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fish
18
Nov

Spawning and rearing habitat for important forage-fish species in San Francisco Bay apparently shifts geographically by many miles depending on how much freshwater is flowing into the Estuary.

In a recent study, a team of scientists found that in a dry year, Pacific herring and longfin smelt larvae occurred farther up the Estuary than in a wet year, when spawning and recruitment was pushed seaward. The results suggest that the fish have broader geographic ranges than previously believed, a finding that could inform efforts to manage and protect their habitat. Biologists have long assumed that longfin smelt, a protected species in steep decline for decades, spawn strictly in...
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22
Sep

Heavy Lifting for Fish

Ted Frink recalls watching Jacques Cousteau’s television specials when he was growing up in coastal Orange County. “I envisioned myself as Cousteau,” says Frink, a fisheries biologist with the California Department of Water Resources (DWR) now approaching retirement. “My folks encouraged my interest in science. I knew I could be a biologist.” That early inspiration sparked a long and varied career, culminating in his work as chief of DWR’s Special Restoration Initiatives Branch and his role in mitigating obstacles to...
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22
Sep

Retrofitted Houseboat IDs Fish in the Shallows

On a hazy Delta morning at Isleton’s B & W Resort, more than a dozen trucks are already neatly arrayed in the double-long parking spaces with empty trailers facing the boat launch: evidence of fishers and boaters getting an early start on their Labor Day weekend. Randy Mager, sporting a flannel shirt and worn baseball cap, radiates earnest enthusiasm, which for a 20-year state government veteran is as refreshing and rare as a Delta smelt. “I am more excited about...
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13
Sep

By looking solely at the results of a single annual fish-counting survey, Californians may be seeing an incomplete reflection of Bay-Delta fish population trends.

A team of scientists analyzed 14 survey programs carried out by state and federal agencies, as well as UC Davis, and concluded that employing such a diverse variety of long-term surveys is essential for accurately tracking and assessing the overall health of San Francisco Estuary’s ecosystem and its resident fishes. The research is described in the June issue of San Francisco Estuary and Watershed Science. Lead author Dylan Stompe, of UC Davis, explains that the research arose from concerns that...
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13
Sep

A unique adaptive behavioral trait that may once have helped winter-run Chinook salmon thrive in the Sacramento River system could now be working against the fish as they face extinction.

The trait – which cues fish when to spawn based on water temperature – isn’t syncing up with current conditions in the Sacramento River below Shasta Dam. A paper published in the June issue of San Francisco Estuary and Watershed Science, reports that cooler springtime river temperatures seem to prompt earlier winter-run spawning while warmer temperatures push back the peak spawning period by a week or two. Under historic conditions, when winter-run Chinook spawned in high-elevation streams now inaccessible to...
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05
Aug

More than half the water diverted from Central Valley rivers is used to irrigate cattle-feed crops, implicating beef and dairy as top drivers of recent fish declines.

Recent findings, published in Nature Sustainability in March, strengthen the environmental arguments for going vegan while rewriting the familiar narrative that almonds and other high-value tree crops are the top hogs of Central Valley water resources. The study’s authors, led by Brian Richter of Virginia-based Sustainable Waters, focused on the arid West and found that irrigated crops like alfalfa and hay, more than any others, are drying out rivers. The reduced flows are pushing dozens of fish species toward extinction....
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19
Mar

Kinky Fish Spines Linked to Selenium

By Joe Eaton Scientists with the U.S. Geological Survey and the National Oceanic and Atmospheric Administration are using new tools to track selenium, with the Sacramento splittail, a California-endemic fish, as an indicator species. Robin Stewart, lead author of a new paper on splittail and selenium, is one of the region’s most seasoned current experts on bioaccumulation of metals in estuarine species. In some sampled splittail, selenium levels exceeded the proposed EPA protective criteria for fish ovaries. Liver levels, not...
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05
Mar

A career spent monitoring imperiled fish has given Randy Baxter a strong sense of the vulnerability of aquatic ecosystems.

“We’ve overtaxed the system,” he says. Baxter officially retired from the California Department of Fish and Wildlife last August, but still works two or three days a week as a “reemployed annuitant”—a big change from supervising a staff of 14 studying the threatened longfin smelt and other native fish. The reduced schedule gives him more time to fish, in California and on British Columbia’s Skeena River, and tend his orchids and carnivorous plants. Chicago-born Baxter grew up in Pacifica with...
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05
Mar

Bob Fujimura spent his entire career with the California Department of Fish and Wildlife.

Bob Fujimura spent his entire career with the California Department of Fish and Wildlife. From 1987 until his retirement in late 2018, Fujimura served in a variety of roles at the department—but he is likely best known for heading up its long-term monitoring of native fishes in the Bay and Delta. Beginning in the mid-2000s, he oversaw annual smelt surveys with far-reaching implications for management and conservation, including the Spring Kodiak Trawl, which determines the relative abundance and distribution of...
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22
Jan

Manmade features in the Delta, including riprap-armored banks, water diversion pipes, pilings, and woody debris, may be sending juvenile native fishes into the jaws of finned invaders.

“We know from a decade of doing survival studies that migrating juvenile salmon are dropping out of the system pretty much everywhere in the Delta,” says UC Santa Cruz fisheries biologist Brendan Lehman. “Physical habitat features are potentially aggregating predators and prey in ways detrimental to salmon smolts and steelhead.” The scientists report in the December 2019 San Francisco Estuary and Watershed Science that artificial light and submerged aquatic vegetation pose the most severe and widespread risks to native fishes....
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22
Jan

A recent test found more than 250 chemicals in the Delta’s Cache Slough, but “Dr Doom” says figuring out what they all are, and their concentrations, is beside the point in our efforts to understand stressors on native fish resilience.

“Knowing the effect on the fish is more informative than knowing which chemicals may be causing it,” says UC Davis’ Richard Connon (whose colleagues gave him his sinister title), referring to taking an ecological rather than regulatory perspective on fish health, and also to the less obvious sublethal effects of contaminants on fish behavior and reproduction. Connon is the lead author of a wide-ranging journal article in the December 2019 issue of SFEWS on how to better focus contaminants research...
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08
Aug

New shoreline strategies piloted in Puget Sound could help young fish in urbanized estuaries elsewhere.

When Seattle rebuilt its seawall in 2017, they hoped to make the hardened shoreline a little less daunting for the young salmon that hug it closely on their journey to the ocean. Project managers took a three-pronged approach. First, they added texture and complexity into the new concrete seawall to encourage invertebrates, food for the young fish, to settle in nooks and crannies and on horizontal “shelves” built into the wall. Mussels, ecosystem engineers, have settled on the shelves and...
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13
Feb

Pied-billed grebes are providing valuable biocontrol services in the Estuary by consuming red swamp crayfish, an invasive crustacean known to disrupt ecosystems.

Although grebes are primarily fish-eaters (they swallow their own feathers to cushion the sharp bones), this species also consumes significant numbers of crayfish, sometimes detaching the pincers before swallowing the good part. Native to southern swamps and bayous, the red swamp crayfish has been introduced in the Sacramento Valley and San Francisco Delta. According to the US Geological Survey, the species is established at Coyote Hills Regional Park and elsewhere around the Bay. The crayfish preys on the larval stages of...
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13
Feb

For the first time ever, an annual fish-counting survey has turned up zero Delta smelt—a dire milestone in Bay Area aquatic biology.

This does not mean the fish is extinct—yet—but it does mean that the Sacramento-San Joaquin Delta ecosystem is in disarray. The species, which lives its entire life in the estuary, is a key ecological indicator—and it was prolific until just a couple of decades ago. According to the California Department of Fish and Wildlife’s Fall Midwater Trawl survey, which provides an annual index on abundance for several fish species in the Delta, the Delta smelt index generally averaged several hundred fish...
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13
Feb

A marriage of robotics and artificial intelligence promises to automate the detection of harmful algal blooms, which can trigger shellfish harvesting bans and fill wildlife rescue centers with sickened animals.

The Imaging FlowCytobot (IFCB) takes water samples around the clock and photographs phytoplankton cells floating within. “It’s got a huge amount of potential for figuring out what plankton is in the water column and monitoring for HABs,” says Alexis Fischer, a postdoctoral fellow at the University of California, Santa Cruz with Raphael Kudela. Fischer and colleagues are building a phytoplankton image classifier already capable of identifying more than 90 percent of cells photographed by IFCB at the Santa Cruz Wharf. The...
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13
Nov

Incidental findings of a long-term study of brown bear predation on salmon have revealed a hidden link between the fish and forest health.

For 20 years, Tom Quinn, a professor in Aquatic and Fishery Sciences at the University of Washington, waded in southwestern Alaska’s Hansen Creek with his students, counting and measuring sockeye salmon carcasses in the stream. Quinn asked his students to toss the bodies on the north bank of the creek to avoid double counting; over the years, they tossed close to 295 tons of salmon onto the north bank. In 2016, Quinn and his colleagues and students took core samples...
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26
Sep

Dioxins Are Sticking Around Nearshore and in Fish, RMP Reports

As the “Fish-SMART” signs on local piers warn, the tissues of fish reeled in from San Francisco Bay waters can contain mercury or PCBs, but a new RMP report reminds us of a third contaminant of concern to human health: dioxins. The report, due out in October 2018 and prepared by staff of the San Francisco Estuary Institute and the SF Bay Regional Water Quality Control Board, confirms that while levels of this toxic contaminant in sediments nearshore have declined...
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13
Aug

Nighttime lights on bridges shining into bays and rivers can attract and confuse fish as they migrate at night, leaving them vulnerable to predation.

“Well-lighted bridges and dams can create twilight conditions that predators love, especially other fish,” says Peter Moyle, professor emeritus at UC Davis. He recounts that at one point the Red Bluff Diversion Dam was lit up at night and pikeminnow took the opportunity to prey on juvenile salmon. “Opening up the gates helped because the pikeminnow were headed upstream to spawn so didn’t really want to be there, and the juvenile salmon could move past the dam quickly at night.”...
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07
Feb

A wide-ranging Habitat Conservation Plan that could eventually protect up to 4800 acres of endangered species habitat in the Bay Area is the linchpin of a November agreement between the U.S. Fish and Wildlife Service and Pacific Gas and Electric Company.

Under the agreement, FWS issued the utility a 30-year incidental take permit for operations and maintenance activities in the nine Bay Area counties. The HCP includes strategies to avoid, minimize, and offset potential direct, indirect, and cumulative effects of PG&E’s O&M and minor new construction activities on 32 threatened or endangered species. The parties are hailing the landscape-scale plan as an improvement over the project-by-project process they previously operated under, as it will enable PG&E to complete projects more quickly...
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13
Nov

In hot water due to climate change, many ocean fish are moving to higher latitudes or deeper waters to find the conditions they need to survive.

These include lobster, black bass, and Atlantic cod, all of which have supported iconic fisheries along the Eastern seaboard of the United States. “Ocean animals are moving ten times faster than animals fleeing climate change on land,” says Rutgers University marine biologist Malin Pinsky, whose Rutgers OceanAdapt website enables visitors to explore changes in marine species distributions over recent decades. These range shifts are causing headaches for fishing fleets, which are forced to head farther out to sea or hundreds of miles further from...
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About Us

The San Francisco Bay-Delta is named in the federal Clean Water Act as one of 28 “estuaries of national significance." For over 20 years, the San Francisco Estuary Partnership has worked together with local communities and federal and state agencies to improve the health of California’s most urbanized estuary.

San Francisco Estuary Partnership 1515 Clay Street, Suite 1400 Oakland, CA 94612 (510) 622-2304

Association of Bay Area Governments