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 A bay is a recessed, coastal body of water that directly connects to a larger main body of water, such as an ocean, a lake, or another bay. A large bay is usually called a gulf, sea, sound, or bight. A cove is a small, circular bay with a na ...

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 San Pablo Bay is a tidal estuary that forms the northern extension of San Francisco Bay in the East Bay and North Bay regions of the San Francisco Bay Area in northern California. Most of the Bay is shallow; however, there is a deep wate ...

, immediately north of the Central Bay; the

Carquinez Strait The Carquinez Strait (; Spanish: ''Estrecho de Carquinez'') is a narrow tidal strait in Northern California. It is part of the tidal estuary of the Sacramento and the San Joaquin rivers as they drain into the San Francisco Bay. The strait is lo ...

, a narrow, deep channel leading to

Suisun Bay Suisun Bay ( ; Wintun for "where the west wind blows") is a shallow tidal estuary (a northeastern extension of the San Francisco Bay) in Northern California. It lies at the confluence of the Sacramento River and San Joaquin River, forming the ent ...

; and the

Delta Delta commonly refers to: * Delta (letter) (Δ or δ), a letter of the Greek alphabet * River delta, at a river mouth * D ( NATO phonetic alphabet: "Delta") * Delta Air Lines, US * Delta variant of SARS-CoV-2 that causes COVID-19 Delta may also ...

of the

Sacramento ) , image_map = Sacramento County California Incorporated and Unincorporated areas Sacramento Highlighted.svg , mapsize = 250x200px , map_caption = Location within Sacramento ...

and San Joaquin rivers. Until the 20th century, the LSZ of the estuary was fringed by

tule ''Schoenoplectus acutus'' (syn. ''Scirpus acutus, Schoenoplectus lacustris, Scirpus lacustris'' subsp. ''acutus''), called tule , common tule, hardstem tule, tule rush, hardstem bulrush, or viscid bulrush, is a giant species of sedge in the p ...

-dominated freshwater

wetlands A wetland is a distinct ecosystem that is flooded or saturated by water, either permanently (for years or decades) or seasonally (for weeks or months). Flooding results in oxygen-free ( anoxic) processes prevailing, especially in the soils. The ...

. 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 Pelagic fish live in the pelagic zone of ocean or lake waters—being neither close to the bottom nor near the shore—in contrast with demersal fish that do live on or near the bottom, and reef fish that are associated with coral reef ...

species, by increasing vulnerability to predation. The

intertidal The intertidal zone, also known as the foreshore, is the area above water level at low tide and underwater at high tide (in other words, the area within the tidal range). This area can include several types of habitats with various species of ...

and

benthic The benthic zone is the ecological region at the lowest level of a body of water such as an ocean, lake, or stream, including the sediment surface and some sub-surface layers. The name comes from ancient Greek, βένθος (bénthos), meaning "t ...

estuary is presently dominated by mudflats that are largely the result of sedimentation derived from gold mining in the

Sierra Nevada The Sierra Nevada () is a mountain range in the Western United States, between the Central Valley of California and the Great Basin. The vast majority of the range lies in the state of California, although the Carson Range spur lies primarily ...

in the late 19th century. The trend toward high sediment loads was reversed in the 1950s with the advent of the

Central Valley Project The Central Valley Project (CVP) is a federal power and water management project in the U.S. state of California under the supervision of the United States Bureau of Reclamation (USBR). It was devised in 1933 in order to provide irrigation and m ...

, locking up most sediment behind dams, and resulting in an annual net loss of sediments from the estuary. 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. 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 Intensive agriculture, also known as intensive farming (as opposed to extensive farming), conventional, or industrial agriculture, is a type of agriculture, both of crop plants and of animals, with higher levels of input and output per unit of ag ...

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. 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. 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.

Hydrodynamics

The LSZ centers around 2 psu (

practical salinity unit Salinity () is the saltiness or amount of salt dissolved in a body of water, called saline water (see also soil salinity). It is usually measured in g/L or g/kg (grams of salt per liter/kilogram of water; the latter is dimensionless and equal ...

s, 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

and the

State Water Project The California State Water Project, commonly known as the SWP, is a state water management project in the U.S. state of California under the supervision of the California Department of Water Resources. The SWP is one of the largest public wat ...

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 The Golden Gate is a strait on the west coast of North America that connects San Francisco Bay to the Pacific Ocean. It is defined by the headlands of the San Francisco Peninsula and the Marin Peninsula, and, since 1937, has been spanned by th ...

), 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 Zooplankton are the animal component of the planktonic community ("zoo" comes from the Greek word for ''animal''). Plankton are aquatic organisms that are unable to swim effectively against currents, and consequently drift or are carried along by ...

, 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 The delta smelt (''Hypomesus transpacificus'') is an endangered slender-bodied smelt, about long, in the family Osmeridae. Non-Indigenous to the upper Sacramento-San Joaquin Estuary of California, it mainly inhabits the freshwater-saltwater ...

, a small endemic fish; unexceptional except that it has been described as being tremendously abundant in historical accounts. 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. 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. 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. 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 Physical geography (also known as physiography) is one of the three main branches of geography. Physical geography is the branch of natural science which deals with the processes and patterns in the natural environment such as the atmosphere, ...

and hydrology of the estuary, including nutrient inputs, sediment load, turbidity, environmental stochasticity,

climate Climate is the long-term weather pattern in an area, typically averaged over 30 years. More rigorously, it is the mean and variability of meteorological variables over a time spanning from months to millions of years. Some of the meteorologi ...

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 In ecology, the term productivity refers to the rate of generation of biomass in an ecosystem, usually expressed in units of mass per volume (unit surface) per unit of time, such as grams per square metre per day (g m−2 d−1). The unit of mas ...

, food web and

trophic dynamics A food web is the natural interconnection of food chains and a graphical representation of what-eats-what in an ecological community. Another name for food web is consumer-resource system. Ecologists can broadly lump all life forms into one ...

, energetic transfer, advection and dispersal in and out of the system, survival and

mortality Mortality is the state of being mortal, or susceptible to death; the opposite of immortality. Mortality may also refer to: * Fish mortality, a parameter used in fisheries population dynamics to account for the loss of fish in a fish stock throug ...

, predation, and

competition Competition is a rivalry where two or more parties strive for a common goal which cannot be shared: where one's gain is the other's loss (an example of which is a zero-sum game). Competition can arise between entities such as organisms, indivi ...

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 Copepods (; meaning "oar-feet") are a group of small crustaceans found in nearly every freshwater and saltwater habitat. Some species are planktonic (inhabiting sea waters), some are benthic (living on the ocean floor), a number of species have p ...

Eurytemora affinis ''Eurytemora'' is a genus of copepods in the family Temoridae. The World Register of Marine Species The World Register of Marine Species (WoRMS) is a taxonomic database that aims to provide an authoritative and comprehensive list of names of ...

'', and large macrozooplankton typified by San Francisco bay shrimp and mysid shrimps. These provided nutrition and energy to native filter feeders such as the northern

anchovy An anchovy is a small, common forage fish of the family Engraulidae. Most species are found in marine waters, but several will enter brackish water, and some in South America are restricted to fresh water. More than 140 species are placed in ...

(''Engraulis mordax''), and planktivores such as

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 Benthos (), also known as benthon, is the community of organisms that live on, in, or near the bottom of a sea, river, lake, or stream, also known as the benthic zone.rotifers and

ciliates The ciliates are a group of alveolates characterized by the presence of hair-like organelles called cilia, which are identical in structure to eukaryotic flagella, but are in general shorter and present in much larger numbers, with a different ...

. 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

, longfin smelt, striped bass, and threadfin shad have been declared "species of interest" because of a stepwise decline in abundance beginning in 2001. 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 In ecology, primary production is the synthesis of organic compounds from atmospheric or aqueous carbon dioxide. It principally occurs through the process of photosynthesis, which uses light as its source of energy, but it also occurs through ...

by phytoplankton fixes energy and key nutrients into a biologically available form (i.e., food), via

photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in ...

. 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.Dugdale 2003 In spite of this, the estuary is unique in that it tends to have a relatively depressed rate of primary production. This is probably due to two factors: large inputs of nitrogen in the form of

ammonium The ammonium cation is a positively-charged polyatomic ion with the chemical formula or . It is formed by the protonation of ammonia (). Ammonium is also a general name for positively charged or protonated substituted amines and quaterna ...

, which suppresses nitrate uptake by phytoplankton, which prefer the metabolically cheaper NH₄+, and high turbidity, which limits light required for photosynthesis to the top few centimeters of the water column. This turbidity is a legacy of hydraulic gold mining in the

in the 1850s. 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. 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.

Herbivory A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage or marine algae, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthpart ...

also removes phytoplankton from the water column. While the pelagic food web 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-1980s, and have not rebounded.

Photosynthetic production

The main source of photosynthetically derived energy is

phytoplankton Phytoplankton () are the autotrophic (self-feeding) components of the plankton community and a key part of ocean and freshwater ecosystems. The name comes from the Greek words (), meaning 'plant', and (), meaning 'wanderer' or 'drifter'. ...

. Generally speaking,

diatoms A diatom (Neo-Latin ''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twain". is any member of a large group comprising sev ...

and microflagellates produce most of the bioavailable carbon in the estuary.Jassby and Cloern 2000 Other types, notably the

dinoflagellates The dinoflagellates ( Greek δῖνος ''dinos'' "whirling" and Latin ''flagellum'' "whip, scourge") are a monophyletic group of single-celled eukaryotes constituting the phylum Dinoflagellata and are usually considered algae. Dinoflagellates ...

, may produce

harmful algal blooms A harmful algal bloom (HAB) (or excessive algae growth) is an algal bloom that causes negative impacts to other organisms by production of natural algae-produced toxins, mechanical damage to other organisms, or by other means. HABs are sometimes ...

, or

red tide A harmful algal bloom (HAB) (or excessive algae growth) is an algal bloom that causes negative impacts to other organisms by production of natural algae-produced toxins, mechanical damage to other organisms, or by other means. HABs are sometimes ...

s, that are less readily available for assimilation into the foodweb.

from phytoplankton is a function of two different factors: growth rates and accumulation (Fig. 1). Although the LSZ is a sink for high concentrations of

nutrients A nutrient is a substance used by an organism to survive, grow, and reproduce. The requirement for dietary nutrient intake applies to animals, plants, fungi, and protists. Nutrients can be incorporated into cells for metabolic purposes or excr ...

from urban and agricultural sources, phytoplankton production rates are quite low.Jassby et al. 2002

Nitrate Nitrate is a polyatomic ion with the chemical formula . Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are soluble in water. An example of an insolu ...

is optimally used by phytoplankton for growth, but

(largely derived from 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. Another suppressive factor on growth rate is the high turbidity of the estuary, which limits the ability of

photosynthetically active radiation Photosynthetically active radiation (PAR) designates the spectral range (wave band) of solar radiation from 400 to 700 nanometers that photosynthetic organisms are able to use in the process of photosynthesis. This spectral region corresponds more o ...

(PAR) to penetrate beyond the top few centimeters of the water column. This limits phytoplankton photosynthesis to a relatively shallow

photic zone The photic zone, euphotic zone, epipelagic zone, or sunlight zone is the uppermost layer of a body of water that receives sunlight, allowing phytoplankton to perform photosynthesis. It undergoes a series of physical, chemical, and biological pro ...

. Thus, when the

water column A water column is a conceptual column of water from the surface of a sea, river or lake to the bottom sediment.Munson, B.H., Axler, R., Hagley C., Host G., Merrick G., Richards C. (2004).Glossary. ''Water on the Web''. University of Minnesota-D ...

is stratified, turbidity is high, and ammonium is present, the growth rate of phytoplankton is typically suppressed. Phytoplankton accumulation is primarily the result of

residence time The residence time of a fluid parcel is the total time that the parcel has spent inside a control volume (e.g.: a chemical reactor, a lake, a human body). The residence time of a set of parcels is quantified in terms of the frequency distribu ...

. The north Delta and

have relatively low residence times due to the high volume of water moving through the region for downstream flow and for

export An export in international trade is a good produced in one country that is sold into another country or a service provided in one country for a national or resident of another country. The seller of such goods or the service provider is a ...

to southern California. Since water moves more rapidly through this part of the system, the rate of accumulation decreases as productivity is advected out of the system. In contrast, parts of the southern Delta have a higher residence time due to the low volume of water moving through the system; in fact the water on occasion runs backwards, due to the lack of inflow from the San Joaquin River, and export pumping. During summer, phytoplankton density may be an order of magnitude higher here than in other parts of the estuary. Harmful algal blooms (HAB's) of dinoflagellates or

cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...

produce toxic metabolic byproducts that render them noxious to many organisms. Fostered by a combination of high nutrient concentrations and temperatures, HAB's have a doubly negative effect on the food web by competitively excluding diatoms and microflagellates, further reducing bioavailable primary production. While certain

invertebrates Invertebrates are a paraphyletic group of animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This is a grouping including all animals apart from the chordat ...

such as

bivalves Bivalvia (), in previous centuries referred to as the Lamellibranchiata and Pelecypoda, is a class of marine and freshwater molluscs that have laterally compressed bodies enclosed by a shell consisting of two hinged parts. As a group, bival ...

may not be directly affected, they may propagate toxins up the food chain, sickening or killing

predator Predation is a biological interaction where one organism, the predator, kills and eats another organism, its prey. It is one of a family of common feeding behaviours that includes parasitism and micropredation (which usually do not kill t ...

s. It is not well understood how

copepods Copepods (; meaning "oar-feet") are a group of small crustaceans found in nearly every freshwater and saltwater habitat. Some species are planktonic (inhabiting sea waters), some are benthic (living on the ocean floor), a number of species have p ...

are affected. The invasive

algae Algae (; singular alga ) is an informal term for a large and diverse group of photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular micr ...

''Microcystis aeruginosa'' is now common in the Delta during summer months and may reduce copepod productivity (in addition to being potentially

carcinogenic A carcinogen is any substance, radionuclide, or radiation that promotes carcinogenesis (the formation of cancer). This may be due to the ability to damage the genome or to the disruption of cellular metabolic processes. Several radioactive sub ...

for humans).

Detrital production

Enormous quantities of sediment and

detritus In biology, detritus () is dead particulate organic material, as distinguished from dissolved organic material. Detritus typically includes the bodies or fragments of bodies of dead organisms, and fecal material. Detritus typically hosts comm ...

flux through the LSZ. Much of this is organic debris in the form of dissolved and particulate

organic matter Organic matter, organic material, or natural organic matter refers to the large source of carbon-based compounds found within natural and engineered, terrestrial, and aquatic environments. It is matter composed of organic compounds that have c ...

(DOM and POM, respectively). In addition to upstream sources, organic matter may accumulate from local organism mortality and waste production.

Detritivores Detritivores (also known as detrivores, detritophages, detritus feeders, or detritus eaters) are heterotrophs that obtain nutrients by consuming detritus (decomposing plant and animal parts as well as feces). There are many kinds of invertebrates, ...

capitalize upon this energy source, creating an alternate and parallel food web of potentially large importance. This is because

carbon fixation Biological carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide) is converted to organic compounds by living organisms. The compounds are then used to store energy and as ...

into the detrital food web is not limited by stratification, turbidity or day length, all of which limit photosynthesis. Detrital production occurs continuously, limited only by inputs and advection out of the Delta system. Bacteria are the chief agents of transformation of DOM and POM into bioavailable carbon through the microbial loop. This mechanism is particularly important in nutrient limited marine systems, where

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

release nutrients from sinking detritus, allowing it to be recycled back to the photic zone. Little work has been applied to the function of the microbial loop in the San Francisco Estuary, but it may be that the role of bacteria is not critical for recycling nutrients in a

eutrophic Eutrophication is the process by which an entire body of water, or parts of it, becomes progressively enriched with minerals and nutrients, particularly nitrogen and phosphorus. It has also been defined as "nutrient-induced increase in phytoplan ...

system. Rather, they may provide an alternative food chain through direct grazing by

flagellates A flagellate is a cell or organism with one or more whip-like appendages called flagella. The word ''flagellate'' also describes a particular construction (or level of organization) characteristic of many prokaryotes and eukaryotes and their ...

, rotifers and

. The high abundance of the cyclopoid copepod ''Limnoithona tetraspina'' may be due to its reliance on ciliates rather than phytoplankton as a primary food source.Bouley 2006 The major species of

calanoid Calanoida is an order of copepods, a group of arthropods commonly found as zooplankton. The order includes around 46 families with about 1800 species of both marine and freshwater copepods between them. Description Calanoids can be distinguis ...

copepods may also use ciliates as a supplementary or even primary food source, but to what degree is unknown.

Secondary production

Secondary production refers to organisms that feed on primary production and transfer energy to higher

trophic level The trophic level of an organism is the position it occupies in a food web. A food chain is a succession of organisms that eat other organisms and may, in turn, be eaten themselves. The trophic level of an organism is the number of steps it ...

s of the estuarine foodweb. Historically, secondary production in the San Francisco Estuary was dominated by

mysid shrimp Mysida is an order of small, shrimp-like crustaceans in the malacostracan superorder Peracarida. Their common name opossum shrimps stems from the presence of a brood pouch or "marsupium" in females. The fact that the larvae are reared in this ...

production. However, the native mysid ''Neomysis mercedis'' has been largely replaced by the introduced ''Acanthomysis bowmani'', which persists at lower densities. The introduced

amphipod Amphipoda is an order of malacostracan crustaceans with no carapace and generally with laterally compressed bodies. Amphipods range in size from and are mostly detritivores or scavengers. There are more than 9,900 amphipod species so far descri ...

''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

s. The naturalized native

copepod ''

'' is believed to have been introduced near the end of 19th century. It dominated the zooplankton of the low salinity zone until the 1980s when it was largely replaced by another introduced calanoid copepod, ''Pseudodiaptomus forbesi''. 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.Durand2006 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. 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. 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

Primary consumers A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage or marine algae, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthpar ...

rely upon primary production as a main food source. The most important 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 under high predation pressure from the recently introduced Amur River clam (''Corbula amurensis''). Because of this, and because copepods rely upon both photosynthetic and detrital food sources, copepods in the LSZ have limited feedback on primary production, unlike marine 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 fresh water. This wide distribution helps the population maintain an upstream refuge from predation, unlike other species with narrower salinity tolerances. ''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. File:Lottia pelta (23542532150).jpg, Shield limpet (''Lottia pelta'') found in central and south SF bay File:Tegula funebralis.jpg, Black turban snail (''Tegula funebralis'') found in intertidal zones File:Hermissenda crassicornis.jpg, ''Hermissenda crassicornis'' found on Docks, rocks, and pilings. File:Polinices Radula Hole (2132260797).jpg, 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

ballast water Ballast is used in ships to provide moment to resist the lateral forces on the hull. Insufficiently ballasted boats tend to tip or heel excessively in high winds. Too much heel may result in the vessel capsizing. If a sailing vessel needs to voy ...

exchange since the 1980s. Generally, they are not in sufficient abundance to negatively impact copepod consumers; however, periodic blooms of ''S. doerri'' and ''A. sinensis'' occur which have not been well studied.

Macroinvertebrates

While capable of filter-feeding, mysids (tiny shrimp-like creatures) are largely carnivorous, feeding on copepod adults. They provided an energetic conduit between plankton and planktivorous fishes, including juvenile fishes,

sturgeon Sturgeon is the common name for the 27 species of fish belonging to the family Acipenseridae. The earliest sturgeon fossils date to the Late Cretaceous, and are descended from other, earlier acipenseriform fish, which date back to the Early ...

Chinook salmon The Chinook salmon (''Oncorhynchus tshawytscha'') is the largest and most valuable species of Pacific salmon in North America, as well as the largest in the genus '' Oncorhynchus''. Its common name is derived from the Chinookan peoples. Other ...

, and

American shad The American shad (''Alosa sapidissima'') is a species of anadromous clupeid fish naturally distributed on the North American coast of the North Atlantic, from Newfoundland to Florida, and as an introduced species on the North Pacific coast. Th ...

. Mysids were once abundant until the native ''Neomysis mercedis'' was replaced in the mid-1980s by the invasive ''Acanthomysis bowmani'', which is smaller and less abundant. Mysid decline has been linked to the subsequent decline in a number of fish species in the estuary in the 1980s and '90s.

Shrimp Shrimp are crustaceans (a form of shellfish) with elongated bodies and a primarily swimming mode of locomotion – most commonly Caridea and Dendrobranchiata of the decapod order, although some crustaceans outside of this order are ref ...

are generalist carnivores who prey largely on mysids and

amphipods Amphipoda is an order of malacostracan crustaceans with no carapace and generally with laterally compressed bodies. Amphipods range in size from and are mostly detritivores or scavengers. There are more than 9,900 amphipod species so far describ ...

. ''Crangon franciscorum'' represents one of two remaining commercial fisheries in the estuary. While no longer used for "San Francisco Bay shrimp cocktails", they are harvested for bait. Other predators include striped bass and

adults and smolts.

Fish

Because fish are a

taxonomically In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given ...

and morphologically diverse group, species vary in their

trophic Trophic, from Ancient Greek τροφικός (''trophikos'') "pertaining to food or nourishment", may refer to: * Trophic cascade * Trophic coherence * Trophic egg * Trophic function * Trophic hormone * Trophic level index * Trophic level ...

ecologies. In general, fish can be divided into four broad feeding categories:

filter feeder Filter feeders are a sub-group of suspension feeding animals that feed by straining suspended matter and food particles from water, typically by passing the water over a specialized filtering structure. Some animals that use this method of feedin ...

s, planktivores, piscivores and

feeders. Filter feeders strain the water column indiscriminately for small prey, typically phyto- and zooplankton. This category of fishes includes threadfin shad (''Dorosoma petenense''),

(''Alosa sapidissima''),

inland silverside The inland silverside (''Menidia beryllina'') is a neotropical silverside native to eastern North America, and introduced into California. It is a fish of estuaries and freshwater environments. Inland silversides are quite elongate even for silv ...

s (''Menidia beryllina''), and

anchovies An anchovy is a small, common forage fish of the family Engraulidae. Most species are found in marine waters, but several will enter brackish water, and some in South America are restricted to fresh water. More than 140 species are placed in 1 ...

(''Engraulis mordax''). Some evidence suggests that some of these species are food-limited due to the depressed levels of plankton after the introduction of the Amur River clam. Anchovies have left the LSZ in favor of more productive regions of the estuary in the San Pablo and Central Bays. File:Jack Silverside.jpg,

Jacksmelt ''Atherinopsis californiensis'', the jack silverside or jacksmelt,Leo PinkasCalifornia Marine Fish Landings For 1972 and Designated Common Names of Certain Marine Organisms of California fish bulletin 161, Marine Resources Region, 1974 is a speci ...

(''Atherinopsis californiensis'') File:Hypomesus transpacificus.jpg, Delta smelt (''Hypomesus transpacificus'') File:Clupea pallasii by OpenCage.jpg, Pacific herring (''Clupea pallasii''), normally off shore but enter the bay to spawn from November through March. File:Anchovy closeup.jpg, northern anchovy (''

Engraulis mordax The Californian anchovy or northern anchovy (''Engraulis mordax'') is a species of anchovy found in the Pacific Ocean, ranging from Mexico to British Columbia. Relationship with humans Commercial fishing As sardine populations declined in the Pa ...

'') found in San Pablo and Suisun bay File:Bay pipefish (Syngnathus leptorhynchus) 01.jpg, Bay pipefish ('' Syngnathus leptorhynchus'') found in intertidal areas commonly among eelgrass Planktivores selectively prey upon individual zooplankton, such as copepods, mysids and

gammarid Gammaridae is a family of amphipods. In North America they are included among the folk taxonomic category of " scuds", and otherwise gammarids is usually used as a common name. They have a wide distribution, centered on Eurasia, and are euryha ...

s. This group includes most fish larvae,

(''

Hypomesus transpacificus The delta smelt (''Hypomesus transpacificus'') is an endangered slender-bodied smelt, about long, in the family Osmeridae. Non-Indigenous to the upper Sacramento-San Joaquin Estuary of California, it mainly inhabits the freshwater-saltwater mi ...

'') and longfin smelt (''

Spirinchus thaleichthys ''Spirinchus'' is a genus of smelt Smelt may refer to: * Smelting, chemical process * The common name of various fish: ** Smelt (fish), a family of small fish, Osmeridae ** Australian smelt in the family Retropinnidae and species ''Retropinna ...

''),

tule perch The tule perch ''Hysterocarpus traskii'' is a surfperch ( Embiotocidae) native to the rivers and estuaries of central California, United States of America. It is the sole member of its genus, and the only freshwater surfperch. The tule perch is ...

(''Hysterocarpus traski''), and salmon smolts. The delta smelt is of particular interest due to its endangered status. It may be food-limited, but the evidence is somewhat contradictory. Other factors, such as entrainment of eggs and larvae in the export pumping of fresh water from the Delta may also explain the decline. File:Cymatogaster aggregata 1zz.jpg, Shiner surfperch(''Cymatogaster aggregata'') found in subtidal zones File:Russian River tule perch.jpg, tule perch (''Hysterocarpus traskii'') File:Steinhart Aquarium 13 2013-03-27.jpg, Walleye surfperch (''Hyperprosopon argenteum'') File:Sebastes auriculatus.jpg, brown rockfish (''Sebastes auriculatus'') File:Plainfin Midshipman - Porichthys notatus (43465733001).jpg, Humming toadfish ('' Porichthys notatus'') found in subtidal zones The main piscivore of the LSZ is the striped bass (''

Morone saxatilis The striped bass (''Morone saxatilis''), also called the Atlantic striped bass, striper, linesider, rock, or rockfish, is an anadromous perciform fish of the family Moronidae found primarily along the Atlantic coast of North America. It has al ...

''), which was introduced in the 1890s and preys heavily upon native fishes. Striped bass are an important sport fishery in the San Francisco Estuary, and as such, represent a minor withdrawal of biomass from the estuary.Radovich 1963 Benthic, or bottom-dwelling, fishes include

white sturgeon White sturgeon (''Acipenser transmontanus'') is a species of sturgeon in the family Acipenseridae of the order Acipenseriformes. They are an anadromous fish species ranging in the Eastern Pacific; from the Gulf of Alaska to Monterey, California. ...

(''Acipenser transmontanus''), white catfish (''Ameiurus catus''), and

starry flounder The starry flounder (''Platichthys stellatus''), also known as the grindstone, emery wheel and long-nosed flounder, is a common flatfish found around the margins of the North Pacific. The distinctive features of the starry flounder include the c ...

(''Platichthys stellatus''). Because of their habitat orientation, they feed primarily on epibenthic organisms such as amphipods, bay shrimp, and bivalves. These fish are known to feed at least occasionally on the Amur River clam, which would represent one of the few channels for energy flow from that species, except for detrital production. The sole

commercial fishery Commercial fishing is the activity of catching fish and other seafood for commercial profit, mostly from wild fisheries. It provides a large quantity of food to many countries around the world, but those who practice it as an industry must often p ...

in the LSZ is for bait shrimp. There are a variety of sports fisheries that represent a minor flow of carbon, but significant flows of capital to local economies around the estuary. Most of the recreational fisheries surround striped bass, sturgeon, and introduced fresh water basses in the freshwater Delta. This paucity of fisheries makes the San Francisco Estuary unique. Nearly all estuaries worldwide support at least remnants of significant fisheries.Nichols et al. 1986 The San Francisco Estuary at one time supported major fisheries for salmon, anchovies, and

Dungeness crab The Dungeness crab (''Metacarcinus magister'') is a species of crab inhabiting eelgrass beds and water bottoms along the west coast of North America. It typically grows to across the carapace and is a popular seafood. Its common name comes from ...

s until the 1950s. The demise of these fisheries was probably due more to

habitat loss Habitat destruction (also termed habitat loss and habitat reduction) is the process by which a natural habitat becomes incapable of supporting its native species. The organisms that previously inhabited the site are displaced or dead, thereby ...

than

overharvesting Overexploitation, also called overharvesting, refers to harvesting a renewable resource to the point of diminishing returns. Continued overexploitation can lead to the destruction of the resource, as it will be unable to replenish. The term ap ...

. File:Triakis semifasciata SI3.jpg,

Leopard shark The leopard shark (''Triakis semifasciata'') is a species of houndshark, in the family Triakidae. It is found along the Pacific coast of North America, from the U.S. state of Oregon to Mazatlán in Mexico. Typically measuring 1.2–1.5 m (3.9� ...

(''Triakis semifasciata'') File:Notorynchus cepedianus head3.jpg,

broadnose sevengill shark The broadnose sevengill shark (''Notorynchus cepedianus'') is the only extant member of the genus ''Notorynchus'', in the family Hexanchidae. It is recognizable because of its seven gill slits, while most shark species have five gill slits, with ...

(''Notorynchus cepedianus'') File:Spiny dogfish hokitika.jpg, spiny dogfish('' Squalus acanthias'') found in the subtidal zone File:Acipenser medirostris FWS 20924.jpg, North American green sturgeon (''Acipenser medirostris'') File:4774 white sturgeon swart odfw (4455048986).jpg, White sturgeon (''

Acipenser transmontanus White sturgeon (''Acipenser transmontanus'') is a species of sturgeon in the family Acipenseridae of the order Acipenseriformes. They are an anadromous fish species ranging in the Eastern Pacific; from the Gulf of Alaska to Monterey, California. ...

'')

Birds

The San Francisco Estuary is a major stop on the

Pacific flyway The Pacific Flyway is a major north-south flyway for migratory birds in the Americas, extending from Alaska to Patagonia. Every year, migratory birds travel some or all of this distance both in spring and in fall, following food sources, heading ...

for migrating waterfowl. Yet little is known about the flow of carbon in or out of the estuary via

birds Birds are a group of warm-blooded vertebrates constituting the class Aves (), characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweigh ...

. Millions of

waterfowl Anseriformes is an order of birds also known as waterfowl that comprises about 180 living species of birds in three families: Anhimidae (three species of screamers), Anseranatidae (the magpie goose), and Anatidae, the largest family, which ...

annually use the bay shallows as a refuge. Most of the birds are dabbling ducks that feed on submerged aquatic vegetation. Diving ducks (such as

scaup Scaup is the common name for three species of diving duck: * Greater scaup, or just "scaup", ''Aythya marila'' * Lesser scaup The lesser scaup (''Aythya affinis'') is a small North American diving duck that migrates south as far as Central Ameri ...

s) feed on epibenthic organisms like C. amurensis, representing a possible flow of carbon from that otherwise dead end. Two

endangered species An endangered species is a species that is very likely to become extinct in the near future, either worldwide or in a particular political jurisdiction. Endangered species may be at risk due to factors such as habitat loss, poaching and inv ...

of birds are found here: the California least tern and the

California clapper rail Ridgway's rail (''Rallus obsoletus'') is a near-threatened species of bird. It is found principally in California's San Francisco Bay to southern Baja California. A member of the rail family, Rallidae, it is a chicken-sized bird that rarely fli ...

. Exposed

bay mud Bay mud consists of thick deposits of soft, unconsolidated silty clay, which is saturated with water; these soil layers are situated at the bottom of certain estuaries, which are normally in temperate regions that have experienced cyclical glac ...

s provide important feeding areas for

shorebird 245px, A flock of Dunlins and Red knots">Red_knot.html" ;"title="Dunlins and Red knot">Dunlins and Red knots Waders or shorebirds are birds of the order Charadriiformes commonly found wikt:wade#Etymology 1, wading along shorelines and mudflat ...

s, but underlying layers of bay mud pose geological hazards for structures near many parts of the bay perimeter. Piscivorous birds such as

double-crested cormorant The double-crested cormorant (''Nannopterum auritum'') is a member of the cormorant family of water birds. It is found near rivers and lakes, and in coastal areas, and is widely distributed across North America, from the Aleutian Islands in A ...

and brown pelicans also inhabit the estuary, but their trophic impact remains poorly studied. 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. File:Pelican Over SF.jpg, Brown Pelican (''Pelecanus occidentalis californicus'') at San Francisco Bay File:Rallus obsoletus, Oakland, California 1.jpg, Ridgway's rail (''Rallus obsoletus'') in Oakland File:Double-crested cormorant at Sutro Baths-6942.jpg, double-crested cormorant File:Larus delawarensis -Oakland -USA-8.jpg,

Ring-billed gull The ring-billed gull (''Larus delawarensis'') is a medium-sized gull. The genus name is from Latin ''Larus'' which appears to have referred to a gull or other large seabird. The specific ''delawarensis'' refers to the Delaware River. Description ...

(''Larus delawarensis'') in Oakland File:California Least Tern adult & chick, Santa Ynez estuary, Vandenberg AFB, California (17323255361).jpg, California least tern

Mammals

Before 1825, Spanish, French, English, Russians and Americans were drawn to the Bay Area to harvest prodigious quantities of

beaver Beavers are large, semiaquatic rodents in the genus ''Castor'' native to the temperate Northern Hemisphere. There are two extant species: the North American beaver (''Castor canadensis'') and the Eurasian beaver (''C. fiber''). Beavers a ...

(''Castor canadensis''), river otter, marten, fisher, mink, fox, weasel, harbor seals and Sea Lions (''

Zalophus californianus The California sea lion (''Zalophus californianus'') is a coastal eared seal native to western North America. It is one of six species of sea lions. Its natural habitat ranges from southeast Alaska to central Mexico, including the Gulf of Califo ...

'') and

sea otter The sea otter (''Enhydra lutris'') is a marine mammal native to the coasts of the northern and eastern North Pacific Ocean. Adult sea otters typically weigh between , making them the heaviest members of the weasel family, but among the smal ...

(''Enhydra lutris''). This early fur trade, known as the

California Fur Rush Before the 1849 California Gold Rush, American, English and Russian fur hunters were drawn to Spanish (and then Mexican) California in a California Fur Rush, to exploit its enormous fur resources. Before 1825, these Europeans were drawn to the north ...

, was more than any other single factor, responsible for opening up the West and the

San Francisco Bay Area The San Francisco Bay Area, often referred to as simply the Bay Area, is a populous region surrounding the San Francisco, San Pablo, and Suisun Bay estuaries in Northern California. The Bay Area is defined by the Association of Bay Area G ...

, in particular, to world trade. By 1817 sea otter in the area were practically eliminated. The Russians maintained a sealing station in the nearby

Farallon Islands The Farallon Islands, or Farallones (from the Spanish ''farallón'' meaning "pillar" or "sea cliff"), are a group of islands and sea stacks in the Gulf of the Farallones, off the coast of San Francisco, California, United States. The isl ...

from 1812 to 1840, taking 1,200 to 1,500 fur seals annually, though American ships had already exploited the islands. By 1818 the seals diminished rapidly until only about 500 could be taken annually and within the next few years, the fur seal was extirpated from the islands until they began to recolonize the islands in 1996. Although 20th-century naturalists were skeptical that beaver were historically extant in coastal streams or the Bay itself, 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.

Thomas McKay Thomas McKay (1 September 1792 – 9 October 1855) was a Canadian businessman who was one of the founders of the city of Ottawa, Ontario. Biography McKay was born in Perth, Scotland and became a skilled stonemason. He emigrated to the C ...

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

and its

Sonoma Creek , name_etymology = , image = Beaver Dam Sonoma Creek, Sonoma Thanksgiving 2009.jpg , image_caption = Beaver dam on Sonoma Creek at Maxwell Farms Regional Park in Sonoma, California, 2009 , image_size = 300 , ma ...

and

Napa River The Napa River is a river approximately long in the U.S. state of California. It drains a famous wine-growing region called the Napa Valley, in the mountains north of the San Francisco Bay. Milliken Creek and Mt. Veeder watersheds are a few ...

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 Matadero Creek is a stream originating in the foothills of the Santa Cruz Mountains in Santa Clara County, California, United States. The creek flows in a northeasterly direction for until it enters the Palo Alto Flood Basin, where it joins Ado ...

Palo Alto Palo Alto (; Spanish for "tall stick") is a charter city in the northwestern corner of Santa Clara County, California, United States, in the San Francisco Bay Area, named after a coastal redwood tree known as El Palo Alto. The city was es ...

North American river otter The North American river otter (''Lontra canadensis''), also known as the northern river otter and river otter, is a semiaquatic mammal that only lives on the North American continent, along its waterways and coasts. An adult North American rive ...

(''Lontra canadensis'') are also re-colonizing the Bay and its tributaries. River otter in the Bay were first reported in Redwood Creek at Muir Beach in 1996, and recently in Corte Madera Creek, and in the south Bay on Coyote Creek, as well as in 2010 in San Francisco Bay itself at the Richmond Marina. For the first time in 65 years, Pacific Harbor Porpoise (''Phocoena phocoena'') returned to the Bay in 2009. Golden Gate Cetacean Research, a non-profit organization focused on research on

cetacean Cetacea (; , ) is an infraorder of aquatic mammals that includes whales, dolphins, and porpoises. Key characteristics are their fully aquatic lifestyle, streamlined body shape, often large size and exclusively carnivorous diet. They propel th ...

s, has developed a photo-identification database enabling the scientists to identify specific porpoise individuals and is trying to ascertain whether a healthier bay has brought their return. Pacific harbor porpoise range from

Point Conception Point Conception (Chumash: ''Humqaq'') is a headland along the Gaviota Coast in southwestern Santa Barbara County, California. It is the point where the Santa Barbara Channel meets the Pacific Ocean, and as the corner between the mostly north ...

, California, to Alaska and across to the

Kamchatka Peninsula The Kamchatka Peninsula (russian: полуостров Камчатка, Poluostrov Kamchatka, ) is a peninsula in the Russian Far East, with an area of about . The Pacific Ocean and the Sea of Okhotsk make up the peninsula's eastern and w ...

and Japan. Recent genetic studies show that there is a local stock from San Francisco to the Russian River and that eastern Pacific coastal populations rarely migrate far, unlike western Atlantic Harbor porpoise. The

common bottlenose dolphin The common bottlenose dolphin or Atlantic bottlenose dolphin (''Tursiops truncatus'') is a wide-ranging marine mammal of the family Delphinidae. The common bottlenose dolphin is a very familiar dolphin due to the wide exposure it gets in captiv ...

(''Tursiops truncatus'') has been extending its current range northwards from the

Southern California Bight The Southern California Bight is a 692-kilometer-long (430 mi) stretch of curved coastline that runs along the west coast of the United States and Mexico, from Point Conception in California to Punta Colonet in Baja California, plus the area o ...

. The first coastal bottlenose dolphin in the

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. File:Beaver Yearling Grooming Alhambra Creek 2008.jpg, Yearling

Alhambra Creek Alhambra Creek is a stream in Contra Costa County, in the East Bay region of the San Francisco Bay Area in northern California. Geography The creek drains into the Carquinez Strait at Martinez, via the historical Arroyo del Hambre. Alhambra ...

, downtown Martinez File:Sea lions at Pier 39 3.jpg, Sea Lions (''

'') at Pier 39 File:Face of Sea Lion.JPG, Pacific Harbor seal ('' Phoca vitulina richardii'') File:River otter Richmond Marina Scott Campbell July 29, 2010.jpg, River otter sunning on rocks in the Richmond Marina File:Humpback Whale underwater shot.jpg,

Humphrey the Whale Humphrey the Whale is a humpback whale that twice deviated from his Mexico to Alaska migration by entering San Francisco Bay. This behavior is unusual for a humpback whale, and Humphrey attracted wide media attention when entering the bay in bot ...

a Humpback whale (''Megaptera novaeangliae'') that entered the bay File:Harbor.Porpoise.4.jpg,

Harbour porpoise The harbour porpoise (''Phocoena phocoena'') is one of eight extant species of porpoise. It is one of the smallest species of cetacean. As its name implies, it stays close to coastal areas or river estuaries, and as such, is the most familiar ...

(''Phocoena phocoena'') File:Salt marsh harvest mouse (Reithrodontomys raviventris), climbing.jpg,

Salt marsh harvest mouse The salt marsh harvest mouse (''Reithrodontomys raviventris''), also known as the red-bellied harvest mouse, is an endangered rodent endemic to the San Francisco Bay Area salt marshes in California. The two distinct subspecies are both endangere ...

(''Reithrodontomys raviventris''), is an endangered species endemic to the wetlands of the San Francisco Bay with a high salt tolerance.

Jellyfish

Jellyfish Jellyfish and sea jellies are the informal common names given to the medusa-phase of certain gelatinous members of the subphylum Medusozoa, a major part of the phylum Cnidaria. Jellyfish are mainly free-swimming marine animals with umbre ...

have not been prevalent in the estuary until recently. In East Coast estuaries such as

Chesapeake Bay The Chesapeake Bay ( ) is the largest estuary in the United States. The Bay is located in the Mid-Atlantic region and is primarily separated from the Atlantic Ocean by the Delmarva Peninsula (including the parts: the Eastern Shore of Maryland / ...

, they are often

top-level predator An apex predator, also known as a top predator, is a predator at the top of a food chain, without natural predators of its own. Apex predators are usually defined in terms of trophic dynamics, meaning that they occupy the highest trophic le ...

s, feeding indiscriminately on both fish and zooplankton. Several small invasive taxa have been identified in the LSZ and freshwater regions. These species strobilate in summer, but maintain

polyps A polyp in zoology is one of two forms found in the phylum Cnidaria, the other being the medusa. Polyps are roughly cylindrical in shape and elongated at the axis of the vase-shaped body. In solitary polyps, the aboral (opposite to oral) end i ...

in the

benthos Benthos (), also known as benthon, is the community of organisms that live on, in, or near the bottom of a sea, river, lake, or stream, also known as the benthic zone.plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a cruc ...

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. File:Corynactis Sp. 2008-03.jpg, ''

Corynactis californica ''Corynactis californica'' is a brightly colored colonial anthozoan corallimorph. Unlike the Atlantic true sea anemone, '' Actinia fragacea'', that bears the same common name, strawberry anemone, this species is a member of the order Corallimor ...

'' found on docks and pilings in the intertidal zones

Benthic consumers

The

community has taken on a disproportionately large role in the food web ecology of the estuary due to key invasions by

bivalve Bivalvia (), in previous centuries referred to as the Lamellibranchiata and Pelecypoda, is a class (biology), class of marine and freshwater Mollusca, molluscs that have laterally compressed bodies enclosed by a shell consisting of two hing ...

s. The use of these clams, the Amur River clam (''Corbula amurensis'') has a wide salinity tolerance that extends into the low salinity zone, but not into freshwater. It filter feeds on phytoplankton and small zooplankton, such as calanoid copepod nauplii. The clam has few predators in the San Francisco Estuary and this allows it to grow to high densities (on the order of tens of thousands/m2). Because of its high clearance rates, it is capable of clearing the entire water column of portions of the estuary in a few days, leading to drastically depleted plankton populations. This is thought to be the main cause of a decline in ecosystem productivity after the invasion of the clams in the mid-1980s. File:Starry Flounder.JPG,

Starry flounder The starry flounder (''Platichthys stellatus''), also known as the grindstone, emery wheel and long-nosed flounder, is a common flatfish found around the margins of the North Pacific. The distinctive features of the starry flounder include the c ...

(''Platichthys stellatus'') File:Citharichthys stigmaeus (Speckled Sanddab).jpg, Speckled Sanddab (''Citharichthys stigmaeus'') found in subtidal zones with sandy bottoms File:A Nap for Batoids.jpg, Bat Ray (''

Myliobatis californica The bat ray (''Myliobatis californica'')Gill, T.N. (1865). "Note on the family of myliobatoids, and on a new species of ''Aetobatis''". ''Ann. Lyc. Nat. Hist. N. Y.'' 8, 135–138. is an eagle ray found in muddy or sandy sloughs, estuaries and ...

'') and a Big skate ('' Beringraja binoculata'') in the Aquarium of the Bay both found in subtidal areas of the bay This decline in productivity is essentially due to the redirection of the pelagic network to a benthic chain by this one species. Because the Amur River clam feeds on primary producers, consumers and predators, it impacts multiple

s. Consequently, nearly all plankton exhibit signs of

apparent competition Competition is an interaction between organisms or species in which both require a resource that is in limited supply (such as food, water, or territory). Competition lowers the fitness of both organisms involved since the presence of one of th ...

, in that production at one trophic level impacts all others by increasing clam abundance. This results in a negative

feedback loop Feedback occurs when outputs of a system are routed back as inputs as part of a chain of cause-and-effect that forms a circuit or loop. The system can then be said to ''feed back'' into itself. The notion of cause-and-effect has to be handled c ...

: ''C. amurensis'' limits plankton biomass, which in turn limits ''C. amurensis''. However, inputs from outside the system due to tidal advection or upstream sources may increase ''C. amurensis'' biomass, further driving plankton limitation. This feedback loop is further amplified because the clam may persist for more than one or two years, which puts added pressure on plankton populations 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 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

and microflagellates which are too 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 microbial food web and the invasion of ''L. tetraspina'' capitalize are the result of an untapped alternative path for energy flow in the food web, facilitated by C. amurensis. Subsequent patterns of invasion may reflect a similar pattern. File:2011-08-14 San Francisco 043 Pier 39, Aquarium of the Bay (6092202672).jpg,

Dungeness Crab The Dungeness crab (''Metacarcinus magister'') is a species of crab inhabiting eelgrass beds and water bottoms along the west coast of North America. It typically grows to across the carapace and is a popular seafood. Its common name comes from ...

(''Metacarcinus magister'') File:Cancer productus.jpg, Red rock crab (''Cancer productus'') File:Metacarcinus gracilis.jpg, Graceful Crab (''Metacarcinus gracilis'') File:Red Rock Crab (Cancer antennarius) (2281653819).jpg, California rock crab(''Romaleon antennarium'') File:Hemigrapsus oregonensis 6158.JPG, Yellow Shore crab (''Hemigrapsus oregonensis'') found in shallow intertidal areas File:Pyromaia tuberculata.jpg, American spider crab (''Pyromaia tuberculata'') found under rocks and near dock pilings File:Pagurus hirsutiusculus 3017.JPG, Hairy hermit crab(''Pagurus hirsutiusculus'') File:Pisaster ochraceus (23729798342).jpg, Ochre Starfish (''Pisaster ochraceus'') found in intertidal zone

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,

, fish and both rooted and floating plants. Many pelagic species have been introduced most recently through

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. Species have also been introduced via attachment to sporting boats which are trailered between regions. This is the probable source of a number of low salinity plants like Egeria densa and

water hyacinth ''Pontederia crassipes'' (formerly ''Eichhornia crassipes''), commonly known as common water hyacinth is an aquatic plant native to South America, naturalized throughout the world, and often invasive outside its native range.Eichhornia crassipes ''Pontederia crassipes'' (formerly ''Eichhornia crassipes''), commonly known as common water hyacinth is an aquatic plant native to South America, naturalized throughout the world, and often invasive outside its native range.piscivorous fish like the striped bass,

, itself intentionally introduced in the late 1800s from the

. The freshwater

quagga mussel The quagga mussel (''Dreissena rostriformis'', also known as ''Dreissena bugensis'' or ''Dreissena rostriformis bugensis'') is a species (or subspecies) of freshwater mussel, an aquatic bivalve mollusk in the family Dreissenidae. It has an aver ...

, originally from Europe, is expected to be introduced by boaters within the next two to ten years, in spite of precautionary measures. Furthermore, the young age and isolated environment of the San Francisco estuary has resulted in the success of invasive invertebrates due to the lack of biodiversity.

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

climate change In common usage, climate change describes global warming—the ongoing increase in global average temperature—and its effects on Earth's climate system. Climate change in a broader sense also includes previous long-term changes to ...

. Future ecological changes will be driven on an ecosystem wide scale, particularly as

sea level rise Globally, sea levels are rising due to human-caused climate change. Between 1901 and 2018, the globally averaged sea level rose by , or 1–2 mm per year on average.IPCC, 2019Summary for Policymakers InIPCC Special Report on the Ocean and Cr ...

tectonic Tectonics (; ) are the processes that control the structure and properties of the Earth's crust and its evolution through time. These include the processes of mountain building, the growth and behavior of the strong, old cores of continents ...

instability and infrastructure decline cause levee 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.

Notes

References

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Limnology and Oceanography 38:949-964. {{aquatic ecosystem topics San Francisco Bay Environment of California Ecosystems Science and technology in the San Francisco Bay Area Environment of the San Francisco Bay Area San Francisco Bay watershed