Is it possible to gather biological information without disturbing the subjects? Do scientists want to know which species inhabit a region, whether they are moving in or out, or if endangered or very rare species remain present? Can such questions be answered by monitoring the health of an ecosystem? The answer is yes, thanks to environmental genetics.
With current techniques, researchers can sample water and detect the DNA of every species that leaves traces in that environment. For instance, just over a year ago a team of scientists found evidence for 187 taxonomic groups from only 20 liters of water collected near Everest.
Environmental genetics opens up many possibilities for studying ecosystems. It offers high reliability in detecting and identifying species, especially when traditional observation is challenging. DNA itself is a fundamental molecule—the code for all life on Earth containing the instructions to build every organism, from bacteria to humans.
Because DNA is unique to each species, it acts like a barcode that helps identify what is present without the need to see or capture organisms. In most environments there is typically enough DNA to determine its origin, enabling researchers to infer biodiversity without direct observation.
This approach is particularly valuable when rare or very small species are involved or when environments make observation and trapping impractical.
Sea creatures naturally shed DNA into their surroundings through mucus, feces, and tissue particles. Scientists refer to this shed material as environmental DNA or eDNA. By collecting a water sample, researchers can capture this DNA and create a genetic snapshot of the entire ecosystem, revealing which creatures inhabit the area.
High sensitivity and precision
eDNA enables the genetic identification of species in aquatic systems with high sensitivity, even when individuals are scarce, and without harming them. This makes the technology especially useful for biosecurity studies, early warning of invasive or pathogenic species, and monitoring of protected or endangered organisms.
Collecting eDNA from marine environments is fast, cost‑effective, and safe compared with traditional methods such as visual surveys, video monitoring, sonar, or fishing records.
How it works: scientists collect water from a site using standard sampling tools. Each sample is documented with geographic coordinates, depth, filter material, salinity, and temperature. The eDNA is then separated from the water using a membrane filter and stored for preservation. Proper storage allows DNA to remain intact for years, which is crucial when facing unknown species and the need to reanalyze samples.
After collection, samples are sent to a laboratory for testing. DNA consists of four bases—adenine, guanine, cytosine, and thymine—and each organism exhibits a unique pattern of these bases. This pattern helps scientists identify the organism from the sample.
Non-invasive technology
Scientists assign a unique label to each DNA sequence in a process sometimes called barcode coding. The labeled sequences are then compared with a growing DNA database to determine the family, genus, or species of the organism present in the sample.
eDNA is an emerging technology with many benefits. It avoids direct interaction with living organisms, offering a window into species that may not be videotaped or easily observed by conventional means. It can reveal a broad range of life, from bacteria to large marine mammals, expanding the scope of field surveys.
Recent work from a major research organization in Australia has outlined a roadmap for integrating eDNA technologies into large-scale marine monitoring, highlighting expectations for future capabilities and applications. Such guidance underscores the potential for eDNA to inform conservation and management decisions.
Historically, most eDNA work focused on aquatic species because collecting and extracting DNA from water is comparatively straightforward. Today, eDNA can also be sourced from soil, air, and sediments, and even from biological traces like feces, hair, leaves, pollen, and honey, enabling broad ecological inventories.
Applications in environmental monitoring and management include detecting pest species, identifying rare or endangered species, and providing multi-species data to characterize ecosystems and monitor environmental changes.
Citation: CSIRO Roadmap for eDNA in Marine Monitoring. A detailed report outlining how eDNA technologies can be scaled for large-scale monitoring and future developments has been published as part of ongoing research efforts. [CSIRO Roadmap, attribution without direct link]