Tiny sensors that detect DNA in seawater

Collin Closek is a marine scientist at the Stanford Center for Oceans Solutions in the Woods Institute for the Environment. Halleh Balch is an optical physicist in the School of Engineering’s Materials Science and Engineering Department. Last year they joined forces on a Sustainability Accelerator seed grant project titled “Protecting Ocean Biodiversity: Developing and Deploying Real-Time Environmental DNA Sensors in International Marine Sanctuaries,” under the leadership of co-PIs Fiorenza Micheli and Jennifer Dionne.
 

Leveraging the team’s interdisciplinary expertise, they have developed a groundbreaking optical sensor that measures DNA and other key molecules in seawater using light, potentially revolutionizing the study of biodiversity in the enigmatic depths below the ocean’s surface.

What is the sustainability problem you are working on?

Closek: The ocean is on the front lines of climate change and the effects aren’t always easy to see or to track. The main gap is having a better understanding of the biodiversity and the biological changes that might be happening due to climate change and other human-related stresses, like pollution and fishing, in the ocean.

There are ways to do this now, but it is labor intensive. You typically have to collect samples by hand and bring them back to the lab. The marine protected area we are working in is 24 nautical miles offshore and it stretches out to 200 nautical miles. It is massive, hard to get to, and it’s not always safe to be out in those environments. The idea for the future is to develop an autonomous, remote sensor able to detect organisms continually and in real time for months at a time. Halleh is developing sensors that allow us to do that – to detect DNA and other molecules in the water.

Balch: Marine biodiversity is fundamental to our understanding of marine ecosystems, food security, and the economy of coastal ecosystems, but is challenging to measure.

Collin is a pioneer in developing approaches to use environmental DNA detection for biodiversity monitoring in the Palau eDNA Project. He and colleagues have demonstrated that you can use environmental DNA to capture relative abundance of species across Palau’s National Marine Sanctuary and use this information to inform management practices.

My research is focused on the development of optical sensors based on nanophotonics and spectroscopy to enable new measurements of marine and freshwater ecosystems. In this project, we are developing an optical platform that can simultaneously detect marine metabolites and target DNA sequences for in situ measurements. Our platform is based on dense arrays of optical resonators made of nanoscale silicon blocks, pioneered by my lab members Varun Dolia and Jack Hu in the Dionne Lab (see Hu, Dionne, Nature Communications 2023 and Dolia, Dionne, Nature Nanotechnology in press). Each resonator forms an independent sensing element that traps and amplifies specific colors of laser light. We develop surface chemistries that allow us to attach small molecules like DNA and metabolites across different sensing elements. When a target molecule binds to a resonator, the color of light trapped in that resonator shifts. We also developed a relatively simple approach to optically read out data from hundreds or thousands of sensing elements simultaneously, which allows us to both make many measurements at a time and also diversify the potential species, toxins, and metabolites we are able to detect using a single sensor platform.

Micheli: This project represents a critical step forward in our ability to understand and protect marine ecosystems, which are increasingly threatened by human activities and climate change.

Dionne: Many marine organisms are like superheroes – cephalopods can change their color and texture to camouflage themselves; mantis shrimp can see colors and polarizations that our eyes can’t detect; and phytoplankton, despite being just 1% of all biomass, contribute 40% of global carbon capture and storage. How can we glean new insights from the ocean while protecting its health? Our eDNA sensors can monitor biodiversity and ecosystem health, and also provide insight into “extremophiles” that could inspire new synthetic biology solutions. When deployed at scale, we believe our sensors can enable a shift from “reactive” and crisis-based approaches to “proactive” solutions for sustainability.

What did your Sustainability Accelerator grant allow you to do that you couldn’t before?

Closek: The funding allowed us to start working with different groups – such as fisher, NGOs, and governments – to understand what their measurement priorities were, what challenges eDNA could help them address, and potential applications for this new technology. Being able to detect organisms, but also other types of metabolites and chemicals, adds an important novel layer of understanding. It’s not just temperature change that causes organisms to differ in how they're using an environment. It might be pollution or toxins that are entering the environment causing them to leave or mortality events. The seed funding allowed us to come together and start talking through some of these challenges and opportunities. You don’t typically get funding to do that type of initial exploration work.

Balch: The Sustainability Accelerator grant has enabled us to come together across different disciplines to identify the technological gaps and the engineering requirements to translate our work from the lab into the field. One of the important parts of this study has been our early outreach and engagement with community members including local marine preserve managers, fishers, and educators. These discussions are helping us understand how potential end-users see eDNA impacting their work. Several aspects of our research goals have been driven through these conversations. One example is understanding what species of fish might be valuable to both fishers and managers of marine sanctuaries to be able to monitor. Another example is that the frequency of data sampling and collection is a potentially important engineering parameter that could enable more efficient use of resources and provide early warning signals of toxins or target species within a marine sanctuary.

What makes you excited about this technology?

Closek: It would be a game changer. New technologies can democratize the way that we approach ocean observation. I’m excited because our understanding of how organisms move around the ocean is fairly poorly understood. We have a lot of autonomous technologies that allow us to understand physical properties, like currents and waves. We have ways to detect sea temperature and salinity and so forth. But biological organisms and chemical attributes, which this platform targets, are more difficult to observe autonomously. Being able to understand where organisms are, how they might be adapting – or not – to environmental change and anomalous events, will allow us to draw better conclusions on what factors might be causing these changes. All of that extrapolates out to fisheries and other aspects of society that are important to humans, not just the ecosystems, but also in how we choose to use and manage those natural resources. 

Dionne: This seed project has demonstrated that we can do targeted DNA detection. In the coming months, we’re excited to expand this technology for a portable, low-cost platform for de novo, long-read eDNA sequencing. This technology could open entirely new windows into the incredible inhabitants of the ocean, including many we have not yet discovered. 

Micheli: Seeing this technology come to life through such a collaborative effort has been incredibly rewarding. With further development, this technology could greatly accelerate ocean biodiversity discovery and our ability to track change, enabling us to make informed decisions that will positively impact marine conservation efforts worldwide.

Fiorenza Micheli is the David and Lucile Packard Professor in Marine Science and professor of oceans in the Stanford Doerr School of Sustainability. She is also a professor, by courtesy, of biology in the School of Humanities and Sciences and senior fellow at the Stanford Woods Institute for the Environment.

Jennifer Dionne is associate professor of materials science and engineering in the School of Engineering and, by courtesy, of radiology at Stanford Medicine, and a senior fellow at the Precourt Institute for Energy.