Bay Nature magazineFall 2004

The Bay

Still Hanging On

October 1, 2004

If you were to walk into the shallow water of San Francisco Bay, it’s quite likely you would find yourself sinking in up to your knees—unless you’re a black-necked stilt with long, slender legs and toes. Yet where today we have tidal flats coated in viscous Bay mud, there once were jumbled, sharp-edged clusters of oyster reefs cemented to shoreline fringes.

In prehistoric times, generations of oysters grew on top of one another, forming near-shore labyrinths of tunnels, nooks, and crannies, refuge and spawning habitat for myriad fish, barnacles, mussels, sponges, and other small estuarine animals. Fish eggs clung to the shells of live and dead oysters, young fish hid from predators, and tiny volcano-shaped barnacles rhythmically kicked microscopic food into their mouths with infinitesimal legs. Surrounding the reefs, oyster gardens of clams, worms, snails, and thousands of other minute invertebrates burrowed and crawled among wispy strands of eelgrass, ingesting food that haloed from above.

Today the reefs are gone, buried under layers of silt. But shell remnants of these complex underwater communities are still present in the Bay ecosystem, whirling about in the currents with the remains of nonnative oysters and clams from a more recent era. Scoured shells pile up into long banks and wash up on the mudflats in the South Bay. And hiding below the surface, ancient oyster remains still form thick layers, despite decades of commercial dredging of the calcium-rich shells for use in making cement, chicken feed, and even the surfacing for bocce ball courts.

Though the prolific reefs have disappeared, remnant oyster populations cling to boats, dock pilings, floating piers, and shoreline rocks, says Holly Harris, a San Francisco State University graduate student researching Ostrea conchaphila, the West Coast native oyster.

For over a year, Harris combed the Bay’s fringes in search of live native oysters. First she searched the subtidal zone (the shallow waters below low tide), where reefs once formed. Using a dredge boat, she scooped up mud, exotic jellyfish and sea squirts, worms, and shell fragments, but she found only a few live oysters in one place: Point Pinole near Richmond. However, as she kept searching, she discovered clusters of live oysters cemented to pier pilings and shoreline rocks around the Bay—especially at China Camp State Park in Marin.

Recognized as some of the most pristine wetland left in the estuary, the salt marsh and shoreline areas in China Camp State Park on the southwest shores of San Pablo Bay became part of the region’s first National Estuarine Research Reserve one year ago. On a warm June day here, I am strolling along the park’s main beach with Harris and her thesis adviser, Michael McGowan. We pass the site of the Chinese shrimp-fishing village that thrived here in the late 1800s and look out at the glistening mudflat strewn with rocks, scurrying crabs, green algae, and craters full of salt water.

Crouching on the shore, McGowan picks up a rock covered by shelled creatures of many sizes. Pointing to one, he says, “That’s a live native oyster; it’s low tide, so it’s closed up.” At first glance, the clump looks like nothing more than a muddy rock. “Once you know what you are looking for, then you see them,” says McGowan. “See this light-colored one? This is what they look like when they’re small, but for some reason this one died at about one year.” When an oyster is about the size of a thumbnail, or two months old, its elliptical brown shells become visible. Gradually adding shell in radiating ridges, it forms an oblong shape resembling an earlobe and is fully grown in about four years.

Holding another clump, McGowan points out some live baby oysters adorning the edge of a large exotic clam. A fisheries biologist researching the restoration of this forgotten native mollusk, McGowan envisions a time when they will form reefs again. “Here are some small ones as well as some larger ones; now, you can imagine if that became more successful and expanded, they could build out onto the mudflats,” he says.

The tide is creeping back in, and in less than six hours, water will inundate the mudflat cluttered with clumps of miniature reefs—oysters, barnacles, and mussels on rock foundations.

When covered by water, the cilia of the oyster’s gills beat to siphon in the current of water, allowing the oyster to breathe and filter-feed on microscopic plants called phytoplankton. Animals in the estuary live by the rhythms of the tides, which bring in food and send out waste. “They don’t have to pay water and sewer bills; that is all taken care of,” says McGowan. But as with most things in life, there is a cost. Bat rays, native fish up to six feet across, invade the intertidal zone on the flooding tide. Pointing to a water-filled pit in the mud, McGowan says, “When bat rays are feeding, they flap their ‘wings’ to wash away the sediments.” Then they devour the oysters, clams, and other shellfish by crushing the shells with their teeth.

We are here in the midst of spawning season, which runs from May to September. Males release several million sperm each by opening their shells, called valves. Females filter the sperm as it billows through the water. Like many mollusks, the oyster is a hermaphrodite, though it does not produce sperm and eggs simultaneously. All native oysters begin life as males, but, after releasing sperm, they can undergo multiple sex changes to reproduce as much as possible.

Once the female’s eggs are fertilized, larvae develop inside the female’s gill chamber for about 10 days, changing color from white to gray to black, explains Harris. When larvae turn black, females open their valves, releasing about 250,000 little oysters, one-eighth of a millimeter in size, to the mercy of the currents. Looking like a diaphanous swirl of tiny shells, they first drift and then swim upside down using tiny cilia for one or more weeks until they get eaten, die, or find a hard surface that is suitable for life-long attachment. A tiny foot, used solely as an attaching organ, protrudes above the infinitesimal creature’s shell until it attaches to something. Ideally, the foot will find a place where another oyster managed to grow—that is, another shell to settle on. (As its scientific name, Ostrea conchaphila, implies, the larvae are “shell-loving.”) But almost any hard surface will do—a rock or a piece of wood, or washed-up iron pipe. Once it finds the surface that it will call home for life, the oyster’s foot secretes a kind of permanent cement and latches on.

Like many rocky shorelines along the Bay, this one at China Camp Beach is not natural. Rocks were placed here to protect the historic Chinese buildings, which might otherwise sink into the mud. For now, these shoreline rocks and marina docks are the primary habitat for remnants of an ancient oyster population that was once a mainstay of the Native American diet.

Native Californians lived in hundreds of small villages near streams and alongside the evolving tidal wetlands of San Francisco Bay. Over thousands of years, generations of Coast Miwok and Ohlone built mounds of shells that attested to enormous populations of shellfish in the Bay. The oldest shellmounds, dating back several millennia, were about the same age as the ancient reefs buried in the South Bay.

By the time the Spanish arrived in the Bay Area, some mounds had bases as large as football fields and reached 40 feet in height, says Mark Hylkema, a state park archaeologist who specializes in Bay Area prehistory. Before they were destroyed by urban development in the 20th century, many of these mounds were studied extensively by archaeologists. Oysters and mussels dominated the oldest layers of many mounds, and bent-nose clams dominated the younger layers. Hylkema attributes the implied shift in the native diet to a shift in the estuary’s habitats. “The oyster thrived with a rocky bottom and hard sediment, then it became nothing but mud,” he says. Many scientists believe that the Bay took shape 6,000 to 7,000 years ago with the rise of sea level at the end of the last ice age. The sea continued to fill in the Bay, slowing and stopping about 3,000 to 4,000 years ago. Subsequently, shorelines began to fill in with soft sediments, creating vast salt marshes and mudflats.

The shellmounds and buried reefs in the South Bay testify to an oyster heyday more than 2,000 years ago. It is impossible to say how abundant oysters were in the subsequent period. However, we do know that as soon as the gold-seeking immigrants arrived in the Bay Area after 1848, they fixated on fishing the little mollusks out of the Bay. Apparently the local oysters did not satisfy their appetites, either because of their size and taste, or because there simply weren’t enough left. In any case, within a couple of years the connoisseurs began importing oysters from Willapa Bay in Washington State, where they were more abundant and larger, though the same species. San Franciscans soon began calling the West Coast native the Olympia oyster, the common name in Washington. Near Alameda, Richmond, Point San Quentin, Point Pinole, and Sausalito, oyster entrepreneurs stored the “Olys” in artificial shoreline beds staked with underwater fences to keep out bat rays.

The oyster business based on the Washington imports was short-lived. As soon as the transcontinental railroad was completed in 1869, the “Olys” were replaced by Crassostrea virginica, the Atlantic coast native preferred for its flavor and size. San Franciscans imported over 100 trainloads of virginicas per year for “fattening” in tidal beds. While the East Coast oysters never successfully reproduced in the Bay, their shells hosted invertebrates that eventually established thriving populations here.

As the train cars poured in, the oyster business shifted south to San Mateo County due to heavy siltation of the north and central Bay. Hydraulic mining in the Sierra washed massive quantities of sediment down from the foothills into the Delta, blanketing the northern parts of the Bay with silt and smothering live oysters in commercial beds. The South Bay was spared, but the tidal mudflats there were isolated from shore by extensive marshes, and thus vulnerable to poachers—the “oyster pirates” of Alameda and Oakland made famous by author Jack London, who worked both with and against them in his youth.

In the early 1900s, raw sewage and industrial pollution from rapid and unchecked urbanization suffocated and poisoned the commercial oysters. After a typhoid scare, public demand for shellfish waned, and by 1939, San Francisco Bay no longer had an oyster industry.

While the native oyster was not actually displaced by its farmed eastern counterpart, its populations likely suffered from the chronic pollution that afflicted all Bay wildlife in the century following the Gold Rush. Today, despite environmental legislation such as the Clean Water Act, pollution and siltation from shoreline erosion remain significant problems in the Bay. Habitat loss and invasive nonnative species continue to threaten Bay ecosystems. Over 200 exotics now dwell in San Francisco Bay, making it one of the most invaded estuaries in the world. Invasives such as the Atlantic oyster drill and European green crab prey directly on oysters; nonnative sea squirts crowd them out; and the rapidly multiplying Asian overbite clam consumes untold quantities of phytoplankton in some parts of the Bay, starving out other species.

Despite the many stresses of urbanization, native oysters “are going to hang in there,” says Tom Moore, a California Fish and Game marine biologist. But “it would take large-scale restoration” for the species to flourish, and the science to make that happen is still “unknown,” says Moore.

McGowan believes such a project would be well worth undertaking, given the spawning and refuge habitat that oyster reefs can provide for native fish and invertebrates, which in turn feed numerous birds and marine mammals. As filter feeders, oysters also clear up water so that eelgrass can photosynthesize and grow, providing habitat and nutrients to the estuary. While the mainstay of their diet is marine phytoplankton, oysters also “repackage” small particles of organic matter that wash in from the Delta and Bay tributaries. These particles stick to the mucus in the oysters’ filtering channels, aggregating into little packets that are nutritious for other bottom-dwellers in the mud.

Scientists and community volunteers are now working together to find out if, with a little help, native oyster populations can rebound and bring their unique reef habitat back to the Bay. A similar experiment is under way in Tomales Bay, and large-scale restoration is already taking place in Chesapeake Bay, where the eastern oyster once formed reefs so vast that they posed a hazard to ships in the 19th century.

In 2001, the local environmental nonprofit Save the Bay organized the Native Oyster Project with a grant from the National Oceanic and Atmospheric Administration’s (NOAA) Community-Based Restoration Program and scientific support from McGowan and Harris. Led by Marilyn Latta, Save the Bay’s habitat restoration manager, five teams of volunteers hung ropes strung with shells, called “oyster necklaces,” from shoreline docks Bay-wide to find out if and where oyster larvae drift in the currents.

By the third month of the oyster project, volunteers found baby oysters on necklaces hanging near the shores of Coyote Point in San Mateo, the Oakland estuary, and Richardson Bay in Marin. Along with the oysters, an array of exotics, some impossible to name, covered the necklaces. Exotic sea squirts, which look like translucent balloons with pant legs, made the oyster necklaces weigh as much as 100 pounds.

The necklace experiment proved that oyster larvae are in fact still drifting in the currents in many places around the Bay. From these results, McGowan hypothesized that if oysters had places to settle, they could expand their populations. To take that next step, McGowan is partnering with the Tiburon Audubon Center to test the effects of introducing larger artificial reef habitat into one subregion of the Bay, the calm and relatively clean waters of the Richardson Bay Audubon Sanctuary. This summer, the crew began testing whether artificial reefs—wooden palettes with bags of oyster shells stacked on them—placed in the low intertidal and shallow subtidal areas could jump-start the local population.

Supported by NOAA and the Tiburon Peninsula Foundation, McGowan, Harris, and volunteers from Tiburon Audubon are now monitoring the reefs, counting the leopard sharks, bat rays, starry flounders, surfperch, and other fish that routinely cruise the waters to feed. They are also surveying the reefs themselves to see which creatures are finding a niche there.

But will conchaphila dominate the reef? Will juvenile chinook salmon linger in the shallow waters to feed and grow before going to sea? Will small endangered fish like the bay goby find a safe place to lay their eggs? Will large flocks of wintering greater scaups dive in the shallows to forage? Definitive answers to these questions are a long way off, but McGowan certainly hopes so. “The oysters are just one part of a mosaic of interrelated habitats that include salt marshes, eelgrass beds, and mudflats,” he says. “Restoration of individual parts of the system may seem insignificant, but the synergistic effects can really amount to something over time.”

To find out more about the Richardson Bay restoration efforts, call the Tiburon Audubon Center at (415)388-2524. This article was funded by the U.S. Environmental Protection Agency and the San Francisco Estuary Project.

Update: January 2005

In “Still Hanging On: The Bay’s Native Oysters” (Oct-Dec 2004), Bay Nature reported on fisheries biologist Michael McGowan and San Francisco State University graduate student Holly Harris’ research on restoring the San Francisco Bay’s native oyster, Ostrea conchaphila. In the last three months, McGowan and Harris have made several strides in their work. Over the summer, McGowan introduced larger artificial “reefs”—bags of oysters stacked on wooden palettes—to provide an alternative substrate for oyster larvae. In September, McGowan’s team retrieved several of their reefs from Tiburon’s Richardson Bay and, according to McGowan, the “native oysters had colonized the shells in very high numbers and they had grown to remarkable size in such a short time.” In the course of their monitoring, McGowan’s team also collected a thornback (Platyrhinoidis triseriata), a fish that has been collected only once before in the Bay in the last 20 years.

In perhaps the best news yet for the future of oyster restoration efforts, McGowan and Michele Pearson of the Tiburon Audubon Center have been awarded a grant to put together a guidebook for restoring native oysters in San Francisco Bay. The book, scheduled to debut by the end of 2005, will include the history and biology of the Bay’s native oysters, as well as recommended approaches for restoration efforts in the San Francisco Bay. [Matthew Bettelheim]

About the Author

Christine Sculati is a Bay Nature contributor and writes about state park closures and nature on her blog,