Funding for the University of California-San Diego’s Scripps Institution of Oceanography supports the work of scientists researching new ways to understand life in the ocean by identifying the genetic traces organisms leave in seawater. Using environmental DNA (eDNA), scientists can detect what lives across the deep ocean, including regions that have long remained out of reach for traditional observation, as well as measuring the biological response to climate change. This project is one of three Scripps research programs supported by FFST. The foundation is also funding Scripps’ research into the mechanisms driving ice loss in the Thwaites Glacier and West Antarctic Ice Sheet as well as the expansion of the international Argo program through development of new Deep Argo floats. These grants enable the continuation of ongoing, long-term research initiatives to understand how the changing environment impacts critical ecological processes.
Dr. Margaret Leinen, Director Emeritus and Vice Chancellor Emeritus of Scripps Institution of Oceanography, is one of the world’s preeminent deep ocean experts. Throughout her career, she has held positions at coastal universities across the United States, at the U.S. National Science Foundation, and in the private sector working to understand the complex secrets of the ocean and its impact on our climate. When she stepped down from her leadership positions at the famed University of California-San Diego institution in September 2025, she was looking forward to spending more time with friends, family, and her hobbies. But the people in her life knew her well enough to know she would do much more than that.
Dr. Leinen has been busy dreaming up new modes and applications of biomolecular observation that utilize data and techniques from genetics, physical oceanography, biochemistry, and many other disciplines of biology and oceanography. With the support of a grant from FFST, Dr. Leinen’s team at Scripps is setting out to map where organisms reside in the ocean through collection and analysis of environmental DNA (eDNA) and other biomolecules, the genetic material that organisms shed throughout their lifetimes. Dr. Leinen noted that the “biology of the deep ocean is the least known ecosystem on the planet,” and that, too often, the greatest barrier to studying the deep ocean is the amount of time and money required to participate in a research cruise.
With these techniques, researchers sample the water at different parts of the ocean and analyze the entire ecosystem of organisms identified only by their nucleic acids, which in turn tell scientists what kinds of organisms are present, their quantity, and broader ecosystem dynamics. By taking water samples at various depths and locations throughout previously understudied parts of the deep ocean where sunlight begins to fade and photosynthesis is no longer possible, Dr. Leinen hopes to expand on global efforts to map the open ocean and help people understand that it’s “not just a big bucket of water out there.”
The work builds on the genomics revolution that began almost 20 years ago with efforts to understand the ecosystem of fish and other organisms in U.S. rivers. While traditional observation required scientists to physically capture the organisms they measured for – be it with nets, or trawls, or the help of scuba equipment – the new generation of observation allows scientists to understand what creatures exist and where, without ever having to lay eyes on them. When she first saw these practices in action for river observation, Dr. Leinen immediately began imagining the implications for understanding the big blue ocean.
This transformational thinking is also inspired, in part, by a Ph.D. thesis that crossed her desk from a Scripps student who joined a research cruise as part of a cross-collaborative effort with ocean chemists and physicists. For every one to two degrees the research cruise traveled in latitude, the Ph.D. candidate collected samples at various depths. She continued this practice for the duration of the expedition from Antarctica to the Equator and found that every water mass had its own distinct ecosystem of microbes – all identifiable using genomic techniques.
The first phase of Scripps’ research will utilize traditional sampling approaches to build on this work, with researchers like Dr. Melissa Brock, one of the post-graduate researchers supporting Dr. Leinen’s work, setting out on a weeks-long expedition from Cape Verde to Germany. As they travel, Dr. Brock and others will collect new samples for every few degrees of latitude they cover. The samples will be analyzed for biomolecules and cataloged as a part of the Ocean Biomolecular Observing Network, so that researchers around the world may reference and build on them as a part of a collective effort to map the ocean’s organisms. Over time, this record of samples will help ocean scientists understand how changes to the ocean environment – temperature, salinity, oxygen, pH, etc. – impact the organisms that live there.
According to Dr. Brock, FFST’s grant has given the research team the unique ability to attain a comprehensive understanding of not only what organisms exist in parts of the deep ocean, but also under what conditions. Analysis of the eDNA samples they collect will then allow them to build a more expansive picture of marine ecosystems, making it possible to detect species and track how communities of species are changing across regions and depths.
Simultaneously, the Scripps team is working with others who are developing tools for autonomous sampling vehicles suitable for open ocean collection efforts. This kind of robotic collection technology could truly transform the research process, enabling the autonomous collection and analysis of samples, with the data relayed back to labs on land via satellite. Autonomous sampling also has the potential to generate foundational data that improves our understanding, forecasting, and stewardship of the ocean as part of the integrated Earth system by enabling collection at scale.
Their efforts all ladder up into a process that Dr. Leinen calls “intelligent discovery,” pairing new tools with established methods and data. The process gives researchers the opportunity to discover new things with rich context around them. “Everyone in science is desperate for the ability to test hypotheses that are still untested,” she noted.
Neither Dr. Leinen nor Dr. Brock originally thought they would spend their lives studying the ocean. Dr. Brock wanted to be a medical doctor. Dr. Leinen first wanted to be a baseball player, then later, a lawyer, and ultimately found a love for paleoceanography. For both women, the path to their current work was shaped over decades by teachers, professors, and advocates who encouraged them to pursue new subjects and ways of doing things, and to take the opportunity to be surprised by what they found in the process. Now, as scientists, they express that FFST has taken on a similar role, allowing them the opportunity to face the unknown in the name of discovery yet again.
The unknown will always exist alongside discovery. Explorers and innovators across history have long accepted this principle and been called brave for their willingness to face it head on. Science is the same. FFST’s grantmaking strategy supports big bets and long bets in research because when scientists are empowered to pursue a new approach they unlock the opportunity for discovery. Through this work, Dr. Leinen hopes to inspire the next generation of scientists to pursue research that sits on the cutting edge and to always lead with curiosity. Because if science has made one thing clear, it’s that discovery begins with curiosity, and the greatest breakthroughs often come from the relentless pursuit of understanding the unknown.
Research at Scripps Institution of Oceanography is transforming how scientists observe life across the ocean. By unlocking new ways to observe and study marine ecosystems, scientists are building the knowledge needed to better understand our planet, inform global decision-making, and protect the systems that sustain life on Earth.