Articles | Volume 17, issue 4
https://doi.org/10.5194/gmd-17-1729-2024
© 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-17-1729-2024
© 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
| 
27 Feb 2024
Model description paper |
| 27 Feb 2024
| 27 Feb 2024
A diatom extension to the cGEnIE Earth system model – EcoGEnIE 1.1
Aaron A. Naidoo-Bagwell
CORRESPONDING AUTHOR
Department of Geology, Lund University, Lund, Sweden
School of Geographical Sciences, BRIDGE, University of Bristol, Bristol, UK
Fanny M. Monteiro
CORRESPONDING AUTHOR
School of Geographical Sciences, BRIDGE, University of Bristol, Bristol, UK
Katharine R. Hendry
School of Earth Sciences, University of Bristol, Bristol, UK
Polar Oceans Team, British Antarctic Survey, Cambridge, UK
Scott Burgan
Met Office, Exeter, UK
Jamie D. Wilson
School of Earth Sciences, University of Bristol, Bristol, UK
Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, UK
Ben A. Ward
School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, UK
Andy Ridgwell
Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
Daniel J. Conley
Department of Geology, Lund University, Lund, Sweden
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Marco Puglia, Thomas Bibby, Jamie Wilson, and Ben Ward
EGUsphere, https://doi.org/10.5194/egusphere-2025-3050, https://doi.org/10.5194/egusphere-2025-3050, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
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Mixotrophs use both photosynthesis and predation as source of nutrition. Simulations show they can increase ocean carbon storage, but long-term effects are not yet understood. Using a low-resolution ocean-ecology model that ran for 10,000 years, we compared simulations with and without mixotrophs. Mixotrophs increased global carbon storage by trapping more organic carbon in the ocean interior, although interactions with the ocean circulation offset these effects in the North Atlantic.
Kirsty M. Edgar, Maria Grigoratou, Fanny M. Monteiro, Ruby Barrett, Rui Ying, and Daniela N. Schmidt
Biogeosciences, 22, 3463–3483, https://doi.org/10.5194/bg-22-3463-2025, https://doi.org/10.5194/bg-22-3463-2025, 2025
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Planktic foraminifera are microscopic marine organisms whose calcium carbonate shells provide valuable insights into past ocean conditions. A promising means of understanding foraminiferal ecology and their environmental interactions is to constrain their key functional traits relating to feeding, symbioses, motility, calcification, and reproduction. Here we review what we know of their functional traits, key gaps in our understanding, and suggestions on how to fill them.
Mara Y. McPartland, Tomas Lovato, Charles D. Koven, Jamie D. Wilson, Briony Turner, Colleen M. Petrik, José Licón-Saláiz, Fang Li, Fanny Lhardy, Jaclyn Clement Kinney, Michio Kawamiya, Birgit Hassler, Nathan P. Gillett, Cheikh Modou Noreyni Fall, Christopher Danek, Chris M. Brierley, Ana Bastos, and Oliver Andrews
EGUsphere, https://doi.org/10.5194/egusphere-2025-3246, https://doi.org/10.5194/egusphere-2025-3246, 2025
This preprint is open for discussion and under review for Geoscientific Model Development (GMD).
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The Coupled Model Intercomparison Project (CMIP) is an international consortium of climate modeling groups that produce coordinated experiments in order to evaluate human influence on the climate and test knowledge of Earth systems. This paper describes the data requested for Earth systems research in CMIP7. We detail the request for model output of the carbon cycle, the flows of energy among the atmosphere, land and the oceans, and interactions between these and the global climate.
Isabell Hochfeld, Ben A. Ward, Anke Kremp, Juliane Romahn, Alexandra Schmidt, Miklós Bálint, Lutz Becks, Jérôme Kaiser, Helge W. Arz, Sarah Bolius, Laura S. Epp, Markus Pfenninger, Christopher A. Klausmeier, Elena Litchman, and Jana Hinners
Biogeosciences, 22, 2363–2380, https://doi.org/10.5194/bg-22-2363-2025, https://doi.org/10.5194/bg-22-2363-2025, 2025
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Marine ecosystem models (MEMs) are valuable for assessing the threats of global warming to biodiversity and ecosystem functioning, but their predictions vary widely. We argue that MEMs should consider evolutionary processes and undergo independent validation. Here, we present a novel framework for MEM development using validation data from sediment archives, which map long-term environmental and evolutionary change. Our approach is a crucial step towards improving the predictive power of MEMs.
David A. Stappard, Jamie D. Wilson, Andrew Yool, and Toby Tyrrell
EGUsphere, https://doi.org/10.5194/egusphere-2025-436, https://doi.org/10.5194/egusphere-2025-436, 2025
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This research explores nutrient limitations in oceanic primary production. While traditional experiments identify the immediate limiting nutrient at specific locations, this study aims to identify the ultimate limiting nutrient (ULN), which governs long-term productivity. A mathematical model incorporating nitrogen, phosphorus, and iron nutrient cycles is used. The model's results are compared with ocean observational data to assess its effectiveness in investigating the ULN.
Keyi Cheng, Andy Ridgwell, and Dalton S. Hardisty
Biogeosciences, 21, 4927–4949, https://doi.org/10.5194/bg-21-4927-2024, https://doi.org/10.5194/bg-21-4927-2024, 2024
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The carbonate paleoredox proxy, I / Ca, has shown its potential to quantify the redox change in the past ocean, which is of broad importance for understanding climate change and evolution. Here, we tuned and optimized the marine iodine cycling embedded in an Earth system model, “cGENIE”, against modern ocean observations and then tested its ability to estimate I / Ca in the Cretaceous ocean. Our study implies cGENIE’s potential to quantify redox change in the past using the I / Ca proxy.
Joost de Vries, Fanny Monteiro, Gerald Langer, Colin Brownlee, and Glen Wheeler
Biogeosciences, 21, 1707–1727, https://doi.org/10.5194/bg-21-1707-2024, https://doi.org/10.5194/bg-21-1707-2024, 2024
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Calcifying phytoplankton (coccolithophores) utilize a life cycle in which they can grow and divide into two different phases. These two phases (HET and HOL) vary in terms of their physiology and distributions, with many unknowns about what the key differences are. Using a combination of lab experiments and model simulations, we find that nutrient storage is a critical difference between the two phases and that this difference allows them to inhabit different nitrogen input regimes.
Giulia Lodi, Julia Cooke, Rebecca A. Pickering, Lucie Cassarino, Mike Murray-Hudson, Keotshephile Mosimane, and Daniel J. Conley
EGUsphere, https://doi.org/10.5194/egusphere-2024-225, https://doi.org/10.5194/egusphere-2024-225, 2024
Preprint archived
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Papyrus, Cyperus papyrus, is abundant in the Okavango Delta. We explored nutrient and Silicon (Si) isotopes distribution in papyrus to learn more about how this species affects nutrient cycles which are still moderately understood in Botswana. We found large amounts of Si in roots, rhizomes, stems and umbels. We showed that this plant takes up lighter Si isotopes and deposits lighter isotopes first, starting in the roots, leading to an enrichment in heavy isotopes along the transpiration stream.
Anna Belcher, Sian F. Henley, Katharine Hendry, Marianne Wootton, Lisa Friberg, Ursula Dallman, Tong Wang, Christopher Coath, and Clara Manno
Biogeosciences, 20, 3573–3591, https://doi.org/10.5194/bg-20-3573-2023, https://doi.org/10.5194/bg-20-3573-2023, 2023
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The oceans play a crucial role in the uptake of atmospheric carbon dioxide, particularly the Southern Ocean. The biological pumping of carbon from the surface to the deep ocean is key to this. Using sediment trap samples from the Scotia Sea, we examine biogeochemical fluxes of carbon, nitrogen, and biogenic silica and their stable isotope compositions. We find phytoplankton community structure and physically mediated processes are important controls on particulate fluxes to the deep ocean.
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.
Michael J. Whitehouse, Katharine R. Hendry, Geraint A. Tarling, Sally E. Thorpe, and Petra ten Hoopen
Earth Syst. Sci. Data, 15, 211–224, https://doi.org/10.5194/essd-15-211-2023, https://doi.org/10.5194/essd-15-211-2023, 2023
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We present a database of Southern Ocean macronutrient, temperature and salinity measurements collected on 20 oceanographic cruises between 1980 and 2009. Vertical profiles and underway surface measurements were collected year-round as part of an integrated ecosystem study. Our data provide a novel view of biogeochemical cycling in biologically productive regions across a critical period in recent climate history and will contribute to a better understanding of the drivers of primary production.
James P. J. Ward, Katharine R. Hendry, Sandra Arndt, Johan C. Faust, Felipe S. Freitas, Sian F. Henley, Jeffrey W. Krause, Christian März, Allyson C. Tessin, and Ruth L. Airs
Biogeosciences, 19, 3445–3467, https://doi.org/10.5194/bg-19-3445-2022, https://doi.org/10.5194/bg-19-3445-2022, 2022
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The seafloor plays an important role in the cycling of silicon (Si), a key nutrient that promotes marine primary productivity. In our model study, we disentangle major controls on the seafloor Si cycle to better anticipate the impacts of continued warming and sea ice melt in the Barents Sea. We uncover a coupling of the iron redox and Si cycles, dissolution of lithogenic silicates, and authigenic clay formation, comprising a Si sink that could have implications for the Arctic Ocean Si budget.
Katherine A. Crichton, Andy Ridgwell, Daniel J. Lunt, Alex Farnsworth, and Paul N. Pearson
Clim. Past, 17, 2223–2254, https://doi.org/10.5194/cp-17-2223-2021, https://doi.org/10.5194/cp-17-2223-2021, 2021
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The middle Miocene (15 Ma) was a period of global warmth up to 8 °C warmer than present. We investigate changes in ocean circulation and heat distribution since the middle Miocene and the cooling to the present using the cGENIE Earth system model. We create seven time slices at ~2.5 Myr intervals, constrained with paleo-proxy data, showing a progressive reduction in atmospheric CO2 and a strengthening of the Atlantic Meridional Overturning Circulation.
Yoshiki Kanzaki, Dominik Hülse, Sandra Kirtland Turner, and Andy Ridgwell
Geosci. Model Dev., 14, 5999–6023, https://doi.org/10.5194/gmd-14-5999-2021, https://doi.org/10.5194/gmd-14-5999-2021, 2021
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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.
Jun Shao, Lowell D. Stott, Laurie Menviel, Andy Ridgwell, Malin Ödalen, and Mayhar Mohtadi
Clim. Past, 17, 1507–1521, https://doi.org/10.5194/cp-17-1507-2021, https://doi.org/10.5194/cp-17-1507-2021, 2021
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Planktic and shallow benthic foraminiferal stable carbon isotope
(δ13C) data show a rapid decline during the last deglaciation. This widespread signal was linked to respired carbon released from the deep ocean and its transport through the upper-ocean circulation. Using numerical simulations in which a stronger flux of respired carbon upwells and outcrops in the Southern Ocean, we find that the depleted δ13C signal is transmitted to the rest of the upper ocean through air–sea gas exchange.
Markus Adloff, Andy Ridgwell, Fanny M. Monteiro, Ian J. Parkinson, Alexander J. Dickson, Philip A. E. Pogge von Strandmann, Matthew S. Fantle, and Sarah E. Greene
Geosci. Model Dev., 14, 4187–4223, https://doi.org/10.5194/gmd-14-4187-2021, https://doi.org/10.5194/gmd-14-4187-2021, 2021
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We present the first representation of the trace metals Sr, Os, Li and Ca in a 3D Earth system model (cGENIE). The simulation of marine metal sources (weathering, hydrothermal input) and sinks (deposition) reproduces the observed concentrations and isotopic homogeneity of these metals in the modern ocean. With these new tracers, cGENIE can be used to test hypotheses linking these metal cycles and the cycling of other elements like O and C and simulate their dynamic response to external forcing.
Sebastiaan J. van de Velde, Dominik Hülse, Christopher T. Reinhard, and Andy Ridgwell
Geosci. Model Dev., 14, 2713–2745, https://doi.org/10.5194/gmd-14-2713-2021, https://doi.org/10.5194/gmd-14-2713-2021, 2021
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Biogeochemical interactions between iron and sulfur are central to the long-term biogeochemical evolution of Earth’s oceans. Here, we introduce an iron–sulphur cycle in a model of Earth's oceans. Our analyses show that the results of the model are robust towards parameter choices and that simulated concentrations and reactions are comparable to those observed in ancient ocean analogues (anoxic lakes). Our model represents an important step forward in the study of iron–sulfur cycling.
Petra Zahajská, Carolina Olid, Johanna Stadmark, Sherilyn C. Fritz, Sophie Opfergelt, and Daniel J. Conley
Biogeosciences, 18, 2325–2345, https://doi.org/10.5194/bg-18-2325-2021, https://doi.org/10.5194/bg-18-2325-2021, 2021
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The drivers of high accumulation of single-cell siliceous algae (diatoms) in a high-latitude lake have not been fully characterized before. We studied silicon cycling of the lake through water, radon, silicon, and stable silicon isotope balances. Results showed that groundwater brings 3 times more water and dissolved silica than the stream inlet. We demonstrate that groundwater discharge and low sediment deposition have driven the high diatom accumulation in the studied lake in the past century.
Joost de Vries, Fanny Monteiro, Glen Wheeler, Alex Poulton, Jelena Godrijan, Federica Cerino, Elisa Malinverno, Gerald Langer, and Colin Brownlee
Biogeosciences, 18, 1161–1184, https://doi.org/10.5194/bg-18-1161-2021, https://doi.org/10.5194/bg-18-1161-2021, 2021
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Coccolithophores are important calcifying phytoplankton with an overlooked life cycle. We compile a global dataset of marine coccolithophore abundance to investigate the environmental characteristics of each life cycle phase. We find that both phases contribute to coccolithophore abundance and that their different environmental preference increases coccolithophore habitat. Accounting for the life cycle of coccolithophores is thus crucial for understanding their ecology and biogeochemical impact.
Katherine A. Crichton, Jamie D. Wilson, Andy Ridgwell, and Paul N. Pearson
Geosci. Model Dev., 14, 125–149, https://doi.org/10.5194/gmd-14-125-2021, https://doi.org/10.5194/gmd-14-125-2021, 2021
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Temperature is a controller of metabolic processes and therefore also a controller of the ocean's biological carbon pump (BCP). We calibrate a temperature-dependent version of the BCP in the cGENIE Earth system model. Since the pre-industrial period, warming has intensified near-surface nutrient recycling, supporting production and largely offsetting stratification-induced surface nutrient limitation. But at the same time less carbon that sinks out of the surface then reaches the deep ocean.
Christopher T. Reinhard, Stephanie L. Olson, Sandra Kirtland Turner, Cecily Pälike, Yoshiki Kanzaki, and Andy Ridgwell
Geosci. Model Dev., 13, 5687–5706, https://doi.org/10.5194/gmd-13-5687-2020, https://doi.org/10.5194/gmd-13-5687-2020, 2020
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We provide documentation and testing of new developments for the oceanic and atmospheric methane cycles in the cGENIE Earth system model. The model is designed to explore Earth's methane cycle across a wide range of timescales and scenarios, in particular assessing the mean climate state and climate perturbations in Earth's deep past. We further document the impact of atmospheric oxygen levels and ocean chemistry on fluxes of methane to the atmosphere from the ocean biosphere.
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Short summary
As an extension to the EcoGEnIE 1.0 Earth system model that features a diverse plankton community, EcoGEnIE 1.1 includes siliceous plankton diatoms and also considers their impact on biogeochemical cycles. With updates to existing nutrient cycles and the introduction of the silicon cycle, we see improved model performance relative to observational data. Through a more functionally diverse plankton community, the new model enables more comprehensive future study of ocean ecology.
As an extension to the EcoGEnIE 1.0 Earth system model that features a diverse plankton...
