Building a Library of Life: How Smithsonian Collections Are Revolutionizing Ocean eDNA Research

Unlocking natural history collections is key to monitoring and protecting Earth’s environments using eDNA

Trees line a winding river, and the blue sky is reflected in the water
The Indian River Lagoon, one of the most diverse waterways in the country, is the National Museum of Natural History’s primary eDNA monitoring and testing site. Holly Sweat

Even if you can’t always see them, traces of life on Earth are all around you. A small scoop of water from the ocean or a cup of dirt from your backyard may seem unremarkable, but these environmental samples hold a treasure trove of information: hundreds of genetic fingerprints left behind by fish darting beneath the water and tiny insects burrowing into the soft earth. 

This environmental DNA (eDNA) is transforming the way scientists are able to sample ecosystems and monitor life on a rapidly changing planet.  Just as detectives use clues to solve a case, researchers sift through this genetic soup of skin, blood and hair cells to piece together a comprehensive picture of life. 

Since launching its Ocean DNA program in 2019, the National Museum of Natural History (NMNH) has been pioneering eDNA research at marine sample sites around the world.  The revolutionary technology allows researchers to catalogue the biodiversity of entire ecosystems efficiently and without destroying natural habitats. But to make sense of these genetic whispers, they need a reference guide – a library of life.  

Chris Meyer, NMNH invertebrate zoologist and curator of mollusks, has been leading the Smithsonian’s efforts to curate a reference library cataloguing all of the specimens held in the museum’s collections. James Di Loreto

This is where the Smithsonian’s vast collections come into play. By sequencing the genetics of physical museum specimens, the Ocean DNA team has begun creating a Rosetta Stone for marine life. The database lists species names and characteristics alongside their genetic barcodes, bridging the gap between isolated eDNA fragments collected in the field and centuries of natural history knowledge.  

“Right now, you can think of the genetic barcodes we are getting from eDNA like a series of phone numbers, except the phone numbers aren’t connected to any people,” said Chris Meyer, an invertebrate zoologist and head of the museum’s Ocean DNA program. “As the world’s largest collection of marine life, the museum’s job is to create a phone book that links those genetic phone numbers to the species they represent.”

A kaleidoscope of creatures from a plankton sample taken in Bali, Indonesia. Chris Meyer

But with hundreds of thousands of marine species to choose from, how do you even begin building a library of life? Meyer and his team of collaborators decided to start where the need was the greatest, by cataloguing all U.S. marine fishes. 

There are more than 4,000 species of marine fishes in the U.S., all critical indicators of ocean health, and NMNH holds over 90% of these fish in its collections. With the oldest and most comprehensive fish collection in the country, the museum has access to hundreds of years of specimens that can be added to the national reference library. The Ocean DNA team has already sequenced over a third of the museum’s U.S. marine fish collection, a process that they intend to complete within the next two years. 

“Agencies like the National Oceanic and Atmospheric Administration and U.S. Fish and Wildlife Service have pivoted to eDNA for biodiversity monitoring and marine protection projects,” Meyer said. “We have this unique role as the national museum to unlock our collections and help our partnering agencies understand their eDNA samples to the fullest potential.”

Meyer samples a basket star from the Gulf of Mexico to generate reference libraries that will be used in eDNA research. Smithsonian Institution

Another goal of the Ocean DNA project is to create a resource that will support the Smithsonian’s own long-term monitoring programs.  Marine biologist Holly Sweat has been working with the Army Corps of Engineers at the Smithsonian’s Marine Station in Fort Pierce, Florida for over 20 years, taking benthic samples to monitor the effects of runoff pollutants in the Indian River Lagoon. 

Currently, the team has to collect and count every species by hand, but they are starting to implement much quicker and more cost-efficient eDNA technology. In addition to testing these new molecular techniques against traditional sampling methods, these demonstration sites will be used as a method to build the museum’s reference library. As they continue to collect environmental samples, the team will run their results through the growing reference database and fill in any gaps they don’t already have catalogued.

(Left to right) Former program coordinator Jess Glanz, principal investigator Holly Sweat and former technician Garrett O’Donnell sample for benthic organisms on the Indian River Lagoon. Scott Jones

“Eventually the eDNA and reference library processes will converge and create a solar eclipse, and we will know every species in that area,” Meyer said. “And once we are done with a certain category of life, we can move on to the next.” 

The long-term goal of the project is to sequence every species on Earth and make biodiversity accessible to everyone. Meyer hopes that in 10 or 20 years, researchers and communities around the world will be able to collect their own eDNA samples and figure out exactly what species are in their environments.  

eDNA has become one of the most rapidly advancing fields in marine science, and a growing number of government agencies now rely on this technology for a variety of essential applications. From monitoring climate change and the impacts of the oil and fishing industries to detecting invasive species and pathogens, eDNA is at the center of research that will help to protect and preserve Earth’s environments. 

A sampling of benthic infauna that were found living on the bottom of the Indian River Lagoon near the Atlantic coast of Florida. Holly Sweat

However, a problem emerged as each agency began conducting their own individual eDNA research, all gathering similar data without a standardized and efficient method to share resources. This week, the White House Office of Science and Technology Policy released a “National Aquatic Environmental DNA Strategy,” co-chaired by Meyer. The strategy provides a unified roadmap for how multiple agencies can work together to share data and coordinate large-scale eDNA analyses and applications.  

“An essential part of the national strategy is for NMNH to be the national clearing house for curated reference libraries, so that each agency doesn’t spend all their time sequencing the same species over and over again,” Meyer said. "If everyone agrees to gather biodiversity data in a uniform way, then we can combine it and look across space and time to learn where the gaps in our knowledge really are.” 

Former program coordinator Jess Glanz examines a sample jar from a collection site on the Indian River Lagoon. Holly Sweat

But releasing the strategy is only the beginning of the process. The next step is implementation, and each agency will need to decide how they are going to turn possibility into action. Meyer and colleagues have built NMNH’s Ocean DNA project as a direct example of how agencies can contribute to successful eDNA monitoring programs, with an approach that already follows the suggestions outlined in the national strategy. 

"We have this unique role as the national museum to unlock our collections and help our partnering agencies understand their eDNA samples to the fullest potential." — Chris Meyer, NMNH Invertebrate Zoologist

Today, ahead of World Ocean Day on June 8th, NMNH is hosting the final meeting of the National Workshop on Marine eDNA with Johns Hopkins University, bringing researchers, practitioners and policymakers together to discuss the strategy and their plans for the future of eDNA.  

The workshop is a call to action; a way for interested parties to learn how government agencies are planning to use this simple, scalable, non-destructive and non-invasive eDNA sampling to meet the challenges we are seeing in a changing world, and what it will take to get there.  

“We have the technology, we have the natural history collections and we have the need,” Meyer said. “The ocean science community is out there banging on our door saying we need this reference library now, so we’re getting to work.” 

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