On a warm day this spring, an airplane carrying Stanford experimental physicist Halleh Balch touched down on the island nation of Palau in the Western Pacific as a brewing typhoon piled dark clouds on the horizon. In her luggage, Balch had packed a thumbnail-sized sensor that had been months in the making in California to detect fragments of DNA recently shed into the ocean by passing marine life.
Other technologies have enabled scientists for years to detect species in a habitat based on sloughed scales, tissues, and other genetic material known as environmental DNA, or eDNA. But few have been able to deliver that information in close to real time, especially in a marine environment, where scientists and natural resource managers say there’s an urgent need to track the array of marine life facing climate change impacts like coral bleaching, warming seas, and fish migrations.
Among the challenges scientists face when collecting eDNA from the ocean environment are salt and debris, which can make water samples difficult to filter and analyze. Plus, most current approaches require large laboratory-based equipment. The tiny sensor in Balch’s luggage was being designed in collaboration with Collin Closek, a staff scientist at the Stanford Center for Ocean Solutions, for exactly these challenges.
Balch, who’s a Howard Hughes Medical Institute Hanna Gray Fellow, had led technological development of the sensor over the past year in the lab of Stanford materials science and engineering professor Jennifer Dionne. Now, after months of iteration, she was bringing the latest prototype of the device to get feedback from local stakeholders and colleagues who had just returned from a five-day expedition collecting eDNA throughout the Palau National Marine Sanctuary. Together, the team aims to eventually use the sensor to accelerate their ability to identify and monitor species in one of the largest marine protected areas on Earth.
Today, conservation and management is not such a far-fetched idea for Palauans to support because it has already been instilled in us for generations. We’re just doing it at a greater scale and in a more modern way than before. ”
Sampling at sea
Hours before Balch arrived in Palau, a ship called the PSS Remeliik II docked alongside a concrete pier outside the archipelago’s capital city of Koror. The 100-foot vessel, operated by Palau’s Division of Marine Law Enforcement, had taken Balch’s collaborators to the outermost reaches of the marine sanctuary. Among those on board were Closek and Ikelau Otto, chief researcher at the Palau International Coral Reef Center, or PICRC, which the Palauan government appointed to carry out scientific monitoring of the sanctuary.
“We don’t know how many species call the sanctuary home,” said Otto, who was raised in Palau, a nation of 18,000 people with centuries-long practices of stewarding their regional waters that are central to the community’s culture, economy, and food security. “We need to understand what’s out there.”
Historically, when communities noticed a change in certain fish populations, they alerted their chief, who would mandate a moratorium on fishing that species until its population could recover. “Today, conservation and management is not such a far-fetched idea for Palauans to support because it has been instilled in us for generations,” said Otto. “We’re just doing it at a greater scale and in a more modern way than before.”
Otto and the PICRC team established the Palau eDNA Project with the Stanford Center for Ocean Solutions in 2020, with the goal of optimizing eDNA for large ocean areas and establishing a robust scientific inventory of biodiversity in Palau’s marine waters.
The work requires trained researchers to spend days at sea, collecting and filtering hundreds of samples from specific sites, then freezing the filtered DNA to minus 80 degrees Celsius (112 degrees below zero Fahrenheit) to preserve them for laboratory analysis. “Because this is such a vast area, and sampling takes a lot of time and resources, there are many unknowns,” said Otto. Targeted, near real-time monitoring could help address some of the information gaps.
Navigating the future of oceans
Capricious weather can complicate fieldwork, requiring researchers to adjust their sampling schedule at a moment’s notice. Aboard the PSS Remeliik II this spring, the researchers adapted their sampling plan to dodge the worst of the heaving swells stirred up by Typhoon Mawar, which ended up flooding homes and knocking out power for thousands in Guam and prompting evacuation of more than a million people in Japan after veering east from Palau.
In spite of the weather, the researchers completed their sampling goals. But as the typhoon barreled across the North Pacific, it offered a stark reminder of how the ocean can be both a lifeline and a threat to the very existence of island nations that have offshore territories several times their landmass. As sea levels rise and storms become more intense due to global warming, Palau and other countries in the Micronesia region north of Australia share a common need to understand and protect their marine resources and the livelihoods they provide. “We’re trying to find new, innovative ways to study Palau’s sanctuary,” Otto said.
If the group of researchers working on the new sensor achieve their highest hopes, the device would complement and likely reduce the need for organized expeditions with complex logistics like those required for sampling trips aboard the PSS Remeliik II. The labor-intensive fieldwork would reveal which species exist throughout the sanctuary, like a census of local marine life. PICRC could then use these census data to make decisions about which species and areas to prioritize when monitoring for early indicators of change to ocean health over time.
Changes in the abundance or distribution of species in an area can provide clues about whether current protections are working, or perhaps need to evolve. For example, if the genetic fingerprint of a harmful algal bloom is detected in a habitat that’s normally a haven for locally consumed reef fish, then Palau’s Ministry of Agriculture, Fisheries, and the Environment can restrict harvesting in the area to minimize the risk of people getting sick from eating the fish.
“Monitoring changes in marine biodiversity over time is crucially important for understanding overall ocean health,” said Center for Ocean Solutions co-director Fiorenza Micheli, a marine ecologist who’s part of the Stanford team that has partnered with PICRC and local stakeholders to develop science objectives for the sanctuary. “Building this scientific baseline allows us to track and better forecast abrupt or gradual changes, like coral bleaching events or movements of fish stocks due to climate change, that pose a risk to the health and livelihoods of millions of people around the world.
Building this scientific baseline allows us to track and better forecast abrupt or gradual changes, like coral bleaching events or movements of fish stocks due to climate change, that pose a risk to the health and livelihoods of millions of people around the world. ”
Illuminating new approaches
To the naked eye, the sensor resembles a conventional microscope slide. Zoom in, and you would see a sapphire chip lithographically patterned with dense arrays of nanoscale silicon blocks. The carefully designed structures act like optical antennae that can amplify specific colors of infrared light.
Scientists chemically coat the chip with gene fragments that complement the DNA of a target species, such as the Napoleon wrasse, a large fish which interests researchers and local stakeholders because it is endangered and one of few predators that can keep coral-eating crown-of-thorns starfish in check. If eDNA data in the future begin to show shifts or declines in the population, it could give Palau’s natural resource managers an early warning so they can expedite tracking and management of Napoleon wrasse populations and habitats.
Like pieces of a molecular puzzle, the gene fragments on the chip selectively bind to the DNA of the target species when it’s present in the water flowing over the chip. Under infrared illumination, the color of light trapped in the silicon antennae will change when a molecule binds to the surface, thereby changing the associated light signal. By imaging the chip with an infrared camera, the team can determine which DNA fragments have bound to it by virtue of how the chip is lighting up.
“Rather than amplifying the DNA molecule, we can amplify light,” said Balch. “One of the gaps we are hoping to help fill is the ability to make hundreds of thousands of measurements with little to no DNA amplification.”
In the coming years, the researchers aim to integrate the sensor with autonomous sampling platforms that can be left tethered to a mooring or buoy, relaying environmental DNA data from open water to shore via satellite in nearly real time. Longer term, they hope the device might even track chemicals and pathogens along with measures of biodiversity.
“One of the most important outcomes of this technology would be simultaneous detection of an organism’s DNA alongside chemical signatures that could reveal ecosystem trends and perhaps help us understand what factors drive change in ocean health,” said Closek.
For PICRC staff charged with implementing the Palau National Marine Sanctuary’s science and monitoring strategy, detection of toxins or pathogens in combination with which species are present nearby means fisheries managers can better protect the health of Palauans and the region’s marine biodiversity.
Bridging disciplines
The chip’s optical sensing capabilities build on technology developed by the Dionne Lab to monitor trends in environmental and human health. To study how light behaves at the nanoscale, researchers in the lab mount custom configurations of mirrors and lenses to bend and direct different wavelengths of laser light, looking to an untrained eye like a miniature obstacle course for light.
A presentation by Dionne about her lab’s work on the Stanford campus in 2017 piqued the curiosity of Micheli, who partners with small-scale fishers across the globe. Micheli wondered if this rapid sensing technology could be brought to the marine environment for coastal communities like those in Palau. Several years later, she approached Dionne, and the pair agreed to explore the possibility with Balch, Closek, and PICRC colleagues. The group received seed funding from the Sustainability Accelerator at the Stanford Doerr School of Sustainability to develop a real-time eDNA sensor for the ocean.
In the coming months, the team will work to validate the device’s ability to accurately detect species, including yellowfin tuna and others identified as priorities by local stakeholders and scientists. They’ll also use years of environmental DNA samples collected through the Palau eDNA Project to test the feasibility of the new technology and refine the process for analyzing future samples.
“Democratizing science is one of the most urgent needs of our time,” said Micheli. “This project has the potential to scale environmental monitoring and analytical capacity across coastal regions around the world."
Balch is also a National Science Foundation Ocean Sciences Postdoctoral Research Fellow. Dionne is also a senior fellow at the Precourt Institute for Energy and an associate professor, by courtesy, of radiology and a Chan Zuckerberg Biohub Investigator. Micheli is also a professor and chair of the Oceans Department at the Stanford Doerr School of Sustainability, a senior fellow at the Stanford Woods Institute for the Environment, and a professor, by courtesy, of biology.
The Palau eDNA Project is supported by the Waitt Foundation and Oceankind. The optical eDNA sensor project was supported by an accelerator planning grant from the Stanford Doerr School of Sustainability and by the Chan Zuckerberg Biohub Investigator Program. Shared facilities including the Stanford Product Realization Lab, the Stanford Nano Shared Facilities, and the Stanford Nanofabrication Facility enabled sensor prototype development.
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