Janet Thompson

Biography

I am an aquatic ecologist in the National Research Program in Menlo Park, California.    My research has focused on the function of the benthic community  as both consumers and prey in the food web  and as contaminant vectors in estuarine and tidal freshwater ecosystems. I specifically study (1) how and when the structure and function of the benthic community reflects changes in the overlying quality water, (2) how and when processes within the benthic community control the productivity, food web complexity, and ulitmately the health of aquatic ecosystems, and (3) how invasive non-indigenous species affect community and ecosystem dynamics.   I have mostly used the San Francisco Estuary and tidal freshwater Delta as my field laboratory in my 30+ years of study, but have also worked on the benthos on  the coastal shelf in Northern California and in Washington and Oregon estuaries.   I am the project chief for the project "Mechanisms of biological and ecological response in disturbed aquatic ecosystems."

 

EDUCATION 

Stanford University, Ph.D., Environmental Fluid Mechanics, Department of Civil Engineering, 1999 

California State University,  M.A., Marine Biology, 1979

Lewis and Clark College, B.S., Biology, 1972

 

Employment

  • U.S. Geological Survey, Water Resources Division, Biologist (1985-present)
  • U.S. Geological Survey, Geologic Division, Biologist  (1972-1985)

 Awards and Honors

  • USGS Western Region Diversity Award – Supervisor.  2007.  
  • U.S. Department of the Interior, Superior Service Award, 2003
  • U.S.G.S. Graduate School Program Recipient, 1992
  • Special Achievement Award for Outstanding Performance, USGS, 1989

Academic Theses/Dissertation Committees

  • Post-Doctoral Fellows:  Dr. Laurent Chauvaud, Dr. Rene Takesue 
  • PhD:  Simons (Stanford University, Civil and Environmental Engineering, 2004), Jones (Stanford University, Civil and Environmental Engineering,  2007) 
  • MS:  Winternitz (University of San Francisco, Marine Science 1986), Kaplan (CSU Monterey, Marine Science 2000), Shouse  (CSU San Francisco, Marine Biology 2002), Peterson  (CSU San Francisco, Marine Biology  2002), Kleckner (CSU San Francisco, Marine Biology  2010), Green (CSU San Francisco, Marine Biology  2010), Simmons (Massachusetts Institute of Technology, Department of Urban Studies and Planning 2013)
  • Intern Advisor:  Environmental Engineering Stanford University, 1991-1999; Environmental Sciences Senior Research Studies, UC Berkeley, 1992-1996;  Environmental Studies, University of San Francisco 1995-2000
  • Honors College Advisor:  Stanford Univeristy 1995-1997

Editorial Boards:

  • Associate Editor, San Francisco Estuary and Watershed Science 2008-present

Review, advisory duties(examples):

  • Coordinator, San Francisco Estuary Priority Ecosystem Science Project (2003-2010), California
  • Advisor, Puget Sound Working Group, Seatle, WA  (2004-2006)
  • Technical Review Panal, Delta Vision (State of California), Sacramento, CA (2007-2008)
  • National Center for Ecological Analysis and Synthesis, member of panal examining effects of off-shore processes on SF Estuary, Santa Barbara, CA (2009-2010)
  • Review, Chesapeake Research Consortium, Maryland (2002)
  • Workshop member, NATO, Roles of Suspension Feeders in Natural and Aquaculture Ecosystems, Lithuania (2004-2005)
  • Panal member, International Seminar on Restoration of Damaged Lagoon Environments, Matsue, Japan (2004)
  • CALFED Advisory Panal, Exotic Species Effect on Restoration Plans of SF Bay and Delta (1998-2004
  • Subtidal/Intertidal/Marsh Goals for San Francisco Estuary with Climate Change (Adviser to NOAA 2006-present)

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Publications:

Clifton, H. Edward, and Thompson, Janet K., 1978.  Macaronichnus segregatis - a feeding structure of shallow marine polychaetes: Journal of Sedimentary Petrology, v. 48, no. 4, p. 1293 1302.   

Thompson, Janet K., 1979.  Population dynamics and sediment relations of Gemma gemma in San Francisco Bay, MA Thesis, California State Univ., San Francisco: 139 p. Published in Thompson 1982.

Thompson, Janet K., Nichols, Frederic H., and Wienke, Sally M., 1981. Distribution of benthic chlorophyll in Francisco Bay, California, February 1980-February 1981:  U.S. Geological Survey Open-File Report 81 1134, 36 p.

Thompson, Janet K. and Nichols, F.H., 1981.  Benthic macrofaunal biomass of San Francisco Bay, January/February and August 1973:  U.S. Geological Survey Open-File Report 81 1331, 39p.

Thompson, Janet K. 1981. Sediment grain size distribution in San Francisco Bay, California,   33p.

Nichols, F.H., and Thompson,  Janet K., 1982b.  Seasonal growth in the bivalve Macoma balthica near the southern limit of its range:  Estuaries, v. 5, no. 2,p. 110 120.  

Thompson, Janet K. 1982.  Population structure of Gemma gemma (Bivalvia: Veneridae) in South San Francisco bay, with a comparison to some northeastern United States estuarine populations: VELIGER v. 24, no. 3, p. 281 290.

Hill, Gary H., Chin, John L., and Thompson (McHendrie), Janet K., 1982. Distribution of macrobenthic infauna in tidal flat deposits,  Willapa Bay, Washington - Summer 1978:  U.S. Geological survey Open-File Report 82 461, 47 p. 

Thompson, Janet K., and Nichols, Frederic H., 1984.  Benthic macrofauna of a South San Francisco Bay, California mudflat, 1974 to 1983:  U.S. Geological Survey Open-File Report 84 759, 200 p.

Nichols, Frederic H., and Janet K., 1985a.  Persistence of an introduced mudflat community in South San Francisco Bay, California:  Marine Ecology Progress Series v. 24, p. 83 97.

Nichols, F.H., and Thompson Janet K., 1985b.  Time Scales of change in the San Francisco Bay benthos: Hydrobiologia, v. 129, p. 121 138. 

Thompson, Janet K. and Nichols, F.H., 1988.  Food availability controls the seasonal cycle of growth in the bivalve Macoma balthica. Journal Exp. Marine Biol. Ecol., v. 116, p. 43 61.

Nichols, F.H., Cacchione, D.A, Drake, D.E., Thompson, J. K. 1989.  Emergence of burrowing urchins from California continental shelf sediments - a response to alongshore current reversals:  Estuarine Coastal Shelf Science v. 29, p. 171 182.  

Carlton, J. T., Thompson, J. K., Schemel, L.E., Nichols, F.H. 1990. The remarkable invasion of San Francisco Bay, California (USA) by the Asian Clam Potamocorbula amurensis (Mollusca: Bivalvia):  Marine Ecology Progress Series v. 66, no. 1 2, p. 81 94. 

Nichols, Frederic H., Thompson, J. K., Schemel, L.E. 1990.  The remarkable invasion of San Francisco Bay (California, USA) by the Asian clamPotamocorbula amurensis.  II Displacement of a former community: Marine Ecology Progress Series v. 66, no. 1 2, p. 95 101.  

Monismith, Stephen G., Koseff, J. R., Thompson Janet K., O'Riordan, Catherine A., and Nepf, Heidi M. 1990. A study of Model Bivalve  Siphon Currents: Limnology & Oceanography v. 35, no. 3, p. 680 696 

Cole, B.E., Thompson, J. K., and Cloern, J.E..  1992. Measurement of filtration rates by infaunal bivalves in a recirculating flume: Marine Biology v. 113, p. 219-225. 

Thompson, J.K, Parchaso, F., Brown, C.L., Luoma, S.N.  In situ Ecosystem Effects of Trace Contaminants in the San Francisco bay Estuary:  The Necessary Link to Establishing Water Quality Standards:  U.S. Geological Survey Open-File Report 96-437, 98 p.

Lucas, L.V., Cloern, J.E., Koseff, J.R., Monismith, S.G., Thompson, J.K.  1998 Does the Sverdrup Critical Depth Model Explain Bloom Dynamics in the Coastal Zone?  Journal of Marine Research, v. 56, pp.375-415  

Parchaso, F., Brown, C. L., Thompson, J. K., Luoma, S. N., 1997, In situ effects of trace contaminants on the ecosystem in the San Francisco Bay estuary, 1995:  The necessary link to establishing water quality standards, II:  U. S. Geological Survey Open File Report 97-420  

Hornberger, M., Luoma, S., Cain, D., Parchaso, F., Brown, C., Bouse, R., Wellise, C., and Thompson, J., 1999:   Bioaccumulation of metals by the bivalve Macoma balthica at a site in South San Francisco Bay between 1977-1997: Long-term trends and associated biological effects with changing pollutant loadings: U.S. Geological Survey Open-File Report 99-55, 42 p  

Thompson, Janet K., 1999.  The effect of infaunal bivalve grazing on phytoplankton bloom development in South San Francisco Bay, PhD Thesis, Stanford University, Dept. of Civil and Environmental Engineering, Stanford, CA: 419p.

Lucas, L.V., Koseff, J.R., Cloern, J.E., Monismith, S.G., Thompson, J.K. 1999 Processes governing phytoplankton blooms in estuaries. I. The local production-loss balance:  Marine Ecology Progress Series, v. 187, pp. 1-15 

Lucas, L.V., Koseff, J.R., Monismith, S.G., Cloern, J.E., Thompson, J.K.  1999 Processes governing phytoplankton blooms in estuaries. II. The role of horizontal transport:  Marine Ecology Progress Series, v. 187, pp. 17-30

Hornberger, M., Luoma, S., Cain, D., Parchaso, F., Brown, C., Bouse, R., Wellise, C., and Thompson, J., 2000:   Linkage of bioaccumulation and biological effects to changes in pollutant loads in South San Francisco Bay:  Environmental Science and Technology, v. 34:2401-2409..

Thompson, Janet K.  2002.  The evolving benthic community.  in Science and strategies for restoration.  San Francisco Estuary Project Eds, p. 66-67.

Thompson, J.K., Stewart, A.R., and Parchaso, F. 2001.  Behind the energetics of the Asiatic clam, Potamocorbula amurensis in San Francisco Bay: Interagency Ecological Program for the San Francisco Estuary Newsletter 14(4):30

Lucas, L.V., J. E. Cloern, J.K. Thompson, and N.E. Monsen. 2002. Functional variability of shallow tidal habitats in the Sacramento-San Joaquin Delta: restoration implications. Ecol. Appl. 12(5): 1528-1547. 

Crimaldi, J.P. J.K. Thompson, J.H. Rosman, R. J. Lowe, J. R. Koseff.  2002. Hydrodynamics of larval settlement:  The influence of turbulent stress events at potential recruitment sites.  Limnol. and Ocean. 47(4):1137-1151 

Parchaso, F. and J.K. Thompson, 2002, The Influence of Hydrologic Processes on Reproduction of the Introduced Bivalve Potamocorbula amurensis in Northern San Francisco Bay, California, Pacific Science, 56(3):329-345  

Brown, C.L., F. Parchaso, J.K. Thompson, S.N. Luoma. 2003.  Assessing toxicant effects in a complex estuary: A case study of effects of silver on reproduction in the bivalve, Potamocorbula amurensis, in San Francisco Bay.  Human and Ecological Risk Assessment. 9(1):95-119.  

Chauvaud, L., J. K. Thompson, J. E. Cloern, and G. Thouzeau.  2003.  Clams as CO2 generators:  The Potamocorbula amurensis example in San Francisco Bay.  Limnol. and Ocean. 48(6):2086-2092.  

Thompson, J.K. F. Parchaso, and M.K. Shouse.  2002.  Near-field receiving water monitoring of a benthic community near the Palo Alto water quality control plant in south San Francisco Bay:  February 1974 through December 2002.    U.S. GEOLOGICAL SURVEY Open-File Report 02-394  http://pubs.water.usgs.gov/ofr02394/

Shouse, M.K, F.  Parchaso, and J. K. Thompson.  2003.  Near-field receiving water monitoring of a benthic community near the Palo Alto water quality control plant in south San Francisco Bay:  February 1974 through December 2000.    U.S. GEOLOGICAL SURVEY Open-File Report 03-224  http://water.usgs.gov/pubs/of/2003/ofr03-224/ofr03_224.html  

Brown, C. L., Luoma, S. N., Parchaso, F., and Thompson, J. K. 2004. Lessons learned about metals in the estuary: The importance of long-term clam accumulation data. San Francisco Estuary Institute (SFEI). 2004. The Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary. SFEI Contribution 78. San Francisco Estuary Institute, Oakland, CA 24, 38-45.  

Jones, N.L., S.G. Monismith, and J.K. Thompson 2005. “Preliminary results from a shallow water benthic grazing study,”  I.E.P. Newsletter 18(1), pp. 7-13

Moon, E., Shouse, M. K., Parchaso, F. Thompson, J.K., Luoma, S.N., Cain, D. J. and Hornberger, M.I., 2005, Near-Field Receiving Water Monitoring of Trace Metals and a Benthic Community Near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California: 2004. U.S. Geological Survey Open File Report 2005-1279. Menlo Park, California. 118pp.  

Thompson, JK, 2005.  One estuary, one invasion, two responses:  phytoplankton and benthic community dynamics determine the effect of an estuarine invasive suspension feeder. In: Olenin S, Dame R, eds. The Comparative Roles of Suspension Feeders in Ecosystems. Amsterdam, Netherlands: Springer, 291-316.

Asmus, H, Asmus R., Bushek, D., Burlakova, L., Davme, R., Dauunys, D., Duarte, P., Herman, P.M., Karatayev, Kholodkevich, S., Kotta, J., Malej, A., Newell, R., Olenin, S., Ostroumov, S., Prins, T., Safronova, D., Shadrin, N.,  N., Shpigel, M., Smaal, A., Thompson, J., Wolff, W., Wolowica, M., Zemlys, P. 2005 The Roles of Suspension-Feeders in Ecosystems: Synthesis and Conclusions.  In: Olenin S, Dame R, eds. The Comparative Roles of Suspension Feeders in Ecosystems. Amsterdam, Netherlands: Springer, 345-353 

Cain, D. J., Parchaso, F. Thompson, J.K., Luoma, S.N., Lorenzi, A.H., Moon, E., Shouse, M. K., Hornberger, M.I., and J.L. Dyke. 2006. Near-Field Receiving Water Monitoring of Trace Metals and a Benthic Community Near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California: 2005. U.S. Geological Survey Open File Report 2006-1152. Menlo Park, California. 128pp.  

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 restoration of disturbed ecosystems, Ecosystems 9: 422-440. 

Lorenzi, A.H., Cain, D. J., Parchaso, F. Thompson, J.K., Luoma, S.N., Hornberger, M.I., Dyke, J.L. Dyke, Cervantes, R., and Shouse, M. K. 2007. Near-Field Receiving Water Monitoring of Trace Metals and a Benthic Community Near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California: 2006. U.S. Geological Survey Open File Report 2007-1199. Menlo Park, California. 128pp 

Brown L.R., Thompson, J.K, Higgins, K., and Lucas, L.V.  2007.  Population density, biomass, and age-class structure of an invasive clam  Corbicula fluminea  in rivers of the lower San Joaquin River watershed, California: Western North American Naturalist.67(4):572-586.  

Thompson JK, Hieb K, McGourty K, Cosentio-Manning N, Wainwright-De La Cruz S, Elliot M, Allen S, 2007.  Habitat type and associated biological assemblages: soft bottom substrate.  In: Schaeffer K, McGourty K, Cosentio-Manning N, eds. Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. Santa Rosa, CA, US.  National Oceanic and Atmospheric Administration, 18-23 (Table 3a), 37-46

Cloern, J.E., Jassby, A.D., Thompson, J.K, Hieb, K.  2007. A cold phase of the east Pacific triggers new phytoplankton blooms in San Francisco Bay. Proceedings National Acad. Science 104(47):18561-18565. 

Jones, N.L., Thompson, J.K., and Monismith, S.G., 2008, A note on the effect of wind waves on vertical mixing in Franks Tract Sacramento-San Joaquin Delta, California: San Francisco Estuary and Watershed Science, v. 6, no. 2, Article 4. 

Takesue, R.K., C.R. Bacon, and J.K. Thompson.  2008.  Influences of organic matter and calcification rate on trace elements in aragonitic estuarine bivalve shells.  Geochemica et Cosmochimica Acta 72(22): 5431-5445.    

Thompson, J.K., J.R. Koseff, S.G. Monismith, and L. V. Lucas. 2008.  Shallow water processes govern system-wide phytoplankton bloom dynamics: A Field Study. Journal of Marine Systems 74:153-166.

Kimmerer, W., Brown, L, Culberson, S., Moyle, P., Nobriga, M., Thompson, J.  2008. Aquatic Ecosystems.   In. Healey, M.C., M.D. Dettinger, and R.B. Norgaard, eds. The State of Bay-Delta Science, 2008, p.81-101.  CA: CALFED Science Program. 174 pp.  

Jones, N.L., Thompson, J.K., Arrigo, K.R., Monismith, S.G. 2009. Hydrodynamic control of phytoplankton loss to the benthos in an estuarine environment. Limnology and Oceanography, v. 54, no. 3, p. 952-969. 

Cain, Daniel J. Thompson, Janet K., Dyke, Jessica, L., Parchaso, Francis, Luoma, Samuel N., and Hornberger, Michelle, I. 2009. Near-Field Receiving Water Monitoring of Trace Metals and a Benthic Community Near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California: 2008. Open-file Report 2009-1193. pp. 120. 

Lucas, L.V., J.K. Thompson, and L.R. Brown.  2009.  Why are diverse relationships observed between phytoplankton biomass and transport time?  Limnology and Oceanography 54(1):381-390. 

Lucas, L.V., J.R. Koseff, S.G. Monismith, and J.K. Thompson.  2009.  Shallow water processes govern system-wide phytoplankton bloom dynamics: A Modeling Study. Journal of Marine Systems 75:70-86. 

Dyke, J.L., Parchaso, F., Thompson, J.K., Cain, D.J., Luoma, S.N., and Hornberger, M.I., 2010.  Near-field receiving water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California: 2009, U.S. Geological Survey Open-File Report 2010-1188, 142 p.(Available online at: http://pubs.usgs.gov/of/2010/1188).  

Thompson, J.K., 2011. Corbula amurensis.  Invasive Species Compendium (produced by CABI) Hard copy and web book will be available.   In Beta Release at: http://www.cabi.org/isc/?compid=5&dsid=107736&loadmodule=datasheet&page=...

Dyke, J.L., Parchaso, F., Thompson, J.K., Cain, D.J., Luoma, S.N., and Hornberger, M.I. 2011. Near-field receiving water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California: 2010, U.S. Geological Survey Open-File Report 2011-1163, 114 p. http://pubs.usgs/of/2011/1163.  

Greene, V.E., Sullivan, L.J., Thompson, J.K., Kimmerer, W.J. 2011 Grazing impact of the invasive clam Corbula amurensis on the microplankton assemblage of the northern San Francisco Estuary.  Mar. Ecol. Prog. Series. 431:183-193.  

Janssen, E.M.L., Thompson, J.K., Luoma, S.N., Luthy, R.G.  2011.  PCB-induced changes of a benthic community and expected ecosystem recovery following in situ sorbent amendment.  Environmental Toxicology and Chemistry 30(8):1819-1826.  

Franco, J.N., Ceia, F.R., Patrício, J., Modesto, V., Thompson, J., Marques, J.C., Neto J.M. In press.  Population dynamics of Corbicula fluminea(Müller, 1774) in mesohaline and oligohaline habitats: Invasion success in a Southern Europe estuary.  Estuarine Coastal Shelf Science.  doi:10.1016/j.ecss.2011.07.014.   

Dyke, J.L., Thompson, J.K., Cain, D.J., Kleckner, A.E., Parchaso, F., Luoma, S.N., and Hornberger, M.I., 2012, Near-field receiving water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California; 2011: U.S. Geological Survey Open-File Report 2012-1165, 108 p. (Available at http://pubs.usgs.gov/of/2012/1165/.)

Lucas, LV and JK Thompson.  2012.  Changing restoration rules: Exotic bivalves interact with residence time and depth to control phytoplankton productivity.  Ecosphere 3(12): article 117.  http://www.esajournals.org/doi/pdf/10.1890/ES12-00251.1