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Exploring species and functional diversity of fishes in Cambodian coastal habitats using eDNA metabarcoding

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Abstract

Previous studies investigating marine fish diversity in Cambodia’s coastal ecosystems focused on visual methods, concentrating on reporting ecologically and economically important indicator taxa. This study, however, presents the first comprehensive assessment of marine fish biodiversity along the coast of two regions in Cambodia using environmental DNA (eDNA) metabarcoding methods. Water samples were collected above coral reefs, seagrass meadows, estuarine sites and open water in the Northern Koh Kong region and the Koh Rong Archipelago, a marine national park. A region of the 12S rDNA was targeted for fish diversity. Additionally, for the detection of marine mammals, 16S ribosomal DNA was amplified. A total of 204 unique fish species were identified across 78 families and 17 orders, revealing significant differences in species richness and community composition across different habitat types and sampling locations. Functional diversity analyses categorized species into 18 distinct functional groups, shedding light on their ecological roles within the investigated habitats. Comparison with existing fish surveys and databases highlighted the effectiveness of eDNA metabarcoding in providing comparable or better biodiversity estimates. The study also identified two marine mammal species, including the endangered Irrawaddy dolphin, emphasizing the importance of eDNA in detecting elusive and threatened species. The study highlights the effectiveness of eDNA metabarcoding for marine biodiversity monitoring, offering valuable baseline data for conservation efforts in Cambodia and beyond, supporting the creation of marine protected areas (MPAs) to safeguard marine biodiversity. Advocating for the designation of Koh Kong as an MPA, the research points to its rich biodiversity, endangered species presence, and unique functional composition, suggesting its potential as a focal point for conservation initiatives.

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Data availability

Sequence data (demultiplexed, unfiltered reads) that support the findings of this study have been deposited on the Zenodo repository https://doi.org/10.5281/zenodo.11095946.

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Acknowledgements

This work was supported by Fauna & Flora, funded by Arcadia, Blue Action Fund and FAO under the Cambodia Marine Program. Field surveys were led by Matthew Glue, Morokot Long and Srey Oun Ith, and we would like to thank Sorn Srenh and the Song Saa Foundation for their tireless field survey efforts. We also like to thank the Fisheries Administration and the Ministry of Environment, Royal Government of Cambodia for their support in permission to conduct these surveys.

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Authors and Affiliations

  1. School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK

    Charlotte G. Clay

  2. Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan

    Fabian Gösser & James D. Reimer

  3. Fauna & Flora, Cambodia, #19 St 360, BKK1, Phnom Penh, 12100, Cambodia

    Matthew Glue, Morokot Long, Stefanie M. Rog & Pablo Sinovas

  4. Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan

    James D. Reimer

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Clay, C.G., Gösser, F., Glue, M. et al. Exploring species and functional diversity of fishes in Cambodian coastal habitats using eDNA metabarcoding. Coral Reefs 44, 221–241 (2025). https://doi.org/10.1007/s00338-024-02599-1

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