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

Abstract

Environmental 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.

Knowledge Gaps in the Biology, Ecology, and Management of the Pacific Crown-of-Thorns Sea StarAcanthastersp. on Australia’s Great Barrier Reef

“…This is not to understate the very significant progress in COTS research over recent decades, which has effectively redressed many critical knowledge gaps (Moran, 1986;Pratchett et al, 2017). Indeed, many of the research questions posed herein have arisen directly from new knowledge (e.g., Allen et al, 2019) or are possible only because of the recent sequencing of the COTS genome (Hall et al, 2017) and development of novel sampling methods (Doyle et al, 2017;Doyle and Uthicke, 2020). However, renewed impetus and opportunities for COTS research should carefully consider the myriad knowledge gaps and potential research questions.…”

The Future of DNA Barcoding: Reflections from Early Career Researchers

“…Another innovation is where single-species biomonitoring techniques have been developed based on barcoding primers designed to detect target species in complex samples with a dip-stick. Doyle and Uthicke [62] designed the tool by combining a lateral flow assay with species-specific primers to successfully detect the presence of crown-of-thorn starfish on the Great Barrier Reef. This dip-stick method may potentially detect a wide variety of species from environmental samples, requiring little scientific training or laboratory access, making it well-suited for citizen science and remote conservation projects.…”

The Promise and Pitfalls of Environmental DNA and RNA Approaches for the Monitoring of Human and Animal Pathogens from Aquatic Sources

“…This can reduce bias introduced by the PCR step because of unequal gene amplification and will be informative for future work examining species or pathogen abundance and biomass. In addition, advancement and increased accessibility of current molecular technologies, such as ddPCR and high-throughput sequencing, will be able to provide near-term improvements in eDNA detection sensitivity, all while adapting to enable low-cost nonexpert citizen scientists to evaluate and monitor the health of their own ecosystems (Goldberg et al 2016 , AIMS 2018 , 2020 , Doyle and Uthicke 2020 ). For example, Doyle and Uthicke ( 2020 ) have successfully developed a sensitive eDNA detection device that uses a lateral flow assay to detect the highly invasive crown-of-thorns sea star ( Acanthaster cf.…”

“…solaris ) in the form of a handheld dipstick, similar to a home glucose or pregnancy test (AIMS 2018 , 2020). The adaptation of eDNA detection from a solely laboratory environment to a technology that is applicable and accessible to the general public has the potential to vastly improve the field of eDNA (and eRNA) analysis (AIMS 2018 , 2020, Doyle and Uthicke 2020 ). In addition, portable high-throughput sequencing machines are being used to detect pathogens in both field and laboratory conditions (Urban et al 2021 ) and hold the promise of significantly improving pathogen detection in clinical and clean manufacturing settings, especially for unculturable species.…”