Abstract
This study conducted underwater visual census (UVC) and eDNA metabarcoding to survey fish fauna in the coastal waters off Busan (Cheongsapo) and Ulsan (Bangeojin), Southeast sea of Korea, after which the two survey methods were compared. A total of 49 species were identified in Cheongsapo (eDNA metabarcoding: 29 species; UVC: 29 species) and 60 were identified in Bangeojin (eDNA metabarcoding: 43 species; UVC: 30 species), which accounted for 70 species in both areas. Except for 13 species without GenBank sequence data, 80% of the species detected using UVC were detected through eDNA metabarcoding. In addition, eDNA metabarcoding enabled the detection of 33 species that were otherwise not detected by UVC. Thus, eDNA can be used to conduct fast and wide fish diversity surveys and is applicable to microhabitats in coastal areas. Therefore, eDNA could become an important complement to traditional surveys for monitoring marine biodiversity.
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References
Akiyama S, Naganuma M, Katayama S (2009) Annual life cycle of rabbitfish Siganus fuscescens in Tateyama Bay, Chiba prefecture. Fish Eng 46:107–115
Bellwood DR, Alcala AC (1988) The effect of a minimum length specification on visual estimates of density and biomass of coral reef fishes. Coral Reefs 7:23–27
Brock VE (1954) A preliminary report on a method of estimating reef fish populations. J Wildl Manag 18:297–308. https://doi.org/10.2307/3797016
Brock RE (1982) A critique of the visual census method for assessing coral reef fish populations. Bull Mar Sci 32:269–276
Choi KH, Han MH, Kang CK, Park JM, Choi JH, Park JH, Sohn MH, Back GW, Choy EJ, Lee CI (2012) Seasonal variations in species composition of fish assemblage collected by trammel net in coastal waters of the East Sea. J Korean Soc Fish Technol 48:415–427. https://doi.org/10.3796/KSFT.2012.48.4.415
Choi Y, Kim B, Lee HH (2013) The fish fauna of little Munsom in Jeju-do, Korea. Korean J Environ Biol 31:45–52. https://doi.org/10.11626/KJEB.2013.31.1.045
Chyung MK (1977) The fishes of Korea. Iljisa, Seoul, p 727
Cole VJ, Harasti D, Lines R, Stat M (2021) Estuarine fishes associated with intertidal oyster reefs characterized using environmental DNA and baited remote underwater video. Environ DNA 142:123. https://doi.org/10.1002/edn3.190
Davis GE, Anderson TW (1989) Population estimates of four kelp forest fishes and an evaluation of three in situ assessment techniques. Bull Mar Sci 44:1138–1151
Dejean T, Valentini A, Duparc A, Pellier-Cuit S, Pompanon F, Taberlet P, Miaud C (2011) Persistence of environmental DNA in freshwater ecosystems. PLoS ONE 6:e23398. https://doi.org/10.1371/journal.pone.0023398
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. https://doi.org/10.1093/bioinformatics/btq461
Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4:423–425. https://doi.org/10.1098/rsbl.2008.0118
Froese R, Pauly D (2018) FishBase. http://www.fishbase.org Accessed 1 June 2018
Gong Y, Suh YS, Seong KT, Han IS (2010) Climate change and marine ecosystem. Academy Book, Seoul, p 278
Guo X, Miyazawa Y, Yamagata T (2006) The Kuroshio onshore intrusion along the shelf break of the East China Sea: the origin of the Tsushima Warm Current. J Phys Oceanogr 36:2205–2231. https://doi.org/10.1175/JPO2976.1
Han KH, Kim JH, Baek SR (2002) Seasonal variation of species composition of fishes collected by set net in coastal waters of Ulsan, Korea. Korean J Ichthyol 14:61–69
Hänfling B, Handley LL, Read DS, Hahn C, Li J, Nichols P, Blackman RC, Oliver A, Winfield IJ (2016) Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Mol Ecol 25:3101–3119. https://doi.org/10.1111/mec.13660
Harmelin-Vivien ML, Harmelin JG, Chauvet C, Duval C, Galzin R, Lejeune P, Barnabé G, Blanc F, Ghevalier R, Duclerc J, Lasserre G (1985) Evaluation visuelle des peuplements et populations de poissons: methodes et problemes. Rev Ecol 40:467–539
Horinouchi M, Nakamura Y, Sano M (2005) Comparative analysis of visual censuses using different width strip-transects for a fish assemblage in a seagrass bed. Estuar Coast Shelf Sci 65:53–60. https://doi.org/10.1016/j.ecss.2005.05.003
Hwang CH, Park YJ (2017) Seasonal variation of species composition of fish by otter trawl in the coastal waters off Gijang, Busan, Korea. Korean J Fish Aquat Sci 50:429–436. https://doi.org/10.5657/KFAS.2017.0429
Jang PG, Hyun B, Cha HG, Chung HS, Jang MC, Shin K (2013) Seasonal variation of phytoplankton assemblages related to surface water mass in the Eastern part of the South Sea in Korea. Ocean Polar Res 35:157–170. https://doi.org/10.4217/OPR.2013.35.2.157
Jerde CL, Chadderton WL, Mahon AR, Renshaw MA, Corush J, Budny ML, Mysorekar S, Lodge DM (2013) Detection of Asian carp DNA as part of a great lakes basin-wide surveillance program. Can J Fish Aquat Sci 70:522–526. https://doi.org/10.1139/cjfas-2012-0478
Kang JH, Kim YG, Park JY, Kim JK, Ryu JH, Kang CB, Park JH (2014) Comparison of fish species composition collected by set net at Hupo in Gyeong-Sang-Buk-Do, and Jangho in Gang-Won-Do, Korea. Korean J Fish Aquat Sci 47:424–430. https://doi.org/10.5657/KFAS.2014.0424
Kelly RP, Port JA, Yamahara KM, Martone RG, Lowell N, Thomsen PF, Mach ME, Bennett M, Prahler E, Caldwell MR, Crowder LB (2014) Harnessing DNA to improve environmental management. Science 344:1455–1456. https://doi.org/10.1126/science.1251156
KHOA (2018) Korea Ocean Observing and Forecasting System. http://www.khoa.go.kr/koofs/kor/observation/obs_real.do Accessed 15 Jan 2020
Kim BJ, An JH (2010) New record of Blenny Omobranchus loxozonus (Perciformes: Blenniidae) from Jeju Island, Korea. Korean J Ichthyol 22:61–64
Kim YH, Jeon BS, Kang YJ (2000) Seasonal variation in species composition of fish in Suyoung Bay, Korea. Korean J Fish Aquat Sci 33:320–324
Kim MJ, Han SH, Song CB (2010) First record of the Goby Redigobius bikolanus (Perciformes: Gobiidae) from Korea. Korean J Ichthyol 22:206–209
Kim JS, Lee YD, Lee SH, Park JS, Gwak WS (2018) Seasonal variation in fish species composition in the coastal water of Samdong-myeon, Namhae, Korea. Korean J Ichthyol 30:55–64
Kim JH, Jo HB, Chang MH, Woo SH, Cho YH, Yoon JD (2020) Application of environmental DNA for monitoring of freshwater fish in Korea. Korean J Ecol Environ 53:63–72. https://doi.org/10.11614/KSL.2020.53.1.063
Kim IS, Choi Y, Lee CL, Lee YJ, Kim BJ, Kim JH (2005) Illustrated book of Korean fishes. Kyohak Publishing, Seoul, p 515
Kinoshita Y (1935) Hibernation and sleeping of Halichoeres poecilopterus. Zool Soc Jpn 47:795–799
Ko JC, Seo YI, Kim HY, Lee SK, Cha HK, Kim JI (2010) Distribution characteristics of eggs and larvae of the anchovy Engraulis japonica in the Yeosu and Tongyeong coastal waters of Korea. Korean J Ichthyol 22:256–266
Ko JC, Kim BY, Kim MJ, Park SE, Kim JB, Cho HK (2015) A seasonal characteristic of marine environment and fish assemblage in the coastal waters Jeju Island, Korea from 2012 to 2013. J Fish Mar Sci Educ 27:319–344. https://doi.org/10.13000/JFMSE.2015.27.2.319
Kwak SN, Park JM (2016) Fish assemblage in a rocky subtidal habitat around Jam-do, Jinhae. Korean J Ichthyol 28:273–278
Lamy T, Pitz KJ, Chavez FP, Yorke CE, Miller RJ (2021) Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities. Sci Rep 11:1–13. https://doi.org/10.1038/s41598-021-93859-5
Lee DJ, Kang SK, Choi KH, Jung KM (2014) Species composition and seasonal variations of fishes collected by set net in coastal waters of Gijang, Korea. Korean J Fish Aquat Sci 47:983–996. https://doi.org/10.5657/KFAS.2014.0983
Lee SJ, Kim MJ, Han SH (2019) Reproductive ecology of rabbit fish, Siganus fuscescens in the coastal waters off Jeju Island of Korea. J Korean Soc Fish Ocean Technol 55:349–355. https://doi.org/10.3796/KSFOT.2019.55.4.349
Lie HJ, Cho CH (2002) Recent advances in understanding the circulation and hydrography of the East China Sea. Fish Oceanogr 11:318–328. https://doi.org/10.1046/j.1365-2419.2002.00215.x
Mahon AR, Jerde CL, Galaska M, Bergner JL, Chadderton WL, Lodge DM, Hunter ME, Nico LG (2013) Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLoS ONE 8:e58316. https://doi.org/10.1371/journal.pone.0058316
Min MA, Barber PH, Gold Z (2021) MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes). Conserv Genet Resour 13:447–456. https://doi.org/10.1007/s12686-021-01219-2
Minamoto T, Yamanaka H, Takahara T, Honjo MN, Kawabata Z (2012) Surveillance of fish species composition using environmental DNA. Limnology 13:193–197. https://doi.org/10.1007/s10201-011-0362-4
Mitani I (2000) A view on warming of sea surface temperature in Sagami Bay. Kanagawa Pref Fish Res Agen 5:71–75
Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Soc Open Sci 2:150088. https://doi.org/10.1098/rsos.150088
Miya M, Minamoto T, Yamanaka H, Oka SI, Sato K, Yamamoto S, Sado T, Doi H (2016) Use of a filter cartridge for filtration of water samples and extraction of environmental DNA. J Vis Exp 117:54741. https://doi.org/10.3791/54741
Nakamura Y, Sano M (2004) Comparison between community structures of fishes in Enhalus acoroides- and Thalassia hemprichii-dominated seagrass beds on fringing coral reefs in the Ryukyu Islands, Japan. Ichthyol Res 51:38–45. https://doi.org/10.1007/s10228-003-0191-5
Nakazono A (2002) Fate of tropical reef fish juveniles that settle to a temperate habitat. Fish Sci 68:127–130. https://doi.org/10.2331/fishsci.68.sup1_127
Oksanen J (2013) Vegan: ecological diversity. R Project 368:1–11
Park JH, Kim JK, Choi JH, Choi YM (2008) First record of a Jawfish, Opistognathus hongkongiensis (Opistognathidae: Perciformes) from Korea. Korean J Ichthyol 20:74–77
Park JM, Baeck GW, Huh SH (2018) Variations in demersal fish assemblage in the Southern coast of East Sea, Korea. Korean J Fish Aquat Sci 51:426–434. https://doi.org/10.5657/KFAS.2018.0426
Polanco Fernández A, Marques V, Fopp F, Juhel JB, Borrero-Pérez GH, Cheutin MC, Dejean T, González Corredor JD, Acosta-Chaparro A, Hocdé R, Eme D, Maire E, Spescha M, Valentini A, Manel S, Mouillot D, Albouy C, Pellissier L (2021) Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environ DNA 3:142–156. https://doi.org/10.1002/edn3.140
Shimizu N, Kadota T, Tsuboi M, Sakai Y (2010) Fish fauna in the coastal area of Kurahashi Island, Seto Inland Sea, Japan. Bull Hiroshima Univ Mus 2:43–52
Sigsgaard EE, Carl H, Møller PR, Thomsen PF (2015) Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples. Biol Conserv 183:46–52. https://doi.org/10.1016/j.biocon.2014.11.023
Song YK, Kim JH, Won SY, Park C (2019) Possibility in identifying species composition of fish communities using the environmental DNA metabarcoding technique. J Korean Env Res Technol 22:125–138. https://doi.org/10.13087/kosert.2019.22.6.125
Stat M, John J, DiBattista JD, Newman SJ, Bunce M, Harvey ES (2019) Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity. Conserv Biol 33:196–205. https://doi.org/10.1111/cobi.13183
Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH (2012) Environmental DNA. Mol Ecol 21:1789–1793. https://doi.org/10.1111/j.1365-294X.2012.05542.x
Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata ZI (2012) Estimation of fish biomass using environmental DNA. PLoS ONE 7:e35868. https://doi.org/10.1371/journal.pone.0035868
Thomsen PF, Møller PR, Sigsgaard EE, Knudsen SW, Jørgensen OA, Willerslev E (2016) Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes. PLoS ONE 11:e0165252. https://doi.org/10.1371/journal.pone.0165252
Toshihiro S, Hironori U (2012) Predation on the short-neck clam Ruditapes philippinarum by intertidal fishes: a list of fish predators. J Fish Technol 5:1–19
Watanabe T (1982) Distribution of eggs and larvae of metric migratory fish in relation to the Kuroshio. Bull Coast Oceanogr 19:149–162
Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE 8:e59520. https://doi.org/10.1371/journal.pone.0059520
Yamamoto S, Masuda R, Sato Y, Sado T, Araki H, Kondoh M, Minamoto T, Miya M (2017) Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci Rep 7:1–12. https://doi.org/10.1038/srep40368
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Funding was provided by the National Research Foundation of Korea Grant (NRF-2016R1D1A1B03931588).
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Lee, YD., Lee, GM., Park, JY. et al. Comparing Environmental DNA Metabarcoding and Underwater Visual Census to Monitor Korean Coastal Fish Community. Ocean Sci. J. 57, 592–606 (2022). https://doi.org/10.1007/s12601-022-00082-y
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DOI: https://doi.org/10.1007/s12601-022-00082-y