Ecology of the San Francisco Estuary low salinity zone

Ecology of the San Francisco Estuary low salinity zone

The low salinity zone (LSZ) of the San Francisco Estuary and Delta represents a highlyaltered ecosystem. The region has been heavily re-engineered to accommodate the needs ofwater delivery, shipping, agriculture, and most recently, suburban development. These needshave wrought direct changes in the movement of water and the nature of the landscape, andindirect changes have arisen from the introduction of non-native species. New species havealtered the architecture of the food web as surely as levies have altered the landscape of islandsand channels that form the complex system known as the Delta (Kimmerer 2004).

Reconstructing a historic foodweb 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 mostof their 10,000 year history, and so describing the “natural” condition of the Estuary is muchlike “hitting a moving target” (Kimmerer 2004). Climate change, hydrologic engineering,shifting water needs, and newly introduced species will continue to alter the food webconfiguration of the Estuary. This model provides a snapshot of the current state, with notesabout recent changes or species introductions that have altered the configuration of the foodweb. Understanding the dynamics of the current foodweb may prove useful for restorationefforts to improve the functioning and species diversity of the Estuary.

Primary Producers

Photosynthetic Production

The main source of photosynthetically derived energy is phytoplankton. Generallyspeaking, diatoms and microflagellates produce most of the bioavailable carbon in the Estuary(Jassby and Cloern 2000). Other types, notably the dinoflagellates, may produce harmful algalblooms, or red tides, that are less readily available for assimilation into the foodweb (Andersonet al. 2002).

Phytoplankton production is a function of two different factors: growth rates andaccumulation (Fig. 1). Although the LSZ is a sink for high concentrations of nutrients fromurban and agricultural sources, phytoplankton production rates are quite low (Jassby et al.2002). Nitrate is optimally used by phytoplankton for growth, but ammonium (largely derivedfrom sewage outfalls) has a suppressive effect on growth rate. Thus, while not nutrient limited,phytoplankton tend to grow more slowly due to the kinds of nitrogen present (Dugdale et al.2003). Another suppressive factor on growth rate is the high turbidity of the Estuary, whichlimits the ability of photosynthetically active radiation (PAR) to penetrate beyond the top fewcentimeters of the water column. This limits phytoplankton photosynthesis to a relativelyshallow photic zone. Thus, when the water column is stratified, turbidity is high, andammonium is present, the growth rate of phytoplankton is typically suppressed (Cloern 1987,Cole and Cloern 1987).

Phytoplankton accumulation is primarily the result of residence time (Jassby et al.2002). The north Delta and Suisun Bay have relatively low residence times due to the highvolume of water moving through the region for downstream flow and for export to southernCalifornia. Since water moves more rapidly through this part of the system, the rate ofaccumulation decreases as productivity is advected out of the system. In contrast, parts of thesouthern Delta have a higher residence time due to the low volume of water moving throughthe system; in fact the water on occasion runs backwards, due to the lack of inflow from the SanJoaquin River, and export pumping. During summer, phytoplankton density may be an order ofmagnitude higher here than in other parts of the Estuary (Ball and Arthur 1979).

Harmful algal blooms (HAB’s) of dinoflagellates or cyanobacteria produce toxicmetabolic byproducts that render them noxious to many organisms. Fostered by a combinationof high nutrient concentrations and temperatures, HAB’s have a doubly negative affect on thefood web by competitively excluding diatoms and microflagellates, further reducingbioavailable primary production. While certain invertebrates such as bivalves may not bedirectly affected, they may propagate toxins up the food chain, sickening or killing predators. It is not well understood how copepods are affected. The invasive algae "Microcystis aeruginosa" isnow common in the Delta during summer months and may reduce copepod productivity (inaddition to being potentially carcinogenic for humans) (Lehman and Waller 2003).

Detrital Production

Enormous quantities of sediment and detritus flux through the LSZ. Much of this isorganic debris in the form of dissolved and particulate organic matter (DOM and POM,respectively). In addition to upstream sources, organic matter may accumulate from localorganism mortality and waste production (Murrell et al. 1999, Murrell and Hollibaugh 2000).
Detritivores capitalize upon this energy source, creating an alternate and parallel foodweb ofpotentially large importance. This is because carbon fixation into the detrital food web is notlimited by stratification, turbidity or day length, all of which limit photosynthesis. Detritalproduction occurs continuously, limited only by inputs and advection out of the Delta system(Jassby et al. 1993, Jassby and Cloern 2000).

Bacteria are the chief agents of transformation of DOM and POM into bioavailablecarbon through the microbial loop. This mechanism is particularly important in nutrient limited
marine systems, where bacteria release nutrients from sinking detritus, allowing it to berecycled back to the photic zone. Little work has been applied to the function of the microbialloop in the San Francisco Estuary, but it may be that the role of bacteria is not critical forrecycling nutrients in a eutrophic system. Rather, they may provide an alternative food chainthrough direct grazing by flagellates, rotifers and ciliates (Hollibaugh and Wong 1996).

The high abundance of the cyclopoid copepod "Limnoithona tetraspina" may be due to itsreliance on ciliates rather than phytoplankton as a primary food source (Bouley P. 2006). Themajor species of calanoid copepods may also use ciliates as a supplementary or even primaryfood source, but to what degree is unknown (Rollwagen-Bollens and Penry 2003, Rollwagen-Bollens et al. 2006).

Primary Consumers

Primary consumers rely upon primary production as a main food source. The mostimportant consumers of the pelagic web of the LSZ are copepods, along with the rotifers,flagellates and ciliates mentioned above. All species of calanoid copepods have declined underhigh predation pressure from the recently introduced Amur River clam ("Corbula amurensis")(Kimmerer 1996). Because of this, and because copepods rely upon both photosynthetic anddetrital food sources, copepods in the LSZ have limited feedback on primary production, unlikemarine and lentic systems where copepods can graze down blooms in a matter of days.

"Pseudodiaptomus forbesi" is the dominant calanoid copepod of the LSZ in terms of biomass. It has a sufficiently wide salinity tolerance that it can persist both at low salinity and in freshwater. This wide distribution helps the population maintain an upstream refuge from predation,unlike other species with narrower salinity tolerances (Durand 2006).

"Limnoithona tetraspina" has become the numerically dominant cyclopoid copepod since itsintroduction in 1993. It feeds primarily upon ciliates and microflagellates, but unlike "P. forbesi",it is relatively impervious to predation by clams or fish, hence its abundance. Energetically, "L. tetraspina" may be a dead end for the food web; these copepods are either advected out of thesystem by tides and currents, or die and fall down to the benthos, where they may be availableto the microbial loop, or to detritivores (Bouley and Kimmerer 2006).


Predatory Copepods

A number of predatory copepods exist throughout the Delta, about which relativelylittle is known. "Sinocalanus doerri", "Acartiella sinensis", and "Tortanus dextrilobatus" all appear to bemorphologically capable of predation upon other copepods. Each was introduced to theEstuary, probably through ballast water exchange since the 1980’s. Generally, they are not insufficient abundance to negatively impact copepod consumers; however, periodic blooms of "S.doerri" and "A. sinensis" occur which have not been well studied (Orsi and Ohtsuka 1999).


While capable of filter-feeding, mysids are largely carnivorous, feeding on copepodadults. They provided an energetic conduit between plankton and planktivorous fishes,including juvenile fishes, sturgeon, Chinook salmon, and American shad. Mysids were onceabundant until the native "Neomysis mercedis" was replaced in the mid-1980’s by the invasive"Acanthomysis bowmani", which is smaller and less abundant. Mysid decline has been linked to thesubsequent decline in a number of fish species in the Estuary in the 1980’s and 90’s (Orsi andKnutson 1979, Modlin and Orsi 1997).

Shrimp are generalist carnivores who prey largely on mysids and amphipods. "Crangonfranciscorum" represents one of two remaining commercial fisheries in the Estuary. While nolonger used for “San Francisco Bay Shrimp Cocktails”, they are harvested for bait. Otherpredators include striped bass and Chinook salmon adults and smolts (Sitts and Knight 1979).


Because fish are a taxonomically and morphologically diverse group, species vary intheir trophic ecologies. In general, fish can be divided into four broad feeding categories: filterfeeders, planktivores, piscivores and benthic feeders.

Filter feeders strain the water column indiscriminately for small prey, typically phyto- andzooplankton. This category of fishes includes threadfin shad ("Dorosoma petenense"), Americanshad ("Alosa sapidissima") , inland silversides ("Menidia beryllina") , and anchovies ("Engraulismordax"). Some evidence suggests that some of these species are food-limited due to thedepressed levels of plankton after the introduction of Corbula amurensis. Anchovies have left theLSZ in favor of more productive regions of the Estuary in the San Pablo and Central Bays(Kimmerer 2006).

Planktivores selectively prey upon individual zooplankton, such as copepods, mysidsand gammarids. This group includes most fish larvae, Delta smelt ("Hypomesus transpacificus") and
longfin smelt ("Spirinchus thaleichthys"), tule perch ("Hysterocarpus traski"), and salmon smolts. TheDelta smelt is of particular interest due to its endangered status. It may be food-limited, but theevidence is somewhat contradictory. Other factors, such as entrainment of eggs and larvae inthe export pumping of fresh water from the Delta may also explain the decline (Bennett 2006).

The main piscivore of the LSZ is the striped bass ("Morone saxatilis"), which wasintroduced in the 1890’s and preys heavily upon native fishes. Striped bass are an importantsport fishery in the San Francisco Estuary, and as such, represent a minor withdrawal ofbiomass from the Estuary (Radovich 1963).

Benthic, or bottom-dwelling, fishes include white sturgeon ("Acipenser transmontanus"),
white catfish ("Ameiurus catus"), and starry flounder ("Platichthys stellatus"). Because of their habitatorientation, they feed primarily on epibenthic organisms such as amphipods, bay shrimp, andbivalves. These fish are known to feed at least occasionally on Corbula amurensis, which wouldrepresent one of the few channels for energy flow from that species, except for detritalproduction (Peterson 1997).


The San Francisco Estuary is a major stop on the Pacific flyway for migratingwaterfowl. Yet little is known about the flow of carbon in or out of the Estuary via birds. Mostof the birds are dabbling ducks that feed on submerged aquatic vegetation. Diving ducks (suchas scaups) feed on epibenthic organisms like C. amurensis, representing a possible flow of carbonfrom that otherwise dead end (Poulton et al. 2002, Richman and Lovvorn 2004). Piscivorousbirds such as cormorants and pelicans also inhabit the Estuary, but their trophic impactremains poorly studied.


Humans represent the main mammalian predator. The sole commercial fishery in theLSZ is for bait shrimp. There are a variety of sports fisheries that represent a minor flow ofcarbon, but significant flows of capital to local economies around the Estuary. Most of therecreational fisheries surround striped bass, sturgeon, and introduced fresh water basses in thefreshwater Delta. This paucity of fisheries makes the San Francisco Estuary unique. Nearly allestuaries world-wide support at least remnants of significant fisheries (Nichols et al. 1986). TheSan Francisco Estuary at one time supported major fisheries for salmon, anchovies, and
Dungeness crabs until the 1950’s. The demise of these fisheries was probably due more to
habitat loss than overharvesting (Conomos 1979).


Jellies have not been prevalent in the Estuary until recently. In east coast estuaries suchas the Chesapeake, they are often top-level predators, feeding indiscriminately on both fish andzooplankton. Several small invasive taxa have been identified in the LSZ and freshwaterregions. These species strobilate in summer, but maintain polyps in the benthos year round.Their impact on the plankton is unknown, but research is underway to quantify it. In sufficientdensity, jellies may have a complementary role to C. amurensis in suppressing zooplankton, byinhabiting areas of low salinity outside the range of the clams, where planktonic species havehad a predation-free refuge.

Benthic Consumers

The benthic community has taken on a disproportionately large role in the food webecology of the Estuary due to key invasions by bivalves (Kimmerer 1996). The mostubiquitous of these clams, the Amur River clam ("Corbula amurensis") has a wide salinity tolerancethat extends into the low salinity zone, but not into freshwater. It filter feeds on phytoplanktonand small zooplankton, such as calanoid copepod nauplii. The clam has few predators in the SanFrancisco Estuary and this allows it to grow to high densities (on the order of tens ofthousands/m2). Because of its high clearance rates, it is capable of clearing the entire watercolumn of portions of the Estuary in a few days, leading to drastically depleted planktonpopulations (Werner and Hollibaugh 1993). This is thought to be the main cause of a decline inecosystem productivity after the invasion of the clams in the mid-1980’s (Carlton et al. 1990,Nichols et al. 1990, Kimmerer 1996).

This decline in productivity is essentially due to the redirection of the pelagic networkto a benthic chain by this one species (Kimmerer 1996). Because the Amur River clam feeds onprimary producers, consumers and predators, it impacts multiple trophic levels. Consequently,nearly all plankton exhibit signs of apparent competition, in that production at one trophiclevel impacts all others by increasing clam abundance. This results in a negative feedback loop:"C. amurensis" limits plankton biomass, which in turn limits "C. amurensis". However, inputs fromoutside the system due to tidal advection or upstream sources may increase "C. amurensis"biomass, further driving plankton limitation. This feedback loop is further amplified becausethe clam may persist for more than one or two years, which puts added pressure on planktonpopulations during cycles of low productivity.

The redirection of carbon by C. amurensis to the benthos has created a limited chain,leaving the pelagic web depauperate. Detrital production from clam excretion and death mayfuel bacterial production, which may be circulated into the detrital food web, or microbial loop.While the recycled nutrients may support some phytoplankton growth, it ultimately feeds backto increased C. amurensis populations. The recent invasion success of Limnoithona tetraspina maybe understood in terms of this phenomenon. It feeds on ciliates and microflagellates which aretoo small to be grazed by the clam, thereby avoiding competition. Additionally, "L. tetraspina"appears impervious to predation by the clam or (almost) anything else. The rise of the microbialfood web and the invasion of "L. tetraspina" capitalize are the result of an untapped alternativepath for energy flow in the food web, facilitated by C. amurensis. Subsequent patterns ofinvasion may reflect a similar pattern.

Future Invasions

The modern food web is derived from a series of invasions and trophic substitutions.This process is expected to continue, as new organisms arrive through accidental or intentionalintroductions. What is less clear is the extent to which previous introductions pave the way forfuture invasions. This may occur in one of three ways.
*An early invader may provide a resource that is unutilized in the new system until a new predator is introduced ("L. tetraspina" and the microbial loop, as described above).
*Early invaders may facilitate new ones by altering habitat and making it suitable for subsequent invasions (jelly polyps using Amur River clam shells for substrate).
*Apparent competition between old and new residents may increase the possibilities for invasion and settlement of new organisms that can capitalize on unexploited resources (the subsidization of the Amur River clam by upstream populations of the introduced copepod P. forbesi, creating pressure on native copepods).


The LSZ food web of the San Francisco Estuary operates in two parallel andasymmetrical directions. The bulk of carbon is assimilated into the benthic and microbial loops,which represent energetic dead ends. A smaller fraction is delivered to higher pelagic trophiclevels which may support copepods, fish, birds and fisheries. This redirection of the food webinto these two narrow loops may be responsible for the decline in macroinvertebrates and fishesin the Estuary, which operate outside of these chains. Restoration of the Estuary to a higherdegree of function relies upon the probability of delivering increased benefits to the pelagic webwithout subsidizing the benthic.


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