Sains Malaysiana 53(1)(2024): 11-21

http://doi.org/10.17576/jsm-2024-5301-02

The Viability and Potential of Environmental DNA (eDNA) Detection of Freshwater Fish Based on Current Genetic Resources in Malaysia

(Daya Maju dan Potensi Pengesanan DNA Persekitaran Ikan Air Tawar Berdasarkan Sumber Genetik Terkini di Malaysia)

KAVIARASU MUNIAN^1,2, FARAH FARHANA RAMLI¹, NURSYUHADA OTHMAN¹, HIDAYAH HARIS¹, NUR HARTINI SARIYATI¹, NUR AINA AMIRA MAHYUDIN², MOHD FAUDZIR NAJMUDDIN¹, MOHD SHAHFIZ AZMAN² & MUHAMMAD ABU BAKAR ABDUL-LATIFF^1,*

¹Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600 Muar, Johor, Malaysia

²Zoology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), 52019 Kepong, Selangor, Malaysia

Received: 26 June 2022/Accepted: 12 December 2023

Abstract

Environmental DNA (eDNA) metabarcoding is a promising tool for regular biological monitoring, especially for freshwater fish, which are facing tremendous threats worldwide. The application of eDNA detection is a dramatic improvement on common methods of biomonitoring as it produces tangible results in a short time with low effort and little expense. However, the accuracy of the technique is largely dependent on the availability of genetic references for the target organisms. In this study, we investigated the availability of genetic resources for freshwater fish in Malaysia in three public depositories, National Center for Biotechnology Information (NCBI), Barcode of Life Data System (BOLD), and Mitochondrial Genome Database of Fish (MitoFish), focusing on seven targeted genes of mitochondrial DNA. We found that only 68.6% of freshwater fish found in Malaysia had information on at least one of the seven targeted genes, with data on Cytochrome C Oxidase Subunit I being most commonly available. Genetic information for threatened and endemic species were underrepresented (33.3%-41.7%), yet fish of commercial value and invasive species were well explored genetically. Although there is still room for improvement to achieve comprehensive and reliable genetic resource information for freshwater fish in Malaysia, the application of eDNA metabarcoding is still highly relevant. This is since the current decline in freshwater fish diversity in Malaysia is alarming and because the technique will assist in the ongoing effort to generate new genetic references for Malaysian freshwater fish.

Keywords: Environmental DNA; Cytochrome b; Cytochrome C Oxidase Subunit I ; freshwater fish; metabarcoding and Next-Generation Sequencing (NGS)

Abstrak

Metabarkod DNA persekitaran (eDNA) ialah kaedah yang berpotensi dalam memantau sumber biologi terutamanya dalam pemantauan ikan air tawar terancam di seluruh dunia. Penggunaan teknik eDNA dalam pemantauan sumber biologi merupakan kaedah beteknologi tinggi kerana ia mampu memberikan hasil yang ketara dalam masa yang singkat dengan penggunaan tenaga dan kos yang minimum. Walau bagaimanapun, ketepatan teknik ini sebahagian besarnya bergantung kepada ketersediaan rujukan genetik untuk organisma yang disasar. Dalam penyelidikan ini, kami mengkaji ketersediaan sumber genetik untuk ikan air tawar di Malaysia di tiga depositori awam, iaitu Pusat Maklumat Bioteknologi Kebangsaan, Sistem Data Kehidupan Kod Bar dan Pangkalan Data Genom Mitokondria Ikan dan memfokuskan kepada tujuh gen DNA mitokondria yang terpilih. Hasil keputusan kami menunjukkan hanya 68.6% daripada ikan air tawar yang ditemui di Malaysia mempunyai maklumat tentang sekurang-kurangnya satu daripada tujuh gen yang disasarkan, manakala gen subunit Sitokrom C Oksidase Subunit I merupakan gen yang paling tersedia untuk digunakan. Keputusan kami juga menunjukkan maklumat tentang genetik spesies terancam dan endemik masih kurang dikaji (33.3%-41.7%), tetapi ikan air tawar komersial dan spesies ikan invasif telah dikaji dengan lebih baik dari aspek genetik. Fenomenon penurunan kepelbagaian ikan air tawar di Malaysia yang membimbangkan pada masa kini memberikan kewajaran kepada pelaksanaan aplikasi metabarkod eDNA untuk kajian ikan air tawar. Walaupun masih terdapat ruang penambahbaikan untuk mencapai maklumat sumber genetik yang komprehensif dan boleh dipercayai di Malaysia, aplikasi metabarkod (eDNA) ini wajar diteruskan sebagai sebahagian usaha berterusan para pengkaji dalam menjana rujukan genetik baharu untuk ikan air tawar Malaysia.

Kata kunci: DNA persekitaran; ikan air tawar; metabarkod dan penjujuran generasi hadapan (NGS); sitokrom b; Sitokrom Oksidase Subumit I

REFERENCES

Allan, J.D. & Flecker, A.S. 1993. Biodiversity conservation in running waters. BioScience 43(1): 32-43.

Allentoft, M.E., Collins, M., Harker, D., Haile, J., Oskam, C.L., Hale, M.L., Campos, P.F., Samaniego, J.A., Gilbert, M.T.P., Willerslev, E. & Zhang, G. 2012. The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society B: Biological Sciences 279(1748): 4724-4733.

Bohmann, K., Evans, A., Gilbert, M.T.P., Carvalho, G.R., Creer, S., Knapp, M., Douglas, W.Y. & De Bruyn, M. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution 29(6): 358-367.

Centre for Biodiversity Genomics, Canada. 2021. Barcode of Life Data System. Bold Systems.  https://www.boldsystems.org/ Accessed 10 August 2021.

Chen, C., Li, Q., Fu, R., Wang, J., Xiong, C., Fan, Z., Hu, R., Zhang, H. & Lu, D. 2019. Characterization of the mitochondrial genome of the pathogenic fungus Scytalidium auriculariicola (Leotiomycetes) and insights into its phylogenetics. Scientific Reports 9: 17447.

Chong, V.C., Lee, P.K.Y. & Lau, C.M. 2010. Diversity, extinction risk and conservation of Malaysian fishes. Journal of Fish Biology 76(9): 2009-2066.

Coleman, C.O. 2015. Taxonomy in times of the taxonomic impediment–examples from the community of experts on amphipod crustaceans. Journal of Crustacean Biology 35(6): 729-740.

Darling, J.A. & Mahon, A.R. 2011. From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research 111(7): 978-988.

de Carvalho, C.B.V. 2014. DNA barcoding in forensic vertebrate species identification. Brazilian Journal of Forensic Sciences, Medical Law and Bioethics 4(1): 12-23.

De Moor, F.C. 1996. The importance of voucher specimens. Southern African Journal of Aquatic Science 22(1-2): 117-118.

Deagle, B.E., Jarman, S.N., Coissac, E., Pompanon, F. & Taberlet, P. 2014. DNA metabarcoding and the cytochrome c oxidase subunit I marker: Not a perfect match. Biology Letters 10(9): 20140562.

Deiner, K., Bik, H.M., Mächler, E., Seymour, M., Lacoursière‐Roussel, A., Altermatt, F., Creer, S., Bista, I., Lodge, D.M., de Vere, N. & Pfrender, M.E. 2017. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology 26(21): 5872-5895.

Dudgeon, D., Arthington, A.H., Gessner, M.O., Kawabata, Z.I., Knowler, D.J., Lévêque, C., Naiman, R.J., Prieur-Richard, A.H., Soto, D., Stiassny, M.L. & Sullivan, C.A. 2006. Freshwater biodiversity: Importance, threats, status and conservation challenges. Biological Reviews 81(2): 163-182.

Ficetola, G.F., Miaud, C., Pompanon, F. & Taberlet, P. 2008. Species detection using environmental DNA from water samples. Biology Letters 4(4): 423-425.

Froese, R. & Pauly, D. 2017. FishBase. www.fishbase.org Accessed 10 August 2021.

Gehri, R.R., Larson, W.A., Gruenthal, K., Sard, N.M. & Shi, Y. 2021. eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine‐scale heterogeneity in a temperate freshwater lake. Environmental DNA 3(5): 912-929.

Hebert, P.D., Ratnasingham, S. & De Waard, J.R. 2003. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences 270(suppl_1): S96-S99.

Jackson, J.B., Kirby, M.X., Berger, W.H., Bjorndal, K.A., Botsford, L.W., Bourque, B.J., Bradbury, R.H., Cooke, R., Erlandson, J., Estes, J.A. & Hughes, T.P. 2001. Historical overfishing and the recent collapse of coastal ecosystems. Science 293(5530): 629-637.

Jarman, S.N., McInnes, J.C., Faux, C., Polanowski, A.M., Marthick, J., Deagle, B.E., Southwell, C. & Emmerson, L. 2013. Adélie penguin population diet monitoring by analysis of food DNA in scats. PLoS ONE 8(12): e82227.

Kartzinel, T.R., Chen, P.A., Coverdale, T.C., Erickson, D.L., Kress, W.J., Kuzmina, M.L., Rubenstein, D.I., Wang, W. & Pringle, R.M. 2015. DNA metabarcoding illuminates dietary niche partitioning by African large herbivores. Proceedings of the National Academy of Sciences 112(26): 8019-8024.

Kottelat, M. 2013. The fishes of the inland waters of Southeast Asia: A catalogue and core bibliography of the fishes known to occur in freshwaters, mangroves and estuaries. Raffles Bulletin of Zoology 2013(Supplement No. 27): 1-663.

Kounosu, A., Murase, K., Yoshida, A., Maruyama, H. & Kikuchi, T. 2019. Improved 18S and 28S rDNA primer sets for NGS-based parasite detection. Scientific Reports 9(1): 1-12.

Liu, H., Li, H., Song, F., Gu, W., Feng, J., Cai, W. & Shao, R. 2017. Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus. Scientific Reports 7: 4284.

Liu, J., Jiang, J., Song, S., Tornabene, L., Chabarria, R., Naylor, G.J. & Li, C. 2017. Multilocus DNA barcoding–species identification with multilocus data. Scientific Reports 7: 16601.

Lundberg, J.G., Kottelat, M., Smith, G.R., Stiassny, M.L. & Gill, A.C. 2000. So many fishes, so little time: An overview of recent ichthyological discovery in continental waters. Annals of the Missouri Botanical Garden 87(1): 26-62.

Ma, X., Yang, H., Zhong, X., Zeng, P., Zhou, X., Zeng, S., Dong, X., Min, W. & Huang, F. 2022. eDNA metabarcoding analysis of the composition and spatial patterns of fish communities in the Sanbanxi Reservoir, China. Sustainability 14(20): 12966.

McElroy, M.E., Dressler, T.L., Titcomb, G.C., Wilson, E.A., Deiner, K., Dudley, T.L., Eliason, E.J., Evans, N.T., Gaines, S.D., Lafferty, K.D. & Lamberti, G.A. 2020. Calibrating environmental DNA metabarcoding to conventional surveys for measuring fish species richness. Frontiers in Ecology and Evolution 8: 276.

McInnes, J.C. 2017. The development and application of DNA metabarcoding to non-invasively assess seabird diets, using albatrosses as a model. Doctoral dissertation, University of Tasmania (Unpublished).

MitoFish: Mitochondrial Genome Database of Fish. 2021. MitoFish. http://mitofish.aori.u-tokyo.ac.jp/ accessed on 10 August 2021.

Milhau, T., Valentini, A., Poulet, N., Roset, N., Jean, P., Gaboriaud, C. & Dejean, T. 2021. Seasonal dynamics of riverine fish communities using eDNA. Journal of Fish Biology 98(2): 387-398.

Naiman, R.J., Magnuson, J.J., Stanford, J.A. & McKnight, D.M. 1995. The Freshwater Imperative: A Research Agenda. Covelo: Island Press. p. 200.

Nakagawa, H., Yamamoto, S., Sato, Y., Sado, T., Minamoto, T. & Miya, M. 2018. Comparing local‐and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods. Freshwater Biology 63(6): 569-580.

National Library of Medicine (US), National Center for Biotechnology Information. National Center for Biotechnology Information (NCBI). https://www.ncbi.nlm.nih.gov/ Accessed on 10 August 2021.

Ng, C.K.C., Abdullah, F., Biun, H., Ibrahim, M.K., Mustapha, S. & Sade, A. 2017. A working checklist of the freshwater fish diversity for habitat management and conservation work in Sabah, Malaysia, North Borneo. Biodiversitas Journal of Biological Diversity 18(2): 560-574.

Othman, N., Haris, H., Fatin, Z., Najmuddin, M.F., Sariyati, N.H., Md-Zain, B.M. & Abdul-Latiff, M.A.B. 2021. A review on environmental DNA (eDNA) metabarcoding markers for wildlife monitoring research. IOP Conference Series: Earth and Environmental Science 736(1): 012054.

Pentinsaari, M., Salmela, H., Mutanen, M. & Roslin, T. 2016. Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life. Scientific Reports 6: 35275.

Revenga, C., Campbell, I., Abell, R., De Villiers, P. & Bryer, M., 2005. Prospects for monitoring freshwater ecosystems towards the 2010 targets. Philosophical Transactions of the Royal Society B: Biological Sciences 360(1454): 397-413.

Roberts, T.R. 1999. Fishes of the cyprinid genus Tor in the Nam Theun watershed (Mekong basin) of Laos, with description of a new species. Raffles Bulletin of Zoology 47: 225-236.

Saba, A.O., Ismail, A., Zulkifli, S.Z., Halim, M.R.A., Wahid, N.A.A. & Amal, M.N.A. 2020. Species composition and invasion risks of alien ornamental freshwater fishes from pet stores in Klang Valley, Malaysia. Scientific Reports 10: 17205.

Sala, O.E., Stuart Chapin, F.I.I.I., Armesto, J.J., Berlow, E., Bloomfield, J., Dirzo, R., Huber-Sanwald, E., Huenneke, L.F., Jackson, R.B., Kinzig, A. & Leemans, R. 2000. Global biodiversity scenarios for the year 2100. Science 287(5459): 1770-1774.

Sanger, F., Nicklen, S. & Coulson, A.R. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74(12): 5463-5467.

Schnell, I.B., Thomsen, P.F., Wilkinson, N., Rasmussen, M., Jensen, L.R., Willerslev, E., Bertelsen, M.F. & Gilbert, M.T.P. 2012. Screening mammal biodiversity using DNA from leeches. Current Biology 22(8): R262-R263.

Schwarz, C., Debruyne, R., Kuch, M., McNally, E., Schwarcz, H., Aubrey, A.D., Bada, J. & Poinar, H. 2009. New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic Acids Research 37(10): 3215-3229.

Shaw, J.L., Clarke, L.J., Wedderburn, S.D., Barnes, T.C., Weyrich, L.S. & Cooper, A. 2016. Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biological Conservation 197: 131-138.

Singh, M.P., Janso, J.E. & Brady, S.F. 2007. Cytoskyrins and cytosporones produced by Cytospora sp. CR200: Taxonomy, fermentation and biological activities. Marine Drugs 5(3): 71-84.

Stoeckle, M.Y., Das Mishu, M. & Charlop-Powers, Z. 2020. Improved environmental DNA reference library detects overlooked marine fishes in New Jersey, United States. Frontiers in Marine Science https://doi.org/10.3389/fmars.2020.00226

Tarkan, A.S., Marr, S.M. & Ekmekçi, F.G. 2015. Non-native and translocated freshwater fish. FiSHMED Fishes in Mediterranean Environments 3: 1-28.

Tedesco, P.A., Beauchard, O., Bigorne, R., Blanchet, S., Buisson, L., Conti, L., Cornu, J.F., Dias, M.S., Grenouillet, G., Hugueny, B. & Jézéquel, C. 2017. A global database on freshwater fish species occurrence in drainage basins. Scientific Data 4: 170141.

Waldron, A., Mooers, A.O., Miller, D.C., Nibbelink, N., Redding, D., Kuhn, T.S., Roberts, J.T. & Gittleman, J.L. 2013. Targeting global conservation funding to limit immediate biodiversity declines. Proceedings of the National Academy of Sciences 110(29): 12144-12148.

Wang, J., Zhang, L.I., Zhang, Q.L., Zhou, M.Q., Wang, X.T., Yang, X.Z. & Yuan, M.L. 2017. Comparative mitogenomic analysis of mirid bugs (Hemiptera: Miridae) and evaluation of potential DNA barcoding markers. PeerJ 5: e3661.

*Corresponding author; email: latiff@uthm.edu.my