, Volume 28, Issue 1, pp 160–172 | Cite as

Adapting the CHEMTAX method for assessing phytoplankton taxonomic composition in Southeastern U.S. estuaries

  • Alan J. LewitusEmail author
  • David L. White
  • Raphael G. Tymowski
  • Mark E. Geesey
  • Sabrina N. Hymel
  • Peter A. Noble


CHEMTAX is a matrix factorization program used to derive taxonomic structure of phytoplankton from photosynthetic pigment vitios. The program was originally developed from and applied to the analysis of oceanic phytoplankton assemblages. We found that application of the original CHEMTAX reference matrix to southeastern United States estuarine systems produced inaccurate results, as verified by microscopy. Modification of the matrix, based primarily on the pigment ratios of 33 estuarine isolates, improved the predictive capabilities of CHEMTAX for our samples. Limitations of the method included an overstimation of diatom biomass (due to the inability to differentiate diatoms from taxa with chloroplasts derived from diatom endosymbionts, notably some dinoflagellates) and a tendency to exclude some raphidophyte species. In complement with microscopic verification, the method was shown to improve assessment of phytoplankton taxonomic composition.


Phytoplankton Pigment Composition North Inlet Accessory Pigment Pigment Ratio 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Literature Cited

  1. Bidigare, R. R., O. Schofield, andB. B. Prézelin. 1989. Influence of zeaxanthin on quantum yield of photosynthesis of aSynechococcus clone WH7803 (CD2).Marine Ecology Progress Series 56:177–188.CrossRefGoogle Scholar
  2. Booth, B. C. 1987. The use of autofluorescence for analyzing oceanic phytoplankton communities.Botanica Marina 30:101–108.CrossRefGoogle Scholar
  3. DiTullio, G. R., M. E. Geesey, D. R. Jones, K. Daly, W. O. Smith, andL. Campbell. 2003. Phytoplankton assemblage structure and primary productivity along 170°W in the South Pacific Ocean.Marine Ecology Progress Series 255:55–80.CrossRefGoogle Scholar
  4. Everitt, D. A., S. W. Wright, J. K. Volkman, D. P. Thomas, andE. J. Lindstrom. 1990. Phytoplankton community compositions in the western equatorial Pacific determined from chlorophyll and carotenoid pigment distributions.Deep-Sea Research. 37:975–997.CrossRefGoogle Scholar
  5. Furuya, K., M. Hayashi, Y. Yabushita, andA. Ishikawa. 2003. Phytoplankton dynamics in the East China Sea in spring and summer as revealed by HPLC-derived pigment signatures.Deep-Sea Research II 50:367–387.CrossRefGoogle Scholar
  6. Gieskes, W. W. andG. W. Kraay. 1986. Floristic and physiological difference between the shallow and the deep nanoplankton community in the euphotic zone of the open tropical Atlantic revealed by HPLC analysis of pigments.Marine Biology 91:567–576.CrossRefGoogle Scholar
  7. Gieskes, W. W. C., G. W. Kraay, A. Notji, D. Setiapermana, andD. Sutomo. 1988. Monsoonal alteration of a mixed and layered structure in the phytoplankton of the euphotic zone of the Banda Sea (Indonesia): A mathematical analysis of algal pigment fingerprints.Netherlands Journal of Sea Research 22: 123–137.CrossRefGoogle Scholar
  8. Guillard, R. R. L. 1975. Culture of phytoplankton for feeding marine invertebrates, p. 29–60.In W. L. Smith and M. H. Chaney (eds.), Culture of Marine Invertebrate Animals. Plenum Press, New York.Google Scholar
  9. Henriksen, P., B. Riemann, H. Kaas, H. M. Sørensen, andH. L. Sørensen. 2002. Effects of nutrient-limitation and irradiace on marine phytoplankton pigments.Journal of Plankton Research 24:835–858.CrossRefGoogle Scholar
  10. Higgins, H. W. andD. J. Mackey 2000. Algal class abundances, estimated from chlorophyll and carotenoid pigments, in the western Equatorial Pacific under El Niño and non-El Niño conditions.Deep-Sea Research 147:1461–1483.Google Scholar
  11. Hillebrand, H., C.-D. Dürselen, D. Kirschtel, U. Pollingher, andT. Zohary. 1999. Biovolume calculation for pelagic and benthic microalgae.Journal of Phycology 35:403–424.CrossRefGoogle Scholar
  12. Jeffrey, S. W., R. F. C. Mantoura, andS. W. Wright (eds.). 1997. Phytoplankton Pigments in Oceanography: Guidelines to Modern Methods. UNESCO Publishing, Paris, France.Google Scholar
  13. Kana, T. M. andP. M. Gilbert. 1987. Effect of irradiances up to 2000 μE m−2 s−1 on marineSynechococcus WH7803—I. Growth, pigmentation, and cell composition.Deep-Sea Research 34:479–495.CrossRefGoogle Scholar
  14. Kana, T. M., P. M. Glibert, R. Goericke, andN. A. Welschmeyer. 1988. Zeaxanthin and β-carotene inSynechococcus WH7803 respond differently to irradiance.Limnology and Oceanography, 33:1623–1627.Google Scholar
  15. Kawaguchi, T., A. J. Lewitus, C. M. Aelion, andH. N. McKellar. 1997. Can urbanization limit iron availability to estuarine algae?Journal of Experimental Marine Biology and Ecology 213:53–69.CrossRefGoogle Scholar
  16. Klein, B. andA. Sournia 1987. A daily study of the diatom spring bloom at Roscoff (France) in 1985. II. Phytoplankton pigment composion studied by HPLC analysis.Marine Ecology Progress Series 37:265–275.CrossRefGoogle Scholar
  17. Letelier, R. M., R. R. Bidigare, D. V. Hebel, M. Ondrusek, C. D. Winn, andD. M. Calr. 1993. Temporal variability of phytoplankton community structure based on pigment analysis.Limnology and Oceanography 38:1420–1437.Google Scholar
  18. Lewitus, A., K. Hayes, J. Kempton, L. Mason, S. Wilde, B. Williams, and J. Wolny. 2004. Prevalence of raphidophyte blooms in South Carolina brackish ponds associated with housing and golf courses.In K. A. Steidinger, J. A. Landsberg, C. R. Tomas, and G. A. Vargo (eds.), Proceedings of the Xth International Conference on Harmful Algae (in press).Google Scholar
  19. Lewitus, A. J., E. T. Koepfler andJ. T. Morris. 1998. Seasonal variation in the regulation of phytoplankton by nitrogen and grazing in a salt marsh estuary.Limnology and Oceanography 43:636–646.CrossRefGoogle Scholar
  20. Lewitus, A. J., E. T. Koepfler, andR. Pigg. 2000. Use of dissolved organic nitrogen by a salt marsh phytoplankton bloom community.Archives of Hydrobiology Special Issues on Advances in Limnology 55:441–456.Google Scholar
  21. Lewitus, A. J., L. B. Schmidt, L. J. Mason, J. W. Kempton, S. B. Wilde, J. L. Wolny, B. J. Williams, K. C. Hayes, S. N. Hymel, C. J. Keppler, andA. H. Ringwood. 2003. Harmful algal blooms in South Carolina residential and golf course ponds.Population and Environment 24:387–413.CrossRefGoogle Scholar
  22. Mackey, D. J., H. W. Higgins, M. D. Mackey, andD. Holdsworth. 1998. Algal class abundances in the western equatorial Pacific: Estimation from HPLC measurements of chloroplast pigments using CHEMTAX.Deep-Sea Research I 45:1441–1468.CrossRefGoogle Scholar
  23. Mackey, M. D., D. J. Mackey, H. W. Higgins, andS. W. Wright. 1996. CHEMTAX—A program for estimating class abundances from chemical markers: Application to HPLC measurements of phytoplankton.Marine Ecology Progress Series 144:265–283.CrossRefGoogle Scholar
  24. Menden-Deuer, S. andE. J. Lessard. 2000. Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton.Limnology and Oceanography 45:569–579.Google Scholar
  25. Menden-Deuer, S., E. J. Lessard, andJ. Satterberg. 2001. Effect of preservation on dinoflagellate and diatom cell volume and consequences for carbon biomass predictions.Marine Ecology Progress Series 222:41–50.CrossRefGoogle Scholar
  26. Millie, D. F., H. W. Paerl, andJ. P. Hurley. 1993. Microalgal pigment assessments using high-performance liquid chromatography: A synopsis of organismal and ecological applications.Canadian Journal of Fish and Aquatic Sciences 50:2513–2527.CrossRefGoogle Scholar
  27. Montagnes, D. J. S., J. A. Berges, P. J. Harrison, andF. J. R. Taylor. 1994. Estimating carbon, nitrogen, protein, and chlorophylla from volume in marine phytoplankton.Limnology and Oceanography 39:1044–1060.Google Scholar
  28. Riegman, R. andG. W. Kraay. 2001. Phytoplankton community structure derived from HPLC analysis of pigments in the Faroe-Shetland Channel during summer 1999: The distribution of taxonomic groups in relation to physical/chemical conditions in the photic zone.Journal of Plankton Research 23:191–205.CrossRefGoogle Scholar
  29. Schlüter, L., F. Møhlenberg, H. Havskum, andS. Larsen. 2000. The use of phytoplankton pigments for identifying and quantifying phytoplankton groups in coastal areas: Testing the influence of light and nutrients on pigment/chlorophylla ratios.Marine Ecology Progress Series 192:49–63.CrossRefGoogle Scholar
  30. Van Heukelem, L., A. J. Lewitus, T. M. Kana, andN. E. Craft. 1994. Improved separations of phytoplankton pigments using temperature-controlled high performance liquid chromatography.Marine Ecology Progress Series 114:303–313.CrossRefGoogle Scholar
  31. Van Heukelem, L. andC. S. Thomas. 2001. Computer-assisted high-performance liquid chromatography method development with applications to the isolation and analysis of phytoplankton pigments.Journal of Chromatography A 910:31–49.CrossRefGoogle Scholar
  32. Verity, P. G., C. Y. Robertson, C. R. Tronzo, M. G. Andrews, J. R. Nelson, andM. E. Sieracki. 1992. Relationships between cell volume and the carbon and nitrogen content of marine photosynthetic nanoplankton.Limnology and Oceanography 37:1434–1446.CrossRefGoogle Scholar
  33. Wright, S. W., S. W. Jeffrey, R. F. C. Mantoura, C. A. Llewellyn, T. Bjørnland, D. Repeta, andN. Welschmeyer. 1991. Improved HPLC method for the analysis of chlorophylls and carotenoids from marine phytoplankton.Marine Ecology Progress Series 77:183–196.CrossRefGoogle Scholar
  34. Wright, S. W., D. P. Thomas, H. J. Marchant, H. W. Higgins, M. D. Mackey, andD. J. Mackey. 1996. Analysis of phytoplankton of the Australian sector of the Southern Ocean: Comparison of microscopy and size frequency data with interpretations of pigment HPLC data using the ‘CHEMTAX’ matrix factorisation program.Marine Ecology Progress Series 144:285–298.CrossRefGoogle Scholar

Copyright information

© Estuarine Research Federation 2005

Authors and Affiliations

  • Alan J. Lewitus
    • 1
    Email author
  • David L. White
    • 2
  • Raphael G. Tymowski
    • 3
  • Mark E. Geesey
    • 4
  • Sabrina N. Hymel
    • 1
  • Peter A. Noble
    • 5
  1. 1.Bell W. Baruch Institute for Marine and Coastal SciencesUniversity of South Carolina, and Marine Resources Research Institute, South Carolina Department of Natural Resources, Hollings Marine LaboratorySouth CarolinaCharleston
  2. 2.Marine Science ProgramUniversity of South CarolinaColumbia
  3. 3.Baruch Marine LaboratoryBelle W. Baruch Institute for Marine and Coastal Sciences, University of South CarolinaGeorgetown
  4. 4.Grice Marine LaboratoryCollege of CharlestonCharleston
  5. 5.Civil and Environmental Engineering DepartmentUniversity of WashingtonSeattle98195

Personalised recommendations