Please use this identifier to cite or link to this item: http://hdl.handle.net/2122/2588
DC FieldValueLanguage
dc.contributor.authorallVichi, M.; Istituto Nazionale di Geofisica e Vulcanologia, Sezione Bologna, Bologna, Italiaen
dc.contributor.authorallPinardi, N.; Istituto Nazionale di Geofisica e Vulcanologia, Sezione Bologna, Bologna, Italiaen
dc.contributor.authorallMasina, S.; Istituto Nazionale di Geofisica e Vulcanologia, Sezione Bologna, Bologna, Italiaen
dc.date.accessioned2007-10-09T10:25:07Zen
dc.date.available2007-10-09T10:25:07Zen
dc.date.issued2006en
dc.identifier.urihttp://hdl.handle.net/2122/2588en
dc.description.abstractThe 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.en
dc.language.isoEnglishen
dc.publisher.nameElsevieren
dc.relation.ispartofJournal of Marine Systemsen
dc.relation.ispartofseries1-4 / 64 (2007)en
dc.subjectMarine biogeochemistryen
dc.subjectBiomass-based ecosystem modelen
dc.titleA generalized model of pelagic biogeochemistry for the global ocean ecosystem. Part I: theoryen
dc.typearticleen
dc.description.statusPublisheden
dc.type.QualityControlPeer-revieweden
dc.description.pagenumber89-109en
dc.subject.INGV03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modelingen
dc.subject.INGV03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactionsen
dc.subject.INGV03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cyclesen
dc.identifier.doi10.1016/j.jmarsys.2006.03.006en
dc.relation.referencesAllen, 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 ocean: a comment. Mar. Chem. 57, 169–172. Sunda, W.G., Huntsman, S.A., 1995. Iron uptake and growth limitation in oceanic and coastal phytoplankton. Mar. Chem. 50, 189–206. Sunda, W.G., Huntsman, S.A., 1997. Interrelated influence of iron, light and cell size on marine phytoplankton growth. Nature 390, 389–392. Taylor, A.H., Allen, J.I., Clark, P.A., 2002. Extraction of a weak climatic signal by an ecosystem. Nature 416, 629–632. Timmermans, K.R., van der Wagt, B., de Baar, H.J.W., 2004. Growth rates, half-saturation constants, and silicate, nitrate, and phosphate depletion in relation to iron availability of four large, open-ocean diatoms from the Southern ocean. Limnol. Oceanogr. 49, 2141–2151. Timmermans, K.R., van derWagt, B., Veldhuis, M.J.W., Maatman, A., de Baar, H.J.W., 2005. Physiological responses of three species of marine picophytoplankton to ammonium, phosphate, iron and light limitation. J. Sea Res. 53, 109–120. Varela, R., Cruzado, A., Gabaldon, J., 1995. Modelling primary production in the North Sea using the European Regional Seas Ecosystem Model. J. Sea Res. 33 (3–4), 337–361. Vichi, M., 2002. Predictability studies of coastal marine ecosystem behavior. Ph.D. thesis,University of Oldenburg, Oldenburg, Germany. URL http://docserver.bis.uni-oldenburg.de/publikationen/dissertation/ 2002/vicpre02/vicpre02.html. Vichi, M., Zavatarelli, M., Pinardi, N., 1998. Seasonal modulation of microbial-mediated carbon fluxes in the Northern Adriatic Sea. Fisheries Oceanogr. 7 (3/4), 182–190. Vichi, M., May, W., Navarra, A., 2003a. Response of a complex ecosystem model of the northern Adriatic Sea to a regional climate change scenario. Clim. Res. 24, 141–159. Vichi, M., Oddo, P., Zavatarelli, M., Coluccelli, A., Coppini, G., Celio, M., Fonda Umani, S., Pinardi, N., 2003b. Calibration and validation of a one-dimensional complex marine biogeochemical fluxes model in different areas of the northern Adriatic shelf. Ann. Geophys. 21, 413–436. Vichi, M., Ruardij, P., Baretta, J.W., 2004. Link or sink: a modelling interpretation of the open Baltic biogeochemistry. Biogeosciences 1, 79–100. Vichi, M., Masina, S., Navarra, A. 2006-this isssue. A generalized model of pelagic biogeochemistry for the global ocean ecosystem: Part II. Numerical simulations. J. Mar. Syst. doi:10.1016/j.jmarsys.2006.03.014. Webb, W., Newton, M., Starr, D., 1974. Carbon dioxide exchange of Alnus rubra: a mathematical model. Ecologia 17, 281–291. Worden, A.Z., Nolan, J.K., Palenik, B., 2004. Assessing the dynamics and ecology of marine picophytoplankton: the importance of the eukaryotic component. Limnol. Oceanogr. 49, 168–179. Zavatarelli, M., Baretta, J., Baretta-Bekker, J., Pinardi, N., 2000. The dynamics of the Adriatic Sea ecosystem; an idealized model study. Deep-Sea Res., Part 1, Oceanogr. Res. Pap. 47, 937–970. Zeebe, R.E., Wolf-Gladrow, D.A., 2001. CO2 in Seawater: Equilibrium, Kinetics, Isotopes. Vol. 65 of Oceanography Book Series. Elsevier, Amsterdam.en
dc.description.journalTypeJCR Journalen
dc.description.fulltextreserveden
dc.contributor.authorVichi, M.en
dc.contributor.authorPinardi, N.en
dc.contributor.authorMasina, S.en
dc.contributor.departmentIstituto Nazionale di Geofisica e Vulcanologia, Sezione Bologna, Bologna, Italiaen
dc.contributor.departmentIstituto Nazionale di Geofisica e Vulcanologia, Sezione Bologna, Bologna, Italiaen
dc.contributor.departmentIstituto Nazionale di Geofisica e Vulcanologia, Sezione Bologna, Bologna, Italiaen
item.openairetypearticle-
item.cerifentitytypePublications-
item.languageiso639-1en-
item.grantfulltextrestricted-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.fulltextWith Fulltext-
crisitem.author.deptIstituto Nazionale di Geofisica e Vulcanologia (INGV), Sezione Bologna, Bologna, Italia-
crisitem.author.deptIstituto Nazionale di Geofisica e Vulcanologia (INGV), Sezione Bologna, Bologna, Italia-
crisitem.author.orcid0000-0003-4765-0775-
crisitem.author.orcid0000-0001-6273-7065-
crisitem.author.parentorgIstituto Nazionale di Geofisica e Vulcanologia-
crisitem.author.parentorgIstituto Nazionale di Geofisica e Vulcanologia-
crisitem.classification.parent03. Hydrosphere-
crisitem.classification.parent03. Hydrosphere-
crisitem.classification.parent03. Hydrosphere-
crisitem.department.parentorgIstituto Nazionale di Geofisica e Vulcanologia-
crisitem.department.parentorgIstituto Nazionale di Geofisica e Vulcanologia-
crisitem.department.parentorgIstituto Nazionale di Geofisica e Vulcanologia-
Appears in Collections:Article published / in press
Files in This Item:
File Description SizeFormat Existing users please Login
633.pdf544.23 kBAdobe PDF
Show simple item record

WEB OF SCIENCETM
Citations

131
checked on Feb 10, 2021

Page view(s)

175
checked on Apr 24, 2024

Download(s)

25
checked on Apr 24, 2024

Google ScholarTM

Check

Altmetric