Sensitive environmental DNA detection via lateral flow assay (dipstick)—A case study on corallivorous crown‐of‐thorns sea star (Acanthaster cf. solaris) detection

Abstract

AbstractEnvironmental DNA (eDNA) represents an emerging opportunity for species monitoring in the marine environment. One aspect that poses challenges is the ability to detect target DNA without the complexity of specialized laboratory equipment. Lateral flow is an analytical technique that has been adopted in point‐of‐care diagnostics for human, veterinary, and agricultural health. Here, we aim to use lateral flow assay as a detection method for eDNA monitoring using a commercially available nucleic acid lateral flow device (PCRD™) in combination with previously developed species‐specific mtDNA primers. Episodic population explosions of coral‐eating crown‐of‐thorns sea star (CoTS) contribute significantly to the coral reef crisis on tropical Pacific coral reefs. Laboratory testing revealed our lateral flow assay developed for CoTS was as sensitive as digital droplet PCR and able to detect < 10 copies of target DNA, per PCR. Furthermore, the lateral flow assay was completed in less than half the time compared with digital droplet PCR and cost less than half that of digital droplet PCR. We applied this method to eDNA water samples collected in field locations where CoTS were present in low (=nonoutbreak) population densities and found lateral flow assay to be sufficiently sensitive to detect these populations. Detection of low‐density CoTS populations is critical for early warning of outbreaks and leads to early management interventions (e.g., culling). Importantly, we demonstrate that with species‐specific primers, the development and application of lateral flow assay methods for eDNA detection are feasible, for example, for invasive or threatened species, or those with high conservation value.