The San Francisco Estuary together with the Sacramento–San Joaquin River Delta represents a highly altered ecosystem. The region has been heavily re-engineered to accommodate the needs of water delivery, shipping, agriculture, and most recently, suburban development. These needs have wrought direct changes in the movement of water and the nature of the landscape, and indirect changes from the introduction of non-native species. New species have altered the architecture of the food web as surely as levees have altered the landscape of islands and channels that form the complex system known as the Delta.Kimmerer 2004
This article deals particularly with the ecology of the low salinity zone (LSZ) of the estuary. Reconstructing a historic food web for the LSZ is difficult for a number of reasons. First, there is no clear record of the species that historically have occupied the estuary. Second, the San Francisco Estuary and Delta have been in geologic and hydrologic transition for most of their 10,000 year history, and so describing the "natural" condition of the estuary is much like "hitting a moving target". Climate change, hydrologic engineering, shifting water needs, and newly introduced species will continue to alter the food web configuration of the estuary. This model provides a snapshot of the current state, with notes about recent changes or species introductions that have altered the configuration of the food web. Understanding the dynamics of the current food web may prove useful for restoration efforts to improve the functioning and species diversity of the estuary.
Physical geography
The San Francisco Bay is both a bay and an estuary. The former term refers to any inlet or cove providing a physical refuge from the open ocean. An estuary is any physiographic feature where freshwater meets an ocean or sea. The northern portion of the bay is a brackish estuary, consisting of a number of physical embayments which are dominated by both marine and fresh water fluxes. These geographic entities are, moving from saline to fresh (or west to east): San Pablo Bay, immediately north of the Central Bay; the Carquinez Strait, a narrow, deep channel leading to Suisun Bay; and the Delta of the Sacramento and San Joaquin rivers.
Until the 20th century, the LSZ of the estuary was fringed by tule-dominated freshwater wetlands. Between 80 and 95% of these historic wetlands have been filled to facilitate land use and development around the Bay Area.Conomos 1979 Habitat loss at the edges of the pelagic zone is thought to create a loss of native pelagic fish species, by increasing vulnerability to predation.
The intertidal and benthic estuary is presently dominated by mudflats that are largely the result of sedimentation derived from gold mining in the Sierra Nevada in the late 19th century. The trend toward high sediment loads was reversed in the 1950s with the advent of the Central Valley Project, locking up most sediment behind dams, and resulting in an annual net loss of sediments from the estuary.Vayssieres 2006 Thus the mudflats appear to be slowly receding, although turbidity remains extremely high. The high turbidity of the water is responsible for the unique condition that exists in the San Francisco Estuary wherein high nutrient availability does not lead to high phytoplankton production. Instead, most algae photosynthetic organisms are light-limited.Jassby 2000
The Delta has likewise experienced heavy alteration. Beginning in the 19th century, naturally occurring levees were reinforced for permanency, to protect farmlands from regular flooding. Many of these farms were established on peat islands occurring in the middle of the Delta waterways. Intensive farming oxidized the high carbon content of the soil, causing considerable loss of soil mass. As a consequence, these islands have subsided, or sunk, to nearly 6 meters below sea level.Deverel 1998 The Delta today consists of highly riprapped waterways, punctuated by islands that appear like "floating bowls" with their basins far below the surface of the water.Philip 2007 These islands are at high risk for flooding due to levee collapse. The subsequent eastward shift in salinity is expected to dramatically alter the ecology of the entire LSZ of the San Francisco Estuary.Lund 2007
Hydrodynamics
The LSZ centers around 2 psu (practical salinity units, a measurement of salinity) and ranges from about 6 psu down to 0.5 psu. The primary fresh water inputs to the estuary derive from runoff of regional precipitation, the Sacramento River, and the San Joaquin River.Kimmerer 2002
River inflow is largely controlled by upstream reservoir releases. A significant fraction of this inflow is exported out of the Delta by the federal Central Valley Project and the State Water Project to southern California for agricultural and urban use. These alterations have removed much of the variation in through-estuary outflow (i. e., freshwater that makes it out the Golden Gate), creating lower outflow in the winter and higher outflow in the summer than historically found in the estuary. On average, freshwater flows into the estuary are 50% of historic flows. Phytoplankton, zooplankton, and larval and adult fish can become entrained in the export pumps, causing a potentially significant but unknown impact on the abundance of these organisms. This may be particularly true of the endangered delta smelt, a small endemic fish; unexceptional except that it has been described as being tremendously abundant in historical accounts.Moyle 1992 The delta smelt is believed to migrate and spawn upstream in the Delta during the early summer, placing its eggs and larvae at high risk for entrainment.Bennett 2006 Management for the smelt is currently the source of controversy as its ecology brings into collision course the disparate water needs of conservation, development and agriculture in California.
The movement of water out of the estuary is complex and dependent upon a number of factors. Tidal cycles cause water to move toward and away from the Golden Gate four times in a 24-hour period.
Using 2 psu as a marker for the Low Salinity Zone, the direction and magnitude of fluctuations can be tracked as its distance in kilometers from the Golden Gate, or X2. Because the position of X2 relies upon a number of physical parameters including inflow, export, and tides, its position shifts over many kilometers on a daily and seasonal cycle; over the course of a year, it can range from San Pablo Bay during high flow periods, up into the Delta during the summer drought. The position of X2 is carefully monitored and maintained by releasing water from upstream reservoirs in anticipation of export demand. This is mandated by State Water Board Decision 1641 and requires that state and federal pumping be curtailed if X2 is shifted east of Chipps Island (75 river kilometers upstream of the Golden Gate Bridge) during the months of February through May, or east of Collinsville (81 river kilometers upstream of the Golden Gate Bridge) during the months of January, June, July and August. (D-1641 pp 150)
Gravitational circulation causes stratified high salinity water at depth to flow landward while low salinity water on top flows seaward.Monismith 1996 The effect of gravitational circulation may be most pronounced during periods of high fresh water flow, providing a negative feedback for maintaining the salt field and the distribution of pelagic organisms in the estuary.
Mixing is important at the landward edge of gravitational circulation, often around X2, where the water column becomes less stratified.Burau 1998 A fixed mixing zone occurs at the "Benicia Bump" at the east end of the Carquinez Strait, where the deep channel becomes dramatically shallower as it enters Suisun Bay.Schoellhamer 2001 Mixing is critical in maintaining salinity such that extremely large inputs of fresh water are required to move X2 a short distance to the west. Mixing also assists pelagic organisms in maintaining position in the estuary, slowing the advection of primary and secondary production out of the system.
Pelagic zone Pelagic organisms spend all or part of their lives in the open water, where habitat is defined not by edges but by physiological tolerance to salinity and temperature. The Low Salinity Zone (LSZ) of the San Francisco Estuary constitutes a habitat for a suite of organisms that are specialized to survive in this unique confluence of terrestrial, freshwater, and marine influences. While there are many habitats with distinct ecologies that are part of the estuary (including marine, freshwater, intertidal marsh and benthic mudflat systems) each is linked to the LSZ by export and import of freshwater, nutrients, carbon, and organisms.
The distribution and abundance of organisms in the LSZ is dependent upon both abiotic and biotic factors. Abiotic factors include the physical geography and hydrology of the estuary, including nutrient inputs, sediment load, turbidity, environmental stochasticity, climate and anthropogenic influences. Abiotic factors tend to drive production in the estuarine environment, and are mediated by biotic factors.
Biotic factors include nutrient uptake and primary production, secondary production of zooplankton, food web and trophic dynamics, energetic transfer, advection and dispersal in and out of the system, survival and mortality, predation, and competition from introduced species.
Food web It is difficult to characterize the historic food web of the San Francisco Estuary because of the dramatic changes in geography, hydrology, and species composition that have occurred in the past century. However, monitoring begun in the 1970s gives some information about the historic dynamics of the foodweb. Prior to the 1980s the LSZ was dominated by a phytoplankton-driven foodweb, a stable mesoplankton population dominated by the copepod Eurytemora affinis, and large macrozooplankton typified by San Francisco bay shrimp and mysid shrimps.Orsi 1986 These provided nutrition and energy to native filter feeders such as the northern anchovy (Engraulis mordax), and planktivores such as delta smelt and juvenile salmon.
Food web change has been driven historically by increased turbidity, and more recently by introduced species, as described in the sections on primary and secondary production.
Notably, the high clearance rate of the introduced Amur River clam Potamocorbula amurensis population has produced a ten-fold decline in plankton density, resulting in a carbon trap in the benthos and an assumed increase in waste detrital production.Kimmerer 1996 This waste is hypothesized to fuel the microbial loop, resulting in an increase in microzooplankton such as the copepod Limnoithona tetraspina, which utilize rotifers and ciliates.
These changes are one cause for declining fish stocks. For example, the northern anchovy, Engraulis mordax, was until the 1980s quite abundant in the Low Salinity Zone, until its range in the estuary became restricted to the Central and South Bays.Kimmerer 2006 This is probably due to a behavioral response following the introduction of the Amur River (Potamocorbula amurensis) clam and the subsequent decline in plankton availability.
More recently, a general pelagic organism decline (POD) was described, and this has been the source of much concern within the scientific, managerial, and political communities.
Several key species, including delta smelt, longfin smelt, striped bass, and threadfin shad have been declared "species of interest" because of a stepwise decline in abundance beginning in 2001.Taugher 2005 This was attended by a similar decline in secondary productivity and is currently the source of much research. A number of hypotheses have been proposed to explain the POD, including food web decline, water exports from the Delta, and toxics from urban, industrial, or agricultural sources.
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