Environmental DNA (eDNA) sampling for detecting stream fish assemblages in comparison with traditional sampling methods
- 주제(키워드) 환경유전자 , eDNA , Metabarcoding , Fish , Diversity , Stream , Hantangang
- 주제(DDC) 570
- 발행기관 아주대학교
- 지도교수 박상규
- 발행년도 2023
- 학위수여년월 2023. 8
- 학위명 석사
- 학과 및 전공 일반대학원 생명과학과
- 실제URI http://www.dcollection.net/handler/ajou/000000033089
- 본문언어 영어
- 저작권 아주대학교 논문은 저작권에 의해 보호받습니다.
초록/요약
Recently, environmental DNA (eDNA) has been drawing attention as a powerful tool for detecting fish community structure. Since traditional capture-based methods are limited due to incomplete sampling efficiency, particularly when investigators cannot approach sampling sites, several studies have applied the eDNA method as a complementary tool. These previous studies also put an emphasis on fine-tuning methods for a specific ecosystem type to adopt the eDNA survey due to complicate relationships between eDNA and environmental factors. Thus, the aim of this study is to evaluate the eDNA method and suggest reasonable sampling methods that are highly likely to be applicable in stream fish sampling surveys. I compared the fish community structures observed with the eDNA and the traditional methods, and estimated the number of required sample replicates in the three study sites: Upstream; Midstream; and Downstream in Yeongpyeongcheon Stream, located in the Imjingang River Basin, a part of the Hangang River Basin in South Korea. I simultaneously conducted traditional fish sampling and eDNA sampling at 6 different sampling spots in each study site. Surveys were performed twice, in summer and autumn, to consider seasonal variations in fish assemblages. To clarify factors influencing the eDNA survey results, I conducted a permutational multivariate analysis of variance (PERMANOVA). The number of sample replicates needed was calculated via species accumulation curve fitted to the Michaelis-Menten equation. As a result, I could detect 22 and 33 species using traditional fish sampling and the eDNA method, respectively. Eighteen fish were detected from both methods, and the species undetected from the eDNA method were Rhinogobius brunneus, Hemibarbus labeo, Sarcocheilichthys variegatus, and Coreoperca herzi. From the PERMANOVA result, only site and seasonal factors were significant statistically among the factors including site, season, and mesohabitat types. When comparing the number of required sample replicates, eDNA sampling required less sampling efforts in autumn than traditional fish sampling. On the contrary, the number of sample replicates should be increased in summer, except for the Downstream site. In the Downstream site, eDNA sampling required less effort in both seasons. Six replicate samples per each study site covered an average of 80 percent of expected species in the region. Overall, the eDNA survey worked as a powerful tool for detecting fish fauna with less effort compared to traditional method. Sampling site and seasonal variation must be considered since the effect of these two variables were prominent. However, biological indices showed unrealistic values when calculated with the eDNA result. Further studies would be needed for applying eDNA read counts as a quantity data.
more목차
1. Introduction 1
2. Materials and Methods 3
2.1 Study sites and sampling methods for both surveys 3
2.2 Environmental factors 6
2.3 DNA extraction and metabarcoding 6
2.4 eDNA data analysis 7
2.5 Statistical analyses 8
3. Results 10
3.1 Environmental factors 10
3.2 Comparison with traditional survey 12
3.2.1 Species composition 12
3.2.2 Characteristics of traditional method and eDNA method 19
3.2.3 Sampling efforts 25
4. Discussion 27
5. References 30
6. Abstract 39
