Delta Smelt’s Fate Worries Scientists

Last summer, state fish and game workers dragged a net dozens of times through the milk-chocolate waters of the Sacramento-San Joaquin Delta, looking for a tiny, steely blue fish found nowhere else in the world. The catch, 17 delta smelt, was shockingly small.

Never in the nearly five decades that the state has monitored smelt in the sprawling delta, where two of the state’s biggest rivers converge just east of San Francisco Bay, have their numbers been as dismal. So abundant a generation ago that fishermen used the translucent, finger-length fish for bait, the delta smelt population has plummeted from the millions to an estimated 100,000 or less -- bringing it, some warn, to the brink of extinction.

The smelt’s recent collapse, coupled with the decline of three other fish species that swim in the delta, has launched a multimillion-dollar scientific detective hunt for the reason.

There is a sense of urgency because the smelt’s only home is one of California’s most important, if troubled, ecosystems. The hub of the state’s giant water system and a Bay Area playground, the delta is a vital link in the estuary chain that supports most of California’s commercial fish species.

If the smelt is lost, it will be one more sign that the delta is too taxed to give Californians everything they demand of it.

“The only way we’ll be able to save this estuary and the valuable resources it provides ... is by figuring out what’s going wrong for this little fish,” said Tina Swanson, a senior scientist with the Bay Institute, which last month petitioned the federal government to upgrade the smelt’s protected status to endangered.

Environmental safeguards in place for more than a decade have altered the operation of the big government water projects, sometimes even shutting down the enormous delta pumps that supply two out of three Californians. But that hasn’t been enough.

“I think for delta smelt it’s looking pretty gloomy,” said UC Davis research ecologist Bill Bennett, who has spent much of the last decade studying the fish’s decline. The delta “is really not a good place for them to live anymore. It’s a very different aquarium these fish are in than it was 30 years ago.”

The delta’s degradation started with the Gold Rush, when settlers drained its vast, rich tidal marshes for cropland and walled its meandering waterways with earthen levees. More recently, the estuary’s natural rhythms of flow and saltiness have been broken by upstream dams and delta water exports that rocketed after completion of the State Water Project in the late 1960s. Farm and urban runoff has brought a stew of pesticides and other contaminants, and an ever-expanding array of nonnative species competes for food and habitat.

Yet scientists aren’t sure exactly what in that grim summary is pushing the smelt to the edge of survival.

“Is it one more straw on the camel’s back or did something new creep in?” asked Bruce Herbold, a U.S. Environmental Protection Agency fish biologist who is helping coordinate the scientific sleuthing by a consortium of federal and state agencies.

The smelt’s numbers began to plunge in the early 1980s. In 1993, the fish was listed as threatened under the Endangered Species Act. The Bay Institute and two other groups say the listing should now be changed to endangered.

“Many of us watching the situation fully expected, because last year was a good water year, the numbers would be better,” said David Harlow, an assistant field supervisor with the U.S. Fish and Wildlife Service. “They aren’t.”

Moreover, three other delta fish have also taken a dive since 2002: the native longfin smelt, young striped bass and -- most surprising to biologists -- the threadfin shad.

“That blew everyone away because they had been doing wonderfully for years,” said Ted Sommer, a state Department of Water Resources environmental specialist.

After a year of data-crunching, the science team suspects there is not one culprit, but many.

Inevitably, any look at the delta turns to the mammoth government pumping operations in the south delta that fill the aqueducts carrying water to the vegetable fields of the San Joaquin Valley and the subdivisions of Southern California. The pumps are so powerful that they can reverse the natural flow in delta channels.

In 2003, enough fresh water was sucked out of the delta to fill a lake the size of Los Angeles to a depth of nearly 22 feet. Delta water exports in the last five years have been among the highest on record, according to state figures, and the timing of exports has also changed. Less water is being pumped in the spring and more at other times of the year, particularly during winter, a shift that was intended to protect spawning female fish.

“You can’t really deny that smelt have gone down while pumping has gone up, and the big crash took place when they changed the time of the pumping,” observed Peter Moyle, a UC Davis professor of fisheries biology who thinks the operation of the state and federal water projects “is clearly playing a major role.”

Although screens steer fish from the pumps into collection tanks for transport back to the delta, the smelt are so small and fragile that many are sucked into the pump apparatus or don’t survive the tanks.

The higher pumping rates, Moyle speculates, may be pulling water through the delta so quickly that it’s interfering with the production of beneficial algae and hurting the food web. And more fish may be dying at the pumps during the winter, before they can spawn.

Moyle, whose work helped win the smelt endangered species protection, started studying the fish in the early 1970s.

“You’d go out there and do a 20-minute trawl for striped bass and you’d come back with a tub of fish that was mostly delta smelt,” Moyle recalled. “You know you’ve got them even before you see them. You get this waft of cucumbers” -- their signature smell.

So delicate it can die if held for an instant, the smelt remains somewhat mysterious. It lives for only a year, and scientists don’t even know exactly where in the delta it spawns -- only one egg has been collected in the wild.

The effect of the water projects extends beyond the pumps. Delta hydrology has been fundamentally altered by upstream dam releases that maintain a year-round supply of fresh water, disrupting the natural inflow pattern along with the balance of fresh and salt water.

“It used to be salty in the summer and really fresh all the way down to Suisun Bay in the springtime, every year,” Herbold said. “And now it’s fresh all the time. It’s just stable. It’s the Mississippi River.”

That has made the delta a better home for exotic species, many of which were dumped into San Francisco Bay with ballast water emptied by ships from distant ports. Scientists have documented more than 200 kinds of alien plants, fish and invertebrates. More arrive every year, making the bay-delta one of the most invaded estuaries in the world.

For natives such as the smelt, that means more competition for food. And it means the food itself has changed.

One invader in particular, an Asian clam known as the overbite clam for its mismatched shells, is a delta villain. Since its 1986 discovery, the voracious eater has carpeted parts of Suisun Bay and marsh -- an important fish nursery and one of the least altered parts of the delta.

“It’s aliens, aliens, aliens, aliens -- that’s what’s going on in the delta, this huge invasion and dominance of alien species,” said B.J. Miller, an environmental engineer who consults for major federal water contractors dependent on delta supplies. He argues that the focus on water exports is overblown.

Scientists are also examining the effect of toxics. Pesticides, industrial pollutants, mercury from 1860s Sierra gold mining -- all can be found in the delta. In recent years, Central Valley farmlands that drain into its waters have switched from a class of pesticides harmful to humans to pyrethroids, which are better for people but poisonous to aquatic organisms.

At the Aquatic Toxicology Laboratory at the UC Davis School of Veterinary Medicine, researchers bathe amphipods, tiny crustaceans, in beakers of delta water for 10 days to see if they grow or die. In similar testing last year, 5% of the delta water samples were toxic to the creatures, a crucial part of the food chain.

Using hatchery fish, the lab is about to conduct the same sort of experiment with striped bass and delta smelt. “Is the water toxic to aquatic organisms, and if it is, can we identify what is causing the toxicity?” asked lab director Inge Werner.

At another Davis lab, pathobiologist David Ostrach has been studying striped bass since the late 1980s. A few years ago he found that eggs from females captured in the Sacramento River upstream from the delta were contaminated with chemicals such as PCBs and flame retardants that interfered with larval growth and development.

“You have an animal that right at first feeding is set up to fail,” Ostrach said. “Those are fairly disturbing results.”

But he can’t say if that sort of individual effect helps explain the recent tumble in overall fish numbers.

The delta’s fish troubles, Ostrach suspects, are manifold.

“I don’t believe they’re going to put their finger on any one thing,” he said of researchers. “It’s multiple things causing multiple problems.”