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

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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

This project has analyzed environmental-DNA (eDNA) metabarcode sequence data from the Mekong River's water. The bacterial diversity derived from 16S rRNA metabarcode sequence data showed more than 10,000 occurrences of identified bacteria in the Mekong River samples collected during March - December 2021.

At final reporting, the project published these results on GBIF as an occurrence dataset comprising 12,614 records, as well as its accompanying sampling event dataset.

In order to achieve the goal of sharing the eDNA-derived biodiversity information of microorganisms in Mekong river, the metabarcode sequence data were also deposited to NCBI Bioproject database. The diversity and occurrence datasets have also been integrated to AmiBase system and the data sharing API was developed at (

During project implementation and to raise awareness of importance of eDNA data for Mekong biodiversity study and conservation in local communities around Mekong river, four eDNA data analysis and data mobilization workshops have been conducted in January 2022, March 2022, June 2022 and October 2022 respectively. The 4th and final workshop being conducted in conjunction with the WDCM global training course: ASEAN satellite training course and held as a hybrid seminar including onsite and online sessions. These events attracted a total of 250 participants including a variety of audience from university students, lecturers, researchers, and R&D personnels in private sectors. The success of these workshop activities hopefully paving the foundation of an eDNA-based diversity study network in Thailand.

In addition to this and to increase project visibility, project workshop activity has been publicized on the MekongDNA’s Citizen Science program website. Project news and information has also posted to social networks such as TBRCNetwork Facebook page, for example the news post to announce the start of the project and the news post to summarize the success of the 4th workshop and seminar.

Due to the COVID-19 pandemic the project team experienced some delays in workshop events and had lower attendance rates than expected. In response to participant’s requests for the expansion of the workshop to live online events, the project team were able to address this and conduct its 4th workshop and seminar as a hybrid event.

€ {{ 17981 | localNumber }}
€ {{ 970 | 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