The Underwater Library at Scripps Institution of Oceanography

For decades, the Scripps Oceanographic Collections have amassed millions of marine organisms and geological samples that continue to yield scientific discoveries

The Scripps Oceanographic Collections are the largest university-based oceanographic collections in the world. It is comprised of the Marine Vertebrate, Benthic Invertebrate, Pelagic Invertebrate, and Geological Collections. Photo by Oriana Poindexter.

T he bucket of preserved fish opens, but it doesn’t smell as bad as you might think. Like vinegar, with a hint of sardine. OK, maybe it’s bad, but if you’re Ben Frable, manager of the Marine Vertebrate Collection at Scripps Institution of Oceanography, you’re used to it.

Frable removes the contents: an oarfish, the longest bony fish alive, tightly curled to fit inside its shipping container.

The 15-foot creature uncurls in front of me like a fishy Fruit Roll-Up. Frable and an undergraduate assistant measure and photograph the fish before preparing it for its future afterlife in the Marine Vertebrate Collection.

In a windowless area of Vaughan Hall, shielded from the San Diego sun that would otherwise damage the preserved organisms, the oarfish will join the other two million fish suspended silently in their alcohol seas, a mausoleum of 140,000 jars representing more than 6,000 different marine fish species.

But they’re not entombed here; these specimens are all available to the scientific community, both near and far, and have many tales to tell even in their lifeless state.

One big happy family

The Marine Vertebrate Collection is one of four that comprise the Oceanographic Collections at Scripps Institution of Oceanography at UC San Diego, the largest university-based oceanographic collections in the world. It shares Vaughan Hall with the Benthic Invertebrate Collection and the Pelagic Invertebrate Collection , both home to their own impressive assortment of marine organisms. And to the north, a refrigerated room chills part of the Geological Collections.

“This is only a small portion of this collection,’ Alex Hangsterfer, manager of the Geological Collections, tells me as the lights flicker on. “The rest, large rocks and dredged samples, are located in a warehouse off campus.’

It’s not your average rock collection. This assortment of over 3,500 dredged samples fills a 9,000-square-foot building. Rocks from all major tectonic features—including hot spots, island chains, seamounts, and abyssal plains—are represented. There are also pieces of drowned coral reefs, ice-rafted cobbles, manganese nodules, as well as very rare igneous, metamorphic, and mantle rocks.

Home to someof the largest samples, the Geological Collection also has some of the smallest: opal microfossils looking all the world like carnival spun glass, which are neatly secured in 40,000 glass slides used for microscope observation.

Inside the room before me are sediment cores—about 7,500 of them—which are cylinders of mud pulled from the bottom of the ocean. Though most are less than ten feet long, their layers go back hundreds or thousands of years. Each core is a snapshot of Earth’s history and are, along with the dredged rocks, a dream for geochemists, geophysicists, and paleoceanographers (those who study past life in the sea).

Back in Vaughan Hall, the Pelagic Invertebrate and Benthic Invertebrate Collections share a massive room of movable shelves, stocked with millions of spineless specimens. Most were collected from the Pacific Ocean, but all the world’s seas are represented on these shelves.

It’s easy to focus on the large sea urchins and crab shells in the entrance to the Benthic Collection, or the six-foot-long Humboldt squid in its cylindrical tank near the doors of the Pelagic Collection. To Charlotte Seid and Linsey Sala, managers of the respective collections, the excitement only starts there.

“This is only a fraction of what we have here,’ said Seid. “We have upwards of 56,000 jars and 800,000 individual animals.’ In these jars are those creatures found on the seafloor, such as sea stars, lobsters, mollusks, and sea cucumbers.

Across the room, one searching a shelf for pelagic invertebrates would come upon squid, krill, and strange curiosities like salps. Like their benthic roommates, they’re also invertebrates, but inhabit the water column instead of the ocean floor.

“Our collection is unique in that we house more than 140,000 whole zooplankton samples in addition to reference specimens,’ Sala said. “These are a mixture of many different pelagic animals collected by fine mesh nets and preserved as a single collection event. They must be carefully sorted under a microscope to identify specific groups and we can reconstruct populations of these organisms quantitatively.’

All of the specimens and samples, large to small, old to new, are used for scientific research in one way or another, and have been since the founding of Scripps in 1903, when a few dedicated scientists made the initial effort to start collecting locally.

A tale as old as Scripps

Since the institution’s earliest days as a small marine research center at the Hotel Del Coronado Boathouse, there have always been preserved curiosities lining Scripps shelves. These earliest specimens included barnacles and mollusks collected along San Diego’s beaches, copepods and other plankton, as well as deep-sea corals from the U.S. Fisheries Steamer Albatross cruise off California, led by Scripps’ founding director William E. Ritter in 1904.

When Scripps moved to its final and current location in La Jolla, the specimens made the move as well, slowly growing in quantity until a new era of seagoing research blossomed in the 1940s and 1950s.

After the collapse of the California sardine fishery in the mid-1940s, scientists began a push to understand how overfishing and environmental changes were at play. As a result, the California Cooperative Oceanic Fisheries Investigations (CalCOFI) was formed in 1949, setting sail to sample the biological communities offshore of the state and Baja California. This exploration led to an explosive growth in plankton samples, forming the foundation for the Pelagic Invertebrate Collection, which at that time was joined with benthic samples and didn’t yet have its formal name.

When World War II ended, a fleet of former war ships became available to scientists, who jumped at the opportunity to use the modern vessels and their high-tech capabilities for ocean exploration. Sonar transformed oceanography and the Collections, which began dramatic growth during this time as both biological and geological samples were hauled to the surface and brought back to campus for study.

Carl Hubbs, a prominent ichthyologist, joined Scripps in 1944 and set to work researching coastal fish in Southern California and the California Current. His samples, along with a small collection of fish accumulated byScripps Aquarium Curator Percy S. Barnhart, were the beginnings of the Marine Vertebrate Collection. Aboard those WWII-era ships, researchers in the 1950s were making heavy use of the newly developed Isaacs-Kidd Midwater Trawl, bringing a significant number of midwater fishes to the collection in this cone-shaped net that is dragged through the water column instead of on the bottom of the ocean.

With the collection managed mainly by graduate students in the early days, Hubbs saw an opportunity to advocate for a curatorial position. In 1958, Richard Rosenblatt was appointed as Curator of Fishes. Under his care, the collection continued to grow as pelagic, midwater, and deep-sea specimens from around the world were added. Rosenblatt and Hubbs also made numerous collections of shore fishes from the tropical eastern Pacific, especially Mexico and Panama.

Scripps was one of the first U.S. institutions to begin taking core samples from the deep sea, with some dating back to the 1910s. When sonar became widely available after World War II, science’s ability to map the ocean floor led to a flurry of geological sampling. At the time when the Marine Vertebrate Collection was taking formal shape, so too did the Geological Collection. William Riedel, a renowned micropaleontologist, became the first curator of the Collection in 1955 and his research on core samples and dredged rocks began what is now one of the world’s largest geological collections.

While still joined as one, Benthic and Pelagic Invertebrate Collections were undergoing their own growth at this time as well, as new seafloor and midwater trawls were bringing up organisms never seen before. In the 1960s, the two split into their own, with Pelagic taking a focus on time series data such as the CalCOFI samples and Benthic delving into the documentation of new deep-sea life.

Curators and managers were hired, samples were collected, scientific enterprise in collections grew exponentially, and by the end of the 1990s each Collection was firmly rooted in its own endeavors and current locations on the Scripps campus. Built with a solid foundation and encompassing millions of oceanographic treasures, the Collections are now powerhouses—of discovery, collaboration, and education.

Discoveries from the dead

“The word ’collections’ sounds old, dusty, static, something shoved away,’ said Pelagic Invertebrate Collection Curator Mark Ohman. “It doesn’t show the dynamic side of the Collections: the teaching, research, education and outreach, and marine resource management to which we contribute.’

Take a superficial look at the shelves and it might be easy to think that. But talk to the grateful scientific users or search in any online scientific journal and it will become evident that this idea is far from the truth.

“There’s an exciting story to be told,’ said Ohman. “Not just from the thrilling time spent at sea collecting, but from what these specimens can continue to tell us.’

The story of one jar’s contents isn’t static like the specimen within. The Collections operate as a sort of library—yes, a large collection of material, but a treasure trove of knowledge and discovery just waiting to happen once a lid is unscrewed.

A favorite story from the Pelagic InvertebrateCollection involves an unlikely catalyst: Alfred Hitchcock’s The Birds. A tale about a small seaside California town under attack from berserk birds is actually based on a true story, and the reason for the birds’ behavior was found in plankton samples. Domoic acid, a neurotoxin produced by single-celled algae, can build up in plankton-eating fish like sardines and anchovies, which in turn are consumed by predators like sea lions and seabirds. The resulting poisoning can lead to erratic behavior and ultimately death. Archived zooplankton specimens from the time of the movie’s setting showed that domoic acid was present in the plankton and provided the explanation.

The powerful stories, however, are the ones completely reshaping our knowledge of the ocean. With the most consistent time series of plankton in the world, the Pelagic Invertebrate Collection has been paramount in increasing our understanding of physical and biological processes in the Pacific Ocean, particularly Pacific Decadal Oscillation (PDO), El Niño, and La Niña. Plankton samples from CalCOFI’s earliest cruises helped scientists in the mid-1900s understand how unfavorable environmental conditions—like PDO, a shifting pattern of warm and cold surface water—was related to the collapse of the sardine fishery. Today, researchers are using decades-old krill and plankton samples to look for trends in species and abundance in the years leading up to past El Niño and La Niña events. By looking for these trends, they can compare recent samples to older ones for signals that could help forecast future El Niño or La Niña events.

With its focus on time series data, even specimens from the collections’ earliest days are still making headlines in research journals. Beyond helping the National Oceanic and Atmospheric Administration forecast an El Nño, the Pelagic Invertebrate Collection is allowing Scripps scientists to study the “flavors? of these events. Using samples from ten different El Niños, Scripps PhD graduate Laura Lilly found that scientists can predict how future events will affect different groups of plankton, such as krill, a vital prey item for whales, penguins, and other marine animals.

“None of these discoveries or forecasting tools would be possible without long-term records that we have in Pelagic Invertebrate Collection, and all the collections quite frankly,’ said Ohman. These records are also revealing clues to how other oceanographic phenomena, like harmful algal blooms, acidification, and deoxygenation, are affecting the ocean. And, Ohman stresses, how we’re affecting it.

Jennifer Brandon, a marine scientist who completed her PhD at Scripps, relied heavily on the Pelagic and Geological Collections for her research on plastic pollution. With the help of Linsey Sala, Brandon documented microplastics in salps, pelagic invertebrates that form long, colonial chains. In a 2019 study , she estimated the ocean is contaminated by 8.3 million pieces of so-called mini-microplastics per cubic meter of water, a million times more than previously thought.

In a separate 2019 study , Brandon worked with Ohman, Hangsterfer and Geological Collections Curator Richard Norris to look at pollution in seafloor cores collected in the Santa Barbara Basin. She found that the amount of plastic fragments has been increasing exponentially since the end of World War II. Sifting through nearly 200 years of sediments, she noted that since the 1940s the amount of microscopic plastics has doubled about every 15 years. Similar projects are using the Geological Collections to analyze plastic accumulation in San Diego’s Mission Bay and other coastal areas.

Most recently, researchers are turning their attention to the Collections after the discovery of DDT waste barrels off the coast of Southern California. Because Scripps and CalCOFI maintain a collection of biological specimens pulled from the ocean at known locations across space and time for the better part of a century, the program has the potential to broach historical samples with modern science in order to understand the scope and scale of DDT pollution in the coastal ecosystem.

“CalCOFI, like other long-term monitoring programs, is perennially on the funding chopping block, because the justification for such programs is largely, ’some day, you might need it for eventualities you can’t imagine,’- said associate professor and CalCOFI Director Brice Semmens. “The rediscovery of the DDT dumping ground of southern California is a classic eventuality: how has the DDT, leaked from thousands of barrels, made its way to the parts of the food chain that Californians rely on?

We’re only scratching the surface when it comes to what past samples can tell us about our changing world. As wildfires become more frequent, scientists are beginning to think about their effects on the pelagic environment, looking to CalCOFI samples for clues around past and recent fires. They can also give us insights into ocean acidification. Pteropods, a type of pelagic sea snail with a calcium carbonate shell, are canaries in the coal mine for ocean acidification in the open ocean environment. Researchers are looking at their abundance and shell strength in past samples to see if more acidic waters are depleting them.

“These are the kinds of questions that come out later that you never would have thought of at the time,’ said Moira Decima, an assistant professor who will curate the Pelagic Invertebrate Collection starting in July 2021. “With the Collections we can address problems that we become aware of many years or decades after the sampling was completed.’

Marine biologists and ecologists are thinking about how changing ocean conditions are compressing or shifting habitat for certain species. By referencing where specimens were collected in the past to where the same species are seen now, scientists can lay the framework for conservation and management plans amid a quickly altering environment.

Specimens in the Marine Vertebrate Collection allow researchers to understand how fish populations, sizes, and other variations have changed over time, and how they might continue to change in a warming world. Sometimes Ben Frable stumbles upon a fish so rare that it merits scientific publication.

“I was checking old identifications and found a fish collected near Midway Atoll in 1959,’ he said. “It was very similar to a rare species only known from Japan that was just described in 2013. It turned out to be this species and I was able to describe the fourth known specimen and extend the known range 3,400 kilometers (over 2,100 miles) east into the central Pacific.’

Frable and Phil Hastings, Curator of the Marine Vertebrate Collection, frequently use the Collection in their own research. In research worldwide, these specimens have been cited in more than 1,500 scientific papers.

“Collections inspire scientists,’ said Hastings. “They generate new ideas, about species, about ecology. They make you think about evolution and how things have come to be how they are.’

Like the Marine Vertebrate Collection, the Benthic Invertebrate Collection is a hotbed for new species discovery. The Benthic Invertebrate Collection’s strengths - deep-sea and chemosynthesis-based ecosystems - represent some of the most extreme and least explored environments on our planet, so it is common for the collection to support dozens of new species descriptions each year. Doctoral, masters, and even undergraduate students routinely encounter invertebrates that were previously unknown to science and often known only from a single location - hinting at the immense scope of how much we still need to learn about the deep sea.

The scientist who completes the rigorous work and due diligence of describing a newfound species is also entitled to name it. To support the research costs involved in these projects, the Benthic Invertebrate Collection invites the public to share in the process by donating to the Name a Species Program. Donors can choose the name for a new species—often commemorating the donor’s own name, honoring the memory of a loved one, or serving as a truly unique birthday or wedding gift. The new name is declared in a scientific publication that permanently establishes the new species, and the donor receives a copy of the publication and a framed print of the new discovery.

In the early 2000s, Curator Greg Rouse was part of a team that described deep-sea worms of the genus Osedax, which are unique in their ability to feed on the bones of whale carcasses by secreting acid and hosting symbiotic bacteria. In 2018, fourteen new species were described in Monterey Bay alone. The Rouse lab continues to investigate these unusual worms and the broader evolutionary and ecological roles of whale falls.

In 2020 Rouse and colleagues described four new species of Elvis worms , named for their shimmering scales, that also inhabit the deep. Another recent publication by Rouse and colleagues described a local species of parchment worm, named Chaetopterus dewysee after a longtime research supporter. These worms are abundant in southern California and have inspired bioluminescence research at Scripps, but until last year they had not been formally recognized as unique. For each of these new species and more than 100 others, the Benthic Invertebrate Collection houses the all-important holotype, the single specimen that serves as the defining example and “gold standard? of that species. By serving as the repository for these priceless reference specimens, the Scripps Collections attract international interest and play a crucial role in biodiversity research.

The excitement of describing a new species highlights what the curators and managers of the Collections strive to make prominent among the scientific and public communities: that our world still has many secrets to yield, but our actions could wipe out what we don’t even know is there. For example, deep-sea mining threatens to perturb both seafloor and midwater habitats where the animal residents, let alone the long-term ecological consequences, are poorly understood.

“Deep sea organisms can be hundreds of years old; we can’t assume they will simply come back after their habitats are demolished,’ said Charlotte Seid. “We’re doing our best to keep up with the rate of discovery before these creatures and their ecosystems could be destroyed.’

From ship to shelf to shipping

The specimens and samples aren’t confined to the labs at Scripps; they help scientists around the world in their own research.

Each Collection acts as a shipping warehouse in a sense, bringing in goods (organisms and sediments), packaging them for preservation and research, and then processing and sending orders to customers (other researchers and institutions); these goods are only on loan, however, and return to their respective homes.

The specimens don’t ship themselves, of course. Seid, Frable, Sala, and Hangsterfer process hundreds of requests each year, while conducting their own research, maintaining current specimens and samples, and prepping new ones for the Collections. An average day on the job is a balance of checking specimens, logging data and photos, research in the lab, fulfilling requests from around the world, helping Scripps students and faculty with their own research, coordinating research cruises and other projects, and leading outreach and tours of the Collections

A perk, they all agree, is the opportunity to spend time at sea on these cruises, which bring in many of the new additions to their shelves.

“Visiting the deep sea myself, inside the submersible Alvin, has given me an amazing perspective on the ecosystems we study and the individual animal lives inside our jars,’ said Seid, reflecting on one of her dives to 1497 meters (0.93 miles) off Costa Rica. “It’s incredible and humbling to spend a full day among these animals, alive in full glory in their own element.’

As nonliving material, the marine sediment and dredge samples don’t require the alcohol preservation techniques, but are maintained at constant cool temperatures to safeguard their chemistry and structure. The fish and invertebrates that make their way into the sister Collections are often first fixed in formalin and then preserved in alcohol. Some jars won’t leave their final shelves, but every one is checked regularly for signs of damage and to maintain an adequate liquid level. Since formalin treatment interferes with the ability to extract DNA, tissue samples for genetic purposes are taken from the fish and benthic invertebrates prior to fixing the specimen in formalin.

The location, date, depth, and personnel information are all recorded for each specimen. This data will eventually be digitized into each collection’s online database, a system that both helps our own scientists track our samples and opens the Collections to researchers around the world.

“It takes a tremendous amount of time to maintain what we have, and each of the Collections continue to grow,’ said Sala. “It’s exciting to give new purpose to samples that have been used in past scientific work and bring to light some we have yet to use for science.’ To add to them, the managers are constantly chipping away at backlogged specimens. Scripps has become a home for valuable orphaned organisms from fellow institutions that no longer have the space or funding to maintain them. When UCLA closed their collections doors in 2015, 10,000 jars made their way to the Marine Vertebrate Collection. In 2017-2019, the Benthic Invertebrate Collection took in more than 8,000 specimens upon the retirement of eminent deep-sea researchers Bob Vrijenhoek from the Monterey Bay Aquarium Research Institute and Verena Tunnicliffe from the University of Victoria in British Columbia. These new arrivals were acquired over decades of expeditions, representing millions of dollars of ship time and grant funds and encompassing many careers’ worth of scientific achievements. For example, specimens in the Tunnicliffe collection served as the raw material for research and advocacy that led to the Endeavour Hydrothermal Vents being designated as Canada’s first marine protected area in 2003.

“These particular jars of snails, sea spiders, tube worms, and other animals played a direct, pioneering role in the conservation of their own habitat,’ said Seid, “even though we couldn’t have anticipated those implications at the time.’

Vital beyond belief

Most well-known, large scientific collections are located in museums, like the Smithsonian or American Museum of Natural History, and rarely at universities. The Scripps Collections’ campus connection is crucial; students learn about biodiversity, collection science, and use the specimens and samples in their research. Fifty PhD graduates from Scripps alone have relied on the Marine Vertebrate Collection for their dissertations.

Many of the labs and research centers at Scripps can trace their work back to the collection, whether it’s related to deep sea food webs, fisheries management, climate change, or biomedicine. Some are directly linked to a Collection, like the Scripps Center for Marine Archaeology’s ties to the Geological Collections. Specimens and samples from each Collection are widely used in classrooms for many UC San Diego courses and are frequently on display at Birch Aquarium, such as the Oddities exhibit.

Being university-based, the Collections are at the doorstep of technological advancements and scientific breakthroughs. Notably, the revolution in genetics research has greatly increased the importance of these specimens. The curators and managers save versatile source material (like the frozen tissue samples), anticipating that new technology and research methods will come along that open new doors of discovery.

Environmental DNA, or eDNA, is genetic material collected from environmental samples, like water, air, and soil. From those samples, scientists can now rapidly assess the biodiversity of those environments. For Sala, Ohman, and Décima, sequencing techniques give them a novel look at the species diversity in samples that may easily contain hundreds of species of zooplankton.

Continued expertise of plankton identification in combinations with new technologies, such as Zooglider , and the use of computer-based plankton classification has led to us seeing animals we have never seen before and those that we are familiar with but in natural positions otherwise absent from physical collections,’ said Sala. “This lends to better understand their life strategies and role in the food web.’

The managers and curators are also hard at work modernizing the collections, digitizing the information for each and every specimen and sample. This is crucial for inventory management, and for opening up the collections to more researchers around the world looking for specific material or reference specimens.

This is a massive undertaking. With slim staff and thousands upon thousands of jars, the process of taking written information and photographs and adding them to a database is painfully detailed, but vital for the scientific community. Having well collected, labeled, and preserved material with its associated data are crucial for depositing and continued use of each sample. Many specimens and samples can be accessed through the respective Collections’ websites.

Having the Collections at Scripps opens up a world of possibilities to the general public, especially around education. The managers frequently conduct tours, speak at events (including virtual ones), collaborate with artists and writers, and field general inquiries, such as curious beachgoers seeking to identify mystery creatures.

Since 2018, the Geological Collections has been participating in GEOPATHS, a collaborative project between UC San Diego, the University of San Diego, and California State University-Bakersfield. This collaboration was designed to inspire underrepresented students to pursue careers in the geosciences. The project takes undergraduate students out to sea to collect geological samples, and engages them in research with the samples in the classroom or as a part of a summer internship. They’re also working with high school teachers to develop curricula based on the geosciences and oceanography fields.

The Collections might be hidden in refrigerated rooms, sitting behind heavy doors in a basement, or stored on dozens of shelves out of sight, but look a little closer and you’ll see specimens and samples on classroom desks, making headlines in the latest scientific research, and sparking wonder in wide-eyed children at Birch Aquarium. And they continue to be the foundation for an incredible amount of discovery, past, present, and future.


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