Journal of Environmental Impact Assessment (환경영향평가)

Korean Society of Environmental Impact Assessment (한국환경영향평가학회)
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Identification of Freshwater Fish Species in Korea Using Environmental DNA Technique - From the Experiment at the Freshwater Fish Ecological Learning Center in Yangpyeong, Gyeonggi Do -

환경DNA 기술을 이용한 국내 담수어류종 탐지 가능성 - 경기도 민물고기생태학습관 중심으로 -

  • Kim, Gawoo (Dept. of Landscape Architecture, Graduate School of Environmental Studies, Seoul National University) ;
  • Song, Youngkeun (Dept. of Landscape Architecture, Graduate School of Environmental Studies, Seoul National University)
  • 김가우 (서울대학교 환경대학원 환경조경학과) ;
  • 송영근 (서울대학교 환경대학원 환경조경학과)
  • Received : 2020.09.10
  • Accepted : 2021.02.08
  • Published : 2021.02.28
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Abstract

This study focused on verifying the identification of freshwater fish species in Korea using Environmental DNA (eDNA) technique. The research of DNA is increasing in the field of ecology, since this is more sensitive of identify rather than traditional investigation method. Which is difficult to detect species hidden in water and be easily influenced by diverse factors (sites, bad weather, researchers and so on). We applied the pilot test in aquarium (Freshwater Fish Ecological Learning Center in Yangpyeong, Gyeonggi Do), where freshwater fish species are inhabits. We conducted to sampling and analyzing the sixteen water samples (50 species from 7 orders and 13 families) using MiFish primer set. The results showed that 45 species (90%) was investigated by eDNA. It highlight that eDNA with universal primer is possible to detect freshwater fish species of Korean. However, the errors on species identification seems to be caused by the primer that be not suited perfectly and the pollution such as aquarium, sampling collectors.

본 연구는 환경DNA 기술을 이용한 국내 담수어류종 탐지방법 도입 및 적용가능성을 확인하기 위해 수행되었다. 환경DNA를 이용한 모니터링 기술은 기존의 현장조사 모니터링 방식에 비하여 교란이 적고 편의성이 높으며 조사에 대한 감도가 높아 급변하는 하천 생태계 모니터링을 위한 효율적인 방법으로 주목받고 있다. 본 연구의 대상지는 경기도 민물고기 생태학습관으로 수족관 내 수조, 생태연못, 양식장에 서식하는 국내 대표적 담수어류종에 대해 7월부터 10월까지 3차례의 물 환경시료를 수집하여 환경DNA 분석을 실시하였다. 국내 담수생태계의 다양한 서식환경을 고려하여 선정된 종에 대해 기 구축된 유전자생물종 DNA 염기서열 특성을 검토하고, 종 검출 여부 확인을 위해 채수된 16개의 환경시료를 Miya et al(2015)에서 제시된 환경DNA 분석 프로토콜에 준하여 분석하였다. 그 결과 대상 어종 총 7목 11과 50종 중 7목 11과 45종(90%)이 검출되었다. 이는 환경DNA 기술과 기 구축된 어류종 DNA DB를 활용하여 다양한 환경조건에서도 단순한 채수 샘플링으로부터 국내 서식하고 있는 주요 민물고기 어종이 검출되었다는 점에서 의의가 있다. 나아가 실험 중 발생된 수족관 내 시료 오염, 불균질한 DNA 채집, 생물종 유전자정보 누락 등의 오차요인들을 분석하여 자연환경에서 적용 시 앞으로의 보완 방향에 대하여 제시하였다.

Keywords

References

  1. Alice V, Francois P, Pierre T. 2009. DNA bar oding for ecologists. Trends in Ecology & Evolution 24(2): 110-117. https://doi.org/10.1016/j.tree.2008.09.011
  2. Ficetola GF, Miaud C, Pompanon F, Taberlet P. 2008. Species detection using environmental DNA from water samples. Biology Letter 4(4): 423-425. https://doi.org/10.1098/rsbl.2008.0118
  3. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessiere J, Taberlet P, Pompanon F. 2010. An in silico approach for the evaluation of DNA barcodes. BMC Genomics 11(434): 2-8. https://doi.org/10.1186/1471-2164-11-2
  4. Fukumoto S, Shimaru A and Minamoto T. 2015. A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan. Journal of Applied Ecology 52(2): 358-365. https://doi.org/10.1111/1365-2664.12392
  5. Hopkins GW, Freckleton RP. 2002. Declines in the numbers of amateur and professional taxonomists: implications for conservation. Animal Conservation 5: 245-249. https://doi.org/10.1017/S1367943002002299
  6. Kim HM, Kim SY, Park YS, Lee HJ, Kim KT, Kim Y, Kim HJ, Kawk MH, Lim TY, Park C, Song WK. 2020. Review and application of environmental DNA (eDNA) investigation of terrestrial species in urban ecosystem. The Korea Society of Environmental Restoration Technology 23(2): 69-89. [Korean Literature]
  7. Magoc T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21): 2957-2963. https://doi.org/10.1093/bioinformatics/btr507
  8. Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, S 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 Society Open Science 2(7): p. 3-34.
  9. Nelson JS. 1994. Fishes of the world. 3rd edn Wiley, New York, p. 600.
  10. Naiman R, Prieur-Richard A, Arthington A, Dudgeon D, Gessner M, Kawabata Z, Knowler D, O'Keefe J, Leveque C, Soto D, Stiassny M, Sullivan C. 2006. Challenges for freshwater biodiversity research : Science plan and implementation strategy. DIVERSITAS, Report No. 5. DIVERSITAS, Paris, pp. 13-15.
  11. Rees HC, Maddison BC, Middleditch DJ, Patmore JR, Gough KC. 2014. The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology. Journal of Applied Ecology 51: 1450-1459. https://doi.org/10.1111/1365-2664.12306
  12. Song YK, Kim JH, Won SY, Park C. 2019. Possibility in identifying species composition of fish communities using the environmental DNA metabarcoding technique - with the preliminary results at urban ecological streams. The Korea Society of Environmental Restoration Technology 22(6): 125-138. [Korean Literature]
  13. Thomsen PF, Willerslev E. 2015. Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity, Biological Conservation 183: 4-18. https://doi.org/10.1016/j.biocon.2014.11.019
  14. Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z. 2012. Estimation of fish biomass using environmental DNA. PLoS ONE. 7(4): e35868(1)-e35868(9). https://doi.org/10.1371/journal.pone.0035868
  15. Takahara T, Minamoto T, Doi H. 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
  16. Wheeler Q, Raven P, Wilson E. 2004. Taxonomy: impediment or expedient. Science 303: 285. https://doi.org/10.1126/science.303.5656.285
  17. 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. Scientific Reports 7(40368): 2-11. https://doi.org/10.1038/s41598-017-00046-6