Articles | Volume 15, issue 5
https://doi.org/10.5194/gmd-15-2105-2022
© Author(s) 2022. 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-15-2105-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
11 Mar 2022
Model description paper |
| 11 Mar 2022
| 11 Mar 2022
RADIv1: a non-steady-state early diagenetic model for ocean sediments in Julia and MATLAB/GNU Octave
Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
Department of Earth and Planetary Sciences, McGill University, Montreal, Canada
Matthew P. Humphreys
Department of Ocean Systems (OCS), NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
Monica M. Wilhelmus
Center for Fluid Mechanics, School of Engineering, Brown University, Providence, USA
Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
Dustin Carroll
Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
Moss Landing Marine Laboratories, San José State University, Moss Landing, USA
William M. Berelson
Department of Earth Sciences, University of Southern California, Los Angeles, USA
Dimitris Menemenlis
Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
Jack J. Middelburg
Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
Jess F. Adkins
Geological and Planetary Sciences, California Institute of Technology, Pasadena, USA
Related authors
Olivier Sulpis, Siv K. Lauvset, and Mathilde Hagens
Ocean Sci., 16, 847–862, https://doi.org/10.5194/os-16-847-2020, https://doi.org/10.5194/os-16-847-2020, 2020
Short summary
Short summary
As direct measurements of seawater carbonate system variables, such as pH, are difficult to obtain, scientists use equilibrium constants to compute them from known variables. Using a compilation of in situ data, we show that the set of equilibrium constants preferred by the community is not consistent with measurements in cold, polar waters, where human-made ocean acidification is spreading rapidly. Closing knowledge gaps regarding seawater carbon chemistry in polar regions should be a priority.
Yoshihiro Nakayama, Alena Malyarenko, Hong Zhang, Ou Wang, Matthis Auger, Ian Fenty, Matthew Mazloff, Köhl Armin, and Dimitris Menemenlis
EGUsphere, https://doi.org/10.5194/egusphere-2024-727, https://doi.org/10.5194/egusphere-2024-727, 2024
Short summary
Short summary
Global and basin-scale ocean reanalyses are becoming easily accessible. Yet, such ocean reanalyses are optimized for their entire model domains and their ability to simulate the Southern Ocean requires evaluations. We conduct intercomparison analyses of Massachusetts Institute of Technology general circulation model (MITgcm)-based ocean reanalyses. They generally perform well for the open ocean, but open ocean temporal variability and Antarctic continental shelves require improvements.
Matthew P. Humphreys
EGUsphere, https://doi.org/10.5194/egusphere-2024-626, https://doi.org/10.5194/egusphere-2024-626, 2024
Short summary
Short summary
The ocean absorbs carbon dioxide (CO2) from the atmosphere, which slows down climate change. Seawater CO2 absorption is controlled by a property called ƒCO2. This ƒCO2 changes as seawater warms up or cools down, but we haven’t known for sure how much it changes, with different measurements and calculations giving inconsistent results. Here, we work out how ƒCO2 should theoretically respond to temperature change and show that this is consistent with both measurements and calculations.
Milan Y. Patel, Pietro F. Vannucci, Jinsol Kim, William M. Berelson, and Ronald C. Cohen
Atmos. Meas. Tech., 17, 1051–1060, https://doi.org/10.5194/amt-17-1051-2024, https://doi.org/10.5194/amt-17-1051-2024, 2024
Short summary
Short summary
Low-cost particulate matter (PM) sensors are becoming increasingly common in community monitoring and atmospheric research, but these sensors require proper calibration to provide accurate reporting. Here, we propose a hygroscopic growth calibration scheme that evolves in time to account for seasonal changes in hygroscopic growth. In San Francisco and Los Angeles, CA, applying a seasonal hygroscopic growth calibration can account for sensor biases driven by the seasonal cycles in PM composition.
Ellen Margaret Buckley, Leela Cañuelas, Mary-Louise Timmermans, and Monica Martinez Wilhelmus
EGUsphere, https://doi.org/10.5194/egusphere-2024-89, https://doi.org/10.5194/egusphere-2024-89, 2024
Short summary
Short summary
The Arctic sea ice cover seasonally evolves from large plates separated by long, linear leads in the winter to a mosaic of smaller sea ice floes in the summer. Here, we present a new image segmentation algorithm applied to thousands of images and identifying over 9 million individual pieces of ice. We observe the characteristics of the floes and how they evolve throughout the summer as the ice breaks up.
Siv K. Lauvset, Nico Lange, Toste Tanhua, Henry C. Bittig, Are Olsen, Alex Kozyr, Marta Álvarez, Kumiko Azetsu-Scott, Peter J. Brown, Brendan R. Carter, Leticia Cotrim da Cunha, Mario Hoppema, Matthew P. Humphreys, Masao Ishii, Emil Jeansson, Akihiko Murata, Jens Daniel Müller, Fiz F. Perez, Carsten Schirnick, Reiner Steinfeldt, Toru Suzuki, Adam Ulfsbo, Anton Velo, Ryan J. Woosley, and Robert Key
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2023-468, https://doi.org/10.5194/essd-2023-468, 2024
Revised manuscript accepted for ESSD
Short summary
Short summary
GLODAP is a data product for ocean inorganic carbon and related biogeochemical variables measured by the chemical analysis of water bottle samples from scientific cruises. GLODAPv2.2023 is the fifth update of GLODAPv2 from 2016. The data that are included have been subjected to extensive quality controlling, including systematic evaluation of measurement biases. This version contains data from 1108 hydrographic cruises covering the world's oceans from 1972 to 2021.
Katharina Gallmeier, J. Xavier Prochaska, Peter Cornillon, Dimitris Menemenlis, and Madolyn Kelm
Geosci. Model Dev., 16, 7143–7170, https://doi.org/10.5194/gmd-16-7143-2023, https://doi.org/10.5194/gmd-16-7143-2023, 2023
Short summary
Short summary
This paper introduces an approach to evaluate numerical models of ocean circulation. We compare the structure of satellite-derived sea surface temperature anomaly (SSTa) instances determined by a machine learning algorithm at 10–80 km scales to those output by a high-resolution MITgcm run. The simulation over much of the ocean reproduces the observed distribution of SSTa patterns well. This general agreement, alongside a few notable exceptions, highlights the potential of this approach.
Jinsol Kim, John B. Miller, Charles E. Miller, Scott J. Lehman, Sylvia E. Michel, Vineet Yadav, Nick E. Rollins, and William M. Berelson
Atmos. Chem. Phys., 23, 14425–14436, https://doi.org/10.5194/acp-23-14425-2023, https://doi.org/10.5194/acp-23-14425-2023, 2023
Short summary
Short summary
In this study, we present the partitioning of CO2 signals from biogenic, petroleum and natural gas sources by combining CO, 13CO2 and 14CO2 measurements. Using measurements from flask air samples at three sites in the greater Los Angeles region, we find larger and positive contributions of biogenic signals in winter and smaller and negative contributions in summer. The largest contribution of natural gas combustion generally occurs in summer.
Christopher Horvat, Ellen Buckley, Madelyn Stewart, Poom Yoosiri, and Monica M. Wilhelmus
EGUsphere, https://doi.org/10.5194/egusphere-2023-2312, https://doi.org/10.5194/egusphere-2023-2312, 2023
Preprint withdrawn
Short summary
Short summary
The decline of sea ice area variability is a leading indicator of climate change, and accurate measurement of sea ice area are of high importance. We develop new measurement of sea ice area coverage using the ICESat-2 laser altimeter, typically used to measure the height of the ice surface. The new method performs as well or better than typical passive microwave measurements, especially for sea ice populated with thin fractures in winter.
Brendan Byrne, David F. Baker, Sourish Basu, Michael Bertolacci, Kevin W. Bowman, Dustin Carroll, Abhishek Chatterjee, Frédéric Chevallier, Philippe Ciais, Noel Cressie, David Crisp, Sean Crowell, Feng Deng, Zhu Deng, Nicholas M. Deutscher, Manvendra K. Dubey, Sha Feng, Omaira E. García, David W. T. Griffith, Benedikt Herkommer, Lei Hu, Andrew R. Jacobson, Rajesh Janardanan, Sujong Jeong, Matthew S. Johnson, Dylan B. A. Jones, Rigel Kivi, Junjie Liu, Zhiqiang Liu, Shamil Maksyutov, John B. Miller, Scot M. Miller, Isamu Morino, Justus Notholt, Tomohiro Oda, Christopher W. O'Dell, Young-Suk Oh, Hirofumi Ohyama, Prabir K. Patra, Hélène Peiro, Christof Petri, Sajeev Philip, David F. Pollard, Benjamin Poulter, Marine Remaud, Andrew Schuh, Mahesh K. Sha, Kei Shiomi, Kimberly Strong, Colm Sweeney, Yao Té, Hanqin Tian, Voltaire A. Velazco, Mihalis Vrekoussis, Thorsten Warneke, John R. Worden, Debra Wunch, Yuanzhi Yao, Jeongmin Yun, Andrew Zammit-Mangion, and Ning Zeng
Earth Syst. Sci. Data, 15, 963–1004, https://doi.org/10.5194/essd-15-963-2023, https://doi.org/10.5194/essd-15-963-2023, 2023
Short summary
Short summary
Changes in the carbon stocks of terrestrial ecosystems result in emissions and removals of CO2. These can be driven by anthropogenic activities (e.g., deforestation), natural processes (e.g., fires) or in response to rising CO2 (e.g., CO2 fertilization). This paper describes a dataset of CO2 emissions and removals derived from atmospheric CO2 observations. This pilot dataset informs current capabilities and future developments towards top-down monitoring and verification systems.
Siv K. Lauvset, Nico Lange, Toste Tanhua, Henry C. Bittig, Are Olsen, Alex Kozyr, Simone Alin, Marta Álvarez, Kumiko Azetsu-Scott, Leticia Barbero, Susan Becker, Peter J. Brown, Brendan R. Carter, Leticia Cotrim da Cunha, Richard A. Feely, Mario Hoppema, Matthew P. Humphreys, Masao Ishii, Emil Jeansson, Li-Qing Jiang, Steve D. Jones, Claire Lo Monaco, Akihiko Murata, Jens Daniel Müller, Fiz F. Pérez, Benjamin Pfeil, Carsten Schirnick, Reiner Steinfeldt, Toru Suzuki, Bronte Tilbrook, Adam Ulfsbo, Anton Velo, Ryan J. Woosley, and Robert M. Key
Earth Syst. Sci. Data, 14, 5543–5572, https://doi.org/10.5194/essd-14-5543-2022, https://doi.org/10.5194/essd-14-5543-2022, 2022
Short summary
Short summary
GLODAP is a data product for ocean inorganic carbon and related biogeochemical variables measured by the chemical analysis of water bottle samples from scientific cruises. GLODAPv2.2022 is the fourth update of GLODAPv2 from 2016. The data that are included have been subjected to extensive quality controlling, including systematic evaluation of measurement biases. This version contains data from 1085 hydrographic cruises covering the world's oceans from 1972 to 2021.
Hector S. Torres, Patrice Klein, Jinbo Wang, Alexander Wineteer, Bo Qiu, Andrew F. Thompson, Lionel Renault, Ernesto Rodriguez, Dimitris Menemenlis, Andrea Molod, Christopher N. Hill, Ehud Strobach, Hong Zhang, Mar Flexas, and Dragana Perkovic-Martin
Geosci. Model Dev., 15, 8041–8058, https://doi.org/10.5194/gmd-15-8041-2022, https://doi.org/10.5194/gmd-15-8041-2022, 2022
Short summary
Short summary
Wind work at the air-sea interface is the scalar product of winds and currents and is the transfer of kinetic energy between the ocean and the atmosphere. Using a new global coupled ocean-atmosphere simulation performed at kilometer resolution, we show that all scales of winds and currents impact the ocean dynamics at spatial and temporal scales. The consequential interplay of surface winds and currents in the numerical simulation motivates the need for a winds and currents satellite mission.
Matthew P. Humphreys, Erik H. Meesters, Henk de Haas, Szabina Karancz, Louise Delaigue, Karel Bakker, Gerard Duineveld, Siham de Goeyse, Andreas F. Haas, Furu Mienis, Sharyn Ossebaar, and Fleur C. van Duyl
Biogeosciences, 19, 347–358, https://doi.org/10.5194/bg-19-347-2022, https://doi.org/10.5194/bg-19-347-2022, 2022
Short summary
Short summary
A series of submarine sinkholes were recently discovered on Luymes Bank, part of Saba Bank, a carbonate platform in the Caribbean Netherlands. Here, we investigate the waters inside these sinkholes for the first time. One of the sinkholes contained a body of dense, low-oxygen and low-pH water, which we call the
acid lake. We use measurements of seawater chemistry to work out what processes were responsible for forming the acid lake and discuss the consequences for the carbonate platform.
Matthew P. Humphreys, Ernie R. Lewis, Jonathan D. Sharp, and Denis Pierrot
Geosci. Model Dev., 15, 15–43, https://doi.org/10.5194/gmd-15-15-2022, https://doi.org/10.5194/gmd-15-15-2022, 2022
Short summary
Short summary
The ocean helps to mitigate our impact on Earth's climate by absorbing about a quarter of the carbon dioxide (CO2) released by human activities each year. However, once absorbed, chemical reactions between CO2 and water reduce seawater pH (
ocean acidification), which may have adverse effects on marine ecosystems. Our Python package, PyCO2SYS, models the chemical reactions of CO2 in seawater, allowing us to quantify the corresponding changes in pH and related chemical properties.
Gerrit Müller, Jack J. Middelburg, and Appy Sluijs
Earth Syst. Sci. Data, 13, 3565–3575, https://doi.org/10.5194/essd-13-3565-2021, https://doi.org/10.5194/essd-13-3565-2021, 2021
Short summary
Short summary
Rivers are major freshwater resources, connectors and transporters on Earth. As the composition of river waters and particles results from processes in their catchment, such as erosion, weathering, environmental pollution, nutrient and carbon cycling, Earth-spanning databases of river composition are needed for studies of these processes on a global scale. While extensive resources on water and nutrient composition exist, we provide a database of river particle composition.
Luca Possenti, Ingunn Skjelvan, Dariia Atamanchuk, Anders Tengberg, Matthew P. Humphreys, Socratis Loucaides, Liam Fernand, and Jan Kaiser
Ocean Sci., 17, 593–614, https://doi.org/10.5194/os-17-593-2021, https://doi.org/10.5194/os-17-593-2021, 2021
Short summary
Short summary
A Seaglider was deployed for 8 months in the Norwegian Sea mounting an oxygen and, for the first time, a CO2 optode and a chlorophyll fluorescence sensor. The oxygen and CO2 data were used to assess the spatial and temporal variability and calculate the net community production, N(O2) and N(CT). The dataset was used to calculate net community production from inventory changes, air–sea flux, diapycnal mixing and entrainment.
Yang Feng, Dimitris Menemenlis, Huijie Xue, Hong Zhang, Dustin Carroll, Yan Du, and Hui Wu
Geosci. Model Dev., 14, 1801–1819, https://doi.org/10.5194/gmd-14-1801-2021, https://doi.org/10.5194/gmd-14-1801-2021, 2021
Short summary
Short summary
Simulation of coastal plume regions was improved in global ECCOv4 with a series of sensitivity tests. We find modeled SSS is closer to SMAP when using daily point-source runoff as well as increasing the resolution from coarse to intermediate. The plume characteristics, freshwater transport, and critical water properties are modified greatly. But this may not happen with a further increase to high resolution. The study will advance the seamless modeling of land–ocean–atmosphere feedback in ESMs.
Junjie Liu, Latha Baskaran, Kevin Bowman, David Schimel, A. Anthony Bloom, Nicholas C. Parazoo, Tomohiro Oda, Dustin Carroll, Dimitris Menemenlis, Joanna Joiner, Roisin Commane, Bruce Daube, Lucianna V. Gatti, Kathryn McKain, John Miller, Britton B. Stephens, Colm Sweeney, and Steven Wofsy
Earth Syst. Sci. Data, 13, 299–330, https://doi.org/10.5194/essd-13-299-2021, https://doi.org/10.5194/essd-13-299-2021, 2021
Short summary
Short summary
On average, the terrestrial biosphere carbon sink is equivalent to ~ 20 % of fossil fuel emissions. Understanding where and why the terrestrial biosphere absorbs carbon from the atmosphere is pivotal to any mitigation policy. Here we present a regionally resolved satellite-constrained net biosphere exchange (NBE) dataset with corresponding uncertainties between 2010–2018: CMS-Flux NBE 2020. The dataset provides a unique perspective on monitoring regional contributions to the CO2 growth rate.
Liang Yu, Joachim C. Rozemeijer, Hans Peter Broers, Boris M. van Breukelen, Jack J. Middelburg, Maarten Ouboter, and Ype van der Velde
Hydrol. Earth Syst. Sci., 25, 69–87, https://doi.org/10.5194/hess-25-69-2021, https://doi.org/10.5194/hess-25-69-2021, 2021
Short summary
Short summary
The assessment of the collected water quality information is for the managers to find a way to improve the water environment to satisfy human uses and environmental needs. We found groundwater containing high concentrations of nutrient mixes with rain water in the ditches. The stable solutes are diluted during rain. The change in nutrients over time is determined by and uptaken by organisms and chemical processes. The water is more enriched with nutrients and looked
dirtierduring winter.
Anne Roepert, Lubos Polerecky, Esmee Geerken, Gert-Jan Reichart, and Jack J. Middelburg
Biogeosciences, 17, 4727–4743, https://doi.org/10.5194/bg-17-4727-2020, https://doi.org/10.5194/bg-17-4727-2020, 2020
Short summary
Short summary
We investigated, for the first time, the spatial distribution of chlorine and fluorine in the shell walls of four benthic foraminifera species: Ammonia tepida, Amphistegina lessonii, Archaias angulatus, and Sorites marginalis. Cross sections of specimens were imaged using nanoSIMS. The distribution of Cl and F was co-located with organics in the rotaliids and rather homogeneously distributed in miliolids. We suggest that the incorporation is governed by the biomineralization pathway.
Olivier Sulpis, Siv K. Lauvset, and Mathilde Hagens
Ocean Sci., 16, 847–862, https://doi.org/10.5194/os-16-847-2020, https://doi.org/10.5194/os-16-847-2020, 2020
Short summary
Short summary
As direct measurements of seawater carbonate system variables, such as pH, are difficult to obtain, scientists use equilibrium constants to compute them from known variables. Using a compilation of in situ data, we show that the set of equilibrium constants preferred by the community is not consistent with measurements in cold, polar waters, where human-made ocean acidification is spreading rapidly. Closing knowledge gaps regarding seawater carbon chemistry in polar regions should be a priority.
Jingjing Guo, Miriam Glendell, Jeroen Meersmans, Frédérique Kirkels, Jack J. Middelburg, and Francien Peterse
Biogeosciences, 17, 3183–3201, https://doi.org/10.5194/bg-17-3183-2020, https://doi.org/10.5194/bg-17-3183-2020, 2020
Short summary
Short summary
The fluxes of soil organic carbon (OC) transport from land to sea are poorly constrained, mostly due to the lack of a specific tracer for soil OC. Here we evaluate the use of specific molecules derived from soil bacteria as a tracer for soil OC in a small river catchment. We find that the initial soil signal is lost upon entering the aquatic environment. However, the local environmental history of the catchment is reflected by these molecules in the lake sediments that act as their sink.
Hannah K. Donald, Gavin L. Foster, Nico Fröhberg, George E. A. Swann, Alex J. Poulton, C. Mark Moore, and Matthew P. Humphreys
Biogeosciences, 17, 2825–2837, https://doi.org/10.5194/bg-17-2825-2020, https://doi.org/10.5194/bg-17-2825-2020, 2020
Short summary
Short summary
The boron isotope pH proxy is increasingly being used to reconstruct ocean pH in the past. Here we detail a novel analytical methodology for measuring the boron isotopic composition (δ11B) of diatom opal and apply this to the study of the diatom Thalassiosira weissflogii grown in culture over a range of pH. To our knowledge this is the first study of its kind and provides unique insights into the way in which diatoms incorporate boron and their potential as archives of palaeoclimate records.
Nathaniel Kemnitz, William M. Berelson, Douglas E. Hammond, Laura Morine, Maria Figueroa, Timothy W. Lyons, Simon Scharf, Nick Rollins, Elizabeth Petsios, Sydnie Lemieux, and Tina Treude
Biogeosciences, 17, 2381–2396, https://doi.org/10.5194/bg-17-2381-2020, https://doi.org/10.5194/bg-17-2381-2020, 2020
Short summary
Short summary
Our paper shows how sedimentation in a very low oxygen setting provides a unique record of environmental change. We look at the past 250 years through the filter of sediment accumulation via radioisotope dating and other physical and chemical analyses of these sediments. We conclude, remarkably, that there has been very little change in net sediment mass accumulation through the past 100–150 years, yet just prior to 1900 CE, sediments were accumulating at 50 %–70 % of today's rate.
Mark J. Hopwood, Dustin Carroll, Thorben Dunse, Andy Hodson, Johnna M. Holding, José L. Iriarte, Sofia Ribeiro, Eric P. Achterberg, Carolina Cantoni, Daniel F. Carlson, Melissa Chierici, Jennifer S. Clarke, Stefano Cozzi, Agneta Fransson, Thomas Juul-Pedersen, Mie H. S. Winding, and Lorenz Meire
The Cryosphere, 14, 1347–1383, https://doi.org/10.5194/tc-14-1347-2020, https://doi.org/10.5194/tc-14-1347-2020, 2020
Short summary
Short summary
Here we compare and contrast results from five well-studied Arctic field sites in order to understand how glaciers affect marine biogeochemistry and marine primary production. The key questions are listed as follows. Where and when does glacial freshwater discharge promote or reduce marine primary production? How does spatio-temporal variability in glacial discharge affect marine primary production? And how far-reaching are the effects of glacial discharge on marine biogeochemistry?
Robyn E. Tuerena, Raja S. Ganeshram, Matthew P. Humphreys, Thomas J. Browning, Heather Bouman, and Alexander P. Piotrowski
Biogeosciences, 16, 3621–3635, https://doi.org/10.5194/bg-16-3621-2019, https://doi.org/10.5194/bg-16-3621-2019, 2019
Short summary
Short summary
The carbon isotopes in algae can be used to predict food sources and environmental change. We explore how dissolved carbon is taken up by algae in the South Atlantic Ocean and how this affects their carbon isotope signature. We find that cell size controls isotope fractionation. We use our results to investigate how climate change may impact the carbon isotopes in algae. We suggest a shift to smaller algae in this region would decrease the carbon isotope ratio at the base of the food web.
Wim Joost van Hoek, Lauriane Vilmin, Arthur H. W. Beusen, José M. Mogollón, Xiaochen Liu, Joep J. Langeveld, Alexander F. Bouwman, and Jack J. Middelburg
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2019-205, https://doi.org/10.5194/gmd-2019-205, 2019
Revised manuscript not accepted
Short summary
Short summary
In this study we present CARBON-DISC 1.0. It couples the global water balance model PCR-GLOBWB with global carbon inputs from the Integrated Model to Assess the Global Environment (IMAGE) at a 0.5° resolution and calculates gridcell-to-gridcell transport, C transformations, C emissions, C burial and primary production on a monthly timestep and without calibration.
Yingxu Wu, Mathis P. Hain, Matthew P. Humphreys, Sue Hartman, and Toby Tyrrell
Biogeosciences, 16, 2661–2681, https://doi.org/10.5194/bg-16-2661-2019, https://doi.org/10.5194/bg-16-2661-2019, 2019
Short summary
Short summary
This study takes advantage of the GLODAPv2 database to investigate the processes driving the surface ocean dissolved inorganic carbon distribution, with the focus on its latitudinal gradient between the polar oceans and the low-latitude oceans. Based on our quantitative study, we find that temperature-driven CO2 gas exchange and high-latitude upwelling of DIC- and TA-rich deep waters are the two major drivers, with the importance of the latter not having been previously realized.
Joep Langeveld, Alexander F. Bouwman, Wim Joost van Hoek, Lauriane Vilmin, Arthur H. W. Beusen, José M. Mogollón, and Jack J. Middelburg
Biogeosciences Discuss., https://doi.org/10.5194/bg-2019-238, https://doi.org/10.5194/bg-2019-238, 2019
Preprint withdrawn
Short summary
Short summary
We compiled a global database on annual average dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) in soil solutions. We use this database to construct the first global models and maps on DOC in soil pore water. Highest concentrations in shallow soils occur in forests of cooler, humid zones. Highest concentrations in deeper soils are calculated for Histosols. Our research enables a spatially explicit first estimation of dissolved carbon in soil solution on the global scale.
Nicole M. J. Geerlings, Eva-Maria Zetsche, Silvia Hidalgo-Martinez, Jack J. Middelburg, and Filip J. R. Meysman
Biogeosciences, 16, 811–829, https://doi.org/10.5194/bg-16-811-2019, https://doi.org/10.5194/bg-16-811-2019, 2019
Short summary
Short summary
Multicellular cable bacteria form long filaments that can reach lengths of several centimeters. They affect the chemistry and mineralogy of their surroundings and vice versa. How the surroundings affect the cable bacteria is investigated. They show three different types of biomineral formation: (1) a polymer containing phosphorus in their cells, (2) a sheath of clay surrounding the surface of the filament and (3) the encrustation of a filament via a solid phase containing iron and phosphorus.
Ilja J. Kocken, Margot J. Cramwinckel, Richard E. Zeebe, Jack J. Middelburg, and Appy Sluijs
Clim. Past, 15, 91–104, https://doi.org/10.5194/cp-15-91-2019, https://doi.org/10.5194/cp-15-91-2019, 2019
Short summary
Short summary
Marine organic carbon burial could link the 405 thousand year eccentricity cycle in the long-term carbon cycle to that observed in climate records. Here, we simulate the response of the carbon cycle to astronomical forcing. We find a strong 2.4 million year cycle in the model output, which is present as an amplitude modulator of the 405 and 100 thousand year eccentricity cycles in a newly assembled composite record.
Jack J. Middelburg
Biogeosciences, 15, 413–427, https://doi.org/10.5194/bg-15-413-2018, https://doi.org/10.5194/bg-15-413-2018, 2018
Short summary
Short summary
Organic carbon processing at the seafloor is studied by geologists to better understand the sedimentary record, by biogeochemists to quantify burial and respiration, by organic geochemists to elucidate compositional changes, and by ecologists to follow carbon transfers within food webs. These disciplinary approaches have their strengths and weaknesses. This award talk provides a synthesis, highlights the role of animals in sediment carbon processing and presents some new concepts.
Joost Frieling, Gert-Jan Reichart, Jack J. Middelburg, Ursula Röhl, Thomas Westerhold, Steven M. Bohaty, and Appy Sluijs
Clim. Past, 14, 39–55, https://doi.org/10.5194/cp-14-39-2018, https://doi.org/10.5194/cp-14-39-2018, 2018
Short summary
Short summary
Past periods of rapid global warming such as the Paleocene–Eocene Thermal Maximum are used to study biotic response to climate change. We show that very high peak PETM temperatures in the tropical Atlantic (~ 37 ºC) caused heat stress in several marine plankton groups. However, only slightly cooler temperatures afterwards allowed highly diverse plankton communities to bloom. This shows that tropical plankton communities may be susceptible to extreme warming, but may also recover rapidly.
Meike Becker, Nils Andersen, Helmut Erlenkeuser, Matthew P. Humphreys, Toste Tanhua, and Arne Körtzinger
Earth Syst. Sci. Data, 8, 559–570, https://doi.org/10.5194/essd-8-559-2016, https://doi.org/10.5194/essd-8-559-2016, 2016
Short summary
Short summary
The stable carbon isotope composition of dissolved inorganic carbon (δ13C-DIC) can be used to quantify fluxes within the marine carbon system such as the exchange between ocean and atmosphere or the amount of anthropogenic carbon in the water column. In this study, an internally consistent δ13C-DIC dataset for the North Atlantic is presented. The data have undergone a secondary quality control during which systematic biases between the respective cruises have been quantified and adjusted.
Dick van Oevelen, Christina E. Mueller, Tomas Lundälv, and Jack J. Middelburg
Biogeosciences, 13, 5789–5798, https://doi.org/10.5194/bg-13-5789-2016, https://doi.org/10.5194/bg-13-5789-2016, 2016
Short summary
Short summary
Cold-water corals form true hotspots of biodiversity in the cold and dark deep sea, but need to live off of only small amounts of food that reach the deep sea. Using chemical tracers, this study investigated whether cold-water corals are picky eaters. We found that under low food conditions, they do not differentiate between food sources but they do differentiate at high food concentrations. This adaptation suggests that they are well adapted to exploit short food pulses efficiently.
Dorothee C. E. Bakker, Benjamin Pfeil, Camilla S. Landa, Nicolas Metzl, Kevin M. O'Brien, Are Olsen, Karl Smith, Cathy Cosca, Sumiko Harasawa, Stephen D. Jones, Shin-ichiro Nakaoka, Yukihiro Nojiri, Ute Schuster, Tobias Steinhoff, Colm Sweeney, Taro Takahashi, Bronte Tilbrook, Chisato Wada, Rik Wanninkhof, Simone R. Alin, Carlos F. Balestrini, Leticia Barbero, Nicholas R. Bates, Alejandro A. Bianchi, Frédéric Bonou, Jacqueline Boutin, Yann Bozec, Eugene F. Burger, Wei-Jun Cai, Robert D. Castle, Liqi Chen, Melissa Chierici, Kim Currie, Wiley Evans, Charles Featherstone, Richard A. Feely, Agneta Fransson, Catherine Goyet, Naomi Greenwood, Luke Gregor, Steven Hankin, Nick J. Hardman-Mountford, Jérôme Harlay, Judith Hauck, Mario Hoppema, Matthew P. Humphreys, Christopher W. Hunt, Betty Huss, J. Severino P. Ibánhez, Truls Johannessen, Ralph Keeling, Vassilis Kitidis, Arne Körtzinger, Alex Kozyr, Evangelia Krasakopoulou, Akira Kuwata, Peter Landschützer, Siv K. Lauvset, Nathalie Lefèvre, Claire Lo Monaco, Ansley Manke, Jeremy T. Mathis, Liliane Merlivat, Frank J. Millero, Pedro M. S. Monteiro, David R. Munro, Akihiko Murata, Timothy Newberger, Abdirahman M. Omar, Tsuneo Ono, Kristina Paterson, David Pearce, Denis Pierrot, Lisa L. Robbins, Shu Saito, Joe Salisbury, Reiner Schlitzer, Bernd Schneider, Roland Schweitzer, Rainer Sieger, Ingunn Skjelvan, Kevin F. Sullivan, Stewart C. Sutherland, Adrienne J. Sutton, Kazuaki Tadokoro, Maciej Telszewski, Matthias Tuma, Steven M. A. C. van Heuven, Doug Vandemark, Brian Ward, Andrew J. Watson, and Suqing Xu
Earth Syst. Sci. Data, 8, 383–413, https://doi.org/10.5194/essd-8-383-2016, https://doi.org/10.5194/essd-8-383-2016, 2016
Short summary
Short summary
Version 3 of the Surface Ocean CO2 Atlas (www.socat.info) has 14.5 million CO2 (carbon dioxide) values for the years 1957 to 2014 covering the global oceans and coastal seas. Version 3 is an update to version 2 with a longer record and 44 % more CO2 values. The CO2 measurements have been made on ships, fixed moorings and drifting buoys. SOCAT enables quantification of the ocean carbon sink and ocean acidification, as well as model evaluation, thus informing climate negotiations.
Clare Woulds, Steven Bouillon, Gregory L. Cowie, Emily Drake, Jack J. Middelburg, and Ursula Witte
Biogeosciences, 13, 4343–4357, https://doi.org/10.5194/bg-13-4343-2016, https://doi.org/10.5194/bg-13-4343-2016, 2016
Short summary
Short summary
Estuarine sediments are important locations for carbon cycling and burial. We used tracer experiments to investigate how site conditions affect the way in which seafloor biological communities cycle carbon. We showed that while total respiration rates are primarily determined by temperature, total carbon processing by the biological community is strongly related to
its biomass. Further, we saw a distinct pattern of carbon cycling in sandy sediment, in which uptake by bacteria dominates.
Matthew P. Humphreys, Florence M. Greatrix, Eithne Tynan, Eric P. Achterberg, Alex M. Griffiths, Claudia H. Fry, Rebecca Garley, Alison McDonald, and Adrian J. Boyce
Earth Syst. Sci. Data, 8, 221–233, https://doi.org/10.5194/essd-8-221-2016, https://doi.org/10.5194/essd-8-221-2016, 2016
Short summary
Short summary
This paper reports the stable isotope composition of dissolved inorganic carbon in seawater for a transect from west to east across the North Atlantic Ocean. The results can be used to study oceanic uptake of anthropogenic carbon dioxide, and also to investigate the natural biological carbon pump. We also provide stable DIC isotope results for two batches of Dickson seawater CRMs to enable intercomparisons with other studies.
Arthur H. W. Beusen, Alexander F. Bouwman, Ludovicus P. H. Van Beek, José M. Mogollón, and Jack J. Middelburg
Biogeosciences, 13, 2441–2451, https://doi.org/10.5194/bg-13-2441-2016, https://doi.org/10.5194/bg-13-2441-2016, 2016
Short summary
Short summary
Intensifying anthropogenic activity over the 20th century including agriculture, water consumption, urbanization, and aquaculture has almost doubled the global nitrogen (N) and phosphorus (P) delivery to streams and steadily increased the N : P ratio in freshwater bodies. Concurrently, the cumulative number of reservoirs has driven a rise in freshwater nutrient retention and removal. Still, river nutrient transport to the ocean has also nearly doubled, potentially stressing coastal environments.
A. H. W. Beusen, L. P. H. Van Beek, A. F. Bouwman, J. M. Mogollón, and J. J. Middelburg
Geosci. Model Dev., 8, 4045–4067, https://doi.org/10.5194/gmd-8-4045-2015, https://doi.org/10.5194/gmd-8-4045-2015, 2015
Short summary
Short summary
The IMAGE-Global Nutrient Model (GNM) is used to study the impact of multiple environmental changes on N and P delivery to surface water and transport and in-stream retention in rivers, lakes, wetlands and reservoirs over prolonged time periods. N and P are delivered to water bodies via diffuse sources (agriculture and natural ecosystems) and wastewater. N and P retention in a water body is calculated on the basis of the residence time of the water and nutrient uptake velocity.
M. P. Humphreys, E. P. Achterberg, A. M. Griffiths, A. McDonald, and A. J. Boyce
Earth Syst. Sci. Data, 7, 127–135, https://doi.org/10.5194/essd-7-127-2015, https://doi.org/10.5194/essd-7-127-2015, 2015
Short summary
Short summary
We present measurements of the stable carbon isotope composition of seawater dissolved inorganic carbon. The samples were collected during two research cruises in boreal summer 2012 in the northeastern Atlantic and Nordic Seas. The results can be used to investigate the marine carbon cycle, providing information about biological productivity and oceanic uptake of anthropogenic carbon dioxide.
M. Hagens, C. P. Slomp, F. J. R. Meysman, D. Seitaj, J. Harlay, A. V. Borges, and J. J. Middelburg
Biogeosciences, 12, 1561–1583, https://doi.org/10.5194/bg-12-1561-2015, https://doi.org/10.5194/bg-12-1561-2015, 2015
Short summary
Short summary
This study looks at the combined impacts of hypoxia and acidification, two major environmental stressors affecting coastal systems, in a seasonally stratified basin. Here, the surface water experiences less seasonality in pH than the bottom water despite higher process rates. This is due to a substantial reduction in the acid-base buffering capacity of the bottom water as it turns hypoxic in summer. This highlights the crucial role of the buffering capacity as a modulating factor in pH dynamics.
A. de Kluijver, P. L. Schoon, J. A. Downing, S. Schouten, and J. J. Middelburg
Biogeosciences, 11, 6265–6276, https://doi.org/10.5194/bg-11-6265-2014, https://doi.org/10.5194/bg-11-6265-2014, 2014
J. J. Middelburg
Biogeosciences, 11, 2357–2371, https://doi.org/10.5194/bg-11-2357-2014, https://doi.org/10.5194/bg-11-2357-2014, 2014
C. E. Mueller, A. I. Larsson, B. Veuger, J. J. Middelburg, and D. van Oevelen
Biogeosciences, 11, 123–133, https://doi.org/10.5194/bg-11-123-2014, https://doi.org/10.5194/bg-11-123-2014, 2014
L. Pozzato, D. Van Oevelen, L. Moodley, K. Soetaert, and J. J. Middelburg
Biogeosciences, 10, 6879–6891, https://doi.org/10.5194/bg-10-6879-2013, https://doi.org/10.5194/bg-10-6879-2013, 2013
B. Veuger, A. Pitcher, S. Schouten, J. S. Sinninghe Damsté, and J. J. Middelburg
Biogeosciences, 10, 1775–1785, https://doi.org/10.5194/bg-10-1775-2013, https://doi.org/10.5194/bg-10-1775-2013, 2013
A. de Kluijver, K. Soetaert, J. Czerny, K. G. Schulz, T. Boxhammer, U. Riebesell, and J. J. Middelburg
Biogeosciences, 10, 1425–1440, https://doi.org/10.5194/bg-10-1425-2013, https://doi.org/10.5194/bg-10-1425-2013, 2013
K. A. Koho, K. G. J. Nierop, L. Moodley, J. J. Middelburg, L. Pozzato, K. Soetaert, J. van der Plicht, and G-J. Reichart
Biogeosciences, 10, 1131–1141, https://doi.org/10.5194/bg-10-1131-2013, https://doi.org/10.5194/bg-10-1131-2013, 2013
A. F. Bouwman, M. F. P. Bierkens, J. Griffioen, M. M. Hefting, J. J. Middelburg, H. Middelkoop, and C. P. Slomp
Biogeosciences, 10, 1–22, https://doi.org/10.5194/bg-10-1-2013, https://doi.org/10.5194/bg-10-1-2013, 2013
Related subject area
Oceanography
Implementation of additional spectral wave field exchanges in a three-dimensional wave–current coupled WAVEWATCH-III (version 6.07) and CROCO (version 1.2) configuration: assessment of their implications for macro-tidal coastal hydrodynamics
Comparison of 4-dimensional variational and ensemble optimal interpolation data assimilation systems using a Regional Ocean Modeling System (v3.4) configuration of the eddy-dominated East Australian Current system
LOCATE v1.0: numerical modelling of floating marine debris dispersion in coastal regions using Parcels v2.4.2
New insights into the South China Sea throughflow and water budget seasonal cycle: evaluation and analysis of a high-resolution configuration of the ocean model SYMPHONIE version 2.4
MQGeometry-1.0: a multi-layer quasi-geostrophic solver on non-rectangular geometries
Parameter estimation for ocean background vertical diffusivity coefficients in the Community Earth System Model (v1.2.1) and its impact on El Niño–Southern Oscillation forecasts
Great Lakes wave forecast system on high-resolution unstructured meshes
Impact of increased resolution on Arctic Ocean simulations in Ocean Model Intercomparison Project phase 2 (OMIP-2)
StraitFlux – Precise computations of Water Strait fluxes on various Modelling Grids
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)
CAR36, a regional high-resolution ocean forecasting system for improving drift and beaching of Sargassum in the Caribbean Archipelago
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
Comparison of the Coastal and Regional Ocean Community Model (CROCO) and NCAR-LES in Non-hydrostatic Simulations
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
DELWAVE 1.0: Deep-learning surrogate model of surface wave climate in the Adriatic Basin
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)
Intercomparisons of five ocean particle tracking software packages
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
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
A nonhydrostatic oceanic regional model, ORCTM v1, for internal solitary wave simulation
How does 4DVar data assimilation affect the vertical representation of mesoscale eddies? A case study with observing system simulation experiments (OSSEs) using ROMS v3.9
An ensemble Kalman filter-based ocean data assimilation system improved by adaptive observation error inflation (AOEI)
GULF18, a high-resolution NEMO-based tidal ocean model of the Arabian/Persian Gulf
The Baltic Sea Model Intercomparison Project (BMIP) – a platform for model development, evaluation, and uncertainty assessment
An ensemble Kalman filter system with the Stony Brook Parallel Ocean Model v1.0
Gaetano Porcile, Anne-Claire Bennis, Martial Boutet, Sophie Le Bot, Franck Dumas, and Swen Jullien
Geosci. Model Dev., 17, 2829–2853, https://doi.org/10.5194/gmd-17-2829-2024, https://doi.org/10.5194/gmd-17-2829-2024, 2024
Short summary
Short summary
Here a new method of modelling the interaction between ocean currents and waves is presented. We developed an advanced coupling of two models, one for ocean currents and one for waves. In previous couplings, some wave-related calculations were based on simplified assumptions. Our method uses more complex calculations to better represent wave–current interactions. We tested it in a macro-tidal coastal area and found that it significantly improves the model accuracy, especially during storms.
Colette Gabrielle Kerry, Moninya Roughan, Shane Keating, David Gwyther, Gary Brassington, Adil Siripatana, and Joao Marcos A. C. Souza
Geosci. Model Dev., 17, 2359–2386, https://doi.org/10.5194/gmd-17-2359-2024, https://doi.org/10.5194/gmd-17-2359-2024, 2024
Short summary
Short summary
Ocean forecasting relies on the combination of numerical models and ocean observations through data assimilation (DA). Here we assess the performance of two DA systems in a dynamic western boundary current, the East Australian Current, across a common modelling and observational framework. We show that the more advanced, time-dependent method outperforms the time-independent method for forecast horizons of 5 d. This advocates the use of advanced methods for highly variable oceanic regions.
Ivan Hernandez, Leidy M. Castro-Rosero, Manuel Espino, and Jose M. Alsina Torrent
Geosci. Model Dev., 17, 2221–2245, https://doi.org/10.5194/gmd-17-2221-2024, https://doi.org/10.5194/gmd-17-2221-2024, 2024
Short summary
Short summary
The LOCATE numerical model was developed to conduct Lagrangian simulations of the transport and dispersion of marine debris at coastal scales. High-resolution hydrodynamic data and a beaching module that used particle distance to the shore for land–water boundary detection were used on a realistic debris discharge scenario comparing hydrodynamic data at various resolutions. Coastal processes and complex geometric structures were resolved when using nested grids and distance-to-shore beaching.
Ngoc B. Trinh, Marine Herrmann, Caroline Ulses, Patrick Marsaleix, Thomas Duhaut, Thai To Duy, Claude Estournel, and R. Kipp Shearman
Geosci. Model Dev., 17, 1831–1867, https://doi.org/10.5194/gmd-17-1831-2024, https://doi.org/10.5194/gmd-17-1831-2024, 2024
Short summary
Short summary
A high-resolution model was built to study the South China Sea (SCS) water, heat, and salt budgets. Model performance is demonstrated by comparison with observations and simulations. Important discards are observed if calculating offline, instead of online, lateral inflows and outflows of water, heat, and salt. The SCS mainly receives water from the Luzon Strait and releases it through the Mindoro, Taiwan, and Karimata straits. SCS surface interocean water exchanges are driven by monsoon winds.
Louis Thiry, Long Li, Guillaume Roullet, and Etienne Mémin
Geosci. Model Dev., 17, 1749–1764, https://doi.org/10.5194/gmd-17-1749-2024, https://doi.org/10.5194/gmd-17-1749-2024, 2024
Short summary
Short summary
We present a new way of solving the quasi-geostrophic (QG) equations, a simple set of equations describing ocean dynamics. Our method is solely based on the numerical methods used to solve the equations and requires no parameter tuning. Moreover, it can handle non-rectangular geometries, opening the way to study QG equations on realistic domains. We release a PyTorch implementation to ease future machine-learning developments on top of the presented method.
Zheqi Shen, Yihao Chen, Xiaojing Li, and Xunshu Song
Geosci. Model Dev., 17, 1651–1665, https://doi.org/10.5194/gmd-17-1651-2024, https://doi.org/10.5194/gmd-17-1651-2024, 2024
Short summary
Short summary
Parameter estimation is the process that optimizes model parameters using observations, which could reduce model errors and improve forecasting. In this study, we conducted parameter estimation experiments using the CESM and the ensemble adjustment Kalman filter. The obtained initial conditions and parameters are used to perform ensemble forecast experiments for ENSO forecasting. The results revealed that parameter estimation could reduce analysis errors and improve ENSO forecast skills.
Ali Abdolali, Saeideh Banihashemi, Jose Henrique Alves, Aron Roland, Tyler J. Hesser, Mary Anderson Bryant, and Jane McKee Smith
Geosci. Model Dev., 17, 1023–1039, https://doi.org/10.5194/gmd-17-1023-2024, https://doi.org/10.5194/gmd-17-1023-2024, 2024
Short summary
Short summary
This article presents an overview of the development and implementation of Great Lake Wave Unstructured (GLWUv2.0), including the core model and workflow design and development. The validation was conducted against in situ data for the re-forecasted duration for summer and wintertime (ice season). The article describes the limitations and challenges encountered in the operational environment and the path forward for the next generation of wave forecast systems in enclosed basins like the GL.
Qiang Wang, Qi Shu, Alexandra Bozec, Eric P. Chassignet, Pier Giuseppe Fogli, Baylor Fox-Kemper, Andy McC. Hogg, Doroteaciro Iovino, Andrew E. Kiss, Nikolay Koldunov, Julien Le Sommer, Yiwen Li, Pengfei Lin, Hailong Liu, Igor Polyakov, Patrick Scholz, Dmitry Sidorenko, Shizhu Wang, and Xiaobiao Xu
Geosci. Model Dev., 17, 347–379, https://doi.org/10.5194/gmd-17-347-2024, https://doi.org/10.5194/gmd-17-347-2024, 2024
Short summary
Short summary
Increasing resolution improves model skills in simulating the Arctic Ocean, but other factors such as parameterizations and numerics are at least of the same importance for obtaining reliable simulations.
Susanna Winkelbauer, Michael Mayer, and Leopold Haimberger
EGUsphere, https://doi.org/10.5194/egusphere-2023-2883, https://doi.org/10.5194/egusphere-2023-2883, 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 is complicated by the distortion of the used modelling grids and the large number of different grid-types. We present two new methods that allow to calculate oceanic fluxes of volume, heat, salinity and ice through almost arbitrary sections for various models and reanalyses, independent of the used modelling grids.
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.
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. Discuss., https://doi.org/10.5194/gmd-2023-183, https://doi.org/10.5194/gmd-2023-183, 2023
Revised manuscript accepted for GMD
Short summary
Short summary
In order to improve the 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 were found to be quite realistic.
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.
Xiaoyu Fan, Baylor Fox-Kemper, Nobuhiro Suzuki, Qing Li, Patrick Marchesiello, Francis Auclair, Peter P. Sullivan, and Paul S. Hall
EGUsphere, https://doi.org/10.5194/egusphere-2023-1657, https://doi.org/10.5194/egusphere-2023-1657, 2023
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 similarly accurate, but CROCO’s additional features (e.g., nesting and realism) and its compressible turbulence formulation carry additional costs.
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.
Peter Mlakar, Antonio Ricchi, Sandro Carniel, Davide Bonaldo, and Matjaž Ličer
EGUsphere, https://doi.org/10.5194/egusphere-2023-718, https://doi.org/10.5194/egusphere-2023-718, 2023
Short summary
Short summary
We propose a new point-prediction DEep Learning WAVe Emulating model (DELWAVE) which successfully emulates the ocean wave 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 modeling is substantially weaker than the climate change signal.
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.
Jilian Xiong and Parker MacCready
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2023-45, https://doi.org/10.5194/gmd-2023-45, 2023
Revised manuscript accepted for GMD
Short summary
Short summary
A new offline particle tracking model, Tracker, was introduced to work with the Regional Ocean Modeling System (ROMS). Its performance was compared with four other particle tracking models and passive dye, which span a representative range of tracking algorithms. All tracking models perform similarly, especially for the first day. The comparison of multiple tracking codes in the same circulation model establishes confidence in all, and allows comparison of performance and ease of use.
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.
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.
Hao Huang, Pengyang Song, Shi Qiu, Jiaqi Guo, and Xueen Chen
Geosci. Model Dev., 16, 109–133, https://doi.org/10.5194/gmd-16-109-2023, https://doi.org/10.5194/gmd-16-109-2023, 2023
Short summary
Short summary
The Oceanic Regional Circulation and Tide Model (ORCTM) is developed to reproduce internal solitary wave dynamics. The three-dimensional nonlinear momentum equations are involved with the nonhydrostatic pressure obtained via solving the Poisson equation. The validation experimental results agree with the internal wave theories and observations, demonstrating that the ORCTM can successfully describe the life cycle of nonlinear internal solitary waves under different oceanic environments.
David E. Gwyther, Shane R. Keating, Colette Kerry, and Moninya Roughan
Geosci. Model Dev., 16, 157–178, https://doi.org/10.5194/gmd-16-157-2023, https://doi.org/10.5194/gmd-16-157-2023, 2023
Short summary
Short summary
Ocean eddies are important for weather, climate, biology, navigation, and search and rescue. Since eddies change rapidly, models that incorporate or assimilate observations are required to produce accurate eddy timings and locations, yet the model accuracy is rarely assessed below the surface. We use a unique type of ocean model experiment to assess three-dimensional eddy structure in the East Australian Current and explore two pathways in which this subsurface structure is being degraded.
Shun Ohishi, Takemasa Miyoshi, and Misako Kachi
Geosci. Model Dev., 15, 9057–9073, https://doi.org/10.5194/gmd-15-9057-2022, https://doi.org/10.5194/gmd-15-9057-2022, 2022
Short summary
Short summary
An adaptive observation error inflation (AOEI) method was proposed for atmospheric data assimilation to mitigate erroneous analysis updates caused by large observation-minus-forecast differences for satellite brightness temperature around clear- and cloudy-sky boundaries. This study implemented the AOEI with an ocean data assimilation system, leading to an improvement of analysis accuracy and dynamical balance around the frontal regions with large meridional temperature differences.
Diego Bruciaferri, Marina Tonani, Isabella Ascione, Fahad Al Senafi, Enda O'Dea, Helene T. Hewitt, and Andrew Saulter
Geosci. Model Dev., 15, 8705–8730, https://doi.org/10.5194/gmd-15-8705-2022, https://doi.org/10.5194/gmd-15-8705-2022, 2022
Short summary
Short summary
More accurate predictions of the Gulf's ocean dynamics are needed. We investigate the impact on the predictive skills of a numerical shelf sea model of the Gulf after changing a few key aspects. Increasing the lateral and vertical resolution and optimising the vertical coordinate system to best represent the leading physical processes at stake significantly improve the accuracy of the simulated dynamics. Additional work may be needed to get real benefit from using a more realistic bathymetry.
Matthias Gröger, Manja Placke, H. E. Markus Meier, Florian Börgel, Sandra-Esther Brunnabend, Cyril Dutheil, Ulf Gräwe, Magnus Hieronymus, Thomas Neumann, Hagen Radtke, Semjon Schimanke, Jian Su, and Germo Väli
Geosci. Model Dev., 15, 8613–8638, https://doi.org/10.5194/gmd-15-8613-2022, https://doi.org/10.5194/gmd-15-8613-2022, 2022
Short summary
Short summary
Comparisons of oceanographic climate data from different models often suffer from different model setups, forcing fields, and output of variables. This paper provides a protocol to harmonize these elements to set up multidecadal simulations for the Baltic Sea, a marginal sea in Europe. First results are shown from six different model simulations from four different model platforms. Topical studies for upwelling, marine heat waves, and stratification are also assessed.
Shun Ohishi, Tsutomu Hihara, Hidenori Aiki, Joji Ishizaka, Yasumasa Miyazawa, Misako Kachi, and Takemasa Miyoshi
Geosci. Model Dev., 15, 8395–8410, https://doi.org/10.5194/gmd-15-8395-2022, https://doi.org/10.5194/gmd-15-8395-2022, 2022
Short summary
Short summary
We develop an ensemble-Kalman-filter-based regional ocean data assimilation system in which satellite and in situ observations are assimilated at a daily frequency. We find the best setting for dynamical balance and accuracy based on sensitivity experiments focused on how to inflate the ensemble spread and how to apply the analysis update to the model evolution. This study has a broader impact on more general data assimilation systems in which the initial shocks are a significant issue.
Cited articles
Adkins, J. F., Naviaux, J. D., Subhas, A. V., Dong, S., and Berelson, W. M.: The Dissolution Rate of CaCO3 in the Ocean, Annu. Rev. Mar. Sci., 13, 57–80, https://doi.org/10.1146/annurev-marine-041720-092514, 2021.
Aller, R. C.: Transport and reactions in the bioirrigated
zone, in: The benthic boundary layer: transport processes and
biogeochemistry, edited by: Boudreau, B. P. and Jørgensen, B. B., Oxford University Press, New York,
269–301, ISBN-13 978-0195118810, 2001.
Anderson, L. A.: On the hydrogen and oxygen content of marine phytoplankton, Deep-Sea Res. Pt. I, 42, 1675–1680, https://doi.org/10.1016/0967-0637(95)00072-E, 1995.
Anderson, L. A. and Sarmiento, J. L.: Redfield ratios of remineralization determined by nutrient data analysis, Global Biogeochem. Cy., 8, 65–80, https://doi.org/10.1029/93GB03318, 1994.
Archer, D.: Modeling the calcite lysocline, J. Geophys. Res., 96, 17037–17050, https://doi.org/10.1029/91JC01812, 1991.
Archer, D. E.: An atlas of the distribution of calcium carbonate in sediments of the deep sea, Global Biogeochem. Cy., 10, 159–174, https://doi.org/10.1029/95GB03016, 1996.
Archer, D., Emerson, S., and Reimers, C.: Dissolution of calcite in deep-sea sediments: pH and O2 microelectrode results, Geochim. Cosmochim. Ac., 53, 2831–2845, https://doi.org/10.1016/0016-7037(89)90161-0, 1989a.
Archer, D., Emerson, S., and Smith, C. R.: Direct measurement of the diffusive sublayer at the deep sea floor using oxygen microelectrodes, Nature, 340, 623–626, https://doi.org/10.1038/340623a0, 1989b.
Archer, D. E., Morford, J. L., and Emerson, S. R.: A model of suboxic sedimentary diagenesis suitable for automatic tuning and gridded global domains, Global Biogeochem. Cy., 16, 171–1721, https://doi.org/10.1029/2000GB001288, 2002.
Arndt, S., Jørgensen, B. B., LaRowe, D. E., Middelburg, J. J., Pancost, R. D., and Regnier, P.: Quantifying the degradation of organic matter in marine sediments: A review and synthesis, Earth-Sci. Rev., 123, 53–86, https://doi.org/10.1016/j.earscirev.2013.02.008, 2013.
Bender, M., Martin, W., Hess, J., Sayles, F., Ball, L., and Lambert, C.: A whole-core squeezer for interfacial pore-water sampling, Limnol. Oceanogr., 32, 1214–1225, https://doi.org/10.4319/lo.1987.32.6.1214, 1987.
Berelson, W. M., Hammond, D. E., McManus, J., and Kilgore, T. E.: Dissolution kinetics of calcium carbonate in equatorial Pacific sediments, Global Biogeochem. Cy., 8, 219–235, https://doi.org/10.1029/93GB03394, 1994.
Berg, P., Huettel, M., Glud, R. N., Reimers, C. E., and Attard, K. M.: Aquatic Eddy Covariance: The Method and Its Contributions to Defining Oxygen and Carbon Fluxes in Marine Environments, 14, 431–455, Annu. Rev. Mar. Sci., https://doi.org/10.1146/annurev-marine-042121-012329, 2022.
Berner, R. A.: Early diagenesis: A theoretical approach, Princeton University Press, 256 pp., ISBN 13 9780691082585, 1980.
Bezanson, J., Edelman, A., Karpinski, S., and Shah, V. B.: Julia: A Fresh Approach to Numerical Computing, SIAM Rev., 59, 65–98, https://doi.org/10.1137/141000671, 2017.
Billett, D. S. M., Lampitt, R. S., Rice, A. L., and Mantoura, R. F. C.: Seasonal sedimentation of phytoplankton to the deep-sea benthos, Nature, 302, 520–522, https://doi.org/10.1038/302520a0, 1983.
Boudreau, B. P.: On the equivalence of nonlocal and radial-diffusion models for porewater irrigation, J. Mar. Res., 42, 731–735, https://doi.org/10.1357/002224084788505924, 1984.
Boudreau, B. P.: Is burial velocity a master parameter for bioturbation?, Geochim. Cosmochim. Ac., 58, 1243–1249, https://doi.org/10.1016/0016-7037(94)90378-6, 1994.
Boudreau, B. P.: The diffusive tortuosity of fine-grained unlithified sediments, Geochim. Cosmochim. Ac., 60, 3139–3142, https://doi.org/10.1016/0016-7037(96)00158-5, 1996a.
Boudreau, B. P.: A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments, Comput. Geosci., 22, 479–496, https://doi.org/10.1016/0098-3004(95)00115-8, 1996b.
Boudreau, B. P.: Diagenetic Models and Their Implementation, Springer-Verlag, Berlin, 414 pp., ISBN-13 978-0387611259, 1997.
Boudreau, B. P. and Guinasso Jr., N. L.: The influence of
a diffusive boundary layer on accretion, dissolution, and diagenesis
at the sea floor, in: The Dynamic Environment of the Ocean Floor,
edited by: Fanning, K. A., Manheim, F. T., Lexington Books, Lexington, 115–145, ISBN 13 9780669028096, 1982.
Boudreau, B. P., Sulpis, O., and Mucci, A.: Control of CaCO3 dissolution at the deep seafloor and its consequences, Geochim. Cosmochim. Ac., 268, 90–106, https://doi.org/10.1016/j.gca.2019.09.037, 2020.
Brendel, P. J. and Luther, G. W. I.: Development of a Gold Amalgam Voltammetric Microelectrode for the Determination of Dissolved Fe, Mn, O2, and S(-II) in Porewaters of Marine and Freshwater Sediments, Environ. Sci. Technol., 29, 751–761, https://doi.org/10.1021/es00003a024, 1995.
Buesseler, K. O., Antia, A. N., Chen, M., Fowler, S. W.,
Gardner, W. D., Gustafsson, O., Harada, K., Michaels, A. F., van der Loeff,
M. R., Sarin, M., Steinberg, D. K., and Trull, T.: An assessment of the use of sediment traps for estimating upper ocean particle fluxes, J. Mar. Res., 65, 345–416, 2007.
Burdige, D. J.: Preservation of Organic Matter in Marine Sediments: Controls, Mechanisms, and an Imbalance in Sediment Organic Carbon Budgets?, Chem. Rev., 107, 467–485, https://doi.org/10.1021/cr050347q, 2007.
Burdige, D. J. and Gieskes, J. M.: A pore water/solid phase diagenetic model for manganese in marine sediments, Am. J. Sci., 283, 29–47, https://doi.org/10.2475/ajs.283.1.29, 1983.
Cai, W.-J. and Reimers, C. E.: The development of pH and pCO2 microelectrodes for studying the carbonate chemistry of pore waters near the sediment-water interface, Limnol. Oceanogr., 38, 1762–1773, https://doi.org/10.4319/lo.1993.38.8.1762, 1993.
Cai, W.-J., Zhao, P., and Wang, Y.: pH and pCO2 microelectrode measurements and the diffusive behavior of carbon dioxide species in coastal marine sediments, Mar. Chem., 70, 133–148, https://doi.org/10.1016/S0304-4203(00)00017-7, 2000.
Cai, W.-J., Ma, Y., Hopkinson, B. M., Grottoli, A. G., Warner, M. E., Ding, Q., Hu, X., Yuan, X., Schoepf, V., Xu, H., Han, C., Melman, T. F., Hoadley, K. D., Pettay, D. T., Matsui, Y., Baumann, J. H., Levas, S., Ying, Y., and Wang, Y.: Microelectrode characterization of coral daytime interior pH and carbonate chemistry, Nat. Commun., 7, 11144, https://doi.org/10.1038/ncomms11144, 2016.
Carroll, D., Menemenlis, D., Adkins, J. F., Bowman, K. W., Brix, H., Dutkiewicz, S., Fenty, I., Gierach, M. M., Hill, C., Jahn, O., Landschützer, P., Lauderdale, J. M., Liu, J., Manizza, M., Naviaux, J. D., Rödenbeck, C., Schimel, D. S., Van der Stocken, T., and Zhang, H.: The ECCO-Darwin Data-Assimilative Global Ocean Biogeochemistry Model: Estimates of Seasonal to Multidecadal Surface Ocean pCO2 and Air-Sea CO2 Flux, J. Adv. Model. Earth Sy., 12, e2019MS001888, https://doi.org/10.1029/2019MS001888, 2020.
Chriss, T. M. and Caldwell, D. R.: Evidence for the influence of form drag on bottom boundary layer flow, J. Geophys. Res., 87, 4148–4154, https://doi.org/10.1029/JC087iC06p04148, 1982.
Cook, P. G., Rodellas, V., Andrisoa, A., and Stieglitz, T. C.: Exchange across the sediment-water interface quantified from porewater radon profiles, J. Hydrol., 559, 873–883, https://doi.org/10.1016/j.jhydrol.2018.02.070, 2018.
Couture, R.-M., Sfafei, B., Van Cappellen, P., Tessier, A., and Gobeil, C.: Non-Steady State Modeling of Arsenic Diagenesis in Lake Sediments, Environ. Sci. Technol., 44, 197–203, https://doi.org/10.1021/es902077q, 2010.
Cowie, G. L. and Hedges, J. I.: Biochemical indicators of diagenetic alteration in natural organic matter mixtures, Nature, 369, 304–307, https://doi.org/10.1038/369304a0, 1994.
Cui, Y., Kump, L. R., Ridgwell, A. J., Charles, A. J., Junium, C. K., Diefendorf, A. F., Freeman, K. H., Urban, N. M., and Harding, I. C.: Slow release of fossil carbon during the Palaeocene–Eocene Thermal Maximum, Nat. Geosci., 4, 481–485, https://doi.org/10.1038/ngeo1179, 2011.
Dade, W. B.: Near-bed turbulence and hydrodynamic control of diffusional mass transfer at the sea floor, Limnol. Oceanogr., 38, 52–69, https://doi.org/10.4319/lo.1993.38.1.0052, 1993.
de Beer, D., Bissett, A., de Wit, R., Jonkers, H., Köhler-Rink, S., Nam, H., Kim, B. H., Eickert, G., and Grinstain, M.: A microsensor for carbonate ions suitable for microprofiling in freshwater and saline environments, Limnol. Oceanogr.-Meth., 6, 532–541, https://doi.org/10.4319/lom.2008.6.532, 2008.
De Borger, E., Tiano, J., Braeckman, U., Rijnsdorp, A. D., and Soetaert, K.: Impact of bottom trawling on sediment biogeochemistry: a modelling approach, Biogeosciences, 18, 2539–2557, https://doi.org/10.5194/bg-18-2539-2021, 2021.
Dickson, A. G.: An exact definition of total alkalinity and a procedure for the estimation of alkalinity and total inorganic carbon from titration data, Deep-Sea Res., 28, 609–623, https://doi.org/10.1016/0198-0149(81)90121-7, 1981.
Dong, S., Berelson, W. M., Rollins, N. E., Subhas, A. V., Naviaux, J. D., Celestian, A. J., Liu, X., Turaga, N., Kemnitz, N. J., Byrne, R. H., and Adkins, J. F.: Aragonite dissolution kinetics and calcite/aragonite ratios in sinking and suspended particles in the North Pacific, Earth Planet. Sc. Lett., 515, 1–12, https://doi.org/10.1016/j.epsl.2019.03.016, 2019.
Egbert, G. D. and Erofeeva, S. Y.: Efficient Inverse Modeling of Barotropic Ocean Tides, J. Atmos. Ocean. Tech., 19, 183–204, https://doi.org/10.1175/1520-0426(2002)019<0183:EIMOBO>2.0.CO;2, 2002.
Emerson, S., Jahnke, R., and Heggie, D.: Sediment-water exchange in shallow water estuarine sediments, J. Mar. Res., 42, 709–730, https://doi.org/10.1357/002224084788505942, 1984.
Fiadeiro, M. E. and Veronis, G.: On weighted-mean schemes for the finite-difference approximation to the advection-diffusion equation, Tellus, 29, 512–522, https://doi.org/10.3402/tellusa.v29i6.11385, 1977.
Froelich, P. N., Klinkhammer, G. P., Bender, M. L., Luedtke, N. A., Heath, G. R., Cullen, D., Dauphin, P., Hammond, D., Hartman, B., and Maynard, V.: Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis, Geochim. Cosmochim. Ac., 43, 1075–1090, https://doi.org/10.1016/0016-7037(79)90095-4, 1979.
Glud, R. N., Gundersen, J. K., Revsbech, N. P., and Jørgensen, B. B.: Effects on the benthic diffusive boundary layer imposed by microelectrodes, Limnol. Oceanogr., 39, 462–467, https://doi.org/10.4319/lo.1994.39.2.0462, 1994.
Gruber, N., Clement, D., Carter, B. R., Feely, R. A.,
van Heuven, S., Hoppema, M., Ishii, M., Key, R. M., Kozyr, A., Lauvset, S. K., Monaco, C. L., Mathis, J. T., Murata, A., Olsen, A., Perez, F. F., Sabine, C. L., Tanhua, T., and Wanninkhof, R.: The oceanic sink for anthropogenic CO2 from 1994 to 2007, Science, 363, 1193–1199, https://doi.org/10.1126/science.aau5153, 2019.
Gundersen, J. K. and Jørgensen, B. B.: Microstructure of diffusive boundary layers and the oxygen uptake of the sea floor, Nature, 345, 604–607, https://doi.org/10.1038/345604a0, 1990.
Haffert, L., Haeckel, M., de Stigter, H., and Janssen, F.: Assessing the temporal scale of deep-sea mining impacts on sediment biogeochemistry, Biogeosciences, 17, 2767–2789, https://doi.org/10.5194/bg-17-2767-2020, 2020.
Hales, B., Emerson, S., and Archer, D.: Respiration and dissolution in the sediments of the western North Atlantic: estimates from models of in situ microelectrode measurements of porewater oxygen and pH, Deep-Sea Res. Pt. I, 41, 695–719, https://doi.org/10.1016/0967-0637(94)90050-7, 1994 (data available at: https://doi.org/10.1594/PANGAEA.730420).
Hammond, D. E., McManus, J., Berelson, W. M., Kilgore, T. E., and Pope, R. H.: Early diagenesis of organic material in equatorial Pacific sediments: stpichiometry and kinetics, Deep-Sea Res. Pt. II, 43, 1365–1412, https://doi.org/10.1016/0967-0645(96)00027-6, 1996.
Han, C., Cai, W.-J., Wang, Y., and Ye, Y.: Calibration and evaluation of a carbonate microsensor for studies of the marine inorganic carbon system, J. Oceanogr., 70, 425–433, https://doi.org/10.1007/s10872-014-0243-7, 2014.
Han, X., Fang, H., He, G., and Reible, D.: Effects of roughness and permeability on solute transfer at the sediment water interface, Water Res., 129, 39–50, https://doi.org/10.1016/j.watres.2017.10.049, 2018.
Hedges, J. I., Baldock, J. A., Gélinas, Y., Lee, C., Peterson, M. L., and Wakeham, S. G.: The biochemical and elemental compositions of marine plankton: A NMR perspective, Mar. Chem., 78, 47–63, https://doi.org/10.1016/S0304-4203(02)00009-9, 2002.
Higashino, M. and Stefan, H. G.: Diffusive boundary layer development above a sediment – water interface, Water Environ. Res., 76, 292–300, https://doi.org/10.2175/106143004X141870, 2004.
Homoky, W. B., Weber, T., Berelson, W. M., Conway, T. M., Henderson, G. M., van Hulten, M., Jeandel, C., Severmann, S., and Tagliabue, A.: Quantifying trace element and isotope fluxes at the ocean–sediment boundary: a review, Philos. T. Roy. Soc., 374, 20160246, https://doi.org/10.1098/rsta.2016.0246, 2016.
Hondzo, M.: Dissolved oxygen transfer at the sediment-water interface in a turbulent flow, Water Resour. Res., 34, 3525–3533, https://doi.org/10.1029/1998WR900009, 1998.
Huettel, M., Berg, P., and Kostka, J. E.: Benthic exchange and biogeochemical cycling in permeable sediments, Annu. Rev. Mar. Sci., 6, 23–51, https://doi.org/10.1146/annurev-marine-051413-012706, 2014.
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.
Humphreys, M. P. and Sulpis, O.: Radi.jl: the
reactive-advective-diffusive-irrigative diagenetic sediment module
in Julia, Zenodo [code], https://doi.org/10.5281/zenodo.5005650, 2021.
Humphreys, M. P., Lewis, E. R., Sharp, J. D., and Pierrot, D.: PyCO2SYS v1.8: marine carbonate system calculations in Python, Geosci. Model Dev., 15, 15–43, https://doi.org/10.5194/gmd-15-15-2022, 2022.
Jahnke, R. A.: The global ocean flux of particulate organic carbon: Areal distribution and magnitude, Global Biogeochem. Cy., 10, 71–88, https://doi.org/10.1029/95GB03525, 1996.
Jørgensen, B. B.: A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments, Geomicrobiol. J., 1, 29–47, https://doi.org/10.1080/01490457809377722, 1978.
Jørgensen, B. B. and Revsbech, N. P.: Diffusive boundary layers and the oxygen uptake of sediments and detritus, Limnol. Oceanogr., 30, 111–122, https://doi.org/10.4319/lo.1985.30.1.0111, 1985.
Jutras, M., Dufour, C. O., Mucci, A., Cyr, F., and Gilbert, D.: Temporal Changes in the Causes of the Observed Oxygen Decline in the St. Lawrence Estuary, J. Geophys. Res.-Oceans, 125, e2020JC016577, https://doi.org/10.1029/2020JC016577, 2020.
Keir, R. S.: The dissolution kinetics of biogenic calcium carbonates in seawater, Geochim. Cosmochim. Ac., 44, 241–252, https://doi.org/10.1016/0016-7037(80)90135-0, 1980.
Lampitt, R. S.: Evidence for the seasonal deposition of detritus to the deep-sea floor and its subsequent resuspension, Deep-Sea Res., 32, 885–897, https://doi.org/10.1016/0198-0149(85)90034-2, 1985.
Lampitt, R. S., Hillier, W. R., and Challenor, P. G.: Seasonal and diel variation in the open ocean concentration of marine snow aggregates, Nature 362, 737–739, https://doi.org/10.1038/362737a0, 1993.
Lampitt, R. S., Salter, I., de Cuevas, B. A., Hartman, S., Larkin, K. E., and Pebody, C. A.: Long-term variability of downward particle flux in the deep northeast Atlantic: Causes and trends, Deep-Sea Res. Pt. II, 57, 1346–1361, https://doi.org/10.1016/j.dsr2.2010.01.011, 2010.
Larkum, A. W. D., Koch, E. M. W., and Kühl, M.: Diffusive boundary layers and photosynthesis of the epilithic algal community of coral reefs, Mar. Biol., 142, 1073–1082, https://doi.org/10.1007/s00227-003-1022-y, 2003.
Lauvset, S. K., Key, R. M., Olsen, A., van Heuven, S.,
Velo, A., Lin, X., Schirnick, C., Kozyr, A., Tanhua, T., Hoppema,
M., Jutterström, S., Steinfeldt, R., Jeansson, E., Ishii, M.,
Perez, F. F., Suzuki, T., and Watelet, S.: A new global interior
ocean mapped climatology: the
Lee, C., Wakeham, S. G., and Hedges, J. I.: Composition and flux of particulate amino acids and chloropigments in equatorial Pacific seawater and sediments, Deep-Sea Res. Pt. I, 47, 1535–1568, https://doi.org/10.1016/S0967-0637(99)00116-8, 2000.
Levich, V. G.: Physicochemical Hydrodynamics, Prentice-Hall Inc., Englewood Cliffs, 1962.
Li, Y.-H. and Gregory, S.: Diffusion of ions in sea water and in deep-sea sediments, Geochim. Cosmochim. Ac., 38, 703–714, https://doi.org/10.1016/0016-7037(74)90145-8, 1974.
Lorke, A., Müller, B., Maerki, M., and Wüest, A.: Breathing sediments: The control of diffusive transport across the sediment – water interface by periodic boundary-layer turbulence, Limnol. Oceanogr., 48, 2077–2085, https://doi.org/10.4319/lo.2003.48.6.2077, 2003.
Lueker, T. J., Dickson, A. G., and Keeling, C. D.: Ocean pCO2 calculated from dissolved inorganic carbon, alkalinity, and equations for K1 and K2: validation based on laboratory measurements of CO2 in gas and seawater at equilibrium, Mar. Chem., 70, 105–119, https://doi.org/10.1016/S0304-4203(00)00022-0, 2000.
Martin, W. R. and Bender, M. L.: The variability of benthic fluxes and sedimentary remineralization rates in response to seasonally variable organic carbon rain rates in the deep sea; a modeling study, Am. J. Sci., 288, 561–574, https://doi.org/10.2475/ajs.288.6.561, 1988.
Martiny, A. C., Pham, C. T. A., Primeau, F. W., Vrugt, J. A., Moore, J. K., Levin, S. A., and Lomas, M. W.: Strong latitudinal patterns in the elemental ratios of marine plankton and organic matter, Nat. Geosci., 6, 279–283, https://doi.org/10.1038/ngeo1757, 2013.
Meysman, F. J. and Montserrat, F.: Negative CO2 emissions via enhanced silicate weathering in coastal environments, Biol. Lett.-UK, 13, 20160905, https://doi.org/10.1098/rsbl.2016.0905, 2017.
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.
Middelburg, J. J.: A simple rate model for organic matter decomposition in marine sediments, Geochim. Cosmochim. Ac., 53, 1577–1581, https://doi.org/10.1016/0016-7037(89)90239-1, 1989.
Middelburg, J. J.: Marine Carbon Biogeochemistry: A Primer for Earth System Scientists, Springer International Publishing, 118 pp., https://doi.org/10.1007/978-3-030-10822-9, 2019.
Middelburg, J. J., Soetaert, K., and Herman, P. M. J.: Empirical relationships for use in global diagenetic models, Deep-Sea Res. Pt. I, 44, 327–344, https://doi.org/10.1016/S0967-0637(96)00101-X, 1997.
Millero, F. J.: Thermodynamics of the carbon dioxide system in the oceans, Geochim. Cosmochim. Ac., 59, 661–677, https://doi.org/10.1016/0016-7037(94)00354-O, 1995.
Montserrat, F., Renforth, P., Hartmann, J., Leermakers, M., Knops, P., and Meysman, F. J.: Olivine Dissolution in Seawater: Implications for CO2 Sequestration through Enhanced Weathering in Coastal Environments, Environ. Sci. Technol., 51, 3960–3972, https://doi.org/10.1021/acs.est.6b05942, 2017.
Morse, J. W.: Calculation of diffusive fluxes across the sediment-water interface, J. Geophys. Res., 79, 5045–5048, https://doi.org/10.1029/JC079i033p05045, 1974.
Mucci, A.: The solubility of calcite and aragonite in seawater at various salinities, temperatures and one atmosphere total pressure, Am. J. Sci., 283, 780–799, https://doi.org/10.2475/ajs.283.7.780, 1983.
Munhoven, G.: Glacial–interglacial rain ratio changes: Implications for atmospheric and ocean–sediment interaction, Deep-Sea Res. Pt. II, 54, 722–746, https://doi.org/10.1016/j.dsr2.2007.01.008, 2007.
Munhoven, G.: Model of Early Diagenesis in the Upper Sediment with Adaptable complexity – MEDUSA (v. 2): a time-dependent biogeochemical sediment module for Earth system models, process analysis and teaching, Geosci. Model Dev., 14, 3603–3631, https://doi.org/10.5194/gmd-14-3603-2021, 2021.
Naviaux, J. D., Subhas, A. V., Dong, S., Rollins, N. E., Liu, X., Byrne, R. H., Berelson, W. M., and Adkins, J. F.: Calcite dissolution rates in seawater: Lab vs. in-situ measurements and inhibition by organic matter, Mar. Chem., 215, 103684, https://doi.org/10.1016/j.marchem.2019.103684, 2019a.
Naviaux, J. D., Subhas, A. V., Rollins, N. E., Dong, S., Berelson, W. M., and Adkins, J. F.: Temperature dependence of calcite dissolution kinetics in seawater, Geochim. Cosmochim. Ac., 246, 363–384, https://doi.org/10.1016/0016-7037(84)90276-X, 2019b.
Paraska, D. W., Hipsey, M. R., and Salmon, S. U.: Sediment diagenesis models: Review of approaches, challenges and opportunities, Environ. Modell. Softw., 61, 297–325, https://doi.org/10.1016/j.envsoft.2014.05.011, 2014.
Perez, F. F., Fontela, M., García-Ibáñez, M., Mercier, H., Velo, A., Lherminier, P., Zunino, P., de la Paz, M., Alonso-Pérez, F., Guallart, E. F., and Padin, X. A.: Meridional overturning circulation conveys fast acidification to the deep Atlantic Ocean, Nature, 554, 515–518, https://doi.org/10.1038/nature25493, 2018.
Pugh, D. T.: Tides, surges and mean sea level, John Wiley & Sons Ltd., 472 pp., ISBN 13 9780471915058, 1987.
Rabouille, C. and Gaillard, J.-F.: Towards the EDGE: Early diagenetic global explanation. A model depicting the early diagenesis of organic matter, O2, NO3, Mn, and PO4, Geochim. Cosmochim. Ac., 55, 2511–2525, https://doi.org/10.1016/0016-7037(91)90369-G, 1991.
Redfield, A. C.: The biological control of chemical factors in the environment, Am. Sci., 46, 205–221, 1958.
Reimers, C. E.: An in situ microprofiling instrument for measuring interfacial pore water gradients: methods and oxygen profiles from the North Pacific Ocean, Deep-Sea Res., 34, 2023–2035, https://doi.org/10.1016/0198-0149(87)90096-3, 1987.
Revsbech, N. P., Jørgensen, B. B., and Blackburn, T. H.: Oxygen in the Sea Bottom Measured with a Microelectrode, Science, 207, 1355–1356, https://doi.org/10.1126/science.207.4437.1355, 1980.
Riley, J. S., Sanders, R., Marsay, C., Le Moigne, F. A. C., Achterberg, E. P., and Poulton, A. J.: The relative contribution of fast and slow sinking particles to ocean carbon export, Global Biogeochem. Cy., 26, GB1026, https://doi.org/10.1029/2011GB004085, 2012.
Røy, H., Hüttel, M., and Jørgensen, B. B.: The role of small-scale sediment topography for oxygen flux across the diffusive boundary layer, Limnol. Oceanogr., 47, 837–847, https://doi.org/10.4319/lo.2002.47.3.0837, 2002.
Santschi, P. H., Bower, P., Nyffeler, U. P., Azevedo, A., and Broecker, W. S.: Estimates of the resistance to chemical transport posed by the deep-sea boundary layer, Limnol. Oceanogr., 28, 899–912, https://doi.org/10.4319/lo.1983.28.5.0899, 1983.
Santschi, P. H., Anderson, R. F., Fleisher, M. Q., and Bowles, W.: Measurements of diffusive sublayer thicknesses in the ocean by alabaster dissolution, and their implications for the measurements of benthic fluxes, J. Geophys. Res.-Oceans, 96, 10641–10657, https://doi.org/10.1029/91JC00488, 1991.
Sayles, F. L.: The composition and diagenesis of interstitial solutions – I. Fluxes across the seawater-sediment interface in the Atlantic Ocean, Geochim. Cosmochim. Ac., 43, 527–454, https://doi.org/10.1016/0016-7037(79)90163-7, 1979.
Sayles, F. L., Martin, W. R., and Deuser, W. G.: Response of benthic oxygen demand to particulate organic carbon supply in the deep sea near Bermuda, Nature, 371, 686–689, https://doi.org/10.1038/371686a0, 1994.
Sayles, F. L., Martin, W. R., Chase, Z., and Anderson,
R. F.: Benthic remineralization and burial of biogenic
SiO2, CaCO3, organic carbon, and detrital
material in the Southern Ocean along a transect at 170∘
West, Deep-Sea Res. Pt. II, 48, 4323–4383, https://doi.org/10.1016/S0967-0645(01)00091-1, 2001 (data available at: http://usjgofs.whoi.edu/jg/dir/jgofs/southern/nbp98_2/, last access: March 2022).
Schulz, H. D.: Quantification of Early Diagenesis:
Dissolved Constituents in Pore Water and Signals in the Solid Phase,
in: Marine Geochemistry, edited by: Schulz, H. D. and Zabel, M., Springer, Berlin, Heidelberg, ISBN 13 9783540321439, 2006.
Sillén, L. G., Martell, A. E., and Bjerrum, J.: Stability constants of metal-ion complexes, Special publication, 17 edn., Chemical Society, London, UK, https://doi.org/10.1021/ed042p521.1, 1964.
Smith, C. R. and Rabouille, C.: What controls the mixed-layer depth in deep-sea sediments? The importance of POC flux, Limnol. Oceanogr., 47, 418–426, https://doi.org/10.4319/lo.2002.47.2.0418, 2002.
Smith, C. R., Berelson, W., Demaster, D. J., Dobbs, F. C., Hammond, D., Hoover, D. J., Pope, R. H., and Stephens, M.: Latitudinal variations in benthic processes in the abyssal equatorial Pacific: control by biogenic particle flux, Deep-Sea Res. Pt. II, 44, 2295–2317, https://doi.org/10.1016/S0967-0645(97)00022-2, 1997.
Smith Jr., K. L. and Baldwin, R. J.: Seasonal fluctuations in deep-sea sediment community oxygen consumption: central and eastern North Pacific, Nature, 307, 624–626, https://doi.org/10.1038/307624a0, 1984.
Smith, K. L., Baldwin, R. J., and Williams, P. M.: Reconciling particulate organic carbon flux and sediment community oxygen consumption in the deep North Pacific, Nature, 359, 313–316, https://doi.org/10.1038/359313a0, 1992.
Smith, K. L., Kaufmann, R. S., and Baldwin, R. J.: Coupling of near-bottom pelagic and benthic processes at abyssal depths in the eastern North Pacific Ocean, Limnol. Oceanogr., 39, 1101–1118, https://doi.org/10.4319/lo.1994.39.5.1101, 1994.
Soetaert, K., Herman, P. M. J., and Middelburg, J. J.: Dynamic response of deep-sea sediments to seasonal variations: A model, Limnol. Oceanogr., 41, 1651–1668, https://doi.org/10.4319/lo.1996.41.8.1651, 1996a.
Soetaert, K., Herman, P. M. J., and Middelburg, J. J.: A model of early diagenetic processes from the shelf to abyssal depths, Geochim. Cosmochim. Ac., 60, 1019–1040, https://doi.org/10.1016/0016-7037(96)00013-0, 1996b.
Soetaert, K., Herman, P. M. J., Middelburg, J. J., Heip,
C., deStigter, H. S., van Weering, T. C. E., Epping, E., and Helder, W.: Modeling 210Pb-derived mixing activity in ocean margin sediments: Diffusive versus nonlocal mixing, J. Mar. Res., 54, 1207–1227, https://doi.org/10.1357/0022240963213808, 1996c.
Sosna, M., Denuault, G., Pascal, R. W., Prien, R. D., and Mowlem, M.: Development of a reliable microelectrode dissolved oxygen sensor, Sensor. Actuat. B-Chem., 123, 344–351, https://doi.org/10.1016/j.snb.2006.08.033, 2007.
Subhas, A. V., Adkins, J. F., Rollins, N. E., Naviaux,
J., Erez, J., and Berelson, W. M.: Catalysis and chemical mechanisms
of calcite dissolution in seawater, P. Natl. Acad. Sci. USA, 114, 8175–8180, https://doi.org/10.1073/pnas.1703604114, 2017.
Sulpis, O., Lix, C., Mucci, A., and Boudreau, B. P.: Calcite dissolution kinetics at the sediment-water interface in natural seawater, Mar. Chem., 195, 70–83, https://doi.org/10.1016/j.marchem.2017.06.005, 2017.
Sulpis, O., Boudreau, B. P., Mucci, A., Jenkins, C. J.,
Trossman, D. S., Arbic, B. K., and Key, R. M.: Current
CaCO3 dissolution at the seafloor caused by anthropogenic
CO2, P. Natl. Acad. Sci. USA, 115, 11700–11705, https://doi.org/10.1073/pnas.1804250115, 2018.
Sulpis, O., Dufour, C. O., Trossman, D. S., Fassbender, A. J., Arbic, B. K., Boudreau, B. P., Dunne, J. P., and Mucci, A.: Reduced CaCO3 Flux to the Seafloor and Weaker Bottom Current Speeds Curtail Benthic CaCO3 Dissolution Over the 21st Century, Global Biogeochem. Cy., 33, 1654–1673, https://doi.org/10.1029/2019GB006230, 2019.
Sulpis, O., Humphreys, M. P., Wilhelmus, M. M., and
Carroll, D.: Radi.m: the reactive-advective-diffusive-irrigative
diagenetic sediment module in MATLAB/ GNU Octave, Zenodo [code], https://doi.org/10.5281/zenodo.4739205, 2021.
Teng, Y.-C., Primeau, F. W., Moore, J. K., Lomas, M. W., and Martiny, A. C.: Global-scale variations of the ratios of carbon to phosphorus in exported marine organic matter, Nat. Geosci., 7, 895–898, https://doi.org/10.1038/ngeo2303, 2014.
Thompson, K. F., Miller, K. A., Currie, D., Johnston, P., and Santillo, D.: Seabed Mining and Approaches to Governance of the Deep Seabed, Frontiers in Marine Science, 5, 480, https://doi.org/10.3389/fmars.2018.00480, 2018.
Trimmer, M., Petersen, J., Sivyer, D. B., Mills, C.,
Young, E., and Parker, E. R.: Impact of long-term benthic trawl disturbance on sediment sorting and biogeochemistry in the southern North Sea, Mar. Ecol. Prog. Ser., 298, 79–94, https://doi.org/10.3354/meps298079, 2005.
Uppström, L. R.: The boron/chlorinity ratio of deep-sea water from the Pacific Ocean, Deep-Sea Res., 21, 161–162, https://doi.org/10.1016/0011-7471(74)90074-6, 1974.
Van Cappellen, P. and Wang, Y.: Cycling of iron and manganese in surface sediments; a general theory for the coupled transport and reaction of carbon, oxygen, nitrogen, sulfur, iron, and manganese, Am. J. Sci., 296, 197–243, https://doi.org/10.2475/ajs.296.3.197, 1996.
van de Velde, S., Van Lancker, V., Hidalgo-Martinez, S., Berelson, W. M., and Meysman, F. J. R.: Anthropogenic disturbance keeps the coastal seafloor biogeochemistry in a transient state, Sci. Rep., 8, 5582, https://doi.org/10.1038/s41598-018-23925-y, 2018.
Walter, L. M. and Morse, J. W.: The dissolution kinetics of shallow marine carbonates in seawater: A laboratory study, Geochim. Cosmochim. Ac., 49, 1503–1513, https://doi.org/10.1016/0016-7037(85)90255-8, 1985.
Wenzhöfer, F., Oguri, K., Middelboe, M., Turnewitsch, R., Toyofuku, T., Kitazato, H., and Glud, R. N.: Benthic carbon mineralization in hadal trenches: Assessment by in situ O2 microprofile measurements, Deep-Sea Res. Pt. I, 116, 276–286, https://doi.org/10.1016/j.dsr.2016.08.013, 2016.
Westrich, J. T. and Berner, R. A.: The role of sedimentary organic matter in bacterial sulfate reduction: The G model tested, Limnol. Oceanogr., 29, 236–249, https://doi.org/10.4319/lo.1984.29.2.0236, 1984.
Yakushev, E. V., Protsenko, E. A., Bruggeman, J., Wallhead, P., Pakhomova, S. V., Yakubov, S. Kh., Bellerby, R. G. J., and Couture, R.-M.: Bottom RedOx Model (BROM v.1.1): a coupled benthic–pelagic model for simulation of water and sediment biogeochemistry, Geosci. Model Dev., 10, 453–482, https://doi.org/10.5194/gmd-10-453-2017, 2017.
Yao, W. and Millero, F. J.: The chemistry of the anoxic waters in the Framvaren Fjord, Norway, Aquat. Geochem., 1, 53–88, https://doi.org/10.1007/BF01025231, 1995.
Zachos, J. C., Röhl, U., Schellenberg, S. A., Sluijs, A., Hodell, D. A., Kelly, D. C., Thomas, E., Nicolo, M., Raffi, I., Lourens, L. J., McCarren, H., and Kroon, D.: Rapid Acidification of the Ocean During the Paleocene-Eocene Thermal Maximum, Science, 308, 1611–1615, https://doi.org/10.1126/science.1109004, 2005.
Zhao, P. and Cai, W.-J.: An Improved Potentiometric pCO2 Microelectrode, Anal. Chem., 69, 2052–5058, https://doi.org/10.1021/ac970747g, 1997.
Zhao, P. and Cai, W.-J.: pH polymeric membrane microelectrodes based on neutral carriers and their application in aquatic environments, Anal. Chim. Acta, 395, 285–291, https://doi.org/10.1016/S0003-2670(99)00359-1, 1999.
Zuddas, P. and Mucci, A.: Kinetics of calcite precipitation from seawater: II. The influence of the ionic strength, Geochim. Cosmochim. Ac., 62, 757–766, https://doi.org/10.1016/S0016-7037(98)00026-X, 1998.
Short summary
A quarter of the surface of the Earth is covered by marine sediments rich in calcium carbonates, and their dissolution acts as a giant antacid tablet protecting the ocean against human-made acidification caused by massive CO2 emissions. Here, we present a new model of sediment chemistry that incorporates the latest experimental findings on calcium carbonate dissolution kinetics. This model can be used to predict how marine sediments evolve through time in response to environmental perturbations.
A quarter of the surface of the Earth is covered by marine sediments rich in calcium carbonates,...
