Using microbial metabarcoding to monitor biodiversity and bioindicators in the Mekong River

How to link datasets to a project

{{result.description | stripTags | limitTo:200 }}

{{ result.publishingOrganizationTitle | limitTo:100 }}

... ...

How to link events and news to a project

A dinoflagelate from the genus Alexandrium, collected in the Gulf of Siam, Thailand. Photo Maria Faust via NMNH Extant Specimen Records.

River microbes have great potential for assessment and monitoring of biodiversity and environmental conditions in freshwater ecosystems. However, generating biodiversity data based on traditional sampling and morphological identification is time-consuming and error-prone. Recently, metabarcoding of environmental DNA (eDNA) technique offers novel opportunities. It is a non-invasive, cost-effective method to assess biodiversity and bioindicators accurately with the aid of advanced next-generation sequencing (NGS) and high-throughput sequencing (HTS) technologies.

However, the metabarcoding studies and eDNA data in Mekong River are scarce. The goal of this project is to promote the use of data on microbial biodiversity in river monitoring and conservation through a series of training workshops and the construction of an integrated data platform for collecting, managing and sharing eDNA biodiversity data.

The project team will compile eDNA data (primarily bacterial 16S rDNA and fungal ITS metabarcoding data) from studies into a database of Mekong River’s microbial communities. The main original source of eDNA data used in this project will be derived from the MekongDNA Project led by Dr Supawadee Ingsriswang of the National Center for Genetic Engineering and Biotechnology (BIOTEC) in Thailand. The resulting database will be incorporated into a web-based platform.

Moreover, in order to facilitate data use and sharing in scientific communities, the biodiversity data and metadata of the project can be accessed via API which enables automated data sharing between relevant biodiversity databases such as AmiBase. The mobilization of Mekong eDNA data will have implications in sustainable development in research communities and general public.

Project progress

During the first half of the project, the project team has compiled, analyzed eDNA metabarcode sequence, conducted data standardization and shared data with GBIF.

The eDNA 16S rRNA metabarcoding sequence data from Mekong river has been analyzed and initial analyses showed the temporal and taxonomic composition in the Mekong river’s bacterial communities. These results were cleaned and re-translated to occurrence-level data and by midterm reporting the project published to GBIF the eDNA-derived occurrence dataset and sampling metadata with Darwin Core terms, with 82 records.

The first stage of data API development was implemented and tested with the data examples so far.

During implementation and to raise awareness of the importance of eDNA data for Mekong biodiversity study and conservation in local communities around Mekong river, three eDNA data analysis and data mobilization workshops have been conducted in January 2022, March 2022 and June 2022 at various institutes and universities in Northern and Northeastern Thailand. These workshops have successfully attracted audiences from university students, lecturers, researchers, and research organization, which is paving the foundation of an eDNA-based diversity study network in Mekong local communities in Thailand.

In addition to this and to increase project visibility, project activity updates have also been published in the MekongDNA’s Citizen Science program and information about the project posted to social networks such as TBRCNetwork Facebook page (see example here).

€ {{ 17984 | localNumber }}
€ {{ 979 | localNumber }}
2 September 2021 - 28 February 2023
Project identifier
Contact details

Somsak Likhitrattanapisal
National Center for Genetic Engineering and Biotechnology
113 Thailand Science Park Paholyothin Rd., Khlong Neung, Khlong Luang, Pathum Thani
12120 Pathum Thani