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 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.
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.
Keyi Cheng, Andy Ridgwell, and Dalton Hardisty
EGUsphere, https://doi.org/10.5194/egusphere-2024-677, https://doi.org/10.5194/egusphere-2024-677, 2024
Short summary
Short summary
The carbonate paleoredox proxy, I:Ca, has shown its potential in quantifying 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 observation, and then tested its ability to estimate I:Ca in the Cretaceous ocean. Our study implies cGENIE’s potential in quantifying redox change in the past using the I:Ca proxy.
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
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
An optimal transformation method applied to diagnosing the ocean carbon sink
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
Towards a real-time modeling of global ocean waves by the fully GPU-accelerated spectral wave model WAM6-GPU
Great Lakes wave forecast system on high-resolution unstructured meshes
Development of a Novel Storm Surge Inundation Model Framework for Efficient Prediction
Skin Sea Surface Temperature schemes in coupled ocean-atmosphere modeling: the impact of chlorophyll-interactive e-folding depth
A simple approach to represent precipitation-derived freshwater fluxes into nearshore ocean models: an FVCOM4.1 case study
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)
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 1: Evolution of ecosystem composition under limited light and nutrient conditions
Ocean wave tracing v.1: a numerical solver of the wave ray equations for ocean waves on variable currents at arbitrary depths
Design and evaluation of an efficient high-precision ocean surface wave model with a multiscale grid system (MSG_Wav1.0)
Evaluation of the CMCC global eddying ocean model for the Ocean Model Intercomparison Project (OMIP2)
Barents-2.5km v2.0: an operational data-assimilative coupled ocean and sea ice ensemble prediction model for the Barents Sea and Svalbard
Open-ocean tides simulated by ICON-O, version icon-2.6.6
Using Probability Density Functions to Evaluate Models (PDFEM, v1.0) to compare a biogeochemical model with satellite-derived chlorophyll
Data assimilation sensitivity experiments in the East Auckland Current system using 4D-Var
Using the COAsT Python package to develop a standardised validation workflow for ocean physics models
Improving Antarctic Bottom Water precursors in NEMO for climate applications
Formulation, optimization, and sensitivity of NitrOMZv1.0, a biogeochemical model of the nitrogen cycle in oceanic oxygen minimum zones
Waves in SKRIPS: WAVEWATCH III coupling implementation and a case study of Tropical Cyclone Mekunu
Adding sea ice effects to a global operational model (NEMO v3.6) for forecasting total water level: approach and impact
Enhanced ocean wave modeling by including effect of breaking under both deep- and shallow-water conditions
An internal solitary wave forecasting model in the northern South China Sea (ISWFM-NSCS)
The 3D biogeochemical marine mercury cycling model MERCY v2.0 – linking atmospheric Hg to methylmercury in fish
Global seamless tidal simulation using a 3D unstructured-grid model (SCHISM v5.10.0)
Arctic Ocean simulations in the CMIP6 Ocean Model Intercomparison Project (OMIP)
ChemicalDrift 1.0: an open-source Lagrangian chemical-fate and transport model for organic aquatic pollutants
The Met Office operational wave forecasting system: the evolution of the regional and global models
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. II): Towards a better representation of total alkalinity when modelling the carbonate system and air-sea CO2 fluxes
4DVarNet-SSH: end-to-end learning of variational interpolation schemes for nadir and wide-swath satellite altimetry
Development and validation of a global 1∕32° surface-wave–tide–circulation coupled ocean model: FIO-COM32
Reproducible and relocatable regional ocean modelling: fundamentals and practices
Barotropic tides in MPAS-Ocean (E3SM V2): impact of ice shelf cavities
Using the two-way nesting technique AGRIF with MARS3D V11.2 to improve hydrodynamics and estimate environmental indicators
Multidecadal and climatological surface current simulations for the southwestern Indian Ocean at 1∕50° resolution
The tidal effects in the Finite-volumE Sea ice–Ocean Model (FESOM2.1): a comparison between parameterised tidal mixing and explicit tidal forcing
HIDRA2: deep-learning ensemble sea level and storm tide forecasting in the presence of seiches – the case of the northern Adriatic
Moana Ocean Hindcast – a > 25-year simulation for New Zealand waters using the Regional Ocean Modeling System (ROMS) v3.9 model
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.
Neill Mackay, Jan Zika, Taimoor Sohail, Richard Williams, Oliver Andrews, and Andrew Watson
EGUsphere, https://doi.org/10.5194/egusphere-2023-2448, https://doi.org/10.5194/egusphere-2023-2448, 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.
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.
Ye Yuan, Fujiang Yu, Zhi Chen, Xueding Li, Fang Hou, Yuanyong Gao, Zhiyi Gao, and Renbo Pang
EGUsphere, https://doi.org/10.5194/egusphere-2024-169, https://doi.org/10.5194/egusphere-2024-169, 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, Graphics Processing Unit (GPU)-accelerated computing is introduced in the WAM (Cycle 6). With this effort, global high-resolution wave simulations now can run on GPUs up to tens of times faster than currently available models on a CPU node with just as accurate results.
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.
Xuanxuan Gao, Shuiqing Li, Dongxue Mo, Yahao Liu, and Po Hu
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-12, https://doi.org/10.5194/gmd-2024-12, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
Storm surges generate coastal inundation and expose populations and properties in 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 significantly improves over the 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. Discuss., https://doi.org/10.5194/gmd-2024-13, https://doi.org/10.5194/gmd-2024-13, 2024
Revised manuscript accepted for GMD
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.
Krysten Rutherford, Laura Bianucci, and William Floyd
EGUsphere, https://doi.org/10.5194/egusphere-2023-3064, https://doi.org/10.5194/egusphere-2023-3064, 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, B.C., 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.
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.
Lucille Barré, Frédéric Diaz, Thibaut Wagener, France Van Wambeke, Camille Mazoyer, Christophe Yohia, and Christel Pinazo
Geosci. Model Dev., 16, 6701–6739, https://doi.org/10.5194/gmd-16-6701-2023, https://doi.org/10.5194/gmd-16-6701-2023, 2023
Short summary
Short summary
While several studies have shown that mixotrophs play a crucial role in the carbon cycle, the impact of environmental forcings on their dynamics remains poorly investigated. Using a biogeochemical model that considers mixotrophs, we study the impact of light and nutrient concentration on the ecosystem composition in a highly dynamic Mediterranean coastal area: the Bay of Marseille. We show that mixotrophs cope better with oligotrophic conditions compared to strict auto- and heterotrophs.
Trygve Halsne, Kai Håkon Christensen, Gaute Hope, and Øyvind Breivik
Geosci. Model Dev., 16, 6515–6530, https://doi.org/10.5194/gmd-16-6515-2023, https://doi.org/10.5194/gmd-16-6515-2023, 2023
Short summary
Short summary
Surface waves that propagate in oceanic or coastal environments get influenced by their surroundings. Changes in the ambient current or the depth profile affect the wave propagation path, and the change in wave direction is called refraction. Some analytical solutions to the governing equations exist under ideal conditions, but for realistic situations, the equations must be solved numerically. Here we present such a numerical solver under an open-source license.
Jiangyu Li, Shaoqing Zhang, Qingxiang Liu, Xiaolin Yu, and Zhiwei Zhang
Geosci. Model Dev., 16, 6393–6412, https://doi.org/10.5194/gmd-16-6393-2023, https://doi.org/10.5194/gmd-16-6393-2023, 2023
Short summary
Short summary
Ocean surface waves play an important role in the air–sea interface but are rarely activated in high-resolution Earth system simulations due to their expensive computational costs. To alleviate this situation, this paper designs a new wave modeling framework with a multiscale grid system. Evaluations of a series of numerical experiments show that it has good feasibility and applicability in the WAVEWATCH III model, WW3, and can achieve the goals of efficient and high-precision wave simulation.
Doroteaciro Iovino, Pier Giuseppe Fogli, and Simona Masina
Geosci. Model Dev., 16, 6127–6159, https://doi.org/10.5194/gmd-16-6127-2023, https://doi.org/10.5194/gmd-16-6127-2023, 2023
Short summary
Short summary
This paper describes the model performance of three global ocean–sea ice configurations, from non-eddying (1°) to eddy-rich (1/16°) resolutions. Model simulations are obtained following the Ocean Model Intercomparison Project phase 2 (OMIP2) protocol. We compare key global climate variables across the three models and against observations, emphasizing the relative advantages and disadvantages of running forced ocean–sea ice models at higher resolution.
Johannes Röhrs, Yvonne Gusdal, Edel S. U. Rikardsen, Marina Durán Moro, Jostein Brændshøi, Nils Melsom Kristensen, Sindre Fritzner, Keguang Wang, Ann Kristin Sperrevik, Martina Idžanović, Thomas Lavergne, Jens Boldingh Debernard, and Kai H. Christensen
Geosci. Model Dev., 16, 5401–5426, https://doi.org/10.5194/gmd-16-5401-2023, https://doi.org/10.5194/gmd-16-5401-2023, 2023
Short summary
Short summary
A model to predict ocean currents, temperature, and sea ice is presented, covering the Barents Sea and northern Norway. To quantify forecast uncertainties, the model calculates ensemble forecasts with 24 realizations of ocean and ice conditions. Observations from satellites, buoys, and ships are ingested by the model. The model forecasts are compared with observations, and we show that the ocean model has skill in predicting sea surface temperatures.
Jin-Song von Storch, Eileen Hertwig, Veit Lüschow, Nils Brüggemann, Helmuth Haak, Peter Korn, and Vikram Singh
Geosci. Model Dev., 16, 5179–5196, https://doi.org/10.5194/gmd-16-5179-2023, https://doi.org/10.5194/gmd-16-5179-2023, 2023
Short summary
Short summary
The new ocean general circulation model ICON-O is developed for running experiments at kilometer scales and beyond. One targeted application is to simulate internal tides crucial for ocean mixing. To ensure their realism, which is difficult to assess, we evaluate the barotropic tides that generate internal tides. We show that ICON-O is able to realistically simulate the major aspects of the observed barotropic tides and discuss the aspects that impact the quality of the simulated tides.
Bror F. Jönsson, Christopher L. Follett, Jacob Bien, Stephanie Dutkiewicz, Sangwon Hyun, Gemma Kulk, Gael L. Forget, Christian Müller, Marie-Fanny Racault, Christopher N. Hill, Thomas Jackson, and Shubha Sathyendranath
Geosci. Model Dev., 16, 4639–4657, https://doi.org/10.5194/gmd-16-4639-2023, https://doi.org/10.5194/gmd-16-4639-2023, 2023
Short summary
Short summary
While biogeochemical models and satellite-derived ocean color data provide unprecedented information, it is problematic to compare them. Here, we present a new approach based on comparing probability density distributions of model and satellite properties to assess model skills. We also introduce Earth mover's distances as a novel and powerful metric to quantify the misfit between models and observations. We find that how 3D chlorophyll fields are aggregated can be a significant source of error.
Rafael Santana, Helen Macdonald, Joanne O'Callaghan, Brian Powell, Sarah Wakes, and Sutara H. Suanda
Geosci. Model Dev., 16, 3675–3698, https://doi.org/10.5194/gmd-16-3675-2023, https://doi.org/10.5194/gmd-16-3675-2023, 2023
Short summary
Short summary
We show the importance of assimilating subsurface temperature and velocity data in a model of the East Auckland Current. Assimilation of velocity increased the representation of large oceanic vortexes. Assimilation of temperature is needed to correctly simulate temperatures around 100 m depth, which is the most difficult region to simulate in ocean models. Our simulations showed improved results in comparison to the US Navy global model and highlight the importance of regional models.
David Byrne, Jeff Polton, Enda O'Dea, and Joanne Williams
Geosci. Model Dev., 16, 3749–3764, https://doi.org/10.5194/gmd-16-3749-2023, https://doi.org/10.5194/gmd-16-3749-2023, 2023
Short summary
Short summary
Validation is a crucial step during the development of models for ocean simulation. The purpose of validation is to assess how accurate a model is. It is most commonly done by comparing output from a model to actual observations. In this paper, we introduce and demonstrate usage of the COAsT Python package to standardise the validation process for physical ocean models. We also discuss our five guiding principles for standardised validation.
Katherine Hutchinson, Julie Deshayes, Christian Éthé, Clément Rousset, Casimir de Lavergne, Martin Vancoppenolle, Nicolas C. Jourdain, and Pierre Mathiot
Geosci. Model Dev., 16, 3629–3650, https://doi.org/10.5194/gmd-16-3629-2023, https://doi.org/10.5194/gmd-16-3629-2023, 2023
Short summary
Short summary
Bottom Water constitutes the lower half of the ocean’s overturning system and is primarily formed in the Weddell and Ross Sea in the Antarctic due to interactions between the atmosphere, ocean, sea ice and ice shelves. Here we use a global ocean 1° resolution model with explicit representation of the three large ice shelves important for the formation of the parent waters of Bottom Water. We find doing so reduces salt biases, improves water mass realism and gives realistic ice shelf melt rates.
Daniele Bianchi, Daniel McCoy, and Simon Yang
Geosci. Model Dev., 16, 3581–3609, https://doi.org/10.5194/gmd-16-3581-2023, https://doi.org/10.5194/gmd-16-3581-2023, 2023
Short summary
Short summary
We present NitrOMZ, a new model of the oceanic nitrogen cycle that simulates chemical transformations within oxygen minimum zones (OMZs). We describe the model formulation and its implementation in a one-dimensional representation of the water column before evaluating its ability to reproduce observations in the eastern tropical South Pacific. We conclude by describing the model sensitivity to parameter choices and environmental factors and its application to nitrogen cycling in the ocean.
Rui Sun, Alison Cobb, Ana B. Villas Bôas, Sabique Langodan, Aneesh C. Subramanian, Matthew R. Mazloff, Bruce D. Cornuelle, Arthur J. Miller, Raju Pathak, and Ibrahim Hoteit
Geosci. Model Dev., 16, 3435–3458, https://doi.org/10.5194/gmd-16-3435-2023, https://doi.org/10.5194/gmd-16-3435-2023, 2023
Short summary
Short summary
In this work, we integrated the WAVEWATCH III model into the regional coupled model SKRIPS. We then performed a case study using the newly implemented model to study Tropical Cyclone Mekunu, which occurred in the Arabian Sea. We found that the coupled model better simulates the cyclone than the uncoupled model, but the impact of waves on the cyclone is not significant. However, the waves change the sea surface temperature and mixed layer, especially in the cold waves produced due to the cyclone.
Pengcheng Wang and Natacha B. Bernier
Geosci. Model Dev., 16, 3335–3354, https://doi.org/10.5194/gmd-16-3335-2023, https://doi.org/10.5194/gmd-16-3335-2023, 2023
Short summary
Short summary
Effects of sea ice are typically neglected in operational flood forecast systems. In this work, we capture these effects via the addition of a parameterized ice–ocean stress. The parameterization takes advantage of forecast fields from an advanced ice–ocean model and features a novel, consistent representation of the tidal relative ice–ocean velocity. The new parameterization leads to improved forecasts of tides and storm surges in polar regions. Associated physical processes are discussed.
Yue Xu and Xiping Yu
Geosci. Model Dev., 16, 2811–2831, https://doi.org/10.5194/gmd-16-2811-2023, https://doi.org/10.5194/gmd-16-2811-2023, 2023
Short summary
Short summary
An accurate description of the wind energy input into ocean waves is crucial to ocean wave modeling, and a physics-based consideration of the effect of wave breaking is absolutely necessary to obtain such an accurate description, particularly under extreme conditions. This study evaluates the performance of a recently improved formula, taking into account not only the effect of breaking but also the effect of airflow separation on the leeside of steep wave crests in a reasonably consistent way.
Yankun Gong, Xueen Chen, Jiexin Xu, Jieshuo Xie, Zhiwu Chen, Yinghui He, and Shuqun Cai
Geosci. Model Dev., 16, 2851–2871, https://doi.org/10.5194/gmd-16-2851-2023, https://doi.org/10.5194/gmd-16-2851-2023, 2023
Short summary
Short summary
Internal solitary waves (ISWs) play crucial roles in mass transport and ocean mixing in the northern South China Sea. Massive numerical investigations have been conducted in this region, but there was no systematic evaluation of a three-dimensional model about precisely simulating ISWs. Here, an ISW forecasting model is employed to evaluate the roles of resolution, tidal forcing and stratification in accurately reproducing wave properties via comparison to field and remote-sensing observations.
Johannes Bieser, David J. Amptmeijer, Ute Daewel, Joachim Kuss, Anne L. Soerensen, and Corinna Schrum
Geosci. Model Dev., 16, 2649–2688, https://doi.org/10.5194/gmd-16-2649-2023, https://doi.org/10.5194/gmd-16-2649-2023, 2023
Short summary
Short summary
MERCY is a 3D model to study mercury (Hg) cycling in the ocean. Hg is a highly harmful pollutant regulated by the UN Minamata Convention on Mercury due to widespread human emissions. These emissions eventually reach the oceans, where Hg transforms into the even more toxic and bioaccumulative pollutant methylmercury. MERCY predicts the fate of Hg in the ocean and its buildup in the food chain. It is the first model to consider Hg accumulation in fish, a major source of Hg exposure for humans.
Y. Joseph Zhang, Tomas Fernandez-Montblanc, William Pringle, Hao-Cheng Yu, Linlin Cui, and Saeed Moghimi
Geosci. Model Dev., 16, 2565–2581, https://doi.org/10.5194/gmd-16-2565-2023, https://doi.org/10.5194/gmd-16-2565-2023, 2023
Short summary
Short summary
Simulating global ocean from deep basins to coastal areas is a daunting task but is important for disaster mitigation efforts. We present a new 3D global ocean model on flexible mesh to study both tidal and nontidal processes and total water prediction. We demonstrate the potential for
seamlesssimulation, on a single mesh, from the global ocean to a few estuaries along the US West Coast. The model can serve as the backbone of a global tide surge and compound flooding forecasting framework.
Qi Shu, Qiang Wang, Chuncheng Guo, Zhenya Song, Shizhu Wang, Yan He, and Fangli Qiao
Geosci. Model Dev., 16, 2539–2563, https://doi.org/10.5194/gmd-16-2539-2023, https://doi.org/10.5194/gmd-16-2539-2023, 2023
Short summary
Short summary
Ocean models are often used for scientific studies on the Arctic Ocean. Here the Arctic Ocean simulations by state-of-the-art global ocean–sea-ice models participating in the Ocean Model Intercomparison Project (OMIP) were evaluated. The simulations on Arctic Ocean hydrography, freshwater content, stratification, sea surface height, and gateway transports were assessed and the common biases were detected. The simulations forced by different atmospheric forcing were also evaluated.
Manuel Aghito, Loris Calgaro, Knut-Frode Dagestad, Christian Ferrarin, Antonio Marcomini, Øyvind Breivik, and Lars Robert Hole
Geosci. Model Dev., 16, 2477–2494, https://doi.org/10.5194/gmd-16-2477-2023, https://doi.org/10.5194/gmd-16-2477-2023, 2023
Short summary
Short summary
The newly developed ChemicalDrift model can simulate the transport and fate of chemicals in the ocean and in coastal regions. The model combines ocean physics, including transport due to currents, turbulence due to surface winds and the sinking of particles to the sea floor, with ocean chemistry, such as the partitioning, the degradation and the evaporation of chemicals. The model will be utilized for risk assessment of ocean and sea-floor contamination from pollutants emitted from shipping.
Nieves G. Valiente, Andrew Saulter, Breogan Gomez, Christopher Bunney, Jian-Guo Li, Tamzin Palmer, and Christine Pequignet
Geosci. Model Dev., 16, 2515–2538, https://doi.org/10.5194/gmd-16-2515-2023, https://doi.org/10.5194/gmd-16-2515-2023, 2023
Short summary
Short summary
We document the Met Office operational global and regional wave models which provide wave forecasts up to 7 d ahead. Our models present coarser resolution offshore to higher resolution near the coastline. The increased resolution led to replication of the extremes but to some overestimation during modal conditions. If currents are included, wave directions and long period swells near the coast are significantly improved. New developments focus on the optimisation of the models with resolution.
Lucille Barré, Frédéric Diaz, Thibaut Wagener, Camille Mazoyer, Christophe Yohia, and Christel Pinazo
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2023-34, https://doi.org/10.5194/gmd-2023-34, 2023
Revised manuscript accepted for GMD
Short summary
Short summary
Carbonate system is typically studied using measurements, yet modelling 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 their variations are strongly impacted by the hydrodynamic processes that affect the bay.
Maxime Beauchamp, Quentin Febvre, Hugo Georgenthum, and Ronan Fablet
Geosci. Model Dev., 16, 2119–2147, https://doi.org/10.5194/gmd-16-2119-2023, https://doi.org/10.5194/gmd-16-2119-2023, 2023
Short summary
Short summary
4DVarNet is a learning-based method based on traditional data assimilation (DA). This new class of algorithms can be used to provide efficient reconstructions of a dynamical system based on single observations. We provide a 4DVarNet application to sea surface height reconstructions based on nadir and future Surface Water and Ocean and Topography data. It outperforms other methods, from optimal interpolation to sophisticated DA algorithms. This work is part of on-going AI Chair Oceanix projects.
Bin Xiao, Fangli Qiao, Qi Shu, Xunqiang Yin, Guansuo Wang, and Shihong Wang
Geosci. Model Dev., 16, 1755–1777, https://doi.org/10.5194/gmd-16-1755-2023, https://doi.org/10.5194/gmd-16-1755-2023, 2023
Short summary
Short summary
A new global surface-wave–tide–circulation coupled ocean model (FIO-COM32) with a resolution of 1/32° × 1/32° is developed and validated. Both the promotion of the horizontal resolution and included physical processes are shown to be important contributors to the significant improvements in FIO-COM32 simulations. It is time to merge these separated model components (surface waves, tidal currents and ocean circulation) and start a new generation of ocean model development.
Jeff Polton, James Harle, Jason Holt, Anna Katavouta, Dale Partridge, Jenny Jardine, Sarah Wakelin, Julia Rulent, Anthony Wise, Katherine Hutchinson, David Byrne, Diego Bruciaferri, Enda O'Dea, Michela De Dominicis, Pierre Mathiot, Andrew Coward, Andrew Yool, Julien Palmiéri, Gennadi Lessin, Claudia Gabriela Mayorga-Adame, Valérie Le Guennec, Alex Arnold, and Clément Rousset
Geosci. Model Dev., 16, 1481–1510, https://doi.org/10.5194/gmd-16-1481-2023, https://doi.org/10.5194/gmd-16-1481-2023, 2023
Short summary
Short summary
The aim is to increase the capacity of the modelling community to respond to societally important questions that require ocean modelling. The concept of reproducibility for regional ocean modelling is developed: advocating methods for reproducible workflows and standardised methods of assessment. Then, targeting the NEMO framework, we give practical advice and worked examples, highlighting key considerations that will the expedite development cycle and upskill the user community.
Nairita Pal, Kristin N. Barton, Mark R. Petersen, Steven R. Brus, Darren Engwirda, Brian K. Arbic, Andrew F. Roberts, Joannes J. Westerink, and Damrongsak Wirasaet
Geosci. Model Dev., 16, 1297–1314, https://doi.org/10.5194/gmd-16-1297-2023, https://doi.org/10.5194/gmd-16-1297-2023, 2023
Short summary
Short summary
Understanding tides is essential to accurately predict ocean currents. Over the next several decades coastal processes such as flooding and erosion will be severely impacted due to climate change. Tides affect currents along the coastal regions the most. In this paper we show the results of implementing tides in a global ocean model known as MPAS–Ocean. We also show how Antarctic ice shelf cavities affect global tides. Our work points towards future research with tide–ice interactions.
Sébastien Petton, Valérie Garnier, Matthieu Caillaud, Laurent Debreu, and Franck Dumas
Geosci. Model Dev., 16, 1191–1211, https://doi.org/10.5194/gmd-16-1191-2023, https://doi.org/10.5194/gmd-16-1191-2023, 2023
Short summary
Short summary
The nesting AGRIF library is implemented in the MARS3D hydrodynamic model, a semi-implicit, free-surface numerical model which uses a time scheme as an alternating-direction implicit (ADI) algorithm. Two applications at the regional and coastal scale are introduced. We compare the two-nesting approach to the classic offline one-way approach, based on an in situ dataset. This method is an efficient means to significantly improve the physical hydrodynamics and unravel ecological challenges.
Noam S. Vogt-Vincent and Helen L. Johnson
Geosci. Model Dev., 16, 1163–1178, https://doi.org/10.5194/gmd-16-1163-2023, https://doi.org/10.5194/gmd-16-1163-2023, 2023
Short summary
Short summary
Ocean currents transport things over large distances across the ocean surface. Predicting this transport is key for tackling many environmental problems, such as marine plastic pollution and coral reef resilience. However, doing this requires a good understanding ocean currents, which is currently lacking. Here, we present and validate state-of-the-art simulations for surface currents in the southwestern Indian Ocean, which will support future marine dispersal studies across this region.
Pengyang Song, Dmitry Sidorenko, Patrick Scholz, Maik Thomas, and Gerrit Lohmann
Geosci. Model Dev., 16, 383–405, https://doi.org/10.5194/gmd-16-383-2023, https://doi.org/10.5194/gmd-16-383-2023, 2023
Short summary
Short summary
Tides have essential effects on the ocean and climate. Most previous research applies parameterised tidal mixing to discuss their effects in models. By comparing the effect of a tidal mixing parameterisation and tidal forcing on the ocean state, we assess the advantages and disadvantages of the two methods. Our results show that tidal mixing in the North Pacific Ocean strongly affects the global thermohaline circulation. We also list some effects that are not considered in the parameterisation.
Marko Rus, Anja Fettich, Matej Kristan, and Matjaž Ličer
Geosci. Model Dev., 16, 271–288, https://doi.org/10.5194/gmd-16-271-2023, https://doi.org/10.5194/gmd-16-271-2023, 2023
Short summary
Short summary
We propose a new fast and reliable deep-learning architecture HIDRA2 for sea level and storm surge modeling. HIDRA2 features new feature encoders and a fusion-regression block. We test HIDRA2 on Adriatic storm surges, which depend on an interaction between tides and seiches. We demonstrate that HIDRA2 learns to effectively mimic the timing and amplitude of Adriatic seiches. This is essential for reliable HIDRA2 predictions of total storm surge sea levels.
Joao Marcos Azevedo Correia de Souza, Sutara H. Suanda, Phellipe P. Couto, Robert O. Smith, Colette Kerry, and Moninya Roughan
Geosci. Model Dev., 16, 211–231, https://doi.org/10.5194/gmd-16-211-2023, https://doi.org/10.5194/gmd-16-211-2023, 2023
Short summary
Short summary
The current paper describes the configuration and evaluation of the Moana Ocean Hindcast, a > 25-year simulation of the ocean state around New Zealand using the Regional Ocean Modeling System v3.9. This is the first open-access, long-term, continuous, realistic ocean simulation for this region and provides information for improving the understanding of the ocean processes that affect the New Zealand exclusive economic zone.
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...
