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.

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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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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Paddlers Monitor Plovers

By Ashleigh Papp “It sounds fun and glamorous to kayak to work, but it’s not always the case,” says Ben Pearl, plover program director for the San Francisco Bay Bird Observatory. Pearl spends six months of the year in the field researching predator threats, habitat status, and breeding behavior of the local snowy plover population. “All of this habitat used to be tidal marsh and was converted to salt ponds, so the ground is sometimes soft and nearly impossible to...
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Just Shy of Splendor in the Grass

By Jacoba Charles Tobias Rohmer and Ben Chen’s careful work in Hayward’s Cogswell Marsh represents one small moment in the massive, nearly 20-year-old Invasive Spartina Project. To date an initial total of 805 acres of non-native cordgrass, spread across 70,000 acres of the San Francisco Bay’s marshlands, has been reduced to less than 40 net acres. Treatment of the southern section of Cogswell marsh was halted in 2011, however, due to concerns about Ridgway’s rails who’d made homes in the...
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California Sun Podcast Interview with ESTUARY’s Editor Dives into All Things Bay & Delta on the Front Burner Today

This August the California Sun’s Jeff Schechtman interviewed ESTUARY magazine’s editor in chief Ariel Rubissow Okamoto, also a long-time Bay Area science writer, about her personal opinions on the resiliency of the largest estuary on the West Coast, the challenges facing the Sacramento–San Joaquin Delta, and the potential impacts of climate change and sea level rise on the San Francisco Bay.  Listen to the 20-minute podcast here. Mentions: Nutrients, Toxics, Giant Marsh, Adaptation Atlas, Resilience, Sea Level Rise impacts, BCDC...
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Two long-scarce freshwater mammal species are staging a comeback in Bay Area waterways.

The California Department of Fish and Wildlife (CDFW) recently updated its distribution map for the state’s river otters, reflecting sightings by citizen-scientist “otter-spotters.” River Otter Ecology Project director Megan Isadore says the map fills in major gaps in the North Bay and East Bay, increasing otters’ documented range by 4,100 square miles. “It’s interesting to find how well they’re doing in very populated cities,” she says. Absent from the Bay Area for decades, river otters were observed near Tomales in...
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Coyote Valley, an important wildlife corridor connecting the Santa Cruz and Diablo Mountain ranges, would receive new protections under state legislation introduced in April.

AB 948 would create a new Coyote Valley Conservation Program, to be administered by the Santa Clara Open Space Authority. The bill would expand the existing protected area from 7,400 acres to 17,000 acres, and boost new efforts to preserve its resources. Coyote Valley, which drains the ecologically rich upper watershed of Coyote Creek, has long faced development threats as surrounding South Bay communities expand. The area provides critical habitat for critters large and small, which use the valley—especially its...
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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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While it’s been a tough year for marine mammals along the California coast, local San Francisco Bay conditions may have afforded scientists a unique opportunity to study emerging ocean problems.

The Marine Mammal Center participated in 12 necropsies of deceased gray whales in and around the Bay. Later in the year, malnourished Guadalupe fur seals stranded along the coast at a historically high rate. In June, a surprisingly early toxic algae bloom off the coast of San Luis Obispo caused a rash of cases of Domoic Acid Toxicity among pregnant and yearling California sea lions. Dr. Cara Field, staff veterinarian at The Marine Mammal Center, has some theories as to...
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Tailing a Thrush

By Joe Eaton Researchers like Point Blue Conservation Science ecologist Tom Gardali have equipped Swainson’s thrushes, weighing just over an ounce, with tiny, one-gram GPS tags. If recovered, the tag shows the thrush’s exact winter destination, information vital to border-crossing conservation efforts. “You only get a few readings,” says Gardali, “and you still need to get the tag back. But GPS goes to a spot on the map. This is Holy Grail stuff.”  Sierra/Cascade thrushes were presumed to migrate to...
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Brinkmanship for Frail Smelt

By Joe Eaton Delta smelt had a bad year in 2017. Although scientists are still analyzing the data, the message seems to be that strong freshwater flows alone are not sufficient to allow the population to increase. The resulting sense of urgency has led fish biologists to consider how cultured smelt, raised in hatcheries, could be used to supplement the wild population. “We’ve considered the cultured smelt as a lifeboat,” says California Department of Water Resources biologist Ted Sommer. “Now...
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High Road or High Water for Wildlife

By Ashleigh Papp While we were cooped up inside waiting out February’s storms, many animals were on the move. Cameras positioned along a creek in the Pacheco Pass wildlife corridor captured footage of animals passing through a culvert under a bridge on SR-152 that crosses Pacheco Creek. “We caught a bobcat on camera walking through the creek,” says Tanya Diamond, researcher with Pathways for Wildlife. “With her ears back and elbow-deep in water, you can tell she’s miserable.” As storms...
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Putah Creek Pipeline for Salmon

By Robin Meadows “The dream is to reestablish a natural run of salmon in Putah Creek,” says UC Davis professor emeritus Peter Moyle. In 1972 Putah creek was a trickle of water between heavy machinery mining gravel for the campus roads. Moyle and others urged the university to cease mining and by the end of the decade the machinery was gone and the administration designated a riparian reserve along the creek on campus. After droughts and an ensuing long legal...
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SOS for Finicky Native

By Lisa Owens Viani In 2016, restoration managers with The Nature Conservancy discovered that western sycamores planted along the Sacramento River had hybridized with the non-native London plane tree. The native sycamore is “kind of a messy tree,” says project manager Ryan Luster. “The branches break off and create cavities that wildlife love to use.” Concerns about the tree’s status first arose in the 1990s when the California Department of Fish and Wildlife found only 17 sycamore stands larger than...
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