Oceanography The Official Magazine of
The Oceanography Society
Volume 23 Issue 03

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Volume 23, No. 3
Pages 126 - 139


Models: Tools for Synthesis in International Oceanographic Research Programs

Dennis J. McGillicuddy Jr. Brad deYoungScott C. DoneyPatricia M. GlibertDetlef Stammer Francisco E. Werner
First Paragraph

Through its promotion of coordinated international research programs, the Intergovernmental Oceanographic Commission (IOC) has facilitated major progress on some of the most challenging problems in oceanography. Issues of global significance—such as general ocean circulation, the carbon cycle, the structure and dynamics of ecosystems, and harmful algal blooms—are so large in scope that they require international collaboration to be addressed systematically. International collaborations are even more important when these issues are affected by anthropogenic processes—such as climate change, CO2 enhancement, ocean acidification, pollution, and eutrophication—whose impacts may differ greatly throughout the global ocean. These problems require an entire portfolio of research activities, including global surveys, regional process studies, time-series observations, laboratory-based investigations, and satellite remote sensing. Synthesis of this vast array of results presents its own set of challenges (Hofmann et al., 2010), and models offer an explicit framework for integration of the knowledge gained as well as detailed investigation of the underlying dynamics. Models help us to understand what happened in the past, and to make predictions of future changes—both of which support the development of sound policy and decision making. We review examples of how models have been used for this suite of purposes, focusing on areas where IOC played a key role in organizing and coordinating the research activities.


McGillicuddy, D.J. Jr., B. deYoung, S.C. Doney, P.M. Glibert, D. Stammer, and F.E. Werner. 2010. Models: Tools for synthesis in international oceanographic research programs. Oceanography 23(3):126–139, https://doi.org/10.5670/oceanog.2010.28.


Anderson, D.M., B. Reguera, G.C. Pitcher, and H.O. Enevoldsen. 2010. The IOC International Harmful Algal Bloom Program: History and science impacts. Oceanography 23(3):72–85. [CrossRef]

Anderson, D.A., P.M. Glibert, and J.M. Burkholder. 2002. Harmful algal blooms and eutrophication: Nutrient sources, composition, and consequences. Estuaries 25:562­–584. [CrossRef]

Backer, L.C., and D.J. McGillicuddy Jr. 2006. Harmful algal blooms at the interface between coastal oceanography and human health. Oceanography 19(2):94–106. [pdf]

Barange, M., J.G. Field, R.H. Harris, E. Hofmann, R.I. Perry, and F.E. Werner, eds. 2010. Marine Ecosystems and Global Change. Oxford University Press, New York, 464 pp.

Barton, A.D., S. Dutkiewicz, J. Bragg, G. Flierl, and M.J. Follows. 2010. Patterns of marine phytoplankton diversity. Science 327:1,509–1,511. [CrossRef]

Bartsch, J., K. Brander, M. Heath, P. Munk, K. Richardson, and E. Svendsen. 1989. Modelling the advection of herring larvae in the North Sea. Nature 340:632–636. [CrossRef]

Batchelder, H.P., C.A. Edwards, and T.M. Powell. 2002. Individual-based models of copepod populations in coastal upwelling regions: Implications of physiologically and environmentally influenced diel vertical migration on demographic success and nearshore retention. Progress in Oceanography 53:307–333. [CrossRef]

Burkholder, J.M., P.M. Glibert, and H.M. Skelton. 2008. Mixotrophy, a major mode of nutrition for harmful algal species in eutrophic waters. Harmful Algae 8:77–93. [CrossRef]

Caley, M.J., M.H. Carr, M.A. Hixon, T.P. Hughes, G.P. Jones, and B.A. Menge. 1996. Recruitment and the local dynamics of open marine populations. Annual Review of Ecology and Systematics 27:477–500. [CrossRef]

Chai, F., M. Jiang, R.T. Barber, R.C. Dugdale, and Y. Chao. 2003. Interdecadal variation of the transition zone chlorophyll front, a physical-biological model simulation between 1960 and 1990. Journal of Oceanography 59:461–475. [CrossRef]

Cowen, R.K., K.M.M. Lwiza, S. Sponaugle, C.B. Paris, and D.B. Olson. 2000. Connectivity of marine populations: Open or closed? Science 287:857–859. [CrossRef]

Cowen, R.K., S. Thorrold, J. Pineda, G. Gawarkiewicz, and F. Werner. 2007. Population connectivity in marine systems: An overview. Oceanography 20(3):16–23. [pdf]

deYoung, B., M. Heath, F. Werner, F. Chai, B. Megrey, and P. Monfray. 2004. Challenges of modeling ocean basin ecosystems. Science 304:1,463–1,466.

Doney, S.C., and H.W. Ducklow. 2006. A decade of synthesis and modeling in the US Joint Global Ocean Flux Study. Deep-Sea Research Part II 53(5­–7):451–458. [CrossRef]

Doney, S.C., B. Tilbrook, S. Roy, N. Metzl, C. Le Quéré, M. Hood, R.A. Feely, and D. Bakker. 2009. Surface ocean CO2 variability and vulnerability. Deep-Sea Research Part II 56:504–511. [CrossRef]

Dumont, E., J.H. Harrison, C. Kroeze, E.J. Bakker, and S.P. Seitzinger. 2005. Global distribution and sources of dissolved inorganic nitrogen export to the coastal zone: Results from a spatially explicit, global model. Global Biogeochemical Cycles 19(4):1–14. [CrossRef]

Dutkiewicz, S., M.J. Follows, and J.G. Bragg. 2009. Modeling the coupling of ocean ecology and biogeochemistry. Global Biogeochemical Cycles 23, GB4017. [CrossRef]

Fasham, M.J.R., B.M. Balino, M.C. Bowles, R. Anderson, D. Archer, U. Bathmann, P. Boyd, K. Buesseler, P. Burkill, A. Bychkov, and others. 2001. A new vision of ocean biogeochemistry after a decade of the Joint Global Ocean Flux Study (JGOFS). AMBIO, Special Issue 10:4–31.

Flynn, K.J., and A. Mitra. 2009. Building the “perfect beast”: Modelling mixotrophic plankton. Journal of Plankton Research 31:965–992. [CrossRef]

Fogarty, M.J., and L.W. Botsford. 2007. Population connectivity and spatial management of marine fisheries. Oceanography 20(3):112–123. [pdf]

Follows, M.J., S. Dutkiewicz, S. Grant, and S.W. Chisholm. 2007. Emergent biogeography of microbial communities in a model ocean. Science 315:1,843–1,846. [CrossRef]

Friedlingstein, P., P. Cox, R. Betts, L. Bopp, W. von Bloh, V. Brovkin, P. Cadule, S. Doney, M. Eby, I. Fung, and others. 2006. Climate–carbon cycle feedback analysis: Results from the C4MIP model intercomparison. Journal of Climate 19(14):3,337–3,353.

Friedrichs, M.A.M., J.A. Dusenberry, L.A. Anderson, R. Armstrong, F. Chai, J.R. Christian, S.C. Doney, J. Dunne, M. Fujii, R. Hood, and others. 2007. Assessment of skill and portability in regional marine biogeochemical models: The role of multiple planktonic groups. Journal of Geophysical Research 112, C08001. [CrossRef]

Gell, F.R., and C.M. Roberts. 2003. Benefits beyond boundaries: The fishery effects of marine reserves. Trends in Ecology and Evolution 18:448–455. [CrossRef]

Giering, R., and T. Kaminski. 1998. Recipes for adjoint code construction. ACM Transactions on Mathematical Software 24:437–474. [CrossRef]

Glibert, P.M., S. Seitzinger, C.A. Heil, J.M. Burkholder, M.W. Parrow, L.A. Codispoti, and V. Kelly. 2005. The role of eutrophication in the global proliferation of harmful algal blooms: New perspectives and new approaches. Oceanography 18(2):198–209. [pdf]

Glibert, P.M., and J.M. Burkholder. 2006. The complex relationships between increasing fertilization of the earth, coastal eutrophication and proliferation of harmful algal blooms. Pp. 341–354 in Ecology of Harmful Algae. E. Graneli and J. Turner, eds, Springer, Netherlands. [CrossRef]

Glibert, P.M., E. Mayorga, and S. Seitzinger. 2008. Prorocentrum minimum tracks anthropogenic nitrogen and phosphorus inputs on a global basis: Application of spatially explicit nutrient export models. Harmful Algae 8(1):33–38. [CrossRef]

Glibert, P.M., J.I. Allen, L. Bouwman, C. Brown, K.J. Flynn, A. Lewitus, and C. Madden. 2010. Modeling of HABs and eutrophication: Status, advances, challenges. Journal of Marine Systems. [CrossRef]

Glibert, P.M., J. Alexander, D.W. Meritt, E.W. North, and D.K. Stoecker. 2007. Harmful algae pose additional challenges for oyster restoration: Impacts of the harmful algae Karlodinium veneficum and Prorocentrum minimum on early life stages of the oysters Crassostrea virginica and Crassostrea ariakensis. Journal of Shellfish Research 26:919–925. [CrossRef]

Glibert, P.M., J. Harrison, C. Heil, and S. Seitzinger. 2006. Escalating worldwide use of urea: A global change contributing to coastal eutrophication. Biogeochemistry 77:441–463. [CrossRef]

Glibert, P.M., R. Magnien, M.W. Lomas, J. Alexander, C. Fan, E. Haramoto, M. Trice, and T.M. Kana. 2001. Harmful algal blooms in the Chesapeake and Coastal Bays of Maryland, USA: Comparisons of 1997, 1998, and 1999 events. Estuaries 24:875–883. [CrossRef]

Gruber, N., H. Frenzel, S.C. Doney, P. Marchesiello, J.C. McWilliams, J.R. Moisan, J.J. Oram, G.-K. Plattner, and K.D. Stolzenbach. 2006. Eddy-resolving simulation of plankton ecosystem dynamics in the California current system. Deep-Sea Research Part I 53:1,483–1,516. [CrossRef]

Gruber, N., M. Gloor, S.E. Mikaloff, S.C. Fletcher, S. Doney, S. Dutkiewicz, M.J. Follows, M. Gerber, A.R. Jacobson, F. Joos, and others. 2009. Oceanic sources, sinks, and transport of atmospheric CO2. Global Biogeochemical Cycles 23, GB1005. [CrossRef]

Hall, J., D.E. Harrison, and D. Stammer, eds. 2010. Proceedings of the “OceanObs’09: Sustained Ocean Observations and Information for Society” Conference. Venice, Italy, 21–25 September 2009, European Space Agency Publication WPP-306, Paris.

Heisler, J., P.M. Glibert, J.M. Burkholder, D.M. Anderson, W. Cochlan, W.C. Dennison, Q. Dortch, C.J. Gobler, C.A. Heil, E. Humphries, and others. 2008. Eutrophication and harmful algal blooms: A scientific consensus. Harmful Algae 8:3–13. [CrossRef]

Hjort, J. 1914. Fluctuations in the great fisheries of northern Europe. Rapports et Procès-Verbaux des Réunions du Conseil International pour l’Exploration de la Mer 20:1–228.

Hood, R.R., E.A. Laws, R.A. Armstrong, N.R. Bates, C.W. Brown, C.A. Carlson, F. Chai, S.C. Doney, P.G. Falkowski, R.A. Feely, and others. 2006a. Pelagic functional group modeling: Progress, challenges and prospects. Deep-Sea Research Part II 53(5–7):459–512. [CrossRef]

Hood, R.R., X. Zhang, P.M. Glibert, M.R. Roman, and D. Stoecker. 2006b. Modeling the influence of nutrients, turbulence and grazing on Pfiesteria dynamics. Harmful Algae 5:459–479. [CrossRef]

Hofmann, E.E., and E. Gross. 2010. IOC contributions to science synthesis. Oceanography 23(3):152–159. [CrossRef]

Howarth, R.W. 2008. Coastal nitrogen pollution: A review of sources and trends globally and regionally. Harmful Algae 8:14–20. [CrossRef]

Irigoien, X., K.J. Flynn, and R.P. Harris. 2005. Phytoplankton blooms: A “loophole” in microzooplankton grazing impact? Journal of Plankton Research 27:313–321. [CrossRef]

Key, R.M., A. Kozyr, C.L. Sabine, K. Lee, R. Wanninkhof, J. Bullister, R.A. Feely, F. Millero, C. Mordy, and T.-H. Peng. 2004. A global ocean carbon climatology: Results from GLODAP. Global Biogeochemical Cycles 18, GB4031. [CrossRef]

Kishi, M.J., M. Kashiwai, D.M. Ware, B.A. Megrey, D.L. Eslinger, F.E. Werner, M.N. Aita, T. Azumaya, M. Fujii, S. Hashimoto, and others. 2007. NEMURO: A lower trophic level model for the North Pacific marine ecosystem. Ecological Modelling 202(1–2):12–25. [CrossRef]

Köhl, A., and D. Stammer. 2008. Variability of the meridional overturning in the North Atlantic from 50-year GECCO state estimation. Journal of Physical Oceanography 38:1,913–1,930.

Landsberg, J. 2002. The effects of harmful algal blooms on aquatic organisms. Reviews in Fisheries Science 10:113–190. [CrossRef]

Lee, T., D. Stammer, T. Awaji, M. Balmaseda, D. Behringer, J. Carton, N. Ferry, A. Fischer, I. Fukumori, B. Giese, and others. 2010. Ocean state estimation for climate research. In Proceedings of the “OceanObs’09: Sustained Ocean Observations and Information for Society” Conference (Vol. 2). Venice, Italy, 21–25 September 2009, European Space Agency Publication WPP-306, Paris, 13 pp. Available online at http://www.oceanobs09.net/blog/?p=106 (accessed May 28, 2010).

Lehodey, P., F. Chai, and J. Hampton. 2003. Modelling climate-related variability of tuna populations from a coupled ocean- biogeochemical-populations dynamics model. Fisheries Oceanography 12:483–494. [CrossRef]

Le Quéré, C., S.P. Harrison, I.C. Prentice, E.T. Buitenhuis, O. Aumont, L. Bopp, H. Claustre, L.C. Da Cunha, R. Geider, X. Giraud, and others. 2005. Ecosystem dynamics based on plankton functional types for global ocean biogeochemistry models. Global Change Biology 11:2,016–2,040.

Le Quéré, C., M.R. Raupach, J.G. Canadell, G. Marland, L. Bopp, P. Ciais, T.J. Conway, S.C. Doney, R.A. Feely, P. Foster, and others. 2009. Trends in the sources and sinks of carbon dioxide. Nature Geoscience 2:831–836. [CrossRef]

Marotzke, J., R. Giering, Q.K. Zhang, D. Stammer, C.N. Hill, and T. Lee. 1999. Construction of the adjoint MIT ocean general circulation model and application to Atlantic heat transport sensitivity. Journal of Geophysical Research 104(29):529–548.

Marshall, J., A. Adcroft, C. Hill, L. Perelman, and C. Heisey. 1997. A finite-volume, incompressible Navier-Stokes model for studies of the ocean on parallel computers. Journal of Geophysical Research 102:5,753–5,766.

Matsumoto, K., J.L. Sarmiento, R.M. Key, J.L. Bullister, K. Caldeira, J.M. Campin, S.C. Doney, H. Drange, J.C. Dutay, M. Follows, and others. 2004. Evaluation of ocean carbon cycle models with data-based metrics. Geophysical Research Letters 31, L07303. [CrossRef]

McGillicuddy, D.J. Jr., L.A. Anderson, S.C. Doney, and M.E. Maltrud. 2003. Eddy-driven sources and sinks of nutrients in the upper ocean: Results from a 0.1 degree resolution model of the North Atlantic. Global Biogeochemical Cycles 17(2), 1035. [CrossRef]

Moore, J.K., S.C. Doney, and K. Lindsay. 2004. Upper ocean ecosystem dynamics and iron cycling in a global 3-D model. Global Biogeochemical Cycles 18, GB4028. [CrossRef]

Mullon, C., P. Cury, and P. Penven. 2002. Evolutionary individual-based model for the recruitment of anchovy (Engraulis capensis) in the southern Benguela. Canadian Journal of Fisheries and Aquatic Science 59:910–922. [CrossRef]

Mullon, C., P. Fréon, C. Parada, C. van der Lingen, and J. Huggett. 2003. From particles to individuals: Modeling the early stages of anchovy in the Southern Benguela. Fisheries Oceanography 12(4):396–406. [CrossRef]

Munk, W., and C. Wunsch. 1982. Observing the ocean in the 1990s. Philosophical Transactions of the Royal Society London A 307:439–464. [CrossRef]

Najjar, R.G., H.A. Walker, P.J. Anderson, E.J. Barron, R.J. Bord, J.R. Gibson, V.S. Kennedy, C.G. Knight, J.P. Megonigal, R.E. O’Connor, and others. 2000. The potential impacts of climate change on the mid-Atlantic coastal region. Climate Research 14:219–233. [CrossRef]

Najjar, R.G., X. Jin, F. Louanchi, O. Aumont, K. Caldeira, S.C. Doney, J.C. Dutay, M. Follows, N. Gruber, F. Joos, and others. 2007. Impact of circulation on export production, dissolved organic matter and dissolved oxygen in the ocean: Results from phase II of the Ocean Carbon-cycle Model Intercomparison Project (OCMIP-2). Global Biogeochemical Cycles 21, GB3007. [CrossRef]

Orr, J.C., V.J. Fabry, O. Aumont, L. Bopp, S.C. Doney, R.A. Feely, A. Gnanadesikan, N. Gruber, A. Ishida, F. Joos, and others. 2005. Anthropogenic ocean acidification over the twenty-first century and its impact on marine calcifying organisms. Nature 437:681–686. [CrossRef]

Oschlies, A. 2002. Can eddies make ocean deserts bloom? Global Biogeochemical Cycles 16(4), 1106. [CrossRef]

Palumbi, S.R. 2004. Marine reserves and ocean neighbourhoods: The spatial scale of marine populations and their management. Annual Reviews of Environmental Resources 29:31–68. [CrossRef]

Parada, C., C. Mullon, C. Roy, P. Freon, L. Hutchings, and C. van der Lingen. 2008. Does vertical migratory behaviour retain fish larvae inshore in upwelling ecosystems? A modeling study of anchovy in the southern Benguela. African Journal of Marine Science 18(3):437–452. [CrossRef]

Raven, J.A., J. Beardall, K.J. Flynn, and S.C. Maberly. In press. Phagotrophy in the origins of photosynthesis in eukaryotes and as a complementary mode of nutrition in phototrophs: Relation to Darwin’s insectivorous plants. Journal of Experimental Botany.

Rose, K.A., B.A. Megrey, D. Hay, F. Werner, and J. Schweigert. 2008. Climate regime effects on Pacific herring growth using coupled nutrient-phytoplankton-zooplankton and bioenergetics models. Transactions of the American Fisheries Society 137:278–297. [CrossRef]

Sarmiento, J., R. Slater, R. Barber, L. Bopp, S.C. Doney, A.C. Hirst, J. Kleypas, R. Matear, U. Mikolajewicz, P. Monfray, and others. 2004. Response of ocean ecosystems to climate warming. Global Biogeochemical Cycles 18, GB3003. [CrossRef]

Seitzinger, S.P., J.A. Harrison, E. Dumont, A.H.W. Beusen, and A.F. Bouwman. 2005. Sources and delivery of carbon, nitrogen and phosphorous to the coastal zone: An overview of global nutrient export from watersheds (NEWS) models and their application. Global Biogeochemical Cycles 19, GB4S01. [CrossRef]

Speirs, D.C., W.S.C. Gurney, M.R. Heath, W. Horbelt, S.N. Wood, and B.A. de Cuevas. 2006. Ocean-scale modelling of the distribution, abundance, and seasonal dynamics of the copepod Calanus finmarchicus. Marine Ecology Progress Series 313:173–192. [CrossRef]

Stammer, D., C. Wunsch, I. Fukumori, and J. Marshall. 2002. State estimation improves prospects for ocean research. Eos, Transactions, American Geophysical Union 83(27):294–295.

Stammer, D., A. Köhl, T. Awaji, M. Balmaseda, D. Behringer, J. Carton, N. Ferry, A. Fischer, I. Fukumori, B. Giese, and others. 2010. Ocean information provided through ensemble ocean syntheses. Pp. 21–25 in Proceedings of OceanObs’09: Sustained Ocean Observations and Information for Society (Vol. 2). Venice, Italy, September 2009, J. Hall, D.E. Harrison, and D. Stammer, eds, European Space Agency Publication WPP-306, Paris. Available online at: http://ecco2.org/manuscripts/2009/StammerOceanObs09.pdf (accessed June 17, 2010).

Steinacher, M., F. Joos, T.L. Frölicher, L. Bopp, P. Cadule, V. Cocco, S.C. Doney, M. Gehlen, K. Lindsay, J.K. Moore, and others. 2009. Projected 21st century decrease in marine productivity: A multi-model analysis. Biogeosciences 7:979–1,005.

Stoecker, D.K., A.E. Thessen, and D.E. Gustafson. 2008. “Windows of opportunity” for dinoflagellate blooms: Reduced microzooplankton net growth coupled to eutrophication. Harmful Algae 8:140–151. [CrossRef]

Stumpf, R.P. 2008. Developing operational capabilities for nowcasts and forecasts of harmful algal blooms. Pp. 96–98 in Proceedings XII International Conference on Harmful Algae. Copenhagen, September 2006, IOC of UNESCO, Paris.

Tiedeken, J.A., and J.S. Ramsdell. 2007. Embryonic exposure to domoic acid increases the susceptibility of zebrafish larvae to the chemical convulsant pentylenetetrazole. Environmental Health Perspectives 115(11):1,547–1,552.

Werner, F.E., F.H. Page, D.R. Lynch, J.W. Loder, R.G. Lough, R.I. Perry, D.A. Greenberg, and M.M. Sinclair. 1993. Influence of mean 3-D advection and simple behavior on the distribution of cod and haddock early life history stages on Georges Bank. Fisheries Oceanography 2:43–64. [CrossRef]

Werner, F.E., R.K. Cowen, and C.B. Paris. 2007. Coupled biological and physical models: Present capabilities and necessary developments for future studies of population connectivity. Oceanography 20(3):54–69. [pdf]

Wunsch, C., R.M. Ponte, and P. Heimbach. 2007. Decadal trends in sea level patterns: 1993–2004. Journal of Climate 20:5,889–5,911.

Wunsch, C. 2006. Discrete Inverse and State Estimation Problems With Geophysical Fluid Applications. Cambridge University Press, Cambridge, 371 pp. [CrossRef]

Wunsch, C., P. Heimbach, R. Ponte, I. Fukumori, and the ECCO-Consortium members. 2009. The global general circulation of the oceans estimated by the ECCO-Consortium. Oceanography 22(2):88–103. [pdf]

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