Ecology of the San Francisco Estuary
The
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".[1] 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
Until the 20th century, the LSZ of the estuary was fringed by
The
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.[5] 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.[6] 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.[7]
Hydrodynamics
The LSZ centers around 2 psu (
River inflow is largely controlled by upstream reservoir releases. A significant fraction of this inflow is exported out of the Delta by the federal
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)
Mixing is important at the landward edge of gravitational circulation, often around X2, where the water column becomes less stratified.[13] 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.[14] 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,[1] slowing the advection of primary and secondary production out of the system.
Pelagic zone
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.[8] Abiotic factors tend to drive production in the estuarine environment, and are mediated by biotic factors.
Biotic factors include nutrient uptake and
Food web
It is difficult to characterize the historic
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
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.[17] 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.[18]
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.[19] 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.
Producers
Primary production and nutrient uptake
Primary production by phytoplankton fixes energy and key nutrients into a biologically available form (i.e., food), via photosynthesis. Phytoplankton production is largely structured by physical parameters: nutrient availability, sunlight, turbidity, and temperature.
The San Francisco Estuary has a numerous sources of nutrients that can be used for primary production, derived largely from waste water treatment facilities, agricultural and urban drainage, and the ocean.
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.[1] The latter is typical of the main channels of the estuary during periods of high flow, when surface waters tend to flush particles and plankton downstream.
Photosynthetic production
The main source of
Phytoplankton accumulation is primarily the result of
Harmful algal blooms (HAB's) of dinoflagellates or
Detrital production
Enormous quantities of sediment and detritus flux through the LSZ. Much of this is organic debris in the form of dissolved and particulate organic matter (DOM and POM, respectively). In addition to upstream sources, organic matter may accumulate from local organism mortality and waste production.[33][34]
Bacteria are the chief agents of transformation of DOM and POM into bioavailable carbon through the
The high abundance of the
Secondary production
Secondary production refers to organisms that feed on primary production and transfer energy to higher
Today, the main source of secondary production derives from
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.[45]
Yet another invasive copepod, the very small cyclopoid Limnoithona tetraspina, appeared in the Low Salinity Zone in the 1990s. 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.[37] 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.
Consumers
Primary consumers
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 fresh water. This wide distribution helps the population maintain an upstream refuge from predation, unlike other species with narrower salinity tolerances.[44]
Limnoithona tetraspina has become the numerically dominant cyclopoid copepod since its introduction 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 the system by tides and currents, or die and fall down to the benthos, where they may be available to the microbial loop, or to detritivores.[46]
-
Shield limpet (Lottia pelta) found in central and south SF bay[47]
-
Black turban snail (Tegula funebralis) found in intertidal zones[47]
-
Hermissenda crassicornis found on Docks, rocks, and pilings.[47]
-
Nuttall's cockle (Clinocardium nuttallii) in intertidal zones
Predatory copepods
A number of predatory copepods exist throughout the Delta, about which relatively little is known. Sinocalanus doerri, Acartiella sinensis, and Tortanus dextrilobatus all appear to be morphologically capable of predation upon other copepods. Each was introduced to the estuary, probably through
Macroinvertebrates
While capable of
Fish
Because fish are a taxonomically and morphologically diverse group, species vary in their trophic ecologies. In general, fish can be divided into four broad feeding categories: filter feeders, planktivores, piscivores and benthic feeders.
Filter feeders strain the water column indiscriminately for small prey, typically phyto- and zooplankton. This category of fishes includes
-
Jacksmelt (Atherinopsis californiensis)[47]
-
Delta smelt (Hypomesus transpacificus)[47]
-
Pacific herring (Clupea pallasii), normally off shore but enter the bay to spawn from November through March.[47]
-
northern anchovy (Engraulis mordax) found in San Pablo and Suisun bay[47]
-
Bay pipefish (Syngnathus leptorhynchus) found in intertidal areas commonly among eelgrass [47]
Planktivores selectively prey upon individual zooplankton, such as copepods, mysids and
-
Shiner surfperch(Cymatogaster aggregata) found in subtidal zones[47]
-
tule perch (Hysterocarpus traskii)
-
Walleye surfperch (Hyperprosopon argenteum)[47]
-
brown rockfish (Sebastes auriculatus)
-
Humming toadfish (Porichthys notatus) found in subtidal zones[47]
The main piscivore of the LSZ is the
Benthic, or bottom-dwelling, fishes include
The sole
-
Leopard shark (Triakis semifasciata)[47]
-
broadnose sevengill shark (Notorynchus cepedianus)[47]
-
spiny dogfish(Squalus acanthias) found in the subtidal zone[47]
-
North American green sturgeon (Acipenser medirostris)
-
White sturgeon (Acipenser transmontanus)
Birds
The San Francisco Estuary is a major stop on the
In January 2015, scientists were working to identify a gray, thick, sticky, odorless substance coating on birds along San Francisco Bay shorelines. Hundreds of birds have died, and hundreds more have been coated with the substance. Scientists are concerned about other wildlife that may be at risk from the substance.[57]
-
Brown Pelican (Pelecanus occidentalis californicus) at San Francisco Bay
-
Ridgway's rail (Rallus obsoletus) in Oakland
-
double-crested cormorant
-
Ring-billed gull (Larus delawarensis) in Oakland
Mammals
Before 1825, Spanish, French, English, Russians and Americans were drawn to the Bay Area to harvest prodigious quantities of
Although 20th-century naturalists were skeptical that beaver were historically extant in coastal streams or the Bay itself,[62] earlier records show that the California golden beaver (Castor canadensis ssp. subauratus) was one of the most valued of the animals taken, and apparently was found in great abundance.[58] Thomas McKay reported that in one year the Hudson's Bay Company took 4,000 beaver skins on the shores of San Francisco Bay. Recently, beaver have recolonized the brackish Napa Sonoma Marsh in north San Pablo Bay and its Sonoma Creek and Napa River tributaries. Beaver are also recolonizing the South Bay, having been translocated to upper Los Gatos Creek at Lexington Reservoir in the 1980s. They subsequently migrated downstream to the Guadalupe River, and upon reaching saltwater, have used it to recolonize east to Coyote Creek and northwest to Matadero Creek in Palo Alto.[63]
For the first time in 65 years,
The common bottlenose dolphin (Tursiops truncatus) has been extending its current range northwards from the Southern California Bight. The first coastal bottlenose dolphin in the San Francisco Bay Area in recent times was spotted in 1983 off the San Mateo County coast in 1983. In 2001 bottlenose dolphins were first spotted east of the Golden Gate Bridge and confirmed by photographic evidence in 2007. Zooarcheological remains of bottlenose dolphins indicated that bottlenose dolphins inhabited San Francisco Bay in prehistoric times until at least 700 years before present, and dolphin skulls dredged from the Bay suggest occasional visitors in historic times.[69]
-
Sea Lions (Zalophus californianus) at Pier 39
-
Pacific Harbor seal (Phoca vitulina richardii)
-
River otter sunning on rocks in the Richmond Marina
-
Humphrey the Whale a Humpback whale (Megaptera novaeangliae) that entered the bay
-
Harbour porpoise (Phocoena phocoena)
-
Salt marsh harvest mouse(Reithrodontomys raviventris), is an endangered species endemic to the wetlands of the San Francisco Bay with a high salt tolerance.
Jellyfish
Their impact on the plankton is unknown, but research is underway to quantify it. In sufficient density, jellies may have a complementary role to C. amurensis in suppressing zooplankton, by inhabiting areas of low salinity outside the range of the clams, where planktonic species have had a predation-free refuge.
-
Corynactis californica found on docks and pilings in the intertidal zones
Benthic consumers
The
-
Starry flounder (Platichthys stellatus)
-
Speckled Sanddab (Citharichthys stigmaeus) found in subtidal zones with sandy bottoms[47]
-
Bat Ray (Beringraja binoculata) in the Aquarium of the Bay both found in subtidal areas of the bay[47]
This decline in productivity is essentially due to the redirection of the pelagic network to a benthic chain by this one species.
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 may fuel 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 back to increased C. amurensis populations. The recent invasion success of Limnoithona tetraspina may be understood in terms of this phenomenon. It feeds on
-
Dungeness Crab (Metacarcinus magister)[47]
-
Red rock crab (Cancer productus)
-
Graceful Crab (Metacarcinus gracilis)
-
California rock crab(Romaleon antennarium)
-
Yellow Shore crab (Hemigrapsus oregonensis) found in shallow intertidal areas[47]
-
American spider crab (Pyromaia tuberculata) found under rocks and near dock pilings[47]
-
Hairy hermit crab(Pagurus hirsutiusculus)
-
Ochre Starfish (Pisaster ochraceus) found in intertidal zone[47]
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,
Species have also been introduced via attachment to sporting boats which are trailered between regions.
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 intentional introductions. What is less clear is the extent to which previous introductions pave the way for future 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).
Summary
The LSZ food web of the San Francisco Estuary operates in two parallel and asymmetrical 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 trophic levels which may support copepods, fish, birds and fisheries. This redirection of the food web into these two narrow loops may be responsible for the decline in macroinvertebrates and fishes in the estuary, which operate outside of these chains. Restoration of the estuary to a higher degree of function relies upon the probability of delivering increased benefits to the pelagic web without subsidizing the benthic.
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
See also
- List of watercourses in the San Francisco Bay Area
- Hydrography of the San Francisco Bay Area
- The Watershed Project
- San Francisco Estuary and Watershed Science
Notes
- ^ a b c d e Kimmerer 2004
- ^ a b Conomos 1979
- ^ Vayssieres 2006
- ^ Jassby 2000
- ^ Deverel 1998
- ^ Philip 2007
- ^ Lund 2007
- ^ a b Kimmerer 2002
- ^ Gunther, Andrew (2011). "The State of the San Francisco Bay 2011, San Francisco Estuary Partnership" (PDF). The State of the San Francisco Bay 2011. Retrieved 6 October 2017.
- ^ Moyle 1992
- ^ a b Bennett 2006
- ^ Monismith 1996
- ^ Burau 1998
- ^ Schoellhamer 2001
- ^ Orsi 1986
- ^ a b c d e f Kimmerer 1996
- ^ a b Kimmerer 2006
- ^ Davis, Jay (September 2006). "The Pulse of the Estuary 2006" (PDF). sfei.org. San Francisco Estuary Institute. Retrieved 2 November 2016.
- ^ Taugher 2005
- ^ Smith 2002
- ^ a b Dugdale 2003
- ^ Jassby 2002
- ^ Nichols 1986
- ^ Kimmerer 1994
- ^ a b Jassby and Cloern 2000
- ^ Anderson et al. 2002
- ^ a b Jassby et al. 2002
- ^ Dugdale et al. 2003
- ^ Cloern 1987
- ^ Cole and Cloern 1987
- ^ Ball and Arthur 1979
- ^ Lehman and Waller 2003
- ^ Murrell et al. 1999
- ^ Murrell and Hollibaugh 2000
- ^ Jassby et al. 1993
- ^ Hollibaugh and Wong 1996
- ^ a b Bouley 2006
- ^ Rollwagen-Bollens and Penry 2003
- ^ Rollwagen-Bollens et al. 2006
- ^ Modlin 1997
- ^ Kimmerer 1998
- ^ Lee 1999
- ^ Orsi 1991
- ^ a b Durand2006
- ^ Orsi 1999
- ^ Bouley and Kimmerer 2006
- ^ OCLC 86174077.
- ^ Orsi and Ohtsuka 1999
- ^ Orsi and Knutson 1979
- ^ Modlin and Orsi 1997
- ^ Sitts and Knight 1979
- ^ a b Radovich 1963
- ^ Peterson 1997
- ^ a b Nichols et al. 1986
- ^ Poulton et al. 2002
- ^ Richman and Lovvorn 2004
- ^ Scientists race to identify goop on birds along San Francisco Bay shorelines(January 2015), The Christian Science Monitor
- ^ a b Skinner, John E. (1962). An Historical Review of the Fish and Wildlife Resources of the San Francisco Bay Area (The Mammalian Resources). California Department of Fish and Game, Water Projects Branch Report no. 1. Sacramento, California: California Department of Fish and Game. Archived from the original on 2011-07-26.
- ^ Suzanne Stewart and Adrian Praetzellis (November 2003). Archeological Research Issues for the Point Reyes National Seashore - Golden Gate National Recreation Area (PDF) (Report). Anthropological Studies Center, Sonoma State University. p. 335. Retrieved Jan 10, 2010.
- ISBN 0-559-89342-6.
- ISBN 0-942087-10-0.
- ^ Tappe, Donald T. (1942). "The Status of Beavers in California". Game Bulletin No. 3. California Department of Fish & Game.
- ^ Sue Dremann (November 4, 2022). "The beaver is back: Pair of the semiaquatic rodents spotted in Palo Alto". Palo Alto Weekly. Retrieved January 18, 2023.
- ^ "Get Outside!". San Francisco Chronicle. April 1966. Retrieved 2011-03-06.
- ^ "Blue Oak Ranch Reserve". University of California. Archived from the original on 2011-05-12. Retrieved 2011-03-06.
- ^ David Perlman (November 8, 2010). "Porpoises return to SF Bay – scientists study why". San Francisco Chronicle. Retrieved July 25, 2011.
- ^ "Harbor Porpoise Project". Golden Gate Cetacean Research. Retrieved July 25, 2011.
- ^ Harbor Porpoise (Phocoena phocoena): San Francisco-Russian River Stock (PDF) (Report). National Marine Fisheries Service. October 15, 2009. Retrieved July 25, 2011.
- S2CID 255918023.
- ^ Werner and Hollibaugh 1993
- ^ Carlton et al. 1990
- ^ Nichols et al. 1990
- ^ a b c Carlton 1996
- ^ Cole 1992
- ^ Dey 2007
- ^ Epstein 2006
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