A new method of environmental DNA monitoring to detect rare and endangered fish species sold in markets

An article recently published in Methods in Ecology and Evolution, researchers from the Environmental Forensics Laboratory at the University of Hong Kong have developed a powerful new tool to monitor the trade in rare and endangered fish species in Hong Kong’s wet markets. Using the DNA of the environment (eDNA), which is present in the wastewater of fish markets, the researchers were able to obtain and sequence enough DNA to identify more than 100 species of fish that have passed through the market.

Different types of vulnerable or endangered species were detected by eDNA during research, including Epinephelus fuscoguttatus, a type of brown marble perch that is listed as vulnerable and declining according to the International Union for Conservation of Nature (IUCN), and three species of eel including Anguilla japonica and Anguilla rostra the endangered IUCN, as well as the European eel of Anguilla, Anguilla, listed by CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora). Two types of bream have been identified, including the golden fin bream (Nemipterus virgatus), which is listed as a vulnerable IUCN, and the Aquinas bream (Acanthopagus sivicolus), which is listed as a vulnerable and declining IUCN.

Metabarking allows species to be identified immediately

Bar coding is a common method of species identification in which specific parts of the body’s genome are sequenced and used to identify the organism in question. Each species has its own unique “barcode” that can provide a more reliable form of identification than traditional morphology-based methods. This technique can be extended to the identification of several species simultaneously (known as metabarcoding) thanks to advanced high-throughput sequencing technology. Even a small amount of DNA released from plants and animals into the environment (eDNA) is sufficient for meta-bartering, allowing the identification of mixed communities of species that may have been present in the area.

In this study, researchers from the Laboratory of Environmental Forensics aimed to develop a method of identification fish the species traded in Hong Kong’s markets do not depend on fish taxonomy experts to spend hours visually identifying every fish sold. In addition, many fishmongers are often reluctant to allow lengthy inspections of their goods because Hong Kong markets can be found for sale endangered fish species.

The method outlined in the paper compared the two most common types of eDNA capture: filtration and sedimentation. In the filtration method, one liter of water collected from sewage in three wet markets was collected and passed through a thin filter that captured tissue, blood and other cellular debris that contained enough DNA to identify the species of fish that dumped it. . The precipitation method used even less water, which allows the identification of fish species present by chemical precipitation of the eDNA present in the cell debris from 45 ml of wastewater. After drainage water collection the eDNA was extracted and sequenced and species of fish were found in three wet markets surveyed over a 5-day period. To confirm the results, a fish taxonomy expert conducted a visual inspection, and a comparison of species detection was compared.

High reliability and easy adaptation

Although it is impossible to be 100% sure of the identification of each species present by any method, the benefits of the DNA-based screening method are many. Basically, DNA-based identifiers can be more reliable than morphological identifiers, and this is especially true if the fish is sold cut or belongs to certain genera and families of a similar species. The method of DNA isolation described in the article is also very simple and can be easily performed by anyone who has basic molecular laboratory training in a few hours. Visual research requires hours and hours of extensive work by many taxonomists, which has been a deterrent to the deployment of regular surveys in Hong Kong.

“We hope that our method will not only push local authorities make more high-tech solutions to control and combat illegal wildlife trade in Hong Kong, but also contribute to the use of eDNA and meta-bargaining in the urban context, ”said John L. Richards, co-author of the journal.