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Ye L, Peng S, Ma Y, Zhang W, Wang L, Sun X, Zhang C, Yeasmin M, Zhao J, Dong Z. Biodiversity and distribution patterns of blooming jellyfish in the Bohai Sea revealed by eDNA metabarcoding. BMC Ecol Evol 2024; 24:37. [PMID: 38500049 PMCID: PMC10946145 DOI: 10.1186/s12862-024-02224-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The mass occurrence of scyphozoan jellyfish severely affects marine ecosystems and coastal economies, and the study of blooming jellyfish population dynamics has emerged in response. However, traditional ecological survey methods required for such research have difficulties in detecting cryptic life stages and surveying population dynamics owing to high spatiotemporal variations in their occurrence. The environmental DNA (eDNA) technique is an effective tool for overcoming these limitations. RESULTS In this study, we investigated the biodiversity and spatial distribution characteristics of blooming jellyfish in the Bohai Sea of China using an eDNA metabarcoding approach, which covered the surface, middle, and bottom seawater layers, and sediments. Six jellyfish taxa were identified, of which Aurelia coerulea, Nemopilema nomurai, and Cyanea nozakii were the most dominant. These three blooming jellyfish presented a marked vertical distribution pattern in the offshore regions. A. coerulea was mainly distributed in the surface layer, whereas C. nozakii and N. nomurai showed a upper-middle and middle-bottom aggregation, respectively. Horizontally, A. coerulea and C. nozakii were more abundant in the inshore regions, whereas N. nomurai was mainly distributed offshore. Spearman's correlation analysis revealed a strong correlation between the eDNA of the three dominant blooming jellyfish species and temperature, salinity, and nutrients. CONCLUSIONS Our study confirms the applicability of the eDNA approach to both biodiverstiy evaluation of blooming jellyfish and investigating their spatial distribution, and it can be used as a supplementary tool to traditional survey methods.
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Affiliation(s)
- Lijing Ye
- Yantai University, 264005, Yantai, Shandong, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
| | - Saijun Peng
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanqing Ma
- Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, 264006, Yantai, Shandong, China
| | - Wenjing Zhang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lei Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiyan Sun
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chen Zhang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Munjira Yeasmin
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jianmin Zhao
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhijun Dong
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003, Yantai, Shandong, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Wu L, Osugi T, Inagawa T, Okitsu J, Sakamoto S, Minamoto T. Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons. Mol Ecol Resour 2024; 24:e13875. [PMID: 37830396 DOI: 10.1111/1755-0998.13875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, the throughput was limited. High-throughput metabarcoding technology can detect the DNA of multiple species simultaneously in a single experiment but does not provide sufficient quantification. In this study, we applied a quantitative metabarcoding approach to simultaneously quantify the eDNA concentration of an entire fish assemblage in a small reservoir over two summer seasons. Traditional surveys were also conducted to investigate the individuals of fish. The eDNA concentrations were quantified using quantitative metabarcoding, and the fish species detected using this approach were highly consistent with the results of traditional fish monitoring. A significant positive relationship was observed between the eDNA concentration and fish species abundance. Seasonal changes in fish community structure were estimated using eDNA concentrations, which may reveal the activity seasons of different fish. The eDNA concentrations of different fish species peaked at different water temperatures, reflecting the differential responses of fish species to this environmental factor. Finally, by detecting outlier eDNA concentrations, the spawning activities of 13 fish species were estimated, 12 of which were roughly consistent with the current knowledge of fish spawning periods. These results indicate that quantitative eDNA metabarcoding with dozens of sampling times is useful for the simultaneous ecological monitoring of multiple fish species.
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Affiliation(s)
- Luhan Wu
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Hyogo, Japan
| | | | | | | | | | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Hyogo, Japan
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Peng S, Wang L, Ma Y, Ye L, Hou C, Liu Y, Li Y, Sun T, Zhao J, Dong Z. Application of environmental DNA metabarcoding and quantitative PCR to detect blooming jellyfish in a temperate bay of northern China. Ecol Evol 2023; 13:e10669. [PMID: 37915801 PMCID: PMC10616739 DOI: 10.1002/ece3.10669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Frequently occurring jellyfish blooms have severe impacts on the socioeconomics of coastal areas, which stress the importance of early detection and assessments of blooming jellyfish taxa. Environmental DNA (eDNA) techniques (quantitative PCR and eDNA metabarcoding) have the advantage of high sensitivity and are an emerging powerful tool for investigations of target species. However, a comprehensive analysis of the biodiversity and biomass of jellyfish taxa in the target area by combining the two eDNA techniques is still lacking. Here, we developed eDNA metabarcoding and quantitative PCR for the detection and assessment of jellyfish taxa in the temperate Yantai Sishili Bay (YSB) and estimated the spatial distribution of Aurelia coerulea. Species-specific quantitative PCR assays targeting the mitochondrial cytochrome c oxidase subunit I gene of A. coerulea were developed. Additionally, eDNA metabarcoding based on the mitochondrial 16S rDNA sequences identified six jellyfish species in YSB. Moreover, our results indicate that A. coerulea aggregations were more likely to occur in the inner part of the bay than in the outer part, and they gathered in the bottom layer of seawater rather than in the surface layer. Our results demonstrate the potential of two eDNA techniques in jellyfish biomass investigation and jellyfish taxa detection. These eDNA techniques may contribute to the discovery of jellyfish aggregation so as to achieve early warning of large-scale jellyfish blooms in coastal areas.
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Affiliation(s)
- Saijun Peng
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Wang
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuanqing Ma
- Shandong Key Laboratory of Marine Ecological RestorationShandong Marine Resource and Environment Research InstituteYantaiShandongChina
| | - Lijing Ye
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
| | - Chaowei Hou
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yongliang Liu
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yongxue Li
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tingting Sun
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jianmin Zhao
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhijun Dong
- Muping Coastal Environment Research StationYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiShandongChina
- University of Chinese Academy of SciencesBeijingChina
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Pragmatic applications of DNA barcoding markers in identification of fish species – a review. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.
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Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art. Foods 2023; 12:foods12010228. [PMID: 36613444 PMCID: PMC9818732 DOI: 10.3390/foods12010228] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.
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Guenay-Greunke Y, Bohan DA, Traugott M, Wallinger C. Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology. Sci Rep 2021; 11:19510. [PMID: 34593851 PMCID: PMC8484467 DOI: 10.1038/s41598-021-98018-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/30/2021] [Indexed: 01/23/2023] Open
Abstract
High-throughput sequencing platforms are increasingly being used for targeted amplicon sequencing because they enable cost-effective sequencing of large sample sets. For meaningful interpretation of targeted amplicon sequencing data and comparison between studies, it is critical that bioinformatic analyses do not introduce artefacts and rely on detailed protocols to ensure that all methods are properly performed and documented. The analysis of large sample sets and the use of predefined indexes create challenges, such as adjusting the sequencing depth across samples and taking sequencing errors or index hopping into account. However, the potential biases these factors introduce to high-throughput amplicon sequencing data sets and how they may be overcome have rarely been addressed. On the example of a nested metabarcoding analysis of 1920 carabid beetle regurgitates to assess plant feeding, we investigated: (i) the variation in sequencing depth of individually tagged samples and the effect of library preparation on the data output; (ii) the influence of sequencing errors within index regions and its consequences for demultiplexing; and (iii) the effect of index hopping. Our results demonstrate that despite library quantification, large variation in read counts and sequencing depth occurred among samples and that the sequencing error rate in bioinformatic software is essential for accurate adapter/primer trimming and demultiplexing. Moreover, setting an index hopping threshold to avoid incorrect assignment of samples is highly recommended.
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Affiliation(s)
- Yasemin Guenay-Greunke
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria. .,Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020, Innsbruck, Austria.
| | - David A Bohan
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Michael Traugott
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Corinna Wallinger
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.,Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020, Innsbruck, Austria
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Yang J, Zhang X, Jin X, Seymour M, Richter C, Logares R, Khim JS, Klymus K. Recent advances in environmental DNA‐based biodiversity assessment and conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Jun Yang
- Aquatic EcoHealth Group Fujian Key Laboratory of Watershed Ecology Key Laboratory of Urban Environment and Health Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Xiaowei Zhang
- School of the Environment State Key Laboratory of Pollution Control & Resource Reuse Nanjing University Nanjing China
| | - Xiaowei Jin
- China National Environmental Monitoring CentreMinistry of Ecology and Environment of the People's Republic of China Beijing China
| | - Mathew Seymour
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Catherine Richter
- Columbia Environmental Research CenterU.S. Geological Survey Columbia MO USA
| | - Ramiro Logares
- Institute of Marine Sciences CSICPasseig Marítim de la Barceloneta Barcelona Spain
| | - Jong Seong Khim
- School of Earth & Environmental Sciences College of Natural Sciences Seoul National University Seoul Republic of Korea
| | - Katy Klymus
- Columbia Environmental Research CenterU.S. Geological Survey Columbia MO USA
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