Articles | Volume 14, issue 5
https://doi.org/10.5194/gmd-14-2713-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-14-2713-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
18 May 2021
Model description paper |
| 18 May 2021
| 18 May 2021
Iron and sulfur cycling in the cGENIE.muffin Earth system model (v0.9.21)
Sebastiaan J. van de Velde
CORRESPONDING AUTHOR
Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
current address: Bgeosys, Geoscience, Environment & Society, Université Libre de Bruxelles, Brussels, Belgium
current address: Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
Dominik Hülse
Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
Christopher T. Reinhard
School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Andy Ridgwell
Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
Related authors
Astrid Hylen, Nils Ekeroth, Hannah Berk, Andy W. Dale, Mikhail Kononets, Wytze K. Lenstra, Aada Palo, Anders Tengberg, Sebastiaan J. van de Velde, Stefan Sommer, Caroline P. Slomp, and Per O. J. Hall
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2025-146, https://doi.org/10.5194/essd-2025-146, 2025
Preprint under review for ESSD
Short summary
Short summary
Phosphorus is an essential element for life and its cycling strongly impact primary production. Here, we present a dataset of sediment-water fluxes of dissolved inorganic phosphorus from the Baltic Sea, an area with a long history of eutrophication. The fluxes were measured in situ with three types of benthic chamber landers at 59 stations over 20 years. The data show clear spatial patterns and will be important for marine management and studies on mechanisms in benthic phosphorus cycling.
Tom Huysmans, Filip J. R. Meysman, and Sebastiaan J. van de Velde
EGUsphere, https://doi.org/10.5194/egusphere-2025-447, https://doi.org/10.5194/egusphere-2025-447, 2025
Short summary
Short summary
To examine the potential of "Accelerated Weathering of Limestone" as a carbon capture and storage technique, we compared the different available reactor designs, and assessed their CO2 sequestration efficiencies, resource usage and limitations. We find that large water volumes are required to efficiently remove CO2 from the gas stream and that very small CaCO3 particle sizes and long residence times are required to achieve reasonable CaCO3 dissolution efficiencies.
Astrid Hylén, Sebastiaan J. van de Velde, Mikhail Kononets, Mingyue Luo, Elin Almroth-Rosell, and Per O. J. Hall
Biogeosciences, 18, 2981–3004, https://doi.org/10.5194/bg-18-2981-2021, https://doi.org/10.5194/bg-18-2981-2021, 2021
Short summary
Short summary
Sediments in oxygen-depleted ocean areas release high amounts of phosphorus, feeding algae that consume oxygen upon degradation, leading to further phosphorus release. Oxygenation is thought to trap phosphorus in the sediment and break this feedback. We studied the sediment phosphorus cycle in a previously anoxic area after an inflow of oxic water. Surprisingly, the sediment phosphorus release increased, showing that feedbacks between phosphorus release and oxygen depletion can be hard to break.
Sebastiaan J. van de Velde, Rebecca K. James, Ine Callebaut, Silvia Hidalgo-Martinez, and Filip J. R. Meysman
Biogeosciences, 18, 1451–1461, https://doi.org/10.5194/bg-18-1451-2021, https://doi.org/10.5194/bg-18-1451-2021, 2021
Short summary
Short summary
Some 540 Myr ago, animal life evolved in the ocean. Previous research suggested that when these early animals started inhabiting the seafloor, they retained phosphorus in the seafloor, thereby limiting photosynthesis in the ocean. We studied salt marsh sediments with and without animals and found that their impact on phosphorus retention is limited, which implies that their impact on the global environment might have been less drastic than previously assumed.
Martin Schobben, Sebastiaan van de Velde, Jana Gliwa, Lucyna Leda, Dieter Korn, Ulrich Struck, Clemens Vinzenz Ullmann, Vachik Hairapetian, Abbas Ghaderi, Christoph Korte, Robert J. Newton, Simon W. Poulton, and Paul B. Wignall
Clim. Past, 13, 1635–1659, https://doi.org/10.5194/cp-13-1635-2017, https://doi.org/10.5194/cp-13-1635-2017, 2017
Short summary
Short summary
Stratigraphic trends in the carbon isotope composition of calcium carbonate rock can be used as a stratigraphic tool. An important assumption when using these isotope chemical records is that they record a globally universal signal of marine water chemistry. We show that carbon isotope scatter on a confined centimetre stratigraphic scale appears to represent a signal of microbial activity. However, long-term carbon isotope trends are still compatible with a primary isotope imprint.
Jelle Bijma, Mathilde Hagens, Jens Hammes, Noah Planavsky, Philip A. E. Pogge von Strandmann, Tom Reershemius, Christopher T. Reinhard, Phil Renforth, Tim Jesper Suhrhoff, Sara Vicca, Arthur Vienne, and Dieter A. Wolf-Gladrow
EGUsphere, https://doi.org/10.5194/egusphere-2025-2740, https://doi.org/10.5194/egusphere-2025-2740, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
Short summary
Short summary
Enhanced rock weathering is a nature based negative emission technology, that permanently stores CO2. It requires rock-flour to be added to arable land with the help of farmers. To be eligible for carbon credits calls for a simple but scientifically solid, so called, Monitoring, Reporting & Verification” (MRV). We demonstrate that the commonly used carbon-based accounting is ill-suited to close the balance in open systems such as arable land, and argue for cation-based accounting strategy.
Astrid Hylen, Nils Ekeroth, Hannah Berk, Andy W. Dale, Mikhail Kononets, Wytze K. Lenstra, Aada Palo, Anders Tengberg, Sebastiaan J. van de Velde, Stefan Sommer, Caroline P. Slomp, and Per O. J. Hall
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2025-146, https://doi.org/10.5194/essd-2025-146, 2025
Preprint under review for ESSD
Short summary
Short summary
Phosphorus is an essential element for life and its cycling strongly impact primary production. Here, we present a dataset of sediment-water fluxes of dissolved inorganic phosphorus from the Baltic Sea, an area with a long history of eutrophication. The fluxes were measured in situ with three types of benthic chamber landers at 59 stations over 20 years. The data show clear spatial patterns and will be important for marine management and studies on mechanisms in benthic phosphorus cycling.
Tom Huysmans, Filip J. R. Meysman, and Sebastiaan J. van de Velde
EGUsphere, https://doi.org/10.5194/egusphere-2025-447, https://doi.org/10.5194/egusphere-2025-447, 2025
Short summary
Short summary
To examine the potential of "Accelerated Weathering of Limestone" as a carbon capture and storage technique, we compared the different available reactor designs, and assessed their CO2 sequestration efficiencies, resource usage and limitations. We find that large water volumes are required to efficiently remove CO2 from the gas stream and that very small CaCO3 particle sizes and long residence times are required to achieve reasonable CaCO3 dissolution efficiencies.
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
Short summary
Short summary
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.
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
Short summary
Short summary
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.
Aaron A. Naidoo-Bagwell, Fanny M. Monteiro, Katharine R. Hendry, Scott Burgan, Jamie D. Wilson, Ben A. Ward, Andy Ridgwell, and Daniel J. Conley
Geosci. Model Dev., 17, 1729–1748, https://doi.org/10.5194/gmd-17-1729-2024, https://doi.org/10.5194/gmd-17-1729-2024, 2024
Short summary
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.
Kazumi Ozaki, Devon B. Cole, Christopher T. Reinhard, and Eiichi Tajika
Geosci. Model Dev., 15, 7593–7639, https://doi.org/10.5194/gmd-15-7593-2022, https://doi.org/10.5194/gmd-15-7593-2022, 2022
Short summary
Short summary
A new biogeochemical model (CANOPS-GRB v1.0) for assessing the redox stability and dynamics of the ocean–atmosphere system on geologic timescales has been developed. In this paper, we present a full description of the model and its performance. CANOPS-GRB is a useful tool for understanding the factors regulating atmospheric O2 level and has the potential to greatly refine our current understanding of Earth's oxygenation history.
Yoshiki Kanzaki, Shuang Zhang, Noah J. Planavsky, and Christopher T. Reinhard
Geosci. Model Dev., 15, 4959–4990, https://doi.org/10.5194/gmd-15-4959-2022, https://doi.org/10.5194/gmd-15-4959-2022, 2022
Short summary
Short summary
Increasing carbon dioxide in the atmosphere is an urgent issue in the coming century. Enhanced rock weathering in soils can be one of the most efficient C capture strategies. On the basis as a weathering simulator, the newly developed SCEPTER model implements bio-mixing by fauna/humans and enables organic matter and crushed rocks/minerals at the soil surface with an option to track their particle size distributions. Those features can be useful for evaluating the carbon capture efficiency.
Philip Pika, Dominik Hülse, and Sandra Arndt
Geosci. Model Dev., 14, 7155–7174, https://doi.org/10.5194/gmd-14-7155-2021, https://doi.org/10.5194/gmd-14-7155-2021, 2021
Short summary
Short summary
OMEN-SED is a model for early diagenesis in marine sediments simulating organic matter (OM) degradation and nutrient dynamics. We replaced the original description with a more realistic one accounting for the widely observed decrease in OM reactivity. The new model reproduces pore water profiles and sediment–water interface fluxes across different environments. This functionality extends the model’s applicability to a broad range of environments and timescales while requiring fewer parameters.
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
Short summary
Short summary
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
Short summary
Short summary
Sedimentary carbonate plays a central role in regulating Earth’s carbon cycle and climate, and also serves as an archive of paleoenvironments, hosting various trace elements/isotopes. To help obtain
trueenvironmental changes from carbonate records over diagenetic distortion, IMP has been newly developed and has the capability to simulate the diagenesis of multiple carbonate particles and implement different styles of particle mixing by benthos using an adapted transition matrix method.
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
Short summary
Short summary
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
Short summary
Short summary
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.
Astrid Hylén, Sebastiaan J. van de Velde, Mikhail Kononets, Mingyue Luo, Elin Almroth-Rosell, and Per O. J. Hall
Biogeosciences, 18, 2981–3004, https://doi.org/10.5194/bg-18-2981-2021, https://doi.org/10.5194/bg-18-2981-2021, 2021
Short summary
Short summary
Sediments in oxygen-depleted ocean areas release high amounts of phosphorus, feeding algae that consume oxygen upon degradation, leading to further phosphorus release. Oxygenation is thought to trap phosphorus in the sediment and break this feedback. We studied the sediment phosphorus cycle in a previously anoxic area after an inflow of oxic water. Surprisingly, the sediment phosphorus release increased, showing that feedbacks between phosphorus release and oxygen depletion can be hard to break.
Sebastiaan J. van de Velde, Rebecca K. James, Ine Callebaut, Silvia Hidalgo-Martinez, and Filip J. R. Meysman
Biogeosciences, 18, 1451–1461, https://doi.org/10.5194/bg-18-1451-2021, https://doi.org/10.5194/bg-18-1451-2021, 2021
Short summary
Short summary
Some 540 Myr ago, animal life evolved in the ocean. Previous research suggested that when these early animals started inhabiting the seafloor, they retained phosphorus in the seafloor, thereby limiting photosynthesis in the ocean. We studied salt marsh sediments with and without animals and found that their impact on phosphorus retention is limited, which implies that their impact on the global environment might have been less drastic than previously assumed.
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
Short summary
Short summary
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
Short summary
Short summary
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.
Malin Ödalen, Jonas Nycander, Andy Ridgwell, Kevin I. C. Oliver, Carlye D. Peterson, and Johan Nilsson
Biogeosciences, 17, 2219–2244, https://doi.org/10.5194/bg-17-2219-2020, https://doi.org/10.5194/bg-17-2219-2020, 2020
Short summary
Short summary
In glacial periods, ocean uptake of carbon is likely a key player for achieving low atmospheric CO2. In climate models, ocean biological uptake of carbon (C) and phosphorus (P) are often assumed to occur in fixed proportions.
In this study, we allow the ratio of C : P to vary and simulate, to first approximation, the complex biological changes that occur in the ocean over long timescales. We show here that, for glacial–interglacial cycles, this complexity contributes to low atmospheric CO2.
Yoshiki Kanzaki, Bernard P. Boudreau, Sandra Kirtland Turner, and Andy Ridgwell
Geosci. Model Dev., 12, 4469–4496, https://doi.org/10.5194/gmd-12-4469-2019, https://doi.org/10.5194/gmd-12-4469-2019, 2019
Short summary
Short summary
This paper provides eLABS, an extension of the lattice-automaton bioturbation simulator LABS. In our new model, the benthic animal behavior interacts and changes dynamically with oxygen and organic matter concentrations and the water flows caused by benthic animals themselves, in a 2-D marine-sediment grid. The model can address the mechanisms behind empirical observations of bioturbation based on the interactions between physical, chemical and biological aspects of marine sediment.
Jamie D. Wilson, Stephen Barker, Neil R. Edwards, Philip B. Holden, and Andy Ridgwell
Biogeosciences, 16, 2923–2936, https://doi.org/10.5194/bg-16-2923-2019, https://doi.org/10.5194/bg-16-2923-2019, 2019
Short summary
Short summary
The remains of plankton rain down from the surface ocean to the deep ocean, acting to store CO2 in the deep ocean. We used a model of biology and ocean circulation to explore the importance of this process in different regions of the ocean. The amount of CO2 stored in the deep ocean is most sensitive to changes in the Southern Ocean. As plankton in the Southern Ocean are likely those most impacted by future climate change, the amount of CO2 they store in the deep ocean could also be affected.
Krista M. S. Kemppinen, Philip B. Holden, Neil R. Edwards, Andy Ridgwell, and Andrew D. Friend
Clim. Past, 15, 1039–1062, https://doi.org/10.5194/cp-15-1039-2019, https://doi.org/10.5194/cp-15-1039-2019, 2019
Short summary
Short summary
We simulate the Last Glacial Maximum atmospheric CO2 decrease with a large ensemble of parameter sets to investigate the range of possible physical and biogeochemical Earth system changes accompanying the CO2 decrease. Amongst the dominant ensemble changes is an increase in terrestrial carbon, which we attribute to a slower soil respiration rate, and the preservation of carbon by the LGM ice sheets. Further investigation into the role of terrestrial carbon is warranted.
Maria Grigoratou, Fanny M. Monteiro, Daniela N. Schmidt, Jamie D. Wilson, Ben A. Ward, and Andy Ridgwell
Biogeosciences, 16, 1469–1492, https://doi.org/10.5194/bg-16-1469-2019, https://doi.org/10.5194/bg-16-1469-2019, 2019
Short summary
Short summary
The paper presents a novel study based on the traits of shell size, calcification and feeding behaviour of two planktonic foraminifera life stages using modelling simulations. With the model, we tested the cost and benefit of calcification and explored how the interactions of planktonic foraminifera among other plankton groups influence their biomass under different environmental conditions. Our results provide new insights into environmental controls in planktonic foraminifera ecology.
Ben A. Ward, Jamie D. Wilson, Ros M. Death, Fanny M. Monteiro, Andrew Yool, and Andy Ridgwell
Geosci. Model Dev., 11, 4241–4267, https://doi.org/10.5194/gmd-11-4241-2018, https://doi.org/10.5194/gmd-11-4241-2018, 2018
Short summary
Short summary
A novel configuration of an Earth system model includes a diverse plankton community. The model – EcoGEnIE – is sufficiently complex to reproduce a realistic, size-structured plankton community, while at the same time retaining the efficiency to run to a global steady state (~ 10k years). The increased capabilities of EcoGEnIE will allow future exploration of ecological communities on much longer timescales than have so far been examined in global ocean models and particularly for past climate.
Tom Dunkley Jones, Hayley R. Manners, Murray Hoggett, Sandra Kirtland Turner, Thomas Westerhold, Melanie J. Leng, Richard D. Pancost, Andy Ridgwell, Laia Alegret, Rob Duller, and Stephen T. Grimes
Clim. Past, 14, 1035–1049, https://doi.org/10.5194/cp-14-1035-2018, https://doi.org/10.5194/cp-14-1035-2018, 2018
Short summary
Short summary
The Paleocene–Eocene Thermal Maximum (PETM) is a transient global warming event associated with a doubling of atmospheric carbon dioxide concentrations. Here we document a major increase in sediment accumulation rates on a subtropical continental margin during the PETM, likely due to marked changes in hydro-climates and sediment transport. These high sedimentation rates persist through the event and may play a key role in the removal of carbon from the atmosphere by the burial of organic carbon.
Dominik Hülse, Sandra Arndt, Stuart Daines, Pierre Regnier, and Andy Ridgwell
Geosci. Model Dev., 11, 2649–2689, https://doi.org/10.5194/gmd-11-2649-2018, https://doi.org/10.5194/gmd-11-2649-2018, 2018
Short summary
Short summary
We present a 1-D analytical diagenetic model resolving organic matter (OM) cycling and the associated biogeochemical dynamics in marine sediments designed to be coupled to Earth system models (ESMs). The reaction network accounts for the most important reactions associated with OM dynamics. The coupling is described and the OM degradation rate constant is tuned. Various observations, such as pore water profiles, sediment water interface fluxes and OM content, are reproduced with good accuracy.
Malin Ödalen, Jonas Nycander, Kevin I. C. Oliver, Laurent Brodeau, and Andy Ridgwell
Biogeosciences, 15, 1367–1393, https://doi.org/10.5194/bg-15-1367-2018, https://doi.org/10.5194/bg-15-1367-2018, 2018
Short summary
Short summary
We conclude that different initial states for an ocean model result in different capacities for ocean carbon storage due to differences in the ocean circulation state and the origin of the carbon in the initial ocean carbon reservoir. This could explain why it is difficult to achieve comparable responses of the ocean carbon system in model inter-comparison studies in which the initial states vary between models. We show that this effect of the initial state is quantifiable.
Martin Schobben, Sebastiaan van de Velde, Jana Gliwa, Lucyna Leda, Dieter Korn, Ulrich Struck, Clemens Vinzenz Ullmann, Vachik Hairapetian, Abbas Ghaderi, Christoph Korte, Robert J. Newton, Simon W. Poulton, and Paul B. Wignall
Clim. Past, 13, 1635–1659, https://doi.org/10.5194/cp-13-1635-2017, https://doi.org/10.5194/cp-13-1635-2017, 2017
Short summary
Short summary
Stratigraphic trends in the carbon isotope composition of calcium carbonate rock can be used as a stratigraphic tool. An important assumption when using these isotope chemical records is that they record a globally universal signal of marine water chemistry. We show that carbon isotope scatter on a confined centimetre stratigraphic scale appears to represent a signal of microbial activity. However, long-term carbon isotope trends are still compatible with a primary isotope imprint.
Natalie S. Lord, Michel Crucifix, Dan J. Lunt, Mike C. Thorne, Nabila Bounceur, Harry Dowsett, Charlotte L. O'Brien, and Andy Ridgwell
Clim. Past, 13, 1539–1571, https://doi.org/10.5194/cp-13-1539-2017, https://doi.org/10.5194/cp-13-1539-2017, 2017
Short summary
Short summary
We present projections of long-term changes in climate, produced using a statistical emulator based on climate data from a state-of-the-art climate model. We use the emulator to model changes in temperature and precipitation over the late Pliocene (3.3–2.8 million years before present) and the next 200 thousand years. The impact of the Earth's orbit and the atmospheric carbon dioxide concentration on climate is assessed, and the data for the late Pliocene are compared to proxy temperature data.
Taraka Davies-Barnard, Andy Ridgwell, Joy Singarayer, and Paul Valdes
Clim. Past, 13, 1381–1401, https://doi.org/10.5194/cp-13-1381-2017, https://doi.org/10.5194/cp-13-1381-2017, 2017
Short summary
Short summary
We present the first model analysis using a fully coupled dynamic atmosphere–ocean–vegetation GCM over the last 120 kyr that quantifies the net effect of vegetation on climate. This analysis shows that over the whole period the biogeophysical effect (albedo, evapotranspiration) is dominant, and that the biogeochemical impacts may have a lower possible range than typically estimated. This emphasises the temporal reliance of the balance between biogeophysical and biogeochemical effects.
J. D. Wilson, A. Ridgwell, and S. Barker
Biogeosciences, 12, 5547–5562, https://doi.org/10.5194/bg-12-5547-2015, https://doi.org/10.5194/bg-12-5547-2015, 2015
Short summary
Short summary
We explore whether ocean model transport rates, in the form of a transport matrix, can be used to estimate remineralisation rates from dissolved nutrient concentrations and infer vertical fluxes of particulate organic carbon. Estimated remineralisation rates are significantly sensitive to uncertainty in the observations and the modelled circulation. The remineralisation of dissolved organic matter is an additional source of uncertainty when inferring vertical fluxes from remineralisation rates.
N. S. Jones, A. Ridgwell, and E. J. Hendy
Biogeosciences, 12, 1339–1356, https://doi.org/10.5194/bg-12-1339-2015, https://doi.org/10.5194/bg-12-1339-2015, 2015
Short summary
Short summary
Production of calcium carbonate by coral reefs is important in the global carbon cycle. Using a global framework we evaluate four models of reef calcification against observed values. The temperature-only model showed significant skill in reproducing coral calcification rates. The absence of any predictive power for whole reef systems highlights the importance of coral cover and the need for an ecosystem modelling approach accounting for population dynamics in terms of mortality and recruitment.
R. Death, J. L. Wadham, F. Monteiro, A. M. Le Brocq, M. Tranter, A. Ridgwell, S. Dutkiewicz, and R. Raiswell
Biogeosciences, 11, 2635–2643, https://doi.org/10.5194/bg-11-2635-2014, https://doi.org/10.5194/bg-11-2635-2014, 2014
G. Colbourn, A. Ridgwell, and T. M. Lenton
Geosci. Model Dev., 6, 1543–1573, https://doi.org/10.5194/gmd-6-1543-2013, https://doi.org/10.5194/gmd-6-1543-2013, 2013
M. Eby, A. J. Weaver, K. Alexander, K. Zickfeld, A. Abe-Ouchi, A. A. Cimatoribus, E. Crespin, S. S. Drijfhout, N. R. Edwards, A. V. Eliseev, G. Feulner, T. Fichefet, C. E. Forest, H. Goosse, P. B. Holden, F. Joos, M. Kawamiya, D. Kicklighter, H. Kienert, K. Matsumoto, I. I. Mokhov, E. Monier, S. M. Olsen, J. O. P. Pedersen, M. Perrette, G. Philippon-Berthier, A. Ridgwell, A. Schlosser, T. Schneider von Deimling, G. Shaffer, R. S. Smith, R. Spahni, A. P. Sokolov, M. Steinacher, K. Tachiiri, K. Tokos, M. Yoshimori, N. Zeng, and F. Zhao
Clim. Past, 9, 1111–1140, https://doi.org/10.5194/cp-9-1111-2013, https://doi.org/10.5194/cp-9-1111-2013, 2013
P. B. Holden, N. R. Edwards, S. A. Müller, K. I. C. Oliver, R. M. Death, and A. Ridgwell
Biogeosciences, 10, 1815–1833, https://doi.org/10.5194/bg-10-1815-2013, https://doi.org/10.5194/bg-10-1815-2013, 2013
Related subject area
Oceanography
GREAT v1.0: Global Real-time Early Assessment of Tsunamis
Using automatic calibration to improve the physics behind complex numerical models: an example from a 3D lake model using Delft3D (v6.02.10) and DYNO-PODS (v1.0)
Improvements to the Met Office's global ocean–sea ice forecasting system including model and data assimilation changes
Resolution dependence of interlinked Southern Ocean biases in global coupled HadGEM3 models
A new global high-resolution wave model for the tropical ocean using WAVEWATCH III version 7.14
sedInterFoam 1.0: a three-phase numerical model for sediment transport applications with free surfaces
The Ross Sea and Amundsen Sea Ice–Sea Model (RAISE v1.0): a high-resolution ocean–sea ice–ice shelf coupling model for simulating the Dense Shelf Water and Antarctic Bottom Water in the Ross Sea, Antarctica
Sensitivity of the tropical Atlantic to vertical mixing in two ocean models (ICON-O v2.6.6 and FESOM v2.5)
CRITER 1.0: A coarse reconstruction with iterative refinement network for sparse spatio-temporal satellite data
HIDRA3: a deep-learning model for multipoint ensemble sea level forecasting in the presence of tide gauge sensor failures
A wave-resolving two-dimensional vertical Lagrangian approach to model microplastic transport in nearshore waters based on TrackMPD 3.0
HOTSSea v1: a NEMO-based physical Hindcast of the Salish Sea (1980–2018) supporting ecosystem model development
Comparing an idealized deterministic-stochastic model (SUP model, version 1) of the tide-and-wind driven sea surface currents in the Gulf of Trieste to HF Radar observations
ISWFM-NSCS v2.0: advancing the internal solitary wave forecasting model with background currents and horizontally inhomogeneous stratifications
Impacts of CICE sea ice model and ERA atmosphere on an Antarctic MetROMS ocean model, MetROMS-UHel-v1.0
DalROMS-NWA12 v1.0, a coupled circulation–ice–biogeochemistry modelling system for the northwest Atlantic Ocean: development and validation
A revised ocean mixed layer model for better simulating the diurnal variation in ocean skin temperature
Evaluating an accelerated forcing approach for improving computational efficiency in coupled ice sheet–ocean modelling
An optimal transformation method for inferring ocean tracer sources and sinks
Data-driven rolling model for global wave height
PPCon 1.0: Biogeochemical-Argo profile prediction with 1D convolutional networks
Wave forecast investigations on downscaling, source terms, and tides for Aotearoa New Zealand
An Effective Communication Topology for Performance Optimization: A Case Study of the Finite Volume WAve Modeling (FVWAM)
Experimental design for the Marine Ice Sheet–Ocean Model Intercomparison Project – phase 2 (MISOMIP2)
Development of a total variation diminishing (TVD) sea ice transport scheme and its application in an ocean (SCHISM v5.11) and sea ice (Icepack v1.3.4) coupled model on unstructured grids
Spurious numerical mixing under strong tidal forcing: a case study in the south-east Asian seas using the Symphonie model (v3.1.2)
Modelling the water isotope distribution in the Mediterranean Sea using a high-resolution oceanic model (NEMO-MED12-watiso v1.0): evaluation of model results against in situ observations
LIGHT-bgcArgo-1.0: using synthetic float capabilities in E3SMv2 to assess spatiotemporal variability in ocean physics and biogeochemistry
PIBM 1.0: An individual-based model for simulating phytoplankton acclimation, diversity, and evolution in the ocean
Towards a real-time modeling of global ocean waves by the fully GPU-accelerated spectral wave model WAM6-GPU v1.0
A simple approach to represent precipitation-derived freshwater fluxes into nearshore ocean models: an FVCOM4.1 case study of Quatsino Sound, British Columbia
An optimal transformation method applied to diagnose the ocean carbon budget
Implementation and assessment of a model including mixotrophs and the carbonate cycle (Eco3M_MIX-CarbOx v1.0) in a highly dynamic Mediterranean coastal environment (Bay of Marseille, France) – Part 2: Towards a better representation of total alkalinity when modeling the carbonate system and air–sea CO2 fluxes
Development of a novel storm surge inundation model framework for efficient prediction
Skin sea surface temperature schemes in coupled ocean–atmosphere modelling: the impact of chlorophyll-interactive e-folding depth
DELWAVE 1.0: deep learning surrogate model of surface wave climate in the Adriatic Basin
StraitFlux – precise computations of water strait fluxes on various modeling grids
Comparison of the Coastal and Regional Ocean COmmunity model (CROCO) and NCAR-LES in non-hydrostatic simulations
Intercomparisons of Tracker v1.1 and four other ocean particle-tracking software packages in the Regional Ocean Modeling System
CAR36, a regional high-resolution ocean forecasting system for improving drift and beaching of Sargassum in the Caribbean archipelago
Implementation of additional spectral wave field exchanges in a three-dimensional wave–current coupled WAVEWATCH-III (version 6.07) and CROCO (version 1.2) configuration: assessment of their implications for macro-tidal coastal hydrodynamics
Comparison of 4-dimensional variational and ensemble optimal interpolation data assimilation systems using a Regional Ocean Modeling System (v3.4) configuration of the eddy-dominated East Australian Current system
LOCATE v1.0: numerical modelling of floating marine debris dispersion in coastal regions using Parcels v2.4.2
New insights into the South China Sea throughflow and water budget seasonal cycle: evaluation and analysis of a high-resolution configuration of the ocean model SYMPHONIE version 2.4
MQGeometry-1.0: a multi-layer quasi-geostrophic solver on non-rectangular geometries
Parameter estimation for ocean background vertical diffusivity coefficients in the Community Earth System Model (v1.2.1) and its impact on El Niño–Southern Oscillation forecasts
Great Lakes wave forecast system on high-resolution unstructured meshes
Impact of increased resolution on Arctic Ocean simulations in Ocean Model Intercomparison Project phase 2 (OMIP-2)
A high-resolution physical–biogeochemical model for marine resource applications in the northwest Atlantic (MOM6-COBALT-NWA12 v1.0)
A flexible z-layers approach for the accurate representation of free surface flows in a coastal ocean model (SHYFEM v. 7_5_71)
Usama Kadri, Ali Abdolali, and Maxim Filimonov
Geosci. Model Dev., 18, 3487–3507, https://doi.org/10.5194/gmd-18-3487-2025, https://doi.org/10.5194/gmd-18-3487-2025, 2025
Short summary
Short summary
The GREAT v1.0 software introduces a novel tsunami warning technology for global real-time analysis. It leverages acoustic signals generated by tsunamis, which propagate faster than the tsunami itself, enabling real-time detection and assessment. Integrating various models, the software provides reliable and rapid assessment, maps risk areas, and estimates tsunami amplitude. This advancement reduces false alarms and enhances global tsunami warning systems' accuracy and efficiency.
Marina Amadori, Abolfazl Irani Rahaghi, Damien Bouffard, and Marco Toffolon
Geosci. Model Dev., 18, 3473–3486, https://doi.org/10.5194/gmd-18-3473-2025, https://doi.org/10.5194/gmd-18-3473-2025, 2025
Short summary
Short summary
Models simplify reality using assumptions, which can sometimes introduce flaws and affect their accuracy. Properly calibrating model parameters is essential, and although automated tools can speed up this process, they may occasionally produce incorrect values due to inconsistencies in the model. We demonstrate that by carefully applying automated tools, we were able to identify and correct a flaw in a widely used model for lake environments.
Davi Mignac, Jennifer Waters, Daniel J. Lea, Matthew J. Martin, James While, Anthony T. Weaver, Arthur Vidard, Catherine Guiavarc'h, Dave Storkey, David Ford, Edward W. Blockley, Jonathan Baker, Keith Haines, Martin R. Price, Michael J. Bell, and Richard Renshaw
Geosci. Model Dev., 18, 3405–3425, https://doi.org/10.5194/gmd-18-3405-2025, https://doi.org/10.5194/gmd-18-3405-2025, 2025
Short summary
Short summary
We describe major improvements of the Met Office's global ocean–sea ice forecasting system. The models and the way observations are used to improve the forecasts were changed, which led to a significant error reduction of 1 d forecasts. The new system performance in past conditions, where subsurface observations are scarce, was improved with more consistent ocean heat content estimates. The new system will be of better use for climate studies and will provide improved forecasts for end users.
David Storkey, Pierre Mathiot, Michael J. Bell, Dan Copsey, Catherine Guiavarc'h, Helene T. Hewitt, Jeff Ridley, and Malcolm J. Roberts
Geosci. Model Dev., 18, 2725–2745, https://doi.org/10.5194/gmd-18-2725-2025, https://doi.org/10.5194/gmd-18-2725-2025, 2025
Short summary
Short summary
The Southern Ocean is a key region of the world ocean in the context of climate change studies. We show that the Met Office Hadley Centre coupled model with intermediate ocean resolution struggles to accurately simulate the Southern Ocean. Increasing the frictional drag that the seafloor exerts on ocean currents and introducing a representation of unresolved ocean eddies both appear to reduce the large-scale biases in this model.
Axelle Gaffet, Xavier Bertin, Damien Sous, Héloïse Michaud, Aron Roland, and Emmanuel Cordier
Geosci. Model Dev., 18, 1929–1946, https://doi.org/10.5194/gmd-18-1929-2025, https://doi.org/10.5194/gmd-18-1929-2025, 2025
Short summary
Short summary
This study presents a new global wave model that improves predictions of sea states in tropical areas by using a high-resolution grid and corrected wind fields. The model is validated globally with satellite data and nearshore using in situ data. The model allows for the first time direct comparisons with in situ data collected at 10–30 m water depth, which is very close to shore due to the steep slope usually surrounding volcanic islands.
Antoine Mathieu, Yeulwoo Kim, Tian-Jian Hsu, Cyrille Bonamy, and Julien Chauchat
Geosci. Model Dev., 18, 1561–1573, https://doi.org/10.5194/gmd-18-1561-2025, https://doi.org/10.5194/gmd-18-1561-2025, 2025
Short summary
Short summary
Most of the tools available to model sediment transport do not account for complex physical mechanisms such as surface-wave-driven processes. In this study, a new model, sedInterFoam, allows us to reproduce numerically complex configurations in order to investigate coastal sediment transport applications dominated by surface waves and to gain insight into the complex physical processes associated with breaking waves and morphodynamics.
Zhaoru Zhang, Chuan Xie, Chuning Wang, Yuanjie Chen, Heng Hu, and Xiaoqiao Wang
Geosci. Model Dev., 18, 1375–1393, https://doi.org/10.5194/gmd-18-1375-2025, https://doi.org/10.5194/gmd-18-1375-2025, 2025
Short summary
Short summary
A coupled fine-resolution ocean–ice model is developed for the Ross Sea and adjacent regions in Antarctica, a key area for the formation of global ocean bottom water, the Antarctic Bottom Water (AABW), which affects global ocean circulation. The model has a high skill level in simulating sea ice production driving the AABW source water formation and AABW properties when assessed against observations. A model experiment shows a significant impact of ice shelf melting on the AABW characteristics.
Swantje Bastin, Aleksei Koldunov, Florian Schütte, Oliver Gutjahr, Marta Agnieszka Mrozowska, Tim Fischer, Radomyra Shevchenko, Arjun Kumar, Nikolay Koldunov, Helmuth Haak, Nils Brüggemann, Rebecca Hummels, Mia Sophie Specht, Johann Jungclaus, Sergey Danilov, Marcus Dengler, and Markus Jochum
Geosci. Model Dev., 18, 1189–1220, https://doi.org/10.5194/gmd-18-1189-2025, https://doi.org/10.5194/gmd-18-1189-2025, 2025
Short summary
Short summary
Vertical mixing is an important process, for example, for tropical sea surface temperature, but cannot be resolved by ocean models. Comparisons of mixing schemes and settings have usually been done with a single model, sometimes yielding conflicting results. We systematically compare two widely used schemes with different parameter settings in two different ocean models and show that most effects from mixing scheme parameter changes are model-dependent.
Matjaž Zupančič Muc, Vitjan Zavrtanik, Alexander Barth, Aida Alvera-Azcarate, Matjaž Ličer, and Matej Kristan
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-208, https://doi.org/10.5194/gmd-2024-208, 2025
Revised manuscript accepted for GMD
Short summary
Short summary
Accurate sea surface temperature data (SST) is crucial for weather forecasting and climate modeling, but satellite observations are often incomplete. We developed a new method called CRITER, which uses machine learning to fill in the gaps in SST data. Our two-stage approach reconstructs large-scale patterns and refines details. Tested on Mediterranean, Adriatic, and Atlantic seas data, CRITER outperforms current methods, reducing errors by up to 44 %.
Marko Rus, Hrvoje Mihanović, Matjaž Ličer, and Matej Kristan
Geosci. Model Dev., 18, 605–620, https://doi.org/10.5194/gmd-18-605-2025, https://doi.org/10.5194/gmd-18-605-2025, 2025
Short summary
Short summary
HIDRA3 is a deep-learning model for predicting sea levels and storm surges, offering significant improvements over previous models and numerical simulations. It utilizes data from multiple tide gauges, enhancing predictions even with limited historical data and during sensor outages. With its advanced architecture, HIDRA3 outperforms current state-of-the-art models by achieving a mean absolute error of up to 15 % lower, proving effective for coastal flood forecasting under diverse conditions.
Isabel Jalón-Rojas, Damien Sous, and Vincent Marieu
Geosci. Model Dev., 18, 319–336, https://doi.org/10.5194/gmd-18-319-2025, https://doi.org/10.5194/gmd-18-319-2025, 2025
Short summary
Short summary
This study presents a novel modeling approach for understanding microplastic transport in coastal waters. The model accurately replicates experimental data and reveals key transport mechanisms. The findings enhance our knowledge of how microplastics move in nearshore environments, aiding in coastal management and efforts to combat plastic pollution globally.
Greig Oldford, Tereza Jarníková, Villy Christensen, and Michael Dunphy
Geosci. Model Dev., 18, 211–237, https://doi.org/10.5194/gmd-18-211-2025, https://doi.org/10.5194/gmd-18-211-2025, 2025
Short summary
Short summary
We developed a 3D ocean model called the Hindcast of the Salish Sea (HOTSSea v1) that recreates physical conditions throughout the Salish Sea from 1980 to 2018. It was not clear that acceptable accuracy could be achieved because of computational and data limitations, but the model's predictions agreed well with observations. When we used the model to examine ocean temperature trends in areas that lack observations, it indicated that some seasons and areas are warming faster than others.
Sofia Flora, Laura Ursella, and Achim Wirth
EGUsphere, https://doi.org/10.5194/egusphere-2024-3391, https://doi.org/10.5194/egusphere-2024-3391, 2025
Short summary
Short summary
We developed a hierarchy of idealized deterministic-stochastic models to simulate the sea surface currents in the Gulf of Trieste. They include tide-and-wind driven sea surface current components, resolving the slowly varying part of the flow and a stochastic signal, representing the fast-varying small-scale dynamics. The comparison with High Frequency Radar observations shows that the non-Gaussian stochastic model captures the essential dynamics and permits to mimic the observed fat-tailed PDF.
Yankun Gong, Xueen Chen, Jiexin Xu, Zhiwu Chen, Qingyou He, Ruixiang Zhao, Xiao-Hua Zhu, and Shuqun Cai
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-165, https://doi.org/10.5194/gmd-2024-165, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
A new internal solitary wave forecasting (ISW) model in the northern South China Sea (ISWFM-NSCS v2.0) improves ISW predictions by incorporating background currents and inhomogeneous stratifications. Additionally, viscosity and diffusivity coefficients are optimized to maintain stable stratifications, extending the forecasting period. Sensitivity experiments illustrate that ISWFM-NSCS v2.0 significantly enhances predictions of various wave properties.
Cecilia Äijälä, Yafei Nie, Lucía Gutiérrez-Loza, Chiara De Falco, Siv Kari Lauvset, Bin Cheng, David A. Bailey, and Petteri Uotila
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-213, https://doi.org/10.5194/gmd-2024-213, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
The sea ice around Antarctica has experienced record lows in recent years. To understand these changes, models are needed. MetROMS-UHel is a new version of an ocean–sea ice model with updated sea ice code and the atmospheric data. We investigate the effect of our updates on different variables with a focus on sea ice and show an improved sea ice representation as compared with observations.
Kyoko Ohashi, Arnaud Laurent, Christoph Renkl, Jinyu Sheng, Katja Fennel, and Eric Oliver
Geosci. Model Dev., 17, 8697–8733, https://doi.org/10.5194/gmd-17-8697-2024, https://doi.org/10.5194/gmd-17-8697-2024, 2024
Short summary
Short summary
We developed a modelling system of the northwest Atlantic Ocean that simulates the currents, temperature, salinity, and parts of the biochemical cycle of the ocean, as well as sea ice. The system combines advanced, open-source models and can be used to study, for example, the ocean capture of atmospheric carbon dioxide, which is a key process in the global climate. The system produces realistic results, and we use it to investigate the roles of tides and sea ice in the northwest Atlantic Ocean.
Eui-Jong Kang, Byung-Ju Sohn, Sang-Woo Kim, Wonho Kim, Young-Cheol Kwon, Seung-Bum Kim, Hyoung-Wook Chun, and Chao Liu
Geosci. Model Dev., 17, 8553–8568, https://doi.org/10.5194/gmd-17-8553-2024, https://doi.org/10.5194/gmd-17-8553-2024, 2024
Short summary
Short summary
Sea surface temperature (SST) is vital in climate, weather, and ocean sciences because it influences air–sea interactions. Errors in the ECMWF model's scheme for predicting ocean skin temperature prompted a revision of the ocean mixed layer model. Validation against infrared measurements and buoys showed a good correlation with minimal deviations. The revised model accurately simulates SST variations and aligns with solar radiation distributions, showing promise for weather and climate models.
Qin Zhou, Chen Zhao, Rupert Gladstone, Tore Hattermann, David Gwyther, and Benjamin Galton-Fenzi
Geosci. Model Dev., 17, 8243–8265, https://doi.org/10.5194/gmd-17-8243-2024, https://doi.org/10.5194/gmd-17-8243-2024, 2024
Short summary
Short summary
We introduce an accelerated forcing approach to address timescale discrepancies between the ice sheets and ocean components in coupled modelling by reducing the ocean simulation duration. The approach is evaluated using idealized coupled models, and its limitations in real-world applications are discussed. Our results suggest it can be a valuable tool for process-oriented coupled ice sheet–ocean modelling and downscaling climate simulations with such models.
Jan D. Zika and Taimoor Sohail
Geosci. Model Dev., 17, 8049–8068, https://doi.org/10.5194/gmd-17-8049-2024, https://doi.org/10.5194/gmd-17-8049-2024, 2024
Short summary
Short summary
We describe a method to relate fluxes of heat and freshwater at the sea surface to the resulting distribution of seawater among categories such as warm and salty or cold and salty. The method exploits the laws that govern how heat and salt change when water mixes. The method will allow the climate community to improve estimates of how much heat the ocean is absorbing and how rainfall and evaporation are changing across the globe.
Xinxin Wang, Jiuke Wang, Wenfang Lu, Changming Dong, Hao Qin, and Haoyu Jiang
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-181, https://doi.org/10.5194/gmd-2024-181, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
Large-scale wave modeling is essential for science and society, typically relying on resource-intensive numerical methods to simulate wave dynamics. In this study, we introduce a rolling AI-based method for modeling global significant wave height. Our model achieves accuracy comparable to traditional numerical methods while significantly improving speed, making it operable on standard laptops. This work demonstrates AI's potential to enhance the accuracy and efficiency of global wave modeling.
Gloria Pietropolli, Luca Manzoni, and Gianpiero Cossarini
Geosci. Model Dev., 17, 7347–7364, https://doi.org/10.5194/gmd-17-7347-2024, https://doi.org/10.5194/gmd-17-7347-2024, 2024
Short summary
Short summary
Monitoring the ocean is essential for studying marine life and human impact. Our new software, PPCon, uses ocean data to predict key factors like nitrate and chlorophyll levels, which are hard to measure directly. By leveraging machine learning, PPCon offers more accurate and efficient predictions.
Rafael Santana, Richard Gorman, Emily Lane, Stuart Moore, Cyprien Bosserelle, Glen Reeve, and Christo Rautenbach
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-110, https://doi.org/10.5194/gmd-2024-110, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
This research explores improving wave forecasts in New Zealand, particularly at Banks Peninsula and Baring Head. We used detailed models, finding that forecasts at Baring Head improved significantly due to its strong tidal currents, but changes at Banks Peninsula were minimal. The study demonstrates that local conditions greatly influence the effectiveness of wave prediction models, highlighting the need for tailored approaches in coastal forecasting to enhance accuracy in the predictions.
Renbo Pang, Fujiang Yu, Yuanyong Gao, Ye Yuan, Liang Yuan, and Zhiyi Gao
EGUsphere, https://doi.org/10.5194/egusphere-2024-2515, https://doi.org/10.5194/egusphere-2024-2515, 2024
Short summary
Short summary
The application of the distributed graph communication topology in earth models has been rarely studied. We tested and compared this topology with the traditional point-to-point communication method using a global wave model. We found that this topology is more efficient. Additionally, using this topology can greatly improve the performance of the wave model and could help improve the performance of other earth models.
Jan De Rydt, Nicolas C. Jourdain, Yoshihiro Nakayama, Mathias van Caspel, Ralph Timmermann, Pierre Mathiot, Xylar S. Asay-Davis, Hélène Seroussi, Pierre Dutrieux, Ben Galton-Fenzi, David Holland, and Ronja Reese
Geosci. Model Dev., 17, 7105–7139, https://doi.org/10.5194/gmd-17-7105-2024, https://doi.org/10.5194/gmd-17-7105-2024, 2024
Short summary
Short summary
Global climate models do not reliably simulate sea-level change due to ice-sheet–ocean interactions. We propose a community modelling effort to conduct a series of well-defined experiments to compare models with observations and study how models respond to a range of perturbations in climate and ice-sheet geometry. The second Marine Ice Sheet–Ocean Model Intercomparison Project will continue to lay the groundwork for including ice-sheet–ocean interactions in global-scale IPCC-class models.
Qian Wang, Yang Zhang, Fei Chai, Y. Joseph Zhang, and Lorenzo Zampieri
Geosci. Model Dev., 17, 7067–7081, https://doi.org/10.5194/gmd-17-7067-2024, https://doi.org/10.5194/gmd-17-7067-2024, 2024
Short summary
Short summary
We coupled an unstructured hydro-model with an advanced column sea ice model to meet the growing demand for increased resolution and complexity in unstructured sea ice models. Additionally, we present a novel tracer transport scheme for the sea ice coupled model and demonstrate that this scheme fulfills the requirements for conservation, accuracy, efficiency, and monotonicity in an idealized test. Our new coupled model also has good performance in realistic tests.
Adrien Garinet, Marine Herrmann, Patrick Marsaleix, and Juliette Pénicaud
Geosci. Model Dev., 17, 6967–6986, https://doi.org/10.5194/gmd-17-6967-2024, https://doi.org/10.5194/gmd-17-6967-2024, 2024
Short summary
Short summary
Mixing is a crucial aspect of the ocean, but its accurate representation in computer simulations is made challenging by errors that result in unwanted mixing, compromising simulation realism. Here we illustrate the spurious effect that tides can have on simulations of south-east Asia. Although they play an important role in determining the state of the ocean, they can increase numerical errors and make simulation outputs less realistic. We also provide insights into how to reduce these errors.
Mohamed Ayache, Jean-Claude Dutay, Anne Mouchet, Kazuyo Tachikawa, Camille Risi, and Gilles Ramstein
Geosci. Model Dev., 17, 6627–6655, https://doi.org/10.5194/gmd-17-6627-2024, https://doi.org/10.5194/gmd-17-6627-2024, 2024
Short summary
Short summary
Water isotopes (δ18O, δD) are one of the most widely used proxies in ocean climate research. Previous studies using water isotope observations and modelling have highlighted the importance of understanding spatial and temporal isotopic variability for a quantitative interpretation of these tracers. Here we present the first results of a high-resolution regional dynamical model (at 1/12° horizontal resolution) developed for the Mediterranean Sea, one of the hotspots of ongoing climate change.
Cara Nissen, Nicole S. Lovenduski, Mathew Maltrud, Alison R. Gray, Yohei Takano, Kristen Falcinelli, Jade Sauvé, and Katherine Smith
Geosci. Model Dev., 17, 6415–6435, https://doi.org/10.5194/gmd-17-6415-2024, https://doi.org/10.5194/gmd-17-6415-2024, 2024
Short summary
Short summary
Autonomous profiling floats have provided unprecedented observational coverage of the global ocean, but uncertainties remain about whether their sampling frequency and density capture the true spatiotemporal variability of physical, biogeochemical, and biological properties. Here, we present the novel synthetic biogeochemical float capabilities of the Energy Exascale Earth System Model version 2 and demonstrate their utility as a test bed to address these uncertainties.
Iria Sala and Bingzhang Chen
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-130, https://doi.org/10.5194/gmd-2024-130, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
Phytoplankton, tiny photosynthetic organisms, produce nearly half of Earth's oxygen. To analyze their physiology, diversity, and evolution in the ocean, we developed a model that treats phytoplankton as individual particles. Moreover, our model considers phytoplankton size, temperature, and light traits, and allows for mutations in phytoplankton cells. Thus, our model provides a valuable tool for advancing the study of phytoplankton physiology, diversity, and evolution.
Ye Yuan, Fujiang Yu, Zhi Chen, Xueding Li, Fang Hou, Yuanyong Gao, Zhiyi Gao, and Renbo Pang
Geosci. Model Dev., 17, 6123–6136, https://doi.org/10.5194/gmd-17-6123-2024, https://doi.org/10.5194/gmd-17-6123-2024, 2024
Short summary
Short summary
Accurate and timely forecasting of ocean waves is of great importance to the safety of marine transportation and offshore engineering. In this study, GPU-accelerated computing is introduced in WAve Modeling Cycle 6 (WAM6). With this effort, global high-resolution wave simulations can now run on GPUs up to tens of times faster than the currently available models can on a CPU node with results that are just as accurate.
Krysten Rutherford, Laura Bianucci, and William Floyd
Geosci. Model Dev., 17, 6083–6104, https://doi.org/10.5194/gmd-17-6083-2024, https://doi.org/10.5194/gmd-17-6083-2024, 2024
Short summary
Short summary
Nearshore ocean models often lack complete information about freshwater fluxes due to numerous ungauged rivers and streams. We tested a simple rain-based hydrological model as inputs into an ocean model of Quatsino Sound, Canada, with the aim of improving the representation of the land–ocean connection in the nearshore model. Through multiple tests, we found that the performance of the ocean model improved when providing 60 % or more of the freshwater inputs from the simple runoff model.
Neill Mackay, Taimoor Sohail, Jan David Zika, Richard G. Williams, Oliver Andrews, and Andrew James Watson
Geosci. Model Dev., 17, 5987–6005, https://doi.org/10.5194/gmd-17-5987-2024, https://doi.org/10.5194/gmd-17-5987-2024, 2024
Short summary
Short summary
The ocean absorbs carbon dioxide from the atmosphere, mitigating climate change, but estimates of the uptake do not always agree. There is a need to reconcile these differing estimates and to improve our understanding of ocean carbon uptake. We present a new method for estimating ocean carbon uptake and test it with model data. The method effectively diagnoses the ocean carbon uptake from limited data and therefore shows promise for reconciling different observational estimates.
Lucille Barré, Frédéric Diaz, Thibaut Wagener, Camille Mazoyer, Christophe Yohia, and Christel Pinazo
Geosci. Model Dev., 17, 5851–5882, https://doi.org/10.5194/gmd-17-5851-2024, https://doi.org/10.5194/gmd-17-5851-2024, 2024
Short summary
Short summary
The carbonate system is typically studied using measurements, but modeling can contribute valuable insights. Using a biogeochemical model, we propose a new representation of total alkalinity, dissolved inorganic carbon, pCO2, and pH in a highly dynamic Mediterranean coastal area, the Bay of Marseille, a useful addition to measurements. Through a detailed analysis of pCO2 and air–sea CO2 fluxes, we show that variations are strongly impacted by the hydrodynamic processes that affect the bay.
Xuanxuan Gao, Shuiqing Li, Dongxue Mo, Yahao Liu, and Po Hu
Geosci. Model Dev., 17, 5497–5509, https://doi.org/10.5194/gmd-17-5497-2024, https://doi.org/10.5194/gmd-17-5497-2024, 2024
Short summary
Short summary
Storm surges generate coastal inundation and expose populations and properties to danger. We developed a novel storm surge inundation model for efficient prediction. Estimates compare well with in situ measurements and results from a numerical model. The new model is a significant improvement on existing numerical models, with much higher computational efficiency and stability, which allows timely disaster prevention and mitigation.
Vincenzo de Toma, Daniele Ciani, Yassmin Hesham Essa, Chunxue Yang, Vincenzo Artale, Andrea Pisano, Davide Cavaliere, Rosalia Santoleri, and Andrea Storto
Geosci. Model Dev., 17, 5145–5165, https://doi.org/10.5194/gmd-17-5145-2024, https://doi.org/10.5194/gmd-17-5145-2024, 2024
Short summary
Short summary
This study explores methods to reconstruct diurnal variations in skin sea surface temperature in a model of the Mediterranean Sea. Our new approach, considering chlorophyll concentration, enhances spatial and temporal variations in the warm layer. Comparative analysis shows context-dependent improvements. The proposed "chlorophyll-interactive" method brings the surface net total heat flux closer to zero annually, despite a net heat loss from the ocean to the atmosphere.
Peter Mlakar, Antonio Ricchi, Sandro Carniel, Davide Bonaldo, and Matjaž Ličer
Geosci. Model Dev., 17, 4705–4725, https://doi.org/10.5194/gmd-17-4705-2024, https://doi.org/10.5194/gmd-17-4705-2024, 2024
Short summary
Short summary
We propose a new point-prediction model, the DEep Learning WAVe Emulating model (DELWAVE), which successfully emulates the Simulating WAves Nearshore model (SWAN) over synoptic to climate timescales. Compared to control climatology over all wind directions, the mismatch between DELWAVE and SWAN is generally small compared to the difference between scenario and control conditions, suggesting that the noise introduced by surrogate modelling is substantially weaker than the climate change signal.
Susanna Winkelbauer, Michael Mayer, and Leopold Haimberger
Geosci. Model Dev., 17, 4603–4620, https://doi.org/10.5194/gmd-17-4603-2024, https://doi.org/10.5194/gmd-17-4603-2024, 2024
Short summary
Short summary
Oceanic transports shape the global climate, but the evaluation and validation of this key quantity based on reanalysis and model data are complicated by the distortion of the used modelling grids and the large number of different grid types. We present two new methods that allow the calculation of oceanic fluxes of volume, heat, salinity, and ice through almost arbitrary sections for various models and reanalyses that are independent of the used modelling grids.
Xiaoyu Fan, Baylor Fox-Kemper, Nobuhiro Suzuki, Qing Li, Patrick Marchesiello, Peter P. Sullivan, and Paul S. Hall
Geosci. Model Dev., 17, 4095–4113, https://doi.org/10.5194/gmd-17-4095-2024, https://doi.org/10.5194/gmd-17-4095-2024, 2024
Short summary
Short summary
Simulations of the oceanic turbulent boundary layer using the nonhydrostatic CROCO ROMS and NCAR-LES models are compared. CROCO and the NCAR-LES are accurate in a similar manner, but CROCO’s additional features (e.g., nesting and realism) and its compressible turbulence formulation carry additional costs.
Jilian Xiong and Parker MacCready
Geosci. Model Dev., 17, 3341–3356, https://doi.org/10.5194/gmd-17-3341-2024, https://doi.org/10.5194/gmd-17-3341-2024, 2024
Short summary
Short summary
The new offline particle tracking package, Tracker v1.1, is introduced to the Regional Ocean Modeling System, featuring an efficient nearest-neighbor algorithm to enhance particle-tracking speed. Its performance was evaluated against four other tracking packages and passive dye. Despite unique features, all packages yield comparable results. Running multiple packages within the same circulation model allows comparison of their performance and ease of use.
Sylvain Cailleau, Laurent Bessières, Léonel Chiendje, Flavie Dubost, Guillaume Reffray, Jean-Michel Lellouche, Simon van Gennip, Charly Régnier, Marie Drevillon, Marc Tressol, Matthieu Clavier, Julien Temple-Boyer, and Léo Berline
Geosci. Model Dev., 17, 3157–3173, https://doi.org/10.5194/gmd-17-3157-2024, https://doi.org/10.5194/gmd-17-3157-2024, 2024
Short summary
Short summary
In order to improve Sargassum drift forecasting in the Caribbean area, drift models can be forced by higher-resolution ocean currents. To this goal a 3 km resolution regional ocean model has been developed. Its assessment is presented with a particular focus on the reproduction of fine structures representing key features of the Caribbean region dynamics and Sargassum transport. The simulated propagation of a North Brazil Current eddy and its dissipation was found to be quite realistic.
Gaetano Porcile, Anne-Claire Bennis, Martial Boutet, Sophie Le Bot, Franck Dumas, and Swen Jullien
Geosci. Model Dev., 17, 2829–2853, https://doi.org/10.5194/gmd-17-2829-2024, https://doi.org/10.5194/gmd-17-2829-2024, 2024
Short summary
Short summary
Here a new method of modelling the interaction between ocean currents and waves is presented. We developed an advanced coupling of two models, one for ocean currents and one for waves. In previous couplings, some wave-related calculations were based on simplified assumptions. Our method uses more complex calculations to better represent wave–current interactions. We tested it in a macro-tidal coastal area and found that it significantly improves the model accuracy, especially during storms.
Colette Gabrielle Kerry, Moninya Roughan, Shane Keating, David Gwyther, Gary Brassington, Adil Siripatana, and Joao Marcos A. C. Souza
Geosci. Model Dev., 17, 2359–2386, https://doi.org/10.5194/gmd-17-2359-2024, https://doi.org/10.5194/gmd-17-2359-2024, 2024
Short summary
Short summary
Ocean forecasting relies on the combination of numerical models and ocean observations through data assimilation (DA). Here we assess the performance of two DA systems in a dynamic western boundary current, the East Australian Current, across a common modelling and observational framework. We show that the more advanced, time-dependent method outperforms the time-independent method for forecast horizons of 5 d. This advocates the use of advanced methods for highly variable oceanic regions.
Ivan Hernandez, Leidy M. Castro-Rosero, Manuel Espino, and Jose M. Alsina Torrent
Geosci. Model Dev., 17, 2221–2245, https://doi.org/10.5194/gmd-17-2221-2024, https://doi.org/10.5194/gmd-17-2221-2024, 2024
Short summary
Short summary
The LOCATE numerical model was developed to conduct Lagrangian simulations of the transport and dispersion of marine debris at coastal scales. High-resolution hydrodynamic data and a beaching module that used particle distance to the shore for land–water boundary detection were used on a realistic debris discharge scenario comparing hydrodynamic data at various resolutions. Coastal processes and complex geometric structures were resolved when using nested grids and distance-to-shore beaching.
Ngoc B. Trinh, Marine Herrmann, Caroline Ulses, Patrick Marsaleix, Thomas Duhaut, Thai To Duy, Claude Estournel, and R. Kipp Shearman
Geosci. Model Dev., 17, 1831–1867, https://doi.org/10.5194/gmd-17-1831-2024, https://doi.org/10.5194/gmd-17-1831-2024, 2024
Short summary
Short summary
A high-resolution model was built to study the South China Sea (SCS) water, heat, and salt budgets. Model performance is demonstrated by comparison with observations and simulations. Important discards are observed if calculating offline, instead of online, lateral inflows and outflows of water, heat, and salt. The SCS mainly receives water from the Luzon Strait and releases it through the Mindoro, Taiwan, and Karimata straits. SCS surface interocean water exchanges are driven by monsoon winds.
Louis Thiry, Long Li, Guillaume Roullet, and Etienne Mémin
Geosci. Model Dev., 17, 1749–1764, https://doi.org/10.5194/gmd-17-1749-2024, https://doi.org/10.5194/gmd-17-1749-2024, 2024
Short summary
Short summary
We present a new way of solving the quasi-geostrophic (QG) equations, a simple set of equations describing ocean dynamics. Our method is solely based on the numerical methods used to solve the equations and requires no parameter tuning. Moreover, it can handle non-rectangular geometries, opening the way to study QG equations on realistic domains. We release a PyTorch implementation to ease future machine-learning developments on top of the presented method.
Zheqi Shen, Yihao Chen, Xiaojing Li, and Xunshu Song
Geosci. Model Dev., 17, 1651–1665, https://doi.org/10.5194/gmd-17-1651-2024, https://doi.org/10.5194/gmd-17-1651-2024, 2024
Short summary
Short summary
Parameter estimation is the process that optimizes model parameters using observations, which could reduce model errors and improve forecasting. In this study, we conducted parameter estimation experiments using the CESM and the ensemble adjustment Kalman filter. The obtained initial conditions and parameters are used to perform ensemble forecast experiments for ENSO forecasting. The results revealed that parameter estimation could reduce analysis errors and improve ENSO forecast skills.
Ali Abdolali, Saeideh Banihashemi, Jose Henrique Alves, Aron Roland, Tyler J. Hesser, Mary Anderson Bryant, and Jane McKee Smith
Geosci. Model Dev., 17, 1023–1039, https://doi.org/10.5194/gmd-17-1023-2024, https://doi.org/10.5194/gmd-17-1023-2024, 2024
Short summary
Short summary
This article presents an overview of the development and implementation of Great Lake Wave Unstructured (GLWUv2.0), including the core model and workflow design and development. The validation was conducted against in situ data for the re-forecasted duration for summer and wintertime (ice season). The article describes the limitations and challenges encountered in the operational environment and the path forward for the next generation of wave forecast systems in enclosed basins like the GL.
Qiang Wang, Qi Shu, Alexandra Bozec, Eric P. Chassignet, Pier Giuseppe Fogli, Baylor Fox-Kemper, Andy McC. Hogg, Doroteaciro Iovino, Andrew E. Kiss, Nikolay Koldunov, Julien Le Sommer, Yiwen Li, Pengfei Lin, Hailong Liu, Igor Polyakov, Patrick Scholz, Dmitry Sidorenko, Shizhu Wang, and Xiaobiao Xu
Geosci. Model Dev., 17, 347–379, https://doi.org/10.5194/gmd-17-347-2024, https://doi.org/10.5194/gmd-17-347-2024, 2024
Short summary
Short summary
Increasing resolution improves model skills in simulating the Arctic Ocean, but other factors such as parameterizations and numerics are at least of the same importance for obtaining reliable simulations.
Andrew C. Ross, Charles A. Stock, Alistair Adcroft, Enrique Curchitser, Robert Hallberg, Matthew J. Harrison, Katherine Hedstrom, Niki Zadeh, Michael Alexander, Wenhao Chen, Elizabeth J. Drenkard, Hubert du Pontavice, Raphael Dussin, Fabian Gomez, Jasmin G. John, Dujuan Kang, Diane Lavoie, Laure Resplandy, Alizée Roobaert, Vincent Saba, Sang-Ik Shin, Samantha Siedlecki, and James Simkins
Geosci. Model Dev., 16, 6943–6985, https://doi.org/10.5194/gmd-16-6943-2023, https://doi.org/10.5194/gmd-16-6943-2023, 2023
Short summary
Short summary
We evaluate a model for northwest Atlantic Ocean dynamics and biogeochemistry that balances high resolution with computational economy by building on the new regional features in the MOM6 ocean model and COBALT biogeochemical model. We test the model's ability to simulate impactful historical variability and find that the model simulates the mean state and variability of most features well, which suggests the model can provide information to inform living-marine-resource applications.
Luca Arpaia, Christian Ferrarin, Marco Bajo, and Georg Umgiesser
Geosci. Model Dev., 16, 6899–6919, https://doi.org/10.5194/gmd-16-6899-2023, https://doi.org/10.5194/gmd-16-6899-2023, 2023
Short summary
Short summary
We propose a discrete multilayer shallow water model based on z-layers which, thanks to the insertion and removal of surface layers, can deal with an arbitrarily large tidal oscillation independently of the vertical resolution. The algorithm is based on a two-step procedure used in numerical simulations with moving boundaries (grid movement followed by a grid topology change, that is, the insertion/removal of surface layers), which avoids the appearance of very thin surface layers.
Cited articles
Adloff, M., Ridgwell, A., Monteiro, F. M., Parkinson, I. J., Dickson, A., Pogge von Strandmann, P. A. E., Fantle, M. S., and Greene, S. E.: Inclusion of a suite of weathering tracers in the cGENIE Earth System Model – muffin release v.0.9.10, Geosci. Model Dev. Discuss. [preprint], https://doi.org/10.5194/gmd-2020-233, in review, 2020. a, b
Alcott, L. J., Mills, B. J. W., and Poulton, S. W.: Stepwise Earth oxygenation is an inherent property of global biogeochemical cycling, Science, 366, 1333–1337, https://doi.org/10.1126/science.aax6459, 2019. a
Balistrieri, L. S., Murray, J. W., and Paul, B.: The cycling of iron and manganese in the water column of Lake Sammamish, Washington, Limnol. Oceanogr., 37, 510–528, 1992. a
Balzano, S., Statham, P. J., Pancost, R. D., and Lloyd, J. R.: Role of microbial populations in the release of reduced iron to the water column from
marine aggregates, Aquat. Microb. Ecol., 54, 291–303, https://doi.org/10.3354/ame01278, 2009. a, b
Beam, J. P., Scott, J. J., McAllister, S. M., Chan, C. S., McManus, J., Meysman, F. J. R., and Emerson, D.: Biological rejuvenation of iron oxides in bioturbated marine sediments, ISME J., 12, 1389–1394,
https://doi.org/10.1038/s41396-017-0032-6, 2018. a
Beard, B. L., Johnson, C. M., Skulan, J. L., Nealson, K. H., Cox, L., and Sun, H.: Application of Fe isotopes to tracing the geochemical and biological cycling of Fe, Chem. Geol., 195, 87–117, 2003. a
Bekker, A., Slack, J. F., Planavsky, N., Krapez, B., Hofmann, A., Konhauser, K. O., and Rouxel, O. J.: Iron Formation: The sedimentary product of a
complex interplay among mantle, tectonic, oceanic, and biospheric processes, Econ. Geol., 105, 467–508, 2010. a
Berg, J. S., Michellod, D., Pjevac, P., Martinez-Perez, C., Buckner, C. R. T., Hach, P. F., Schubert, C. J., Milucka, J., and Kuypers, M. M. M.: Intensive cryptic microbial iron cycling in the low iron water column of the meromictic Lake Cadagno, Environ. Microbiol., 18, 5288–5302, https://doi.org/10.1111/1462-2920.13587, 2016. a
Berner, R. A.: Phosphate removal from sea water by adsorption on volcanogenic ferric oxides, Earth Planet. Sc. Lett., 18, 77–86, 1973. a
Berner, R. A.: Biogeochemical cycles of carbon and sulfur and their effect on atmospheric oxygen over phanerozoic time, Palaeogeogr. Palaeocl., 75, 97–122, 1989. a
Böttcher, M. E., Smock, A. M., and Cypionka, H.: Sulfur isotope fractionation during experimental precipitation of iron(II) and manganese(II) sulfide at room temperature, Chem. Geol., 146, 127–134, 1998. a
Brocks, J. J., Jarrett, A. J. M., Sirantoine, E., Hallmann, C., Hoshino, Y., and Liyanage, T.: The rise of algae in Cryogenian oceans and the emergence of animals, Nature, 548, 578–581, https://doi.org/10.1038/nature23457, 2017. a
Bullen, T. D., White, A. F., Childs, C. W., Vivit, D. V., and Schulz, M. S.: Demonstration of significant abiotic iron isotope fractionation in nature, Geology, 29, 699–702, 2001. a
Campolongo, F., Saltelli, A., and Cariboni, J.: From screening to quantitative sensitivity analysis – A unified approach, Comput. Phys. Commun., 182, 978–988, https://doi.org/10.1016/j.cpc.2010.12.039, 2011. a
Canfield, D. E.: Sulfur isotopes in coal constrain the evolution of the Phanerozoic sulfur cycle, P. Natl. Acad. Sci. USA, 110, 8443–8446, https://doi.org/10.1073/pnas.1306450110, 2013. a
Canfield, D. E. and Teske, A.: Late proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies, Nature, 382, 127–132, https://doi.org/10.1038/382127a0, 1996. a
Canfield, D. E., Rosing, M. T., and Bjerrum, C.: Early anaerobic metabolisms, Philos. T. Roy. Soc. B, 361, 1819–1836, 2006. a
Cao, L., Eby, M., Ridgwell, A., Caldeira, K., Archer, D., Ishida, A., Joos, F., Matsumoto, K., Mikolajewicz, U., Mouchet, A., Orr, J. C., Plattner, G.-K., Schlitzer, R., Tokos, K., Totterdell, I., Tschumi, T., Yamanaka, Y., and Yool, A.: The role of ocean transport in the uptake of anthropogenic CO2, Biogeosciences, 6, 375–390, https://doi.org/10.5194/bg-6-375-2009, 2009. a, b, c
Cloud, P.: A working model of the primitive Earth, Am. J. Sci., 272, 537–548, https://doi.org/10.2475/ajs.272.6.537, 1972. a
Colbourn, G., Ridgwell, A., and Lenton, T. M.: The Rock Geochemical Model (RokGeM) v0.9, Geosci. Model Dev., 6, 1543–1573, https://doi.org/10.5194/gmd-6-1543-2013, 2013. a
Conway, T. M. and John, S. G.: Quantification of dissolved iron sources to
the North Atlantic Ocean, Nature, 511, 212–215, https://doi.org/10.1038/nature13482, 2014. a
Cosmidis, J., Benzerara, K., Morin, G., Busigny, V., Lebeau, O., Jézéquel, D., Noël, V., Dublet, G., and Othmane, G.: Biomineralization
of iron-phosphates in the water column of Lake Pavin (Massif Central, France), Geochim. Cosmochim. Ac., 126, 78–96, https://doi.org/10.1016/j.gca.2013.10.037, 2014. a
Crichton, K. A., Wilson, J. D., Ridgwell, A., and Pearson, P. N.: Calibration of temperature-dependent ocean microbial processes in the cGENIE.muffin (v0.9.13) Earth system model, Geosci. Model Dev., 14, 125–149, https://doi.org/10.5194/gmd-14-125-2021, 2021. a, b
Crockford, P. W., Hayles, J. A., Bao, H., Planavsky, N. J., Bekker, A., Fralick, P. W., Halverson, G. P., Bui, T. H., Peng, Y., and Wing, B. A.: Triple oxygen isotope evidence for limited mid-Proterozoic primary productivity, Nature, 559, 613–616, https://doi.org/10.1038/s41586-018-0349-y, 2018. a
Crosby, S. A., Glasson, D. R., Cuttler, A. H., Butler, I., Turner, D. R.,
Whitfield, M., and Millward, G. E.: Surface areas and porosities of Fe(III)- and Fe(II)-derived oxyhydroxides, Environ. Sci. Technol., 17, 709–713, 1983. a
Crosby, S. A., Roden, E. E., Johnson, C. M., and Beard, B. L.: The mechanisms of iron isotope fractionation produced during dissimilatory Fe(III) reduction by Shewanella putrefaciens and Geobacter sulfurreducens, Geobiology, 5, 169–189, 2007. a
Crowe, S. A., Katsev, S., Leslie, K., Sturm, A., Magen, C., Nomosatryo,
S., Pack, M. A., Kessler, J. D., Reeburgh, W. S., Roberts, J. A., González, L., Douglas Haffner, G., Mucci, A., Sundby, B., and Fowle, D. A.: The methane cycle in ferruginous Lake Matano, Geobiology, 9, 61–78, https://doi.org/10.1111/j.1472-4669.2010.00257.x, 2011. a, b
Crowe, S. A., Jones, C., Canfield, D. E., Paris, G., Adkins, J. F., Sessions, A. L., Katsev, S., Kim, S.-T., Zerkle, A. L., Nomosatryo, S., Fowle,
D. A., and Farquhar, J.: Sulfate was a trace constituent of Archean seawater, Science, 346, 735–739, https://doi.org/10.1126/science.1258966, 2014. a
Dale, A. W., Brüchert, V., Alperin, M., and Regnier, P.: An integrated sulfur isotope model for Namibian shelf sediments, Geochim. Cosmochim. Ac., 73, 1924–1944, https://doi.org/10.1016/j.gca.2008.12.015, 2009. a
Dehairs, F., Baeyens, W., and Goeyens, L.: Accumulation of Suspended Barite at Mesopelagic Depths and Export Production in the Southern Ocean, Science, 20, 1332–1335, https://doi.org/10.1126/science.258.5086.1332, 1990. a
Detmers, J., Bruchert, V., Habicht, K. S., and Kuever, J.: Diversity of sulfur isotope fractionations by sulfate-reducing prokaryotes,
Appl. Environ. Microb., 67, 888–894, 2001. a
Diaz, R. J. and Rosenberg, R.: Spreading dead zones and consequences for
marine ecosystems, Science 321, 926–929, 2008. a
Edwards, N. R. and Shepherd, J. G.: Bifurcations of the thermohaline circulation in a simplified three-dimensional model of the world ocean and the effects of interbasin connectivity, Clim. Dynam., 19, 31–42, 2002. a
Fakhraee, M., Hancisse, O., Canfield, D. E., Crowe, S. A., and Katsev, S.:
Proterozoic seawater sulfate scarcity and the evolution of ocean-atmosphere chemistry, Nat. Geosci., 12, 375–380, https://doi.org/10.1038/s41561-019-0351-5, 2019. a
Ferreira, D., Marshall, J., and Campin, J.: Localization of Deep Water Formation: Role of Atmospheric Moisture Transport and Geometrical Constraints on Ocean Circulation, J. Climate, 23, 1456–1476, https://doi.org/10.1175/2009JCLI3197.1, 2010. a
Finster, K., Liesack, W., and Thamdrup, B.: Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment, Appl. Environ. Microb., 64, 119–125, 1998. a
Froelich, P. N., Klinkhammer, G. P., Bender, M. L., Luedtke, N. A., Heath,
G. R., Cullen, D., and Dauphin, P.: Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis, Geochim. Cosmochim. Ac., 43, 1075–1090, 1979. a
Fry, B., Gest, H., and Hayes, J. M.: 34S/32S fractionation in sulfur cycles catalyzed by anaerobic bacteria, Appl. Environ. Microb., 54, 250–256, 1988. a
Gorby, Y. A., Yanina, S., McLean, J. S., Rosso, K. M., Moyles, D., Dohnalkova, A., Beveridge, T. J., Chang, I. S., Kim, B. H., Kim, K. S., Culley,
D. E., Reed, S. B., Romine, M. F., Saffarini, D. A., Hill, E. A., Shi, L., Elias, D. A., Kennedy, D. W., Pinchuk, G., Watanabe, K., Ishii, S., Logan, B., Nealson, K. H., and Fredrickson, J. K.: Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other
microorganisms, P. Natl. Acad. Sci. USA, 103, 11358–11363, https://doi.org/10.1073/pnas.0604517103, 2006. a
Grotzinger, J. P. and Kasting, J. F.: New Constraints on Precambrian Ocean composition, J. Geol., 101, 235–243, 1993. a
Guilbaud, R., Butler, I. B., and Ellam, R. M.: Abiotic pyrite formation produces a large Fe isotope fractionation, Science, 332, 1548–1551,
2011. a
Guilbaud, R., Poulton, S. W., Butterfield, N. J., Zhu, M., and Shields-Zhou, G. A.: A global transition to ferruginous conditions in the early Neoproterozoic oceans, Nat. Geosci., 8, 466–470, https://doi.org/10.1038/NGEO2434, 2015. a, b
Guilbaud, R., Poulton, S. W., Thompson, J., Husband, K. F., Zhu, M., Zhou, Y., Shields, G. A., and Lenton, T. M.: Phosphorus-limited conditions in the early Neoproterozoic ocean maintained low levels of atmospheric oxygen, Nat. Geosci., 13, 296–301, 2020. a
Halevy, I., Peters, S. E., and Fischer, W. W.: Sulfate burial constraints
on the phanerozoic sulfur cycle, Science, 337, 331–334, https://doi.org/10.1126/science.1220224, 2012. a
Henson, S. A., Sanders, R., Madsen, E., Morris, P. J., Le Moigne, F., and Quartly, G. D.: A reduced estimate of the strength of the ocean's biological carbon pump, Geophys. Res. Lett., 38, L04606, https://doi.org/10.1029/2011GL046735, 2011. a
Holland, H. D.: The Chemical Evolution of the Atmosphere and Oceans, Princeton University Press, Princeton, New Jersey, USA, 582 pp., 1984. a
Hülse, D., Arndt, S., Wilson, J. D., Munhoven, G., and Ridgwell, A.: Understanding the causes and consequences of past marine carbon cycling variability through models, Earth-Sci. Rev., 171, 349–382, https://doi.org/10.1016/j.earscirev.2017.06.004, 2017. a
Hülse, D., Arndt, S., Daines, S., Regnier, P., and Ridgwell, A.: OMEN-SED 1.0: a novel, numerically efficient organic matter sediment diagenesis module for coupling to Earth system models, Geosci. Model Dev., 11, 2649–2689, https://doi.org/10.5194/gmd-11-2649-2018, 2018. a, b, c
Hülse, D., Arndt, S., and Ridgwell, A.: Mitigation of extreme Ocean Anoxic Event conditions by organic matter sulfurization, Paleoceanogr. Paleocl., 34, 476–489, https://doi.org/10.1029/2018PA003470, 2019. a
Jimenez-Lopez, C. and Romanek, C. S.: Precipitation kinetics and carbon isotope partitioning of inorganic siderite at 25 ∘C and 1 atm, Geochim. Cosmochim. Ac., 68, 557–571, 2004. a
Johnson, C. M., Roden, E. E., Welch, S. A., and Beard, B. L.: Experimental
Constraints on Fe isotope fractionation during magnetite and Fe carbonate
formation coupled to dissimilatory hydrous ferric oxide reduction, Geochim. Cosmochim. Ac., 69, 963–993, 2004. a
Johnson, K. S.: Carbon dioxide hydration and dehydration kinetics in seawater, Limnol. Oceanogr., 27, 849–855, https://doi.org/10.4319/lo.1982.27.5.0849, 1982. a
Jones, C., Nomosatryo, S., Crowe, S. A., Bjerrum, C. J., and Canfield, D. E.: Iron oxides, divalent cations, silica, and the early earth phosphorus crisis, Geology, 43, 135–138, https://doi.org/10.1130/G36044.1, 2015. a, b
Kaplan, I. R. and Rittenberg, S. C.: Microbiological fractionation of sulphur isotopes, J. Gen. Microbiol., 34, 195–212, 1964. a
Keeling, R. F., Körtzinger, A., and Gruber, N.: Ocean Deoxygenation in a Warming World, Annu. Rev. Mar. Sci., 2, 199–229, https://doi.org/10.1146/annurev.marine.010908.163855, 2010. a
Kharecha, P., Kasting, J., and Siefert, J.: A coupled atmosphere-ecosystem
model of the early Archean Earth, Geobiology, 2, 53–76, https://doi.org/10.1111/j.1472-4669.2005.00049.x, 2005. a
Konhauser, K. O., Planavsky, N. J., Hardisty, D. S., Robbins, L. J., Warchola, T. J., Haugaard, R., Lalonde, S. V., Partin, C. A., Oonk, P. B. H.,
Tsikos, H., Lyons, T. W., Bekker, A., and Johnson, C. M.: Iron formations:
A global record of Neoarchaean to Palaeoproterozoic environmental history, Earth-Sci. Rev., 172, 140–177, https://doi.org/10.1016/j.earscirev.2017.06.012, 2017. a
Konovalov, S. K., Murray, J. W., Luther, G. W., and Tebo, B. M.: Processes controlling the redox budget for the oxic/anoxic water column of the Black Sea, Deep-Sea Res. Pt. II, 53, 1817–1841, https://doi.org/10.1016/j.dsr2.2006.03.013, 2006. a, b
Kump, L. R. and Seyfried, W. E.: Hydrothermal Fe fluxes during the Precambrian: Effect of low oceanic sulfate concentrations and low hydrostatic pressure on the composition of black smokers, Earth Planet. Sc. Lett., 235, 654–662, https://doi.org/10.1016/j.epsl.2005.04.040, 2005. a
Laakso, T. A. and Schrag, D. P.: Regulation of atmospheric oxygen during the Proterozoic, Earth Planet. Sc. Lett., 388, 81–91, https://doi.org/10.1016/j.epsl.2013.11.049, 2014. a, b, c
Laakso, T. A. and Schrag, D. P.: A small marine biosphere in the Proterozoic, Geobiology, 17, 161–171, https://doi.org/10.1111/gbi.12323, 2019. a
LaRowe, D. E. and Van Cappellen, P.: Degradation of natural organic matter: A thermodynamic analysis, Geochim. Cosmochim. Ac., 75, 2030–2042, https://doi.org/10.1016/j.gca.2011.01.020, 2011. a
Lenton, T. M., Daines, S. J., and Mills, B. J. W.: COPSE reloaded: An improved model of biogeochemical cycling over Phanerozoic time, Earth-Sci. Rev., 178, 1–28, https://doi.org/10.1016/J.EARSCIREV.2017.12.004, 2018. a, b
Lough, A. J. M., Connelly, D. P., Homoky, W. B., Hawkes, J. A., Chavagnac, V., Castillo, A., Kazemian, M., Nakamura, K. I., Araki, T., Kaulich, B.,
and Mills, R. A.: Diffuse hydrothermal venting: A hidden source of iron to the oceans, Front. Marine Sci., 6, 329, https://doi.org/10.3389/fmars.2019.00329, 2019. a
Lovley, D.: Dissimilatory Fe(III) and Mn(IV) Reduction, Microbiol. Rev., 55, 259–287, 1991 a
Marion, G. M., Millero, F. J., Camões, M. F., Spitzer, P., Feistel, R., and Chen, C. T. A.: pH of seawater, Mar. Chem., 126, 89–96, https://doi.org/10.1016/j.marchem.2011.04.002, 2011. a
Marsh, R., Müller, S. A., Yool, A., and Edwards, N. R.: Incorporation of the C-GOLDSTEIN efficient climate model into the GENIE framework: “eb_go_gs” configurations of GENIE, Geosci. Model Dev., 4, 957–992, https://doi.org/10.5194/gmd-4-957-2011, 2011. a, b
Martin, J., Knauer, G. A., Karl, D., and Broenkow, W.: VERTEX: carbon cycling in the northeast Pacific, Deep-Sea Res., 34, 267–285, https://doi.org/10.1016/0198-0149(87)90086-0, 1987. a
Meyer, K. M., Ridgwell, A., and Payne, J. L.: The influence of the biological pump on ocean chemistry: Implications for long-term trends in marine redox chemistry, the global carbon cycle, and marine animal ecosystems, Geobiology, 14, 207–219, https://doi.org/10.1111/gbi.12176, 2016. a
Meysman, F. J. R., Middelburg, J. J., Herman, P. M. J., and Heip, C. H. R.: Reactive transport in surface sediments – II. Media: an object-oriented problem-solving environment for early diagenesis, Comput. Geosci., 29, 301–318, https://doi.org/10.1016/S0098-3004(03)00007-4, 2003. a
Michard, G., Viollier, E., Jézéquel, D., and Sarazin, G.: Geochemical study of a crater lake: Pavin Lake, France – Identification, location
and quantification of the chemical reactions in the lake, Chem. Geol., 115, 103–115, 1994. a
Millero, F. J., Sotolongo, S., and Izaguirre, M.: The oxidation kinetics of Fe(II) in seawater, Geochim. Cosmochim. Ac., 51, 793–207, https://doi.org/10.1016/0016-7037(87)90093-7, 1987. a, b
Millero, F. J., Wensheng, Y., and Aicher, J.: The speciation of Fe(II) and
Fe(III) in natural waters, Mar. Chem., 50, 21–39, 1995. a
Monteiro, F. M., Pancost, R. D., Ridgwell, A., and Donnadieu, Y.: Nutrients as the dominant control on the spread of anoxia and euxinia across the
Cenomanian-Turonian oceanic anoxic event (OAE2): Model-data comparison, Paleoceanography, 27, PA4209, https://doi.org/10.1029/2012PA002351, 2012. a
Morris, M.: Factorial sampling plans for preliminary computational experiments, Technometrics, 33, 161–174, 1991. a
Najjar, R. G. and Orr, J. C.: Biotic-HOWTO, Internal OCMIP Report,
LSCE/CEA Saclay, Gifsur-Yvette, France, 15 pp., 1999. a
Nisbet, E. G. and Sleep, N. H.: The habitat and nature of early life, Nature, 409, 1083–1091, https://doi.org/10.1038/35059210, 2001. a
Olson, S. L., Kump, L. R., and Kasting, J. F.: Quantifying the areal extent and dissolved oxygen concentrations of Archean oxygen oases, Chem. Geol., 362, 35–43, https://doi.org/10.1016/j.chemgeo.2013.08.012, 2013. a
Olson, S. L., Reinhard, C. T., and Lyons, T. W.: Limited role for methane in the mid-Proterozoic greenhouse, P. Natl. Acad. Sci. USA, 113, 11447–11452, 2016. a
Ozaki, K., Tajima, S., and Tajika, E.: Conditions required for oceanic anoxia/euxinia: Constraints from a one-dimensional ocean biogeochemical cycle model, Earth Planet. Sc. Lett., 304, 270–279, https://doi.org/10.1016/J.EPSL.2011.02.011, 2011. a, b
Ozaki, K., Tajika, E., Hong, P. K., Nakagawa, Y., and Reinhard, C. T.: Effects of primitive photosynthesis on Earth's early climate system,
Nat. Geosci., 11, 55–59, https://doi.org/10.1038/s41561-017-0031-2, 2018. a
Ozaki, K., Reinhard, C. T., and Tajika, E.: A sluggish mid-Proterozoic biosphere and its effect on Earth's redox balance, Geobiology, 17, 3–11, https://doi.org/10.1111/gbi.12317, 2019. a, b
Parekh, P., Follows, M. J., and Boyle, E.: Modeling the global ocean iron cycle, Global Biogeochem. Cy., 18, GB1002, https://doi.org/10.1029/2003GB002061, 2004. a, b, c, d
Pellerin, A., Anderson-Trocmé, L., Whyte, L. G., Zane, G. M., Wall, J. D., and Wing, B. A.: Sulfur Isotope Fractionation during the Evolutionary Adaptation of a Sulfate-Reducing Bacterium, Appl. Environ. Microb.,
81, 2676–2689, https://doi.org/10.1128/AEM.03476-14, 2015. a
Pellerin, A., Wenk, C. B., Halevy, I., and Wing, B. A.: Sulfur Isotope Fractionation by Sulfate-Reducing Microbes Can Reflect Past Physiology, Environ. Sci. Technol., 52, 4013–4022, https://doi.org/10.1021/acs.est.7b05119, 2018. a
Pellerin, A., Antler, G., Holm, S. A., Findlay, A. J., Crockford, P. W., Turchyn, A. V., Jørgensen, B. B., and Finster, K.: Large sulfur isotope
fractionation by bacterial sulfide oxidation, Science Advances, 5, eaaw1480, https://doi.org/10.1126/sciadv.aaw1480, 2019. a, b
Picard, A., Kappler, A., Schmid, G., Quaroni, L., and Obst, M.: Experimental diagenesis of organo-mineral structures formed by microaerophilic Fe(II)-oxidizing bacteria, Nat. Commun., 6, 6277, https://doi.org/10.1038/ncomms7277, 2015. a
Planavsky, N. J., McGoldrick, P., Scott, C. T., Li, C., Reinhard, C. T., Kelly, A. E., Chu, X., Bekker, A., Love, G. D., and Lyons, T. W.: Widespread iron-rich conditions in the mid-Proterozoic ocean, Nature, 477, 448–451, https://doi.org/10.1038/nature10327, 2011. a, b
Poser, A., Vogt, C., Knöller, K., Ahlheim, J., Weiss, H., Kleinsteuber, S., and Richnow, H.-H.: Stable Sulfur and Oxygen Isotope Fractionation of Anoxic Sulfide
Oxidation by Two Different Enzymatic Pathway, Environ. Sci. Technol., 48,
9094–9102, https://doi.org/10.1021/es404808r, 2014. a
Postma, D. and Jakobsen, R.: Redox zonation: equilibrium constraints on the
Poulton, S. W. and Canfield, D. E.: Development of a sequential extraction procedure for iron: Implications for iron partitioning in continentally
derived particulates, Chem. Geol., 214, 209–221, https://doi.org/10.1016/j.chemgeo.2004.09.003, 2005. a, b
Poulton, S. W. and Raiswell, R.: The low-temperature geochemical cycle of
iron: from continental fluxes to marine sediment deposition, Am. J. Sci., 302, 774–805, 2002. a
Price, F. T. and Shieh, Y. N.: Fractionation of sulfur isotopes during laboratory synthesis of pyrite at low temperatures, Chem. Geol., 27, 245–253, 1979. a
Reinhard, C. T., Planavsky, N. J., Robbins, L. J., Partin, C. A., Gill, B. C., Lalonde, S. V., Bekker, A., Konhauser, K. O., and Lyons, T. W.: Proterozoic ocean redox and biogeochemical stasis, P. Natl. Acad. Sci. USA, 110, 5357–5362, https://doi.org/10.1073/pnas.1208622110, 2013. a, b
Reinhard, C. T., Planavsky, N. J., Olson, S. L., Lyons, T. W., and Erwin, D. H.: Earth's oxygen cycle and the evolution of animal life, P. Natl. Acad. Sci. USA, 113, 8933–8938, https://doi.org/10.1073/pnas.1521544113, 2016. a
Reinhard, C. T., Planavsky, N. J., Gill, B. C., Ozaki, K., Robbins, L. J., Lyons, T. W., Fischer, W. W., Wang, C., Cole, D. B., and Konhauser, K. O.: Evolution of the global phosphorus cycle, Nature, 541, 386–389, https://doi.org/10.1038/nature20772, 2017. a, b, c, d
Reinhard, C. T., Planavsky, N. J., Ward, B. A., Love, G. D., Le Hir, G., and Ridgwell, A.: The impact of marine nutrient abundance on early eukaryotic ecosystems, Geobiology, 18, 139–151, https://doi.org/10.1111/gbi.12384, 2020b. a, b, c
Ridgwell, A.: Evolution of the ocean's “biological pump”,
P. Natl. Acad. Sci. USA, 108, 16485–16486, https://doi.org/10.1073/pnas.1112236108, 2011. a
Ridgwell, A. and Death, R.: Iron limitation in an efficient model of global carbon cycling and climate, in preparation, 2021. a
Ridgwell, A. and Hargreaves, J. C.: Regulation of atmospheric CO2 by deep‐sea sediments in an Earth system model, Global Biogeochem. Cy., 21, GB2008, https://doi.org/10.1029/2006GB002764, 2007. a
Ridgwell, A., Hargreaves, J. C., Edwards, N. R., Annan, J. D., Lenton, T. M., Marsh, R., Yool, A., and Watson, A.: Marine geochemical data assimilation in an efficient Earth System Model of global biogeochemical cycling, Biogeosciences, 4, 87–104, https://doi.org/10.5194/bg-4-87-2007, 2007. a, b, c, d, e, f, g, h
Ridgwell, A., Hülse, D., Peterson, C., Ward, B., sjszas, evansmn, and Jones, R.: derpycode/muffindoc: (Version v0.9.21), Zenodo [code], https://doi.org/10.5281/zenodo.4651394, 2021a. a
Ridgwell, A., Reinhard, C., van de Velde, S., Adloff, M., Hülse, D., Wilson, J., Ward, B., Vervoort, P., Monteiro, F., Kirtland-Turner, S., and Li, M.: derpycode/cgenie.muffin: van de Velde et al. [revised for GMD] (Version v0.9.21), Zenodo [code], https://doi.org/10.5281/zenodo.4651390, 2021b. a
Rolison, J. M., Stirling, C. H., Middag, R., Gault-Ringold, M., George, E., and Rijkenberg, M. J. A.: Iron isotope fractionation during pyrite formation in a sulfidic Precambrian ocean analogue, Earth Planet. Sc. Lett., 488, 1–13, https://doi.org/10.1016/j.epsl.2018.02.006, 2018. a
Rouxel, O. J., Bekker, A., and Edwards, K. J.: Iron isotope constraints on
the Archean and Paleoproterozoic ocean redox state, Science, 307, 1088–1091, 2005. a
Sharp, J. H., Benner, R., Bennett, L., Carlson, C. A., Fitzwater, S. E., Pletzer, E. T., and Tupas, L., M.: Analyses of dissolved organic carbon in
seawater: the JGOFS EqPac methods comparison, Mar. Chem., 48, 91–108, 1995. a
Shields, G. A., Mills, B. J. W., Zhu, M., Raub, T. D., Daines, S. J., and Lenton, T. M.: Unique Neoproterozoic carbon isotope excursions sustained by coupled evaporite dissolution and pyrite burial, Nat. Geosci., 12, 823–827, https://doi.org/10.1038/s41561-019-0434-3, 2019. a, b
Sim, M. S., Bosak, T., and Ono, S.: Large sulfur isotope fractionation does not require disproportionation, Science, 333, 74–77, 2011. a
Sperling, E. A., Wolock, C. J., Morgan, A. S., Gill, B. C., Kunzmann, M.,
Halverson, G. P., Macdonald, F. A., Knoll, A. H., and Johnston, D. T.: Statistical analysis of iron geochemical data suggests limited late Proterozoic oxygenation, Nature, 523, 451–454, https://doi.org/10.1038/nature14589, 2015. a, b
Steefel, C. I. and Van Cappellen, P.: A new kinetic approach to modeling water-rock interaction: the role of nucleation, precursors, and Ostwald ripening, Geochim. Cosmochim. Ac., 54, 2657–2677, https://doi.org/10.1016/0016-7037(90)90003-4, 1990. a
Suits, N. S. and Wilkin, R. T.: Pyrite formation in the water column and sediments of a meromictic lake, Geology, 26, 1099–1102, 1998. a
Tagliabue, A., Bopp, L., Dutay, J. C., Bowie, A. R., Chever, F., Jean-Baptiste, P., Bucciarelli, E., Lannuzel, D., Remenyi, T., Sarthou, G., Aumont, O., Gehlen, M., and Jeandel, C.: Hydrothermal contribution to the oceanic dissolved iron inventory, Nat. Geosci., 3, 252–256, https://doi.org/10.1038/ngeo818, 2010. a
Tagliabue, A., Aumont, O., DeAth, R., Dunne, J. P., Dutkiewicz, S., Galbraith, E., Misumi, K., Moore, J. K., Ridgwell, A., Sherman, E., Stock, C., Vichi, M., Völker, C., and Yool, A.: How well do global ocean biogeochemistry models simulate dissolved iron distributions?, Global Biogeochem. Cy., 30, 149–174, https://doi.org/10.1002/2015GB005289, 2016. a, b, c, d, e, f, g, h, i, j, k, l, m, n, o
Thompson, K. J., Kenward, P. A., Bauer, K. W., Warchola, T., Gauger, T., Martinez, R., Sinister, R. L., Michiels, C. C., Llirós, M., Reinhard, C. T., Kappler, A., Konhauser, K. O., and Crowe, S. A.: Photoferrotrophy, deposition of banded iron formations, and methane production in Archean oceans, Science Advances, 5, eaav2869, https://doi.org/10.1126/sciadv.aav2869, 2019. a, b, c, d
Tosca, N. J., Jiang, C. Z., Rasmussen, B., and Muhling, J.: Products of the iron cycle on the early Earth, Free Radical Bio. Med., 140, 138–153, https://doi.org/10.1016/j.freeradbiomed.2019.05.005, 2019. a
Tribovillard, N., Algeo, T. J., Lyons, T., and Riboulleau, A.: Trace metals as paleoredox and paleoproductivity proxies: An update, Chem. Geol., 232, 12–32, https://doi.org/10.1016/j.chemgeo.2006.02.012, 2006. a
Van Cappellen, P. and Ingall, E. D.: Redox stabilization of the Atmosphere and Oceans by Phosphorus-Limited Marine Productivity, Science, 271, 493–496, https://doi.org/10.1126/science.271.5248.493, 1996. a, b, c
van de Velde, S. J., Mills, B. J. W., Meysman, F. J. R., Lenton, T. M., and Poulton, S. W.: Early Palaeozoic ocean anoxia and global warming driven by
the evolution of shallow burrowing, Nat. Comm., 9, 2554, https://doi.org/10.1038/s41467-018-04973-4, 2018. a
van de Velde, S. J., Hidalgo-Martinez, S., Callebaut, I., Antler, G., James, R. K., Leermakers, M., and Meysman, F. J. R.: Burrowing fauna mediate alternative stable states in the redox cycling of salt marsh sediments, Geochim. Cosmochim. Ac., 276, 31–49, 2020a. a
van de Velde, S. J., Reinhard, C., Ridgwell, A., and Meysman, F. J. R.: Bistability in the redox chemistry of sediments and oceans, P. Natl. Acad. Sci. USA, 117, 33043–33050, https://doi.org/10.1073/pnas.2008235117, 2020b. a, b
Vervoort, P., Kirtland Tuner, S., Rochholz, F., and Ridgwell, A.: Earth System Model Analysis of how Astronomical Forcing is Imprinted onto the Marine Geological Record, Paleoceanogr. Paleocl., in review, 2021. a
Wallmann, K., Flögel, S., Scholz, F., Dale, A. W., Kemena, T. P., Steinig, S., and Kuhnt, W.: Periodic changes in the Cretaceous ocean and climate caused by marine redox see-saw, Nat. Geosci., 12, 456–461, https://doi.org/10.1038/s41561-019-0359-x, 2019. a, b
Walter, X. A., Picazo, A., Miracle, M. R., Vicente, E., Camacho, A., Aragno, M., and Zopfi, J.: Phototrophic Fe(II)-oxidation in the chemocline of a ferruginous meromictic lake, Front. Microbiol., 5, 713, https://doi.org/10.3389/fmicb.2014.00713, 2014. a
Wan, M., Schröder, C., and Peiffer, S.:
Ward, B. A., Wilson, J. D., Death, R. M., Monteiro, F. M., Yool, A., and Ridgwell, A.: EcoGEnIE 1.0: plankton ecology in the cGEnIE Earth system model, Geosci. Model Dev., 11, 4241–4267, https://doi.org/10.5194/gmd-11-4241-2018, 2018. a, b
Wiesli, R. A., Beard, B. L., and Johnson, C. M.: Experimental determination of Fe isotope fractionation between aqueous Fe(II), siderite and “green
rust” in abiotic systems, Chem. Geol., 211, 343–362, 2004. a
Wing, B. A. and Halevy, I.: Intracellular metabolite levels shape sulfur isotope fractionation during microbial sulfate respiration, P. Natl. Acad. Sci. USA, 111, 18116–18125, https://doi.org/10.1073/pnas.1407502111, 2014. a
Xiong, Y., Guilbaud, R., Peacock, C. L., Cox, R. P., Canfield, D. E., Krom, M. D., and Poulton, S. W.: Phosphorus cycling in Lake Cadagno, Switzerland: A low sulfate euxinic ocean analogue, Geochim. Cosmochim. Ac., 251, 116–135, https://doi.org/10.1016/j.gca.2019.02.011, 2019. a
Zegeye, A., Bonneville, S., Benning, L. G., Sturm, A., Fowle, D. A., Jones, C., Canfield, D. E., Ruby, C., MacLean, L. C., Nomosatryo, S., Crowe, S., and Poulton, S. W.: Green rust formation controls nutrient availability in a ferruginous water column, Geology, 40, 599–602, https://doi.org/10.1130/G32959.1, 2012. a
Short summary
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.
Biogeochemical interactions between iron and sulfur are central to the long-term biogeochemical...
