Skip to main content

Marine Biogeochemical Modelling and Data Assimilation

  • Chapter
  • First Online:
Operational Oceanography in the 21st Century

Abstract

The inclusion of biogeochemistry into the Global Ocean Data Assimilation Experiment systems represents an exciting opportunity that involves significant challenges. To help articulate these challenges we review marine biogeochemical modeling and the existing applications of biogeochemical data assimilation. The challenges of biogeochemical data assimilation stem from the large model errors associated with biogeochemical models, the computational demands of the global data assimilation systems, and the strong non-linearity between biogeochemical state variables. We use the ocean state estimation problem to outline an approach to adding biogeochemical data assimilation to the Global Ocean Data Assimilation Experiment systems. Our approach allows the biogeochemical model parameters to be spatially and temporally varying to enable the data assimilation system to track the observed biogeochemical fields. The approach is based on addressing the challenges of biogeochemical data assimilation to improve both the state estimation of the biogeochemical fields and the underlying biogeochemical model.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Brasseur P, Bahurel P, Bertino L, Birol F, Brankart JM, Ferry N, Losa S, Remy E, Schroeter J, Skachko S, Testut CE, Tranchant B, Leeuwen PJV, Verron J (2005) Data assimilation for marine monitoring and prediction: the MERCATOR operational assimilation systems and the MERSEA developments. Q J R Meteorol Soc 131(613):3561–3582

    Article  Google Scholar 

  • Brasseur P, Gruber N, Barciela R, Brander K, Doron M, Moussaoui AE, Hobday AJ, Huret M, Kremeur A-S, Lehodey P, Matear R, Moulin C, Murtugudde R, Senina I, Svendsen E (2009) Integrating biogeochemistry and ecology into ocean data assimilation systems. Oceanography 22(3):206–215

    Article  Google Scholar 

  • Brassington GB, Pugh T, Spillman C, Schulz E, Beggs H, Schiller A, Oke PR (2007) BLUElink development of operational oceanography and servicing in Australia. J Res Pract Inf Tech 39(2):151–164

    Google Scholar 

  • Brown CJ, Fulton EA, Hobday AJ, Matear RJ, Possingham HP, Bulman C, Christensen V, Forrest RE, Gehrke PC, Gribble NA, Griffiths SP, Lozano-Montes H, Martin JM, Metcalf S, Okey TA, Watson R, Richardson AJ (2010) Effects of climate-driven primary production change on marine food webs: implications for fisheries and conservation. Glob Change Biol 16:1194–1212, doi: 10.1111/j.1365-2486.2009.02046.x

    Google Scholar 

  • Dowd M (2007) Bayesian statistical data assimilation for ecosystem models using Markov Chain Monte Carlo. J Mar Syst 68(3–4):439–456

    Article  Google Scholar 

  • Eknes M, Evensen G (2002) An Ensemble Kalman filter with a 1-D marine ecosystem model. J Mar Syst 36(1–2):75–100

    Article  Google Scholar 

  • Follows MJ, Dutkiewicz S, Grant S, Chisholm SW (2007) Emergent biogeography of microbial communities in a model ocean. Science 315:1843–1846

    Article  Google Scholar 

  • Franks PJS (1997) Models of harmful Algal Blooms. Limnol Oceanogr 42(5):1273–1282

    Article  Google Scholar 

  • Franks PJS (2009) Planktonic ecosystem models: perplexing parameterizations and a failure to fail. J Plankton Res 31(11):1299–1306

    Article  Google Scholar 

  • Friedrichs MAM, Hood RR, Wiggert JD (2006) Ecosystem model complexity versus physical forcing: quantification of their relative impact with assimilated Arabian Sea data. Deep-Sea Res Part I i-Topical Stud Oceanogr 53(5–7):576–600

    Article  Google Scholar 

  • Friedrichs MAM, Dusenberry JA, Anderson LA, Armstrong RA, Chai F, Christian JR, Doney SC, Dunne J, Fujii M, Hood R, McGillicuddy DJ, Moore JK, Schartau M, Spitz YH, Wiggert JD (2007) Assessment of skill and portability in regional marine biogeochemical models: role of multiple planktonic groups. J Geophys Res-Oceans 112(C8):C08001

    Article  Google Scholar 

  • Gabric AJ, Whetton PH, Boers R, Ayers GP (1998) The impact of simulated climate change on the air-sea flux of dimethylsulphide in the subantarctic Southern Ocean. Tellus Ser B-Chem Phys Meteorol 50(4):388–399

    Article  Google Scholar 

  • Gregg WW (2008) Assimilation of SeaWiFS ocean chlorophyll data into a three-dimensional global ocean model. J Mar Syst 69(3–4):205–225

    Article  Google Scholar 

  • Gregg WW, Friedrichs MAM, Robinson AR, Rose KA, Schlitzer R, Thompson KR, Doney SC (2009) Skill assessment in ocean biological data assimilation. J Mar Syst 76(1–2):16–33

    Article  Google Scholar 

  • Hemmings J, Barciela R, Bell M (2008) Ocean color data assimilation with material conservation for improving model estimates of air-sea CO2 flux. J Mar Res 66:87–126

    Article  Google Scholar 

  • Ishizaka J (1990) Coupling of coastal zone color scanner data ot a physical-biological model of the southeastern U. S. continental shelf ecosystem 3. Nutrient and phytoplankton fluxes and CZCS data assimilation. J Geophys Res 95:20201–20212

    Article  Google Scholar 

  • Jones E, Parslow J, Murray L (2010) A Bayesian approach to state and parameter estimation in a Phytoplankton-Zooplankton model. Aust Meteorol Ocean 59:7–15

    Google Scholar 

  • Kidston M, Matear RJ, Baird M (2010) Exploring the ecosystem model parameterzation using inverse studies. Deep-Sea Res Part II

    Google Scholar 

  • Lee T, Awaji T, Balmaseda MA, Greiner E, Stammer D (2009) Ocean state estimation for climate research. Oceanography 22(3):160–167

    Article  Google Scholar 

  • Martin AJ, Hines A, Bell MJ (2007) Data assimilation in the FOAM operational short-range ocean forecasting system: a description of the scheme and its impact. Q J R Meteor Soc 133(625):981–995

    Article  Google Scholar 

  • Matear RJ (1995) Parameter optimization and analysis of ecosystem models using simulated annealing: a case study at Station P. J Mar Res 53:571–607

    Article  Google Scholar 

  • Matear RJ, Holloway G (1995) Modeling the inorganic phosphorus cycle of the North Pacific using an adjoint data assimilation model to assess the role of dissolved organic phosphorus. Glob Biogeochem Cycles 9:101–119

    Article  Google Scholar 

  • Mattern JP, Dowd M, Fennel K (2010) Sequential data assimilation applied to a physical-biological model for the Bermuda Atlantic time series station. J Mar Syst 79(1–2):144–156

    Article  Google Scholar 

  • Moore TM, Matear RJ, Marra J, Clementson L (2007) Phytoplankton variability off the Western Australian Coast: mesoscale eddies and their role in cross-shelf exchange. Deep Sea Res II 54:943–960

    Article  Google Scholar 

  • Natvik L, Evensen G (2003a) Assimilation of ocean colour data into a biochemical model of the North Atlantic—Part I. Data assimilation experiments. J Mar Syst 40:127–153

    Article  Google Scholar 

  • Natvik L, Evensen G (2003b) Assimilation of ocean colour data into a biochemical model of the North Atlantic—Part II. Statistical analysis. J Mar Syst 40:155–169

    Article  Google Scholar 

  • Oke PR, Brassington GB, Griffin DA, Schiller A (2008) The Bluelink Ocean Data Assimilation System (BODAS). Ocean Model 21(1–2):46–70

    Article  Google Scholar 

  • Oschlies A, Schartau M (2005) Basin-scale performance of a locally optimized marine ecosystem model. J Mar Res 63(2):335–358

    Article  Google Scholar 

  • Schartau M, Oschlies A (2003a) Simultaneous data-based optimization of a 1Decosystem model at three locations in the North Atlantic: Part I—method and parameter estimates. J Mar Res 61(6):765–793

    Article  Google Scholar 

  • Schartau M, Oschlies A (2003b) Simultaneous data-based optimization of a 1Decosystem model at three locations in the North Atlantic: Part II—standing stocks and nitrogen fluxes. J Mar Res 61(6):795–821

    Google Scholar 

  • Schlitzer R (2002) Carbon export fluxes in the Southern Ocean: results from inverse modeling and comparison with satellite based estimates. Deep Sea Res II 49:1623–1644 (Special Volume on the Southern Ocean)

    Article  Google Scholar 

  • Vichi M, Pinardi N, Masina S (2007) A generalized model of pelagic biogeochemistry.for the global ocean ecosystem. Part I: theory. J Mar Syst 64(1–4):89–109

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Richard J. Matear .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Matear, R.J., Jones, E. (2011). Marine Biogeochemical Modelling and Data Assimilation. In: Schiller, A., Brassington, G. (eds) Operational Oceanography in the 21st Century. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0332-2_12

Download citation

Publish with us

Policies and ethics