Development of Environmental DNA (eDNA) Detection Tools to Track the Obligate Coral Predator Coralliophila galea to Support Coral Outplant Site Selection
With the support of the Mote Marine Laboratory and Aquarium, USGS researchers will develop and optimize a CRISPR biosensor to detect C. galea eDNA in the field. The development of this tool could assist coral restoration managers and stakeholders to more effectively inform decisions on coral outplant site selection, based on coral predator presence.
The Science Issue and Relevance: The endangered reef-building Acroporid coral species has been devastated by diseases and other stressors in the Caribbean. Coral restoration programs have become an important part of aiding the recovery of these and other coral populations. One common restoration method is to outplant fragmented corals to a new area where their survival success is more likely. A crucial consideration when choosing coral outplant sites (that is, sites where corals are transported from nurseries and secured back onto reef habitats) is determining coral predator abundance. Coral predators, particularly small and cryptic corallivorous snails, not only threaten coral reef viability but are also associated with the spread of various coral diseases. A predatory snail known as Coralliophila galea has been identified as one of the top three immediate threats to the recovery of remnant populations of wild and restored corals in the Caribbean, making it a prime focus for remediation by managers. However, the efforts to detect and remove C. galea from a 150m2 area of coral requires 51 diver minutes – a logistically ineffective procedure, as snails are often hard to find in deep cracks and crevices – and may not remove all snails due to their cryptic nature. To circumvent this limitation, environmental DNA (eDNA) is a useful tool to inform reef restoration site selection. Environmental DNA is genetic material that animals deposit in the environment and that is collected in samples of soil, water, or air. Environmental DNA tools can be used to detect animals that are cryptic, hard to find, small in size, or have low population densities. Because the predatory snail can be difficult to locate by divers, eDNA can be used by scientists and managers to determine whether the snail’s genetic material is present in an area. Environmental DNA methods may be able to be used to monitor the fluctuating presence of cryptic coral predators without disturbing corals and the organisms nearby in the ecosystem. The accessibility to CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based genetic tools has given rise to applications beyond genome editing to also allow for the precise detection of genetic material. In this work, we propose the use of a CRISPR-Cas biosensor for the detection of C. galea eDNA.
Methodology for Addressing the Issue: With the support of the Mote Marine Laboratory and Aquarium, we will obtain snail samples to help us develop and optimize a CRISPR biosensor to detect C. galea eDNA in the field. To this end, testing of multiple C. galea-specific DNA and RNA oligonucleotides that modulate CRISPR recognition will be assessed and compared to other sympatric, non-target snail species. The latter will be tested as controls to ensure that our assays are not just sensitive, but also highly species-specific to only C. galea. This user-friendly tool could assist coral restoration managers and stakeholders to more effectively inform decisions on coral outplant site selection, based on coral predator presence.
Future Steps: Coral reefs are cornerstones to the nation’s economy, and the environmental diversity and health of countless organisms that directly, and indirectly, depend on these animals. The continued development, testing, and validation of novel eDNA CRISPR-based biosensors for the surveillance and tracking of additional biological threats to corals can support coral restoration management decisions by federal, state, and tribal managers.
With the support of the Mote Marine Laboratory and Aquarium, USGS researchers will develop and optimize a CRISPR biosensor to detect C. galea eDNA in the field. The development of this tool could assist coral restoration managers and stakeholders to more effectively inform decisions on coral outplant site selection, based on coral predator presence.
The Science Issue and Relevance: The endangered reef-building Acroporid coral species has been devastated by diseases and other stressors in the Caribbean. Coral restoration programs have become an important part of aiding the recovery of these and other coral populations. One common restoration method is to outplant fragmented corals to a new area where their survival success is more likely. A crucial consideration when choosing coral outplant sites (that is, sites where corals are transported from nurseries and secured back onto reef habitats) is determining coral predator abundance. Coral predators, particularly small and cryptic corallivorous snails, not only threaten coral reef viability but are also associated with the spread of various coral diseases. A predatory snail known as Coralliophila galea has been identified as one of the top three immediate threats to the recovery of remnant populations of wild and restored corals in the Caribbean, making it a prime focus for remediation by managers. However, the efforts to detect and remove C. galea from a 150m2 area of coral requires 51 diver minutes – a logistically ineffective procedure, as snails are often hard to find in deep cracks and crevices – and may not remove all snails due to their cryptic nature. To circumvent this limitation, environmental DNA (eDNA) is a useful tool to inform reef restoration site selection. Environmental DNA is genetic material that animals deposit in the environment and that is collected in samples of soil, water, or air. Environmental DNA tools can be used to detect animals that are cryptic, hard to find, small in size, or have low population densities. Because the predatory snail can be difficult to locate by divers, eDNA can be used by scientists and managers to determine whether the snail’s genetic material is present in an area. Environmental DNA methods may be able to be used to monitor the fluctuating presence of cryptic coral predators without disturbing corals and the organisms nearby in the ecosystem. The accessibility to CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based genetic tools has given rise to applications beyond genome editing to also allow for the precise detection of genetic material. In this work, we propose the use of a CRISPR-Cas biosensor for the detection of C. galea eDNA.
Methodology for Addressing the Issue: With the support of the Mote Marine Laboratory and Aquarium, we will obtain snail samples to help us develop and optimize a CRISPR biosensor to detect C. galea eDNA in the field. To this end, testing of multiple C. galea-specific DNA and RNA oligonucleotides that modulate CRISPR recognition will be assessed and compared to other sympatric, non-target snail species. The latter will be tested as controls to ensure that our assays are not just sensitive, but also highly species-specific to only C. galea. This user-friendly tool could assist coral restoration managers and stakeholders to more effectively inform decisions on coral outplant site selection, based on coral predator presence.
Future Steps: Coral reefs are cornerstones to the nation’s economy, and the environmental diversity and health of countless organisms that directly, and indirectly, depend on these animals. The continued development, testing, and validation of novel eDNA CRISPR-based biosensors for the surveillance and tracking of additional biological threats to corals can support coral restoration management decisions by federal, state, and tribal managers.