Ecology of the San Francisco Estuary

San Francisco Bay

San Francisco Bay is a shallow, productive estuary through which water draining from approximately forty percent of California, flowing in the Sacramento and San Joaquin rivers from the Sierra Nevada mountains, enters the Pacific Ocean...

and delta represents a highly altered ecosystem

Ecosystem

An ecosystem is a biological environment consisting of all the organisms living in a particular area, as well as all the nonliving , physical components of the environment with which the organisms interact, such as air, soil, water and sunlight....

. 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 have arisen from the introduction of non-native species. New species have altered the architecture of the food web as surely as levee

Levee

A levee, levée, dike , embankment, floodbank or stopbank is an elongated naturally occurring ridge or artificially constructed fill or wall, which regulates water levels...

s have altered the landscape of islands and channels that form the complex system known as the Delta.

This article deals particularly with the ecology of the low salinity

Salinity

Salinity is the saltiness or dissolved salt content of a body of water. It is a general term used to describe the levels of different salts such as sodium chloride, magnesium and calcium sulfates, and bicarbonates...

zone (LSZ) of the estuary. Reconstructing a historic foodweb

Food chain

A food web depicts feeding connections in an ecological community. Ecologists can broadly lump all life forms into one of two categories called trophic levels: 1) the autotrophs, and 2) the heterotrophs...

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

Climate change

Climate change is a significant and lasting change in the statistical distribution of weather patterns over periods ranging from decades to millions of years. It may be a change in average weather conditions or the distribution of events around that average...

, hydrologic engineering, shifting water needs, and newly introduced species

Introduced species

An introduced species — or neozoon, alien, exotic, non-indigenous, or non-native species, or simply an introduction, is a species living outside its indigenous or native distributional range, and has arrived in an ecosystem or plant community by human activity, either deliberate or accidental...

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 foodweb. Understanding the dynamics of the current food web

Food web

may prove useful for restoration efforts to improve the functioning and species diversity of the estuary.

Physical geography

The San Francisco Bay

San Francisco Bay

is both a bay

Bay

A bay is an area of water mostly surrounded by land. Bays generally have calmer waters than the surrounding sea, due to the surrounding land blocking some waves and often reducing winds. Bays also exist as an inlet in a lake or pond. A large bay may be called a gulf, a sea, a sound, or a bight...

and an estuary

Estuary

An estuary is a partly enclosed coastal body of water with one or more rivers or streams flowing into it, and with a free connection to the open sea....

. 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

San Pablo Bay is a tidal estuary that forms the northern extension of San Francisco Bay in northern California in the United States. Most of the Bay is shallow; however, there is a deep water channel approximately in mid bay, which allows access to Sacramento, Stockton, Benicia, Martinez, and...

, immediately north of the Central Bay; the Carquinez Strait

Carquinez Strait

The Carquinez Strait 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...

, a narrow, deep channel leading to Suisun Bay

Suisun Bay

Suisun Bay is a shallow tidal estuary at in northern California, USA. It lies at the confluence of the Sacramento and San Joaquin Rivers, forming the entrance to the Sacramento-San Joaquin River Delta, an inverted river delta...

; and the Delta of the Sacramento

Sacramento River

The Sacramento River is an important watercourse of Northern and Central California in the United States. The largest river in California, it rises on the eastern slopes of the Klamath Mountains, and after a journey south of over , empties into Suisun Bay, an arm of the San Francisco Bay, and...

and San Joaquin River

San Joaquin River

The San Joaquin River is the largest river of Central California in the United States. At over long, the river starts in the high Sierra Nevada, and flows through a rich agricultural region known as the San Joaquin Valley before reaching Suisun Bay, San Francisco Bay, and the Pacific Ocean...

s.

Until the 20th Century, the LSZ of the Estuary was fringed by tule

Tule

Schoenoplectus acutus , called tule , common tule, hardstem tule, tule rush, hardstem bulrush, or viscid bulrush, is a giant species of sedge in the plant family Cyperaceae, native to freshwater marshes all over North America...

-dominated freshwater wetlands. Between 80-95% of these historic wetlands have been filled to facilitate land use and development around the Bay Area. Habitat loss at the edges of the pelagic zone

Pelagic zone

Any water in a sea or lake that is not close to the bottom or near to the shore can be said to be in the pelagic zone. The word pelagic comes from the Greek πέλαγος or pélagos, which means "open sea". The pelagic zone can be thought of in terms of an imaginary cylinder or water column that goes...

is thought to create a loss of native pelagic fish

Pelagic fish

Pelagic fish live near the surface or in the water column of coastal, ocean and lake waters, but not on the bottom of the sea or the lake. They can be contrasted with demersal fish, which do live on or near the bottom, and reef fish which are associated with coral reefs.The marine pelagic...

species, by increasing vulnerability to predation.

The intertidal

Intertidal zone

The intertidal zone is the area that is above water at low tide and under water at high tide . This area can include many different types of habitats, with many types of animals like starfish, sea urchins, and some species of coral...

and benthic Estuary is presently dominated by mudflat

Mudflat

Mudflats or mud flats, also known as tidal flats, are coastal wetlands that form when mud is deposited by tides or rivers. They are found in sheltered areas such as bays, bayous, lagoons, and estuaries. Mudflats may be viewed geologically as exposed layers of bay mud, resulting from deposition of...

s that are largely the result of sedimentation derived from gold mining

Gold mining

Gold mining is the removal of gold from the ground. There are several techniques and processes by which gold may be extracted from the earth.-History:...

in the Sierras in the late 19th Century. The trend toward high sediment loads was reversed in the 1950s with the advent of the Central Valley Project

Central Valley Project

The Central Valley Project is a Bureau of Reclamation federal water project in the U.S. state of California. It was devised in 1933 in order to provide irrigation and municipal water to much of California's Central Valley—by regulating and storing water in reservoirs in the water-rich northern...

, 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 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 levy 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 units, a measurement of salinity) and ranges from about 6 psu down to 0.5 psu. The primary fresh water inputs to the Estuary derive from regional precipitation, the Sacramento River, and the San Joaquin River.

River inflow is largely controlled by upstream reservoir releases. A significant fraction of this inflow is exported out of the Delta by the federal Central Valley Project

Central Valley Project

and the State Water Project to southern California

California

California is a state located on the West Coast of the United States. It is by far the most populous U.S. state, and the third-largest by land area...

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

Golden Gate

The Golden Gate is the North American strait connecting San Francisco Bay to the Pacific Ocean. Since 1937 it has been spanned by the Golden Gate Bridge...

), creating lower outflow in the winter and higher outflow in the summer than historically found in the Estuary. Phytoplankton

Phytoplankton

Phytoplankton are the autotrophic component of the plankton community. The name comes from the Greek words φυτόν , meaning "plant", and πλαγκτός , meaning "wanderer" or "drifter". Most phytoplankton are too small to be individually seen with the unaided eye...

, zooplankton

Zooplankton

Zooplankton are heterotrophic plankton. Plankton are organisms drifting in oceans, seas, and bodies of fresh water. The word "zooplankton" is derived from the Greek zoon , meaning "animal", and , meaning "wanderer" or "drifter"...

, 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

Delta smelt

Delta smelt, Hypomesus transpacificus, is an endangered slender-bodied smelt, about long, of the Osmeridae family. Endemic to the upper Sacramento-San Joaquin estuary of California, it mainly inhabits the freshwater-saltwater mixing zone of the estuary, except during its spawning season, which...

, a small endemic fish; unexceptional except that is 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. 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

Tide

Tides are the rise and fall of sea levels caused by the combined effects of the gravitational forces exerted by the moon and the sun and the rotation of the Earth....

cause water to move toward and away from the Golden Gate four times in a 24 hour period. Using 2 psu as a marker for the Low Salinity Zone, the direction and magnitude of fluctuations can be tracked as the distance in kilometers from the Golden Gate, or X2.

Because the position of X2 relies upon a number of physical parameters including inflow, export, and tides, its position shifts over many kilometers on a daily and seasonal cycle; over the course of a year, it can range from San Pablo Bay during high flow periods, up into the Delta during the summer drought. The position of X2 is carefully monitored and maintained by releasing water from upstream reservoirs in anticipation of export demand. This is mandated by in the Vernalis Salinity Standard, which was legally established to maintain habitat quality in the Estuary for wildlife and to prevent salinity from encroaching upstream to the export pumps.

Gravitation

Gravitation

Gravitation, or gravity, is a natural phenomenon by which physical bodies attract with a force proportional to their mass. Gravitation is most familiar as the agent that gives weight to objects with mass and causes them to fall to the ground when dropped...

al 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

Habitat

* Habitat , a place where a species lives and grows*Human habitat, a place where humans live, work or play** Space habitat, a space station intended as a permanent settlement...

is defined not by edges but by physiological tolerance to salinity and temperature. The Low Salinity Zone (LSZ) of the San Francisco Estuary

San Francisco Bay

constitutes a habitat for a suite of organisms that are specialized to survive in this unique confluence of terrestrial, freshwater

Freshwater

Fresh water is naturally occurring water on the Earth's surface in ice sheets, ice caps, glaciers, bogs, ponds, lakes, rivers and streams, and underground as groundwater in aquifers and underground streams. Fresh water is generally characterized by having low concentrations of dissolved salts and...

, and marine

Marine (ocean)

Marine is an umbrella term. As an adjective it is usually applicable to things relating to the sea or ocean, such as marine biology, marine ecology and marine geology...

influences. While there are many habitats with distinct ecologies

Ecology

Ecology is the scientific study of the relations that living organisms have with respect to each other and their natural environment. Variables of interest to ecologists include the composition, distribution, amount , number, and changing states of organisms within and among ecosystems...

that are part of the Estuary

Estuary

An estuary is a partly enclosed coastal body of water with one or more rivers or streams flowing into it, and with a free connection to the open sea....

(including marine, freshwater, intertidal marsh and benthic mudflat

Benthos

Benthos is the community of organisms which live on, in, or near the seabed, also known as the benthic zone. This community lives in or near marine sedimentary environments, from tidal pools along the foreshore, out to the continental shelf, and then down to the abyssal depths.Many organisms...

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

Physical geography is one of the two major subfields of geography. Physical geography is that branch of natural science which deals with the study of processes and patterns in the natural environment like the atmosphere, biosphere and geosphere, as opposed to the cultural or built environment, the...

and hydrology

Hydrology

Hydrology is the study of the movement, distribution, and quality of water on Earth and other planets, including the hydrologic cycle, water resources and environmental watershed sustainability...

of the Estuary, including nutrient

Nutrient

A nutrient is a chemical that an organism needs to live and grow or a substance used in an organism's metabolism which must be taken in from its environment. They are used to build and repair tissues, regulate body processes and are converted to and used as energy...

inputs, sediment

Sediment

Sediment is naturally occurring material that is broken down by processes of weathering and erosion, and is subsequently transported by the action of fluids such as wind, water, or ice, and/or by the force of gravity acting on the particle itself....

load, turbidity

Turbidity

Turbidity is the cloudiness or haziness of a fluid caused by individual particles that are generally invisible to the naked eye, similar to smoke in air. The measurement of turbidity is a key test of water quality....

, environmental stochasticity, climate

Climate

Climate encompasses the statistics of temperature, humidity, atmospheric pressure, wind, rainfall, atmospheric particle count and other meteorological elemental measurements in a given region over long periods...

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

Primary production

400px|thumb|Global oceanic and terrestrial photoautotroph abundance, from September [[1997]] to August 2000. As an estimate of autotroph biomass, it is only a rough indicator of primary production potential, and not an actual estimate of it...

, secondary production of zooplankton

Zooplankton

, foodweb

Food chain

and trophic dynamics, energetic transfer, advection and dispersal in and out of the system, survivorship and mortality

Death

Death is the permanent termination of the biological functions that sustain a living organism. Phenomena which commonly bring about death include old age, predation, malnutrition, disease, and accidents or trauma resulting in terminal injury....

, predation

Predation

In ecology, predation describes a biological interaction where a predator feeds on its prey . Predators may or may not kill their prey prior to feeding on them, but the act of predation always results in the death of its prey and the eventual absorption of the prey's tissue through consumption...

, and competition

Competition

Competition is a contest between individuals, groups, animals, etc. for territory, a niche, or a location of resources. It arises whenever two and only two strive for a goal which cannot be shared. Competition occurs naturally between living organisms which co-exist in the same environment. For...

from introduced species

Introduced species

Food web

It is difficult to characterize the historic food web

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 E. affinis, and large macrozooplankton typified by San Francisco bay shrimp

Shrimp

Shrimp are swimming, decapod crustaceans classified in the infraorder Caridea, found widely around the world in both fresh and salt water. Adult shrimp are filter feeding benthic animals living close to the bottom. They can live in schools and can swim rapidly backwards. Shrimp are an important...

and mysids These provided nutrition and energy to native filter feeders such as the northern anchovy

Anchovy

Anchovies are a family of small, common salt-water forage fish. There are 144 species in 17 genera, found in the Atlantic, Indian, and Pacific Oceans. Anchovies are usually classified as an oily fish.-Description:...

(Engraulis mordax), and planktivores such as delta smelt

Delta smelt

and juvenile salmon

Salmon

Salmon is the common name for several species of fish in the family Salmonidae. Several other fish in the same family are called trout; the difference is often said to be that salmon migrate and trout are resident, but this distinction does not strictly hold true...

.

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 population has produced a ten-fold decline in plankton density, resulting in a carbon trap in the benthos and an assumed increase in waste detrital production. This waste is hypothesized to fuel the microbial loop, resulting in an increase in microzooplankton such as L. tetraspina, which utilize rotifers and ciliates.

These changes are one cause for declining fish stocks. For example, the northern anchovy, Engraulis mordax, was until the 1980s quite abundant in the Low Salinity Zone, until its range in the Estuary became restricted to the Central and South Bays. This is probably due to a behavioral response following the introduction of the Amur River clam and the subsequent decline in plankton availability.

More recently, a general Pelagic Organism Decline (POD) was described, and this has been the source of much concern within the scientific, managerial, and political communities.

Several key species, including delta smelt

Delta smelt

, longfin smelt

Longfin smelt

The longfin smelt, Spirinchus thaleichthys, is a smelt that is found in several estuaries and lakes along the northern Pacific coast of North America....

, striped bass

Striped bass

The striped bass is the state fish of Maryland, Rhode Island, South Carolina, and the state saltwater fish of New York, Virginia, and New Hampshire...

, and threadfin shad

Threadfin shad

The threadfin shad, Dorosoma petenense, is a small pelagic fish common in rivers, large streams, and reservoirs of the Southeastern United States. Like the American gizzard shad, the threadfin shad has an elongated dorsal ray, but unlike the gizzard shad its mouth is more terminal without...

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.

Primary production and nutrient uptake

Primary production

by phytoplankton fixes energy and key nutrients into a biologically available form (ie, food), via photosynthesis

Photosynthesis

Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...

. Phytoplankton production is largely structured by physical parameters: nutrient availability, sunlight, turbidity, and temperature.

The San Francisco Estuary has a non-limiting source of nutrients that can be used for primary production, derived largely from waste water treatment facilities, agricultural and urban drainage, and the ocean. 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, which suppresses nitrate uptake by phytoplankton, and high turbidity, which limits light for photosynthesis to the top few centimeters of the water column. This turbidity is a legacy of hydraulic gold mining in the Sierra Nevada Mountains 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 advect particles and plankton downstream.

Herbivory 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

Photosynthesis

derived energy is phytoplankton

Phytoplankton

. Generally speaking, diatoms and microflagellates produce most of the bioavailable carbon in the Estuary. Other types, notably the dinoflagellates, may produce harmful algal blooms, or red tide

Red tide

Red tide is a common name for a phenomenon also known as an algal bloom , an event in which estuarine, marine, or fresh water algae accumulate rapidly in the water column and results in discoloration of the surface water. It is usually found in coastal areas...

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

Primary production

Primary production

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 from urban and agricultural sources, phytoplankton production rates are quite low. Nitrate

Nitrate

The nitrate ion is a polyatomic ion with the molecular formula NO and a molecular mass of 62.0049 g/mol. It is the conjugate base of nitric acid, consisting of one central nitrogen atom surrounded by three identically-bonded oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a...

is optimally used by phytoplankton for growth, but ammonium

Ammonium

The ammonium cation is a positively charged polyatomic cation with the chemical formula NH. It is formed by the protonation of ammonia...

(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

Turbidity

of the Estuary, which limits the ability of photosynthetically active radiation

Photosynthetically active radiation

Photosynthetically active radiation, often abbreviated PAR, designates the spectral range 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 or less with the range of light visible to...

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

Photic zone

The photic zone or euphotic zone is the depth of the water in a lake or ocean that is exposed to sufficient sunlight for photosynthesis to occur...

. Thus, when the water column is stratified

Stratification (water)

Water stratification occurs when water masses with different properties - salinity , oxygenation , density , temperature - form layers that act as barriers to water mixing...

, turbidity is high, and ammonium is present, the growth rate of phytoplankton is typically suppressed.

Phytoplankton accumulation is primarily the result of residence time

Residence time

Residence time is the average amount of time that a particle spends in a particular system. This measurement varies directly with the amount of substance that is present in the system....

. The north Delta and Suisun Bay

Suisun Bay

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

Water export

Water exports involve exporting freshwater from one country to another. Large increases in human population and economic growth throughout the world during the twentieth century placed a huge stress on the world’s freshwater resources. Combined with climate change, they will place an even greater...

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 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 affect on the food web by competitively excluding diatoms and microflagellates, further reducing bioavailable primary production. While certain invertebrates such as bivalves may not be directly affected, they may propagate toxins up the food chain, sickening or killing predators. It is not well understood how copepods are affected. The invasive algae

Algae

Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...

Microcystis aeruginosa is now common in the Delta during summer months and may reduce copepod productivity (in addition to being potentially carcinogenic for humans).

Detrital production

Enormous quantities of sediment

Sediment

and detritus

Detritus

Detritus is a biological term used to describe dead or waste organic material.Detritus may also refer to:* Detritus , a geological term used to describe the particles of rock produced by weathering...

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

Organic matter

Organic matter is matter that has come from a once-living organism; is capable of decay, or the product of decay; or is composed of organic compounds...

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

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

Carbon fixation

In biology, carbon fixation is the reduction of carbon dioxide to organic compounds by living organisms. The obvious example is photosynthesis. Carbon fixation requires both a source of energy such as sunlight, and an electron donor such as water. All life depends on fixed carbon. Organisms that...

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

Microbial loop

The microbial loop describes a trophic pathway in the marine microbial food web where dissolved organic carbon is returned to higher trophic levels via the incorporation into bacterial biomass, and coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. The term microbial...

. This mechanism is particularly important in nutrient limited marine

Marine (ocean)

Marine is an umbrella term. As an adjective it is usually applicable to things relating to the sea or ocean, such as marine biology, marine ecology and marine geology...

systems, where bacteria

Bacteria

Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

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 system. Rather, they may provide an alternative food chain through direct grazing by flagellates, rotifers and ciliates.

The high abundance of the cyclopoid

Cyclopoida

Cyclopoida is an order of small crustaceans from the subclass Copepoda. Like many other copepods, members of Cyclopoida are small, planktonic animals living both in the sea and in freshwater habitats. They are capable of rapid movement...

copepod Limnoithona tetraspina may be due to its reliance on ciliates rather than phytoplankton as a primary food source. The major species of calanoid 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

Trophic level

The trophic level of an organism is the position it occupies in a food chain. The word trophic derives from the Greek τροφή referring to food or feeding. A food chain represents a succession of organisms that eat another organism and are, in turn, eaten themselves. The number of steps an organism...

s of the estuarine foodweb. Historically, secondary production in the San Francisco Estuary was dominated by mysid shrimp production. However, the native mysid Neomysis mercedis has been largely replaced by the introduced Acanthomysis bowmani, which persists at lower densities. The introduced amphipod Gammurus daiberi may have taken over some of this niche, but it is largely restricted to fresh water.

Today, the main source of secondary production derives from copepod

Copepod

Copepods are a group of small crustaceans found in the sea and nearly every freshwater habitat. Some species are planktonic , some are benthic , and some continental species may live in limno-terrestrial habitats and other wet terrestrial places, such as swamps, under leaf fall in wet forests,...

s. The naturalized native calanoid copepod Eurytemora affinis 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. 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

Cyclopoida

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

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.

Primary consumers

Primary consumers rely upon primary production

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.

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 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

Filter feeder

Filter feeders are 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 feeding are clams, krill, sponges, baleen whales, and many fish and some sharks. Some birds,...

, 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

Sturgeon is the common name used for some 26 species of fish in the family Acipenseridae, including the genera Acipenser, Huso, Scaphirhynchus and Pseudoscaphirhynchus. The term includes over 20 species commonly referred to as sturgeon and several closely related species that have distinct common...

, Chinook salmon

Chinook salmon

The Chinook salmon, Oncorhynchus tshawytscha, is the largest species in the pacific salmon family. Other commonly used names for the species include King salmon, Quinnat salmon, Spring salmon and Tyee salmon...

, and American shad

American shad

-Introduction:The American shad or Atlantic shad, Alosa sapidissima, is a species of anadromous fish in family Clupeidae of order Clupeiformes. It is not closely related to the other North American shads...

. 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 90’s.

Shrimp

Shrimp

are generalist carnivores who prey largely on mysids and amphipods. 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

Striped bass

The striped bass is the state fish of Maryland, Rhode Island, South Carolina, and the state saltwater fish of New York, Virginia, and New Hampshire...

and Chinook salmon

Chinook salmon

adults and smolts

Spawn (biology)

Spawn refers to the eggs and sperm released or deposited, usually into water, by aquatic animals. As a verb, spawn refers to the process of releasing the eggs and sperm, also called spawning...

Fish

Because fish are a taxonomically

Taxonomy

Taxonomy is the science of identifying and naming species, and arranging them into a classification. The field of taxonomy, sometimes referred to as "biological taxonomy", revolves around the description and use of taxonomic units, known as taxa...

and morphologically

Morphology (biology)

In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....

diverse group, species vary in their trophic ecologies. In general, fish can be divided into four broad feeding categories: filter feeder

Filter feeder

s, planktivores, piscivore

Piscivore

A piscivore is a carnivorous animal which eats primarily fish. Piscivory was the diet of early tetrapods , insectivory came next, then in time reptiles added herbivory....

s and benthic

Benthos

feeders.

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

Threadfin shad

(Dorosoma petenense), American shad

American shad

(Alosa sapidissima), inland silverside

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....

s (Menidia beryllina), and anchovies (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.

Planktivores selectively prey upon individual zooplankton, such as copepods, mysids and gammarids. This group includes most fish larvae, delta smelt

Delta smelt

(Hypomesus transpacificus) and longfin smelt

Longfin smelt

The longfin smelt, Spirinchus thaleichthys, is a smelt that is found in several estuaries and lakes along the northern Pacific coast of North America....

(Spirinchus thaleichthys), tule perch

Tule perch

The tule perch Hysterocarpus traskii is a surfperch 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....

(Hysterocarpus traski), and salmon

Salmon

smolts

Spawn (biology)

Spawn refers to the eggs and sperm released or deposited, usually into water, by aquatic animals. As a verb, spawn refers to the process of releasing the eggs and sperm, also called spawning...

. The delta smelt is of particular interest due to its endangered status

Endangered Species Act

The Endangered Species Act of 1973 is one of the dozens of United States environmental laws passed in the 1970s. Signed into law by President Richard Nixon on December 28, 1973, it was designed to protect critically imperiled species from extinction as a "consequence of economic growth and...

. 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.

The main piscivore of the LSZ is the striped bass

Striped bass

The striped bass is the state fish of Maryland, Rhode Island, South Carolina, and the state saltwater fish of New York, Virginia, and New Hampshire...

(Morone saxatilis), 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.

Benthic, or bottom-dwelling, fishes include white sturgeon

White sturgeon

The white sturgeon , also known as the Pacific sturgeon, Oregon sturgeon, Columbia sturgeon, Sacramento sturgeon, and California white sturgeon, is a sturgeon which lives along the west coast of North America from the Aleutian Islands to Central...

(Acipenser transmontanus), white catfish

Ictalurus catus

Ictalurus catus, also known as the white catfish or white bullhead, is a member of the family Ictaluridae of the order Siluriformes.- Distribution :...

(Ameiurus catus), and starry flounder

Starry flounder

The starry flounder is a common flatfish found around the margins of the North Pacific.The distinctive features of the starry flounder include the combination of black and white-to-orange bar on the dorsal and anal fins, as well as the skin covered with scales modified into tiny star-shaped plates...

(Platichthys stellatus). Because of their habitat

Habitat

* Habitat , a place where a species lives and grows*Human habitat, a place where humans live, work or play** Space habitat, a space station intended as a permanent settlement...

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 in the LSZ is for bait shrimp. There are a variety of sports fisheries

Recreational fishing

Recreational fishing, also called sport fishing, is fishing for pleasure or competition. It can be contrasted with commercial fishing, which is fishing for profit, or subsistence fishing, which is fishing for survival....

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. The San Francisco Estuary at one time supported major fisheries for salmon, anchovies, and Dungeness crab

Dungeness crab

The Dungeness crab, Metacarcinus magister , is a species of crab that inhabits eelgrass beds and water bottoms on the west coast of North America. It typically grows to across the carapace and is a popular seafood...

s until the 1950s. The demise of these fisheries was probably due more to habitat loss than overharvesting

Overfishing

Overfishing occurs when fishing activities reduce fish stocks below an acceptable level. This can occur in any body of water from a pond to the oceans....

Birds

The San Francisco Estuary is a major stop on the Pacific flyway

Pacific Flyway

The Pacific Flyway is a major north-south route of travel for migratory birds in America, 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 to breeding grounds, or travelling to...

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

Waterfowl

Waterfowl are certain wildfowl of the order Anseriformes, especially members of the family Anatidae, which includes ducks, geese, and swans....

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

Scaup may refer to:* Scottish Conservative and Unionist Party, a political party in Scotland* One of three species of diving duck:** Greater Scaup or just Scaup, Aythya marila** Lesser Scaup, Aythya affinis...

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

Endangered species

An endangered species is a population of organisms which is at risk of becoming extinct because it is either few in numbers, or threatened by changing environmental or predation parameters...

of birds are found here: the California least tern

California Least Tern

The Least Tern is a species of tern that breeds in North America and locally in northern South America. It is closely related to, and was formerly often considered conspecific with, the Little Tern of the Old World...

and the California clapper rail

California Clapper Rail

The California Clapper Rail is an endangered subspecies of the Clapper Rail . It is found principally in California's San Francisco Bay, and also in Monterey Bay and Morro Bay...

. Exposed bay mud

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 glacial cycles...

s provide important feeding areas for shorebirds, but underlying layers of bay mud pose geological hazards for structures near many parts of the bay perimeter. Piscivorous birds such as cormorants and pelicans also inhabit the Estuary, but their trophic impact remains poorly studied.

Mammals

Before 1825, Spanish, French, English, Russians and Americans were drawn to the Bay Area to harvest prodigious quantities of beaver (Castor canadensis), river otter, marten, fisher, mink, fox, weasel, harbor and fur seal

Fur seal

Fur seals are any of nine species of pinnipeds in the Otariidae family. One species, the northern fur seal inhabits the North Pacific, while seven species in the Arctocephalus genus are found primarily in the Southern hemisphere...

s (Callorhinus ursinus) and sea otter

Sea Otter

The sea otter is a marine mammal native to the coasts of the northern and eastern North Pacific Ocean. Adult sea otters typically weigh between 14 and 45 kg , making them the heaviest members of the weasel family, but among the smallest marine mammals...

((Enhydra lutris)). This early fur trade, known as the California Fur Rush

California Fur Rush

Before the 1849 California Gold Rush, American, English and Russian fur hunters were drawn to Spanish California in a California Fur Rush, to exploit its enormous fur resources...

, was more than any other single factor, responsible for opening up the West and the San Francisco Bay Area

San Francisco Bay Area

The San Francisco Bay Area, commonly known as the Bay Area, is a populated region that surrounds the San Francisco and San Pablo estuaries in Northern California. The region encompasses metropolitan areas of San Francisco, Oakland, and San Jose, along with smaller urban and rural areas...

, 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

Farallon Islands

The Farallon Islands, or Farallones , are a group of islands and sea stacks in the Gulf of the Farallones, off the coast of San Francisco, California, USA. They lie outside the Golden Gate and south of Point Reyes, and are visible from the mainland on clear days...

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 twentieth 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 (fur trader)

Thomas McKay was a Anglo-Métis Canadian Fur trader who worked mainly in the Pacific Northwest for the Pacific Fur Company , the North West Company , and the Hudson's Bay Company . He was a fur brigade leader and explorer of the Columbia District and later became a U.S. citizen and an early settler...

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

Napa Sonoma Marsh

The Napa Sonoma Marsh is a wetland at the northern edge of San Pablo Bay, which is a northern arm of the San Francisco Bay in California, USA. This marsh has an area of 48,000 acres , of which 13,000 acres are abandoned salt evaporation ponds...

in north San Pablo Bay

San Pablo Bay

and its Sonoma Creek

Sonoma Creek

Sonoma Creek is a stream in northern California. It is one of two principal drainages of southern Sonoma County, California, with headwaters rising in the rugged hills of Sugarloaf Ridge State Park and discharging to San Pablo Bay, the northern arm of San Francisco Bay. The watershed drained by...

and Napa River

Napa River

The Napa River, approximately 55 miles long, is a river in the U.S. state of California. It drains a famous wine-growing region, called the Napa Valley, in the mountains northeast of San Francisco. Milliken Creek is a tributary of the Napa River....

tributaries. Also recently re-colonizing the Bay and its tributaries, the North American River Otter (Lontra canadensis) was first reported in Redwood Creek

Redwood Creek (Marin County)

Redwood Creek is a short but significant stream in Marin County, California. long, it drains a watershed which includes the Muir Woods National Monument, and reaches the Pacific Ocean north of the Golden Gate at Muir Beach.-History:...

at Muir Beach

Muir Beach, California

Muir Beach is a census-designated place , unincorporated community, and beach that is located northwest of San Francisco in western Marin County, California, United States...

in 1996, and recently in Corte Madera Creek

Corte Madera Creek (Marin County, California)

Corte Madera Creek is a short stream which flows southeast for in Marin County, California. Corte Madera Creek is formed by the confluence of San Anselmo Creek and Ross Creek in Ross and entering a tidal marsh at Kentfield before connecting to San Francisco Bay near Corte Madera.-History:The...

, and in the south Bay on Coyote Creek, as well as in 2010 in San Francisco Bay itself at the Richmond Marina

Richmond, California

Richmond is a city in western Contra Costa County, California, United States. The city was incorporated on August 7, 1905. It is located in the East Bay, part of the San Francisco Bay Area. It is a residential inner suburb of San Francisco, as well as the site of heavy industry, which has been...

.

Humans are the main mammalian predator in the area.

Jellyfish

Jellyfish are free-swimming members of the phylum Cnidaria. Medusa is another word for jellyfish, and refers to any free-swimming jellyfish stages in the phylum Cnidaria...

have not been prevalent in the Estuary until recently. In east coast estuaries such as the Chesapeake, they are often top-level predators, 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 in the benthos

Benthos

year round.

Their impact on the plankton

Plankton

Plankton are any drifting organisms that inhabit the pelagic zone of oceans, seas, or bodies of fresh water. That is, plankton are defined by their ecological niche rather than phylogenetic or taxonomic classification...

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.

Benthic consumers

The benthic community has taken on a disproportionately large role in the food web ecology of the Estuary due to key invasions by bivalves. 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.

This decline in productivity is essentially due to the redirection of the pelagic network to a benthic chain by this one species. BecaRiver clam feeds on primary producers, consumers and predators, it impacts multiple trophic level

Trophic level

s. Consequently, nearly all plankton exhibit signs of apparent competition, in that production at one trophic level impacts all others by increasing clam abundance. This results in a negative feedback loop: C. amurensis limits plankton biomass, which in turn limits C. amurensis. However, inputs 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 ciliates 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.

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

Shrimp

, amphipods, bivalves, fish and both rooted and floating plants. Many pelagic species have been introduced most recently through ballast water releases from large ships directly into the Estuary. 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

Egeria densa

Egeria densa is a species of Egeria native to warm temperate South America in southeastern Brazil, Argentina, and Uruguay.It is an aquatic plant growing in water up to 4 m deep, with trailings stems to 2 m or more long, producing roots at...

and water hyacinth

Water hyacinth

The seven species of water hyacinth comprise the genus Eichhornia. Water hyacinth are a free-floating perennial aquatic plant native to tropical and sub-tropical South America. With broad, thick, glossy, ovate leaves, water hyacinth may rise above the surface of the water as much as 1 meter in...

(Eichhornia crassipes

Eichhornia crassipes

Eichhornia crassipes, commonly known as Common Water Hyacinth, is an aquatic plant native to the Amazon basin, and is often considered a highly problematic invasive species outside its native range.-Ecology:...

). These plants have created profound changes in the Delta by disrupting water flow, shading phytoplankton, and providing habitat for piscivorous fish like the striped bass

Striped bass

The striped bass is the state fish of Maryland, Rhode Island, South Carolina, and the state saltwater fish of New York, Virginia, and New Hampshire...

, Morone saxatilis, itself intentionally introduced in the late 1800s from the Chesapeake Bay

Chesapeake Bay

The Chesapeake Bay is the largest estuary in the United States. It lies off the Atlantic Ocean, surrounded by Maryland and Virginia. The Chesapeake Bay's drainage basin covers in the District of Columbia and parts of six states: New York, Pennsylvania, Delaware, Maryland, Virginia, and West...

. The freshwater quagga mussel

Quagga mussel

The quagga mussel is a subspecies of freshwater mussel, an aquatic bivalve mollusk.It is one of seven Dreissena species and has an average life span of 3 to 5 years....

, originally from Europe, is expected to be introduced by boaters within the next two to ten years, in spite of precautionary measures.

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

Climate change

. Future ecological changes will be driven on an ecosystem wide scale, particularly as sea level rise, tectonic instability and infrastructure decline cause levy failure in the Delta. 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.

Physical geography

Hydrodynamics

Pelagic zone

Food web

Primary production and nutrient uptake

Photosynthetic production

Detrital production

Secondary production

Primary consumers

Predatory copepods

Macroinvertebrates

Fish

Birds

Mammals

Jellyfish

Benthic consumers

Introduced species

Future invasions

Summary

Future ecology

See also