Ecology of the San Francisco Estuary

[1] Climate change, hydrologic engineering, shifting water needs, and newly introduced species will continue to alter the food web configuration of the estuary.

The intertidal and benthic estuary is presently dominated by mudflats that are largely the result of sedimentation derived from gold mining in the Sierra Nevada in the late 19th century.

[9] Phytoplankton, zooplankton, and larval and adult fish can become entrained in the export pumps, causing a potentially significant but unknown impact on the abundance of these organisms.

This 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.

[12] 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.

[13] A fixed mixing zone occurs at the "Benicia Bump" at the east end of the Carquinez Strait, where the deep channel becomes dramatically shallower as it enters Suisun Bay.

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.

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.

[15] These provided nutrition and energy to native filter feeders such as the northern anchovy (Engraulis mordax), and planktivores such as delta smelt and juvenile salmon.

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 and an assumed increase in waste detrital production.

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.

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.

[22] This is probably due to two factors: large inputs of nitrogen in the form of ammonium, 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.

[28] Another suppressive factor on growth rate is the high turbidity of the estuary, which limits the ability of photosynthetically active radiation (PAR) to penetrate beyond the top few centimeters of the water column.

[27] The north Delta and Suisun Bay have relatively low residence times due to the high volume of water moving through the region for downstream flow and for export to southern California.

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.

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

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.

[16][43] 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.

All species of calanoid copepods have declined under high predation pressure from the recently introduced Amur River clam (Corbula amurensis).

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.

In January 2015, scientists were working to identify a gray, thick, sticky, odorless substance coating on birds along San Francisco Bay shorelines.

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.

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.

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.

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.

These plants have created profound changes in the Delta by disrupting water flow, shading phytoplankton, and providing habitat for piscivorous fish like the striped bass, Morone saxatilis, itself intentionally introduced in the late 1800s from the Chesapeake Bay.

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.

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