Microread 02: CRISPR based SHERLOCK for Wildlife Conservation

Grey-headed Fish Eagle

For ecological monitoring and research, researchers and conservationists need to identify the exact species of the organism. Even though identifying different species is much more convenient visually, in some cases, it is more difficult owing to cryptic speciation and phenotypic plasticity. This genetic method of identification is much more reliable and highly accurate. To date, genetic marker required trained geneticists to receive the sample, conduct molecular techniques, and analyze to get precise data, which sent to the researcher. This process can take from days to months, which delays the research and conservation efforts to carry action-based management based on the findings.

Moreover, genetic identification techniques may not be available for remote field locations and in countries developing scientific infrastructure, making research way more laggy than it already is. A field-deployable system will allow biologists to identify species in the field rapidly. Rapid species identification can be pivotal in conserving critical species that are time-sensitive. Field deployable identification systems will allow scientists to identify species in-situ, thereby reducing the need for invasive methods like the collection of species sample and logging. CRISPR (clustered regularly interspaced short palindromic repeats) based genetic method could be ideal for species identification due to their diagnostic specificity, sensitivity, and speed.

CRISPR-based SHERLOCK nucleic acid detection platform has shown promise in the fields of diagnostic healthcare and agriculture. Many of the qualities of SHERLOCK like rapid detection, single temperature reaction condition, high sensitivity, low cost, etc., make it well suited to transition to an ecological context. A study to prove this principle engineered SHERLOCK DNA assays that do not require DNA extraction or specialized equipment to genetically differentiate three morphologically similar fishes, which has an overlapping range in California’s San Francisco Estuary (SFE). This study sought to reliably distinguish the US threatened, California endangered delta smelt, California threatened longfin smelt and the non-native Wakasagi. These three species are challenging to differentiate in their younger state and belong to the same family Osmeridae. A broader and more general use, a SHERLOCK-enabled field taxonomic identification method could be broadly utilized by non-molecular biologists working in ecology, conservation biology, and environmental monitoring of any targeted species.

Longfin Smelt swabbed for genetic identification with the help of CRISPR based SHERLOCK ; Credit: Alisha Goodbla/UC Davis.

This study found that the SHERLOCK method described in the study had all the necessary field deployment attributes. The versatile use of mucus swabs from the organisms shows its significance outside the laboratory. Along with this, the SHERLOCK test requires a constant low temperature, and the entire reaction can be done in a single tube, making it easily usable in the field. The reaction can also be carried out while holding it in our palms of the hand or when put into a small portable device that maintains a constant temperature and can detect fluorescence. It is anticipated that the entire process from collecting a sample and genetically identifying it can be completed in an hour, making it highly efficient in real-time diagnostics. Thus it is seen that SHERLOCK can be reliably used in a variety of ecological and environmental monitoring situations to obtain accurate, sensitive, and rapid genetic results. A more detailed study can expand its applicability to more specific taxonomic groups like the differentiation of subspecies. Therefore, with the help of CRISPR methods, ecology and conservation biology will bring rapid, genetic-based taxonomic identification in highly remote locations, thereby making conserving species more streamlined and following the path of least resistance.


M. Baerwald et al., "Rapid and accurate species identification for ecological studies and monitoring using CRISPR‐based SHERLOCK", Molecular Ecology Resources, vol. 20, no. 4, pp. 961-970, 2020. Available: 10.1111/1755-0998.13186.

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