Environmental DNA (eDNA) sampling, which can be used to detect the presence of species based on traces of genetic material they shed into the environment, has proven to be a valuable tool for efficiently monitoring aquatic biodiversity. However, the potential of this technique has yet to be fully evaluated in the diverse tropical river system of the Mekong Basin. Since 2022, FISHBIO and the local NGO Young Eco Ambassador (YEA) have undertaken a pilot effort funded by the Wonders of the Mekong Project to conduct eDNA sampling at a landscape scale across the lower Mekong River and its tributaries in Cambodia. The results from this study will represent an important first step in understanding the types of questions that eDNA analysis may help answer in the Mekong, which in turn could pave the way for integrating this technique into fisheries monitoring programs in the region.
As part of project fieldwork, YEA and FISHBIO researchers have collected more than 50 eDNA samples from the Mekong River and its tributaries. Sample collection locations ranged from the Cambodia/Lao border to as far south as Phnom Penh, and included the mainstem Mekong River, Tonle Sap Lake, and the Sekong, Sesan, and Srepok (3S) tributaries in northeastern Cambodia. The samples will be analyzed using metabarcoding, a technique in which fragments of DNA from a specific region of the mitochondrial genome are amplified. These sequence fragments are then compared to genetic reference libraries in order to identify many different species from a single water sample, thereby providing a “snapshot” of the fish community. Once analyzed, these samples will offer a first look at the information eDNA metabarcoding can reveal about Mekong aquatic diversity at a landscape scale. Developing best practices for eDNA sampling is an important step towards efficiently monitoring a multitude of species in the large and biodiverse Mekong River system, which can inform management and conservation actions for the watershed’s vitally important fisheries.