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John Muir Institute of the Environment masthead2


Volume 2, Issue 1 February 2004

Open Water Processes of the San Francisco Estuary: From Physical Forcing to Biological Responses
Wim Kimmerer, San Francisco State University

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Erratum

ABSTRACT:
This paper reviews the current state of knowledge of the open waters of the San Francisco Estuary. This estuary is well known for the extent to which it has been altered through loss of wetlands, changes in hydrography, and the introduction of chemical and biological contaminants. It is also one of the most studied estuaries in the world, with much of the recent research effort aimed at supporting restoration efforts. In this review I emphasize the conceptual foundations for our current understanding of estuarine dynamics, particularly those aspects relevant to restoration. Several themes run throughout this paper. First is the critical role physical dynamics play in setting the stage for chemical and biological responses. Physical forcing by the tides and by variation in freshwater input combine to control the movement of the salinity field, and to establish stratification, mixing, and dilution patterns throughout the estuary. Many aspects of estuarine dynamics respond to interannual variation in freshwater flow; in particular, abundance of several estuarine-dependent species of fish and shrimp varies positively with flow, although the mechanisms behind these relationships are largely unknown. The second theme is the importance of time scales in determining the degree of interaction between dynamic processes. Physical effects tend to dominate when they operate at shorter time scales than biological processes; when the two time scales are similar, important interactions can arise between physical and biological variability. These interactions can be seen, for example, in the response of phytoplankton blooms, with characteristic time scales of days, to stratification events occurring during neap tides. The third theme is the key role of introduced species in all estuarine habitats; particularly noteworthy are introduced waterweeds and fishes in the tidal freshwater reaches of the estuary, and introduced clams there and in brackish water. The final theme is the rather heterogeneous set of results from monitoring and research in the estuary. For example, some topics have been subjects of intense activity both in research and monitoring (e.g., physical dynamics of the upper estuary, phytoplankton blooms), while others have received little attention (e.g., microzooplankton). In addition, both research and monitoring have emphasized some regions of the estuary (e.g., the Sacramento-San Joaquin Delta) over others (e.g., San Pablo Bay). In addition, ecological modeling and synthesis has emphasized lower trophic levels over higher. Opportunities for restoration in the open waters of the estuary are somewhat limited by the lack of scientific basis for restoration, and the difficulty in detecting ecosystem responses in the context of high natural variability.

ERRATUM:

Page 17, paragraph 1: The last sentence originally read:

Analyses of effects of outflow (or X2) together with export flow (not export:inflow ratio) have revealed nonexistent (salinity; Kimmerer unpublished) or very weak (striped bass survival, Kimmerer et al. 2001) effects of export flow.

The last sentence should be replaced with the following to clarify that salinity in the Delta can be affected by export flow:

Analyses of effects of outflow (or X2) together with export flow (not export:inflow ratio) have revealed nonexistent (salinity in Suisun Bay; Kimmerer unpublished) or very weak (striped bass survival, Kimmerer et al. 2001) effects of export flow.

Page 48, paragraph 1: The last sentence originally read:

Blooms of Microcystis have occurred in the southern Delta (Lehman and Waller 2003).

The last sentence should be revised as follows to state that Microcystis blooms throughout the Delta.

Blooms of Microcystis have occurred throughout the Delta (Lehman and Waller 2003).

Page 63, paragraph 1: The first three sentences of the paragraph originally read:

The principal exception to the generally saturated oxygen concentrations occurs in late summer to early fall in the San Joaquin River near Stockton (Hayes and Lee 1998, 1999, 2000; Lehman et al. 2004), a region not included in Figure 32. In that region, a combination of high summer temperature and high organic matter loading and phytoplankton production result in high oxygen demand relative to gas exchange with the atmosphere. Furthermore, stratification presumably limits oxygen transport to the bottom, and together with planktonic and benthic oxygen consumption results in low oxygen concentration (less than ~5 mg L-1) near the bottom. This may impede movement of fish through the area (Hayes and Lee 1998, 1999, 2000), although estuarine organisms may tolerate lower values (e.g., Stalder and Marcus 1997).

The principal exception to the generally saturated oxygen concentrations occurs in late summer to early fall in the San Joaquin River near Stockton (Hayes and Lee 1998, 1999, 2000, Lehman et al. 2004), a region not included in Figure 32. High oxygen demand relative to gas exchange with the atmosphere in that region was previously attributed to high summer temperature and high organic matter loading and phytoplankton production, but Lehman et al. (2004) presented results showing that loading of nitrogenous nutrients from sewage treatment plants could account for most of the biological oxygen demand. Low dissolved oxygen may impede movement of fish through the area (Hayes and Lee 1998, 1999, 2000), although estuarine organisms may tolerate lower values (e.g., Stalder and Marcus 1997).

KEYWORDS:
Ocean, hydrology, geochemistry, tidal processes, physical forcing, fisheries, water management, water diversions, conceptual model, San Francisco Estuary, California

SUGGESTED CITATION:
Kimmerer, Wim. 2004. Open Water Processes of the San Francisco Estuary: From Physical Forcing to Biological Responses. San Francisco Estuary and Watershed Science. Vol. 2, Issue 1 (February), Article 1.
http://repositories.cdlib.org/jmie/sfews/vol2/iss1/art1




 
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