20x20 | Seeing the oceans in a new light

An optical sensor smaller than a postage stamp could help coastal communities monitor some of the world’s largest marine protected areas. In development by a team from the School of Engineering and the Center for Ocean Solutions, the device could one day revolutionize how quickly and precisely scientists can detect events like coral bleaching or pollution and track target species across vast expanses of ocean.

For years, state-of-the-art gene sequencing technologies have enabled scientists to detect animals and plants in a habitat based on sloughed scales, tissues, and other genetic material known as environmental DNA, or eDNA. By filtering these genetic traces from seawater samples, they can see what recently passed through the vicinity. But few technologies have been able to deliver that information in close to real time, especially in a marine environment.

The team is developing a thumbnail-sized prototype that could speed the process up by using light to identify eDNA fragments as they flow over a dense array of thousands of nanoscale silicon blocks. Each block is engineered to light up when it detects a particular gene fragment. When viewed through a custom microscope, the unique light signatures produced when target gene fragments are present could, one day, enable scientists to identify in near real-time the presence of species, pathogens, and toxins in the water. 

Optical physicist Halleh Balch in the School of Engineering’s Materials Science and Engineering Department is leading the sensor’s development with colleagues in Jennifer Dionne’s lab, a professor of materials science and engineering, and in partnership with marine scientist Collin Closek at the Center for Ocean Solutions. They collaborate with marine resource managers in California and the island nation of Palau in the Western Pacific to ensure the device targets data that would be helpful for local monitoring needs. For example, in Palau, the sensor might look for the genetic fingerprint of a harmful algal bloom in a habitat that’s normally a haven for locally consumed reef fish. The Dionne Lab’s latest design, which they continue to develop, incorporates a new structural change that increases the sensor’s sensitivity in order to detect the low concentrations of eDNA commonly found in the natural environment. 

Read more 20x20 features and catch other highlights from our 20th Anniversary celebration.

Keep exploring 

The Center for Ocean Solutions has been developing eDNA methods for marine biodiversity monitoring since 2012. In partnership with institutions like the Monterey Bay Aquarium, NOAA, and the Palau International Coral Reef Center, the Center has designed and tested novel eDNA detection techniques in the California Current ecosystem, and most recently, in the Monterey Bay National Marine Sanctuary and the Palau National Marine Sanctuary. 

This project has been supported by a Sustainability Accelerator seed grant under the leadership of co-principal investigators Fiorenza Micheli, co-director of the Stanford Center for Ocean Solutions and the David and Lucile Packard Professor of Marine Science, and Jennifer Dionne, professor of materials science and engineering.

Learn more about the Center for Ocean Solutions and other Woods Centers, Programs, and Initiatives.

Banner image credit: Andrew Brodhead

We're flashing back! See more stories about high impact research and solutions emerging from our work over the past two decades.

Read the 20x20 series