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E-News Magazine

As organizations and agencies scramble to preserve the Central Valley’s dwindling Chinook salmon runs, a group of scientists believes they may be overlooking a key factor in the decades-long decline of the fish: disease.

In a paper published in September’s issue of San Francisco Estuary and Watershed Science, a research team proposes that diseases—caused by viruses, bacteria and other microbes—could be suppressing juvenile salmon survival in a river system that once hosted millions of adult spawners each year. According to tracking studies, nearly all juvenile Chinook born from natural spawning die before they reach the Golden Gate Bridge; habitat enhancement efforts have failed to mitigate this mortality rate. Short-term studies of Central Valley salmon...
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Current estimates of young salmon lost to the south Delta pumps are based on a smattering of studies from the 1970s and should be updated, according to a new analysis.

“They don’t represent current operations,” says Ukiah-based consultant Andrew Jahn, lead author of the analysis reported in the September 2020 issue of San Francisco Estuary and Watershed Science. Current operations at the State Water Project (SWP) and the Central Valley Project (CVP) can reverse flows in the Old and Middle rivers, diverting salmon on their way to the ocean towards the projects. Existing salmon loss estimates also fail to account for a likely Old River hotspot for predators, drawn to the...
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Fish passage structures can be improved for the benefit of multiple species, if they are designed to account for differences in behavior, physical ability and size, according to a new literature review.

Historically, most fish passages have been designed to help native salmon return to their upstream habitat and spawning grounds, with little consideration for other migrating species such as sturgeon and lampreys. “There is an assumption that if you just build a fish passage structure, fish will go thorough it, but that is not always the case,” says Department of Water Resources fisheries biologist Zoltan Matica, who conducted the review. “The challenge is to understand that this isn’t only a physical...
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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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Science-in-Short ~ Podcast

Wall-to-Wall Sampling of the Delta’s Aquatic Weeds Via Remote Sensing, an interview with Shruti Khanna.  In this episode of the podcast, Estuary News reporter Daniel McGlynn talks to Dr. Shruti Khanna, a senior environmental scientist at the California Department of Fish and Wildlife. Their conversation focuses on Khanna’s use of remote sensing technology to study the Sacramento-San Joaquin Delta. Specifically, Khanna analyzes and processes remote sensing data, or high- resolution images collected by sensors mounted on aircraft, to study invasive...
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Equity with Intention ~ Podcast

It might be a stretch for many of us to see the relationship between keeping the Estuary healthy and racism in our communities. But leaders and staffers in organizations and agencies across the San Francisco Bay Area have been steadily working to make this connection, and recent events – with the death of George Floyd and erupting protests – have made them ask themselves what more do they need to do?  In this first segment of Estuary Voices, the San...
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Science in Short ~ Podcast

David Ayers: How Fish Interact with Wetlands Topography  In this podcast, Estuary News reporter Alastair Bland and UC Davis PhD student and fish researcher David Ayers discuss the Sacramento-San Joaquin Delta, its fish, its marshlands, its flows, and its future. Ayers explains the focus of his research, which seeks to reveal how underwater topography in the wetlands fringing the estuary affects interactions between predators and small fish. While restoration projects often focus on adding more water to this ecosystem and...
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Small Farmers Shortchanged by SGMA

When governor Jerry Brown signed the Sustainable Groundwater Management Act (SGMA) into law in September 2014, he said that “groundwater management in California is best accomplished locally.” With the first round of plans made available for public comment this year, it appears that, while the state certainly ceded control to local management agencies, those same agencies have prioritized the interests of big agriculture and industry over small farmers and disadvantaged communities. A June 2020 paper from UC Davis published in...
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Nursing Salmon on Flooded Farms

In 2012 a team of salmon researchers tried a wild idea: putting pinky-sized Chinook on a rice field in the Yolo Bypass, a vast engineered floodplain designed to protect the city of Sacramento from inundation. The team found that rearing fish on farms works better than they had ever dreamed. Salmon in this managed floodplain grew so fast — averaging more than one millimeter per day — that they outpaced young Chinook elsewhere in the region. Now, after nearly a...
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Londons Roam and Feast on the Bay circa 1910

Jack London usually sailed west whenever he left the Oakland Municipal Wharf, but on December 18, 1913, he headed east — because he could. Although the canal connecting the Oakland Estuary to San Leandro Bay had been completed in 1902, it wasn’t until the U.S. Army Corps of Engineers widened and deepened the canal in 1913 that it became navigable. Aboard the Roamer, a 30-foot yawl London bought used in 1910, Jack and his wife, Charmian, approached the Park Street...
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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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Covid Clues from Wastewater

As COVID-19 continues its unrelenting rampage, wastewater plant managers and university researchers are ramping up their efforts to monitor wastewater for SARS-CoV-2, the virus that causes the disease. Their goal is to give public health departments a powerful tool: an early warning system for new outbreaks in communities. In Yosemite Valley, for instance, wastewater testing revealed the presence of the virus in the community before swab testing of individuals showed a problem. “There’s a time delay before cases appear in...
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Creeks & Quilts for Climate

The Estuary News team has been working behind the scenes with partners on a cool new build out of our sister Acclimatewest project called the California Climate Quilt. Acclimatewest.org is a pilot storytelling site that gathers stories about creeks, sloughs, and shorelines adapting to sea level rise, describing who lives around them and what concerns they have about their environment, as well as exploring the local natural and human history of the area. At the same time, in a world...
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A Fragile Fleet

The naming of boats and ships is a serious matter. Each larger vessel’s name starts with a code that tells what it carries, what propels it, or what purpose it serves. If it were your hobby to keep tabs on traffic on San Francisco Bay, you’d see a lot of big UCCs (container ships) and TCHs and TCRs (tankers). You’d see ferries emblazoned with MV, standing for “motor vessel.” Before COVID-19, you would have spotted the occasional SS, standing for...
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More Grants for Real People

Even as “environmental justice” and “community engagement” have long been watchwords of restoration and resilience efforts, economically disadvantaged communities on San Francisco Bay’s shoreline have often felt sidelined by them. But that may be changing: the summer of 2020 saw new initiatives to give communities more power to shape and participate in restoration projects in their own backyards. In July, the San Francisco Bay Restoration Authority kicked off its new Community Grants Program, allocating $200,000 of its $25 million 2020-21...
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The Delta’s Blooming Problem

Bright-green blotches of algae have been popping up all over the Delta since early summer, from Discovery Bay to the Stockton waterfront, befouling the air and poisoning the water with toxins that can sicken or even kill humans and animals. Veteran Delta watchers believe that this year’s harmful algal blooms may be the worst ever, and worry that some features of Governor Gavin Newsom’s recently released Water Resilience Portfolio for California will aggravate the problem. “We don’t have enough data...
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Match Points in Stormwater Soup

Scientists studying environmental pollutants tend to divide them into two distinct groups. One includes “legacy” contaminants that drew attention during the early stages of the environmental movement, like mercury, PCBs, and some pesticides. The other is a much larger class of “emerging” contaminants whose production or monitoring began more recently and about whom less is known; think pharmaceuticals, plastic additives, and flame retardants. Effluent from wastewater treatment plants is often seen as the primary source of emerging contaminants in San...
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Trolling for Salmon by Kayak

Whales scare us much more than sharks. They erupt from the ocean with a rush of displaced water and a poof of air. A collision could be disastrous. “Whale – go-go-go!” I shout. We pedal double-time to dodge the humpback, behind us and approaching from the left. A moment later it surfaces again, with another poof, now off to our right, moving away. We relax and slow back to our standard trolling speed of about 2.5 miles per hour, and...
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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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Makeover for Delta Weed Patch & Salt Trap?

What began as a project to convert a submerged Delta island into habitat for endangered native fish has morphed into a multi-benefit package with additional payoffs for water quality and recreation. The collaborative design process for the Franks Tract Futures project brought initially skeptical local stakeholders on board and is being hailed as a model for future initiatives. Yet major uncertainties remain as interested parties explore the challenges of implementing a complex redesign of a big chunk of the Delta....
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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