Department of Oceanography, Texas A&M
University
Fall 2009: OCNG 654 Plankton Ecology:
Phytoplankton: References
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REFERENCES
Required reading for each Lecture is given first, followed list of "Background References" for additional information and papers used in lecture.
Lecture 1: Introduction to the Phytoplankton and Diversity of the Algae
REQUIRED READING: Brodie & Lewis 2007. Ch. 1; Delwiche Ch. 2; Cavlier-Smith Ch.3;
Peruse these 3 websites; you may refer back to them over the course:
Background references:
- Baldauf SL 2003. The deep roots of eukaryotes. Science 300:1703–1706
- Reeb, V. C., Peglar, M. T., Yoon, H. S., Bai, J. R., Wu, M., Shiu, P., Grafenberg, J. L., Reyes-Prieto, A., Rümmele, S. E., Gross, J. & Bhattacharya, D. 2009. Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists. Mol. Phylogenet. Evol. 53:202-11.
- Pechenik, JA. A short guide to writing about Biology. Ch.4: Citing sources Ch.5: Revising; Ch.6: Writing Summaries; Ch.7 Writing Term Papers
- Good cell biology refrences: van den Hoek. 1995. Ch. 1 Introduction; Ch. 2 Cyanobacteria; Ch. 3 [Prochlorophyta]; Ch. 6 Heterokonts:Chryso-Parmo- and Sarcinochrysidophyceae; Ch. 8; Eustimatophyceae; Ch. 14 Haptophyta; Ch.15 Cryptophyta; Ch. 16 Dinophyta; Ch. 19 Chlorophyta; Ch. 20 Prasinophyta
Lecture 2: Cyanobacteria: picoplankton
REQUIRED READING:
Background references:
- Taxonomy-:proposed System Naturae http://www.taxonomy.nl/Main/Classification/111362.htm
- Campbell, L., H.A. Nolla and D. Vaulot. 1994. The importance of Prochlorococcus to community structure in the central North Pacific Ocean. Limnology and Oceanography 39(4):954-961.
- Chisholm, S.W., S.L. Frankel, R. Goericke, R.J. Olson, B. Palenik, J.B. Waterbury, L. Westjohnsrud and E.R. Zettler. 1992. Prochlorococcus-marinus nov gen-nov sp - an oxyphototrophic marine prokaryote containing divinyl chlorophyll-a and chlorophyll-b. Archives of Microbiology 157(3):297-300.
- Johnson, Z. I., Zinser, E. R., Coe, A., McNulty, N. P., Woodward, E. M. S. & Chisholm, S. W. 2006. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311:1737-40.
- Rippka et al. 1979/ Bergey's Manual of Systematic Bacteriology,
- Schopf, J. W. & Packer, B. M. Early Archean (3.3 billion to 3.5
billion-year-old) microfossils from Warrawoona Group, Australia. Science 237,
70–73 (1987)
- Tice, M.M. and Lowe, D.R. 2004. Photosynthetic microbial mats in
the 3,416-Myr-old ocean. Nature 431, 549 - 552 (30 September 2004).
- Waterbury, J.B., S.W. Watson, R.R.L. Guillard and L.E. Brand. 1979. Wide-spread occurence of a unicellular, marine planktonic, cyanobacterium. Nature, London 277:293-294.
- Zinser, E. R., Coe, A., Johnson, Z. I., Martiny, A. C., Fuller, N. J., Scanlan, D. J. & Chisholm, S. W. 2006. Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method. Appl. Environ. Microbiol. 72:723-32.
LAB #1: Flow Cytometry
REQUIRED READING:
Campbell, L.2001. Flow cytometric analysis of autotrophic picoplankton. In Methods in Microbiology. Paul, J.H. (ed.) vol. 30, Academic Press, San Diego, pp. 317-343.
Background References:
- Amann, R. I., Binder, B. J., Olson, R. J., Chisholm, S. W., Devereux, R. & Stahl, D. A. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-25.
- Cavendar-Bares, K., Frankel, S. L. & Chisholm, S. W. 1998. A dual sheath flow cytometer for shipboard analyses of phytoplankton communities form the oligotrophic oceans. Limnol. Oceanogr. 43:1383-88
- Chisholm, S. W., Olson, R. J., Zettler, E. R., Goericke, R., Waterbury, J. B. & Welschmeyer, N. A. 1988. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340-43.
- Collier, J. L. & Campbell, L. 1999. Flow cytometry in molecular aquatic ecology. Hydrobiologia 401:33-53.
- Dubelaar, G. B. J. & Jonker, R. R. 2000. Flow cytometry as a tool for the study of phytoplankton. Sci. Mar. 64:135-56.
- DuRand, M. D., Olson, R. J. & Chisholm, S. W. 2001. Phytoplankton population dynamics at the Bermuda Atlantic Time-series station in the Sargasso Sea. Deep-Sea Research II 48:1983-2003.
- Monger, B. M. & Landry, M. R. 1993. Flow cytometric analysis of marine bacteria with Hoechst 33342. Appl. Environ. Microbiol. 59:905-11.
- Olson, R. J., Zettler, E. R., Armbrust, E. V. & Chisholm, S. W. 1990. Pigment, size and distribution of Synechococcus in the North Atlantic and Pacific oceans. Limnol. Oceanogr. 35:45-58.
- Olson, R. J., Zettler, E. R., Chisholm, S. W. & Dusenberry, J. A. 1991. Advances in oceanography through flow cytometry. In: Demers, S. [Ed.] NATO ASI Series G, Ecological Sciences. Springer-Verlag, Berlin, pp. 351-99.
- Shapiro, H. M. 1995. Practical Flow Cytometry 3rd. Edition. Wiley-Liss, New York.
- Vaulot, D. 1989. CYTOPC: processing software for flow cytometric data. Signal and Noise 2:8.
- Wood, A. M., Horan, P. K., Muirhead, K., Phinney, D. A., Yentsch, C. M. & Waterbury, J. B. 1985. Discrimination between types of pigments in marine Synechococcus spp. by scanning spectroscopy, epifluorescence microscopy, and flow cytometry. Limnol. Oceanogr. 30:1303-15.
Lecture 3:Cyanobacteria: Trichodesmium and Croccospaera
REQUIRED READING
- Capone et al.1997. Trichodesmium, a globally significant marine Cyanobacterium. Science 276:1221-1229.
- Zehr, J. P., Waterbury, J. B., Turner, P. J., Montoya, J. P., Omoregie, E., Steward, G. F., Hansen, A. & Karl, D. M. 2001. Unicellular cyanobacteria fix N-2 in the subtropical North Pacific Ocean. Nature 412:635-38.
- Church, M. J., Jenkins, B. D., Karl, D. M. & Zehr, J. P. 2005. Vertical distributions of nitrogen-fixing phylotypes at Stn ALOHA in the oligotrophic North Pacific Ocean. Aquat. Microb. Ecol. 38:3-14.
- Webb, E. A., Ehrenreich, I. M., Brown, S. L., Valois, F. W. & Waterbury, J. B. 2009. Phenotypic and genotypic characterization of multiple strains of the diazotrophic cyanobacterium, Crocosphaera watsonii, isolated from the open ocean. Environmental Microbiology 11:338-48.
- Church, M. J., Mahaffey, C., Letelier, R. M., Lukas, R., Zehr, J. P. & Karl, D. M. 2009. Physical forcing of nitrogen fixation and diazotroph community structure in the North Pacific subtropical gyre. Global Biogeochemical Cycles 23:19.
Background References
- Campbell, L., Carpenter, E. J., Montoya, J. P., Kustka, A. B. & Capone, D. G. 2005. Picoplankton community structure within and outside a Trichodesmium bloom in the southwestern Pacific Ocean. Vie Et Milieu-Life and Environment 55:185-95.
- Dupouy, C., Neveux, J., Subramaniam, A., Mulholland, M. R., Montoya, J. P., Campbell, L., Carpenter, E. J. & Capone, D. G. 2000. Satellite captures Trichodesmium blooms in the Southwestern Tropical Pacific. Eos 81:13-16.
- Goebel, N. L., Edwards, C. A., Church, M. J. & Zehr, J. P. 2007. Modeled contributions of three types of diazotrophs to nitrogen fixation at Station ALOHA. Isme J. 1:606-19.
- Zehr, J. P. & Ward, B. B. 2002. Nitrogen cycling in the ocean: New perspectives on processes and paradigms. Appl. Environ. Microbiol. 68:1015-24.
Lecture 4:
REQUIRED READING:
Recommended: links in lecture notes
Background References:
Lab #2: Microscopy
REQUIRED READING:
Recommended References:
- Slayter & Slayter. 1992. Light and electron microscopy. Cambridge University Press.
- Tomas, C. 2000. Identifying Marine Phytoplankton, Academic Press. (TEXTBOOK)
- Culture Collection of Marine Phytoplankton (Bigelow Laboratory): https://ccmp.bigelow.org/home
Lecture 5:
REQUIRED Readings:
Haptophyta REQUIRED READING:
Protozoa: Dinophyta REQUIRED READING
Recommended: at least look at this one:
Background References:
- Taylor, F.J.R., Ed.1987. The Biology of Dinoflagellates. Botanical Monographs. Oxford, Blackwell Scientific Publications.
- Taylor, F.J.R. 1987. Ecology of Dinoflagellates. In Taylor, F.J.R. (eds.), The Biology of dinoflagellates. Blackwell Scientific Publications, Oxford, pp. 399-501.
- Sournia, A. 1982. Form and function in marine phytoplankton. Biol. Rev., 57, 347-394.
role. J. Phycol. 33: 889-896.
Lecture 6:Ochrophyta [Stamenopiles]: Diatoms
REQUIRED READING:
Recommended:
-
Armbrust, E. V. and others 2004. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306: 79-86.
- Allen, A. E., A. Vardi, and C. Bowler. 2006. An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Curr. Opin. Plant Biol. 9: 264-273.
- Sims, P. A., D. G. Mann, and L. K. Medlin. 2006. Evolution of the diatoms: insights from fossil, biological and molecular data. Phycologia 45: 361-402.
- van den Hoek. 1995. Ch. Diatoms.
- Bowler, C, et al. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456: 239-244.
Background Refrences:
- Round, F.E., Crawford, R.M. and Mann, D.G. 1990. The Diatoms - Biology & morphology of the genera. Cambridge University Press, Cambridge.
- Medlin, L. K., and I. Kaczmarska. 2004. Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia 43: 245-270.
Lab #3
Pictures from lab: see this directory: http://oceanography.tamu.edu/~campbell/654/webpage/Lab3/
REQUIRED:
Guillard & Sieracki. Counting cells in culture with the light microscope. In: Anderson RA (ed) Algal Culturing Techniques, Elsevier.
Recommended:
Background References:
- UNESCO 1974. A review of methods used for quantitative phytoplankton studies, UNESCO Tech. Pap. Mar. Sci 18: 27-
- UNESCO 1978 Phytoplankton Manual, (Sournia, A. ed), Paris.
- Cyanobacteria.ppt
- Cyano references
- Cyano Key
- Tomas, C. 2000. Identifying Marine Phytoplankton
Lecture 7:
Plantae REQUIRED READINGS:
Recommended:
Background:
- Vaulot, D., W. Eikrem, M. Viprey and H. Moreau. 2008. The diversity of small eukaryotic phytoplankton (<= 3 µm) in marine ecosystems. FEMS Microbiology Reviews 32(5):795-820.
- Worden, A. Z. & Not, F. 2008. Ecology and diversity of picoeukaryotes. In Kirchman, D. L. [ed.], Microbial Ecology of the Ocean. Wiley, p. 159-205.
Lecture 8: Nutrients and Biomass
REQUIRED READING:
- Barlati et al. Ch. 4. Biogeochemical Role of Algae. In: Algae: anatomy, biochemistry, and biotechnology.
- MacIntyre & Cullen. Ch.19. Using cultures to investigate the physiological ecology of microalgae. In: Andersen (ed). Algal Culturing Techniques
- Bidigare et al. Ch. 20. Analysis of algal pigments by HPLC. In: Andersen (ed). Algal Culturing Techniques
Recommended:
- Whitfield. 2001. Interactions between phytoplankton and trace metals in the ocean. Adv. Mar. Biol. 41: 1-128, Southward et al. (eds)
- Dugdale, R. C., and F. P. Wilkerson. 1998. Silicate regulation of new production in the equatorial Pacific upwelling. Nature 391: 270-273.
Background:
- Boyd,P. et al. A Mesoscale phytoplankton bloom in the polar Southern Ocean stimulated by iron fertilization. Nature 407, 695-702 (2000).
-
Boyd, P. Environmental factors controlling phytoplankton processes in the Southern Ocean. J. Phycol. 38, 844-861 (2002).
- Chisholm, S. et al. Dis-crediting Ocean Fertilization. Science 294 (2001).
Lab #4
REQUIRED READING:
Lecture 9: Primary Production
REQUIRED READING:
- MacIntyre & Cullen. Ch.19. Using cultures to investigate the physiological ecology of microalgae. In: Andersen (ed). Algal Culturing Techniques
Recommended:
- Ch.3. Photosynthesis
- Falkowski, P. G. 1992. Molecular bases of changes in quantum yields of photosyntheis. In: Falkowski, P. G., and A. D. Woodhead (eds). Primary productivity and biogeochemical cycles in the sea. Plenum Press.
Background:
- Cleveland, J. S., M. J. Perry, D. A. Kiefer, and M. C. Talbot. 1989. Maximal quantum yield of photosynthesis in the northwestern Sargasso Sea. J. Mar. Res. 47: 869-886.
- Kiefer, D. A., W. S. Chamberlin, and C. R. Booth. 1989. Natural fluorescence of chlorophyll a: relationship to photosynthesis and chlorophyll concentration in the western South Pacific gyre. Limnol. Oceanogr. 34: 868-881.
- Kiefer, D. A., and R. A. Reynolds. 1992. Advances in understanding phytoplankton fluorescence and photosynthesis, p. 155-174. In P. G. Falkowski and A. D. Woodhead [eds.], Primary Productivity and Biogeochmeical Cycles in the Sea. Plenum Press.
- Prieto, L., R. D. Vaillancourt, B. Hales, and J. Marra. 2008. On the relationship between carbon fixation efficiency and bio-optical characteristics of phytoplankton. J. Plankton Res. 30: 43-56.
- Vaillancourt, R. D., J. Marra, R. T. Barber, and W. O. Smith. 2003. Primary productivity and in situ quantum yields in the Ross Sea and Pacific Sector of the Antarctic Circumpolar Current. Deep-Sea Research Part Ii-Topical Studies in Oceanography 50: 559-578.
- Williams et al. 2002 Phytoplankton Productivity, Blackwell Science
- Satlantic. http://www.satlantic.com/details.asp?ID=12&CategoryID=3&SubCategoryID=0
- Juneau & Harrison. 2005. PAM Flurometry. Photochemistry and Photobiology, 2005, 81: 649–653
Lecture 10: Phytoplankton Growth rates and nutrient kinetics
REQUIRED READING:
- Goldman, J. C., J. J. McCarthy, and D. G. Peavey. 1979. Growth rate influence on the chemical composition of phytoplankton in oceanic waters. Nature, London 279: 210-215.
Recommended:
- Laws, E. A., and T. T. Bannister. 1980. Nutrient- and light-limited growth of Thalassiosira fluviatilis in continuous culture, with implications for phytoplankton growth in the ocean. Limnol. Oceanogr. 25: 457-473.
- Kang et al. 2009. J. Phycology 45: 864-872
Background Reading
- McCarthy, J. J., and J. C. Goldman. 1979. Nitrogenous nutrition of marine phytoplankton in nutrient-depleted waters. Science 203: 670-672.
Lab #5: Photosynthesis vs. Irradiance (P vs. E)
REQUIRED READING:
Recommended
- Frenette, J. J., S. Demers, L. Legendre, and J. Dodson. 1993. Lack of agreement among models for estimating the photosynthetic parameters. Limnol. Oceanogr. 38: 679-687.
- Sakshaug, E. and others 1997. Parameters of photosynthesis: definitions, theory and interpretation of results. J. Plankton Res. 19: 1637-1670.
Background
- Falkowski & Raven. Ch. 7 (196-201); Ch. 9
- Ch 9.1 Light In: Plant Physiology Online
- Kirk: p. 351-359 In: Kirk, J. T. O. 1983. Light and photosynthesis in aquatic ecosystems. Cambridge University Press.
- Jassby, A. D., and T. Platt. 1976. Mathematical formulation of the relationship between photosynthesis and light for phytoplankton. Limnol. Oceanogr. 21: 540-547.
- Platt, T., C. L. Gallegos, and W. G. Harrison. 1980. Photoinhibition of photosynthesis in natural assemblages of marine phytoplankton. J. Mar. Res. 38: 687-701.
Lecture 11: Biotechnology
REQUIRED READING
Recommended
Background
- Lembi & Waaland (1988) Algae and Human Affairs. Cambridge University Press
- Chini Zittelli, G., F. Lavista, A. Bastianini, L. Rodolfi, M. Vincenzini, and M. R. Tredici. 1999. Production of eicosapentaenoic acid by Nannochloropsis sp. cultures in outdoor tubular photobioreactors. J. Biotechnol. 70: 299-312.
- Bradbury, J. (2004). Nature's Nanotechnologists: Unveiling the Secrets of Diatoms. PLoS Biology 2, 1512-1515.
- Drum, R.W.; Gordon, R. (2003). "Star Trek replicators and diatom nanotechnology". Trends Biotechnology 21: 325–328. doi:10.1016/S0167-7799(03)00169-0.
- Echigoya, R., L. Rhodes, Y. Oshima, and M. Satake. 2005. The structures of five new antifungal and hemolytic amphidinol analogs from Amphidinium carterae collected in New Zealand. Harmful Algae 4: 383-389.
- Rosenberg, J. N., G. A. Oyler, L. Wilkinson, and M. J. Betenbaugh. 2008. A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution. Curr. Opin. Biotechnol. 19: 430-436.
Lecture 12: HABs
REQUIRED READING:
- Margalef 1978. Life-forms of phytoplankton as survival alternatives in an unstable environment. Oceanol. Acta, 1, 493–509.
- Anderson, D. M. 2009. Approaches to monitoring, control and management of harmful algal blooms (HABs), p. 342-347. Elsevier Sci Ltd.
- Anderson, D. M. and others 2008. Harmful algal blooms and eutrophication: Examining linkages from selected coastal regions of the United States. Harmful Algae 8: 39-53.
Recommended
- Anderson et al. 2002. Estuaries 25: 704-726
- Cembella, A. and U. John. 2007. Molecular physiology of toxin production and growth regulation in harmful algae. p. 215-228. In: Graneli & Turner.
- Smayda, T.J. and C.S. Reynolds. 2001. Community Assembly in Marine Phytoplankton: Application of Recent Models to Harmful Dinoflagellate Blooms. J. Plankton Res. 23 (5): 447-461
- Steidinger, K.A. and HL. Melton Penta. 1999. Harmful Microalgae and Associated Public Health Risks in the Gulf of Mexico. US EPA: Gulf of Mexico Program. EPA Grants #MX004729-95-0
Background References:
- Anderson, D. M. & D. J. Garrison (eds.). 1997. The ecology and oceanography of harmful algal blooms. Limnol. Oceanogr. Special Issue 42(5, part 2: 1009-1305
- Anderson, D. M., A. D. Cembella, & G. M. Hallegraeff. 1998. Physiological ecology of harmful algal blooms. NATO ASI Series, Vol. G41, Springer-Verlag, Berlin, Heidelberg, 662 pp.
- Graneli, E. & J.T, Turner (eds.). 2007. Ecology of Harmful Algae. Ecological Studies 189. Springer.
- Margalef, R., Estrada, M. and Blasco, D. 1979. Functional morphology of organisms involved in red tides, as adapted to decaying turbulence. In Taylor, D. and Seliger, H. (eds), Toxic Dinoflagellate Blooms. Elsevier, New York, pp. 89–94.
- Tillmann, U., M. Elbrachter, B. Krock, U. John, and A. Cembella. 2009. Azadinium spinosum gen. et sp nov (Dinophyceae) identified as a primary producer of azaspiracid toxins. Eur. J. Phycol. 44: 63-79.
- ISSHA Conference Proceedings
- IOC publications
- Harmful Algae
- WHOI HAB site
Lab #6 Demonstration of Phylogenetic Tree/ BLAST and NASA's ICE
NASA's NEO website for Image Composite Explorer (AVHRR, MODIS) data: http://neo.sci.gsfc.nasa.gov/Search.html
Lecture 13: Remote Sensing and Ocean Observing
REQUIRED READING:
- Nair, A. and others 2008. Remote sensing of phytoplankton functional types. Remote Sens. Environ. 112: 3366-3375.
- Roesler, C. S. M. Etheridge, and G.C. Pitcher. 2003. Application
of an ocean color algal taxa detection model to red tides in the
Southern Benguela. In K. A. Steidinger, J. H. Lansdberg, C.
R. Tomas and G. A. Vargo [eds.], Proceedings of the Xth
International Conference on Harmful Algae. Florida Fish and
Wildlife Conservation Commission and Intergovernmental
Oceanographic Commission of UNESCO.
- Subramaniam, A., C. W. Brown, R. R. Hood, E. J. Carpenter, and D. G. Capone. 2002. Detecting Trichodesmium blooms in SeaWiFS imagery. Deep-Sea Res. 49: 107-121.
Recommended:
- Behernfeld, M.J., and P.G. Falkowski (1997) Photosynthetic rates derived from satellite-based chlorophyll concentration, Limnol. Oceanogr., 42, 1-20.
- Campbell, J. et al. 1992 Global Biogeochem. Cycles
- Chang, G. et al.. 2004. The new age of hyperspectral oceanography. Oceanography 17: 16–23.
- Ryan, J. et al. 2005. Coastal ocean physics and red tides:
An example from Monterey Bay, California. Oceanography
18: 246–255.
Background:
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Last updated: 4 October 2009
Fall 2009:
OCNG 654, Plankton Ecology: Phytoplankton References
Professor: Lisa
Campbell
For comments and
suggestions about this site contact: lcampbell@ocean.tamu.edu.
Department of Oceanography, Texas A&M
University