Biodiversity in a Drop of Water: The New Opportunity of eDNA

Dr. Claude Miaud, Professor at the Ecole Pratique des Hautes Etudes, is a pioneer of eDNA research. He describes how a species’ DNA can be detected in the environment in which that species is found. This monitoring method is minimally invasive and is aiding the discovery of important information on species and ecosystems. Dr. Miaud takes stock of recent advances in this technique, while assessing its limitations and potential future applications.

Date published: 2015/12/24

Environmental DNA is a molecular tool that has the potential to revolutionize species surveys. In his talk, Biodiversity in a Drop of Water: The New Opportunity of Environmental DNA (eDNA) at the 2015 Fuller Symposium, Dr. Miaud explains, “We have passed from using DNA methods to inventory one species or one group, to the inventory of the biodiversity of the whole system.”

There are an estimated 9 million eukaryotic species on earth. Two million of these are thought to live in the world's oceans. But according to Mora et al., despite 250 years of field work and taxonoimic classification, only 1.2 million species have been catalogued in a central database. 86% of species on earth and 91% of species in the ocean still await description. Impediments to the discovery of new species include cost constraints, the secretiveness of many species, and declining populations, globally. eDNA offers a method of environmental sampling that can reduce these contraints, fundamentally altering the way that we survey our planet for life.

eDNA enables scientists to collect a sample from the natural environment, such as water from a lake or snow from an animal track, and analyze that sample for DNA to determine the presence of multiple organisms. DNA is in every living thing and it can be detected even if it is severely degraded. When this DNA is extracted and amplified using different universal markers, it can be next-generation sequenced to determine a species match in a database.

Water sampling represents one of the most efficient methods of eDNA sampling. For example, in order to sample fish diversity in a freshwater stream, conventional methods require electrofishing nets, significant time and field workers. eDNA enables the collection of a water sample in a tube with alcohol, or a pumped and filtered sample that is stored in a sterile box for lab analysis. This method is rapid, requires a small team, and has minimal environmental impact. Laboratory results take some time and resources.

In a 2015 study by Valentini et al. that used both eDNA and classical methods to survey populations of fish and amphibians, eDNA showed greater detectability in 90% of sites. In a 2012 study by Thomson et al. that inventoried saltwater fish communities in Denmark, classical methods such as netting, snorkeling and seine trawlng yielded an inventory of 15 species. eDNA sampling of the same site, using 1/2 a liter of filtered seawater, identified 23 fish species. Traces of DNA are estimated to persist in marine environments for up to 2 weeks. 

WWF recently used eDNA to inventory both fish and vertebrate populations in the Mekong River. For this process, 10 liters of water were pumped and filtered in different locations along the Mekong. Up to 58 species were detected, including the iconic Mekong giant catfish in the north, the irrawaddy dolphin in the south, and more than 30 fish species, several frogs and salamanders. 

eDNA has also been applied to infer the diets of terrestrial animals. In 2012, Shehzad et al. used fecal samples to dentify the prey of snow leopards in two distinct populations in Pakistan. The presence of domestic chickens in the diet of one population provided evidence of potential conflict with local communities. eDNA has also been used to determine the flower preferences of domestic bees for making honey, with implications for agriculture and conservation planning. 

eDNA analysis from leeches in Vietnam as natural samplers has revealed that mammal DNA can persist up to 40 days after blood feedings. Leeches have since revealed evidence of cryptic species in certain rainforest sites. Carrion flies have also been used for eDNA sampling in the Ivory Coast and Madagascar, using traps baited with rotting meat. The digestive tracts of 200 carrion flies screened in one study yielded the DNA sequences of 22 species in the Ivory Coast -- ranging from hippos to shrews -- and 4 secretive species in Madagascar.

These methods may be standardized and eventually used at large geographic scales to measure change over time. This might enable enhanced monitoring of the impact of climate changes on biodiversity, for example. 

Like all things, eDNA has its limitations. It cannot, for example, yield demographic informaiton such as behavioral data, development stages and gender. But eDNA does represent a remarkable new way to undertake biodiversity monitoring and species identification, at scale.

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