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Uncovering Molluscs Diversity in Mandalika Coastal Through eDNA Metabarcoding
Corresponding Author(s) : Dining Aidil Candri
Jurnal Ilmiah Perikanan dan Kelautan, 2025: JIPK VOLUME 17 ISSUE 3 YEAR 2025 (OCTOBER 2025, ISSUE IN PROGRESS)
Abstract
Graphical Abstract
Highlight Research
- The environmental DNA (eDNA) method successfully identified four species of molluscs (Monetaria , M. annulus, M. obvelata, and Phyllaplysia sp.) and two family taxa (Strombidae and Cypraeidae) from the seagrass and coral reef ecosystems on the Mandalika coast.
- The species annulus, M. obvelata, and Phyllaplysia sp were detected in the coastal area of Mandalika for the first time using the eDNA approach, although they had never been recorded observationally in this area before.
- The eDNA method is able to detect species that are difficult to observe directly, such as Phyllaplysia, which have never been reported in the coral reef ecosystem of Mandalika.
- This study emphasizes the urgency of sustainable coastal area management with an eDNA-based scientific approach to monitor diversity, detect rare species, and evaluate the impact of human activities on the ecosystem.
Abstract
Molluscs are one of the main taxa in coastal ecosystems that play an important role in the food chain, bioindicators, and have high economic value. However, the limitations of conventional methods in detecting species that live hidden in complex ecosystems, such as seagrass and coral reefs, are a challenge in biodiversity monitoring. This study aimed to explore the diversity of mollusc species in the Mandalika coastal area using an eDNA metabarcoding approach. This study used the environmental DNA (eDNA) metabarcoding method to identify the diversity of molluscs in the coastal ecosystem of Mandalika, Central Lombok. The sites including Kuta Beach, Gerupuk Bay, and Aan Cape along the Mandalika coastal that contain both seagrass bed and coral reef ecosystems. Two samples were taken from each site in both the seagrass bed and coral reef ecosystems. Analysis of six water samples resulted in 99 ASVs and 116,611 final sequences, with 10 ASVs (50,960 sequences) identified as Mollusca taxa, all from the Gastropoda class. Four species were successfully identified, including Monetaria sp. M. obvelata, M. annulus and Phyllaplysia sp. that had not previously been reported through direct observation or conventional identification methods in Mandalika coastal area. Species diversity varied between locations and was influenced by environmental factors such as temperature, pH, salinity, phosphate, and anthropogenic pressure. These results show that eDNA metabarcoding is an effective tool in detecting mollusc species, even in hard-to-reach habitats, and support the urgency of scientific data-based mollusc conservation management.
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- Ahyadi, H., Erdin, E., Candri, D. A., Farista, B., Astuti, S. P., & Virhota, A. (2021). Species diversity and health status of seagrass meadows in the Mandalika Coastal area, Central Lombok Regency. Prosiding Saintek LPPM Universitas Mataram, 3(2021):1-5.
- Aji, L. P., Widyastuti, A., & Capriati, A. (2018). Community structure of Mollusca in Seagrass Beds Padaido and Aimando Islands Biak Numfor Regency, Papua. Oseanologi dan Limnologi di Indonesia, 3(3):219-234.
- Berliana, C. G., Candri, D. A., & Ahyadi, H. (2024). Mollusca biodiversity as a quality bioindicator waters in Central Lombok Gerupuk Bay Coastal area. Jurnal Pijar MIPA, 19(2):267-272.
- Bolyen, E., Rideout, J. R., Dillo, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawan, C. J., Brown, C. T., Callahan, B. J., Rodriguez, A. M. C., Chase, J., Cope, E. K., Silva, R. D., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langgille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., Mclver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Molina, J. A. N., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaiugh, P. J., Hasan, S., Hooft, J. J., Vargas, F., Baeza, Y. V., Vogtmann, E., Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Khight, R., & Caporaso, J. G. (2018) Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(7):852-857.
- Bula, W., Leiwakabessy, F., & Rumahlatu, D. (2017). The influence of environmental factors on the diversity of Gastropods in Marsegu Island, Maluku. Jurnal Biosaintifika, 9(3):483-491.
- Callahan, B. J., Mcmurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). Dada2: Highresolution sample inference from illumina amplicon data. Nat. Methods, 13(7):581-583.
- Candri, D. A., Hakimi, B., Ahyadi, H., Suana, I. W., Prasedya, E. S., Ambarwati, K., & Mardiati, A. U. (2023a). Condition of coral reef diversity in Kuta Mandalika Coastal, Central Lombok Regency. Jurnal Biologi Tropis, 23(2):15-26.
- Candri, D. A., Hidayati, L. J., Ahyadi, H., & Zamroni, Y. (2023b). Community structure of Molluscs at Batu Kijuk Village. Jurnal Penelitian Pendidikan IPA, 9(2):856-863.
- Candri, D. A., Rahmani, M. S., Ahyadi, H., & Zamroni, Y. (2022). Diversity and distribution of Gastropoda and Bivalvia in mangrove ecosystem of Pelangan, Sekotong, West Lombok. Jurnal Biologi Tropis, 22(3):1092-1100.
- Candri, D. A., Sani, L. H., Ahyadi, H., & Farista, B. (2020). Mollusk community structure in natural and rehabilitated mangrove areas on the south coast of Lombok Island. Jurnal Biologi Tropis, 20(1):139-147.
- Chahouri, A., Yacoubi, B., Moukrim, A., & Banaoiu, A. (2023). Bivalve Molluscs as bioindicators of multiple stressors in the marine environment: Recent advances. Continental Shelf Research. 264(13):1-14.
- Chen, Z., Song, N., Minamoto, T., Wu, Q. Q., & Gao, T. X. (2020). The eDNA collection method of Zhoushan coastal waters. Acta Hydrobiologica Sinica, 44(1):50-58.
- de Jonge, D. S. W., Merten, V., Bayer, T., Puebla, O., Reusch, T. B. H., & Hoving, H. J. T. (2021). A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. Royal Society Open Science, 8(2):1-16.
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- Irie, T., & Morimoto, N. (2016). Intraspecific variations in shell calculation across thermal window and within constant temperatures: Experimental study on an intertidal Gastropod Monetaria annulus. Journal of Experimental Marine Biology and Ecology, 483(10):130-138.
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References
Ahyadi, H., Erdin, E., Candri, D. A., Farista, B., Astuti, S. P., & Virhota, A. (2021). Species diversity and health status of seagrass meadows in the Mandalika Coastal area, Central Lombok Regency. Prosiding Saintek LPPM Universitas Mataram, 3(2021):1-5.
Aji, L. P., Widyastuti, A., & Capriati, A. (2018). Community structure of Mollusca in Seagrass Beds Padaido and Aimando Islands Biak Numfor Regency, Papua. Oseanologi dan Limnologi di Indonesia, 3(3):219-234.
Berliana, C. G., Candri, D. A., & Ahyadi, H. (2024). Mollusca biodiversity as a quality bioindicator waters in Central Lombok Gerupuk Bay Coastal area. Jurnal Pijar MIPA, 19(2):267-272.
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Bula, W., Leiwakabessy, F., & Rumahlatu, D. (2017). The influence of environmental factors on the diversity of Gastropods in Marsegu Island, Maluku. Jurnal Biosaintifika, 9(3):483-491.
Callahan, B. J., Mcmurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). Dada2: Highresolution sample inference from illumina amplicon data. Nat. Methods, 13(7):581-583.
Candri, D. A., Hakimi, B., Ahyadi, H., Suana, I. W., Prasedya, E. S., Ambarwati, K., & Mardiati, A. U. (2023a). Condition of coral reef diversity in Kuta Mandalika Coastal, Central Lombok Regency. Jurnal Biologi Tropis, 23(2):15-26.
Candri, D. A., Hidayati, L. J., Ahyadi, H., & Zamroni, Y. (2023b). Community structure of Molluscs at Batu Kijuk Village. Jurnal Penelitian Pendidikan IPA, 9(2):856-863.
Candri, D. A., Rahmani, M. S., Ahyadi, H., & Zamroni, Y. (2022). Diversity and distribution of Gastropoda and Bivalvia in mangrove ecosystem of Pelangan, Sekotong, West Lombok. Jurnal Biologi Tropis, 22(3):1092-1100.
Candri, D. A., Sani, L. H., Ahyadi, H., & Farista, B. (2020). Mollusk community structure in natural and rehabilitated mangrove areas on the south coast of Lombok Island. Jurnal Biologi Tropis, 20(1):139-147.
Chahouri, A., Yacoubi, B., Moukrim, A., & Banaoiu, A. (2023). Bivalve Molluscs as bioindicators of multiple stressors in the marine environment: Recent advances. Continental Shelf Research. 264(13):1-14.
Chen, Z., Song, N., Minamoto, T., Wu, Q. Q., & Gao, T. X. (2020). The eDNA collection method of Zhoushan coastal waters. Acta Hydrobiologica Sinica, 44(1):50-58.
de Jonge, D. S. W., Merten, V., Bayer, T., Puebla, O., Reusch, T. B. H., & Hoving, H. J. T. (2021). A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. Royal Society Open Science, 8(2):1-16.
Elbrecht, V., & Leese, F. (2017). PrimerMiner: An R package for development and in silico validation of DNA metabarcoding primers. Methods in Ecology and Evolution, 8(5):622-626.
Gokoglu, N. (2021). Shellfish processing and preservation. Springer.
Goldberg, C. S., Sepulveda, A., Ray, A., Baumgardt, J., & Waits, L. P. (2013). Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshwater Science, 32(3):792-800.
Hallam, J., Clare, E. L., Jones, J. I., & Day, J. J. (2021). Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods. Environmental DNA, 3(6):1247-1266.
Harrison, J. B., Sunday, J. M., & Rogers, S. M. (2019). Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proceedings of the Royal Society B, 286(1915):1-9.
Huang, C., Zhu, S. X., Lin, J., & Dong, Q. (2008). Imposex of Mauritia arabica on the south-eastern coast of China. Journal of the Marine Biological Association of the United Kingdom, 88(7):1451-1457.
Irie, T. (2006). Geographical variation of shell morphology in Cypraeae annulus (Gastropoda: Cypraeidae). Journal of Molluscan Studies, 72(1):31-38.
Irie, T., & Morimoto, N. (2016). Intraspecific variations in shell calculation across thermal window and within constant temperatures: Experimental study on an intertidal Gastropod Monetaria annulus. Journal of Experimental Marine Biology and Ecology, 483(10):130-138.
Jarman, S. N., Redd, K. S., & Gales, N. J. (2006) Group specific primers for amplifying DNA sequences that identify Amphipoda, Cephalopoda, Echinodermata, Gastropoda, Isopoda, Ostracoda and Thoracica. Molucar Ecology Notes, 6(1):268-271.
Katoh, M. (1989). Life history of the golden ring cowry Cypraea annulus (Mollusca: Gastropoda) on Okinawa Island, Japan. Marine Biology, 101(1):227-233.
Kestel, J. H., Field, D. L, Bateman, P. W., White, N. E., Allentoft, M. E., Hopkins, A. J. M., Gibberd, M., & Nevill, P. (2022). Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. Science of the Total Environment, 874(11):1-21.
Kim, E. B., Lee, S. R., Lee, C. I., Park, H., & Kim, H. W. (2019). Development of the cephalopod-specific universal primer set and its application for the metabarcoding analysis of planktonic cephalopods in Korean waters. PeerJ, 7(1):7140-7151.
Kuncoro, I., Zamani, N. P., Subhan, B., & Cahyani, N. K. D. (2023) eDNA assessment of Sclerentinian diversity and distribution in Lemukutan Island, Indonesia. Biodiversitas, 24(7):4185-4191.
Lamy, T., Pointer, J. P., Jarne, P., & David, P. (2012). Testing metapopulation dynamics using genetic, demographic and ecological data. Molecular Genetics, 21(6):1394-1410.
Leray, M., Yang, J. Y., Meyer, C. P., Mills, S. C., Agudelo, N., Ranwez, V., Boehm, J. T., & Machida, R. J. (2013). A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: Application for characterizing coral reef fish gut contents. Frontiers in zoology, 10(1):1-14.
Madduppa, H., Cahyani, N. K. D., Anggoro, A. W., Subhan, B., Jefri, E., Sani, L. M. I., Arafat, D., Akbar, N., & Bengen, D. G. (2021). eDNA metabarcoding illuminates species diversity and composition of three phyla (Chordata, Mollusca and Echinodermata) across Indonesian coral reefs. Biodiversity and Conservation, 30(11):3087-3114.
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