* Corresponding Author
Reef Fish Species Diversity Using Environmental DNA Metabarcoding in Mansinam and Lemon Island Waters, Manokwari Regency
https://doi.org/10.22146/jfs.73037 Bayu Pranata(1), Aradea Bujana Kusuma(2*), Muhamad Ilham Azhar(3)
(1) Department of Fishery, Faculty of Fisheries and Marine Sciences, University of Papua, Manokwari Regency, West Papua, Indonesia
(2) Department of Marine Science, Faculty of Fisheries and Marine Sciences, University of Papua, Manokwari Regency, West Papua, Indonesia
(3) Department of Environmental Science, College of Arts and Sciences, American University, Washington DC, USA
(*) Corresponding Author
Abstract
Biodiversity has an essential role in the stability of an ecosystem. A high level of biodiversity indicates a more stable and stable ecosystem. The decline in the quality of ecosystems such as coral reefs, seagrass beds, and mangrove forests due to anthropogenic factors and global warming threaten biodiversity. This study aims to determine the diversity of reef fish species using an environmental DNA (eDNA) approach in the waters of the Mansinam and Lemon, Manokwari Regency islands. The analysis results detected 158 individual fish comprising 26 species from 10 families (sequence identity 97-100%). The highest species abundance was found in the Pomacentridae Family. The Pomacentridae family is an ornamental fish species in coral reef ecosystems. In addition, several species from the families Serranidae, Caesionidae, Mullidae, Holocentridae, Balistidae, Scaridae, and Labridae were also detected; fish species from these families are catch targets for fishers with economic value. Assessment of fish species diversity using the Shannon-Wiener method. The diversity of fish species in the waters of the islands of Mansinam and Lemon is in the high category, namely 3.17. High diversity indicates a stable and stable ecosystem condition.
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Ahn, H., M. Kume, Y. Terashima, F. Ye, S. Kameyama & M. Miya. 2020. Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding. PLoS ONE 15 (10): e0231127. https://doi.org/10.1371/journal.pone.0231127
Allen, G & J.E. Randall. 2002. A review of the leucogaster species complex of the Indo-Pacific Pomacentrid Genus Amblyglyphidodon, with descriptions of two new species. Journal of Ichthyology and Aquatic Biology. 5 (4): 139-52.
Allen, G &. M.V. Erdmann. 2012. Review of Reef Fishes of the East Indies. University of Hawai’i Press, Volumes I-III. Tropical Reef Research. Perth, Australia. 192 p
Andriyono, S., M.J. Alam & H.W. Kim. 2021. Marine fish detection by environmental DNA (eDNA) metabarcoding approach in the Pelabuhan Ratu Bay, Indonesia. International Journal on Advanced Science, Engineering and Information Technology. 11 (2): 729-737. https://doi.org/10.18517/ijaseit.11.2.9528
Andriyono, S., M.J. Alam & H.W. KIM. 2019. Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap Fish Landing Station, Malang, Indonesia. Biodiversitas Journal of Biological Diversity. 20 (12). 3772-3781. https://doi.org/10.13057/biodiv/d201241
Ayhuan, H.V., N.P. Zamani & D. Soedharma. 2017. Structure analysis of makroalgae community at intertidal coastal area in Manokwari, West Papua. Jurnal Teknologi Perikanan dan Kelautan. 8 (1): 19-38. https://doi.org/10.24319/jtpk.8.19-38
Bellwood, D.R., C.H.R. Goatley, S.J. Brandl & O. Bellwood. 2014. Fifty Million Years of Herbivory on Coral Reefs: Fossils, Fish And functional Innovations. P. 281:20133046 in Proc. R. Soc. B.
Bhattacharjee, M.J., B.A. Laskar, B. Dhar & S.K. Ghosh. 2012. Identification and re-evaluation of freshwater catfishes through DNA barcoding. PLoS ONE. 7 (11): e49950. https://doi.org/10.1371/journal.pone.0049950
Bray, D. J. 2022. Pomacentrus in Fishes of Australia. Fishes of Australia. Retrieved January 5, 2022 (https://fishesofaustralia.net.au/home/genus/1202).
Bylemans, J., D.M. Gleeson, R.P. Duncan, C.M. Hardy & E.M. Furlan. 2019. A Performance evaluation of targeted eDNA and eDNA metabarcoding analyses for freshwater fishes. Environmental DNA. 1 (4): 402-414. https://doi.org/10.1002/edn3.41
Carpenter, K. 2001. Caesionidae. The Living Marine Resources of the Western Central Pacific Volume 5: Bony fishes part 3 (Menidae to Pomacentridae) (PDF), edited by K. E. & V. H. N. In Carpenter. FAO Rome.
Choat, J. 2018. Cephalopholis Cyanostigma. The IUCN Red List of Threatened Species 2018: E.T132808A100454656. Retrieved February 14, 2022 (https://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T132808A100454656.en.).
Dasmasela, Y.H., T.F. Pattiasina, S. Syafril & R.F. Tapilatu. 2019. Evaluasi kondisi terumbu karang Di Pulau Mansinam Menggunakan aplikasi metode Underwater Photo Transect (UPT). Jurnal Ilmu Ilmu Eksata. 11 (2):1-12. https://doi.org/10.33506/md.v11i2.458
Du, J., K. Loh, W. Hu, X. Zheng, Y.A. Affendi, J.L.S. Ooi, Z. Ma, M. Rizman-Idid & A.A. Chan. 2019. An Updated Checklist of the Marine Fish Fauna of Redang Islands, Malaysia. Biodivers Data Journal. 7:e47537.
English, S., C. Wilkinson & V. Baker. 1997. Survey Manual for Tropical Marine Resources. Townsfille, Australia: Australian Institute of Marine Science.
Falah, F.H., I.W. Arthana & N.M. Ernawati. 2020. Struktur komunitas dan tingkah laku ikan pada karang genus acropora di Perairan Desa Bondalem, Provinsi Bali. Current Trends in Aquatic Science. 3 (2):67-75.
Frederich, B., G. Fabri, G. Lepoint, P. Vandewalle & E. Parmentier. 2009. Trophic niches of thirteen damselfishes (Pomacentridae) at the Grand Re’cif of Toliara, Madagascar. Ichthyological Research. 5 (1):10-17. https://doi.org/10.1007/s10228-008-0053-2
Froese, R. & D. Pauly. 2021. “‘Caesionidae.’” In FishBase. Retrieved (http://www.fishbase.org/).
Gelis, E.R.E., M.M. Kamal, B. Subhan, I. Bachtiar, L.M.I. Sani & H. Madduppa. 2021. Environmental biomonitoring of reef fish community structure with eDNA metabarcoding in the Coral Triangle. Environmental Biology of Fishes. 4: 887-903. https://doi.org/10.1007/s10641-021-01118-3
Harahap, Z.A & I.E. Susetya. 2020. Marine Ecotourism Potential in Unggeh Island Tapanuli Tengah Regency, North Sumatra, Indonesia. Jurnal Ilmiah Perikanan dan Kelautan 12 (2): 250-62. https://doi.org/10.20473/jipk.v12i2.17940
Hempson, T. N., N.A.J. Graham, M.A. Macneil, D.H. Williamson, G.P. Jones & G.R. Almany. 2017. Coral Reef mesopredators switch prey, shortening food chains, in response to habitat degradation. Ecology and Evolution. 7 (8): 2626-2635. https://dx.doi.org/10.1002%2Fece3.2805
Hukom, F. D. 1998. Ekostruktur Dan Organisasi SpasialTemporal Ikan Karang Di Perairan Teluk Ambon. Tesis. Bogor. Institut Pertanian Bogor. Indonesia
Kamal, M.M., A.A. Hakim, N.A. Butet, Y. Fitrianingsih & R. Astuti. 2019. Autentikasi spesies ikan kerapu berdasarkan marka gen MT-COI dari Perairan Peukan Bada, Aceh. Jurnal Biologi Tropis. 19 (2): 116-123. https://doi.org/10.29303/jbt.v19i2.1245
Laramie, M.B., D.S. Pilliod, C.S. Goldberg & K.M. Strickler. 2015. Environmental DNA Sampling Protocol-Filtering Water to Capture DNA from Aquatic Organisms: U.S. Geological Survey Techniques and Methods. book 2, chap. A13. 12p
Lefaan, P.Th, D. Setiadi & D. Djokosetiyanto. 2013. Struktur komunitas lamun di Perairan Pesisir Manokwari. Maspari Journal. 5 (2): 69-81. https://doi.org/10.36706/maspari.v5i2.2499
Leray, M., J.Y. Yang, C.P. Meyer, S.C. Mills, N. Agudelo, V. Ranwez, J. T. Boehm &. R. J. Machida. 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 (34): 1-4. https://doi.org/10.1186/1742-9994-10-34
Madduppa, H., N.K.D. Cahyani, A.W. Anggoro, B. Subhan, E. Jefri, L.M.I. Sani, D. Arafat, N. Akbar & D.G. Bengen. 2021. eDNA metabarcoding illuminates species diversity and composition of three phyla (Chordata, Mollusca and Echinodermata) across Indonesian coral reefs. Biodiversity and Conservation. 30 (3) : 3087-3114. https://doi.org/10.1007/s10531-021-02237-0
Madduppa, H., R.U. Ayuningtyas, B. Subhan, D. Arafat & P. Prehadi. 2016. Exploited but Unevaluated: DNA barcoding reveals skates and stingrays (Chordata, Chondrichthyes) species landed in the Indonesian fish market. Ilmu Kelautan: Indonesian Journal of Marine Sciences. 21 (2):77-84. https://doi.org/10.14710/ik.ijms.21.2.77-84
Maulida, S., F.M. Nur, K. Eriani & Z. A. Muchlisin. 2020. A review on the cryopreservation development of sperm of the Indonesian native fish. DEPIK Jurnal Ilmu-Ilmu Perairan, Pesisir Dan Perikanan. 9 (2): 141-150. https://doi.org/10.13170/depik.9.2.16572
McClanahan, T & R. Arthur. 2001. The effect of marine reserves and habitat on populations of East African coral reef fishes. Ecological Applications. 11 (2): 559-569. https://doi.org/10.1890/1051-0761(2001)011[0559:TEOMRA]2.0.CO;2
McClure, E.C., A.S. Hoey, K.T. Sievers, R.A. Abesamis & G.R. Russ. 2021. Relative influence of environmental factors and fishing on coral reef fish assemblages. Conservation Biology. 35 (3): 976-990. https://doi.org/10.1111/cobi.13636
McDevitt, A.D., N.G. Sales, S.S. Browett, A.O. Sparnenn, S. Mariani, O.S. Wangensteen, I. Coscia & C. Benvenuto. 2019. Environmental DNA Metabarcoding as an Effective and Rapid Tool for Fish Monitoring in Canals. Journal of Fish Biology. 95: 679-682. https://doi.org/10.1111/jfb.14053
McKenna, S.A., G.R. Allen & S. Suryadi. 2002. A Marine Rapid Assessment of the Raja Ampat Islands, Papua Province, Indonesia. RAP Bulletin of Biological Assessment. 22. Conservation International, Washington, DC. 191
Miya, M., Y. Sato, T. Fukunaga, T. Sado, J.Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka &. H. Araki. 2015. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. Royal Society Open Science. 2: 150088. https://doi.org/10.1098/rsos.150088
Nelson, J. 1994. Fishes of the World. in Third edition. John Wiley & Sons, Inc. New York. 600
Nelson, J. 2006. Fishes of the World. in 4th Edition, John Wiley and Sons. Hoboken. 601
Nybakken, J. 1992. Biologi Laut. Suatu Pendekatan Ekologis. PT. Gramedia Pustaka Utama. Jakarta
Panggabean, A. 2012. Condition of coral reef in relation to fish diversity at Gof Kecil and Yep Nabi Islands in Raja Ampat Islands. J. Lit. Perikan. Ind. 18 (2):109-115.
Pratchett, M & M.L. Berumen. 2008. Interspecific variation in distributions and diets of coral reef butterflyfishes (Teleostei: Chaetodontidae). Journal of Fish Biology. 73 (7):1730-1747. https://doi.org/10.1111/j.1095-8649.2008.02062.x
Pyle, R.L., J.L. Earle & B.D. Greene. 2008. Five new species of the damselfish genus Chromis (Perciformes: Labroidei: Pomacentridae) from Deep Coral Reefs in the Tropical Western Pacific. Zootaxa. 1671: 3-31. http://hdl.handle.net/10199/15417
Ratnawati, P., H. Priliska & S. Sukmaraharja. 2011. Kondisi dan potensi komunitas ikan karang di wilayah Kepulauan Kayoa, Kabupaten Halmahera Selatan Maluku Utara. Pengembangan Pulau-Pulau Kecil. 1 (1): 11-22.
Rondonuwu, A.B., J.L. Tombokan & U.N. Rembet. 2013. Distribusi dan kelimpahan ikan karang famili pomacentridae di perairan terumbu karang Desa Poopoh Kecamatan Tombariri Kabupaten Minahasa. Jurnal Ilmiah Platax. 1 (2): 2302-3589.
Rosdianto., O.M. Luthfi, D.K. Saputra & W.A. Maulana. 2021. Relationship of coral reef cover with reef fish abundance in the waters of Miang Island, Sangkulirang, Kutai East, East Kalimantan. Journal of Environmental Engineering & Sustainable Technology. 8 (1): 1-9.
Sato, Y., M. Miya, T. Fukunaga, T. Sado & W. Iwasaki. 2018. MitoFish and MiFish pipeline: A mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Molecular Biology and Evolution. 35 (6): 1553-55. https://doi.org/10.1093/molbev/msy074
Spellerberg, I & J.F. Peter. 2003. A tribute to Claude shannon (1916-2001) and a plea for more rigorous use of species richness, species diversity and the ‘Shannon-Wiener’ index.” Global Ecology and Biogeography. 12 (3): 177-179. https://doi.org/10.1046/j.1466-822X.2003.00015.x
Suwartimah, K., S. Redjeki & R.N.W. Pagripto. 2016. Reef fish community of Pamuteran and Sumber Kima Waters, Buleleng, Bali. Buletin Oseanografi Marina. 5 (1): 73-81. https://doi.org/10.14710/buloma.v5i1.11299
Syafei, L & D. Sudinno. 2018. Invasive alien spesies, sustainability aquatic biodiversity challenges. Jurnal Penyuluhan Perikanan Dan Kelautan. 12 (3): 145-161. https://doi.org/10.33378/jppik.v12i3.106
Takahara, T., T. Minamoto & H. Doi. 2013. Using environmental DNA to estimate the distribution of an invasive fish species in ponds.PLoS ONE. 8 (2): e56584. https://doi.org/10.1371/journal.pone.0056584
Tapilatu, R.F., T.S. Tururaja, S. Sipriyadi & A.B. Kusuma. 2021. Molecular phylogeny reconstruction of grouper (Serranidae: Epinephelinae) at Northern Part of Bird’s Head Seascape - Papua Inferred from COI gene. Fish Aquat Sci. 24 (5): 181-190. https://doi.org/10.47853/FAS.2021.e18
Thomsen, P.F., J. Kielgast, L.L. Iversen, P.R. Møller, M. Rasmussen & E. Willerslev. 2012. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One. 7 (8): p.e41732. https://doi.org/10.1371/journal.pone.0041732
Tony, F., Soemarno, D. G. R. Wiadnya & L. Hakim. 2020. Diversity of reef fish in Halang Melingkau Island, South Kalimantan, Indonesia. Biodiversitas. 21 (10): 4804-4812. https://doi.org/10.13057/biodiv/d211046
Tucker, C.M., M.W. Cadotte, S.B. Carvalho, T.J. Davies, S. Ferrier, S.A. Fritz, R. Grenyer, M.R. Helmus & L.S. Jin. 2017. A guide to phylogenetic metrics for conservation, community ecology and macroecology: A guide to phylogenetic metrics for ecology. Biological Reviews. 92 (2): 698-715. https://doi.org/10.1111/brv.12252
Ushio, M., H. Murakami, R. Masuda, T. Sado, M. Miya, S. Sakurai, H. Yamanaka, T. Minamoto &. M. Kondoh. 2017. Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. BioRxiv. 1-12. https://doi.org/10.1101/113472
White, W.T., P.R. Last, Dharmadi, R. Faizah, U. Chodrijah, B.I. Prisantoso, J.J. Pogonoski, M. Puckridge & S.J.M. Blaber. 2013. Market Fishes of Indonesia (Jenis-Jenis Ikan Di Indonesia). Australian Centre for International Agricu.
Wibowo, K &. M. Adrim. 2013. Komunitas ikan-ikan karang di Teluk Trigi Trenggalek, Jawa Timur. Zoo Indonesia. 22 (2): 29-38. http://dx.doi.org/10.52508/zi.v22i2.320
Wyzer, J.I., S. Hartini & M. Tokede. 2018. Sanitasi pantai dan kualitas perairan Pulau Mansinam pada kondisi arus permukaan monsun timur. Cassowary. 1 (1): 1-20. https://doi.org/10.30862/casssowary.cs.v1.i1.1
Yamamoto, S., R. Masuda, Y. Sato, T. Sado, H. Araki, M. Kondoh, T. Minamoto & M. Miya. 2017. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci. Rep 7: 40368. https://doi.org/10.1038/srep40368
Yanuar, A &. Aunurohim. 2015. Komunitas ikan karang pada tiga model terumbu buatan (artificial reef) di Perairan Pasir Putih Situbondo, Jawa Timur. Jurnal Sains Dan Seni ITS. 4 (1): E19-24. http://dx.doi.org/10.12962/j23373520.v4i1.8947
Yulianto, I., C. Hammer, B. Wiryawan & H. Palm. 2015. Potential and risk of grouper (Epinephelus Spp., Epinephelidae) stock enhancement in Indonesia. Journal of Coastal Zone Management. 18 (1):1-9. http://dx.doi.org/10.4172/jczm.1000394
Zuhdi, M.F., H. Madduppa & N.P. Zamani. 2021. Environmental DNA biomonitoring reveals seasonal patterns in coral reef fish community structure. Research Square. 1-18. https://doi.org/10.21203/rs.3.rs-711425/v1
DOI: https://doi.org/10.22146/jfs.73037
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