Plankton Dynamics in Tidal Estuaries

Phytoplankton photosynthesis drives many biogeochemical and ecological processes in lakes, estuaries, and the ocean. For example, dynamic changes in pH, trace metal speciation, and concentrations of dissolved gases (oxygen, carbon dioxide, methane), inorganic nutrients (nitrate, phosphate, silicate), and organic compounds (amino acids, organosulfur compounds) are all closely associated with fluctuations in phytoplankton photosynthesis. Trophic linkages also exist, between the phytoplankton as primary producers and populations of consumer organisms including bacteria, zooplankton, benthic invertebrates, and fish. Our scientific understanding of lakes and estuaries as dynamic ecosystems is therefore dependent upon a mechanistic understanding of both natural and human-induced variability of phytoplankton abundance, community composition, productivity, and connections to geochemical processes and other biological communities. These topics are central to poorly resolved issues such as: the growing worldwide incidence of toxic algal blooms and associated fish mortality; coastal eutrophication and increasing frequency/extent of hypoxia or anoxia; long-term and cyclic changes in fish stocks; the global significance of phytoplankton to the cycling of key elements such as carbon and nitrogen; and ecosystem- scale responses to both species extinctions and introductions of exotic species. This project's objectives are to: (1) study the distribution, abundance, species composition, and productivity of planktonic microalgae, animals, and bacteria in estuaries; (2) define and quantify processes that regulate population dynamics and productivity of planktonic organisms in estuaries; (3) define and quantify processes through which the plankton alter and reflect water quality in estuaries; (4) define and quantify benthic processes that affect plankton dynamics and productivity of estuaries; and, (5) define anthropogenic impacts on estuarine ecosystems. For additional information, see San Francisco Bay water quality page .

REPORTS PUBLISHED 1999-2008

Smetacek, V., and Cloern, J.E., 2008, On phytoplanton trends - How are phytoplankton at coastal sites around the world responding to ongoing global change?: Science, v. 319, no. 5868, p. 1346-1348.

Thébault, J., Schraga, T.S., Cloern, J.E., and Dunlavey, E.G., 2008, Primary Production and Carrying Capacity of Former Salt Ponds After Reconnection to San Francisco Bay, Wetlands, v. 28, p. 841-851. (on-line abstract of journal article)

Brown, L.R, Thompson, J.K., Higgins, K., and Lucas, L.V., 2007, Population density, biomass, and age-class structure of the invasive clam Corbicula fluminea in rivers of the lower San Joaquin River Watershed, California: Western North American Naturalist, v. 67, p. 572-586. (on-line abstract of journal article)

Cloern, J.E., 2007, Habitat connectivity and ecosystem productivity: Implications from a simple model: American Naturalist, v. 169, p. E21-E33. (on-line article in pdf format - published by University of Chicago Press, copyright not claimed for this article)

Cloern, J.E., Jassby, A.D., Thompson, J.K., and Hieb, K.A., 2007, A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay: Proceedings of the National Academy of Sciences USA, v. 104, p.18,561-18,565, doi:10.1073/pnas.0706151104, (on-line abstract or on-line article in pdf format, 1664 KB, published with Open Access)

Monsen, N.E., Cloern, J.E., and Burau, J.R., 2007, Effects of flow diversions on water and habitat quality: Examples from California's highly manipulated Sacramento-San Joaquin Delta: San Francisco Estuary and Watershed Science, v. 5, no. 3, article 2. (on-line abstract and to download paper in pdf format)

Bachman, R.W., Cloern, J.E., Hecky, R.E., and Schindler, D.W., eds., 2006, Special Issue on Eutrophication of freshwater and marine ecosystems: Limnology and Oceanography, v. 51, p. 351-800.

Cloern, J.E., Jassby, A.D., Schraga, T.S., and Dallas, K.L., 2006, What is causing the phytoplankton increase in San Francisco Bay?: The Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary, Oakland, San Francisco Estuary Institute, p. 62-70. (on-line article in pdf format)

Cloern, J.E., and Krantz, T., 2006, Eutrophication, in Duffy, J.E., ed., Encyclopedia of Earth: Washington, D.C., Environmental Information Coalition, National Council for Science and the Environment. (on-line article)

Lopez, C.B., Cloern , J.E., Schraga, T.S., Little, A.J., Lucas, L.V., Thompson, J.K., and Burau, J.R., 2006, Ecological values of shallow-water habitats: Implications for the restoration of disturbed ecosystems: Ecosystems, v. 9, p. 422-440. (on-line abstract of journal article)

Lucas, L.V., Sereno, D.M., Burau, J.R., Schraga, T.S., Lopez, C.B., Stacey, M.T., Parchevsky, K.V., and Parchevsky, V.P., 2006, Intratidal variability of water quality in a shallow tidal lagoon: Mechanisms and implications: Estuaries and Coasts, v. 29, p. 711-730. (on-line abstract of journal article)

Cloern, J.E., and Dufford, R., 2005, Phytoplankton community ecology: Principles applied in San Francisco Bay: Marine Ecology Progress Series, v. 285, p. 1-28. (on-line abstractof journal article)

Cloern, J.E., Schraga, T.S., and Burns Lopez, C., 2005, Heat wave brings an unprecedented red tide to San Francisco Bay: Eos, Transactions American Geophysical Union, v. 86, p. 66.

Cloern, J.E., Schraga, T.S., Lopez, C.B., Knowles, N., Labiosa, R.G., and Dugdale, R., 2005, Climate anomalies generate an exceptional dinoflagellate bloom in San Francisco Bay , Geophysical Research Letters, v. 32, no. 14, L14608, doi:10.1029/2005GL023321. (on-line abstract of journal article)

Sobczak, W.V., Cloern, J.E., Jassby, A.D., Cole, B.E., Schraga, T.S., and Arnsberg, A., 2005, Detritus fuels ecosystem metabolism but not metazoan food webs in San Francisco estuary's freshwater delta: Estuaries, v. 28, p. 122-135. (on-line abstract of journal article)

Luoma, S.N., and Cloern, J. E., 2004, Water 2025: The CALFED Bay-Delta Program: People, Land and Water, Department of Interior, v.2/04, p. 23.

Chauvaud, L., Thompson, J.K., Cloern, J.E., and Thouzeau, G., 2003, Clams as CO₂ generators: The Potamocorbula amurensis example in San Francisco Bay: Limnology and Oceanography, v. 48, p. 2,086-2,092. (on-line article, pdf format)

Cloern, J.E., Schraga, T.S., Lopez, C.B., and Labiosa, R., 2003, Lessons from monitoring water quality in San Francisco Bay: 2003 Pulse of the Estuary, San Francisco Estuary Institute, p. 15-20. (on-line complete report, pdf format)

Jassby, A.D., Cloern, J.E., and Muller-Solger, A., 2003, Phytoplankton fuels Delta food web: California Agriculture, v. 57, p. 104-109. (cover story - on-line abstract or on-line report in pdf format)

May, C.L., Koseff, J.R., Lucas L.V., Cloern J.E., and Schoellhamer, D.H., 2003, Effects of spatial and temporal variability of turbidity on phytoplankton blooms: Marine Ecology Progress Series, v. 254, p. 111-128. (on-line abstract)

Cloern, J.E., Canuel, E.A., and Harris, D., 2002, Stable carbon and nitrogen isotope composition of aquatic and terrestrial plants of the San Francisco Bay estuarine system: Limnology and Oceanography, v. 47, p. 713-729. (on-line abstract or article in pdf format)

Guarini, J.M, Cloern, J.E., Edmunds, J., and Gros, P., 2002, Microphytobenthic potential productivity estimated in three tidal embayments of the San Francisco Bay: A comparative study: Estuaries, v. 25, p. 409-417.

Jassby, A.D., Cloern, J.E., and Cole, B.E., 2002, Annual primary production: Patterns and mechanisms of change in a nutrient-rich tidal ecosystem: Limnology and Oceanography, v. 47, p. 698-712. (on-line abstract or article in pdf format)

Lucas, L.V., and Cloern, J.E., 2002, Effects of tidal shallowing and deepening on phytoplankton production dynamics: A modeling study: Estuaries, v. 25, p. 497-507.

Lucas, L.V., Cloern, J.E., Thompson, J.K., and Monsen, N.E., 2002, Functional variability of habitats in the Sacramento-San Joaquin Delta: restoration implications: Ecological Applications, v.12, no. 5, p. 1528-1547. (on-line abstract)

Monsen, N.E., Cloern, J.E., Lucas, L.V., and Monismith, S.G., 2002, A comment on the use of flushing time, residence time, and age as transport time scales, Limnology and Oceanography, v. 47, p. 1545-1553. (on-line abstract or on-line pdf file)

Sobczak, W.V., Cloern, J.E., Jassby, A.D., and Muller-Solger, A.B., 2002, Bioavailability of organic matter in a highly disturbed estuary: The role of detrital and algal sources: Proceedings of the National Academy of Sciences, v. 99, p. 8,101-8,105. (on-line abstract)

Arnsberg, A.J., Cole, B.E., and Cleorn, J.E., 2001, Studies of the San Francisco Bay, California, Estuarine Ecosystem, Regional Monitoring Program Results, 1998: U.S. Geological Survey Open-File Report 01-68, 232 p.

Cloern, J.E., 2001, Our evolving conceptual model of the coastal eutrophication problem: Marine Ecology Progress Series, v. 210, p. 223-253. (on-line abstract)

Cloern, J.E., Cole, B.E., Edmunds, J.L., Schraga, T.S., and Arnsberg, A., 2000, Patterns of water-quality variability in San Francisco Bay during the first six years of the RMP, 1993-1998: 1998 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances, San Francisco Esturary Institute. (on-line document)

Grenz, C., Cloern, J.E., Hager, W.W., and Cole, B.E., 2000, Dynamics of nutrient cycling and related benthic nutrient and oxygen fluxes during a spring phytoplankton bloom in South San Franciso Bay (USA): Marine Ecology Progress Series 197, p. 67-80. (on-line abstract or on-line pdf file)

Howarth, R., Anderson, D., Cloern, J., Elfring, C., Hopkinson, C., Lapointe, B., Malone, T., Marcus, N., McGlathery, K., Sharpley, A., and Walker, D., 2000, Nutrient pollution of coastal rivers, bays, and seas: Issues in Ecology, no. 7, p. 1-15. (on-line pdf file)

Jassby, A.D., and Cloern, J.E., 2000, Organic matter sources and rehabilitation of the Sacramento-San Joaquin Delta (California, USA ): Aquatic Conservation -- Marine and Freshwater Ecosystems, vol. 10, p. 323-352. (on-line abstract or on-line pdf file)

Jassby, A.D., and Cloern, J.E., 2000, Primary food resources in the Sacramento-San Joaquin Delta: Newsletter, Interagency Ecological Program for the Sacremento-San Joaquin Estuary, Summer 2000, p. 21-25. (on-line abstract)

Ning, X., Cloern, J.E.., and Cole, B.E., 2000, Spatial and temporal variability of picocyanobacteria Synechoccus sp. in San Francisco Bay: Limnology and Oceanography, v.45, no. 3, p. 695-702. (on-line abstract)

Cloern, J.E., 1999, The relative importance of light and nutrient limitation of phoytopplankon growth: A simple index of coastal ecosystem sensitivity to nutrient enrichment: Aquatic Ecology, v. 33, no. 1, p. 3-15. (on-line abstract)

Cloern, J.E., Cole, B.E., Edmunds, J.L., and Baylosis, J.I., 1999, Water-quality variability in San Francisco Bay: General patterns of change during 1997, in 1997 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances: San Francisco Estuary Institute, p. 67-81.

Edmunds, J.L., Kuivila, K.M., Cole, B.E., and Cloern, J.E., 1999, Do herbicides impair phytoplankton primary production in the Sacramento-San Joaquin River Delta? in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substance Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999: U.S. Geological Survey Water Resources Investigation Report 99-4018B, p. 81-87. (on-line abstract or to obtain pdf file)

Lucas, L., Koseff, J.R., Cloern, J.E., Monismith, S.G., and Thompson, J.K., 1999, Processes governing phytoplankton blooms in estuaries, Part I, The local production-loss balance: Marine Ecology Progress Series, v. 187, p. 1-15. (on-line abstract or on-line pdf file)

Lucas, L.V., Koseff, J.R., Cloern, J.E., Monismith, S.G., and Thompson, J.K., 1999, Processes governing phytoplankton blooms in estuaries, Part II, The role of transport in global dynamics: Marine Ecology Progress Series, v. 187, p. 17-30. (on-line abstract or on-line pdf file)

FOR ADDITIONAL INFORMATION ON THIS PROJECT, CONTACT:
James E. Cloern
U.S. Geological Survey, 345 Middlefield Rd, MS496, Menlo Park, CA 94025
Email: jecloern@usgs.gov
Telephone: 650-329-4594

Lisa V. Lucas
U.S. Geological Survey, 345 Middlefield Rd, MS496, Menlo Park, CA 94025
Email: llucas@usgs.gov
Telephone: 650-329-4327

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