• Title, Summary, Keyword: Metabarcoding

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SoEM: a novel PCR-free biodiversity assessment method based on small-organelles enriched metagenomics

  • Jo, Jihoon;Lee, Hyun-Gwan;Kim, Kwang Young;Park, Chungoo
    • ALGAE
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    • v.34 no.1
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    • pp.57-70
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    • 2019
  • DNA metabarcoding is currently used for large-scale taxonomic identification to understand the community composition in various marine ecosystems. However, before being widely used in this emerging field, this experimental and analytic approach still has several technical challenges to overcome, such as polymerase chain reaction (PCR) bias, and lack of well-established metabarcoding markers, a task which is difficult but not impossible to achieve. In this study, we present an adapted PCR-free small-organelles enriched metagenomics (SoEM) method for marine biodiversity assessment. To avoid PCR bias and random artefacts, we extracted target DNA sequences without PCR amplification from marine environmental samples enriched with small organelles including mitochondria and plastids because their genome sequences provide a valuable source of molecular markers for phylogenetic analysis. To experimentally enrich small organelles, we performed subcellular fractionation using modified differential centrifugation for marine environmental DNA samples. To validate our SoEM method, two marine environmental samples from the coastal waters were tested the taxonomic capturing capacity against that of traditional DNA metabarcoding method. Results showed that, regardless of taxonomic levels, at least 3-fold greater numbers of taxa were identified in our SoEM method, compared to those identified by the conventional multi-locus DNA metabarcoding method. The SoEM method is thus effective and accurate for identifying taxonomic diversity and presents a useful alternative approach for evaluating biodiversity in the marine environment.

Possibility in identifying species composition of fish communities using the environmental DNA metabarcoding technique - with the preliminary results at urban ecological streams (환경DNA 메타바코딩 기술을 활용한 수생태계 어류종 군집조사의 가능성 - 도시 생태하천 초기분석 자료를 중심으로)

  • Song, Young-Keun;Kim, Jong-Hee;Won, Su-Yeon;Park, Chan
    • Journal of the Korean Society of Environmental Restoration Technology
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    • v.22 no.6
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    • pp.125-138
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    • 2019
  • This study aims to highlight the possibility in identifying species composition of fish communities using the environmental DNA (eDNA) metabarcoding technique, from both of the technical introduction and the pilot test at urban ecological streams. This new emerging survey technique using eDNA is getting popular in the world as a compensating way for the conventional field survey. However, the application to the domestic cases has yet to be studied. We attempted to use this technique for identifying fish species observed at four survey points in Hwangguji-chon, Suwon City. As a result, the detected number of species by eDNA sampled once in May was significantly matched with the total number of observed species in annual field surveys. Additionally eDNA results indicated the presence possibility of the unobserved species in field last year, even though the validation may be required. This survey technique seems to be more efficient and applicable to diverse situations of the fields and species, thereby needs to be studied further. We discussed the pros and cons of the application and summarized the research directions in future.

Review and application of environmental DNA (eDNA) investigation of terrestrial species in urban ecosystem (도시 내 육상 생물종 모니터링을 위한 환경DNA 리뷰 및 적용)

  • Kim, Whee-Moon;Kim, Seoung-Yeal;Park, Il-Su;Lee, Hyun-Jung;Kim, Kyeong-Tae;Kim, Young;Kim, Hye-Joung;Kwak, Min-Ho;Lim, Tae-Yang;Park, Chan;Song, Won-Kyong
    • Journal of the Korean Society of Environmental Restoration Technology
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    • v.23 no.2
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    • pp.69-89
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    • 2020
  • 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.