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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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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In 2019 Los Angeles property owners will see a new addition to their tax bill: a tax on impervious surface area to fund stormwater projects.

Measure W, approved by voters last November, will tax residents 2.5 cents per square foot of impermeable surface on their parcels. The initiative will raise an estimated $300 million per year to fund rain gardens, new parks, and watershed restoration in order to capture and clean the precious rainwater sliding off the county’s concrete and asphalt surfaces. Though the county currently captures and stores enough rain to meet the consumption needs of one million residents, the Measure W tax revenue could...
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The Nature Conservancy’s venture in growing food crops for wintering cranes on Staten Island is under fire from an unexpected source—the Wetlands Preservation Foundation.

The nonprofit, headed by Stockton tomato packer Dino Cortopassi, is suing TNC and the California Department of Water Resources, which holds a conservation easement on Staten Island, alleging farming practices that cause soil subsidence and threaten levee integrity, and misuse of revenue from farm operations. The 9200-acre farm, acquired by TNC in 2001, is a major destination for migratory greater and lesser sandhill cranes (the latter a California endangered species) as well as Aleutian cackling geese and other birds. As...
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Restoring wetlands is an extremely effective way to cool land surfaces, a study conducted in the Sacramento-San Joaquin Delta indicates.

For three years, Kyle Hemes of UC Berkeley and colleagues kept tabs on the heat flux and air flow above three restored Delta wetlands on Twitchell and Sherman islands, and an alfalfa field on Twitchell Island. Surface temperatures at wetlands with open water were up to 5.1 degrees Celsius cooler than the crop field during the daytime. As expected, the dark open water absorbed more solar radiation, and released the energy slowly at night. But wetland vegetation played a role...
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Just months after becoming the first project awarded Measure AA funding, the first phase of tidal breaching at the Montezuma Wetlands restoration project will be two-thirds complete by the end of November.

“We are on track to complete the levees and transition zones next year so we can breach into the slough and restore the area to tidal action,” says Jim Levine, managing partner of Montezuma Wetlands LLC, which owns the property. The breach of the first major restoration area is planned for December 2019. This phase of the multi-phase project will restore 600 acres of previously subsided shoreline on the eastern edge of Suisun Bay to tidal, seasonal and some sub-tidal habitat....
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In response to the critical threat that changing ocean chemistry poses to both ecosystems and economies, the California Ocean Protection Council adopted the state’s first Ocean Acidification Action Plan on October 25.

The plan addresses ocean acidification—like climate change, a consequence of rising atmospheric CO2 levels—in the context of other threats such as polluted runoff, warming temperatures, and rising seas. It promotes local solutions that are likely to provide multiple benefits—from improving water quality to promoting healthy seagrass, marsh, and kelp forest habitats. The plan, one of the first released by a member of the International Alliance to Combat Ocean Acidification, identifies six key strategies, and outlines five-year goals and actions for...
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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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Recent discoveries are promising new weapons against red tides, the massive blooms of microscopic marine algae that are notorious for playing havoc with marine ecosystems.

The culprit behind poisoned seabirds, closed crab fisheries, stranded sea lions, and shellfish poisoning in humans are often diatoms producing the neurotoxin domoic acid. Now, scientists have identified the genes and biochemical processes responsible in diatoms of the genus Pseudo-nitzschia. The finding, published in the journal Science, opens the door to rapid genetic monitoring of algal blooms as a means to spot nascent harmful blooms and track their spread. “By identifying the genes that encode domoic acid production, we are...
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Floods and droughts can cause pools and riffles—and the bugs that live in them—to become more homogenous.

For years, scientists monitoring water quality in streams and rivers have collected mixed samples of aquatic invertebrates from riffles, pools, and transition zones. But UC Santa Barbara stream ecologist David Herbst and his colleagues recently finished a 15-year study of the benthic life in small streams of the central Sierra that examined pools and riffles separately. They found that during flood and drought events, these habitats and their inhabitants become more uniform. But while floods come and go, droughts can...
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The recent California Adaptation Forum in Sacramento included more sessions and voices on climate justice and equity issues than in year’s past, but the public was missing.

 “When you have two hundred of the best climate adaptation professionals in the room together, that’s an opportunity…” said Phoenix Armenta from the Resilient Communities Initiative. Armenta and Lucas Zucker from the Central Coast Alliance United for a Sustainable Economy were members of a special equity-tribal advisory committee convened before the conference to help with program development, diversify attendance, and elevate the conversation on equitable climate adaptation. “There’s always tension about whether to weave [equity] into every single session or give it its...
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A Stream of Science Takeaways. ESTUARY News sent reporters to the biennial Bay-Delta Science Conference in September. This special edition of Pearls shares more than 20 takeaways.
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Help may be on the way for critically endangered southern resident killer whales.

NOAA Fisheries and the Washington Department of Fish and Wildlife have partnered to produce a list of the west coast Chinook salmon stocks most important to the whale’s survival. This list comes as a part of a special action plan by NOAA to address the three primary threats to the southern resident killer whales: Chemical contaminants, vessel traffic, and lack of prey. The salmon, themselves endangered, are the preferred food source for the whales, and identifying the salmon runs—which include...
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California’s Wild and Scenic Rivers System expanded for the first time in 13 years in June when Governor Edmund G. Brown Jr. signed legislation protecting 37 miles of the upper Mokelumne River.

It was the culmination of a long struggle for the Jackson-based Foothill Conservancy and other river advocates. Four years ago, a Mokelumne bill was approved by the state Senate but killed by a parliamentary maneuver  that blocked a vote in the Assembly. Despite significant support in Calaveras and Amador counties, the bill was opposed by local water agencies concerned about the potential impact on their water rights. In 2015 Assemblyman Frank Bigelow (R-O’Neals) successfully proposed a state study of the...
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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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California sea lion nurseries are moving north as Año Nuevo Island and the southeast Farallon Islands experience a record-breaking boom in sea lion births.

Zalophus californianus have traditionally preferred nurseries in the Channel Islands, but the population of pups born off Northern California’s coast began skyrocketing in 2016. Births at both sites went from a few dozen pups to more than 500. The trend has only intensified since; more than a thousand pups born at the Farallones, and between 500 and 700 at Año Nuevo, in 2017 according to NOAA; similar numbers are expected this year, although final counts are not yet available. Such...
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California’s groundwater faces widespread chromium contamination risk resulting from natural, rather than industrial sources.

Chromium’s toxic form, known as hexavalent chromium, is used in steel manufacturing, leather tanning, and wood treatment; its lethal effects were popularized in the 2000 movie Erin Brockovich. But today transformation of the benign form of chromium naturally found in soils poses the larger risk, according to a recent Stanford University study. Dr. Debra Hausladen and her colleagues used a statewide groundwater database to trace the origin of 90,000 chromium samples, and discovered toxic chromium from natural sources is affecting...
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A new online portal from the Delta Stewardship Council offers everyone from scientists to tourists an accessible window into the Delta’s identity and importance.

“Although I had studied freshwater and marine ecology, I really was not familiar with the Delta before I started working there,” says 2017 Sea Grant Fellow Heidi Williams, who developed the Beginner’s Guide to the Sacramento-San Joaquin Delta. “I was looking for a way to dive in and learn about the Delta and realized that there wasn’t an easily accessible place to turn for the basics.” As a science communications fellow, Williams suggested to the Council that she create one...
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Innovative stormwater management strategies throughout California are pioneering new ways to capture and use stormwater to augment local water supplies and prepare for climate change, according to a new report.

“Stormwater has traditionally been considered a nuisance or danger in terms of flooding and water quality,” says the Pacific Institute’s Morgan Shimabuku, lead author of Stormwater Capture in California: Innovative Policies and Funding Opportunities, “But we’re starting to see it as more of a resource with potential for water supply.” Shimabuku notes that stormwater capture is also “a great strategy for adapting to climate change, alleviating the impact of high-intensity rainstorms and reducing dependence on other water sources in times...
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The latest casualty in America’s opioid epidemic is a small invertebrate that filters pollutants and feeds hungry shorebirds.

Biologists testing mussels in the waters around Seattle as part of the Puget Sound Mussel Monitoring Program found oxycodone in mussel tissue for the first time, along with antibiotics, antidepressants, chemotherapy drugs, and heart medications. “We have found evidence that these chemicals are in our nearshore marine waters and are being taken up by marine biota living there,” said Washington Department of Fish & Wildlife biologist Jennifer Lanksbury. She also tested juvenile Chinook salmon in Puget Sound estuaries and found...
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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

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