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Title: A generalized model of pelagic biogeochemistry for the global ocean ecosystem. Part I: theory
Authors: Vichi, M.*
Pinardi, N.*
Masina, S.*
Keywords: Marine biogeochemistry
Biomass-based ecosystem model
Issue Date: 2006
Publisher: Elsevier
Title of journal: Journal of Marine Systems
Series/Report no.: 1-4 / 64 (2007)
Abstract: The set of equations for global ocean biogeochemistry deterministic models have been formulated in a comprehensive and unified form in order to use them in numerical simulations of the marine ecosystem for climate change studies (PELAGOS, PELAgic biogeochemistry for Global Ocean Simulations). The fundamental approach stems from the representation of marine trophic interactions and major biogeochemical cycles introduced in the European Regional Seas Ecosystem Model (ERSEM). Our theoretical formulation revisits and generalizes the stoichiometric approach of ERSEM by defining the state variables as Chemical Functional Families (CFF). CFFs are further subdivided into living, non-living and inorganic components. Living CFFs are the basis for the definition of Living Functional Groups, the biomass-based functional prototype of the real organisms. Both CFFs and LFGs are theoretical constructs which allow us to relate measurable properties of marine biogeochemistry to the state variables used in deterministic models. This approach is sufficiently generic that may be used to describe other existing biomass-based ecosystem model.
URI: http://hdl.handle.net/2122/2588
DOI: 10.1016/j.jmarsys.2006.03.006
Appears in Collections:Papers Published / Papers in press
03.01.01. Analytical and numerical modeling
03.04.01. Biogeochemical cycles
03.01.07. Physical and biogeochemical interactions

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  • Allen, J., Blackford, J., Radford, P., 1998. A 1-D vertically resolved
  • modelling study of the ecosystem dynamics of the Middle and
  • Southern Adriatic Sea. J. Mar. Syst. 18, 265–286.
  • Allen, J., Blackford, J., Holt, J., Proctor, R., Ashworth, M., Siddorn, J.,
  • 2001. A highly spatially resolved ecosystem model for the North
  • West European Continental Shelf. Sarsia 86, 423–440.
  • Andersen, T., Elser, J.J., Hessen, D.O., 2004. Stoichiometry and
  • population dynamics. Ecol. Lett. 7, 884–900.
  • Anderson, T.R., 2005. Plankton functional type modelling: running
  • before we can walk? J. Plankton. Res. 27, 1073–1081.
  • Archer, D.E., Johnson, K.S., 2000. A model of the iron cycle in the
  • ocean. Glob. Biogeochem. Cycles 14, 269–279.
  • Aumont, O., Maier-Reimer, E., Monfray, P., Blain, S., 2003. An
  • ecosystem model of the global ocean including Fe, Si, P colimitations.
  • Glob. Biogeochem. Cycles 17 (2), 1060.
  • Baretta, J., Ruardij, P., 1988. Tidal Flat Estuaries: Simulation and
  • Analysis of the Ems Estuary. Vol. 71 of Ecol. Studies. Springer
  • Verlag, Heidelberg.
  • Baretta, J., Ebenhöh, W., Ruardij, P., 1995. The European Regional
  • Seas Ecosystem Model, a complex marine ecosystem model. J. Sea
  • Res. 33 (3–4), 233–246.
  • Baretta-Bekker, J., Baretta, J., Rasmussen, E., 1995. The microbial
  • food web in the European Regional Seas Ecosystem Model. J. Sea
  • Res. 33 (3–4), 363–379.
  • Baretta-Bekker, J., Baretta, J., Ebenhoeh, W., 1997. Microbial
  • dynamics in the marine ecosystem model ERSEM II with
  • decoupled carbon assimilation and nutrient uptake. J. Sea Res.
  • 38 (3/4), 195–212.
  • Batchelor, G., 1967. An Introduction to Fluid Dynamics. Cambridge
  • University Press, Cambridge.
  • Behrenfeld, M.J., Prasil, O., Babin, M., Bruyant, F., 2004. In search of
  • a physiological basis for covariations in light-limited and lightsaturated
  • photosynthesis. J. Phycol. 40, 4–25.
  • Bidle, K.D., Azam, F., 2001. Bacterial control of silicon regeneration
  • from diatom detritus: significance of bacterial ectohydrolases and
  • species identity. Limnol. Oceanogr. 46 (7), 1606–1623.
  • Blackford, J.C., Burkill, P.H., 2002. Planktonic community structure
  • and carbon cycling in the Arabian Sea as a result of monsoonal
  • forcing: the application of a generic model. J. Mar. Syst. 36 (3),
  • 239–267.
  • Blackford, J., Radford, P., 1995. A structure and methodology for
  • marine ecosystem modelling. J. Sea Res. 33 (3–4), 247–260.
  • Blackford, J.C., Allen, J.I., Gilbert, F.J., 2004. Ecosystem dynamics at
  • six contrasting sites: a generic modelling study. J. Mar. Syst. 52,
  • 191–215.
  • Boyd, P.W., Watson, A.J., Law, C.S., Abraham, E.R., Trull, T.,
  • Murdoch, R., Bakker, D.C.E., Bowie, A.R., Buesseler, K.O.,
  • Chang, H., Charette, M., Croot, P., Downing, K., Frew, R., Gall,
  • M., Hadfield, M., Hall, J., Harvey, M., Jameson, G., LaRoche,
  • J., Liddicoat, M., Ling, R., Maldonado, M.T., McKay, R.M.,
  • Nodder, S., Pickmere, S., Pridmore, R., Rintoul, S., Safi, K.,
  • Sutton, P., Strzepek, R., Tanneberger, K., Turner, S., Waite, A.,
  • Zeldis, J., 2000. A mesoscale phytoplankton bloom in the polar
  • Southern Ocean stimulated by iron fertilization. Nature 407,
  • 695–702.
  • M. Vichi et al. / Journal of Marine Systems xx (2006) xxx–xxx 19
  • ARTICLE IN PRESS
  • Broekhuizen, N., Heath, M., Hay, S., Gurney,W., 1995. Modelling the
  • dynamics of the North Sea's mesozooplankton. J. Sea Res. 33 (3–
  • 4), 381–406.
  • Coale, K.H., Fitzwater, S.E., Gordon, R.M., Johnson, K.S., Barber, R.
  • T., 1996. Control of community growth and export production by
  • upwelled iron in the equatorial Pacific ocean. Nature 379,
  • 621–624.
  • Denman, K.L., 2003. Modelling planktonic ecosystems: parameterizing
  • complexity. Prog. Oceanogr. 57, 429–452.
  • deYoung, B., Heath, M.,Werner, F., Chai, F., Megrey, B., Monfray, P.,
  • 2004. Challenges of modeling ocean basin ecosystems. Science
  • 304, 1463–1466.
  • Doney, S.C., Lindsay, K., Caldeira, K., Campin, J.M., Drange, H.,
  • Dutay, J.C., Follows, M., Gao, Y., Gnanadesikan, A., Gruber, N.,
  • Ishida, A., Joos, F., Madec, G., Maier-reimer, E., Marshall, J.C.,
  • Matear, R.J., Monfray, P., Mouchet, A., Najjar, R., Orr, J.C.,
  • Plattner, G.K., Sarmiento, J., Schlitzer, R., Slater, R., Totterdell, I.
  • J., Weirig, M.F., Yamanaka, Y., Yool, A., 2004. Evaluating global
  • ocean carbon models: the importance of realistic physics. Glob.
  • Biogeochem. Cycles 18, 3017.
  • Ebenhöh, W., Baretta-Bekker, J., Baretta, J., 1997. The primary
  • production module in the marine ecosystem model ERSEM II with
  • emphasis on the light forcing. J. Sea Res. 38, 173–193.
  • Elser, J.J., Hessen, D.O., 2005. Biosimplicity via stoichiometry: the
  • evolution of food-web structure and processes. In: Belgrano, A.,
  • Scharler, D., Ulanowicz, U. (Eds.), Aquatic Food Webs: An
  • Ecosystem Approach. Oxford University Press, Oxford, UK,
  • pp. 7–18.
  • Fennel, W., Osborn, T., 2005. A unifying framework for marine
  • ecological model comparison. Deep-Sea Res., Part 2, Top. Stud.
  • Oceanogr. 52, 1344–1357.
  • Flynn, K.J., 2001. A mechanistic model for describing dynamic multinutrient,
  • light, temperature interactions in phytoplankton. J.
  • Plankton. Res. 23, 977–997.
  • Flynn, K.J., Marshall, H., Geider, R.J., 2001. A comparison of two Nirradiance
  • interaction models of phytoplankton growth. Limnol.
  • Oceanogr. 46, 1794–1802.
  • Frost, P.C., Xenopoulos, M.A., Larson, J.H., 2004. The stoichiometry
  • of dissolved organic carbon, nitrogen, and phosphorus release by a
  • planktonic grazer, Daphnia. Limnol. Oceanogr. 49, 1802–1808.
  • Fung, I.Y., Meyn, S.K., Tegen, I., Doney, S.C., John, J.G., Bishop, J.K.
  • B., 2000. Iron supply and demand in the upper ocean. Glob.
  • Biogeochem. Cycles 14, 281–295.
  • Geider, R., MacIntyre, H., Kana, T., 1996. A dynamic model of
  • photoadaptation in phytoplankton. Limnol. Oceanogr. 41 (1), 1–15.
  • Geider, R., MacIntyre, H., Kana, T., 1997. A dynamic model of
  • phytoplankton growth and acclimation: responses of the balanced
  • growth rate and chlorophyll a:carbon ratio to light, nutrient
  • limitation and temperature. Mar. Ecol. Prog. Ser. 148, 187–200.
  • Geider, R., MacIntyre, H., Kana, T., 1998. A dynamic regulatory
  • model of phytoplanktonic acclimation to light, nutrients, and
  • temperature. Limnol. Oceanogr. 43 (3), 679–694.
  • Gentleman, W., Leising, A., Frost, B., Strom, S., Murray, J., 2003.
  • Functional responses for zooplankton feeding on multiple
  • resources: a review of assumptions and biological dynamics.
  • Deep-Sea Res., Part 2, Top. Stud. Oceanogr. 50, 2847–2875.
  • Gibson, G.A., Musgrave, D.L., Hinckley, S., 2005. Non-linear
  • dynamics of a pelagic ecosystem model with multiple predator
  • and prey types. J. Plankton. Res. 27, 427–447.
  • Ho, T.Y., Quigg, A., Finkel, Z.V., Milligan, A.J., Wyman, K.,
  • Falkowski, P.G., Morel, F.M.M., 2003. The elemental composition
  • of some marine phytoplankton. J. Phycol. 39, 1145–1159.
  • Hofmann, E., Lascara, C., 1998. Overview of Interdisciplinary
  • Modeling for Marine Ecosystems. In: Brink, K.H., Robinson, A.
  • R. (Eds.), The Sea, vol. 10. John Wiley & Sons, Inc., New York,
  • pp. 507–540.
  • Johnson, K.S., Gordon, R.M., Coale, K.H., 1997. What controls
  • dissolved iron concentrations in the world ocean? Mar. Chem. 57,
  • 137–161.
  • Kraemer, S.M., 2004. Iron oxide dissolution and solubility in the
  • presence of siderophores. Aquat. Sci. 66, 3–18.
  • Le Quéré, C., Harrison, S., Prentice, I., Buitenhuis, E., Aumont, O.,
  • Bopp, L., Claustre, H., da Cunha, L.C., Geider, R., Giraud, X.,
  • Klaas, C., Kohfeld, K., Legendre, L., Manizza, M., Platt, T.,
  • Rivkin, R., Sathyendranath, S., Uitz, J., Watson, A., Wolf-
  • Gladrow, D., 2005. Ecosystem dynamics based on plankton
  • functional types for global ocean biogeochemistry models. Glob.
  • Chang. Biol. 11, 2016–2040.
  • Lefevre, N., Watson, A.J., 1999. Modeling the geochemical cycle of
  • iron in the oceans and its impact on atmospheric CO2 concentrations.
  • Glob. Biogeochem. Cycles 13, 727–736.
  • Leonard, C.L., Mcclain, C.R., Murtugudde, R., Hofmann, E.E.,
  • Harding, L.W., 1999. An iron-based ecosystem model of the
  • central equatorial Pacific. J. Geophys. Res. 104, 1325–1341.
  • Martin, J.H., Gordon, R.M., Fitzwater, S.E., 1991. The case for iron.
  • Limnol. Oceanogr. 36, 1793–1802.
  • Martin, J.H., Coale, K.H., Johnson, K.S., Fitzwater, S.E., Gordon, R.
  • M., Tanner, S.J., Hunter, C.N., Elrod, V.A., Nowicki, J.L., Coley,
  • T.L., Barber, R.T., Lindley, S., Watson, A.J., Vanscoy, K., Law, C.
  • S., Liddicoat, M.I., Ling, R., Stanton, T., Stockel, J., Collins, C.,
  • Anderson, A., Bidigare, R., Ondrusek, M., Latasa, M., Millero, F.
  • J., Lee, K., Yao, W., Zhang, J.Z., Friederich, G., Sakamoto, C.,
  • Chavez, F., Buck, K., Kolber, Z., Greene, R., Falkowski, P.,
  • Chisholm, S.W., Hoge, F., Swift, R., Yungel, J., Turner, S.,
  • Nightingale, P., Hatton, A., Liss, P., Tindale, N.W., 1994. Testing
  • the iron hypothesis in ecosystems of the equatorial Pacific Ocean.
  • Nature 371, 123–129.
  • McCarthy, J., Robinson, A., Rothschild, B., 2002. Biological–
  • physical interactions in the sea: emergent findings and new
  • directions. In: Robinson, A., McCarthy, J., Rothschild, B. (Eds.),
  • The Sea, vol. 12. John Wiley & Sons, Inc., New York, pp. 1–17.
  • Ch. 1.
  • Mitra, A., Flynn, K.J., 2005. Predator–prey interactions: is ‘ecological
  • stoichiometry’ sufficient when good food goes bad? J. Plankton.
  • Res. 27, 393–399.
  • Obernosterer, I., Ruardij, P., Herndl, G., 2001. Spatial and diurnal
  • dynamics of dissolved organic matter (DOM) fluorescence and
  • H2O2 and the photochemical oxygen demand of surface water
  • DOM across the subtropical Atlantic Ocean. Lymnol. Oceanogr.
  • 46 (3), 632–643.
  • Ogawa, H., Tanoue, E., 2003. Dissolved organic matter in oceanic
  • waters. J. Oceanogr. 59, 129–147.
  • Olsen, A.,Wanninkhof, R., Trinanes, J.A., Johannessen, T., 2005. The
  • effect of wind speed products and wind speed–gas exchange
  • relationships on interannual variability of the air–sea CO2 gas
  • transfer velocity. Tellus B 57, 95–106.
  • Parekh, P., Follows, M.J., Boyle, E., 2004. Modeling the global ocean
  • iron cycle. Glob. Biogeochem. Cycles 18, GB1002.
  • Petihakis, G., Triantafyllou, G., Allen, I.J., Hoteit, I., Dounas, C.,
  • 2002. Modelling the spatial and temporal variability of the Cretan
  • Sea ecosystem. J. Mar. Syst. 36, 173–196.
  • Platt, T., Gallegos, C.L., Harrison, W.G., 1980. Photoinhibition of
  • photosynthesis in natural assemblages of marine phytoplankton. J.
  • Mar. Res. 38, 687–701.
  • 20 M. Vichi et al. / Journal of Marine Systems xx (2006) xxx–xxx
  • ARTICLE IN PRESS
  • Polimene, L., Allen, J.I., Zavatarelli, M., in press. Dissolved Organic
  • Carbon–bacteria interactions in marine systems: a theoretical
  • modelling study. Aquat. Microb. Ecol.
  • Price, N.M., 2005. The elemental stoichiometry and composition of an
  • iron-limited diatom. Limnol. Oceanogr. 50, 1159–1171.
  • Raick, C., Delhez, E.J.M., Soetaert, K., Gregoire, M., 2005. Study
  • of the seasonal cycle of the biogeochemical processes in the
  • Ligurian Sea using a ID interdisciplinary model. J. Mar. Syst.
  • 55, 177–203.
  • Reinart, A., Arst, H., Blanco-Sequeiros, A., Herlevi, A., 1998.
  • Relation between underwater irradiance and quantum irradiance
  • in dependence on water transparency at different depths in the
  • water bodies. J. Geophys. Res. 103 (C4), 7749–7752.
  • Ruardij, P., Van Raaphorst, W., 1995. Benthic nutrient regeneration in
  • the ERSEM ecosystem model of the North Sea. J. Sea Res. 33 (3–
  • 4), 453–483.
  • Ruardij, P., Haren, H.V., Ridderinkhof, H., 1997. The impact of
  • thermal stratification on phytoplankton and nutrient dynamics in
  • shelf seas: a model study. J. Sea Res. 38 (3–4), 311–331.
  • Sakshaug, E., Bricaud, A., Dandonneau, Y., Falkowski, P.G., Kiefer,
  • D.A., Legendre, L., Morel, A., Parslow, J., Takahashi, M., 1997.
  • Parameters of photosynthesis: definitions, theory and interpretation
  • of results. J. Plankton. Res. 19, 1637–1670.
  • Schmidt, M.A., Zhang, Y.H., Hutchins, D.A., 1999. Assimilation of Fe
  • and carbon by marine copepods from Fe-limited and Fe-replete
  • diatom prey. J. Plankton. Res. 21, 1753–1764.
  • Smith, T., Shugart, H.H., Woodward, F.I., 1997. Plant Functional
  • Types: Their Relevance to Ecosystem Properties and Climate
  • Change. Cambridge University Press, Cambridge.
  • Sterner, R.W., Elser, J.J., 2002. Ecological Stoichiometry: The Biology
  • of Elements from Molecules to the Biosphere. Princeton
  • University Press, Princeton, NJ.
  • Strzepek, R.F., Harrison, P.J., 2004. Photosynthetic architecture differs
  • in coastal and oceanic diatoms. Nature 431, 689–692.
  • Sunda, W.G., 1997. Control of dissolved iron concentrations in the
  • world oc