Optical eDNA sensors

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.

This 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. 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. The team’s latest design increases the device’s sensitivity in order to detect the low concentrations of eDNA commonly found in the natural environment. 

Optical physicist Halleh Balch in the Oceans Department leads the sensor’s development with colleagues in the lab of Jennifer Dionne, a professor of materials science and engineering, and in partnership with marine scientist Collin Closek at the Center for Ocean Solutions. 

Collaborators also include marine resource managers from California and the Western Pacific, who help ensure that the data that the device is designed to collect is meaningful for monitoring local marine sanctuaries. For example, in the Republic of 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 next phase of the project focuses on developing a liquid-handling platform to aid in situ sample collection and processing.