The DNA in a single cup of water can track wildlife, monitor pollution and survey pathogens in waterways and their surroundings, all at the same time.DNA is contained in each cell of every plant, animal, fungus and microbe. It carries the genetic instructions needed for an organism’s survival, growth and function, and the DNA of each species is unique.Organisms shed DNA into their environments. This environmental DNA, or eDNA, can come from cells shed from skin, spores and pollen blowing on the wind, or even just a cough or sneeze. It can provide huge amounts of information. Researchers can use it to assess biodiversity, monitor the spread of invasive species and detect pathogens.Advances in technology have allowed researchers to parse the DNA of hundreds of species floating in the Avoca River. David Duffy, CC BY-NDTraditional monitoring methods, such as field observation or trapping, can be difficult, intrusive and time-consuming. Tracking an elusive species in the wild can mean hours or days without a sighting, perhaps in difficult terrain or remote locations. Trapping wildlife can be stressful for the animals and relies on expert knowledge to properly handle wildlife and position traps.AdvertisementAdvertisementWith eDNA, researchers can collect information about a species without ever needing to see or interact with it. Moreover, a cup of water, a few ounces of sand or even air sucked through a filter can hold enough information to determine what has been in the area, including people, wildlife and infectious pathogens.Cracking the DNA codeResearchers sequence DNA fragments collected from sand, water or air to decode the order of the chemical building blocks that make up DNA. These sequences can be used to not only identify the species that the fragments of DNA came from, but also to narrow down the area where the organism originated.Until recently, researchers typically used an approach called metabarcoding to sequence eDNA. This method creates many copies of specific, short genetic markers that researchers can use to identify particular species.Although powerful, metabarcoding is selective by design. It finds only what it is designed to find – typically small but informative regions of DNA called barcodes – and ignores everything else. Because the DNA fragments are so short, it’s difficult to link these bits of information. A single barcode cannot cover all species in an area, and it cannot provide information about the genetic traits of species in the area.[embedded content]My team at the Duffy Lab at the University of Florida took a different approach. Rather than focusing on one short region of DNA in a sample, we used a technique researchers call long-read shotgun meta …
