On the use of data assimilation in biogeochemical modelling

Ocean Weather Forecasting: An Integrated View of Oceanography

Volumn , Issue , 2006, Pages 525-547

  Oschlies, Andreas ^a  

^a NATIONAL OCEANOGRAPHY CENTRE   (United Kingdom)

Author keywords

data assimilation; Marine ecosystem models; parameter optimisation

Indexed keywords

EID: 84890244401     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/1-4020-4028-8_24     Document Type: Chapter

References (62)

1. Anderson, L. A., and J. L. Sarmiento, 1995: Global ocean phosphate and oxygen simulations. Global Biogeochem. Cycles, 9, 621-636.
2. Athias, V., P. Mazzega, and C. Jeandel, 2000: Selecting a global optimization method to estimate the oceanic particle cycling rate constants. J. Mar. Res., 58, 675-707.
3. Aumont, O., E. Maier-Reimer, S. Blain, and P. Monfray, An ecosystem model of the global ocean including Fe, Si, P co-limitations. Global Biogeochem. Cycles, 17(2), doi:10.1029/2001GB001745, 2003.
4. Bacastow, R., and E. Maier-Reimer, 1990: Ocean-circulation model of the carbon cycle. Climate Dynamics, 4, 95-125.
5. Bennett, A. F., 1989: The Kalman smoother for a linear quasi-geostrophic model of ocean circulation. Dyn. Atmos. Oceans, 13, 219-267.
6. Bertino, L., G. Evensen, and H. Wackernagel, 2003: Sequential data assimilation techniques in oceanography. Int. Stat. Rev., 71, 223-242.
7. Carmillet, V., J.-M. Brankart, P. Brasseur, H. Drange, G. Evensen, and J. Verron, 2001: A singular evolutive extended Kalman filter to assimilate ocean color data in a coupled physical-biochemical model of the North Atlantic ocean. Ocean Modelling, 3, 167-192.
8. Chai, F., R. T. Barber, and S. T. Lindley, 1996: Origin and maintenance of high nutrient condition in the equatorial Pacific. Deep-Sea Res. II, 43, 1031-1064.
9. 14C uptake by phytoplankton really measure? A theoretical modelling approach. Proc. R. Soc. Lond., B 214, 351-368.
10. Ebenhöh, W., J. G. Baretta, and J. W. Baretta, 1997: The primary production module in the marine ecosystem model ERSEM II with emphasis on the light forcing. J. Sea Res., 38, 173-193.
11. Evans, G. T., 2003: Defining misfit between biogeochemical models and data sets. J. Mar. Syst., 40-41, 49-54.
12. Evensen, G., 1992: Using the extended Kalman filter with a multilayer quasi-geostrophic ocean model. J. Geophys. Res., 97(C11), 17,905-17,924.
13. Evensen, G., 2003: The Ensemble Kalman Filter: theoretical formulation and practical implementation. Ocean Dynamics, 53, 343-367.
14. Fasham, M. J. R., H. W. Ducklow, and S. M. McKelvie, 1990: A nitrogen-based model of plankton dynamics in the oceanic mixed layer. J. Mar. Res., 48, 591-639
15. Fasham, M. J. R., J. L. Sarmiento, R. D. Slater, H. W. Ducklow, and R. Williams, 1993: Ecosystem behavior at Bermuda Station S "and Ocean Weather Station India": a general circulation model and observational analysis. Global Biogeochem. Cycles, 7, 379-415.
16. Fasham, M. J. R., and G. T. Evans, 1995: The use of optimisation techniques to model marine ecosystem dynamics at the JGOFS station at 47N 20W. Phil. Trans. Roy. Soc. Lond. B, 348, 203-209.
17. Fennel, K., M. Losch, J. Schröter, and M. Wenzel, 2001: Testing a marine ecosystem model: sensitivity analysis and parameter optimization. J. Mar. Syst., 28, 45-63.
18. Friedrichs, M. A. M., 2002: Assimilation of JGOFS EqPac and SeaWiFS data into a marine ecosystem model of the central equatorial Pacific Ocean. Deep-Sea Res. II, 49, 289-319.
19. Gabric, A. J., R. Simo, R. A. Cropp, A. C. Hirst, and J. Dachs (2004), Modeling estimates of the global emission of dimethylsulfide under enhanced greenhouse conditions, Global Biogeochem. Cycles, 18, GB2014, doi:10.1029/2003GB002183.
20. Gunson, J., A. Oschlies, and V. Garçon, 1999: Sensitivity of ecosystem parameters to simulated satellite ocean colour data using a coupled physical-biological model of the North Atlantic. J. Mar. Res., 57, 613-639.
21. Harmon, R., and P. Challenor, 1997: A Markov chain Monte Carlo method for estimation and assimilation into models. Ecol. Model., 101, 41-59.
22. Hemmings, J. C. P., M. A. Srokocz, P. Challenor, and M. J. R. Fasham, 2003: Assimilating satellite ocean-colour observations into oceanic ecosystem models. Phil. Trans. R. Soc. Lond., A 361, 33-39.
23. Hurtt, G. C., and R. A. Armstrong, 1996: A pelagic ecosystem model calibrated with BATS data. Deep-Sea Res. II, 43, 653-683.
24. Hurtt, G. C., and R. A. Armstrong, 1999: A pelagic ecosystem model calibrated with BATS and OWSI data. Deep-Sea Res. I, 46, 27-61.
25. Kähler, P., and W. Koeve, 2001: Marine dissolved organic matter: can its C:N ratio explain carbon overconsumption? Deep-Sea Res. I, 48, 49-62.
26. Kalman, R. E., 1960: A new approach to linear filtering and prediction problems. J. Basic. Eng., 82 D, 35-45.
27. Klausmeier, C. A., E. Litchman, T. Daufresne, and S. A. Levin, 2004: Optimal nitrogen-to-phosphorus stoichiometry of phytoplankton. Nature, 429, 171-174.
28. Körtzinger, A., W. Koeve, P. Kähler, and L. Mintrop, 2001: C:N ratios in the mixed layer during the productive season in the Northeast Atlantic Ocean. Deep-Sea Res. I, 48, 661-688.
29. Lawson, L. M., Y. H. Spitz, E. E. Hofmann, and R. B. Long, 1995: A data assimilation technique applied to a predator-prey model. Bull. Math. Biology, 57, 625-651.
30. Loukos, H., P. Monfray, L. Bopp, and P. Lehody, 2003: Potential changes in skipjack tuna (Katsuwonus pelamis) habitat from a global warming scenario: modelling approach and preliminary results. Fisheries Oceanography, 12, 474-482.
31. Losa, S. N., G. A. Kivman, and V. A. Ryabchenko, 2004: Weak constraint parameter estimation for a simple ocean ecosystem model: what can we learn about the model and data? J. Mar. Syst., 45, 1-20.
32. Marotzke, J., R. Giering, K. Q. Zhang, D. Stammer, C. Hill, and T. Lee, 1999: Construction of the adjoint MIT ocean general circulation model and application to Atlantic heat transport sensitivity. J. Geophys. Res., 104, 29,529-29,547.
33. Matear, R. J., 1995: Parameter optimization and analysis of ecosystem models using simulated annealing: a case study at Station P. J. Mar. Res., 53, 571-607.
34. McCreary, J. P., K. E. Kohler, R. R. Hood, and D. B. Olson, 1996: A four-component ecosystem of biological activity in the Arabian Sea. Prog. Oceanog., 37, 193-240.
35. Moore, J. K., S. C. Doney, J. A. Kleypas, D. M. Glover, and I. Y. Fung, 2002: An intermediate complexity marine ecosystem model for the global domain. Deep-Sea Res. II, 49, 403-462.
36. Najjar, R. G., J. L. Sarmiento, and J. R. Toggweiler, 1992: Downward transport and fate of organic matter in the ocean: simulations with a general circulation model. Global Biogeochem. Cycles, 6, 45-76.
37. Orr, J. C., 1999: Ocean Carbon-Cycle Model Intercomparison Project (OCMIP), Research GAIM, 2, 7.
38. Oschlies, A., 1999: On spurious interactions among a mixed layer model, convective adjustment, and isopycnal mixing in ocean circulation models. Mon. Weather Rev., 127, 1920-1927.
39. Oschlies, A., 2002: Can eddies make ocean deserts bloom? Global Biogeochem. Cycles, 16, 1106, doi:10.1029/2001GB001830.
40. Oschlies, A., 2004: Feedbacks of biotically induced radiative heating on upper-ocean heat budget, circulation, and biological production in a coupled ecosystem-circulation model. J. Geophys. Res., 110, doi:10.1029/2004JC002430.
41. Oschlies, A., and V. Garçon, 1998: Eddy-induced enhancement of primary production in a model of the North Atlantic Ocean. Nature, 394, 266-269.
42. Oschlies, A., and V. Garçon, 1999: An eddy-permitting coupled physical-biological model of the North Atlantic. 1. Sensitivity to advection numerics and mixed layer physics. Global Biogeochem. Cycles, 13, 135-160.
43. Popova, E. E., M. J. R. Fasham, A. V. Osipov, and V. A. Ryabchenko, 1997: Chaotic behaviour of an ocean ecosystem model under seasonal external forcing. J. Plank. Res., 19, 1495-1515.
44. Popova, E. E., M. A. Srokosz, and D. A. Smeed, 2002: Real-time forecasting of biological and physical dynamics at the Island-Faeroes Front in June 2001. Geophys. Res. Lett., 29, 10.1029/2001GL013706.
45. Prunet, P., J. F. Minster, D. Ruiz-Pino, and I. Dadou, 1996: Assimilation of surface data in a one-dimensional physical-biogeochemical model of the surface ocean. 1. Method and preliminary results. Global Biogeochem. Cycles, 10, 111-138.
46. 2 data. Global Biogeochem. Cycles, 10, 139-158.
47. Redfield, A. C., 1934: On the proportions of organic derivatives in sea water and their relation to the composition of plankton. James Johnstone Memorial Volume, Liverpool, 176-192.
48. Redfield, A. C., B. H. Ketchum, F. A. Richards, 1963: The influence of organisms on the composition of sea water. In The Sea, Vol. 2, M. N. Hill (Ed.), Interscience, New York, 26-77.
49. Sarmiento, J. L., R. D. Slater, M. J. R. Fasham, H. W. Ducklow, J. R. Toggweiler, and G. T. Evans, 1993: A seasonal three-dimensional ecosystem model of nitrogen cycling in the North Atlantic euphotic zone. Global Biogeochem. Cycles, 7, 417-450.
50. 2 transfer and the carbon budget of the North Atlantic. Philos. Trans. R. Soc. London Ser. B, 348, 211-219.
51. Schartau, M., A. Oschlies, and J. Willebrand, 2001: Parameter estimates of a zerodimensional ecosystem model applying the adjoint method. Deep-Sea Res. II, 48, 1769-1800.
52. Schartau, M., and A. Oschlies, 2003: Simulataneous data-based optimization of a 1D-ecosystem model at three locations in the North Atlantic: Part I-Method and parameter estimates. J. Mar. Res., 61, 765-793.
53. Schartau, M., and A. Oschlies, 2003: Simulataneous data based optimization of a 1D-ecosystem model at three locations in the North Atlantic: Part II-Standing stocks and nitrogen fluxes. J. Mar. Res., 61, 795-821.
54. Schofield, O., J. Grzymski, W. P. Bissett, G. J. Kirkpatrick, D. F. Millie, M. Moline, and C. S. Roesler, 1999: Optical monitoring and forecasting systems for harmful algal blooms: possibility of pipe dream? J. Phycol., 35, 1477-1496.
55. Six, K. D., and E. Maier-Reimer, 1996: Effects of plankton dynamics on seasonal carbon fluxes in an ocean general circulation model. Global Biogeochem. Cycles, 10, 559-583.
56. Smetacek, V., 2001: A watery arms race. Nature, 411, 745.
57. Spitz, Y. H., J. R. Moisan, M. R. Abbott, and J. G. Richman, 1998: Data assimilation and a pelagic ecosystem model: parameterization using time series observations. J. Mar. Syst., 16, 51-68.
58. Spitz, Y. H., J. R. Moisan, and M. R. Abbott, 2001: Configuring an ecosystem model using data from the Bermuda Atlantic Time Series (BATS). Deep-Sea Res. II, 48, 1733-1768.
59. Sterner, R. W., and J. J. Elser, 2002: Ecological Stoichiometry: the biology of elements from molecules to the biosphere, Princeton Univ. Press, Princeton, 439pp.
60. Vallino, J. J., 2000: Improving marine ecosystem models: Use of data assimilation and mesocosm experiments. J. Mar. Res., 58, 117-164.
61. 2: Natural Variations, Archean to Present, edited by E. Sundquist and W. Broecker, pp. 99-110, AGU Geophysical Monograph, 32, Washington D. C.
62. Williams, P. L. le B., 1995: Evidence for the seasonal accumulation of carbon-rich dissolved organic material, its scale in comparison with changes in particulate material and the consequential effect on net C/N assimilation rates. Mar. Chem., 51, 17-29.