All organisms leave traces of their DNA behind in the environment, for example, in hair, skin, faeces, eggs, larvae etc. By extracting and sequencing DNA from environmental samples such as soil or river water, we can identify the species that have contributed DNA to that sample, in the same way that a forensics expert can determine who was present at a crime scene. Environmental DNA (eDNA) methods were first applied to microbial communities such as bacteria and fungi. In the last few years, the breadth of eDNA studies has expanded to include plants, invertebrate and vertebrates. In one (slightly gruesome) study, researchers were able to detect DNA from over 20 different mammal species by extracting DNA from flesh-eating carrion flies in tropical Africa!
Courtesy: L. Clarke
Several eDNA projects are currently underway at ACAD. I’m developing non-invasive methods for flora and fauna surveys by extracting DNA from soil or faeces rather than sampling the actual plant or animal. I’ve applied these methods to sites across South Australia, including the Arid Recovery reserve, Roxby Downs, conservation parks, and the Iluka Jacinth-Ambrosia mineral sands mine site. Paul Czechowski, in collaboration with the South Australian Museum, is using environmental DNA to explore Antarctic soil biodiversity. Jennifer Shaw is working with SA Water to develop DNA-based assessments of drinking water quality and freshwater ecosystem health. Jennifer Young (yes, there are two Jennifers) is applying eDNA methods to identify the source of forensic soil samples in conjunction with the Australian Federal Police.
Environmental DNA studies have been made possible by next-generation DNA sequencing (NGS) technology that can generate millions of sequences in a single run. One of the key aspects of eDNA studies is making sense of the massive amounts of data that NGS produces. Luckily, we have a team of bioinformaticians to help (thank you Dr. Julien Soubrier, Dr. Jimmy Breen and Oliver Wooley for your computer programming skills!).
eDNA holds promise as a rapid and sensitive method for assessing biodiversity with a broad range of applications, such as detecting invasive species, monitoring the response of biological communities to climate change and forensic techniques. You may never look at soil the same way again…
Australian Centre for Ancient DNA (ACAD) 