National Research Program

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 .


Cloern, J.E., Jassby, A.D., Carstensen, J., Bennett, W.A., Kimmerer, W., Mac Nally, R., Schoellhamer, D.H., and Winder, M., 2012, Perils of correlating CUSUM-transformed variables to infer ecological relationships (Breton et al. 2006, Glibert 2010): Limnology and Oceangraophy, v. 57, no. 2, p. 665-668. (on-line article in pdf format, 250 KB)

Cloern J.E., Knowles N., Brown L.R., Cayan D., Dettinger M.D., Morgan, T.L., Schoellhamer, D.H., Stacey, M.T., van der Wegen, M., Wagner, R.W., and Jassby, A.D., 2011, Projected evolution of California’s San Francisco Bay-Delta-River System in a Century of Climate Change. PLoS ONE 6(9): e24465. doi:10.1371/journal.pone.0024465. (on-line abstract or on-line journal article in pdf format, 937 KB, PLoS ONE is an open-access journal)

Guarini, J.-M., Chauvaud, L., Cloern, J.E., Clavier, J., Coston-Guarini, J., and Patry, Y., 2011, Seasonal variations in ectotherm growth rates: Quantifying growth as an intermittent non steady state compensatory process: Journal of Sea Research, v. 65, no. 3, p. 355-361. doi:10.1016/j.seares.2011.02.001 (on-line abstract of journal article)

Paerl, H., Yin, K., and Cloern, J., 2011, Meeting Report, Global Patterns of Phytoplankton Dynamics in Coastal Ecosystems: Comparative Analysis of Time Series Observations, SCOR Working Group 137 Meeting, Hangzhou, China, 17-21 October 2010: Eos, v. 92, no. 10, p. 85

Cloern, J.E. and Dugdale, R., 2010, San Francisco Bay, in Glibert, P.M. et al., eds, Nutrients in Estuaries: A Summary Report of the National Estuarine Experts Workgroup 2005-2007, p. 117-126. (on-line report in pdf format, 2220 KB)

Cloern, J.E., Hieb, K.A., Jacobson, T., Sansó, B., Di Lorenzo, E., Stacey, M.T., Largier, J.L., Meiring, W.,. Peterson, W.T., Powell, T.M., Winder, M., and Jassby , A.D., 2010, Biological communities in San Francisco Bay track large-scale climate forcing over the North Pacific: Geophysical Research Letters, v. 37, L21602, doi:10.1029/2010GL044774. (on-line abstract of journal article)

Cloern, J.E. and Jassby, A.D., 2010, Patterns and scales of phytoplankton variability in estuarine-coastal ecosystems: Estuaries and Coasts, v. 33, no. 2, p. 230-241. DOI: 10.1007/s12237-009-9195-3 (on-line abstract or on-line article in pdf format, 342 KB, published by SpringerLink with open-access)

Jassby, A.D. and J.E. Cloern, 2010, R package wq0.2-2: Exploring water quality monitoring data. (on-line package )

Lucas, L.V., 2010, Implications of estuarine transport for water quality, in: Contemporary Issues in Valle-Levinson, A., ed., Estuarine Physics: Cambridge University Press, p. 273-307. ISBN-13: 9780521899673,

Winder, M. and Cloern, J.E., 2010, The annual cycles of phytoplankton biomass: Philosophical Transactions of the Royal Society B, v. 365, p. 3215-3226 doi: 10.1098/rstb.2010.0125 (on-line abstract of journal article)

Lucas, L.V., Koseff, J.R., Monismith, S.G., and Thompson, J.K., 2009, Shallow water processes govern system-wide phytoplankton bloom dynamics - A modeling study: Journal of Marine Systems, v. 75, no. 1-2, p. 70-86. doi:10.1016/j.jmarsys.2008.07.011. (on-line abstract of journal article)

Lucas, L.V., Thompson, J.K., and Brown, L.R., 2009, Why are diverse relationships observed between phytoplankton biomass and transport time?: Limnology and Oceanography, v. 54, no. 1, 381-390. (on-line abstract or on-line article in pdf format, 694 KB, published by the Americal Society of Limnology and Oceanography with open acess)

Cloern, J.E. and Jassby, A.D., 2008, Complex seasonal patterns of primary producers at the land–sea interface: Ecology Letters, v. 11, doi: 10.1111/j.1461-0248.2008.01244.x (on-line abstract of journal article)

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)

Thompson, J.K., Koseff, J.R., Monismith, S.G., and Lucas, L.V., 2008, Shallow water processes govern system-wide phytoplankton bloom dynamics: A field study. Journal of Marine Systems, v. 74, no. 1-2, p.153-166, doi:10.1016/j.jmarsys.2007.12.006. ((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)

James E. Cloern
U.S. Geological Survey, 345 Middlefield Rd, MS496, Menlo Park, CA 94025
Telephone: 650-329-4594

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

 For information on additional projects in the National Research Program, see Indexes to NRP projects and bibliographies

*For articles in Adobe® (.PDF) format, please note that you can download a free copy of Adobe® Acrobat® Reader® here. Also see Adobe® accessibility information, Information for users with disabilities, if applicable.

Accessibility FOIA Privacy Policies and Notices

Take Pride in America logo logo U.S. Department of the Interior | U.S. Geological Survey
Page Contact Information: Linda Friedman
Page Last Modified: Tuesday, 04-Mar-2014 11:28:26 EST