[en] This study describes the coupling of the process-based Model of Early Diagenesis in the Upper Sediment with Adaptable complexity (MEDUSA version 2) to an existing ocean biogeochemistry model consisting of the Finite-volumE Sea ice–Ocean Model (FESOM version 2.1) and the Regulated Ecosystem Model (REcoM version 3). Atmospheric CO2 in the model is a prognostic variable which is determined by the carbonate chemistry in the surface ocean. The model setup and its application to a pre-industrial control climate state is described in detail. In the coupled model, 1390 PgC is stored in the top 10 cm of the bioturbated sediment, mainly as calcite, but also as organic matter (10 %). In the coupled simulation, atmospheric CO2 stabilizes at ∼295 ppm after 2000 years, in line with the CO2 level expected from the climate forcing conditions. Sediment burial of carbon, alkalinity, and nutrients in the coupled simulation is set to be compensated by riverine input. The spatial distribution of biological production is altered depending on the location of riverine input and reduction in sedimentary input, as well as the strength of local nutrient limitation, while the global productivity is not affected substantially. With this coupled ocean–sediment system the model is able to simulate the carbonate compensation feedback under moderate perturbation of CO2 in the atmosphere.
Research Center/Unit :
SPHERES - ULiège Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung (AWI) MARUM — Center for Marine Environmental Sciences
Disciplines :
Earth sciences & physical geography
Author, co-author :
Ye, Ying
Munhoven, Guy ; Université de Liège - ULiège > Département d'astrophysique, géophysique et océanographie (AGO) > Labo de physique atmosphérique et planétaire (LPAP)
Köhler, Peter
Butzin, Martin
Hauck, Judith
Gürses, Özgür
Völker, Christoph
Language :
English
Title :
FESOM2.1-REcoM3-MEDUSA2: an ocean–sea ice–biogeochemistry model coupled to a sediment model
Publication date :
21 February 2025
Journal title :
Geoscientific Model Development
ISSN :
1991-959X
eISSN :
1991-9603
Publisher :
Copernicus
Volume :
18
Issue :
4
Pages :
977-1000
Peer reviewed :
Peer Reviewed verified by ORBi
Development Goals :
13. Climate action 14. Life below water
Name of the research project :
PalMod MARCARA MarESys SEdiment REsponse to NATural and Anthropogenic carbon cycle perturbations — SERENATA
Funders :
BMBF - Bundesministerium für Bildung und Forschung F.R.S.-FNRS - Fonds de la Recherche Scientifique DFG - Deutsche Forschungsgemeinschaft HGF - Helmholtz Association of German Research Centres
Funding number :
01LP1919A; YE 170/2-1; 490763579; J.0123.19; VH-NG-1301
Funding text :
Y.Y., P.K., C.V., and M.B. are supported by the German Federal Ministry of Education and Research (BMBF) through the PalMod project (grant no. 01LP1919A), which is part of the Research for Sustainability initiative (FONA; https://www.fona.de). Y.Y. Ye is additionally supported by the German Research Foundation (DFG; grant no. YE 170/2-1). M.B. is additionally funded through DFG-ANR project MARCARA (grant no. 490763579). Financial support for Guy Munhoven’s
work on MEDUSA was provided by the Belgian Fund for Scientific Research – F.R.S.-FNRS (project SERENATA, grant no. CDR J.0123.19). Guy Munhoven is a Research Associate with the Belgian Fund for Scientific Research – F.R.S.-FNRS. J.H. and Ö.G. were funded by the Initiative and Networking Fund of the Helmholtz Association (Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys), grant no. VH-NG-1301).
Albani, S., Mahowald, N. M., Perry, A. T., Scanza, R. A., Zender, C. S., Heavens, N. G., Maggi, V., Kok, J. F., and Otto-Bliesner, B. L.: Improved Dust Representation in the Community Atmosphere Model, J. Adv. Model. Earth Sy., 6, 541–570, https://doi.org/10.1002/2013MS000279, 2014.
Amon, R. and Benner, R.: Rapid cycling of high-molecular-weight dissolved organic matter in the ocean, Nature, 369, 549–552, https://doi.org/10.1038/369549a0, 1994.
Andersson, J. H., Wijsman, J. W. M., Herman, P. M. J., Middelburg, J. J., Soetaert, K., and Heip, C.: Respiration patterns in the deep ocean, Geophys. Res. Lett., 31, L03304, https://doi.org/10.1029/2003GL018756, 2004.
Archer, D. and Brovkin, V.: The Millennial Atmospheric Lifetime of Anthropogenic CO2, Climatic Change, 90, 283–297, https://doi.org/10.1007/s10584-008-9413-1, 2008.
Archer, D., Kheshgi, H., and Maier-Reimer, E.: Multiple timescales for neutralization of fossil fuel CO2, Geophys. Res. Lett., 24, 405–408, https://doi.org/10.1029/97GL00168, 1997.
Archer, D., Eby, M., Brovkin, V., Ridgwell, A., Cao, L., Mikolajewicz, U., Caldeira, K., Matsumoto, K., Munhoven, G., Montenegro, A., and Tokos, K.: Atmospheric Lifetime of Fossil Fuel Carbon Dioxide, Annu. Rev. Earth Pl. Sci., 37, 117–134, https://doi.org/10.1146/annurev.earth.031208.100206, 2009.
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.
Aumont, O., Ethé, C., Tagliabue, A., Bopp, L., and Gehlen, M.: PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies, Geosci. Model Dev., 8, 2465–2513, https://doi.org/10.5194/gmd-8-2465-2015, 2015.
Broecker, W. S. and Peng, T.-H.: The role of CaCO3 compensation in the glacial to interglacial atmospheric CO2 change, Global Biogeochem. Cy., 1, 15–29, 1987.
Brovkin, V., Ganopolski, A., Archer, D., and Munhoven, G.: Glacial CO2 cycle as a succession of key physical and biogeochemical processes, Clim. Past, 8, 251–264, https://doi.org/10.5194/cp-8-251-2012, 2012.
Buitenhuis, E. T., Le Quéré, C., Bednaršek, N., and Schiebel, R.: Large Contribution of Pteropods to Shallow CaCO3 Export, Global Biogeochem. Cy., 33, 458–468, https://doi.org/10.1029/2018GB006110, 2019.
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.
Butzin, M., Ye, Y., Völker, C., Gürses, Ö., Hauck, J., and Köhler, P.: Carbon isotopes in the marine biogeochemistry model FESOM2.1-REcoM3, Geosci. Model Dev., 17, 1709–1727, https://doi.org/10.5194/gmd-17-1709-2024, 2024.
Canfield, D. E., Kristensen, E., and Thamdrup, B.: The Sulfur Cycle, in: Aquatic Geomicrobiology, vol. 48 of Advances in Marine Biology, Elsevier, Amsterdam (NL), 313–381, https://doi.org/10.1016/S0065-2881(05)48009-8, 2005.
Cartapanis, O., Bianchi, D., Jaccard, S. L., and Galbraith, E. D.: Global pulses of organic carbon burial in deep-sea sediments during glacial maxima, Nat. Commun., 7, 10796, https://doi.org/10.1038/ncomms10796, 2016.
Cartapanis, O., Galbraith, E. D., Bianchi, D., and Jaccard, S. L.: Carbon burial in deep-sea sediment and implications for oceanic inventories of carbon and alkalinity over the last glacial cycle, Clim. Past, 14, 1819–1850, https://doi.org/10.5194/cp-14-1819-2018, 2018.
Christensen, J. P.: Carbon export from continental shelves, denitrification and atmospheric carbon dioxide, Cont. Shelf Res., 14, 547–576, 1994.
Christensen, J. P.: A relationship between deep-sea benthic oxygen demand and oceanic primary productivity, Oceanol. Acta, 23, 65–82, https://doi.org/10.1016/S0399-1784(00)00101-8, 2000.
Christensen, J. P., Murray, J. W., Devol, A. H., and Codispoti, L. A.: Denitrification in continental shelf sediments has major impact on the oceanic nitrogen budget, Global Biogeochem. Cy., 1, 97–116, 1987.
Ciais, P., Sabine, C., Bala, G., Bopp, L., Brovkin, V., Canadell, J., Chhabra, A., DeFries, R., Galloway, J., Heimann, M., Jones, C., Quéré, C. L., Myneni, R. B., Piao, S., and Thornton, P.: Carbon and Other Biogeochemical Cycles, in: Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, edited by: Stocker, T. F., Qin, D., Plattner, G.-K., Tignor, M. M. B., Allen, S. K., Boschung, J., Nauels, A., Xia, Y., Bex, V., and Midgley, P. M., Cambridge University Press, chap. 6, 465–570, https://www.ipcc.ch/site/assets/uploads/2018/02/WG1AR5_Chapter06_FINAL.pdf (last access: 14 February 2025), 2013.
Codispoti, L. and Christensen, J.: Nitrification, denitrification and nitrous oxide cycling in the eastern tropical South Pacific Ocean, Mar. Chem., 16, 277–300, 1985.
de Baar, H. J. W. and de Jong, J.: Distributions, Sources and Sinks of Iron in Seawater, in: The Biogeochemistry of Iron in Seawater, edited by: Turner, D. R. and Hunter, K. A., vol. 7 of IUPAC Ser. Anal. Phys. Chem. Environ. Syst., John Wiley & Sons, 123–253, IBSN 0-471-49068-7, 2001.
DeVries, T., Deutsch, C., Rafter, P. A., and Primeau, F.: Marine denitrification rates determined from a global 3-D inverse model, Biogeosciences, 10, 2481–2496, https://doi.org/10.5194/bg-10-2481-2013, 2013.
Dickson, A. G., Sabine, C. L., and Christian, J. R., eds.: Guide to Best Practices for Ocean CO2 Measurements, vol. 3 of PICES Special Publication, Carbon Dioxide Information and Analysis Center, Oak Ridge (TN), https://www.nodc.noaa.gov/ocads/oceans/Handbook_2007.html (last access: 5 December 2004), 2007.
Dunne, J. P., Sarmiento, J. L., and Gnanadesikan, A.: A synthesis of global particle export from the surface ocean and cycling through the ocean interior and on the seafloor, Global Biogeochem. Cy., 21, GB4006, https://doi.org/10.1029/2006GB002907, 2007.
Dunne, J. P., Hales, B., and Toggweiler, J. R.: Global calcite cycling constrained by sediment preservation controls, Global Biogeochem. Cy., 26, GB3023, https://doi.org/10.1029/2010GB003935, 2012.
Elrod, V. A., Berelson, W. M., Coale, K. H., and Johnson, K. S.: The flux of iron from continental shelf sediments: A missing source for global budgets, Geophys. Res. Lett., 31, L12307, https://doi.org/10.1029/2004GL020216, 2004.
Emerson, S. and Hedges, J. I.: Processes controlling the organic carbon content of open ocean sediments, Paleoceanography, 3, 621–634, https://doi.org/10.1029/PA003i005p00621, 1988.
Friedlingstein, P., O’Sullivan, M., Jones, M. W., Andrew, R. M., Gregor, L., Hauck, J., Le Quéré, C., Luijkx, I. T., Olsen, A., Peters, G. P., Peters, W., Pongratz, J., Schwingshackl, C., Sitch, S., Canadell, J. G., Ciais, P., Jackson, R. B., Alin, S. R., Alkama, R., Arneth, A., Arora, V. K., Bates, N. R., Becker, M., Bellouin, N., Bittig, H. C., Bopp, L., Chevallier, F., Chini, L. P., Cronin, M., Evans, W., Falk, S., Feely, R. A., Gasser, T., Gehlen, M., Gkritzalis, T., Gloege, L., Grassi, G., Gruber, N., Gürses, Ö., Harris, I., Hefner, M., Houghton, R. A., Hurtt, G. C., Iida, Y., Ilyina, T., Jain, A. K., Jersild, A., Kadono, K., Kato, E., Kennedy, D., Klein Goldewijk, K., Knauer, J., Korsbakken, J. I., Landschützer, P., Lefèvre, N., Lindsay, K., Liu, J., Liu, Z., Marland, G., Mayot, N., McGrath, M. J., Metzl, N., Monacci, N. M., Munro, D. R., Nakaoka, S.-I., Niwa, Y., O’Brien, K., Ono, T., Palmer, P. I., Pan, N., Pierrot, D., Pocock, K., Poulter, B., Resplandy, L., Robertson, E., Rödenbeck, C., Rodriguez, C., Rosan, T. M., Schwinger, J., Séférian, R., Shutler, J. D., Skjelvan, I., Steinhoff, T., Sun, Q., Sutton, A. J., Sweeney, C., Takao, S., Tanhua, T., Tans, P. P., Tian, X., Tian, H., Tilbrook, B., Tsujino, H., Tubiello, F., van der Werf, G. R., Walker, A. P., Wanninkhof, R., Whitehead, C., Willstrand Wranne, A., Wright, R., Yuan, W., Yue, C., Yue, X., Zaehle, S., Zeng, J., and Zheng, B.: Global Carbon Budget 2022, Earth Syst. Sci. Data, 14, 4811–4900, https://doi.org/10.5194/essd-14-4811-2022, 2022.
Garcia, H. E., Locarnini, R. A., Boyer, T. P., Antonov, J. I., Baranova, O. K., Zweng, M. M., Reagan, J. R., and Johnson, D. R.: World Ocean Atlas 2013, Volume 4: Dissolved Inorganic Nutrients (Phosphate, Nitrate, Silicate), edited by: Levitus, S. and Mishonov, A., Tech. rep., NOAA Atlas NESDIS 76, http://www.nodc.noaa.gov/OC5/indprod.html (last access: 14 February 2025), 2014.
Garcia, H. E., Weathers, K. W., Paver, C. R., Smolyar, I., Boyer, T. P., Locarnini, R. A., Zweng, M. M., Mishonov, A. V., Baranova, O. K., Seidov, D., and Reagan, J. R.: World Ocean Atlas 2018, Volume 3: Dissolved Oxygen, Apparent Oxygen Utilization, and Oxygen Saturation, edited by: Mishonov, A., Tech. rep., NOAA Atlas NESDIS 83, https://www.nodc.noaa.gov/OC5/woa18/pubwoa18.html (last access: 14 February 2025), 2019.
Glud, R. N.: Oxygen dynamics of marine sediments, Mar. Biol. Res., 4, 243–289, https://doi.org/10.1080/17451000801888726, 2008.
Guieu, C., Huang, W. W., Martin, J.-M., and Yong, Y. Y.: Outflow of trace metals into the Laptev Sea by the Lena River, Mar. Chem., 53, 255–267, https://doi.org/10.1016/0304-4203(95)00093-3, 1996.
Gürses, Ö., Oziel, L., Karakus̹, O., Sidorenko, D., Völker, C., Ye, Y., Zeising, M., Butzin, M., and Hauck, J.: Ocean biogeochemistry in the coupled ocean–sea ice–biogeochemistry model FESOM2.1–REcoM3, Geosci. Model Dev., 16, 4883–4936, https://doi.org/10.5194/gmd-16-4883-2023, 2023.
Hansell, D. A., Carlson, C. A., Repeta, D. J., and Schlitzer, R.: Dissolved Organic Matter in the Ocean: A Controversy Stimulates New Insights, Oceanography, 22, 202–211, https://doi.org/10.5670/oceanog.2009.109, 2009.
Hattori, A.: Denitrification and dissimilatory nitrate reduction, in: Nitrogen in the marine environment, edited by: Carpenter, E. J. and Capone, D. G., chap. 6, Academic Press, New York (NY), 1st Edn., 191–232, ISBN 978-0-12-160280-2, 1983.
Hayes, C. T., Costa, K. M., Anderson, R. F., Calvo, E., Chase, Z., Demina, L. L., Dutay, J.-C., German, C. R., Heimbürger-Boavida, L.-E., Jaccard, S. L., Jacobel, A., Kohfeld, K. E., Kravchishina, M. D., Lippold, J., Mekik, F., Missiaen, L., Pavia, F. J., Paytan, A., Pedrosa-Pamies, R., Petrova, M. V., Rahman, S., Robinson, L. F., Roy-Barman, M., Sanchez-Vidal, A., Shiller, A., Tagliabue, A., Tessin, A. C., Van Hulten, M., and Zhang, J.: Global Ocean Sediment Composition and Burial Flux in the Deep Sea, Global Biogeochem. Cy., 35, e2020GB006769, https://doi.org/10.1029/2020GB006769, 2021.
Hilton, R. G. and West, A. J.: Mountains, erosion and the carbon cycle, Nat. Rev. Earth Environ., 1, 284–299, https://doi.org/10.1038/s43017-020-0058-6, 2020.
Himstedt, K.: Multiple execution of the same MPI application to exploit parallelism at hotspots with minimal code changes: a case study with FESOM2-Iceberg and FESOM2-REcoM, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-756, 2023.
Hohn, S.: Coupling and decoupling of biogeochemical cycles in marine ecosystems, Ph.D. thesis, Universität Bremen, Fachbereich Biologie, 2009.
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.: Processes at the sediment-water interface, in: The Major Biogeochemical Cycles and Their Interactions, edited by: Bolin, B. and Cook, R. B., vol. 21 of SCOPE Reports, John Wiley and Sons, New York (NY), 477–509, ISBN 9780471105220, 1983.
Jørgensen, B. B. and Kasten, S.: Sulfur Cycling and Methane Oxidation, in: Marine Geochemistry, edited by: Schulz, H. D. and Zabel, M., chap. 8, Springer-Verlag, Berlin, Heidelberg (DE), 271–309, https://doi.org/10.1007/3-540-32144-6_8, 2006.
Jørgensen, B. B., Wenzhöfer, F., Egger, M., and Glud, R. N.: Sediment oxygen consumption: Role in the global marine carbon cycle, Earth-Sci. Rev., 228, 103987, https://doi.org/10.1016/j.earscirev.2022.103987, 2022.
Keppler, L., Landschützer, P., Gruber, N., Lauvset, S. K., and Stemmler, I.: Seasonal Carbon Dynamics in the Near-Global Ocean, Global Biogeochem. Cy., 34, e2020GB006571, https://doi.org/10.1029/2020GB006571, 2020.
Knecht, N. S., Benedetti, F., Hofmann Elizondo, U., Bednaršek, N., Chaabane, S., de Weerd, C., Peijnenburg, K. T. C. A., Schiebel, R., and Vogt, M.: The Impact of Zooplankton Calcifiers on the Marine Carbon Cycle, Global Biogeochem. Cy., 37, e2022GB007685, https://doi.org/10.1029/2022GB007685, 2023.
Köhler, P.: Anthropogenic CO2 of high emission scenario compensated after 3500 years of ocean alkalinization with an annually constant dissolution of 5 Pg of olivine, Front. Climate, 2, 575744, https://doi.org/10.3389/fclim.2020.575744, 2020.
Köhler, P. and Munhoven, G.: Late Pleistocene carbon cycle revisited by considering solid Earth processes, Paleoceanography and Paleoclimatology, 35, e2020PA004020, https://doi.org/10.1029/2020PA004020, 2020.
Krachler, R., Jirsa, F., and Ayromlou, S.: Factors influencing the dissolved iron input by river water to the open ocean, Biogeosciences, 2, 311–315, https://doi.org/10.5194/bg-2-311-2005, 2005.
Kriest, I. and Oschlies, A.: Swept under the carpet: organic matter burial decreases global ocean biogeochemical model sensitivity to remineralization length scale, Biogeosciences, 10, 8401–8422, https://doi.org/10.5194/bg-10-8401-2013, 2013.
Kurahashi-Nakamura, T., Paul, A., Munhoven, G., Merkel, U., and Schulz, M.: Coupling of a sediment diagenesis model (MEDUSA) and an Earth system model (CESM1.2): a contribution toward enhanced marine biogeochemical modelling and long-term climate simulations, Geosci. Model Dev., 13, 825–840, https://doi.org/10.5194/gmd-13-825-2020, 2020.
Lan, X., Tans, P., and Thoning, K. W.: Trends in globally-averaged CO2 determined from NOAA Global Monitoring Laboratory measurements, Version 2023-06, https://doi.org/10.15138/9N0H-ZH07, 2023.
Large, W. G. and Yeager, S. G.: The Global Climatology of an Interannually Varying Air-Sea Flux Data Set, Clim. Dynam., 33, 341–364, https://doi.org/10.1007/s00382-008-0441-3, 2009.
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 1° × 1° GLODAP version 2, Earth Syst. Sci. Data, 8, 325–340, https://doi.org/10.5194/essd-8-325-2016, 2016. .
Liu, K.-K. and Kaplan, I. R.: Denitrification rates and availability of organic matter in marine environments, Earth Planet. Sc. Lett., 68, 88–100, 1984.
Martin, J. H., Knauer, G. A., Karl, D. M., and Broenkow, W. W.: VERTEX: carbon cycling in the northeast Pacific, Deep-Sea Res. Pt. I, 34, 267–285, https://doi.org/10.1016/0198-0149(87)90086-0, 1987.
Meinshausen, M., Smith, S. J., Calvin, K., Daniel, J. S., Kainuma, M. L., Lamarque, J.-F., Matsumoto, K., Montzka, S. A., Raper, S. C., Riahi, K., Thomson, A., Velders, G. J. M., and van Vuuren, D. P. P.: The RCP greenhouse gas concentrations and their extensions from 1765 to 2300, Climatic Change, 109, 213–241, 2011.
Meinshausen, M., Vogel, E., Nauels, A., Lorbacher, K., Meinshausen, N., Etheridge, D. M., Fraser, P. J., Montzka, S. A., Rayner, P. J., Trudinger, C. M., Krummel, P. B., Beyerle, U., Canadell, J. G., Daniel, J. S., Enting, I. G., Law, R. M., Lunder, C. R., O’Doherty, S., Prinn, R. G., Reimann, S., Rubino, M., Velders, G. J. M., Vollmer, M. K., Wang, R. H. J., and Weiss, R.: Historical greenhouse gas concentrations for climate modelling (CMIP6), Geosci. Model Dev., 10, 2057–2116, https://doi.org/10.5194/gmd-10-2057-2017, 2017.
Middelburg, J. J., Soetaert, K., Herman, P. M. J., and Heip, C. H. R.: Denitrification in marine sediments: A model study, Global Biogeochem. Cy., 10, 661–673, https://doi.org/10.1029/96GB02562, 1996.
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.
Moreira Martinez, S., Roche, D. M., Munhoven, G., and Waelbroeck, C.: Coupling MEDUSA sediment model to iLOVECLIM (v1.1β) Earth system model, in: 12th International Conference on Paleoceanography (ICP12), Utrecht (NL), 368 pp., https://hdl.handle.net/2268/219749 (last access: 28 May 2021), 2016.
Muller-Karger, F. E., Varela, R., Thunell, R., Luers sen, R., Hu, C., and Walsh, J. J.: The importance of continental margins in the global carbon cycle, Geophys. Res. Lett., 32, L01602, https://doi.org/10.1029/2004GL021346, 2005.
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.
Nelson, D. M., Tréguer, P., Brzezinski, M. A., Leynaert, A., and Qu’eguiner, B.: Production and dissolution of biogenic silica in the ocean: Revised global estimates, comparison with regional data and relationship to biogenic sedimentation, Global Biogeochem. Cy., 9, 359–372, https://doi.org/10.1029/95GB01070, 1995.
Parameswaran, N., González, E., Burwicz-Galerne, E., Braack, M., and Wallmann, K.: NN-TOC v1: global prediction of total organic carbon in marine sediments using deep neural networks, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2024-1360, 2024.
Picard, A., Davis, R. S., Gläser, M., and Fujii, K.: Revised formula for the density of moist air (CIPM-2007), Metrologia, 45, 149–155, https://doi.org/10.1088/0026-1394/45/2/004, 2008.
Sarmiento, J. L. and Gruber, N.: Ocean Biogeochemical Dynamics, Princeton University Press, https://doi.org/10.2307/j.ctt3fgxqx, 2006.
Sarmiento, J. L., Dunne, J., Gnanadesikan, A., Key, R. M., Matsumoto, K., and Slater, R.: A new estimate of the CaCO3 to organic carbon export ratio, Global Biogeochem. Cy., 16, 1107, https://doi.org/10.1029/2002GB001919, 2002.
Schartau, M., Engel, A., Schröter, J., Thoms, S., Völker, C., and Wolf-Gladrow, D.: Modelling carbon overconsumption and the formation of extracellular particulate organic carbon, Biogeosciences, 4, 433–454, https://doi.org/10.5194/bg-4-433-2007, 2007.
Scholz, P., Sidorenko, D., Gurses, O., Danilov, S., Koldunov, N., Wang, Q., Sein, D., Smolentseva, M., Rakowsky, N., and Jung, T.: Assessment of the Finite-volumE Sea ice-Ocean Model (FESOM2.0) – Part 1: Description of selected key model elements and comparison to its predecessor version, Geosci. Model Dev., 12, 4875–4899, https://doi.org/10.5194/gmd-12-4875-2019, 2019.
Scholz, P., Sidorenko, D., Danilov, S., Wang, Q., Koldunov, N., Sein, D., and Jung, T.: Assessment of the Finite-VolumE Sea ice–Ocean Model (FESOM2.0) – Part 2: Partial bottom cells, embedded sea ice and vertical mixing library CVMix, Geosci. Model Dev., 15, 335–363, https://doi.org/10.5194/gmd-15-335-2022, 2022.
Séférian, R., Berthet, S., Yool, A., Palmiéri, J., Bopp, L., Tagliabue, A., Kwiatkowski, L., Aumont, O., Christian, J., Dunne, J., Gehlen, M., Ilyina, T., John, J. G., Li, H., Long, M. C., Luo, J. Y., Nakano, H., Romanou, A., Schwinger, J., Stock, C., Santana-Falcón, Y., Takano, Y., Tjiputra, J., Tsujino, H., Watanabe, M., Wu, T., Wu, F., and Yamamoto, A.: Tracking Improvement in Simulated Marine Biogeochemistry Between CMIP5 and CMIP6, Curr. Clim. Change Rep., 6, 95–119, https://doi.org/10.1007/s40641-020-00160-0, 2020.
Seifert, M., Nissen, C., Rost, B., and Hauck, J.: Cascading effects augment the direct impact of CO2 on phytoplankton growth in a biogeochemical model, Elementa, 10, 00104, https://doi.org/10.1525/elementa.2021.00104, 2022.
Seiter, K., Hensen, C., Schröter, J., and Zabel, M.: Organic Carbon Content in Surface Sediments – Defining Regional Provinces, Deep-Sea Res. Pt. I, 51, 2001–2026, https://doi.org/10.1016/j.dsr.2004.06.014, 2004.
Seiter, K., Hensen, C., and Zabel, M.: Benthic carbon mineralization on a global scale, Global Biogeochem. Cy., 19, GB1010, https://doi.org/10.1029/2004GB002225, 2005.
Shi, X., Cauquoin, A., Lohmann, G., Jonkers, L., Wang, Q., Yang, H., Sun, Y., and Werner, M.: Simulated stable water isotopes during the mid-Holocene and pre-industrial periods using AWI-ESM-2.1-wiso, Geosci. Model Dev., 16, 5153–5178, https://doi.org/10.5194/gmd-16-5153-2023, 2023.
Smith, S. V. and Hollibaugh, J. T.: Coastal Metabolism and the Oceanic Organic Carbon Balance, Rev. Geophys., 31, 75–89, https://doi.org/10.1029/92RG02584, 1993.
Snelgrove, P. V., Soetaert, K., Solan, M., Thrush, S., Wei, C.-L., Danovaro, R., Fulweiler, R. W., Kitazato, H., Ingole, B., Norkko, A., Parkes, R. J., and Volkenborn, N.: Global Carbon Cycling on a Heterogeneous Seafloor, Trends Ecol. Evol., 33, 96–105, https://doi.org/10.1016/j.tree.2017.11.004, 2018.
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, 1996.
Steele, M., Morley, R., and Ermold, W.: PHC: A Global Ocean Hydrography with a High-Quality Arctic Ocean, J. Climate, 14, 2079–2087, https://doi.org/10.1175/15200442(2001)014<2079:PAGOHW>2.0.CO;2, 2001.
Stratmann, T., Wei, C.-L., Lin, Y.-S., and van Oevelen, D.: The SCOC database, a large, open, and global database with sediment community oxygen consumption rates, Sci. Data, 6, 242, https://doi.org/10.1038/s41597-019-0259-3, 2019.
Thullner, M., Dale, A. W., and Regnier, P.: Global-scale quantification of mineralization pathways in marine sediments: A reaction-transport modeling approach, Geochem. Geophy., Geosy., 10, Q10012, https://doi.org/10.1029/2009GC002484, 2009.
Tréguer, P., Nelson, D. M., Bennekom, A. J. V., DeMaster, D. J., Leynaert, A., and Quéguiner, B.: The Silica Balance in the World Ocean: A Reestimate, Science, 268, 375–379, https://doi.org/10.1126/science.268.5209.375, 1995.
Tréguer, P. J. and De La Rocha, C. L.: The World Ocean Silica Cycle, Annu. Rev. Mar. Sci., 5, 477–501, https://doi.org/10.1146/annurev-marine-121211-172346, 2013.
Tréguer, P. J., Sutton, J. N., Brzezinski, M., Charette, M. A., Devries, T., Dutkiewicz, S., Ehlert, C., Hawkings, J., Leynaert, A., Liu, S. M., Llopis Monferrer, N., López-Acosta, M., Maldonado, M., Rahman, S., Ran, L., and Rouxel, O.: Reviews and syntheses: The biogeochemical cycle of silicon in the modern ocean, Biogeosciences, 18, 1269–1289, https://doi.org/10.5194/bg-18-1269-2021, 2021.
Trenberth, K. E. and Smith, L.: The Mass of the Atmosphere: A Constraint on Global Analyses, J. Climate, 18, 864–875, https://doi.org/10.1175/JCLI-3299.1, 2005.
Volk, T. and Hoffert, M. I.: Ocean Carbon Pumps: Analysis of Relative Strengths and Efficiencies in Ocean-Driven Atmospheric CO2 Changes, in: The Carbon Cycle and Atmospheric CO2: Natural Variations Archean to Present, edited by: Sundquist, E. T. and Broecker, W. S., vol. 32 of Geophysical Monograph Series, American Geophysical Union (AGU), Washington (DC), 99–110, https://doi.org/10.1029/GM032p0099, 1985. Wanninkhof, R.: Relationship between wind speed and gas exchange over the ocean revisited, Limnol. Oceanogr., 12, 351–362, https://doi.org/10.4319/lom.2014.12.351, 2014.
Ye, Y.: Ocean biogeochemistry model FESOM2.1-REcoM3 coupled with a sediment model MEDUSA2, Zenodo [code], https://doi.org/10.5281/zenodo.8315240, 2023.
Ye, Y.: FESOM2.1-REcoM3-MEDUSA2: an ocean-sea ice-biogeochemistry model coupled to a sediment model, Zenodo [data set], https://doi.org/10.5281/zenodo.14887815, 2025.
Zeebe, R. E. and Wolf-Gladrow, D. A.: CO2 in Seawater: Equilibrium, Kinetics, Isotopes, vol. 65 of Elsevier Oceanography Book Series, Elsevier Science Publishing, Amsterdam, The Netherlands, ISBN 978-0-444-50946-8, 2001.
