Skip to main content
Log in

Development and Assessment of NEMO(v3.6)-TOPAZ(v2), a Coupled Global Ocean Biogeochemistry Model

  • Original Article
  • Published:
Asia-Pacific Journal of Atmospheric Sciences Aims and scope Submit manuscript

Abstract

Earth System Models (ESMs) simulating the interrelationship between atmospheric chemistry, ocean biogeochemistry, terrestrial ecology, and climate processes are used to understand current climate and predict future climate change. However, ocean biogeochemical results show wide variability between ESMs. We have implemented the Tracers of Phytoplankton with Allometric Zooplankton (TOPAZ) ocean biogeochemistry model into the National Institute of Meteorological Sciences ESM. The offline version (Nucleus for European Modelling of the Ocean – Tracers of Ocean Phytoplankton with Allometric Zooplankton v2 (NEMO-TOPAZ) of the coupled global ocean biogeochemistry model has been evaluated compared to both observational data and another biogeochemistry model (NEMO-Pelagic Interactions Scheme for Carbon and Ecosystem Studies volume 2 [PISCES]) with the same ocean physics model. Biogeochemical tracers simulated by these models showed horizontal and vertical spatial distributions similar to observations. However, limitations caused by the shared ocean physical model were found in both models. While NEMO-TOPAZ tended to overestimate surface chlorophyll and nutrients, variation of simulated equatorial surface chlorophyll has a significant relationship with the El Niño-Southern Oscillation (ENSO) consistent with the observational result. NEMO-TOPAZ achieved superior simulation of dissolved inorganic carbon and alkalinity along with vertical distributions of biogeochemical variables in the Pacific and Atlantic Oceans. For nutrients, NEMO-PISCES showed better results overall. This model will improve scientific understanding of ocean biogeochemical processes and can be used in combination with other models for other components of the Earth’s system to develop a new ESM.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14
Fig. 15
Fig. 16

Similar content being viewed by others

Data Availability

NEMO–TOPAZ is freely available at https://doi.org/10.5281/zenodo.2648099 (Jung and Moon 2019).

References

  • ARCCSS: MOM5 input data, Australian Research Council’s Centre of Excellence for Climate System Science (2018). http://climate-cms.unsw.wikispaces.net/Data. Accessed 22 November 2018 (note: resource no longer exists online)

  • Arsouze, T., Dutay, J.-C., Kageyama, M., Lacan, F., Alkama, R., Marti, O., Jeandel, C.: A modeling sensitivity study of the influence of the Atlantic meridional overturning circulation on neodymium isotopic composition at the last glacial maximum. Clim. Past. 4, 191–203 (2008). https://doi.org/10.5194/cp-4-191-2008

    Article  Google Scholar 

  • Aumont, O., Bopp, L.: Globalizing results from ocean in-situ iron fertilization studies. Glob. Biogeochem. Cycles. 20, GB2017 (2006). https://doi.org/10.1029/2005GB002591

    Article  Google Scholar 

  • Aumont, O., Ethe, C., Tagliabue, A., Bopp, L., Gehlen, M.: PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies. Geosci. Model Dev. 8, 2465–2513 (2015). https://doi.org/10.5194/gmd-8-2465-2015

    Article  Google Scholar 

  • Barnier, B., Madec, G., Penduff, T., Molines, J.-M., Treguier, A.-M., le Sommer, J., Beckmann, A., Biastoch, A., Böning, C., Dengg, J., Derval, C., Durand, E., Gulev, S., Remy, E., Talandier, C., Theetten, S., Maltrud, M., McClean, J., de Cuevas, B.: Impact of partial steps and momentum advection schemes in a global circulation model at eddy permitting resolution. Ocean Dyn. 56(5–6), 543–567 (2006). https://doi.org/10.1007/s10236-006-0082-1

    Article  Google Scholar 

  • Carton, J.A., Chepurin, G.A., Chen, L.: SODA3: a new ocean climate reanalysis. J. Clim. 31, 6967–6983 (2018). https://doi.org/10.1175/JCLI-D-18-0149.1

    Article  Google Scholar 

  • DeVries, T., Holzer, M., Primeau, F.: Recent increase in oceanic carbon uptake driven by weaker upper-ocean overturning. Nature. 542, 215–218 (2017). https://doi.org/10.1038/nature21068

    Article  Google Scholar 

  • Dunne, J.P., John, J.G., Adcroft, A.J., Griffies, S.M., Hallberg, R.W., Shevliakova, E.N., Stouffer, R.J., Cooke, W., Dunne, K.A., Harrison, M.J., Krasting, J.P., Malyshev, S.L., Milly, P.C.D., Phillipps, P.J., Sentman, L.A., Samuels, B.L., Spelman, M.J., Winton, M., Wittenberg, A.T., Zadeh, N.: GFDL’s ESM2 global coupled climate-carbon earth system models part I: physical formulation and baseline simulation characteristics. J. Clim. 25, 6646–6665 (2012a). https://doi.org/10.1175/JCLI-D-11-00560.1

    Article  Google Scholar 

  • Dunne, J.P., John, J.G., Shevliakova, E., Stouffer, R.J., Krasting, J.P., Malyshev, S.L., Milly, P.C.D., Sentman, L.T., Adcroft, A.J., Cooke, W., Dunne, K.A., Griffies, S.M., Hallberg, R.W., Harrison, M.J., Levy, H., Wittenberg, A.T., Phillips, P.J., Zadeh, N.: GFDL’s ESM2 global coupled climate–carbon earth system models. Part II: carbon system formulation and baseline simulation characteristics. J. Clim. 26, 2247–2267 (2012b). https://doi.org/10.1175/jcli-d-12-00150.1

    Article  Google Scholar 

  • Dutkiewicz, S., Follows, M.J., Parekh, P.: Interactions of the iron and phosphorus cycles: a three-dimensional model study. Glob. Biogeochem. Cycles. 19, GB1021 (2005). https://doi.org/10.1029/2004GB002342

    Article  Google Scholar 

  • Fogli, P. G., Iovino, D.: CMCC–CESM–NEMO: Toward the new CMCC Earth System Model. CMCC Research Rep. RP0248, 19 pp. (2014). [Available online at http://www.cmcc.it/wp-content/uploads/2015/02/rp0248-ans-12-2014.pdf]. Accessed 11 April 2019

  • Garcia, H. E., Locarnini, R. A., Boyer, T. P., Antonov, J. I., Baranova, O. K., Zweng, M. M., Reagan, J. R., Johnson, D. R.: World Ocean Atlas 2013, Volume 4: Dissolved Inorganic Nutrients (phosphate, nitrate, silicate). S. Levitus, Ed., A. Mishonov Technical Ed.; NOAA Atlas NESDIS 76, 25 pp (2014)

  • Gnanadesikan, A., Slater, R.J., Gruber, N., Sarmiento, J.L.: Oceanic vertical exchange and new production: a comparison between models and observations. Deep Sea Res. Pt II. 49, 363–401 (2002). https://doi.org/10.1016/S0967-0645(01)00107-2

    Article  Google Scholar 

  • Griffies, S.M., Biastoch, A., Böning, C., Bryan, F., Danabasoglu, G., Chassignet, E.P., England, M.H., Gerdes, R., Haak, H., Hallberg, R.W., Hazeleger, W., Jungclaus, J., Large, W.G., Madec, G., Pirani, A., Samuels, B.L., Scheinert, M., Gupta, A.S., Severijns, C.A., Simmons, H.L., Trguier, A.-M., Winton, M., Yeager, S., Yin, J.: Coordinated Ocean-ice reference experiments (COREs). Ocean Model. 26, 1–46 (2009). https://doi.org/10.1016/j.ocemod.2008.08.007

    Article  Google Scholar 

  • Griffies, S.M., Danabasoglu, G., Durack, P.J., Adcroft, A.J., Balaji, V., Böning, C.W., Chassignet, E.P., Curchitser, E., Deshayes, J., Drange, H., Fox-Kemper, B., Gleckler, P.J., Gregory, J.M., Haak, H., Hallberg, R.W., Heimbach, P., Hewitt, H.T., Holland, D.M., Ilyina, T., Jungclaus, J.H., Komuro, Y., Krasting, J.P., Large, W.G., Marsland, S.J., Masina, S., McDougall, T.J., Nurser, A.J.G., Orr, J.C., Pirani, A., Qiao, F., Stouffer, R.J., Taylor, K.E., Treguier, A.M., Tsujino, H., Uotila, P., Valdivieso, M., Wang, Q., Winton, M., Yeager, S.G.: OMIP contribution to CMIP6: experimental and diagnostic protocol for the physical component of the ocean model Intercomparison project. Geosci. Model Dev. 9(9), 3231–3296 (2016). https://doi.org/10.5194/gmd-9-3231-2016

    Article  Google Scholar 

  • Hense, I., Stemmler, I., Sonntag, S.: Ideas and perspectives: climate-relevant marine biologically driven mechanisms in earth system models. Biogeosciences. 14, 403–413 (2017). https://doi.org/10.5194/bg-14-403-2017

    Article  Google Scholar 

  • Hood, R.R., Kohler, K.E., McCreary, J.P., Smith, S.L.: A four-dimensional validation of a coupled physical-biological model of the Arabian Sea. Deep Sea Res. Pt II. 50, 2917–2945 (2003). https://doi.org/10.1016/j.dsr2.2003.07.004

    Article  Google Scholar 

  • Huang, B., Banzon, V. F., Freeman, E., Lawrimore, J., Liu, W., Peterson, T. C., Smith, T. M., Thorne, P. W., Woodruff, S. D., Zhang, H.-M.: Extended Reconstructed Sea surface temperature (ERSST), version 4. NOAA National Centers for Environmental Information, (2015). https://doi.org/10.7289/V5KD1VVF

  • Jochum, M., Yeager, S., Lindsay, K., Moore, K., Murtugudde, R.: Quantification of the feedback between phytoplankton and ENSO in the community climate system model. J. Clim. 23, 2916–2925 (2009). https://doi.org/10.1175/2010JCLI3254.1

    Article  Google Scholar 

  • Jones, C., Sellar, A.: Development of the 1st version of the UK Earth system model, UKESM newsletter no. 1 – August 2015 (2015). https://ukesm.ac.uk/ukesm-newsletter-no-1-august-2015/. Accessed 4 Nov 2018

  • Jung, H.-C., Moon, B.-K., Wie, J., Park, H.-S., Lee, J., Byun, Y.-H.: A single-column ocean biogeochemistry model. Geosci. Model Dev. 12, 699–722 (2019). https://doi.org/10.5194/gmd-12-699-2019

    Article  Google Scholar 

  • Koné, V., Aumont, O., Lévy, M., Resplandy, L.: Physical and biogeochemical controls of the phytoplankton seasonal cycle in the Indian Ocean: a modeling study. Geophys. Monogr. 185, 147–166 (2009). https://doi.org/10.1029/2008GM000700

    Article  Google Scholar 

  • Large, W. G., Yeager, S. G.: Diurnal to Decadal Global Forcing for Ocean and Sea-Ice Models: the Data Sets and Flux Climatologies, NCAR Technical Note, NCAR/TN-460+STR, CGD Division of the National Center for Atmospheric Research (2004)

  • Large, W.G., Yeager, S.G.: The global climatology of an interannually varying air-sea flux data set. Clim. Dyn. 33, 341–364 (2009). https://doi.org/10.1007/s00382-008-0441-3

    Article  Google Scholar 

  • 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., Pérez, F.F., Suzuki, T., Watelet, S.: A new global interior ocean mapped climatology: the 1°x1° GLODAP version 2. Earth Syst. Sci. Data. 8, 325–340 (2016). https://doi.org/10.5194/essd-8-325-2016

    Article  Google Scholar 

  • Lee, C.M., Jones, B.H., Brink, K.H., Fischer, A.S.: The upper-ocean response to monsoonal forcing in the Arabian Sea: seasonal and spatial variability. Deep Sea Res. Pt II. 47, 1177–1226 (2000)

    Article  Google Scholar 

  • Lim, H.-G., Park, J.-Y., Kug, J.-S.: Impact of chlorophyll bias on the tropical Pacific mean climate in an earth system model. Clim. Dyn. 51, 2681–2694 (2017). https://doi.org/10.1007/s00382-017-4036-8

    Article  Google Scholar 

  • Madec, G.: NEMO ocean engine. Note du Pole de modélisation, Version 3.6 27 ISSN No 1288–1619, Institut Pierre-Simon Laplace (IPSL), France (2016)

  • Madec, G., Delecluse, P., Imbard, M., Lévy, C.: OPA 8.1 Ocean General Circulation Model Reference Manual, Technical Report 11, Note du Pole de Modélisation, Institut Pierre Simon Laplace, Paris, France, 91 pp. (1998)

  • Manizza, M., Le Quéré, C., Watson, A.J., Buitenhuis, E.T.: Bio-optical feedbacks among phytoplankton, upper ocean physics and sea-ice in a global model. Geophys. Res. Lett. 32, L05603 (2005). https://doi.org/10.1029/2004GL020778

    Article  Google Scholar 

  • McClain, C.R., Cleave, M.L., Feldman, G.C., Gregg, W.W., Hooker, S.B., Kuring, N.: Science quality seaWIFS data for global biosphere research. Seal. Technol. 39, 10–16 (1998)

    Google Scholar 

  • Mignot, J., Swingedouw, D., Deshayes, J., Marti, O., Talandier, C., Séférian, R., Lengaigne, M., Madec, G.: On the evolution of the oceanic component of the IPSL climate models from CMIP3 to CMIP5: a mean state comparison. Ocean Model. 72, 167–184 (2013). https://doi.org/10.1016/j.ocemod.2013.09.001

    Article  Google Scholar 

  • Najjar, R., Orr, J. C.: Design of OCMIP-2 simulations of chlorofluorocarbons, the solubility pump and common biogeochemistry, Internal report of the Ocean Carbon-Cycle Model Intercomparison Project (OCMIP), 25 pp., LSCE/CEA Saclay, Gif-sur-Yvette, France (1998)

  • NEMO Consortium.: NEMO Reference configurations inputs (Version v3.6.1), Zenodo, (2019). https://doi.org/10.5281/zenodo.2640767

  • Orr, J.C., Najjar, R.G., Aumont, O., Bopp, L., Bullister, J.L., Danabasoglu, G., Doney, S.C., Dunne, J.P., Dutay, J.-C., Graven, H., Griffies, S.M., John, J.G., Joos, F., Levin, I., Lindsay, K., Matear, R.J., McKinley, G.A., Mouchet, A., Oschlies, A., Romanou, A., Schlitzer, R., Tagliabue, A., Tanhua, T., Yool, A.: Biogeochemical protocols and diagnostics for the CMIP6 ocean model Intercomparison project (OMIP). Geosci. Model Dev. 10, 2169–2199 (2017). https://doi.org/10.5194/gmd-10-2169-2017

    Article  Google Scholar 

  • Park, J.-Y., Kug, J.-S., Park, J.-S., Yeh, S.-W., Jang, C.J.: Variability of chlorophyll associated with ENSO and its possible biological feedback in the equatorial Pacific. J. Geophys. Res. 116, C10001 (2011). https://doi.org/10.1029/2011JC007056

    Article  Google Scholar 

  • Park, J.-Y., Kug, J.S., Seo, H., Bader, J.: Impact of bio-physical feedbacks on the tropical climate in coupled and uncoupled GCMs. Clim. Dyn. 43, 1811–1827 (2014). https://doi.org/10.1007/s00382-013-2009-0

    Article  Google Scholar 

  • Park, H.-J., Moon, B.-K., Wie, J., Kim, K.-Y., Lee, J., Byun, Y.-H.: Biophysical effects simulated by an ocean general circulation model coupled with a biogeochemical model in the tropical Pacific. J. Korean Earth Sci. Soc. 38(7), 469–480 (2017). https://doi.org/10.5467/JKESS.2017.38.7.469

    Article  Google Scholar 

  • Park, J.-Y., Dunne, J.P., Stock, C.A.: Ocean chlorophyll as a precursor of ENSO: an earth system modeling study. Geophys. Res. Lett. 45, 1939–1947 (2018). https://doi.org/10.1002/2017GL076077

    Article  Google Scholar 

  • Penduff, T., Le Sommer, J., Barnier, B., Treguier, A.-M., Molines, J.-M., Madec, G.: Influence of numerical schemes on current-topography interactions in 1/4_ global ocean simulations. Ocean Sci. 3, 509–524 (2007). https://doi.org/10.5194/os-3-509-2007

    Article  Google Scholar 

  • Rousset, C., Vancoppenolle, M., Madec, G., Fichefet, T., Flavoni, S., Barthélemy, A., Benshila, R., Chanut, J., Levy, C., Masson, S., Vivier, F.: The Louvain-La-Neuve Sea ice model LIM3.6: global and regional capabilities. Geosci. Model Dev. 8, 2991–3005 (2015). https://doi.org/10.5194/gmd-8-2991-2015

    Article  Google Scholar 

  • Sauerland, V., Löptien, U., Leonhard, C., Oschlies, A., Srivastav, A.: Error assessment of biogeochemical models by lower bound methods (NOMMA-1.0). Geosci. Model Dev. 11, 1181–1198 (2018). https://doi.org/10.5194/gmd-11-1181-2018

    Article  Google Scholar 

  • Séférian, R., Bopp, L., Gehlen, M., Orr, J.C., Ethé, C., Cadule, P., Aumont, O., Mélia, D.S., Voldoire, A., Madec, G.: Skill assessment of three earth system models with common marine biogeochemistry. Clim. Dyn. 40, 2549–2573 (2013). https://doi.org/10.1007/s00382-012-1362-8

    Article  Google Scholar 

  • Séférian, R., Gehlen, M., Bopp, L., Resplandy, L., Orr, J.C., Marti, O., Dunne, J.P., Christian, J.R., Doney, S.C., Ilyina, T., Lindsay, K., Halloran, P.R., Heinze, C., Segschneider, J., Tjiputra, J., Aumont, O., Romanou, A.: Inconsistent strategies to spin up models in CMIP5: implications for ocean biogeochemical model performance assessment. Geosci. Model Dev. 9, 1827–1851 (2016). https://doi.org/10.5194/gmd-9-1827-2016

    Article  Google Scholar 

  • Smith, G.C., Haines, K., Kanzow, T., Cunningham, S.: Impact of hydrographic data assimilation on the modelled Atlantic meridional overturning circulation. Ocean Sci. 6, 761–774 (2010). https://doi.org/10.5194/os-6-761-2010

    Article  Google Scholar 

  • Sokolov, A., Kicklighter, D., Schlosser, C.A., Wang, C., Monier, E., Brown-Steiner, B., Prinn, R., Forest, C., Gao, X., Libardoni, A., Eastham, S.: Description and evaluation of the MIT earth system model (MESH). J. Adv. Model. Earth Syst. 10, 1759–1789 (2018). https://doi.org/10.1029/2018MS001277

    Article  Google Scholar 

  • Sonntag, S., Hense, I.: Phytoplankton behavior affects ocean mixed layer dynamics through biological-physical feedback mechanisms. Geophys. Res. Lett. 38, L15610 (2011). https://doi.org/10.1029/2011GL048205

    Article  Google Scholar 

  • Steele, M., Morley, R., Ermold, W.: Phc-a global ocean hydrography with a high-quality arctic ocean. J. Clim. 14(9), 2079–2087 (2001). https://doi.org/10.1175/1520-0442(2001)014<2079:PAGOHW>2.0.CO;2

    Article  Google Scholar 

  • Stute, M., Clement, A., Lohmann, G.: Global climate models: past, present, and future. Proc. Natl. Acad. Sci. U. S. A. 98, 10529–10530 (2001). https://doi.org/10.1073/pnas.191366098

    Article  Google Scholar 

  • Taylor, K.E.: Summarizing multiple aspects of model performance in a single diagram. J. Geophys. Res.-Atmos. 106, 7183–7192 (2001). https://doi.org/10.1029/2000JD900719

    Article  Google Scholar 

  • Timmermann, R., Goosse, H., Madec, G., Fichefet, T., Ethe, C., Duliere, V.: On the representation of high latitude processes in the ORCA-LIM global coupled sea ice-ocean model. Ocean Model. 8, 175–201 (2005). https://doi.org/10.1016/j.ocemod.2003.12.009

    Article  Google Scholar 

  • Wanninkhof, R.: Relationship between wind speed and gas exchange over the ocean. J. Geophys. Res. 97, 7373–7382 (1992). https://doi.org/10.1029/92JC00188

    Article  Google Scholar 

  • Wunsch, C., Heimbach, P.: How long to oceanic tracer and proxy equilibrium? Quat. Sci. Rev. 27, 637–651 (2008). https://doi.org/10.1016/j.quascirev.2008.01.006

    Article  Google Scholar 

Download references

Acknowledgements

This work was funded by the Korea Meteorological Administration Research and Development Program under grant KMI (KMI2018-03513). The main calculations were performed by using the supercomputing resource of the Korea Meteorological Administration (National Center for Meteorological Supercomputer). This work is a park of Dr. Jung's Ph.D. thesis.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Byung-Kwon Moon.

Additional information

Responsible Editor: Soon-Il An.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jung, HC., Moon, BK., Lee, H. et al. Development and Assessment of NEMO(v3.6)-TOPAZ(v2), a Coupled Global Ocean Biogeochemistry Model. Asia-Pacific J Atmos Sci 56, 411–428 (2020). https://doi.org/10.1007/s13143-019-00147-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13143-019-00147-4

Keywords

Navigation