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Applied Optics

Applied Optics


  • Editor: Joseph N. Mait
  • Vol. 52, Iss. 11 — Apr. 10, 2013
  • pp: 2257–2273

Multivariate approach for the retrieval of phytoplankton size structure from measured light absorption spectra in the Mediterranean Sea (BOUSSOLE site)

Emanuele Organelli, Annick Bricaud, David Antoine, and Julia Uitz  »View Author Affiliations

Applied Optics, Vol. 52, Issue 11, pp. 2257-2273 (2013)

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Models based on the multivariate partial least squares (PLS) regression technique are developed for the retrieval of phytoplankton size structure from measured light absorption spectra (BOUSSOLE site, northwestern Mediterranean Sea). PLS-models trained with data from the Mediterranean Sea showed good accuracy in retrieving, over the nine-year BOUSSOLE time series, the concentrations of total chlorophyll a [Tchl a ], of the sum of seven diagnostic pigments and of pigments associated with micro, nano, and picophytoplankton size classes separately. PLS-models trained using either total particle or phytoplankton absorption spectra performed similarly, and both reproduced seasonal variations of biomass and size classes derived by high performance liquid chromatography. Satisfactory retrievals were also obtained using PLS-models trained with a data set including various locations of the world’s oceans, with however a lower accuracy. These results open the way to an application of this method to absorption spectra derived from hyperspectral and field satellite radiance measurements.

© 2013 Optical Society of America

OCIS Codes
(010.0010) Atmospheric and oceanic optics : Atmospheric and oceanic optics
(010.4450) Atmospheric and oceanic optics : Oceanic optics
(010.7340) Atmospheric and oceanic optics : Water
(010.1030) Atmospheric and oceanic optics : Absorption

ToC Category:
Atmospheric and Oceanic Optics

Original Manuscript: November 12, 2012
Revised Manuscript: February 5, 2013
Manuscript Accepted: February 11, 2013
Published: April 4, 2013

Virtual Issues
Vol. 8, Iss. 5 Virtual Journal for Biomedical Optics

Emanuele Organelli, Annick Bricaud, David Antoine, and Julia Uitz, "Multivariate approach for the retrieval of phytoplankton size structure from measured light absorption spectra in the Mediterranean Sea (BOUSSOLE site)," Appl. Opt. 52, 2257-2273 (2013)

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  1. J. A. Raven and P. G. Falkowski, “Ocean sink for atmospheric CO2,” Plant Cell Environ. 22, 741–755 (1999). [CrossRef]
  2. O. Aumont, E. Meier-Reimer, S. Blain, and P. Monfray, “An ecosystem model of the global ocean including Fe, Si, P colimitations,” Glob. Biogeochem. Cycles 17, 23–29 (2003). [CrossRef]
  3. C. Le Quéré, S. P. Harrison, I. C. Prentice, E. T. Buitenhuis, O. Aumont, L. Bopp, H. Claustre, L. Cotrim da Cunha, R. Geider, X. Giraud, C. Klaas, K. E. Kohfeld, L. Legendre, M. Manizza, T. Platt, R. B. Rivkin, S. Sathyendranath, J. Uitz, A. J. Watson, and D. Wolf-Gladrow, “Ecosystem dynamics based on plankton functional types for global ocean biogeochemistry models,” Glob. Chang. Biol. 11, 2016–2040 (2005). [CrossRef]
  4. R. R. Hood, 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, M. A. Friedrichs, M. R. Landry, J. K. Moore, D. M. Nelson, T. L. Richardson, B. Salihoglu, M. Schartau, D. A. Toole, and J. D. Wiggert, “Pelagic functional group modeling: progress, challenges and prospects,” Deep Sea Res. Part II 53, 459–512 (2006). [CrossRef]
  5. T. Platt, S. Sathyendranath, and V. Stuart, “Why study biological oceanography?” Aquabiology 28, 542–557 (2006).
  6. T. Platt and S. Sathyendranath, “Ecological indicators for the pelagic zone of the ocean from remote sensing,” Remote Sens. Environ. 112, 3426–3436 (2008). [CrossRef]
  7. S. Sathyendranath and T. Platt, “Ocean-colour radiometry: achievements and future perspectives,” in Oceanography from Space-Revisited, V. Barale, J. F. R. Gower, and L. Alberotanza, eds., (Springer, 2010), pp. 349–359.
  8. S. Alvain, C. Moulin, Y. Dandonneau, and F. M. Bréon, “Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS imagery,” Deep Sea Res. Part I 52, 1989–2004 (2005). [CrossRef]
  9. J. Aiken, J. R. Fishwick, S. Lavender, R. Barlow, G. F. Moore, H. Sessions, S. Bernard, J. Ras, and N. J. Hardman-Mountford, “Validation of MERIS reflectance and chlorophyll during the BENCAL cruise October 2002: preliminary validation of new demonstration products for phytoplankton functional types and photosynthetic parameters,” Int. J. Remote Sens. 28, 497–516 (2007). [CrossRef]
  10. D. E. Raitsos, S. J. Lavender, C. D. Maravelias, J. Haralabous, A. J. Richardson, and P. C. Reid, “Identifying four phytoplankton functional types from space: an ecological approach,” Limnol. Oceanogr. 53, 605–613 (2008). [CrossRef]
  11. J. Uitz, H. Claustre, A. Morel, and S. B. Hooker, “Vertical distribution of phytoplankton communities in open ocean: an assessment based on surface chlorophyll,” J. Geophys. Res. 111, C08005 (2006). [CrossRef]
  12. E. Devred, S. Sathyendranath, V. Stuart, H. Maas, O. Ulloa, and T. Platt, “A two-component model of phytoplankton absorption in the open ocean: theory and applications,” J. Geophys. Res. 111, C03011 (2006). [CrossRef]
  13. T. Hirata, J. Aiken, N. J. Hardman-Mountford, T. J. Smyth, and R. G. Barlow, “An absorption model to determine phytoplankton size classes from satellite ocean colour,” Remote Sens. Environ. 112, 3153–3159 (2008). [CrossRef]
  14. R. J. W. Brewin, S. Sathyendranath, T. Hirata, S. J. Lavender, R. M. Barciela, and N. J. Hardman-Mountford, “A three-component model of phytoplankton size class for the Atlantic Ocean,” Ecol. Model. 221, 1472–1483 (2010). [CrossRef]
  15. A. Fujiwara, T. Hirawake, K. Suzuki, and S. I. Saitoh, “Remote sensing of size structure of phytoplankton communities using optical properties of the Chukchi and Bering Sea shelf region,” Biogeosciences 8, 3567–3580 (2011). [CrossRef]
  16. A. M. Ciotti and A. Bricaud, “Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water leaving radiances at SeaWiFS channels in a continental shelf region off Brazil,” Limnol. Oceanogr. Methods 4, 237–253 (2006). [CrossRef]
  17. C. B. Mouw and J. A. Yoder, “Optical determination of phytoplankton size composition from global SeaWiFS imagery,” J. Geophys. Res. 115, C12018 (2010). [CrossRef]
  18. C. B. Mouw, J. A. Yoder, and S. C. Doney, “Impact of phytoplankton community size on a linked global ocean optical and ecosystem model,” J. Mar. Syst. 89, 61–75 (2012). [CrossRef]
  19. T. S. Kostadinov, D. A. Siegel, and S. Maritorena, “Retrieval of the particle size distribution from satellite ocean color observations,” J. Geophys. Res. 114, C09015 (2009). [CrossRef]
  20. T. S. Kostadinov, D. A. Siegel, and S. Maritorena, “Global variability of phytoplankton functional types from space: assessment via the particle size distribution,” Biogeosciences 7, 3239–3257 (2010). [CrossRef]
  21. T. Hirata, N. J. Hardman-Mountford, R. J. W. Brewin, J. Aiken, R. Barlow, K. Suzuki, T. Isada, E. Howell, T. Hashioka, M. Noguchi-Aita, and Y. Yamanaka, “Synoptic relationships between surface chlorophyll-a and diagnostic pigments specific to phytoplankton functional types,” Biogeosciences 8, 311–327 (2011). [CrossRef]
  22. J. R. Moisan, T. A. H. Moisan, and M. A. Linkswiler, “An inverse modeling approach to estimating phytoplankton pigment concentrations from phytoplankton absorption spectra,” J. Geophys. Res. 116, C09018 (2011). [CrossRef]
  23. E. Torrecilla, D. Stramski, R. A. Reynolds, E. Millán-Núñez, and J. Piera, “Cluster analysis of hyperspectral optical data for discriminating phytoplankton pigment assemblages in the open ocean,” Remote Sens. Environ. 115, 2578–2593 (2011). [CrossRef]
  24. J. M. Sieburth, V. Smetacek, and J. Lenz, “Pelagic ecosystem structure: heterotrophic compartments of the plankton and their relationship to plankton size fractions,” Limnol. Oceanogr. 23, 1256–1263 (1978). [CrossRef]
  25. T. Platt, C. Fuentes-Yaco, and K. T. Frank, “Spring algal bloom and larval fish survival,” Nature 423, 398–399 (2003). [CrossRef]
  26. C. Fuentes-Yaco, P. A. Koeller, S. Sathyendranath, and T. Platt, “Shrimp (Pandalus borealis) growth and timing of the spring phytoplankton bloom on the Newfoundland-Labrador shelf,” Fish. Ocean. 16, 116–129 (2007). [CrossRef]
  27. A. Nair, S. Sathyendranath, T. Platt, J. Morales, V. Stuart, M. H. Forget, E. Devred, and H. Bouman, “Remote sensing of phytoplankton functional types,” Remote Sens. Environ. 112, 3366–3375 (2008). [CrossRef]
  28. C. S. Reynolds, The Ecology of Phytoplankton (Cambridge University, 2006).
  29. A. Morel and A. Bricaud, “Theoretical results concerning light absorption in a discrete medium, and application to specific absorption of phytoplankton,” Deep Sea Res. Part I 28, 1375–1393 (1981). [CrossRef]
  30. A. Bricaud, H. Claustre, J. Ras, and K. Oubelkheir, “Natural variability of phytoplanktonic absorption in oceanic waters: influence of the size structure of algal populations,” J. Geophys. Res. 109, C11010 (2004). [CrossRef]
  31. A. M. Ciotti, M. R. Lewis, and J. J. Cullen, “Assessment of the relationships between dominant cell size in natural phytoplankton communities and the spectral shape of the absorption coefficient,” Limnol. Oceanogr. 47, 404–417 (2002). [CrossRef]
  32. R. J. W. Brewin, N. J. Hardman-Mountford, S. J. Lavender, D. E. Raitsos, T. Hirata, J. Uitz, E. Devred, A. Bricaud, A. Ciotti, and B. Gentili, “An intercomparison of bio-optical techniques for detecting dominant phytoplankton size class from satellite remote sensing,” Remote Sens. Environ. 115, 325–339 (2011). [CrossRef]
  33. H. Martens and T. Næs, Multivariate Calibration (Wiley, 1989).
  34. K. H. Esbensen, T. Midtgaard, and S. Schonkopf, Multivariate Analysis in Practice (Wennberg, 1994).
  35. L. Moberg, B. Karlberg, S. Blomqvist, and U. Larsson, “Comparison between a new application of multivariate regression and current spectroscopy methods for the determination of chlorophylls and their corresponding pheopigments,” Anal. Chim. Acta 411, 137–143 (2000). [CrossRef]
  36. J. Seppäla and K. Olli, “Multivariate analysis of phytoplankton spectral in vivo fluorescence: estimation of phytoplankton biomass during a mesocosm study in the Baltic Sea,” Mar. Ecol. Prog. Ser. 370, 69–85 (2008). [CrossRef]
  37. L. Moberg, B. Karlberg, K. Sørensen, and T. Källqvist, “Assessment of phytoplankton class abundance using absorption spectra and chemometrics,” Talanta 56, 153–160 (2002). [CrossRef]
  38. P. A. Stæhr and J. J. Cullen, “Detection of Karenia mikomotoi by spectral absorption signatures,” J. Plankton Res. 25, 1237–1249 (2003). [CrossRef]
  39. R. Martínez-Guijarro, I. Romero, M. Pachés, J. G. del Río, C. M. Martí, G. Gil, A. Ferrer-Riquielme, and J. Ferrer, “Determination of phytoplankton composition using absorption spectra,” Talanta 78, 814–819 (2009). [CrossRef]
  40. IOCCG, “Remote sensing of inherent optical properties: fundamentals, tests of algorithms, and applications,” Reports of the International Ocean Colour Coordinating Group, No. 5, Z.-P. Lee, ed. (IOCCG, 2006).
  41. A. Bricaud, M. Babin, H. Claustre, J. Ras, and F. Tièche, “Light absorption properties and absorption budget of South East Pacific waters,” J. Geophys. Res. 115, C08009 (2010). [CrossRef]
  42. D. Antoine, M. Chami, H. Claustre, F. D’Ortenzio, A. Morel, G. Bécu, B. Gentili, F. Louis, J. Ras, E. Roussier, A. J. Scott, D. Tailliez, S. B. Hooker, P. Guevel, J. F. Desté, C. Dempsey, and D. Adams, “BOUSSOLE: a joint CNRS-INSU, ESA, CNES and NASA ocean color calibration and validation activity,” NASA Technical Memorandum No. 2006-214147 (2006).
  43. D. Antoine, F. D’Ortenzio, S. B. Hooker, G. Bécu, B. Gentili, D. Tailliez, and A. J. Scott, “Assessment of uncertainty in the ocean reflectance determined by three satellite ocean color sensors (MERIS, SeaWiFS, and MODIS-A) at an offshore site in the Mediterranean Sea (BOUSSOLE project),” J. Geophys. Res. 113, C07013 (2008). [CrossRef]
  44. A. Morel and L. Prieur, “Analysis of variations in ocean color,” Limnol. Oceanogr. 22, 709–722 (1977). [CrossRef]
  45. H. R. Gordon and W. R. Mc Cluney, “Estimation of the depth of sunlight penetration in the sea for remote sensing,” Appl. Opt. 14, 413–416 (1975). [CrossRef]
  46. A. Morel and S. Maritorena, “Bio-optical properties of oceanic waters: a reappraisal,” J. Geophys. Res. 106, 7163–7180 (2001). [CrossRef]
  47. H. Claustre and J. C. Marty, “Specific phytoplankton biomasses and their relation to primary production in the tropical North Atlantic,” Deep Sea Res. Part I 42, 1475–1493 (1995). [CrossRef]
  48. J. Ras, J. Uitz, and H. Claustre, “Spatial variability of phytoplankton pigment distributions in the subtropical South Pacific Ocean: comparison between in situ and modeled data,” Biogeosciences 5, 353–369 (2008). [CrossRef]
  49. F. Vidussi, H. Claustre, J. Bustillos-Guzmàn, C. Cailliau, and J. C. Marty, “Determination of chlorophylls and carotenoids of marine phytoplankton: separation of chlorophyll a from divinyl-chlorophyll a and zeaxanthin from lutein,” J. Plankton Res. 18, 2377–2382 (1996). [CrossRef]
  50. F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, “Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter,” J. Geophys. Res. 106, 19939–19956(2001). [CrossRef]
  51. J. Aiken, Y. Pradhan, R. Barlow, S. Lavender, A. Poulton, P. Holligan, and N. Hardman-Mountford, “Phytoplankton pigments and functional types in the Atlantic Ocean: a decadal assessment, 1995–2005,” Deep Sea Res. Part II 56, 899–917 (2009). [CrossRef]
  52. J. Uitz, Y. Huot, F. Bruyant, M. Babin, and H. Claustre, “Relating phytoplankton photophysiological properties to community structure on large scale,” Limnol. Oceanogr. 53, 614–630 (2008). [CrossRef]
  53. J. Uitz, H. Claustre, N. Garcia, F. B. Griffiths, J. Ras, and V. Sandroni, “A phytoplankton class-specific primary production model applied to the Kerguelen islands region (Southern Ocean),” Deep Sea Res. Part I 56, 541–560 (2009). [CrossRef]
  54. E. Organelli, C. Nuccio, C. Melillo, and L. Massi, “Relationships between phytoplankton light absorption, pigment composition and size structure in offshore areas of the Mediterranean Sea,” Adv. Oceanogr. Limnol. 2, 107–123 (2011). [CrossRef]
  55. K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, “A new method for measuring spectral absorption coefficients of marine particles,” Limnol. Oceanogr. 40, 1526–1532 (1995). [CrossRef]
  56. A. Bricaud, A. Morel, M. Babin, K. Allali, and H. Claustre, “Variations of light absorption by suspended particles with chlorophyll a concentration in oceanic (case 1) waters: analysis and implications for bio-optical models,” J. Geophys. Res. 103, 31033–31044 (1998). [CrossRef]
  57. K. Allali, A. Bricaud, and H. Claustre, “Spatial variations in the chlorophyll-specific absorption coefficients of phytoplankton and photosynthetically active pigments in the equatorial Pacific,” J. Geophys. Res. 102, 12413–12423 (1997). [CrossRef]
  58. A. Bricaud and D. Stramski, “Spectral absorption coefficients of living phytoplankton and nonalgal biogenous matter: a comparison between Peru upwelling area and Sargasso Sea,” Limnol. Oceanogr. 35, 562–582 (1990). [CrossRef]
  59. M. Kishino, M. Takahashi, N. Okami, and S. Ichimura, “Estimation of the spectral absorption coefficients of phytoplankton in the sea,” Bull. Mar. Sci. 37, 634–642 (1985).
  60. R. Bidigare, J. Morrow, and D. Kiefer, “Derivative analysis of spectra absorption by photosynthetic pigments in the western Sargasso Sea,” J. Mar. Res. 47, 323–341 (1989). [CrossRef]
  61. F. Tsai and W. Philpot, “Derivative analysis of hyperspectral data,” Remote Sens. Environ. 66, 41–51 (1998). [CrossRef]
  62. P. Geladi and B. R. Kowalski, “Partial least squares regression: a tutorial,” Anal. Chim. Acta 185, 1–17 (1986). [CrossRef]
  63. B. H. Mevik and R. Wehrens, “The pls package: principal component and partial least squares regression in R,” J. Stat. Softw. 18, 1–24 (2007).
  64. J. C. Marty, J. Chiavérini, M. D. Pizay, and B. Avril, “Seasonal and interannual dynamics of nutrients and phytoplankton pigments in the western Mediterranean Sea at the DYFAMED time-series station (1991–1999),” Deep Sea Res. Part II 49, 1965–1985 (2002). [CrossRef]
  65. J. C. Marty and J. Chiavérini, “Hydrological changes in the Ligurian Sea (NW Mediterranean, DYFAMED site) during 1995–2007 and biogeochemical consequences,” Biogeosciences 7, 2117–2128 (2010). [CrossRef]
  66. N. Hoepffner and S. Sathyendranath, “Effect of pigment composition on absorption properties of phytoplankton,” Mar. Ecol. Prog. Ser. 73, 11–23 (1991). [CrossRef]
  67. E. Bosc, A. Bricaud, and D. Antoine, “Seasonal and interannual variability in algal biomass and primary production in the Mediterranean Sea, as derived from four years of SeaWiFS observations,” Glob. Biogeochem. Cycles 18, GB1005 (2004). [CrossRef]
  68. V. Barale, J. M. Jacquet, and M. Ndiaye, “Algal blooming patterns and anomalies in the Mediterranean Sea as derived from the SeaWifs data set (1998–2003),” Remote Sens. Environ. 112, 3300–3313 (2008). [CrossRef]
  69. M. R. Corson, D. R. Korwan, R. L. Lucke, W. A. Snyder, and C. O. Davis, “The hyperspectral imager for the coastal ocean (HICO) on the international space station,” in Proceedings of IEEE International Geoscience and Remote Sensing Symposium (IEEE, 2008), pp. 101–104.
  70. R. L. Lucke, M. R. Corson, N. McGlothlin, S. Butcher, D. Wood, D. R. Korwan, R. Li, W. A. Snyder, C. O. Davis, and D. Chen, “Hyperspectral imager for the coastal ocean: instrument description and first images,” Appl. Opt. 50, 1501–1516(2011). [CrossRef]
  71. D. F. Millie, O. M. Schofield, G. J. Kirkpatrick, G. Johnsen, P. A. Tester, and B. T. Vinyard, “Detection of harmful algal blooms using photopigments and absorption signatures: a case study of the Florida red tide dinoflagellate, Gymnodinium breve,” Limnol. Oceanogr. 42, 1240–1251 (1997). [CrossRef]
  72. S. E. Craig, S. E. Lohrenz, Z. Lee, K. L. Mahoney, G. J. Kirkpatrick, O. M. Schofield, and R. G. Steward, “Use of hyperspectral remote sensing reflectance for detection and assessment of the harmful alga, Karenia brevis,” Appl. Opt. 45, 5414–5425 (2006). [CrossRef]
  73. B. Lubac, H. Loisel, N. Guiselin, R. Astoreca, L. F. Artigas, and X. Mériaux, “Hyperspectral and multispectral ocean color inversions to detect Phaeocystis globosa blooms in coastal waters,” J. Geophys. Res. 113, C06026 (2008). [CrossRef]
  74. S. Sathyendranath, L. Lazzara, and L. Prieur, “Variations in the spectral values of specific absorption of phytoplankton,” Limnol. Oceanogr. 32, 403–415 (1987). [CrossRef]

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