roccus saxatilis

Pelagic Ecology of the Low Salinity San Francisco Estuary

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 (Kimmerer 2002). 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, foodweb and trophic dynamics, energetic transfer, advection and dispersal in and out of the system, survivorship and mortality, predation, and competition from introduced species.

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 80-95% 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 Sierras in the late 19th Century. The trend toward high sediment loads was reversed in the 1950’s with the advent of the Central Valley Water 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 levies 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 levy 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).


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 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. 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 is 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. tidesTidal 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 the 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 in the Vernalis Salinity Standard, which was legally established to maintain habitat quality in the Estuary for wildlife and to prevent salinity from encroaching upstream to the export pumps (Trott 2006).

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 (Kimmerer 2004) slowing the advection of primary and secondary production out of the system.

Primary Production and Nutrient Uptake

Primary production by phytoplankton fixes energy and key nutrients into a biologically available form (ie, food), via photosynthesis. Phytoplankton production is largely structured by physical parameters: nutrient availability, sunlight, turbidity, and temperature.

The San Francisco Estuary has a non-limiting source of nutrients that can be used for primary production, derived largely from waste water treatment facilities, agricultural and urban drainage, and the ocean (Smith 2002; Dugdale 2003). In spite of this, the Estuary is unique in that it tends to have a relatively depressed rate of primary production (Jassby 2002). This is probably due to two factors: large inputs of nitrogen in the form of ammonium, which suppresses nitrate uptake by phytoplankton, and high turbidity, which limits light for photosynthesis to the top few centimeters of the water column (Dugdale 2003). This turbidity is a legacy of hydraulic gold mining in the Sierra Nevada Mountains in the 1850’s (Nichols 1986).

High residence time of water in the Estuary tends to allow phytoplankton biomass to accumulate, increasing density, while low residence time removes phytoplankton from the Estuary (Kimmerer 2004). The latter is typical of the main channels of the Estuary during periods of high flow, when surface waters tend to advect particles and plankton downstream.

Herbivory also removes phytoplankton from the water column. While the pelagic foodweb is based upon phytoplankton production, most of this production is diverted to the benthos via predation by the introduced Amur River clam, Corbula amurensis. Levels of phytoplankton biomass declined by an order of magnitude after the widespread introduction of C. amurensis in the mid-1980’s, and have not rebounded (Kimmerer 1994).

Secondary Production

Secondary production refers to organisms that feed on primary production and transfer energy to higher trophic levels of the estuarine foodweb. Historically, secondary production in the San Francisco Estuary was dominated by mysid shrimp production (Modlin 1997; Kimmerer 1998). However, the native mysid Neomysis mercedis has been largely replaced by the introduced Acanthomysis bowmani, which persists at lower densities. The introduced amphipod Gammurus daiberi may have taken over some of this niche, but it is largely restricted to fresh water.

Today, the main source of secondary production derives from copepods. The naturalized native calanoid copepod Eurytemora affinis is believed to have been introduced near the end of 19th Century (Lee 1999). It dominated the zooplankton of the low salinity zone until the 1980’s when it was largely replaced by another introduced calanoid copepod, Pseudodiaptomus forbesi (Orsi 1991; Kimmerer 1996). P. forbesi persists by maintaining a source population in freshwater, high-residence regions of the Estuary, particularly in the Delta, outside the range of salinity tolerance of the Amur River clam (Durand 2006). Because the once-dominant E. affinis lacks an upstream range, it is more vulnerable to predation by the clam, and suffers from apparent competition with P. forbesi.

Other calanoid copepods that may be of significance are the recently introduced Sinocalanus doerri and Acartiella sinensis. Little is known about the life histories of these organisms, although based upon their morphology, they may prey on other copepods. They appear in irregular cycles of abundance, during which they may dominate the zooplankton (Orsi 1999). Yet another invasive copepod, the very small cyclopoid Limnoithona tetraspina, appeared in the Low Salinity Zone in the 1990’s. Since then, L. tetraspina has become the numerically dominant copepod, reaching densities on the order of 10,000/m3. It relies on the microbial loop as its food source, feeding upon bacteria, ciliates and rotifers (Bouley P. 2006). In addition, it seems invulnerable to predation by the Amur River clam, for reasons that are unknown. Because of its small size, L. tetraspina is generally not available for consumption by larger predators, particularly fish, making it an energetic dead end.


It is difficult to characterize the historic foodweb 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 1970’s gives some information about the historic dynamics of the foodweb. Prior to the 1980’s the LSZ was dominated by a phytoplankton-driven foodweb, a stable mesoplankton population dominated by E. affinis, and large macrozooplankton typified by San Francisco bay shrimp and mysids (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.

Foodweb 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 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 L. 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 1980’s 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 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 foodweb decline, water exports from the Delta, and toxics from urban, industrial, or agricultural sources.

Introduced species

Species introductions have been increasing since at least the 19th Century as a function of increasing trade and traffic. Introductions include numerous taxa, including copepods, shrimp, amphipods, bivalves, fish and both rooted and floating plants. Many pelagic species have been introduced most recently through ballast water releases from large ships directly into the Estuary (Carlton 1996). As a result, many of these introduced species originate from estuaries around the Pacific Rim, particularly copepods such as P. forbesi and L. tetraspina. The Amur River clam originates from Asia, and has created significant and drastic changes to the ecology of the LSZ, primarily by diverting pelagic food to the benthos and into an accelerated microbial loop (Cole 1992).

Species have also been introduced via attachment to sporting boats which are trailered between regions (Carlton 1996). This is the probable source of a number of low salinity plants like Egeria densa and water hyacinth (Eichhornia crassipes). These plants have created profound changes in the Delta by disrupting water flow, shading phytoplankton, and providing habitat for piscivorous fish like the striped bass, Morone saxatilis, itself intentionally introduced in the late 1800’s from the Chesapeake Bay (Radovich 1963; Carlton 1996). The freshwater quagga mussel, originally from Europe, is expected to be introduced by boaters within the next two to ten years, in spite of precautionary measures (Dey 2007).

Future Ecology

The ecology of the Low Salinity Zone of the San Francisco Estuary is difficult to characterize because it is the result of a complex synergy of both abiotic and biotic factors. In addition, it continues to undergo rapid change resulting from newly introduced species, direct anthropogenic influences and climate change. Future ecological changes will be driven on an ecosystem wide scale, particularly as sea level rise, tectonic instability and infrastructure decline cause levy failure in the Delta (Epstein 2006). The resulting back-surge in water flow is expected to force X2 into the Delta, jeopardizing spatially oriented habitat (like freshwater marshes), channelizing the low salinity zone, and threatening southern California’s water supply, with unknown and unforeseeable consequences for the natural and human ecology of the West coast’s largest estuary.


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