To Unravel Some Of The Ocean’s Mysteries, Scientists Head To Sea

At least twice a year, scientists board the Bell M. Shimada, a National Oceanic and Atmospheric Administration research vessel, to study the Northern California Current ecosystem.
At least twice a year, scientists board the Bell M. Shimada, a National Oceanic and Atmospheric Administration research vessel, to study the Northern California Current ecosystem. CREDIT: Courtney Flatt

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At least twice a year, a team of scientists on NOAA’s research vessel Bell M. Shimada survey waters along the Washington and Oregon coast.

Near the edge of the coastal shelf, off the shore of Grays Harbor, Washington, a 10-foot-long net the shape of two bongo drums slowly lowered into the inky black sea.

Down 10 meters.

Down 20 meters.

Waves knocked against the ship, which held the nets. For a few moments, the scientists aboard the National Oceanic and Atmospheric Administration, or NOAA, research vessel Bell M. Shimada wondered what sea life these nets might catch.

Jonathan Witmer, a survey technician with NOAA, readies equipment for the scientists as waves crash against the side of the ship.

Jonathan Witmer, a survey technician with NOAA, readies equipment for the scientists as waves crash against the side of the ship. CREDIT: Courtney Flatt

One scientist aboard the NOAA ship, Kris Bauer, hoped to find tiny crustaceans known as copepods. These “copes,” as Bauer affectionately called them, play an integral part in the ocean’s food web, filling the bellies of juvenile salmon, sardines and tuna.

“Different species of salmon and tuna and rockfish, they all target these larger copepods because they give fish so many more calories for the effort that they’re expending to hunt,” said Bauer, a second-year Ph.D. student in Oregon State University’s department of integrated biology.

However, climate change could cause big swings in ocean conditions, leaving these tiny copepods to face an inhospitable environment, including warmer, more acidic and increasingly hypoxic waters, which don’t carry all the oxygen that sea life needs to thrive.

It’s unclear exactly what that will mean for hungry, growing fish that feed on copepods. But, some scientists worry a future shifting food web, which could reduce the number of copepods, could further diminish the number of salmon returning to spawning grounds.

These types of changing ocean conditions have other scientists on land wondering whether efforts to save salmon could be for naught. Moreover, some scientists said ocean conditions must be taken into consideration when evaluating how to save salmon.

Effects on salmon

When young salmon first enter the ocean, it’s one of the most important times in their lives, when they bulk up on copepods and grow stronger.

“I think it’s important that we all think about the ocean, especially for salmon. That really is where they get big. It’s clearly an important part of their lifecycle, but we just kind of take it for granted. It’s out of sight, out of mind,” said Laurie Weitkamp, a research fisheries biologist with NOAA.

mysteries of the deep

CREDIT: Courtney Flatt

However, the time salmon spend in the ocean leaves many unanswered questions for scientists, Weitkamp said.

“Right now we don’t understand very much, and we feel like, maybe there really are some critical things that we can be doing that would benefit salmon. But we don’t know what those are at this moment because the ocean is just a big black box,” Weitkamp said.

Salmon spend much of their lives in the ocean, and most of them don’t make it back inland to spawn.

Take the endangered spring/summer chinook on the Snake River. Only about 1% of those salmon that make it to the ocean survive, said Brian Burke, a supervisory research fish biologist with NOAA’s Northwest Fisheries Science Center.

“If we could change ocean survival from 1% to 2% on average, that would dramatically change the entire situation,” Burke said.

Moreover, studies suggesting any single measure to save salmon in freshwater, like increased spill over dams or dam removal, must incorporate data from the years salmon spend at sea, Burke said.

“All of these things we’re doing in freshwater, it would not be a good strategy to interpret the results of these management actions without understanding the impacts of the ocean,” he said.

To that end, the scientists need to better understand predation in the ocean, Burke said. What animals eat juvenile salmon, how much salmon they eat, as well as when and where.

“If we have some of that information, we can start to manage hatchery release timing or fish size,” he said.

Right now, scientists rely more on a variety of ocean indicators such as surface temperature, which can affect the amount of food available for young salmon to eat. Those indicators, like copepod productivity, provide invaluable information, Burke said, but it all tends to correlate to salmon survival not drive it.

To help answer some of those questions, NOAA’s Northwest Fisheries Science Center is drafting a strategy document that could guide future salmon predation studies, Burke said.

Unraveling the ocean’s mysteries

Out at sea, many tiny zooplankton, which include copepods, come alive at night, when they’re less likely to end up in the jaws of larger sea creatures. Under the cover of darkness, the zooplankton can more safely migrate to the upper water columns to catch some dinner of their own.

Crew members on the Bell M. Shimada drop a net into the ocean at night.

Crew members on the Bell M. Shimada drop a net into the ocean at night. CREDIT: Courtney Flatt

Now close to the surface, Bauer hoped to catch copepods in the ship’s bongo nets. For one experiment, he planned to catch live copepods to study in a lab on-shore.

“It’s cool to see them preserved, but when they’re alive, and you see them moving around, and feeding and swimming. No matter how tired I am, it’s always the coolest part,” Bauer said.

The scientists are part of an expedition along California, Oregon and Washington waters, ultimately traveling 1,718 nautical miles. One nautical mile is slightly longer than one mile on land.

On this survey expedition, which lasted from May 6-17, the scientists collected samples of zooplankton, phytoplankton, environmental-DNA, and tested water salinity. The boat cut through water swells up to 13-feet and 40-knot winds deemed dangerous enough to stop sampling efforts. Scientists laughed as a pod of roughly 60 dolphins played in the Shimada’s wake and jumped in excitement at the sight of a sei whale, less frequently identified in these waters.

Talia Davis filters water to collect environmental-DNA, just a portion of the research happening aboard the Bell M. Shimada.

Talia Davis filters water to collect environmental-DNA, just a portion of the research happening aboard the Bell M. Shimada. CREDIT: Courtney Flatt

They hoped all their efforts will help unravel a few threads of the scientific mysteries and secrets the ocean and its creatures hold tight.

For example, Bauer has more questions than answers surrounding the copepods he’s studying. His adviser, Felipe Barreto, who studies a completely different intertidal copepod species, jokes that the 5-millimeter crustaceans Bauer studies are “real copepods” because of their size.

In particular, Bauer is studying Calanus marshallae, a fatty copepod that many fish like to snack on. Calanus marshallae thrive in waters along the Gulf of Alaska to waters off British Columbia, Washington, and Oregon.

Bauer took to calling them “my copes” nearly every time he mentioned the cartoon-like creatures.

“They sort of have this torpedo-like body. Then they have these two giant antennules that stick out on either side of their head, essentially the length of their body. If you’ve ever seen Plankton from ‘SpongeBob,’ that’s exactly what I’m studying,” Bauer said.

But first on the Shimada, Bauer had to catch the Plankton-like copepods.

At 30 meters below the surface, the bongo net stopped.

Jonathan Witmer, a NOAA survey technician, measure the angle of a net in the water.

Jonathan Witmer, a NOAA survey technician, measure the angle of a net in the water. CREDIT: Courtney Flatt

After a few moments drifting at a 45-degree angle, a winch operator pulled the net to the surface. Bauer hoped it had some of his copepods in tow.

Bauer uses copepods to study evolution in the ocean, particularly in response to climate change and oxygen changes on the coastal shelf. Unlike sea life such as fish and whales that are more mobile, he said, plankton can’t just pick up and go somewhere else.

“That’s the thing about plankton. They don’t really have the ability to move when conditions are stressful, unlike fish that are highly mobile and can escape these stressful conditions. Plankton have to endure them,” Bauer said.

But sometimes, ocean conditions bode well for these tiny creatures and the fish that eat them.

Winter conditions stick around

In 2021, an early, nutrient rich-upwelling brought cold waters from deep in the ocean to the coastline. Last year’s upwelling created some of the best ocean conditions in the last 20 years, supplying a bounty of fish food, including copepods.

Calanus marshallae are fatty copepods that many fish like to snack on. They thrive in waters along the Gulf of Alaska to waters off British Columbia, Washington, and Oregon.

Calanus marshallae are fatty copepods that many fish like to snack on. They thrive in waters along the Gulf of Alaska to waters off British Columbia, Washington, and Oregon. CREDIT: Bill Peterson/ Courtesy Of Kris Bauer

However, on this leg of the Shimada’s expedition, the upwelling hadn’t yet arrived. Upwellings usually arrive around tax day, April 15, said Jennifer Fisher, a zooplankton ecologist with NOAA.

As the Shimada maneuvered along the Oregon and Washington coasts, sample after sample showed fewer thriving sea creatures than the previous spring, likely because the 2022 upwelling took its time arriving, Fisher said.

“We saw it all the way up the food chain. From the phytoplankton, to the zooplankton, to the krill, and even the marine mammal folks saw very few whales,” Fisher said.

Prior to the survey, forecasting showed ocean spring conditions would start at the beginning of May.

“Then when we got out here, there were winds from the south and storms,” Fisher said. “The upwelling delay can have cascading consequences for juvenile salmon that are migrating out to have something to feed on. They’re migrating out now.”

The ocean in early May still resembled winter conditions, she said.

“The question still remains: when will the winds turn around? And what’s that going to do to the ecosystem?” she said.

Seeing what, exactly, is happening on the ocean is one reason long-term surveys like these are incredibly important, Fisher said.

By June, Fisher said the delayed upwelling had finally come in, although was weaker than normal.

Decades of work

With the help of these surveys, scientists keep trying to unlock the mysteries of the tiny copepods, even after decades of previous work.

 

Bill Peterson's internationally renowned work set standards for long-term oceanographic monitoring.

Bill Peterson’s internationally renowned work set standards for long-term oceanographic monitoring. Courtesy Of Jennifer Fisher

More than 42 years ago, the Calanus marshallae copepods Bauer now studies drew the interest of young scientist Bill Peterson, whose internationally renowned work would later set standards for long-term oceanographic monitoring. Peterson’s goal was to inform policymakers about climate change and how it affects the ocean ecosystem, Fisher said.

“Bill’s work talking about climate and the effect of climate was pioneering,” Fisher said.

Throughout his career, Peterson continued to love studying zooplankton and the marine ecosystem almost as much as he loved mentoring young minds, including Fisher’s.

“He was the premier zooplankton climate person,” Fisher said. “He was a big thinker, and he really had an amazing understanding of these broad topics. It really broadened my outlook.”

Peterson pushed multidisciplinary scientists to survey the Northern California Current ecosystem. The U.S. Global Ocean Ecosystems Dynamics program, known as GLOBEC, measured how climate change and variability affected abundances of fish, including salmon, and zooplankton in the coastal ocean ecosystem.

Peterson led the start of the Northern California Current survey expeditions that would turn into the Bell M. Shimada sampling surveys. He also restarted a long-term monitoring program off the coast of Newport in 1996.

Fisher now leads these surveys after Peterson died in 2017. Loved ones scattered Peterson’s ashes 25 miles off the coast of Newport, along the stretch of water he studied for so many years, according to an obituary by OPB.

A 2002 report on the GLOBEC North California Current system program noted climate variability over time significantly affects “the abundance, distribution, growth and survival of living marine resources.”

Moreover, according to the report, coastal ocean conditions and the abundance of food, such as copepods, strongly affect juvenile salmon during their first summer at sea.

Scientist Laura Lilly gets a net ready to collect samples from the Pacific Ocean.

Scientist Laura Lilly gets a net ready to collect samples from the Pacific Ocean. CREDIT: Courtney Flatt

During those early GLOBEC years, scientists discussed what seems like a prevailing question today: whether dams and habitat management or natural ocean condition changes pose a greater threat to salmon.

“We’re still talking about the same things,” Fisher said, after recently finding articles from the 1980s and 1990s about fisheries management and climate change in Peterson’s desk.

The GLOBEC ocean surveys aimed to lessen uncertainty for fishery managers, said Jack Barth, executive director of the Marine Studies Initiative at OSU.

Decades ago, Barth helped pioneer the surveying program with Peterson.

“We worked our butts off for two-, three-week periods for two years and put together that whole story relating where the animals were relative to the oceanographic features,” Barth said.

The early team really nailed down the relationship between salmon, zooplankton, marine mammals, and upwelling conditions in the ocean, Barth said. The better the upwelling, the more marine life scientists saw.

‘Coming home’ to Newport

That’s one reason scientists say it’s important to take survey measurements over a long time period. In fact, Fisher estimated the study area outside Newport, Oregon, where she’s based, is one of the most sampled spots of the ocean in the world.

In addition to the Shimada surveys, the team samples the first 25 miles of what’s known as the Newport Hydrographic Line twice a month on the Elakha, the Chinook trading term for sea otter. The Elakha is a 54-foot, $500,000 ship based at OSU’s Hatfield Marine Science Center in Newport. Scientists have sampled this line for the last 26 years.

At least twice a year, scientists sample the deep ocean 200 miles offshore from Newport on the Shimada, aiming to dip nets at least 2,000 meters below the ocean’s surface.

“When we sample the Newport Line, it’s like home. I feel like the copepods know us. It’s like, ‘Hey! We’re here! We’re back!’” Fisher said, of the last night on the 2022 spring Shimada survey.

Vince Welton (right) and Colin Schmidt fix a CTD cable after it broke.

Vince Welton (right) and Colin Schmidt fix a CTD cable after it broke. CREDIT: Courtney Flatt

This spring, an important piece of equipment broke on the deepest 2,000-meter sampling effort, which meant the deepest samples only reached around 1,700 meters below the surface. Vince Welton, the ship’s electronic technician, quickly repaired a damaged cable to get the equipment that measures conductivity, temperature, and depth – or CTD instrument – up and running for the rest of the trip.

The CTD instruments, which weigh around 670 pounds without water, collect independent samples at varying water depths, which Fisher said is extremely important to help better understand how ocean conditions, such as marine heatwaves, will continue to affect sea life.

“The farther down the heatwave goes, the longer the temperature is going to take to get back to normal,” she said.

The survey on the Shimada allows scientists to sample more of the Northern California Current ecosystem, from Trinidad Head in California to La Push in Washington.

The California Current is one of the most productive regions in the ocean because of wind-driven upwelling that delivers nutrient rich water to the Continental Shelf, Fisher said.

‘A bathtub off the coast of Washington’

South of La Push, the ship pushed inland on the Grays Harbor line. Bauer said he believed that his copepods would show up as the ship moved toward the shore – Calanus marshallae aren’t generally found very far off the coastal shelf. And, Washington has a large, almost flat coastal shelf, Bauer said.

“It essentially becomes this bathtub off the coast of Washington, where water is just sitting,” he said.

Scientists collected many zooplankton samples on the Bell M. Shimada survey from May 6-17.

Scientists collected many zooplankton samples on the Bell M. Shimada survey from May 6-17. CREDIT: Courtney Flatt

Those conditions are ripe for hypoxia, which Bauer is studying to better understand how copepods react to stressors. Hypoxia can lead to vast dead zones in the ocean, where marine life isn’t sustainable. As the climate changes, coastal ecosystems could become more vulnerable to hypoxia, according to research from NOAA’s National Centers for Coastal Ocean Science.

“In Washington and Oregon, we’re experiencing really dramatic, intense hypoxic episodes each summer,” Bauer said.

Later in the summer, Bauer will sample live copepods in Oregon and California. Off the California coast, copepods face different conditions than in Washington and Oregon waters.

He spent the last 18 months learning to keep the copepods alive in a lab. To do that, he had to answer lots of questions: When’s the best time to change the water? How often should he turn a light on in the incubator? How much food should be in the water?

After trial and error, Bauer found what he said believed to be the least stressful conditions for copepods in the lab. He placed a single copepod in a 250-milliliter beaker, where it lives for up to two months.

“It’s a daunting task to try to cultivate an organism that has only been cultivated by one or two people a few decades ago,” Bauer said.

Happy copepods are active copepods – swimming around and eating, which Bauer called hilarious to watch.

“They have these feeding appendages that are just moving the water around, and they’re creating this vortex that draws algae into their mouth,” Bauer said.

Catching copepods

In the night’s bewitching hours, the bongo nets broke the water’s surface. A science crew member unclipped the end of the net and collected any number of organisms caught there.

Bauer poured the water inside the cod end through two progressively smaller filters. The filters dumped into a white bucket that collected the seawater.

The first filter removed all the krill and larger organisms. The second collected a boatload of copepods.

“My copes, my copes,” he said.

Scientist Kris Bauer gets a closer look at the Calanus marshallae copepods a bongo net pulled up off the coast of Grays Harbor, Washington.

Scientist Kris Bauer gets a closer look at the Calanus marshallae copepods a bongo net pulled up off the coast of Grays Harbor, Washington. CREDIT: Courtney Flatt

Bauer poured the copepods into a makeshift setup – a clear pyrex dish attached to a light panel.

In this first find, he spotted a large number of male Calanus marshallae, an unusual finding. Bauer said he hoped for more female copepods.

“Females often dive deeper than any other males or earlier life stages, so they’re probably the most vulnerable to low oxygen,” Bauer said.

He drew each copepod into a pipette and dripped the crustacean onto a petri dish for further examination under a microscope.

Bauer kept these copepods alive in a refrigerator to simulate ocean conditions. He cared for them each day the ship remained at sea.

“It’s really this base of the food chain that is so important,” Fisher said.

So, the scientists continue sampling as often as possible, she said.

“We think we know a lot. We sample as often as we can, and we try to understand the system. But, it’s complicated and it’s complex,” Fisher said. “You’re dipping a tiny, little net in this massive ocean, and you’re hoping you’re going to understand something from that.”

Always something surprising

That hope to better understand the ocean drives the scientists onboard the Shimada.

“You never know what you’re going to find. We always find something interesting. There’s always something different. There’s always something that surprises us,” Fisher said.

Over the expedition, the nets brought up many surprises, including a deep sea bristlemouth, a bunch of pyrosomes, and bioluminescent copepods.

Each net dip felt like Christmas morning, Bauer said, the anticipation building as the net closed in on the surface. That Christmas-morning adrenaline kept him from sleeping more than a few hours each day on his first Shimada survey in 2020. “There was too much to see,” Bauer said.

“Everybody’s eyes light up when we bring up the nets,” Bauer said. “It’s like, let’s go out 200 miles and drop a net in the water and see what we get.”

What they get could one day help answer the mysteries of the deep, Bauer said.

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