Methods summary: Applying CRISPR to detect eDNA

Article by Molly-Ann Williams and Anne Parle-McDermott both from Dublin City University

We were challenged to design and build a simple and rapid species monitoring system. Why do we need such a system?  Biodiversity loss is at an all-time high and such a system would help to support the management and conservation of fish species within aquatic environments by acquiring knowledge of species distribution that traditionally is gained through visual detection and counting. These methods are expensive, time consuming and can lead to harm of the species of interest.    We decided that environmental DNA (eDNA) was the way to go but we had to solve the ‘PCR problem’ i.e., avoid having to do cyclical high temperatures as that would see us ending up with a costly, once-off device that would likely not be applied outside our lab.  This got us brainstorming and led us to a novel isothermal detection method, combining Recombinase Polymerase Amplification with CRISPR-Cas detection, which simplifies the adaptation of nucleic acid detection on to a biosensor device.

This innovative methodology utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA, to detect specific species from eDNA. We proved it could work for eDNA by applying the technology to the detection of Salmo salar from eDNA samples collected in Irish rivers, where presence or absence had been previously confirmed using conventional field sampling. The beauty of this advance is that it can be applied to any species in the environment.  Not only does this assay solve the ‘PCR problem’, it is also is a better approach for distinguishing very closely related species.  We look forward to others in the field adapting it to their own favourite species of interest.  

Citation: Williams, M‐A, O’Grady, J, Ball, B, et al. The application of CRISPR‐Cas for single species identification from environmental DNA. Mol Ecol Resour. 2019; 19: 1106– 1114. https://doi.org/10.1111/1755-0998.13045

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