Kim K, Kwon S, Noh A. Detection of frog and aquatic insects by environmental DNA in paddy water ecology. Korean Journal of Agricultural Science 50:299-312.
Korean Journal of Agricultural Science (Korean J. Agric. Sci.) 2023 June, Volume 50, Issue 2, pages 50:299-312. https://doi.org/10.7744/kjoas.20230021
Received on 03 February 2023, Revised on 28 February 2023, Accepted on 26 April 2023, Published on 30 June 2023.
Keonhee Kim1,*, Sera Kwon2, Alongsaemi Noh1
1Human and Eco Care Center, Konkuk University, Seoul 05029, Korea
2Department of Eco Science, Ehwa Woman University, Seoul 03760, Korea
*Corresponding author: passbosko@gmail.com
The paddy environment is classified as a wetland and occupies a very large proportion of the freshwater environment. It is also ecologically important as a habitat and spawning ground for many aquatic insects and amphibian larvae. However, due to climate change and indiscriminate spraying of pesticides, the rice field ecosystem is continuously threatened. In order to restore ecologically damaged rice paddies in the future, information on organisms living in the rice paddy ecosystem, which can serve as a restoration standard, is needed. The eDNA metabarcoding analysis method is a very effective means of accumulating information on many organisms living in the rice field ecosystem because it can indirectly identify the existence of taxa that are no longer found in the target ecosystem due to different adult life periods or metamorphosis. In this study, genes of four species of frogs and nine species of aquatic insects were also discovered, and some taxa were directly discovered in the field. A large number of taxa have been discovered only by DNA searches, and traditional survey methods have only been able to identify very limited taxa. This eDNA-based paddy field biosearch is expected to be very useful in the investigation of biodiversity in agricultural ecosystems due to its strong analytical resolution.
Amphibia, aquatic insect, detection, eDNA, paddy environment
Bang HS, Han MS, Na YE, Kang KK. 2010. Presented at the marco symposium 2009 ‘challenges for agro-environmental research in monsoon asia’. National Institute for Agro-Environmental Sciences, Tsukuba, Japan.
Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM. 2014. Environmental conditions influence edna persistence in aquatic systems. Environmental Science & Technology 48:1819-1827.
Barrett A, Brown L. 2021. Effects of rainfall, temperature and photoperiod on the phenology of ephemeral resources for selected bushveld woody plant species in southern Africa. PLOS One 16:e0251421.
Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Douglas WY, De Bruyn M. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution 29:358-367.
Borzée A, Jang Y. 2015. Description of a seminatural habitat of the endangered suweon treefrog hyla suweonensis. Animal Cells and Systems 19:216-220.
Borzée A, Park S, Kim A, Kim HT, Jang Y. 2013. Morphometrics of two sympatric species of tree frogs in Korea: A morphological key for the critically endangered Hyla suweonensis in relation to H. Japonica. Animal Cells and Systems 17:348-356.
Edmunds RC, Cooper M, Huerlimann R, Robson H, Burrows D. 2019. Environmental DNA survey of eureka creek, upper mitchell, and walsh river for two invasive tilapia species. Jamescook University, Townsville, Austrailia.
Eea JW, Kim MH, Song YJ, Kim ST, Lee JH, Jang IK, Kweon SR, Kang HK, Kim Yi. 2019. Survey on the current status of biodiversity and phenology for impact assessment to climate change. Rural Development Administration, Wanju, Korea.
Ficetola GF, Miaud C, Pompanon F, Taberlet P. 2008. Species detection using environmental DNA from water samples. Biology Letters 4:423-425.
Goldberg CS, Pilliod DS, Arkle RS, Waits LP. 2011. Molecular detection of vertebrates in stream water: A demonstration using rocky mountain tailed frogs and idaho giant salamanders. PLOS One 6:e22746.
Groffen J, Andersen D, Borzée A. 2022. Breeding phenology and landscape use in all amphibian species from the republic of Korea based on open-source data. Frontiers in Environmental Science 10:1641.
Günther R. 1996. Die amphibien und reptilien deutschlands. Springer Spektrum, Berlin, Germany.
Ham C. 2014. Morphology, age structure and mating call characteristics of japanese tree frog (Hyla japonica) and suweon tree frog (Hyla suweonensis). Chonnam National University, Gwangju, Korea. [in Korean]
Hebsgaard MB, Phillips MJ, Willerslev E. 2005. Geologically ancient DNA: Fact or artefact? Trends in Microbiology 13:212-220.
Henry EH, Terando AJ, Morris WF, Daniels JC, Haddad NM. 2022. Shifting precipitation regimes alter the phenology and population dynamics of low latitude ectotherms. Climate Change Ecology 3:100051.
Herder J, Kranenbarg J, De Bruin A, Valentini A. 2013. Op jacht naar DNA–effectief zoeken naar grote modderkruipers. RAVON, Nijmegen, Netherlands.
Herder J, Valentini A, Bellemain E, Dejean T, van Delft J, Thomsen P. 2014. Environmental DNA–a review of the possible applications for the detection of (invasive) species nijmegen: Netherlands food and consumer product safety authority. p. 111. Stichting RAVON, Nijmegen, Netherland.
Hinne IA, Attah SK, Mensah BA, Forson AO, Afrane YA. 2021. Larval habitat diversity and anopheles mosquito species distribution in different ecological zones in Ghana. Parasites & Vectors 14:1-14.
Jang KS, Kim JO, Lee SH, Ji KJ, Seo JB, Shin HS, Yu JH. 2010. A study on the development of ecological infrastructure to improve bio-diversity in paddy wetlands. Korea Rural Community Corporation, Naju, Korea. [in Korean]
Jerde CL, Mahon AR, Chadderton WL, Lodge DM. 2011. “Sight-unseen” detection of rare aquatic species using environmental DNA. Conservation Letters 4:150-157.
Kang HS, Kim C, Kim JS, Kim JO, Kim MH. 2020. Agricultural ecological environment survey/evaluation criteria and manual. National Institute of Agricularal Science, Wanju, Korea. [in Korean]
Kang KK, Han MS, Na YE, Kim MH, Kim MR. 2013. Development of technologies for the management and restoration of paddy ecosystem to improve biodiversity in agro-ecosystem. National Institute of Agricultural Sciences, Wanju, Korea. [in Korean]
Karima Z. 2021. The wonders of Diptera-Characteristics, diversity, and significance for the World’s ecosystems: Chironomidae-biology, ecology and systematics. IntechOpen Limited, London, UK.
Kim EB, Kim ES, Sung HC, Lee DH, Kim GJ, Nam DH. 2021. Comparison of the skeletal features of two sympatric tree frogs (hylidae: Hyla)—Hyla japonica and Hyla suweonensis—using three-dimensional micro-computed tomography. Journal of Asia-Pacific Biodiversity 14:147-153.
Kim H. 2015. A study on establishing a group of biodiversity indicators for benthic macroinvertebrates in the lake ecosystem. Changwon National University 2015:1-138. [in Korean]
Kim JH, Jo H, Chang MH, Woo SH, Cho Y, Yoon JD. 2020. Application of environmental DNA for monitoring of freshwater fish in Korea. Korean Journal of Ecology and Environment 53:63-72. [in Korean]
Kim MH. 2021. Climate change impact assessment through long-term monitoring of biological seasons of indicator organisms. TRKO202200009107. Rural Development Administration, Jeonju, Korea. [in Korean]
Kim SK, Park HS, Park SR. 2016. Distribution of fish and amphibian in rice fields near the yedang reservoir in Korea. Korean Journal of Environment and Ecology 30:48-57. [in Korean]
Ko EM, Kim DY, Kim HJ, Chung YS, Kim CK. 2016. Assessing weediness of herbicide tolerant genetically modified soybean. Korean Journal of Agricultural Science 43:560-566.
Laramie MB, Pilliod DS, Goldberg CS. 2015. Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biological Conservation 183:29-37.
Lee H, Ha J, Cha J, Lee J, Yoon H, Chung C, Oh H, Bae S. 2017. The habitat classification of mammals in Korea based on the national ecosystem survey. Journal of Environmental Impact Assessment 26:160-170. [in Korean]
Lee SD. 2019. Proposition of dragonfly’s appropriate survey period inhabited in temperate zone. Korean Journal of Environment and Ecology 33:16-27. [in Korean]
Lindahl T. 1993. Instability and decay of the primary structure of DNA. Nature 362:709-715.
Minamoto T, Miya M, Sado T, Seino S, Doi H, Kondoh M, Nakamura K, Takahara T, Yamamoto S, Yamanaka H. 2021. An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols. Environmental DNA 3:8-13.
Numata S, Yamaguchi K, Shimizu M, Sakurai G, Morimoto A, Alias N, Noor Azman NZ, Hosaka T, Satake A. 2022. Impacts of climate change on reproductive phenology in tropical rainforests of southeast asia. Communications Biology 5:1-10.
Oh SD, Bae EJ, Park SY, Lee BK, Yun DW, Suh SJ. 2019. Risk assessment of genetically engineered rice Bt-9 resistant to Cnaphalocrocis medinalis: Influence on above-ground arthropods in Korea. Korean Journal of Agricultural Science 46:827-841. [in Korean]
Ramsar-Scientific & Technical Review Panel. 2008. Presented at the 10th meeting of the conference of the parties to the convention on wetlands (COP10-final report). RAMSAR, Changwon, Korea.
RDA (Rural Development Administration). 2019a. An illustrated guide to paddy ecology fauna-fish, amphibians and reptiles. RDA, Jeonju, Korea. [in Korean]
RDA (Rural Development Administration). 2019b. An illustrated guide to paddy ecology fauna-macroinvertebrate. RDA, Jeonju, Korea. [in Korean]
Saito K. 1988. Movement and spawning of several freshwater fishes in temporary waters around paddy fields. Japanes Journal of Ecology 38:35-47.
Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T. 2021. Development and evaluation of pcr primers for environmental DNA (eDNA) metabarcoding of amphibia. bioRxiv 31. DOI:10.1101/2021.10.29.466374.
Sang JH, Jung OS, Yeo HB. 2014. Ecosystem service value evaluation study of paddy wetlands in chungcheongnam-do. Chungnam Development Institute, Gongju, Korea. [in Korean]
Shapiro B. 2008. Engineered polymerases amplify the potential of ancient DNA. Trends in Biotechnology 26:285-287.
Taberlet P, Bonin A, Zinger L, Coissac E. 2018. Environmental DNA: For biodiversity research and monitoring. Oxford University Press, Oxford, UK.
Takahara T, Minamoto T, Doi H. 2013. Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLOS One 8:e56584.
Takeuchi A, Iijima T, Kakuzen W, Watanabe S, Yamada Y, Okamura A, Horie N, Mikawa N, Miller MJ, Kojima T. 2019. Release of edna by different life history stages and during spawning activities of laboratory-reared Japanese eels for interpretation of oceanic survey data. Scientific Reports 9:1-9.
Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10:512-526.
Tamura K, Stecher G, Kumar S. 2021. Mega11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution 38:3022-3027.
Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, Bellemain E, Besnard A, Coissac E, Boyer F. 2016. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology 25:929-942.
Yoccoz NG. 2012. The future of environmental DNA in ecology. Molecular Ecology 21:2031-2038.
Yoon SS, Kim MH, Choi SK, Eo J, Kwon SI, Song YJ. 2017. The development of a sampling instrument for aquatic organisms in rice paddy fields: Submerged funnel traps with attractants. Korean Journal of Environmental Biology 35:640-647. [in Korean]
Zulkefli NS, Kim KH, Hwang SJ. 2019. Effects of microbial activity and environmental parameters on the degradation of extracellular environmental DNA from a eutrophic lake. International Journal of Environmental Research and Public Health 16:3339.
Kim Keonhee, https://orcid.org/0000-0002-5725-1447
Kwon Sera, https://orcid.org/0000-0003-3001-6663
Noh Alongsaemi, https://orcid.org/0000-0003-2073-4573
No potential conflict of interest relevant to this article was reported.
본 논문은 농촌진흥청 공동연구사업(과제번호: PJ015071042023)의 지원에 의해 이루어진 것임.