Forensic ecology? Exploring environmental DNA
What is environmental DNA?
Organisms can leave behind traces of genetic information in the form of skin, hair, feces, mucus, carcasses, and more. These examples of ecological detritus are sources of environmental DNA, or eDNA. Fundamentally, eDNA is exactly what it sounds like: DNA collected from the environment. But what makes eDNA such a valuable source of information is the wide range of places it can be found and the diverse applications of processing this data. Researchers collect the DNA present in these traces—both cellular and extracellular—from water, soil, and air in the environment. Then, they extract, process, sequence, and match the eDNA to a species or individual.
The process of collecting and analyzing eDNA has been likened to forensics and is most commonly used to detect elusive or threatened species for conservation biology research. Like police at a crime scene, researchers can identify organisms by sleuthing out the DNA they’ve accidentally left behind. The analysis of eDNA has enabled researchers to avoid the difficult, time-consuming, and invasive traditional observation methods they would otherwise employ to monitor these species. Yet, some limitations remain. eDNA can degrade when exposed to acidity, heat, certain enzyme proteins, or radiation from sunlight, and both the amount of DNA needed and the costs of processing it can prohibit some research.
Above: Flowchart depicting how eDNA is collected and processed to detect a target species. Image courtesy of World Economic Forum.
What research projects have used eDNA?
Polar bear pawprints: Alaskan polar bears were individually identified without traditional invasive measures like blood tests by sequencing genetic information found in eDNA from hairs left behind in their snowy pawprints. Scientists worked directly with local Iñupiat populations to collect samples before sun exposure degraded the polar bear eDNA. Researchers will use these data to create polar bear family trees to aid in assessing population size and migration patterns for this threatened species.
Above: Snowy polar bear pawprints in Alaska. Image courtesy of BBC.
Agave restoration for bat conservation: Declining agave plant populations in northeast Mexico are linked to declines in the endangered Mexican long-nosed bat, a mutualist that feeds on agave flowers. Researchers recorded bat eDNA from fur and saliva deposited on agave flowers while feeding to track bat population movements. Using this data to follow bat migration corridors, scientists are partnering with conservation groups and local farmers to plant more agave at migratory hotspots and working to revive both bat and agave populations.
Above: Farmers in northern Mexico collect agave seeds for agave restoration efforts. Image courtesy of Yale Environment 360.
Finding hellbender salamanders: The Smithsonian Conservation Biology Institute is teaming up with citizen scientists to track down conservationally vulnerable hellbender salamanders in Virginia by searching stream water for eDNA. Hellbender salamanders are large amphibians that can grow over two feet long yet are extremely elusive. By employing eDNA collection techniques, researchers have had greater success locating salamander populations while also reducing the habitat disturbances typically caused by physical field surveys.
Above: Hellbender salamander camouflaging with rocks. Image courtesy of the Smithsonian National Zoo.
Sponges store eDNA: Sponges are prolific oceanic filter feeders, making them powerful collectors of eDNA from the water column. A team from London’s Natural History Museum harnessed this potential with eDNA sampling and detected 30+ marine vertebrate species in the tissues of Antarctic and Mediterranean sponges. This method provides a shortcut to widespread sampling and is minimally invasive to the sponges. eDNA research has huge potential in aquatic ecosystems, where the DNA traces can oftentimes be found in higher densities and with less risk of degradation than in terrestrial ecosystems.
Above: Sponges form the foundation of reef ecosystems. Image courtesy of the Natural History Museum of London.
Detecting novel viral transmission: Departing from typical conservation biology uses, researchers adapted the eDNA sampling process to detect eRNA. They then used this technology to detect the genetic material of COVID-19 in air and wastewater. These studies helped establish air as a primary mode of viral transmission and revealed more accurately the dates of viral spread via analysis of stored wastewater.
Above: Sewage water sample to be tested for COVID-19. Image courtesy of World Economic Forum.
The above studies are only a brief selection of the large body of research utilizing eDNA. This emerging data source has enabled researchers to target a large variety of organisms across many scientific fields—and innovative ways to collect and analyze eDNA continue to arise.