DNA Sequencing to Survey Ecosystems

The Mekong river is located in Southeast Asia. With an estimated length of 4,350km, it flows from the Tibetan Plateau through China’s Yunnan province, Myanmar, Laos, Thailand, Cambodia and Vietnam, on its way to the South China sea. The Mekong basin is one of the richest areas of biodiversity in the world, second only to the Amazon.

The Mekong river supports the largest inland fishery in the world. Approximately 60 million people live in the lower Mekong basin and an estimated 80% of these people rely directly on the river for their food and livelihood. However, in recent years the Mekong region has seen an increase in economic growth and with this an increase in demand for electricity. The Mekong river has a huge potential for hydroelectric power but currently only a very small amount of the power in the region is generated in this way.

In order to harness the power of this mighty river and supply the increasing electricity needs of the region, there are plans for a series of dams and other hydroelectric projects on the river. Ecologists fear this may threaten the unique species living in and around the river and indeed the entire ecology of the river.

To reduce the environmental impact of these planned hydroelectric dams, scientists intend on using a new environmental monitoring technique to assist developers at the planning stage. If the ecological hotspots can be identified then the positioning of the dams can be planned to minimise ecological damage. All living things shed DNA into their environment. If this environmental DNA (eDNA) is collected and sequenced, the species living in the area can be identified.

Douglas Yu of the Kunming Institute of Zoology in China hopes to work with the Chinese ecologists to carry out these ‘eDNA surveys’ in the Mekong river. This will allow scientists to determine a picture of all the species living in different regions of the Mekong. This method is quick compared to traditional surveying methods, which would take years, and may prove more reliable.

The eDNA survey technique has been shown to work well. A team of European ecologists including Pierre Taberlet at the Joseph Fourier University in Grenoble, France, collected samples of water from rivers and ponds in France and the Netherlands. The eDNA in these water samples was sequenced and the species identified. When compared to traditional survey methods, they found that the eDNA method identified as many, or more, fish species at 89% of the sites they visited.

Douglas Yu said, “eDNA surveys could make wildlife monitoring cheaper, faster and more available to those with fewer resources. The world is just permeated with DNA. You just have to collect it and sequence it in the right way and then you have a much better view of life.”


Molecular Ecology, Volume 25, Issue 4, Feb 2016, pages 929-942. Next Generation Monitoring of Aquatic Biodiversity Using Environmental DNA Metabarcoding.