eDNA

September 01, 2022

Hidden in the back pages of the front section of my local newspaper on Monday was a USA article on how eDNA is being used to unlock some of the world’s oldest mysteries.  While crime shows have used trace amounts of DNA (Deoxyribonucleic acid) to solve cold cases and tabloid talk shows have used it to identify the real father, ecological researchers have been using similar tests to determine the biodiversity of ecosystems.  One example was new information on the elusive loggerhead sea turtle (Caretta caretta).  While the loggerhead’s tracks on the beach are hard to miss, they also leave invisible trails of skin, scat, and saliva.  This environmental DNA (eDNA) can be collected in samples of sand to provided insight into the habits and diets of these reclusive turtles.

When I looked online, I found the use of eDNA began 14 years ago with a study of the invasion of the American bullfrog, (Rana catesbeiana) into Europe, a species that is considered a major cause of decline for native amphibians.  Since the historical data on the invasion was scarce, the study used population genetics data (a partial sequence of the mitochondrial cytochrome b gene) to infer the invasion history and to estimate the number of founders of non-native populations.  The science of eDNA also made a splash during the pandemic when researchers found they could track virus outbreaks (and variants) in municipal wastewater systems.  Identifying eDNA is now being used to verify the biological diversity in areas from the Brazilian Rain Forests to the slopes of Mount Everest.

According to Tracie Seimon, director of the wildlife molecular lab at the Bronx Zoo, the most intriguing aspect of eDNA is being able to learn about rare species without having to disturb them.  Seimon and her colleagues developed a test to amplify eDNA samples to rapidly detect species while reducing the size of the equipment to fit into a backpack.  Seimon’s team found evidence of 187 taxonomic orders in the 5.28 gallons (20 liters) of water collected on Mount Everest at elevations from 15,000 to 18,000 feet (4572 to 5486 m).  Once a baseline inventory is established, they will be able to monitor changes over time.  The non-profit XPRIZE holds competitions to encourage technological development to benefit humanity.  The XPRIZE Rainforest competition challenged teams to develop autonomous technology for rapid appraisal of the forest’s biodiversity, and a lot of interest has been shown using eDNA.  Methods include overland robots traveling the understory and aerial robots flying above the canopy.

THOUGHTS:  Anyone infected with covid sheds the virus each time they wash hands or use the toilet, even if they do not have symptoms.  Scientists have been tracking the virus using eDNA in wastewater for early clues about infections in cities and towns.  A team of researchers designed a system to get more detailed information about the virus variants from wastewater and built a computer program that quickly recognizes small pieces of the genetic material.  This not only picked up new variants like Delta and Omicron weeks before they showed up in clinical tests, but also found variants rarely seen in the clinic.  While this does not identify individuals, it can profile the whole city.  The team is now expanding the program to track other viruses.  Applications for using eDNA can provide early detection for the spread (pathogens) or decline (species) of genetic material.  As with any technology, the critical step will come determining how to use the information.  Act for all.  Change is coming and it starts with you.