Browse > Article
http://dx.doi.org/10.13087/kosert.2020.23.2.69

Review and application of environmental DNA (eDNA) investigation of terrestrial species in urban ecosystem  

Kim, Whee-Moon (Dept. of Environmental Horticulture and Landscape Architecture, Dankook University)
Kim, Seoung-Yeal (Dept. of Environmental Horticulture and Landscape Architecture, Dankook University)
Park, Il-Su (Dept. of Environmental Horticulture and Landscape Architecture, Dankook University)
Lee, Hyun-Jung (School of Environmental Horticulture and Landscape Architecture, Dankook University)
Kim, Kyeong-Tae (School of Environmental Horticulture and Landscape Architecture, Dankook University)
Kim, Young (School of Environmental Horticulture and Landscape Architecture, Dankook University)
Kim, Hye-Joung (School of Environmental Horticulture and Landscape Architecture, Dankook University)
Kwak, Min-Ho (School of Environmental Horticulture and Landscape Architecture, Dankook University)
Lim, Tae-Yang (Dept. of Environmental Horticulture and Landscape Architecture, Dankook University)
Park, Chan (Dept. of Landscape Architecture, University of Seoul)
Song, Won-Kyong (School of Environmental Horticulture and Landscape Architecture, Dankook University)
Publication Information
Journal of the Korean Society of Environmental Restoration Technology / v.23, no.2, 2020 , pp. 69-89 More about this Journal
Abstract
Scientific trust and quantification of traditional species investigation and results that have been used in ecology for decades has always been a problem and concern for ecologists. Global ecologists have proposed DNA-based species investigation studies to find answers to problems. In this study, we reviewed the global trend of research on environmental DNA(eDNA), which is a method for monitoring species by detecting DNA of organisms naturally mixed in environmental samples such as water, soil, and feces. The first eDNA research confirmed the possibility of species investigation at the molecular level, and commercialization of NGS(Next Generation Sequencing) and DNA metabarcoding elicits efficient and quantitative species investigation results, and eDNA research is increasing in the filed of ecology. In this study, mammals and birds were detected using MiMammal universal primers from 23 samples(3 natural reserves; 20 water bowls) out of 4 patches to verify eDNA for urban ecosystems in Suwon, and eDNA was verified by performing camera trapping and field survey. Most terrestrial species were detected through eDNA, and particularly, mice(Mus musculus), and Vinous-throated Parrotbill (Sinosuthora webbiana) were identified only with eDNA, It has been confirmed to be highly effective by investigating techniques for small and internal species. However, due to the lack of resolution of the primer, weasels(Mustela sibirica) and squirrels(Melanochromis auratus) were not detected, and it was confirmed that the traditional investigation method was effective only for a few species, such as Mogera robusta(Mogera robusta). Therefore, it is judged that the effects of species investigation can be maximized only when eDNA is combined with traditional field survey and Camera trapping to complement each other.
Keywords
DNA Metabarcoding; PCR(Polymerase chain reaction); Camera trapping; OTU(Operational Taxonomic Unit); MiMammal; NGS(Next Generation Sequencing); Suwon city;
Citations & Related Records
Times Cited By KSCI : 8  (Citation Analysis)
연도 인용수 순위
1 Rodger, TW and KE Mock. 2015. Drinking water as a source of environmental DNA for the detection of terrestrial wild life species. Conservation Genetics Resources. 7 : 693-696.   DOI
2 Ruppert, K. RJ Kline. 2019. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation 17: e00547.   DOI
3 Saiki, RK. S Scharf and F Faloona. 1985. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230(4732) : 1350-1354.   DOI
4 Sales, NG. MB McKenzie. J Drake. LR Harper. SS Browett. I Coscia. OW Wangensteen. C Baillie. E Bryce. DA Dawson. E Ochu. B Hanfling. LL Handley. S Mariani. X Lambin. C Sutherland and AD McDevitt. 2020. Fishing for mammals: Landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from riverine systems. Journal of Applied Ecology. 57(4) : 707-716.   DOI
5 Sato, Y. M Miya. T Fukunaga. T Sado and W Iwasaki. 2018. MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding. Mol. Biol. Evol. 35(6) : 1553-1555.   DOI
6 Schmidt, DJ. C McDougall. 2018. Complete mitogenomes of five ecologically diverse Australian freshwater fishes. Mitochondrial DNA Part B. 4(1) : 191-193.   DOI
7 Riaz, T. W Shehzad. A Viari. F Pompanon. P Taberlet and E Coissac. 2011. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research 39(21) : e145.   DOI
8 Shapiro, B. 2008. Engineered polymerases amplify the potential of ancient DNA. Trends Biotechnol. 26(6) : 285-287.   DOI
9 Bergmann, GT. JM Craine. MS Robeson 2nd and N Fierer. 2015. Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison). PLoS One 10(11) : e0142409.   DOI
10 Shendure, J and H ji. 2008. Next-generation DNA sequencing. Nature Biotechnology 26(10) : 1135-1145.   DOI
11 Song, WK. 2020. Home Range Analysis of Great Tit (Parus major) before and after Fledging in an Urban Park. J. Korean Env. Res. Tech. 23(1) : 97-106. (in Korean with English summary)
12 Song, WK. EY Kim and DK Lee. 2012. Measuring Connectivity in Heterogenous Landscapes: a Review and Application. Journal of Environmental Impact Assessment. 21(3) : 391-407.   DOI
13 Song, YK. JH Kim. SY Won and C Park. 2019. Possibility in identifying species composition of fish communities using the environmental DNA metabarcoding technique. J. Korean Env. Res. Tech. 22(6) : 125-138. (in Korean with English summary)
14 Staley, ZR. JD Chuong. SJ Hill. J Grabuski. S Shokralla. M Hajibabaei and TA Edge. 2018. Fecal source tracking and eDNA profiling in an urban creek following an extreme rain event. Scientific reports 8(14390) : 1-12.   DOI
15 Stokes, KE. KP O’Neill. WI Montgomery. JTA Dick. CA Maggs and RA McDonald. 2006. The importance of stakeholder engagement in invasive species management: a cross-jurisdictional perspective in Ireland. Biodivers Conserv 15(8) : 2829-2852.   DOI
16 Taberlet, P. E Coissac. M Hajibabaei and LH Rieseberg. 2012a. Environmental DNA. Molecular Ecology 21(8) : 1789-1793.   DOI
17 Taberlet, P. S Prud'homme. E Campione. J Roy. C Miquel. W Shehzad. L Gielly. D Rioux. P Choler. JC Clement. C Melodellima. F Pompanon and E Coissac. 2012b. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Mol. Ecol. 21(8) : 1816-1820.   DOI
18 Tarberlet, P. A Bonin. L Zinger and E Coissac. 2018. Environmental DNA : For Biodiversity Research and Monitoring. Oxford Univ Press.
19 Boessenkool, S.LS Epp. J Haile. E Bellemain. M Edwards. E Coissac. E Willerslev and C Brochmmann. 2012. Blocking Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA. Molecular Ecology. 21(8) : 1806-1815.   DOI
20 Bithell, SL.LTT Tran-Nguyen.MN Hearnden and DM Hartley. 2014. DNA analysis of soil extracts can be used to investigate fine root depth distribution of trees. AoB Plants. 7. plu091.
21 Brenner, S. M Johnson. J Bridgham. G Golda. DH Lloyd. D Johnson. S Luo. S McCurdy. M Foy. M Ewan. R Roth. D George. S Eletr. G Albrecht. E Vermaas. SR Williams. K Moon. T Burcham. M Pallas. RB DuBridge. J Kirchner. K Fearon. J Mao and K Corcoran. 2000. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology 18(6) : 630- 634.   DOI
22 Caporaso, JG. J Kuczynski. J Stombaugh. K Bittinger. FD Bushman. EK Costello. N Fierer. AG Pea. JK Goodrich. JI Gordon. GA Huttley. ST Kelley. D Knights. JE Koenig. RE Lay. CA Lozupone. D McDonald. BD Muegge. M Pirrung. J Reeder. PJ Turnbaugh and WA Walters. 2010. QIIME allows analysis of highthroughput community sequencing data. Nature Methods. 7(5) : 335-336.   DOI
23 Chen, S. Y Zhou. Y Chen and J gu. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17) : i884-i890.   DOI
24 Civade, R. T Dejean. A Valentini. N Roset. JC Raymond. A Bonin. P Taberlet and D Pont. 2016. Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System. PLoS ONE. 11(6): e0157366.   DOI
25 Valentini, A. P Taberlet. C Miaud. R Civade. J Herder. PF Thomsen. E Bellemain. A Besnard. E Coissac. F Boyer. C Gaboriaud. P Jean. N Poulet. N Roset. GH Copp. P Geniez. D Pont. C Argillier. JM Baudoin. T Peroux. AJ Crivelli.A Olivier. M Acqueberge. M Le Brun. PR Moller. E Willerslev and T Dejean. 2016. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol. Ecol. 25(4) : 929-942.   DOI
26 Turner, CR. KL Uy. RC Everhart. 2015. Fish environmental DNA is more concentrated in aquatic sediments than surface water. Biological Conservation 183 : 93-102.   DOI
27 Ushio, M. H Fukuda. T Inoue. K Makoto. O Kishida. K Sato. K Murata. M Nikaido. T Sado. Y Sato. M Takeshita. W Iwasaki. H Yamanaka. M Kondoh and M Miya. 2017. Environmental DNA enables detection of terrestrial mammals from forest pond water. Mol. Ecol. Resour. 17(6) : e63-e75.   DOI
28 Valentini, A. C Miquel and MA Nawaz. 2009. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Mol. Ecol. 9(1) : 51-60.   DOI
29 Valiere, N and P. Taberlet. 2000. Urine collected in the field as a source of DNA for species and individual identification. Mol. Ecol. Resour. 9(12) : 2150-2152.   DOI
30 Watson, JD and FHC Crick. 1953. Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature 171(4356) : 737-738.   DOI
31 Willerslev, E. AJ Hansen and J Binladen. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300(5620) : 791-795.   DOI
32 Yang, C. X Wang. JA Miller. M de Blecourt. Y Ji. C Yang. RD Harrsion and DW Yu. 2014. Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator. Ecological Indicators. 46 : 379-389.   DOI
33 Drummond, AJ. RD Newcomb. TR Buckley. D Xie. A Dopheide. BCM Potter. J Heled. HA Ross. S Grosser. D Park. NJ Demetras. MI Stevens. JC Russell. SH Anderson. A Carter and N Nelson. 2015. Evaluating a multigene environmental DNA approach for biodiversity assessment. Giga-Science. 4(46) : 1-19.
34 Zhang, H. S Yoshizawa. W Iwasaki and W Xian. 2019. Seasonal Fish Assemblage Structure Using Environmental DNA in the Yangtze Estuary and Its Adjacent Waters. Front. Mar. Sci. 6 : 515.   DOI
35 Closek, CJ. JA Santora. HA Starks. ID Schroeder. EA Andruszkiewicz. KM Sakuma. SJ Bograd. EL Hazen. JC Field and AB Boehm. 2019. Marine Vertebrate Biodiversity and Distribution Within the Central California Current Using Environmental DNA (eDNA) Metabarcoding and Ecosystem Surveys. Front. Mar. Sci. 6 : 732.   DOI
36 Clusa, L. L Miralles. A Basanta. C Escot and E Garcia-Vazquez. 2017. eDNA for detection of five highly invasive molluscs. A case study in urban rivers from the Iberian Peninsula. PLoS ONE 12(11) : e0188126.   DOI
37 Degle, BE. A Chiaradia. J McInnes and SN Jarman. 2010. Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?. Conservation Genetics 11(5) : 2039-2048.   DOI
38 Dejean, T. A Valentini. A Duparc. S Pellier-Cuit. F Pompanon. P Taberlet and C Miaud. 2011. Persistence of Environmental DNA in Freshwater Ecosystems. PLoS One 6(8) : e23398.   DOI
39 Evans, NT. BP Olds and MA Renshaw. 2016. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol. Ecol. Resour. 16(1) : 29-41.   DOI
40 Ficetola, GF. C Miaud. F Pompanon and P Taberlet. 2008. Species detection using environmental DNA from water samples. Biology Letters 4(4) : 423-425.   DOI
41 Ficetola, GF. P Taberlet and E Coissac. 2016. How to limit false positives in environmental DNA and metabarcoding? Molecular Ecology Resources 16(3) : 604-607.   DOI
42 Harper, LR. LL Handley. AI Carpenter. M Ghazali. CD Muri. CJ Macgregor. TW Logan. A Law. T Breithaupt. DS Read. AD McDevitt and B Hanfling. 2019. Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals. Biological Conservation 238 : 108225.   DOI
43 Zhang, Z. S Schwartz. L Wagner and W Miller. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational biology 7(1-2) : 203-214.   DOI
44 Zinger, L. J Chave. E Coissac. A Iribar. E Louisanna. S Manzi. V Schilling. H Schimann. G Sommeria-Klein and P Taberlet. 2016. Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA. Soil Biology & Biochemistry. 96 : 16-19.   DOI
45 Giguet-Covex, C. J Pansu. F Arnaud. PJ Rey. C Griggo. L Gielly. I Domaizon. E Coissac. F David. P Choler. J Poulenard and P Taberlet. 2014. Long livestock farming history and human landscape shaping revealed by lake sediment DNA. Nature communications. 5 : 3211.   DOI
46 Giovannoni, SJ. TB Britschgi. CL Moyer and KG Field. 1990 Genetic diversity in Sargasso Sea bacterioplankton. Nature 345(6270) : 60-63   DOI
47 Haile, J. R Holdaway. K Oliver. M Bunce. MTP Gilbert. R Nielsen. K Munch. SYW Ho. B Shaprio and E Willerslev. 2007. Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Molecular Biology and Evolution. 24(4) : 982-989.   DOI
48 Hempel, CA. B Peinert. AJ Beermann. V Elbrecht. JN Macher. TH Macher. G Jacobs and F Leese. 2019. Using environmental DNA to monitor the reintroduction success of the Rhine sculpin (Cottus rhenanus) in a restored stream. PeerJ Preprints 7:e27574v2.
49 Herbert, PD. A Cywinska. SL Ball and JR DeWaard. 2003. Biological identifications through DNA barcodes. Proc. Biol. Sci. 270(1512) : 312-321.
50 Kim, KT. Y Kim. HJ Kim. SY Kim. WM Kim and WK Song. 2019. Usage of Waterbirds on the Artificial Floating Islands in Reservoir using UAV. J. Korean Env. Res. Tech. 22(5):57-67. (in Korean with English summary)
51 Logan, JMJ. KJ Edwards and NA Saunders. 2009. Real-time PCR : current technology and applications. Horizon Scientific Press, Norwich, UK.
52 Kim, SY. WM Kim. WK Song and EJ Hyeong. 2018. Home-range Analysis of Varied Tit (Parus varius) in the Post Fledging Period by Using Radio-tracking. J. Korean Env. Res. Tech. 21(1):95-102. (in Korean with English summary)
53 Lahoz-Monfort, JJ. G Guillera-Arroita and R Tingley. 2016. Statistical approaches to account for false-positive errors in environmental DNA samples. Molecular Ecology Resources 16(3) : 673-685.   DOI
54 Leempoel, K. T Hebert and EA Hadly. 2020. A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity. Proc. R. Soc. B 287 : 20192353.   DOI
55 Levine, JM. M Vila. CM D'Antonio. JS Dukes. K Grigulis and S Lovorel. 2003. Mechanisms underlying the impacts of exotic plant invasions. Proc. R. Soc. B. 270(1517) : 775-781.   DOI
56 Li, W. L Fu. B Niu. S Wu and J Wooley. 2012. Ultrafast clustering algorithms for metagenomic sequence analysis. Briefings in Bioinformatics. 13(6) : 656-668.   DOI
57 Lopes, DM. MD Barba. F Boyer. C Mercier. PJS Filho. LM Heidtmann. D Galiano. BB Kubiak. P Langone. FM Garcias. L Gielly. E Coissac. TRO Freitas and D Taberlet. 2015. DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents. Heredity 114(5) : 525-536.   DOI
58 Lucek, K. A Galli. S Gurten. N Hohmann. A Maccagni. T Patsiou and Y Willi. 2019. Metabarcoding of honey to assess differences in plantpollinator interactions between urban and non-urban sites. Apidologie 50 : 317-329.   DOI
59 Kelly, RP. 2016. Making Making environmental DNA count. Molecular ecology resources 16(1) : 10-12.   DOI
60 Krishnamurthy, K and AF Robert. 2012. A critical review on the utility of DNA barcoding in biodiversity conservation. Biodivers. Conserv. 21(8) : 1901-1919.   DOI
61 Kwok, S and R Higuchi. 1989. Avoiding false positives with PCR. Nature. 339(6221) : 237-238.   DOI
62 Margulies, M. M Egholm. WE Altman. S Attiya. JS Bader. LA Bemben. J Berka. MS Braverman. YJ Chen. Z Chen. SB Dewell. L Du. JM Fierro. XV Gomes. BC Godwin. W He. S Helgesen. CH Ho. GP Irzyk. SC Jando. MLI Alenquer. TP Jarvie. KB Jirage. JB Kim. JR Knight. JR Lanza. JH Leamon. SM Lefkowitz. M Lei. J Li. KL Lohman. H Lu. VB Makhijani. KE McDade. MP McKenna. EW Myers. E Nickerson. JR Nobile. R Plan. BP Puc. MT Ronan. GT Roth. GJ Sarkis. JF Simons. JW Simpson. M Srinivasan. KR Tartaro. A Tomasz. KA Vogt. GA Volkmer. SH Wang. Y Wang. MP Weinr. P Yu. RF Begley and JM Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057) : 376-380.   DOI
63 MacDonald, AJ and S Sarre. 2017. A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA. Molecular Ecology Resources 17(4) : 708-720.   DOI
64 Magoc, T and SL, Salzberg. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21) : 2957-2963.   DOI
65 Magurran, AE and BJ McGill. 2011. Biological diversity-frontiers in measurement and assessment. Oxford University Press.
66 Minamoto, T. M Fukuda. KR Katsuhara. A Fujiwara. S Hidaka and S Yamamoto. 2017. Environmental DNA reflects spatial and temporal jellyfish distribution. PLoS One 12(2) : e0173073.   DOI
67 Ministry of Environment. 2012. Fourth National Survey on Natural Environment. (in Korean).
68 NIER(National In stitute of En viro nmen ta l Research). 2015. Developing guidelines of biotop maps for spatial planning. South Korea. (in Korean with English summary)
69 Ministry of Environment. 2017. Revision of regulations on preparation of environmental impact assessments, etc. (in Korean).
70 Miya, M. Y Sato. T Fukunaga. T Sado. JY Poulsen. K Sato. T Minamoto. S Yamamoto. H Yamanaka. H Araki. M Kondoh and W Iwasaki. 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) : 150088.   DOI
71 Riaz, T. W Shehzad. A Viari. F Pompanon. P Taberlet and E Coissac. 2011. ecoPrimerts : inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res. 39(21) : e145.   DOI
72 Ogram, A.GS Sayler and T Barkay. 1987. The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods 7(2-3) : 57-66.   DOI
73 Oskam, CL. J Haile. E McLay. P Rigby. ME Allentoft. ME Olsen. C Bengtsson. GH Miller. J-L Schwenninger. C Jacomb. R Walter. A Baynes. J Dortch. M Parker-Peason. MTP Gilbert. RN Holdaway. EWillerslev and M Bunce. 2010. Fossil avian eggshell preserves ancient DNA. Proceedings of the Royal Society B. 277(1690) : 1991-2000.   DOI
74 Pansu, J. C Giguet-Covex. GF Ficetola. L Gielly. F Boyer. L Zinger. F Arnaud. J Poulenard. P Taberlet and P Choler. 2015. Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. Mol. Ecol. 24(7) : 1485-1498.   DOI
75 Patel, S. J Waugh. CD Millar and DM Lambert. 2010. Conserved primers for DNA barcoding historical and modern samples from New Zealand and Antarctic birds. Molecular Ecology Resources 10(3) : 431-438.   DOI
76 Pompanon, F. E Coissac and P Taberlet. 2011. Metabarcoding a new way to analyze biodiversity. Biofutur. 319(3) : 30-32.
77 Mullis, KB and FA Faloona. 1987. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in enzymology 155 : 335-350.   DOI
78 Potgieter, LJ. M Gaertner. C Kueffer. BMH Larson. SW Livingstone. PJ O’Farrell and DM Richardson. 2017. Alien plants as mediators of ecosystem services and disservices in urban systems: a global review. Biol Invasions 19(12) : 3571-3588.   DOI
79 Barnes, MA and CR Turnet. 2016. The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics. 17 : 1-17.   DOI
80 Andersen, K. KL Bird. M Rasmussen. J Haile. H Breuning-Madsen. KH Kjaer. L Orlando. MTP Gilbert and E Willerslev. 2012. Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity. Molecular Ecology 21(8) : 1966-1979.   DOI