Development of a lightweight, fully integrated qPCR sensor for environmental DNA

Abstract

Environmental DNA (eDNA) has emerged in recent years as a powerful tool in ecological monitoring. However, conventional eDNA methods are bottlenecked by long wait times due to sample transport and lab analysis. We present a compact and portable eDNA sensor to enable near real-time and in-situ detection of specific eDNA sequences. The instrument has been developed to autonomously sample from the surrounding environment and perform DNA extraction and target amplification. Sample water is rapidly pumped (∼430 mL/min) through a stacked double membrane filter and nucleic acid extraction follows a standardized protocol. A target DNA sequence is amplified and detected through quantitative polymerase chain reaction (qPCR), giving the user a sensitive and specific result on the presence of the target sequence in the environment. Results are obtained in less than 6 h from the beginning of sample capture, enabling same-day decision making. Performance was validated through detection of bowhead whale (Balaena mysticetus) DNA sampled from preserved tissue, with threshold cycles of 19.4 $\pm$ 0.3 for positve controls, 13.3 $\pm$ 0.8 for samples, and 35.2 $\pm$ 1.2 for negative controls. A brief timeline to full sensor validation is presented, that once complete will mark a significant step towards real-time, in-situ eDNA analysis to inform conservation, remediation, and biodiversity management.