Short-Term and Interannual Variability in Primary Production in the Low-Salinity Zone of the San Francisco Estuary

Estuaries and Coasts

Volumn 35, Issue 4, 2012, Pages 913-929

  Kimmerer, Wim J ^a   Parker, Alexander E ^a   Lidström, Ulrika E ^a   Carpenter, Edward J ^a  

^a Romberg Tiburon Center   (United States)

Author keywords

Biomass; Chlorophyll; Phytoplankton; Primary production; San Francisco Estuary; Temporal variability

Indexed keywords

ABUNDANCE; ANNUAL VARIATION; BIOLOGICAL UPTAKE; BIOMASS; BRACKISH WATER; CARBON ISOTOPE; CHLOROPHYLL; ENVIRONMENTAL MONITORING; FOOD WEB; FRESHWATER ENVIRONMENT; PELAGIC ENVIRONMENT; PHTHALATE; PHYTOPLANKTON; PRIMARY PRODUCTION; SALINITY; SPATIOTEMPORAL ANALYSIS; TROPHIC LEVEL;

CALIFORNIA; SAN FRANCISCO ESTUARY; UNITED STATES;

EID: 84861865164     PISSN: 15592723     EISSN: 15592731     Source Type: Journal    
DOI: 10.1007/s12237-012-9482-2     Document Type: Article

References (94)

1. Alpine, A. E., and J. E. Cloern. 1992. Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary. Limnology and Oceanography 37: 946-955.
2. Arar, E. J., and G. B. Collins. 1992. In vitro determination of chlorophyll a and phaeophytin a in marine and freshwater phytoplankton by fluorescence-USEPA Method 445. 0. USEPA methods for determination of chemical substances in marine and estuarine environmental samples. Cincinnati, Ohio.
3. Atlas, D., and T. T. Bannister. 1980. Dependence of mean spectral extinction coefficient of phytoplankton on depth, water color, and species. Limnology and Oceanography 25: 157-159.
4. 14C uptake by phytoplankton for another 50 years? Limnology and Oceanography Bulletin 11: 45-46.
5. Baxter, R., R. Breuer, L. Brown, M. Chotkowski, F. Feyrer, M. Gingras, B. Herbold, A. Mueller-Solger, M. Nobriga, T. Sommer, and K. Souza. 2008. Pelagic organism decline progress report: 2007 synthesis of results. Sacramento. http://www. fws. gov/sacramento/es/documents/POD_report_2007. pdf. Accessed 21 June 2011.
6. Bennett, W. A. 2005. Critical assessment of the delta smelt population in the San Francisco Estuary, California. San Francisco Estuary and Watershed Science 3: Issue 2 Article 1.
7. Berggreen, U., B. Hansen, and T. Kiørboe. 1988. Food size spectra, ingestion and growth of the copepod Acartia tonsa during development: implications for determination of copepod production. Marine Biology 99: 341-352.
8. Bran + Leubbe. 1999. AutoAnalyzer method no. G-177-96 silicate in water and seawater. Buffalo Grove: Bran Luebbe.
9. Brown, L. R., W. Kimmerer, and R. Brown. 2008. Managing water to protect fish: a review of California's Environmental Water Account. Environmental Management 43: 357-368.
10. Cloern, J. E. 1984. Temporal dynamics and ecological significance of salinity stratification in an estuary (South San Francisco Bay, USA). Oceanologica Acta 7: 137-141.
11. Cloern, J. E. 1991. Annual variations in river flow and primary production in the South San Francisco Bay estuary (USA). In Estuaries and coasts: spatial and temporal intercomparisons, ed. M. Elliott and J.-P. Ducrotoy, 91-96. Fredensborg: Olsen and Olsen.
12. Cloern, J. E., and R. T. Cheng. 1981. Simulation model of Skeletonema costatum population dynamics in northern San Francisco Bay, California. Estuarine, Coastal and Shelf Science 12: 83-100.
13. Cloern, J. E., and R. Dufford. 2005. Phytoplankton community ecology: principles applied in San Francisco Bay. Marine Ecology Progress Series 285: 11-28.
14. Cloern, J. E., and A. D. Jassby. 2008. Complex seasonal patterns of primary producers at the land-sea interface. Ecology Letters 11: 1294-1303.
15. Cloern, J., and A. Jassby. 2010. Patterns and scales of phytoplankton variability in estuarine-coastal ecosystems. Estuaries and Coasts 33: 230-241.
16. Cloern, J., A. Alpine, B. Cole, R. Wong, J. Arthur, and M. Ball. 1983. River discharge controls phytoplankton dynamics in the northern San Francisco Bay estuary. Estuarine, Coastal and Shelf Science 16: 415-429.
17. Cloern, J. E., B. E. Cole, R. L. J. Wong, and A. E. Alpine. 1985. Temporal dynamics of estuarine phytoplankton: a case study of San Francisco Bay. Hydrobiologia 129: 153-176.
18. Cloern, J. E., C. Grenz, and L. Vidergar-Lucas. 1995. An empirical model of the phytoplankton chlorophyll/carbon ratio-the conversion factor between productivity and growth rate. Limnology and Oceanography 40: 1313-1321.
19. Cloern, J. E., A. D. Jassby, J. K. Thompson, and K. A. Hieb. 2007. A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay. Proceedings of the National Academy of Sciences, USA 104: 18561-18565.
20. Cole, B. E., and J. E. Cloern. 1984. Significance of biomass and light availability to phytoplankton productivity in San Francisco Bay. Marine Ecology Progress Series 17: 15-24.
21. Cole, B. E., J. E. Cloern, and A. E. Alpine. 1986. Biomass and productivity of three phytoplankton size classes in San Francisco Bay. Estuaries 9: 117-126.
22. Dame, R., T. Chrzanowski, K. Bildstein, B. Kjerfve, H. McKellar, D. Nelson, J. Spurrier, S. Stancyk, H. Stevenson, J. Vernberg, and R. Zingmark. 1986. The outwelling hypothesis and North Inlet, South Carolina. Marine Ecology Progress Series 33: 217-229.
23. Drinkwater, K. F., and K. T. Frank. 1994. Effects of river regulation and diversion on marine fish and invertebrates. Aquatic Conservation: Marine and Freshwater Ecosystems 4: 135-151.
24. Dugdale, R. C., F. P. Wilkerson, V. E. Hogue, and A. Marchi. 2007. The role of ammonium and nitrate in spring bloom development in San Francisco Bay. Estuarine, Coastal and Shelf Science 73: 17-29.
25. Feyrer, F., B. Herbold, S. A. Matern, and P. B. Moyle. 2003. Dietary shifts in a stressed fish assemblage: Consequences of a bivalve invasion in the San Francisco Estuary. Environmental Biology of Fishes 67: 277-288.
26. Fischer, H. B., J. E. List, R. Koh, J. Imberger, and N. H. Brooks. 1979. Mixing in inland and coastal waters. San Diego: Academic.
27. Friederich, G. E., P. M. Walz, M. G. Burczynski, and F. P. Chavez. 2002. Inorganic carbon in the central California upwelling system during the 1997-1999 El Nino-La Nina event. Progress in Oceanography 54: 185-203.
28. Froneman, P. W. 2004. Food web dynamics in a temperate temporarily open/closed estuary (South Africa). Estuarine, Coastal and Shelf Science 59: 87-95.
29. Glibert, P. M. 2010. Long-term changes in nutrient loading and stoichiometry and their relationships with changes in the food web and dominant pelagic fish species in the San Francisco Estuary, California. Reviews in Fisheries Science 18: 211-232.
30. Goosen, N. K., J. Kromkamp, J. Peene, P. van Rijswik, and P. van Breugel. 1999. Bacterial and phytoplankton production in the maximum turbidity zone of three European estuaries: The Elbe, Westerschelde and Gironde. Journal of Marine Systems 22: 151-171.
31. Gould, A. L., and W. J. Kimmerer. 2010. Development, growth, and reproduction of the cyclopoid copepod Limnoithona tetraspina in the upper San Francisco Estuary. Marine Ecology Progress Series 412: 163-177.
32. Greene, V. E., L. J. Sullivan, J. K. Thompson, and W. J. Kimmerer. 2011. Grazing impact of the invasive clam Corbula amurensis on the microplankton assemblage of the northern San Francisco Estuary. Marine Ecology Progress Series 431: 183-193.
33. Guillard, R. R. L. 1978. Counting slides. In Phytoplankton manual, ed. A. Sournia, 182-189. Paris: UNESCO.
34. Harding, L. W., M. E. Mallonee, and E. S. Perry. 2002. Toward a predictive understanding of primary productivity in a temperate, partially stratified estuary. Estuarine, Coastal and Shelf Science 55: 437-463.
35. Hillebrand, H., C.-D. Dürselen, D. Kirschtel, U. Pollingher, and T. Zohary. 1999. Biovolume calculation for pelagic and benthic microalgae. Journal of Phycology 35: 403-424.
36. Holm-Hansen, O., C. J. Lorenzen, R. W. Holmes, and J. D. H. Strickland. 1965. Fluorometric determination of chlorophyll. J. Cons. Perm. Int. Explor. Mer. 30(1): 3-15.
37. Iriarte, A., and D. A. Purdie. 1994. Size distribution of chlorophyll-a biomass and primary production in a temperate estuary (Southampton Water): The contribution of photosynthetic picoplankton. Marine Ecology Progress Series 115: 283-297.
38. Jassby, A. D. 2008. Phytoplankton in the upper San Francisco Estuary: Recent biomass trends, their causes and their trophic significance. San Francisco Estuary and Watershed Science 6: Issue 1 Article 2.
39. Jassby, A. D., and T. Platt. 1976. Mathematical formulation of the relationship between photosynthesis and light for phytoplankton. Limnology and Oceanography 21: 540-547.
40. Jassby, A. D., W. J. Kimmerer, S. G. Monismith, C. Armor, J. E. Cloern, T. M. Powell, J. R. Schubel, and T. J. Vendlinski. 1995. Isohaline position as a habitat indicator for estuarine populations. Ecological Applications 5: 272-289.
41. Jassby, A. D., J. E. Cloern, and B. E. Cole. 2002. Annual primary production: Patterns and mechanisms of change in a nutrient-rich tidal estuary. Limnology and Oceanography 47: 698-712.
42. JGOFS. 1996. JGOFS report no. 19-protocols for the Joint Global Ocean Flux Studies (JGOFS) core measurements. In International JGOFS report series, 128-134 (ISSN 1016-7331).
43. Kimmerer, W. J. 2002. Effects of freshwater flow on abundance of estuarine organisms: physical effects or trophic linkages? Marine Ecology Progress Series 243: 39-55.
44. Kimmerer, W. J. 2004. Open water processes of the San Francisco Estuary: From physical forcing to biological responses. San Francisco Estuary and Watershed Science (Online Serial) 2: Issue 1, Article 1.
45. Kimmerer, W. J. 2005. Long-term changes in apparent uptake of silica in the San Francisco estuary. Limnology and Oceanography 50: 793-798.
46. Kimmerer, W. J. 2006. Response of anchovies dampens effects of the invasive bivalve Corbula amurensis on the San Francisco Estuary foodweb. Marine Ecology Progress Series 324: 207-218.
47. Kimmerer, W. J., and J. J. Orsi. 1996. Causes of long-term declines in zooplankton in the San Francisco Bay estuary since 1987. In San Francisco Bay: The ecosystem, ed. J. T. Hollibaugh, 403-424. San Francisco: AAAS.
48. Kimmerer, W. J., E. Gartside, and J. J. Orsi. 1994. Predation by an introduced clam as the probable cause of substantial declines in zooplankton in San Francisco Bay. Marine Ecology Progress Series 113: 81-93.
49. Kimmerer, W. J., J. R. Burau, and W. A. Bennett. 1998. Tidally-oriented vertical migration and position maintenance of zooplankton in a temperate estuary. Limnology and Oceanography 43: 1697-1709.
50. Kimmerer, W. J., E. S. Gross, and M. MacWilliams. 2009. Variation of physical habitat for estuarine nekton with freshwater flow in the San Francisco Estuary. Estuaries and Coasts 32: 375-389.
51. Kneib, R. T. 1997. The role of tidal marshes in the ecology of estuarine nekton. Oceanography and Marine Biology Annual Review 35: 163-220.
52. 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. Limnology and Oceanography 25: 457-473.
53. Lehman, P. W. 1996. Changes in chlorophyll a concentration and phytoplankton community composition with water-year type in the upper San Francisco Estuary. In San Francisco Bay: The ecosystem, ed. J. T. Hollibaugh, 351-374. San Francisco: AAAS.
54. Lehman, P. W. 2007. The influence of phytoplankton community composition on primary productivity along the riverine to freshwater tidal continuum in the San Joaquin River, California. Estuaries and Coasts 30: 82-93.
55. Lidström, U. E. 2009. Primary production, biomass and species composition of phytoplankton in the low salinity zone of the northern San Francisco Estuary. MS thesis, San Francisco State University.
56. Livingston, R. J., X. F. Niu, F. G. Lewis, and G. C. Woodsum. 1997. Freshwater input to a gulf estuary: Long-term control of trophic organization. Ecological Applications 7: 277-299.
57. Lund, J., E. Hanak, W. Fleenor, R. Howitt, J. Mount, and P. Moyle. 2007. Envisioning futures for the Sacramento-San Joaquin Delta. San Francisco: Public Policy Institute of California.
58. Macedo, M. F., and P. Duarte. 2006. Phytoplankton production modelling in three marine ecosystems-static versus dynamic approach. Ecological Modelling 190: 299-316.
59. MacIsaac, E. A., and J. G. Stockner. 1993. Enumeration of phototrophic picoplankton by autofluorescence microscopy. In Handbook of methods in aquatic microbial ecology, ed. P. F. Kemp, B. F. Sherr, E. B. Sherr, and J. J. Cole. Boca Raton: Lewis.
60. Mallin, M. A., H. W. Paerl, J. Rudek, and P. W. Bates. 1993. Regulation of estuarine primary production by watershed rainfall and river flow. Marine Ecology Progress Series 93: 199-203.
61. Malone, T. C. 1977. Light-saturated photosynthesis by phytoplankton size fractions in New York Bight, USA. Marine Biology 42: 281-292.
62. Mccullagh, P., and J. Nelder. 1989. Generalized linear models. London: Chapman and Hall.
63. Menden-Deuer, S., and E. J. Lessard. 2000. Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton. Limnology and Oceanography 45(3): 569-579.
64. Monismith, S. G., W. J. Kimmerer, J. R. Burau, and M. T. Stacey. 2002. Structure and flow-induced variability of the subtidal salinity field in northern San Francisco Bay. Journal of Physical Oceanography 32: 3003-3019.
65. Morel, A., and R. C. Smith. 1974. Relation between total quanta and total energy for aquatic photosynthesis. Limnology and Oceanography 19: 591-600.
66. Mueller-Solger, A. B., A. D. Jassby, and D. Müller-Navarra. 2002. Nutritional quality of food resources for zooplankton (Daphnia) in a tidal freshwater system (Sacramento-San Joaquin River Delta). Limnology and Oceanography 47: 1468-1476.
67. Murrell, M., J. Hagy, E. Lores, and R. Greene. 2007. Phytoplankton production and nutrient distributions in a subtropical estuary: Importance of freshwater flow. Estuaries and Coasts 30: 390-402.
68. Nichols, F. H. 1985. Increased benthic grazing: An alternative explanation for low phytoplankton biomass in northern San Francisco Bay during the 1976-1977 drought. Estuarine, Coastal and Shelf Science 21: 379-388.
69. Nichols, F. H., J. K. Thompson, and L. E. Schemel. 1990. Remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis. 2. Displacement of a former community. Marine Ecology Progress Series 66: 95-101.
70. Nixon, S. W. 1988. Physical energy inputs and the comparative ecology of lake and marine ecosystems. Limnology and Oceanography 33: 1005-1025.
71. Nixon, S. W. 2003. Replacing the Nile: Are anthropogenic nutrients providing the fertility once brought to the Mediterranean by a great river? Ambio 32: 30-39.
72. Nobriga, M., T. Sommer, F. Feyrer, and K. Fleming. 2008. Long-term trends in summertime habitat suitability for delta smelt, Hypomesus transpacificus. San Francisco Estuary and Watershed Science 6: Issue 1 Article 1.
73. Orsi, J. J., and W. L. Mecum. 1996. Food limitation as the probable cause of a long-term decline in the abundance of Neomysis mercedis the opossum shrimp in the Sacramento-San Joaquin estuary. In San Francisco Bay: The ecosystem, ed. J. T. Hollibaugh, 375-401. San Francisco: AAAS.
74. Pahl-Wostl, C., and D. M. Imboden. 1990. DYPHORA-a dynamic model for the rate of photosynthesis of algae. Journal of Plankton Research 12: 1207-1221.
75. Parker, A. E., W. J. Kimmerer, and U. Lidstro{double acute}m. 2012. Re-evaluating the generality of an empirical model for light-limited primary production in the San Francisco Estuary. Estuaries and Coasts (in press).
76. Revilla, M., A. Ansotegui, A. Iriarte, I. Madariaga, E. Orive, A. Sarobe, and J. M. Trigueros. 2002. Microplankton metabolism along a trophic gradient in a shallow-temperate estuary. Estuaries 25: 6-18.
77. Schoellhamer, D. H. 2011. Sudden clearing of estuarine waters upon crossing the threshold from transport to supply regulation of sediment transport as an erodible sediment pool is depleted: San Francisco Bay, 1999. Estuaries and Coasts 34: 885-899.
78. Sharp, J., K. Yoshiyama, A. Parker, M. Schwartz, S. Curless, A. Beauregard, J. Ossolinski, and A. Davis. 2009. A biogeochemical view of estuarine eutrophication: Seasonal and spatial trends and correlations in the Delaware Estuary. Estuaries and Coasts 32: 1023-1043.
79. Smith, E. M., and W. M. Kemp. 2001. Size structure and the production/respiration balance in a coastal plankton community. Limnology and Oceanography 46: 473-485.
80. Sobczak, W. V., J. E. Cloern, A. D. Jassby, B. E. Cole, T. S. Schraga, and A. Arnsberg. 2005. Detritus fuels ecosystem metabolism but not metazoan food webs in San Francisco estuary's freshwater delta. Estuaries 28: 124-137.
81. Solórzano, L. 1969. Determination of ammonia in natural waters by phenolhypochlorite method. Limnology and Oceanography 14: 799-801.
82. Sommer, T., C. Armor, R. Baxter, R. Breuer, L. Brown, M. Chotkowski, S. Culberson, F. Feyrer, M. Gingras, B. Herbold, W. Kimmerer, A. Mueller Solger, M. Nobriga, and K. Souza. 2007. The collapse of pelagic fishes in the upper San Francisco Estuary. Fisheries 32: 270-277.
83. 14) for measuring organic carbon production in the sea. Journal Cons Perm International Exploration Mer 18: 117-140.
84. Thompson, J. K. 2005. One estuary, one invasion, two responses: Phytoplankton and benthic community dynamics determine the effect of an estuarine invasive suspension-feeder. In Comparative roles of suspension-feeders in ecosystems: NATO Science Series IV Earth and Environmental Sciences 47, 291-316.
85. Thomson, J., W. Kimmerer, L. Brown, K. Newman, R. Mac Nally, W. Bennett, F. Feyrer, and E. Fleishman. 2010. Bayesian change-point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications 1431-1448: 1431-1448.
86. Throndsen, J. 1978. Centrifugation. In Phytoplankton manual, ed. A. Sournia, 98-103. Paris: UNESCO.
87. Tomas, C. R. 1996. Identifying marine diatoms and dinoflagellates. San Diego: Academic.
88. Venables, W. N., and B. N. Ripley. 2003. Modern applied statistics with S, 4th ed. New York: Springer.
89. Verity, P. G., C. Y. Robertson, C. R. Tronzo, M. G. Andrews, J. R. Nelson, and M. E. Sieracki. 1992. Relationships between cell volume and the carbon and nitrogen content of marine photosynthetic nanoplankton. Limnology and Oceanography 37(7): 1434-1446.
90. Wehr, J. D., and R. G. Sheath. 2003. Freshwater algae of North America: Ecology and classification. San Diego: Academic.
91. Werner, I., and J. T. Hollibaugh. 1993. Potamocorbula amurensis-comparison of clearance rates and assimilation efficiencies for phytoplankton and bacterioplankton. Limnology and Oceanography 38: 949-964.
92. Whitledge, T. E., S. Malloy, C. J. Patton, & C. D. Wirick, 1981. Automated nutrient analysis in seawater. Brookhaven National Laboratory Tech. Rep. BNL 51398. 226 pp.
93. Wilkerson, F. P., R. C. Dugdale, V. E. Hogue, and A. Marchi. 2006. Phytoplankton blooms and nitrogen productivity in San Francisco Bay. Estuaries and Coasts 29: 401-416.
94. York, J., B. Costas, and G. McManus. 2010. Microzooplankton grazing in green water-results from two contrasting estuaries. Estuaries and Coasts 34: 373-385.