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Shell stuff: Monitoring the health of California’s shellfish amid climate change

This is the second is a series about Medill News Service reporter Rebecca Fanning’s embedded reporting experience at UC Davis’ Bodega Marine Lab in Bodega Bay, California. Read the original post here. 

By Rebecca Fanning

Endangered black abalone receive an aromatic spa treatment while hundreds of baby oysters float in tiny cages next to winding strands of seagrass, their growth tracked and measured by resident ecologists.

In the world of shelled invertebrates, researchers handle their subjects carefully, especially the babies who are hypersensitive to change and tend to die quickly and without warning, a habit that make them more difficult to study than their more resilient parents.

As these shelled creatures grow, researchers measure their shells, record water chemistry, and take pictures, searching for clues and patterns that will help resolve mysteries about the health of shells and changing ocean environments.

What do these marine invertebrates need to survive in changing ocean conditions? And what is the role of science in rebounding or preparing their populations for the future?

I caught up with Bodega Marine lab ecologists, research scientists and technicians to learn more.



Ph.D. ecologist Aurora Ricart works closely with the Bodega Ocean Acidification Research Group (BOAR), to gather data to answer this question: 

Does the presence of seagrass reduce or increase the pH level of the water where it grows? And if so, how does this affect the growth of calcifiers, shellfish that use carbonate and calcium ions dissolved in seawater to build strong shells and skeletons? 

This question has been debated for years, and marine ecologists have opinions on both sides. But there’s not yet enough data to prove or disprove the power of the plant. That’s what Ricart is hoping to do. And she’s using oysters as her test species.

“I’m very happy to be on the project to try to gain some of this data. The goal of project is to have enough data to be able to give a powerful message, right now we have no evidence at all.” –Ricart


There’s algae everywhere—coating the green seagrass, hanging off of tiny oyster cages and coating the insides of the glass tanks. For Ricart, the productivity of northern California’s marine ecosystem presents new challenges for her research.

A native of Valencia, Spain, Ricart earned her Ph.D. in ecology from the University of Barcelona where she focused on seagrass in the more “oligotrophic,” or nutrient-limited environment of the Mediterranean Sea. While Ricart has never worked in an environment such as the Pacific Ocean before, her seagrass expertise makes her an ideal person for the job. But this algae is an unexpected annoyance in her experiment, one she hasn’t encountered before.

“That’s why I have all of this algae growing, I’m like, ah, what am I going to do with all of you? The productivity you can get around here, it’s crazy,” she says.

“That’s why I have all of this algae growing, I’m like, ah. What am I going to do with all of you? The productivity you can get around here, it’s crazy.”

That productivity is one thing that attracted Ricart to the Bodega Marine Lab for a postdoctoral position in Tessa Hill’s lab. The waters off of Bodega Bay are part of the California Current, one of the most productive in the world thanks to annual upwelling events that bring cold, nutrient-dense water to the surface. That consistent flow of nutrients is to marine animals what protein powder is to a bodybuilder, a fast-track to major growth. So it’s unsurprising that Bodega Bay’s landscape can often feel like nature on steroids.

To deal with the explosion of algae, Ricart moves the seagrass plants into different tanks with “grazers,” tiny slugs who chomp on the algae and clean the plants. She keeps grazers out of her experiments because their respiration rates–the way they breathe–would impact the water’s pH and change her experiment.


While the grazers chomp on green algae, baby oysters are hard at work. Once they leave the larval stage and begin to build their shells, they’re unable to move on their own. So the tiny creatures filter calcium out of ocean water and use it to build strong shells. Oysters and other shell-dwellers who grow this way are called calcifiers because of their reliance on calcium carbonate in the waters where they live.

The three-month-old oysters are barely larger than the head of a thumbtack and it will be two to three years until they’ll resemble the fist-sized adults we see on our plates.

But Ricart’s not raising these oysters to barbecue or squirt with lemon and horseradish for Bay Area weekenders. She’s raising them as part of an experiment to investigate how the amount of seagrass in water can change its chemical makeup and whether this change has an impact on the growth of shell-forming marine invertebrates like oysters.

“We chose oysters because we have a collaboration with Hog Island Oyster Farm, and because this is the main aquaculture product in the area,” she says. The body of research for oysters is also more extensive than other calcifiers because of their economic value as a salty delicacy, allowing the team to use past research to inform their work.

Ricart and her team know that different amounts of seagrass impact fluctuations of pH. In tanks with more seagrass, the pH varies more, while the tank with less or no seagrass experience less photosynthesis and hence have more consistent pH levels throughout the day or night. This is exactly what she expected.

“The first part of the experiment is working,” she says. “What we want to see now is the effect of the fluctuations on the oyster growth.”


The ocean covers seventy percent of the earth’s surface. And as emissions from industry and cars send increasing amounts of CO2 into the atmosphere, it’s the oceans that absorb vast quantities of it,moderating global warming associated with climbing CO2 levels in the atmosphere but transforming the chemical makeup of the water.

The measure of pH (potential of Hydrogen) spans a scale from 0 (very acidic) to 14 (very basic). Bleaches and drain cleaners clock in around 13 or 14 while lemon juice and battery acid measure at 1 and 0 respectively.

Over the past 300 million years, ocean water has remained somewhat basic with a pH of 8.2. But since the industrial revolution and rising CO2 emissions, levels have dropped to 8.1. The ocean is acidifying 100 times faster than it has over the last 55 million years and models project that pH could dip as low as 7.75 by 2100, according to the European Environment Agency.


In a climate of increasing coastal storms and water quality threats, seagrass ecosystems are an ecological powerhouse. They absorb carbon at an incredible rate, removing carbon dioxide from the atmosphere before joining the warming layer around our atmosphere, and they deposit that carbon into the sea floor, burying it in the sediment. They also provide a structural habitat for fish and other ocean dwellers, and act as storm surge buffers for beaches and coastal communities. So when you plant seagrass beds or preserve existing ones, you do a service for the Earth.

Like land plants, seagrass harnesses the power of the sun to grow through photosynthesis. And as it grows, it changes the chemistry of the water. But since the sun only shines during the day, and even then not every day, Ricart must evaluate the impact of day and night on the growth of her baby oysters.

Each morning Ricart arrives at the lab every before sunrise to measure the pH level at her tanks. Then when the sun is highest in the sky, she measures again. This way she’s able to see the impact of periods of extreme darkness and extreme sunlight on the water chemistry.  

She has wanted to study the sea since high school and wanted to be a marine ecologist ever since she heard the term.

“For me, research is not just a job – it’s a way of life,” she says. “It’s being paid to follow your passion and to answer questions of common interest.”

She has wanted to study the sea since high school and wanted to be a marine ecologist ever since she heard the term.

So what is the potential of this common plant? Could the eelgrass that sways in the surf offer part of the solution to changing oceans? Or is the grass just as it looks, a simple plant with ordinary properties, itself in need of saving?





The room smells like fresh beeswax with a hint of coconut. As research scientist Blythe Marshman warms the wax, stirring it occasionally, she prepares the working area. Brushes for coating, an area for the patients to sit, and a notebook to log them by name, keeping track of who was waxed and when.

“It’s important not to let it get too hot,” she says, giving the pot another stir.

“All of these ingredients are organic. We use organic, local honey and organic, fair trade coconut oil. I feel like the Sonoma County niche market would be very supportive of that.”

“All of these ingredients are organic,” junior specialist Malina Loeher adds. “We use organic, local honey and organic, fair trade coconut oil. I feel like the Sonoma County niche market would be very supportive of that.”

Marshman and Loeher don’t work at a day spa, though those are popular in Sonoma County. They work for the California Fish and Wildlife’s Shellfish Health Lab, an operation based at BML. Today they’re waxing endangered black abalone, a process that removes organisms from the marine snails’ ridged outer shell.  

These organisms are all epibionts and endobionts. like polychaete worms, boring bivalves and sponges. These filter-feeding organisms “use and abuse” the abalone’s shell, zapping the animals of energy and fitness in a dangerous game that can lead to infections and death, especially in captivity.

Once the shells are free of these organisms, the abalone can often repair shell damage and dedicate more of its energy expenditures to growth and gonad development—both of which are incredibly important for broodstock in a successful captive breeding program.


The team will wax 12 of the blue-black adults, a process that involves carefully removing each from its happy home suctioned to the bottom of an underwater tank. An inability to clot blood means that the slightest knick of the animal’s “foot” with a knife could spell infection or death for the abalone. Though the Shellfish Health Lab recently completed a study that showed that abalone may be a bit more resilient to small cuts than previously thought. 

While waxing is a common practice for abalone in captivity, the Shellfish Health team still approaches the process cautiously.

“Since abalone need to be removed from their tanks to be waxed, we also have to weigh the cost versus benefit to removing animals for treatment, as there is always the potential risk of injuring them or causing them to spontaneously spawn from stress,” Marshman says.

BML is home to 15 black abalone, most of which were collected from various locations throughout the Central California coast between 1995 and 2003 (prior to being listed as federally endangered in 2009). About a third of the abalone were provided by colleague, Carolyn Friedman, professor of aquatic and fisheries science at the University of Washington.

The team weighs each animal, check its reproductive organs for size before painting each shell with the organic mixture, carefully avoiding small gill-holes and the muscular “foot” of the animal. After a few minutes of drying they’re returned to their underwater homes, smelling slightly better than before and covered in a yellowy coat of wax.


Supervised by research scientist Jim Moore, The Shellfish Health Lab diagnoses and monitors diseases in wild and farmed shellfish throughout California.

The lab is also actively involved in the detection of invasive species and the rehabilitation of native abalone populations up and down the California coast. While lesser-known than the recreationally popular red abalone and less threatened than the critically endangered white abalone, black abalone populations face their own set of threats.

“The black abalone are my favorite,” Marshman says as she examines one with a slightly broken shell. “They are the only abalone species in California that lives solely in the intertidal zone, which means they need to be exceptionally hardy to deal with additional stressors that intertidal organisms face (e.g., desiccation, waves). I guess I have soft spot for animals that have to work harder than others merely to survive. Also, the exterior surface of the black abalone’s shells can range from black to a brilliant bright blue, which is a rare color to find in animals.”

Black abalone are prone to diseases and they live in the shallow waters of the intertidal zone from Baja California, Mexico, to Sonoma County, California. While their tough meat makes them less appetizing for diners, their location close to shore means they’re still prone to poaching like their red cousins.

Over the next month that wax will suffocate any organisms that may have taken up residence in the ridges of the shell, and when it begins to flake, Marshman and her team will use dental tools to chip the wax away, preventing bacteria from growing on top. This part doesn’t smell quite as good. The organisms that the wax has killed tend to give off a strong odor.

There are seven species of abalone that live along the California coast, a small number compared with the roughly 70 species that occupy intertidal and subtidal waters in nearly every continent.

“There’s just something about finding a black abalone in a deep rocky crevasse in the intertidal—kind of like finding a large nugget in a gold mine,” Marshman says. “It makes them one of the more unique abalone species in the world.”

Photo at top: Baby oysters in Aurora Ricart’s oyster hotel at BML. Their growth may help researchers better understand the impact of seagrass presence on shell development. (Rebecca Fanning/MEDILL)

Tracking marine life on the edge of the Pacific

By Rebecca Fanning
Medill Reports

Bodega Bay, California. I’ve spent the past several weeks working with marine ecologists –holding tiny porcelain crabs, named for their propensity for losing limbs, picking seaweed out of small buckets to be dried and weighed for an animal diet experiment, peering through microscopes at fish larvae and gazing at baby oysters, their shells smaller than the head of a tack. The stakes are higher for marine life in an era of climate change, and scientists are weighing the impacts as warming oceans acidify.

The road to UC Davis’ Bodega Marine Lab  leads down a winding road, along a working harbor and past a series of seafood shacks, framed to the south by the calm waters of the bay. The lab itself sits on the edge of the Pacific Ocean, and, thanks to the annual upwelling which brings rich nutrients to the water’s surface, is surrounded by one of the most productive, life-filled marine ecosystems in the world. The lab is home to a thriving community of oceanographers, marine ecologists, naturalists, professors, PhD candidates, undergraduates and boat experts.

As an embedded reporter I saw firsthand the challenges of overnight research, discussed the struggle of attracting attention (and sometimes funding) to the less “charismatic” creatures, and mourned the loss of a beloved professor and marine ecologist whose mark on this community and the world will never be forgotten.

These journal entries are impressions and experiences from my  reporting experience at the lab.  


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Annual blessing of the Bodega Bay fishing fleet marks a shorter and uncertain salmon season

By Rebecca Fanning
Bodega Bay, Calif.

The Karen Jeanne rocks and sways as Dick Ogg steers out of Bodega Harbor, past the rocky breakwall where surf-casting fishermen wave from their perches.

Behind him, an array of boats fall into line, each decorated with signs and flags, their decks full of fishermen, families and friends. To some this route is a familiar morning commute, the first turn on a many-miles journey in pursuit of albacore tuna, salmon, Dungeness crab or sablefish, depending on the season. To commercial fishermen the harbor marks the safe haven after a dangerous journey. For others, today offers a rare boating adventure – a chance to picnic, take photos and crack open a beer before noon.


But today is about more than just socializing. It’s day two of the 45th annual Bodega Bay Fisherman’s Festival and time for the annual Blessing of the Fleet, a centuries-old tradition which began in predominantly Catholic, Mediterranean fishing communities. According to tradition, a priest or pastor blesses the community’s fishing boats to ensure a bountiful harvest and safe return to the harbor.

Family and friends on board Ogg’s boat the Karen Jeanne. (Rebecca Fanning/Medill)

Dick Ogg’s slender build, kind expression and his smooth, tanned skin makes him appear younger than his 65 years. He estimates that he has attended the blessing for more than 25 years, though he’s lived in Sonoma County for much longer, moving here with his family when he was 7. The retired electrician once used fishing as a way to supplement his income, but now he’s taken to the water full-time.

“I’m always reminded of guys I’ve known who aren’t around anymore. Things happen out at sea.” – Dick Ogg

Ogg tells the story of a friend who was run over in a shipping lane, and another who passed away out at sea. But death is only one kind of tragedy that strikes the area’s fishermen.

In Bodega Bay, the blessing tradition began nearly 60 years ago and marked the start of a once-fruitful salmon season. But as regulators scramble to protect declining salmon populations, the season has become shorter and shorter. The California Fish and Wildlife announced earlier this month that commercial salmon fishing in this area would open late – not until July 26 –  and would run for barely two months. The late start cuts the commercial season in half, and with it the chance to make a living.

“The salmon fishery has been diminished to the point that there’s not enough money to make it through the season,” Ogg says, adding that Dungeness crab is the only fishery remaining that provides close to enough money to support working fishermen in the bay. And even then the owners of boats often can’t afford full-time employees when crab season slows.

“I have some bills that aren’t going away,” says one of the crew members on Ogg’s boat.  He tells me about his fear of a less-than-lucrative salmon season and his plan to seek summer work in Alaska’s more fruitful Bristol Bay or as a tuna fisherman in his native Atlantic waters off the east coast.

He says he’s not planning to wait to find out how the salmon yield. He’s already contacted several commercial fishing vessels in hopes of hopping aboard.

For now Pacific salmon join red abalone and Pacific halibut on the list of closed California fisheries. This year marks the first-ever closure for recreational red abalone, though the commercial fishery has been closed since 1996 and other abalone species placed on endangered species lists.


Right now, Ogg is fishing for black cod, a sustainable white fish often called sablefish, considered a best choice or good alternative by the Monterey Bay Aquarium’s seafood watch. But black cod quotas are limited, and the real money still comes from Dungeness crab, a declining industry.

As the boat turns the bend, dense waves crash against Bird Rock, a local landmark named for the persistent birds that land on its surface, their white waste leaving a kind of organic graffiti on the gray stone. The skies are a brilliant blue, but dark clouds linger at their edges, a reminder of the dangers that lurk in open oceans.

Out on the water the harbormaster radio announces the start of the ceremony. The priest leans over a woven flower wreath and the prayers begin.

On board the Karen Jeanne, the crew goes silent, necks craned as all listen to the Lord’s Prayer, reminders of fishermen past and a few references to Jesus and his admiration for fishermen.

Ogg steers the boat closer to the action. “I could use all the blessing I can get,” he says.

As storm clouds cover the sun and boats speed back to the safety of the harbor, the priest blesses each boat, scattering holy water from a gold chalice into the salty air. Before he’s fully docked, raindrops speckle Ogg’s glasses and guests duck into the cabin, reminded of the uncertainty of nature and life on the water.

Photo at top: Fisherman Dick Ogg steers his boat the Karen Jeanne to the Blessing of the Fleet ceremony on Bodega Bay. (Rebecca Fanning/Medill)

Restaurant Week partners with the Greater Chicago Food Depository

By Rebecca Fanning
Medill Reports

It’s Chicago Restaurant Week, the best time to find deals and the worst time to make a reservation at foodie hotspots. But this year there’s a chance to give back. As part of a partnership between Restaurant Week organizers Choose Chicago and the Greater Chicago Food Depository, diners can make donations after finishing their meals.

“It’s an amazing organization. Really the goal is raise awareness and drive donations,” said Jordan Engerman, Director of Partnerships for Choose Chicago.

And every bit counts. According to Food Depository, one dollar provides three meals for those in need, and February is one of the slowest months of the year for donations.

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Local entrepreneur expands compost pickup business to corporate clients, restaurant chains

By Rebecca Fanning
Medill Reports

The United States has a food waste problem. Americans throw more than 130 billion pounds of food into landfills each year according to the U.S. Department of Agriculture. And as it rots, that food releases methane — a greenhouse gas and major contributor to climate change — into the atmosphere.

In Chicago, entrepreneur Jonathan Scheffel is working toward a solution. He’s encouraging individuals and businesses to throw their food in a different bin, and to let him take it away.

“I would say just to try it and see how easy it is. And try to get past thinking that it’s difficult, or its smelly or that it’s going to cause your house to collapse with rodents,” said Scheffel, whose small business, Healthy Soil Compost serves over 400 private residences, offices and restaurants in the city. Continue reading

Wisconsin lures out-of-state anglers by waiving ice-fishing fees

By Rebecca Fanning
Medill Reports

Boating, fishing, cheese and beer. Wisconsin’s identity is rooted in summer fun. But plunging temperatures mean fewer tourists in the chilly months.

In 2012 Wisconsin’s Department of Natural Resources launched free fishing weekends to attract more visitors to their state. For one weekend each January and June, the DNR waives the 50 dollar fishing license and offers free gear and lessons. Their goal: Get locals and visitors outside and excited to kick off the fishing season.

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Ice Monster Number One

By Rebecca Fanning
Medill Reports

It’s noon on a sunny Thursday in October and “Diver Dave” Oliva is sprawled on a black inner tube wearing only a speedo; his mask and snorkel leave a wet mark on the concrete beside
him. He waves to passersby, some seem to know him, others just wave back, amused. Behind him, cars speed down Lake Shore Drive, rushing north from the bustling Loop.

“You’re late,” he says to me when I arrive. “And where’s your swimsuit? Water’s never been this warm in October before.”

Mike Tschantz-Hahn slides over a partially frozen Lake Michigan. (Steve Hernan)

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