. Res.-Oceans, 125, e2019JC015586, https://doi.org/10.1029/2019JC015586, 2020.
Roemmich, D., Alford, M. H., Claustre, H., Johnson, K., King, B., Moum, J., Oke, P., Owens, W. B., Pouliquen, S., Purkey, S., Scanderbeg, M., Suga, T., Wijffels, S., Zilberman, N., Bakker, D., Baringer, M., Belbeoch, M., Bittig, H. C., Boss, E., Calil, P., Carse, F., Carval, T., Chai, F., Conchubhair, D. Ó., d'Ortenzio, F., Dall'Olmo, G., Desbruyeres, D., Fennel, K., Fer, I., Ferrari, R., Forget, G., Freeland, H., Fujiki, T., Gehlen, M., Greenan, B., Hallberg, R., Hibiya, T., Hosoda, S., Jayne, S., Jochum, M., Johnson, G. C., Kang, K., Kolodziejczyk, N., Körtzinger, A., Traon, P.-Y. Le, Lenn, Y.-D., Maze, G., Mork, K. A., Morris, T., Nagai, T., Nash, J., Garabato, A. N., Olsen, A., Pattabhi, R. R., Prakash, S., Riser, S., Schmechtig, C., Schmid, C., Shroyer, E., Sterl, A., Sutton, P., Talley, L., Tanhua, T., Thierry, V., Thomalla, S., Toole, J., Troisi, A., Trull, T. W., Turton, J., Velez-Belchi, P. J., Walczowski, W., Wang, H., Wanninkhof, R., Waterhouse, A. F., Waterman, S., Watson, A., Wilson, C., Wong, A. P. S., Xu, J., and Yasuda, I.: On the Future of Argo: A Global, Full-Depth, Multi-Disciplinary Array, Front. Mar. Sci., 6, 439, https://doi.org/10.3389/fmars.2019.00439, 2019.
Santana-Falcón, Y., Brasseur, P., Brankart, J. M., and Garnier, F.: Assimilation of chlorophyll data into a stochastic ensemble simulation for the North Atlantic Ocean, Ocean Sci., 16, 1297–1315, https://doi.org/10.5194/os-16-1297-2020, 2020.
Schachtschneider, R., Saynisch-Wagner, J., Klemann, V., Bagge, M., and Thomas, M.: An approach for constraining mantle viscosities through assimilation of palaeo sea level data into a glacial isostatic adjustment model, Nonlin. Processes Geophys., 29, 53–75, https://doi.org/10.5194/npg-29-53-2022, 2022.
Simon, E. and Bertino, L.: Gaussian anamorphosis extension of the DEnKF for combined state parameter estimation: Application to a 1D ocean ecosystem model, J. Marine Syst., 89, 1–18, https://doi.org/10.1016/j.jmarsys.2011.07.007, 2012.
Simon, E., Samuelsen, A., Bertino, L., and Mouysset, S.: Experiences in multiyear combined state–parameter estimation with an ecosystem model of the North Atlantic and Arctic Oceans using the Ensemble Kalman Filter, J. Marine Syst., 152, 1–17, https://doi.org/10.1016/j.jmarsys.2015.07.004, 2015.
Skákala, J., Bruggeman, J., Brewin, R. J. W., Ford, D. A., and Ciavatta, S.: Improved Representation of Underwater Light Field and Its Impact on Ecosystem Dynamics: A Study in the North Sea, J. Geophys. Res.-Oceans, 125, e2020JC016122, https://doi.org/10.1029/2020JC016122, 2020.
Skákala, J., Ford, D., Bruggeman, J., Hull, T., Kaiser, J., King, R. R., Loveday, B., Palmer, M. R., Smyth, T., Williams, C. A. J., and Ciavatta, S.: Towards a Multi-Platform Assimilative System for North Sea Biogeochemistry, J. Geophys. Res.-Oceans, 126, e2020JC016649, https://doi.org/10.1029/2020JC016649, 2021.
Skákala, J., Bruggeman, J., Ford, D., Wakelin, S., Akpınar, A., Hull, T., Kaiser, J., Loveday, B. R., O'Dea, E., Williams, C. A. J., and Ciavatta, S.: The impact of ocean biogeochemistry on physics and its consequences for modelling shelf seas, Ocean Model. (Oxf), 172, 101976, https://doi.org/10.1016/j.ocemod.2022.101976, 2022.
Skákala, J., Awty-Carroll, K., Menon, P. P., Wang, K., and Lessin, G.: Future digital twins: emulating a highly complex marine biogeochemical model with machine learning to predict hypoxia, Front. Mar. Sci., 10, 1058837, https://doi.org/10.3389/fmars.2023.1058837, 2023a.
Skákala, J., Wakamatsu, T., Bertino, L., Teruzzi, A., Lazzari, P., Alvarez, E., Cossarini, G., Spada, S., Nerger, L., Vliegen, S., Brankart, J. M., and Brasseur, P.: SEAMLESS Target indicator quality in CMEMS MFCs (D6.1), https://doi.org/10.5281/zenodo.10522305, 2023b.
Sournia, A.: Is there a shade flora in the marine plankton?, J. Plankton Res., 4, 391–399, https://doi.org/10.1093/plankt/4.2.391, 1982.
Teruzzi, A., Bolzon, G., Feudale, L., and Cossarini, G.: Deep chlorophyll maximum and nutricline in the Mediterranean Sea: emerging properties from a multi-platform assimilated biogeochemical model experiment, Biogeosciences, 18, 6147–6166, https://doi.org/10.5194/bg-18-6147-2021, 2021a.
Teruzzi, A., Di Biagio, V., Feudale, L., Bolzon, G., Lazzari, P., Salon, S., Coidessa, G., and Cossarini, G.: Mediterranean Sea Biogeochemical Reanalysis (CMEMS MED-Biogeochemistry, MedBFM3 system) (Version 1), Copernicus Marine Service [data set], https://doi.org/10.25423/CMCC/MEDSEA_MULTIYEAR_BGC _006_008_MEDBFM3, 2021b.
Thomas, R. Q., Figueiredo, R. J., Daneshmand, V., Bookout, B. J., Puckett, L. K., and Carey, C. C.: A Near-Term Iterative Forecasting System Successfully Predicts Reservoir Hydrodynamics and Partitions Uncertainty in Real Time, Water. Resour. Res., 56, e2019WR026138, https://doi.org/10.1029/2019WR026138, 2020.
Torres, R., Allen, J. I., and Figueiras, F. G.: Sequential data assimilation in an upwelling influenced estuary, J. Marine Syst., 60, 317–329, https://doi.org/10.1016/j.jmarsys.2006.02.001, 2006.
Torres, R., Artioli, Y., Kitidis, V., Ciavatta, S., Ruiz-Villarreal, M., Shutler, J., Polimene, L., Martinez, V., Widdicombe, C., Woodward, E. M. S., Smyth, T., Fishwick, J., and Tilstone, G. H.: Sensitivity of Modeled CO2 Air–Sea Flux in a Coastal Environment to Surface Temperature Gradients, Surfactants, and Satellite Data Assimilation, Remote Sens (Basel), 12, 2038, https://doi.org/10.3390/rs12122038, 2020.
Van Leeuwen, P. J., Cheng, Y., and Reich, S.: Nonlinear Data Assimilation, Springer International Publishing, Cham, https://doi.org/10.1007/978-3-319-18347-3, 2015.
Vichi, M., Lovato, T., Butenschön, M., Tedesco, L., Lazzari, P., Cossarini, G., Masina, S., Pinardi, N., Solidoro, C., and Zavatarelli, M.: The Biogeochemical Flux Model (BFM): Equation Description and User Manual. BFM version 5.2., Bologna, Italy, 104 pp., 2020.
Yumruktepe, V. Ç., Samuelsen, A., and Daewel, U.: ECOSMO II(CHL): a marine biogeochemical model for the North Atlantic and the Arctic, Geosci. Model Dev., 15, 3901–3921, https://doi.org/10.5194/gmd-15-3901-2022, 2022.
Short summary
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.
To understand and predict the ocean’s capacity for carbon sequestration, its ability to supply...
