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Home Page San Francisco Bay Ecology
San Francisco Bay has a wide array of interesting wildlife, many of which are detailed in this page. If you would like to read about all of the topics listed below, scroll through the page. If you are interested in a particular topic (i.e. Fish in the Bay), choose that topic below and you will be taken to its spot on the page...
What is an invertebrate?
An invertebrate is an animal without a backbone. Although all invertebrates share this trait, the diversity of shapes and sizes found within invertebrates is tremendous. Invertebrates are found everywhere: on land and in the soil, in freshwater, in saltwater, and even in the bodies of other animals! In fact, invertebrates make up 97% of all animals on the earth.
Invertebrates are very abundant in the muddy, bottom sediments of the San Francisco Bay Estuary. This area is called the benthos and is a habitat for many varieties of plant and animal life. Invertebrates such as crabs, snails, and sea squirts live on top of the mud, while clams, mussels and tube worms are more often found in the mud. Each group of invertebrates has various adaptations to feed, move, and hide from predators.
Common San Francisco Bay Invertebrate Groups:
Invertebrates have been classified into different groups by biologists. The groups are usually based on certain traits that the organisms have in common with others in that group. We will examine the characteristics of 6 different phyla of invertebrates that inhabit San Francisco Bay...
Phylum Porifera
Invertebrates in the Phylum Porifera are pore bearing animals. Common Bay inhabitants in this group are the sponges. A sponge absorbs bacteria and dead plant and animal matter as the particles flow through its porous body. Sponges can act like a mini "hotel" or "apartment complex" for other animals; one sponge may contain hundreds of tiny organisms.
Phylum Molluska
Invertebrates in the Phylum Molluska are soft-bodied animals. Common Bay inhabitants in this group are the clams and mussels. Clams and mussels are filter feeders, filtering out microscopic plants and animals floating in the water. Clams move about by using a hatchet-shaped foot to creep along the muddy bottom of the Bay. Although mussels also have a foot, mussels attach themselves to certain places with "byssal threads" so that they don't move! The sticky threads are produced from a gland near their foot.
Phylum Annelida
Invertebrates in the Phylum Annelida are segmented worms. A common bay inhabitant in this group is the tube worm. Tube worms live in brown mud tubes that the worms make from a mucus and mud mixture. Because the tube worms eat much of the dead plant and animal material decomposing on the bay bottom, the tube worms can be thought of as one of the great trash collectors in the Estuary! The tube worm is not native to San Francisco Bay, it was introduced in the 1800's with the oysters brought over from the east coast to start an oyster industry in the Bay.
Phylum Arthropoda
Invertebrates in the Phylum Arthropoda have jointed limbs. Common bay inhabitants in this group include crabs, crayfish, insects, and spiders. The decorator crab is an arthropod that we often see on MSI's Discovery Voyages. The decorator crab uses its front claws to eat algae and other dead plant or animal life from the bottom of the Bay. This crab gets its nickname for a very good reason. The crab takes its food, algae, and deposits it on its body (carapace) and legs, ensuring camouflage and a meal when desired.
Phylum Cnidaria
Invertebrates in the Phylum Cnidaria have specialized stinging cells. Common bay inhabitants in this group include anemones and jellyfish. The orange anemone is very common in San Francisco Bay. The anemone is small, approximately 1 cm in length, and is often found attached to the inside of empty shells or on sponges. Orange anemones eat zooplankton that are immobilized by stinging cells on the anemone's tentacles. Don't worry...the stinging cells on an orange anemone are too small to hurt us!
Phylum Chordata
A common bay inhabitant in the Phylum Chordata is the tunicate or "sea squirt". Sea squirts have globular bodies that look like a pair of inflated pants (due to 2 siphons at one end). They are filter-feeders, filtering out plankton from the water column as do clams and mussels. A tunicate's body is filled with air and/or water. At times, by gently squeezing its body, a tunicate will squirt out water like a fountain from one of its siphons...hence the nickname!
What is a fish?
If an animal lives in the water, has a backbone, breathes with gills, is cold-blooded (has a body temperature equivalent to its surroundings), and has fins, chances are the animal is a fish. The study of fish is called ichthyology. A look at the external morphology (form and structure) or a fish can tell us a great deal about where it lives and how it makes its living. The shape of the fish's body, the size and shape of its fins, the size and placement of its mouth and the coloration of the fish all have a story to tell. Other information about fish such as reproductive, physiological, and life history characteristics are not so easily determined by simply examining the structure of the fish. To gain access to this knowledge we must first be able to identify the fish and learn the name of the species to which the fish belongs. Once we know the species name of the fish we can look up what others have found out about it.
Common San Francisco Bay Fish
Fish in San Francisco Bay can be classified as either bottom dwellers, middle dwellers, or top dwellers, depending on where the fish lives.
Bottom Dwellers:
Bottom dwellers live on the bottom of the Bay in the muddy sediments. Examples of common bottom dwellers in the Bay are the California Halibut and Leopard Shark.
The California Halibut has an amazing ability to blend in with the environment, itcan change color depending on the type of ground cover in the area. This fish begins life with two eyes in the traditional position (one on each side of the head), but immediately after birth one eye begins to migrate. Eventually both eyes are on one side of the head, a distinct advantage for a fish always lying flat on one side.
The Leopard Shark is grey with heavy black bars and spots. Sharks have no bones; their skeletons are made of cartilage, like our noses! Although they have generally poor eyesight, they have a great sense of contrast. Their eyes have a special layer that intensifies light so that they can see their prey in near dark conditions. Although they have a bad reputation, only 7 out of the 344 species of sharks are truly dangerous to humans.
Middle Dwellers:
Middle Dwellers are fish that dwell in the mid-water zone of the Bay. An example of a Middle Dweller that inhabits San Francisco Bay is the Shiner Surfperch. The Shiner Surfperch is laterally compressed (normal fish shape) and has 2-3 faint yellow stripes on each side. Their front-positioned mouth and small teeth allow them to eat smaller fish and invertebrates in the Bay.
Top Dwellers:
Top Dwellers are fish that inhabit the surface waters of the Bay. An example of a Top Dweller that inhabits San Francisco Bay is the Jacksmelt. Smelt are long, silvery, and torpedo shaped with small mouths located at the front of their body. These fish eat plankton and small crustaceans near the surface. When threatened by predators these fish school together, possibly confusing the predator into believing that the school is one big fish.
California Sea Lions and Harbor Seals are common aquatic mammals inhabiting San Francisco Bay. The Harbor Seals (Phoca vitulina) get their name from the fact that they are frequently observed in protected inlets, bays, and river mouths. These seals are mottled with numerous white and black spots. Although males and females are similar in appearance, males are typically larger. Male Harbor Seals can reach upto 6 feet in length and 300 pounds. Like other seals, the Harbor Seal is well-adapted for diving and can dive to depths of 1000 feet, surface rapidly, and not experience the bends (something we can not do!).
The California Sea Lion (Zalophus californianus) is the most common eared seal on the California coast. Sea Lions get their name from their breeding and social behavior. Males, like African lions, fight for dominance and maintain a harem of females. California Sea Lions are typically larger than Harbor Seals; males can grow up to 8 feet in length and weigh over 600 pounds! California Sea Lions are tan in color but appear dark brown to black when wet. Unlike Harbor Seals that mate in the water, California Sea Lions mate and give birth on land. Since the passage of the Marine Mammal Protection Act in 1972, the number of California Sea Lions has increased and continues to increase each year.
Another interesting mammal inhabiting the San Francisco Bay marshlands is the Salt-marsh Harvest Mouse (Reithrodontomys raviventris). This mouse is endemic to the San Francisco Bay area and has been listed as a federally endangered species. Salt-marsh Harvest mice are unique because they can drink and survive on pure salt-water! Furthermore, these mice build nests in the vegetation similar to the nests of birds. These insulated nests help the Salt-marsh Harvest Mouse to conserve energy. Bair Island, the island adjacent to the Marine Science Institute, is one of the few places in the San Francisco Bay area that the mouse still can inhabit.
Reference:Schoenherr, A. A. 1992. A Natural History of California. University of California Press. Berkeley, California.
San Francisco Bay is very important to numerous species of birds. As part of the Pacific Flyway, thousands of migratory birds use the Bay waters each winter. Other species inhabit the Bay waters year round, using the mudflats, marshlands, and open water. The California Clapper Rail (Rallus longirostris soletus) is an endangered species of bird that inhabits the marshlands of San Francisco Bay. Habitat destruction and predation by introduced Black Rats, has decreased the number of California Clapper Rails to very low levels. Wading birds such as Herons, Egrets, Sandpipers, and Avocets are commonly seen on the mudflats of the Bay. These birds forage for fish and invertebrates in shallow water and muddy areas exposed at low tide. Birds inhabiting the open waters of the Bay include numerous species of ducks, gulls, cormorants, grebes, and brown pelicans. These birds either hunt for prey from a position on the water or dive into the water from the air to capture prey.
Reference: Schoenherr, A. A. 1992. A Natural History of California. University of California Press. Berkeley, California.
Within the last 150 years, increased numbers of humans and increased avenues open to international shipping have greatly contributed to the decline of Bay resources. One way in which these resources have been compromised is the replacement of native flora and fauna with exotic species. Species introductions can be intentional or non-intentional. Most of the species that have been introduced into our Bay during the last 150 years were non-intentionally introduced. One of the most common mechanisms of non-intentional introductions is the release of ballast water carried on ships from foreign ports, a practice still occuring in our Bay today. Although new species are probably introduced into the Bay all of the time, it is the species that are introduced and become established that we need to worry about.
Over the last 140 years, over 100 species of non-native aquatic invertebrates have become established as a part of the San Francisco Bay fauna. Most of the fish that are presently found in the Bay-Delta are non-native. One introduced species, the striped bass, is even used as an indicator species to give us information about the health of our Bay! Andy Cohen, a marine biologist specializing in aquatic species introductions, estimates that one new aquatic species has been introduced into the Bay every 24 weeks since 1970.
Nichols and Patmatmat (1988) stated that accidentally introduced species may have thrived in San Francisco Bay because of the relatively young age of our Bay and the predominance of a single habitat type, soft mud, throughout the Bay. The young age of the Bay may not have allowed a diverse fauna to evolve prior to the introduction of exotic species. A single habitat type limited the number of niches available in the Bay for species to invade and diversify.
Some of the notable introduced species into San Francisco Bay are the Striped Bass, Asian Clam, European Green Crab, Chinese Mitten Crab, and the marsh grass Spartina.
References: Nichols, F. H. and M. M. Patmatmat. 1988. The ecology of the soft-bottom benthos of San Francisco Bay: a community profile. U. S. Fish and Wildlife Service Biological Report 85 (7-23) 73 pp.
Cohen, A. 1997. personal communication. University of Calfornia - Berkeley.
Monroe, M. W. and J. Kelly. 1992. State of the Estuary. San Francisco Estuary Project. U.S. Environmental Protection Agency and the Association of Bay Area Governments. Oakland, CA.
Species that presently require our attention for conservation can be listed as endangered, threatened or of special concern by either the U.S. government or the State of California. There are presently 5 federally endangered species inhabiting the San Francisco Estuary, The San Francisco garter snake, the California clapper rail, the California least tern, the San Joaquin kit fox, and the salt marsh harvest mouse. Three of these species (clapper rail, least tern, and salt marsh harvest mouse) inhabit Bair Island directly across from the Institute.