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algal blooms
16
Apr

A resurgence of dinoflagellates, which can cause harmful algal blooms, may be in the cards for some bays along the U.S. West Coast.

A resurgence of dinoflagellates, which can cause harmful algal blooms, may be in the cards for some bays along the U.S. West Coast. Scientists at UC Santa Cruz have been monitoring phytoplankton weekly at the town’s Municipal Wharf since 2002. In 2018, Alexis Fischer, then a postdoctoral fellow at UC Santa Cruz, augmented these observations with an Imaging FlowCytobot (IFCB) that photographed wharf phytoplankton hourly. She also developed a machine learning classification algorithm to automate identification of the organisms. In 2004-2007 and 2017-2018, the scientists noticed that diatoms, typically dominant, were getting upstaged by dinoflagellates. To get to the root of this role switch, Fischer examined local and regional environmental patterns. She now reports in Limnology and Oceanography that both...
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13
Feb

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 bad actors really stand out in the crowd, Fischer says. “Many of the harmful algal bloom species tend to be larger and more uniquely shaped, which fortunately makes it easier for our classifier to distinguish them.” Phytoplankton from San Francisco...
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31
Aug

In the absence of a government program to contend with harmful algae blooms (HABs) in the Delta, a loose coalition of academics and environmental and community groups has been studying their spread and potential health impacts both from ground level and from the air.

San Francisco Baykeeper has been sending up drones to monitor eight sites between Discovery Bay and downtown Stockton, as well as photo-documenting the spread and intensity of HABs from airplanes flown by Lighthawk Conservation Flying. At the same time, volunteers with Restore the Delta have been conducting water quality testing for HABs and the toxins they produce. “The airplane and drones together allow us to get a really broad geographic understanding of where these neon green HABs are occurring, says Baykeeper’s Jon Rosenfield. “That paired with site specific water quality testing that Restore the Delta is doing allows us to get different spatial scales of analysis of this problem.” These HABs, which Rosenfield says occur during the late-spring and summer...
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13
Nov

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 now able to ask questions about what ocean conditions turn these genes on or off,” said lead author Patrick Brunson of the Scripps Institution of Oceanography. The achievement comes not a moment too soon: with algal blooms getting larger and...
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05
Oct

Toxic Summer for Sea Lions

The Marine Mammal Center in Sausalito is wrapping up a busy summer. A potent neurotoxin called domoic acid, propagated by toxic algal blooms, poses a threat to California sea lions. Originally called “Amnesiac shellfish poisoning,” domoic acid targets the hippocampus and can have devastating effects on sea lions.
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21
Sep

Nutrient Nuances Modeled

San Francisco Bay is becoming less opaque as the sediments power-washed into the Estuary by miners so long ago gradually disperse. This lets sunlight penetrate deeper into the water, creating more favorable conditions for the kind of problematic algal blooms that can shut down crab fisheries and keep people and their pooches out of the water. Scientists have collaborated on some new computer models, however, that may help them predict where and when nutrients, like nitrogen and phosphate from discharges and runoff, may exacerbate the situation.
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03
Mar

Bay Primed for Pea Soup?

Nutrients could be the next big problem for San Francisco Bay — or make that in the Bay, because they’re already here at levels high enough to have caused trouble elsewhere. But despite its excess nitrogen and phosphorus, the Bay has been free of harmful algal blooms and oxygen-depleted dead zones for decades. Indeed, we’ve been so sure of this immunity to nutrients that most wastewater treatment plants don’t even have to remove them before discharging into the Bay. Recent chinks in the Bay’s resistance to nutrients are now alerting us, however, to get ready in case there’s worse to come.
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25
May

Tackling Pollution

Though the Clean Water Act did an amazing job of reducing wastewater and stormwater pollution of the San Francisco Estuary, some contaminants remain thorny problems.  Legacy pollutants like mercury washed into the watershed from upstream gold mining, PCBs from old industrial sites, and selenium from agricultural drainage in the San Joaquin Valley, linger in the sediments, nearly impossible to clean up.  Emerging contaminants from contemporary lifestyles such as herbicides, flame retardants, and fire-fighting foams are being linked to human health problems, while microplastics are turning up everywhere from fish guts to creek bottoms to newborns. More recently, nutrients from both farm and sewage discharges have become a particular challenge for the Estuary. Long protected by its sediment-clouded waters, a recent...
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21
Mar

Saving a Species Struck by Systemic Oversights at Clear Lake

Since the 1950s, four native fish extinctions have taken place in Lake County’s Clear Lake: the thicktail chub, Clear Lake splittail, Pacific lamprey, and hardhead. A fifth endemic species, the Clear Lake hitch, is teetering on the brink. “Agencies view the hitch as just a fish. But for Tribes the hitch is sacred,” explains Big Valley Band of Pomo Indians tribal elder Ron Montez, Sr. “We believe Creator placed this fish here to help us survive for thousands of years. The chi (Pomo word for hitch) not only fed the seven Tribes around the lake, but it fed Tribes who came in from surrounding counties—Sonoma, Napa, Sacramento—and sustained all these people since time immemorial. That’s gone now. Anyone younger than...
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12
Oct

Rocky Road to a Fresh Enough Delta

Nothing reveals just how much the upper Estuary's seesaw of tides and freshwater flows is micro-managed than prolonged drought, and the resulting fiddling with barriers, gates, and water quality standards to prevent the ocean tides and salinity from intruding too far upstream. Come summer, managers begin to talk fearfully of "losing control of the Delta" and the dreaded outcome: salt water too near the export pumps...
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12
Oct

Science in Short: The Hullabaloo About HABS

Dead fish belly up in Lake Merritt and San Francisco Bay this past August sent scientists like Keith Bouma-Gregson scrambling to pinpoint the cause. A harmful bloom of marine algae had taken up residence in the Bay. Bouma-Gregson discusses his observations of the event in this podcast.
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13
Jun

Bagman for Bay Mussels

Martin Trinh practically bounces along the dock at the Coyote Point Yacht Club on a breezy, sunny spring morning. He’s carrying a case full of instruments and scopes out an open slip at the end of the pier. Soon he’s lowering a probe into the water, alongside kelp clinging to the underside of the dock. Another trip back to his Prius, still sporting South Carolina license plates, and he’s got a white plastic dish pan and a scrub brush. He fills and rinses a brown plastic bottle several times before finally capping it while full and placing it into a zip-top plastic bag. Then he lies on his belly, reaches into the water, and with blue nitrile gloves feels amidst...
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15
Feb

Better Living Through Fish – Editor’s Desk

I come from a long line of fisherfolk. My grandparents had a tiny cabin on a Quebec lake. We visited some summers. My grandfather let me drive the big white speedboat at a snail’s pace while he smoked cigars and trolled for trout off the stern. Once, when I caught one bigger than his catch-of-the-day, he “accidentally” knocked it back into the lake with the net. On the dock, we’d sunbathe while he cast lines overhead with a precision worthy of the movie A River Runs Through It. At the lake, we ate trout and eggs, trout salad, baked trout. I survived on spoonfuls of Cool Whip. (Photo above is editor as a teenager with Kay Rubbra, my grandmother, and...
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25
Oct

Tracking Natural Nitrogen Removal

Nitrogen inputs to the San Francisco Bay are among the highest of estuaries worldwide, yet so far have not caused harmful impacts like extreme algal blooms, oxygen depletion, and fish kills. But resistance to this nutrient may not last. Ever since the Gold Rush, excess sediment from pulverized rock has been pouring into the Bay, clouding the water and keeping algae in check by blocking sunlight. Recently, however, that protective sediment has diminished in parts of the Bay, contributing to concerns over nutrient pollution. A new study on a natural nitrogen-removal process is key to predicting whether nitrogen will cause ill effects here, too. The Bay’s nitrogen comes primarily from sewage and, for the most part, this nutrient is not...
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25
Oct

Estuary Summit Pivots from Science to People

“Make the unseen more visible in your work,” urged Amanda Bohl, opening speaker for the largely cameras-off audience of 600 virtually assembled for the 2021 State of the San Francisco Estuary Summit this October. The Delta Stewardship Council staffer’s remarks at the 15th biennial conference, usually a two-day, science-and -policy-heavy networking event but this year an eight-hour Zoom summit, referred to how many things we all work on or people we work with everyday remain invisible. Some of these often unseen yet important things brought up over the course of the day: the indigenous lands upon which so many efforts to restore the Estuary or “manage” its resources take place; the people in local communities left out of government decision-making...
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23
Mar

Delta Study Predicts Stronger Floods and Less Water Supply

Though most don’t realize it, practically all Californians are linked to the Bay-Delta region via its triple function as a source of drinking water for some 27 million Californians, a critical water provider for the Golden State’s hefty agricultural industry, and a rich and unique ecosystem. But for those who live in the legal Delta zone – some 630,000 people – the braided weave of the Sacramento and San Joaquin Rivers and their maze of associated wetlands and levees provides a place of home, community, and recreation. And, as a recent study by the Delta Stewardship Council shows, climate change is tugging on the watery thread holding it all together. “Two-thirds of Californians get their water from here, which is...
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22
Sep

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 to know if this is the worst year ever, because we haven’t been out there every single year for years and years monitoring,” says Meredith Howard, an environmental program manager with the Central Valley Regional Water Quality Control Board. “I...
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22
Sep

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. The proposed project would take a big shallow lake full of weeds, deepen some parts, fill in others with new lands and fish habitats, add beaches and recreational amenities, and stanch the spread of salt water from the ocean toward...
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21
Sep

Estuary News
September 2020

September 21, 2020
This issue of ESTUARY News has a fishy focus, summarizing 12 years of research on the fish-friendly Yolo Bypass, and profiling one man who has spent a lifetime helping fish around dams. Reporters take you out on the Delta to survey fish with cameras not nets, and into the offshore ocean to troll for salmon from a kayak. This issue also covers the latest research on COVID in wastewater, emerging contaminants in stormwater, harmful algal blooms in the Delta, a bold landscape redesign proposal for Franks Tract, as well as concerns about the region’s aging fleet research vessels.  Three stories and a new podcast explore shifts in how the region is distributing environmental dollars and opportunities with more of an...
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16
Aug

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 Art, Oro Loma Horizontal Levee, UC Berkeley, Regional Planning, Franks Tract, Central Delta Corridor, North Delta Arc, State of the Estuary, climate-smart infrastructure and more. Links to Topics Referenced Climate Smart Infrastructure for California- Paying it Forward Report Adapting to...
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