Turning discarded DNA into ecology gold

TECHNOLOGY FEATURE TURNING DISCARDED DNA INTO ECOLOGY GOLD ANDREW TILKER/LEIBNIZ INST. FOR ZOO AND WILDLIFE RES. Ecologists are monitoring biodiversity using DNA shed by wildlife into the environment. Invertebrates such as this Borneo tiger leech (Haemadipsa picta) hold environmental DNA that can be used to monitor other animals. K ristine Bohmann visited Eswatini in 2010 with a mission: to collect bat droppings. She’s not a guano enthusiast. She hoped to show that the bats were eating crop pests to convince sugar-cane farmers to preserve the bats’ habitat. Usually, this would require her to scrutinize bat droppings under a microscope to find and identify insect remains. Instead, Bohmann returned to her master’s programme at the University of Copenhagen with a plan. “I just came back with literally bags of bat shit and an idea.” That idea was to identify the species present in bat faeces — not microscopically, but genetically. Bohmann’s studies showed that sequencing the insect DNA in bat faeces could reveal what the bats ate1. Ecologists are increasingly relying on DNA shed by organisms into the environment, known as environmental DNA (eDNA), for their research. Instead of trekking into the field for weeks or months to collect and taxonomically identify creatures, these scientists are tapping sources such as shed skin cells, fish scales, urine, faeces, blood and saliva for details on rare, endangered and invasive species, and to measure biodiversity. Early eDNA surveys used the polymerase chain reaction (PCR) to amplify DNA from an individual species. But newer techniques, such as the one Bohmann used, can target a whole range of species’ DNA in the same sample. And the latest methods bypass PCR altogether, instead using DNA sequencing to detect organismal signatures. These techniques have enabled eDNA surveys to become more innovative and ambitious in their scope, opening up a whole range of taxonomic groups across large geographical regions for study. The technology still struggles when it comes to estimating population abundance, and requires expensive lab equipment and sophisticated bioinformatics skills. And for all eDNA’s reliance on twenty-first-century technology, ecologists still need to put in the hard yards outdoors to collect the samples. But as eDNA surveys become cheaper and more accessible, it’s increasingly becoming a powerful complement to conventional field-biology techniques. Ecologists could certainly use the help. “Biodiversity is hugely threatened all around the globe and we don’t have the amount of experts actually even to document what we have now,” says Philip Francis Thomsen, a molecular ecologist at Aarhus University, Denmark. “We need to describe what we have while we still have it, and environmental DNA could be one way.” . d e v r e s e r s t h g i r l l A . d e t i m i L e r u t a N r e g n i r p S 9 1 0 2 © B Y S A N D E E P R AV I N D R A N 2 7 J U N E 2 0 1 9 | VO L 5 7 0 | NAT U R E | 5 4 3 LESS LIFTING, MORE FILTERING A big part of ecology and conservation biology is knowing what species are where. To survey reclusive salamanders known as TECHNOLOGY FIELD BIOLOGY hellbenders (Cryptobranchus alleganiensis) in the southeastern United States, wildlife ecologist Stephen Spear had to snorkel or walk through creeks, lifting large rocks and peering underneath. He could survey at most two or three nearby sites in a day. Yet eDNA means he can survey many more — he just needs to collect a litre of water from different points along rivers and streams. “If they’re eDNA-positive, maybe that’s where you focus on going more in depth,” says Spear, director of wildlife ecology at The Wilds, a non-profit safari park and conservation centre in Cumberland, Ohio. Leaving stones unturned reduces physical risks, as well. “I’ve had rocks dropped on my arm, and I’ve had colleagues who’ve actually broken bones from rocks inadvertently dropping,” says Spear. And it’s not only the ecologists who benefit — eDNA “is quite good for biodiversity because we’re not having to kill anything to actually study it”, says Mark de Bruyn, an evolutionary biologist at the University of Sydney, Australia. De Bruyn travelled across southeast Asia for six months during his PhD collecting tiny pieces of freshwater prawns. Now, his PhD student Alice Evans at Bangor University, UK, has only to collect water samples. Whereas de Bruyn needed a week or more at each location, for Evans’ project, she was done in a day or two, spending less than a month overall in the field. FROM ONE SPECIES TO MANY Using PCR to amplify species-specific DNA is a relatively easy way to monitor individual invasive or endangered species. But newer techniques enable ecologists such as Evans to get data from many different taxa at once — in her case, from mammals, fish, crustaceans and amphibians. Back in 2010, Bohmann was faced with the problem of needing to identify dozens of insect species from the same samples of bat guano. Fortuitously, her adviser, Thomas Gilbert at the University of Copenhagen, had just developed a technique that could help. In eDNA ‘metabarcoding’, DNA is amplified by PCR using short segments of DNA, called primers, that have a unique tag at one end and that target genome sequences common to organisms across an entire taxonomic group. In Bohmann’s case, she used universal primers to amplify and sequence insect eDNA from more than 100 faecal samples in parallel, which were then differentiated on the basis of their unique tags. Such data can provide a broad overview of a region’s biodiversity. “Environmental DNA catches more species, in general, than do experts going out [into the field],” says Thomsen. His metabarcoding surveys have detailed fish communities off the coasts of Denmark and Greenland, as well as population-level genetic data from a gathering of whale sharks (Rhincodon typus) near Qatar. “I don’t know of any other method that is so CREATIVE SAMPLING And you can study geographical regions using an ever-widening array of sample sources, from flowers and leeches to air. “The imagination is setting the limits to what sample types you can detect traces of animals and plants in,” says Bohmann. In a study published this year, Thomsen extracted eDNA from wild flowers picked from two grassland sites in Denmark and detected more than 100 species of insects and other arthropods that had visited them, including pollinators, predators and parasites3. Previously, he would have had to spend all day planted next to a flower, watching and identifying the insect species that interacted with it. Yu and his colleagues once followed a brown bear (Ursus arctos) catching salmon for her two cubs in Alaska, hoping to collect bear eDNA. When the bear had finished munching on a fish, they hurriedly grabbed the salivaslathered leftovers and swabbed them. “We were scared out of our minds; we thought we’d die horribly, but in a good cause,” says Yu. Luckily, the researchers were unh (...truncated)