Pearls in the ocean of information that our reporters didn’t want you to miss
Vulnerable homes and office parks in San Mateo County.
August 6, 2017
Cariad Hayes Thronson

Simultaneous lawsuits filed against 37 fossil fuel companies by Marin and San Mateo Counties, along with the City of Imperial Beach, over sea level rise may open new front in climate battle.

The suits, filed in California Superior Court, seek compensatory and punitive damages and other remedies for the ongoing harm that oil, gas and coal cause by contributing to global warming and sea level rise. A 2009 Pacific Institute study calculated that San Mateo has more property and people at risk from sea level rise than any California county, while in Marin more than 12,000 homes, businesses and institutions, with an assessed value of $16 billion could be at risk from tides and surge flooding by the end of the century. The suits claim that the companies have known about the dangers posed by greenhouse gases for nearly fifty years and sought to conceal them from the public and encourage the use of fossil fuels while protecting the companies’ own assets and developing plans to profit from a warmer world. According to some legal experts, the suits may succeed where other efforts to hold fossil fuel companies accountable for climate change damage have failed, thanks to advances in climate science and recent revelations about what the companies knew about global warming and when they knew it. CHT

Man’s best friend is being enlisted in efforts to detect the soil-born pathogen responsible for sudden oak death and other rapidly spreading plant and tree diseases.

Phytophthora is difficult to detect in nurseries, plant materials, and planting sites until it has done its damage. To develop early-detection options, H.T. Harvey and Associates are training a female cattle dog/border collie mix named Bolt to sniff out Phytophthora. Part of the Harvey Dog ecological-scent detection program, Bolt has accurately identified four species of Phytophthora in the lab. If her training in a natural setting is successful, Bolt could get to work helping minimize the spread of Phytophthora. Potential beneficiaries would likely include those working to re-oak the parks, open spaces, and backyards of Silicon Valley to improve habitat for native plants and animals.  KMW

Photo: H.T. Harvey

 Researchers with the U.S. Geological Survey found that adult and sub-adult white sturgeon occupy deep open-water channels and shallow open-water shoals in equal measure, but don’t use shallow wetland channels. As a group, white sturgeon are characterized as amphidromous, meaning they regularly migrate between freshwater and the sea, in both directions, but not for the purpose of breeding. According to the study, which appears in the December 2020 issue of San Francisco Estuary and Watershed Science, adults in the local population use coastal habitats to some degree, but typically remain in the Estuary and lower Sacramento and San Joaquin rivers. There they congregate in deep areas with fine-sediment substrate, and are thought to move into shallow subtidal habitats to feed during high tides. The study may help guide management and conservation of the declining population through habitat restoration and other measures, says lead author Veronica Larwood. Future research could address habitat use for rearing.
 “If we want to restore the ecology of the Delta, we can’t just be looking in the water,” says Kristen E. Dybala of Point Blue Conservation Science. In a paper published in San Francisco Estuary and Watershed Science, Dybala and two co-authors make the case that “birds and their habitat needs are often not addressed in science syntheses, conservation planning, and large-scale restoration initiatives in the Delta.” While some birds use the same sloughs and channels that support such high-profile fishes as Chinook salmon and Delta smelt, other bird species rely on habitat types that fringe the Delta’s waterways. Indeed, while general habitat restoration in the Delta can provide multiple benefits for humans, fish and many birds, the authors observe that numerous bird species “have a specialized set of habitat needs that require particular attention.” Historically, the Delta and the Central Valley provided millions of acres of habitat for uncountable droves of resident and migratory birds. Much has changed: The authors write that “an estimated 97% of historical freshwater emergent wetland in the Delta, 77% of seasonal wetlands, and 77% of riparian forest are now gone, primarily converted to agricultural land.” Still, the Estuary and the farmland fringing it remain...
“There’s no way we can manage them for recovery if we don’t understand the biological processes that govern their dynamics through time and space,” says UC Santa Cruz/NOAA salmon expert Flora Cordoleani, lead author of a study reported in the December 2020 issue of San Francisco Estuary and Watershed Science. Cordoleani and colleagues identified the monitoring gaps while building a model of the spring-run Chinook life cycle. The model accounts for three self-sustaining populations of these at-risk fish, assessing survival of key life stages (eggs, fry, smolts and adults) as well as in key habitats (natal creeks, the Sacramento River, floodplains in the Sutter and Yolo bypasses, the Sacramento-San Joaquin Delta, and San Francisco Bay). “It’s a complex model, and we needed data to fine-tune and test it,” Cordoleani explains. “But there wasn’t much.” Major monitoring gaps include how many juveniles each population produces, and how many survive in the ocean. “Spring-run Chinook haven’t gotten as much attention because they are less endangered than winter-run Chinook,” she continues. That is beginning to change: The California Department of Water Resources is now working to estimate how many spring-run juveniles make it to the Delta. Identifying trouble spots for young salmon is...
 Although past studies have found that the Bay could support 1.5 times the entire current southern sea otter population, a new study from the Estuary & Ocean Science Center at San Francisco State University and published by PeerJ last November indicates that anthropogenic risks like contaminants, vessel traffic, and oil spills may constrain the otter’s ability to gain a foothold. The study, led by Jane Rudebusch, at the time graduate student at SFSU, looked at the types of human stressors present and ranked them according to factors like temporal overlap (frequency of its interaction with otters), intensity (consequence of that interaction), and management effectiveness (how well the stressor is mitigated by human regulation). The study concluded that high-speed vessel traffic, such as commuter ferries, was of primary concern. However, Rudebusch found that “the risk from human disturbance is really not evenly spread throughout the Bay. You can look at pockets of the Bay where there is lower risk and use those to focus a reintroduction effort.” Sites like China Camp on the Marin bayshore are particularly appealing because of their protected status and relative lack of human stressors. Rudebusch says it was important to capture a picture of the entire...
Miniscule polymer pieces the size of a sesame seed or tinier, microplastics pose a growing pollution threat to marine environments worldwide. To understand how microplastics accumulate in nearshore, urbanized environments, researchers quantified the prevalence of microplastics in and around the Zostera marina meadows of Deerness Sound, in the Orkney Islands of Scotland. Mark Hartl and colleagues at Heriot-Watt University found that microplastic flakes, fibers, and fragments were twice as concentrated in the water above eelgrass meadows as in adjacent control areas of sandy sediments. Sediments within the meadows contained 40% more microplastics than in the sandy areas. The scientists also found plastics attached to every one of the 60 blades of eelgrass they examined; in fact, microplastics were 20% more abundant atop eelgrass than in control areas. Eelgrass meadows are prized for their ability to absorb wave energy and increase rates of sedimentation; the researchers suspect this talent for slowing the travel of water helps floating microplastics settle out of the water column onto meadow areas. Meanwhile, biofilms such as algae and the microscopically rough surface of seagrass blades help microplastics adhere to the surface of the plants. The prevalence of these contaminants on eelgrass itself—a source of food for...
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 have indicated high rates of infectious diseases, which lead author Brendan Lehman of UC Santa Cruz says demonstrates the need for ongoing systemwide monitoring. This could involve sampling fish directly for infections or conducting DNA testing of water samples. A monitoring program might also involve using so-called sentinel fish. Born and raised in the controlled environment of a hatchery, a sentinel fish is temporarily released into the wild, then retrieved and screened for diseases or infections. Lehman notes that pathogens occur naturally in river systems. “But the way we’ve changed their environment can exacerbate the effects on the fish,” Lehman says.
“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 influx of salmon and other fish near the two water projects. Evidence of this hotspot lies in the numerous acoustic tags from young salmon to be found in the sediment, which were presumably defecated by striped bass, as well as the fact that it is a popular spot for striped bass fishing. The hotspot is a two-kilometer stretch of Old River between the radial tide gates at the entrance of Clifton Court Forebay, which leads to the SWP, and the trash boom just before the CVP. “The state says ‘our impacts begin at the radial gates’ and federal officials say ‘our impacts being at the trash boom,’ ” Jahn explains. “But you know predators wouldn’t concentrate upstream at the bend...
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 barrier, it can be also a mental barrier.” For example, some species that engage in schooling behavior, such as shad, may refuse to even enter a structure if it limits them to passing one at a time. According to the review, which appears in the September issue of San Francisco Estuary and Watershed Science, other factors that may affect fish passage access include water depth, velocity and turbulence. The key, says Matica, is to take the needs of different species into account from the outset. “You can build a structure that is multi-species friendly in many circumstances,” says Matica.
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 upper reaches of the Estuary. But by towing a weighted hoop net behind a research vessel during the dry year of 2016 and again in the following year of heavy rainfall, the authors of the new study, published in October’s San Francisco Estuary and Watershed Science, put this assumption to rest. In the wet study year, they captured many larval smelt in the shallows of San Francisco Bay. The small size of the young fish indicated that spawning could not have taken place far away. The scientists saw similar patterns among larvae of Pacific herring. The fish spend most of their lives in the open ocean but spawn in coastal estuaries, and the team’s net surveys produced evidence that in...


Former Chronicle reporter Jane Kay spent a year exploring the San Francisco Bay’s 1,000-mile shoreline, focusing on efforts to restore the balance of the bay she loves. She reports that the rising seas and intensified storm surges of climate change may be mitigated by natural buffers, including tidal marsh from reclaimed hayfields and commercial salt ponds as well as restored eelgrass and oyster reefs in subtidal zones. Kay also highlights the ecological role of freshwater flowing though Delta, which benefits species in the Estuary and helps flush treated sewage out of the South Bay. Her story was posted by National Geographic on June 13, 2017. Photo by Ariel Okamoto.

Photo credit here.

No personnel found, please create the personnel post to use the item.