A Fragile Fleet

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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A team of scientists is close to chasing down every last thing that happens to nitrogen in wastewater as it passes through the soils and plants of a horizontal levee.

Not only is 97% of the nitrogen removed, but also trace pharmaceuticals. “You just have to focus on where the water is going,” says environmental engineer Aidan Cecchetti, referring to the UC Berkeley-Stanford-ReNUWIt team’s experimentation with three components of flow through the levee system—under the surface, over the surface, or into the air (through evapotranspiration). “In the wastewater pumped to the subsurface, you see full removal of every contaminant except phosphorous.” What’s most astonishing is how much of the work...
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Surface water diversions in California’s Central Valley can be estimated based on readily available climate data, say researchers—a boon to efforts to track groundwater use.

Valley groundwater pumping is calculated as the total water demand minus surface water deliveries. However, today’s water model relies on individually reported diversions across the entire valley, and compiling all these data is a slow process; by the time the numbers are crunched, assessments of groundwater use are already outdated. “It can take years,” says Jordan Goodrich of University of Waikato in New Zealand. “It’s one of the biggest problems we face in tracking the Central Valley water budget.” Overdrafting...
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New Eyes on Floods and Fire

By Jacoba Charles Flames have become the unofficial face of climate change for Sonoma County, in the wake of the catastrophic Tubbs and Kincade fires that tore through the northern parts of the county in 2017 and 2019. Together the two fires burned more than 114,000 acres, roughly a tenth of the county, claimed 22 lives, and destroyed almost 5,000 homes. However, increased frequency and severity of wildfire is only one of the many ways that climate change is poised...
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Toxins Flock to Beads in a Scientific Tea Bag

By Ashleigh Papp When a New Zealand scientist shared a novel method to test water quality in the early 2000s that didn’t involve harvesting shellfish, UC Santa Cruz’ Raphael Kudela and his team of researchers quickly adopted the idea. After some fine-tuning, they named their new technique Solid Phase Adsorption Toxin Testing (SPATT, for short). The technique takes advantage of custom-built plastic, or resin, beads that are designed to absorb specific things. “It looks a lot like a tea bag,”...
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Tracking Curlews Cross-Country

By Joe Eaton This winter, Jay Carlisle, director of the Intermountain Bird Observatory, teaming with Nils Warnock of Audubon Canyon Ranch and netting expert David Newstead of Coastal Bend Bays and Estuaries Program, caught two long-billed curlews and outfitted them with transmitters. Those birds may reveal where the wintering curlews on the California coast and Bayshore are coming from. While many grassland birds are experiencing catastrophic declines, long-billed curlews had appeared to be an exception. “It’s such a habitat generalist...
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Jan Thompson has always been most interested in what happens down at the bottom of the Bay.

The zone of interaction between the critters in the oozes and the water column above—where specks of sediment, nutrients, and fish food cycle through clam siphons into the Estuary—is the particular specialty of this US Geological Survey scientist. “I’m most proud of the research I’ve done establishing a solid connection between bivalve grazing and phytoplankton growth,” she says. When USGS first hired Thompson, who retired in October 2019, most women in the Menlo Park office were secretaries. She’s since trained...
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Rainer Hoenicke is optimistic about the changes he saw in his five years as the Delta Stewardship Council’s Science Director.

“People are coming to the table and realizing we need to be anticipating and forecasting how to adapt,” he says. Prior to joining the Science Program, Hoenicke served for nearly a decade as deputy and executive director of the San Francisco Estuary Institute, where he managed two Boards of Directors and reorganized the Institute’s program areas. “I felt challenged to do something different,” he says of the move, “since the Delta is much more controversial territory.” In Hoenicke’s eyes, the...
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A new system for treating agricultural drainage water in the Delta could also help rebuild subsided islands.

The approach—known as a Chemically Enhanced Treatment Wetland—combines chemical treatment with natural wetland processes; researchers tested it on Twitchell Island, which features corn and rice crops, as well as wetlands. They dosed agricultural ditch water with dissolved organic material (DOM), then treated it with a coagulant to precipitate the DOM, forming flocculant. The resulting water then passed though treatment wetlands, where the flocculant settled and blended with plant detritus in the sediment. The study, reported in the September 2019 San...
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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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Levels of pyrethroid insecticides spike sharply in the North Delta’s Cache Slough during winter rainstorms, rendering the water so toxic that it decimates laboratory populations of a half-inch crustacean called Hyalella azteca.

However, according to a study reported in the September 2019 San Francisco Estuary and Watershed Science, Hyalella collected in the wild from Cache Slough are resistant to pyrethroids. Genetic analysis revealed that, collectively, Hyalella in the slough have four mutations for pyrethroid resistance. They also have a fifth mutation for resistance to organophosphates and likely carbamates, two additional major classes of pesticides that are applied extensively on agricultural and urban lands. “Hyalella are special,” explains co-author Helen Poynton, a molecular...
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Researchers hope new computer models will help clarify the effects of entrainment on the population of endangered Delta smelt.

Entrainment at the South Delta pumps of the State Water Project and the Central Valley Project has been a concern for years, but disentangling its impact on the dwindling smelt population from those of other environmental and water management factors isn’t easy, and operational differences between the SWP and CVP facilities complicate analysis. Now, US Fish and Wildlife Service statistician Will Smith has developed computer models for entrainment effects on different smelt life stages, part of a larger Delta Smelt...
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While the acreage of wetland restoration projects is growing throughout the Delta, scientists are still working to understand how best to help these areas become fully functioning, complex habitat as quickly and successfully as possible.

A study published in September’s San Francisco Estuary and Watershed Science shed light on some essential questions about what triggers seed generation in wetland habitat. “Wetland restoration practices can be enhanced by a solid understanding of basic plant life history and species ecology,” says co-author Taylor Sloey of Yale-NUS College in Singapore. The researchers looked at three questions: what seeds are present in the seed bank (the viable seeds that accumulate naturally in the soil), and how exposure to cold...
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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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Speakers discuss forward-looking science in a rapidly changing environment, and the neuroscience of persuading people to care about climate change.

Climate Change Planning Mark Gold made the ultimate comment in his opening plenary at the State of the Estuary Conference: “The age of incrementalism, and not moving forward in a bold way, is not getting it done in terms of climate change.” Gold, deputy secretary for ocean and coastal policy for the California Natural Resources Agency, outlined the state’s newly revised strategic plan for a bluer economy, coastal resilience, and rapid response to fisheries emergencies. Following his talk, Geeta Persad...
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Not So Picky Marsh Mouse

The endangered salt marsh harvest mouse (informally “Salty”) is a poster child for tidal marsh restoration in San Francisco Bay. But recent research, presented by University of California at Davis postdoc Katie Smith in a State of the Estuary conference session on tidal wetlands, suggests we’ve misinterpreted what the mouse needs. “It’s been managed as a habitat specialist,” she said, based on assumptions that it requires tidal wetlands and a diet of pickleweed. However, hours of mouse-tracking around the Bay...
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Speakers discuss issues facing Estuary wildlife and their wetland habitats, as well as drones and other new tools that will help future management.

Fish and Wildlife Check-up State of the Estuary Conference presentations featuring decades of data on fish, ducks, seabirds, and cetaceans revealed both hopeful and alarming trends. “The loss of federal funding for the midwinter waterfowl survey, usually conducted using small aircraft, has researchers looking at drone-based alternatives,” said waterfowl biologist Susan De La Cruz of the US Geological Survey. The overall community condition of the Estuary’s fish (abundance, distribution, diversity, proportion of native to non-native species) has declined, reported the...
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Drones Pilot Vegetation Mapping

By Michael Hunter Adamson In the world of conservation, as attested to by multiple speakers at a late summer UC Davis event, drones, or UAVs (unmanned aerial vehicles) may be the vehicle of choice for mapping the future of invasive plant management in the Delta. The California Department of Water Resources began using UAVs in earnest after the Oroville dam failure in the winter of 2017, when drones offered visuals no one could get near on the ground. The Blacklock...
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Invasive clams and freshwater exports from the Delta have created dramatic and unsustainable changes in the San Francisco Estuary’s foodweb over the past 50 years.

 A study by UC Davis researchers found a 97% decline in phytoplankton, the microscopic foundation of the food chain. “Understanding the causes for the decline in the pelagic [water column] community is essential so that efficient solutions can be implemented,” says Bruce Hammock, a research scientist at the UC Davis School of Veterinary Medicine’s Aquatic Health Program. The invasive clams (Potamocorbula amurensis), originally from Asia, have been over-consuming phytoplankton and zooplankton for more than 30 years, and have long been...
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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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