1
|
Van Driessche C, Everts T, Neyrinck S, Halfmaerten D, Haegeman A, Ruttink T, Bonte D, Brys R. Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information. ENVIRONMENTAL RESEARCH 2023; 228:115857. [PMID: 37059322 DOI: 10.1016/j.envres.2023.115857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Monitoring fish communities is central to the evaluation of ecological health of rivers. Both presence/absence of fish species and their relative quantity in local fish assemblages are crucial parameters to measure. Fish communities in lotic systems are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. Analysis of environmental DNA could serve as a non-destructive alternative for detection and quantification of lotic fish communities, but this approach still requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA particles; optimization of predictive power and quality assurance of the molecular detection method. Via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Using a high and low source biomass in two river transects of a species-poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative species abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable from 25 to 300 m, or up to 1 km downstream of the eDNA source, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, might be attributed to variation in species-specific eDNA persistence. Our findings offer crucial insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate eDNA snapshot of the total fish community in the 300-1000 m upstream transect. The potential application for other river systems is further discussed.
Collapse
Affiliation(s)
- Charlotte Van Driessche
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium; Ghent University, Department of Biology, Terrestrial Ecology Unit, Ghent, Belgium.
| | - Teun Everts
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium; KU Leuven, Department of Biology, Plant Conservation and Population Biology, Leuven, Belgium
| | - Sabrina Neyrinck
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
| | - David Halfmaerten
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
| | - Annelies Haegeman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Dries Bonte
- Ghent University, Department of Biology, Terrestrial Ecology Unit, Ghent, Belgium
| | - Rein Brys
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
| |
Collapse
|
2
|
Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
Collapse
Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| |
Collapse
|
3
|
Banerjee P, Dey G, Antognazza CM, Sharma RK, Maity JP, Chan MWY, Huang YH, Lin PY, Chao HC, Lu CM, Chen CY. Reinforcement of Environmental DNA Based Methods ( Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review. BIOLOGY 2021; 10:biology10121223. [PMID: 34943137 PMCID: PMC8698464 DOI: 10.3390/biology10121223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/02/2022]
Abstract
Simple Summary Worldwide biodiversity loss points to a necessity of upgrading to a fast and effective monitoring method that can provide quick conservation action. Newly developed environmental DNA (eDNA) based method found to be more cost-effective, non-invasive, quick, and accurate than traditional monitoring (spot identification, camera trapping). Although the eDNA based methods are proliferating rapidly, as a newly developed branch, it needs more standardization and practitioner adaptation. The present study aims to evaluate the eDNA based methods, and their potential achievements in biodiversity monitoring, and conservation for quick practitioners’ adaption. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community-level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique shows a great promise with its high accuracy and authenticity, and will be applicable alone or alongside other methods in the near future. Abstract Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.
Collapse
Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Gobinda Dey
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Caterina M. Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy;
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan;
| | - Jyoti Prakash Maity
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Michael W. Y. Chan
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
| | - Yi-Hsun Huang
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Pin-Yun Lin
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan;
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Chung-Ming Lu
- Department of Chemical Engineering, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County, Jiayi 62102, Taiwan;
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Correspondence: or ; Tel.: +886-5-2720411 (ext. 66220); Fax: +886-5-2720807
| |
Collapse
|
4
|
Development of a Quantitative PCR Assay for Four Salmon Species Inhabiting the Yangyangnamdae River Using Environmental DNA. BIOLOGY 2021; 10:biology10090899. [PMID: 34571776 PMCID: PMC8471574 DOI: 10.3390/biology10090899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Regular surveys provide essential information to establish strategies for the effective conservation of salmon resources. As an alternative to conventional fish surveys, which are costly and laborious, quantitative PCR (qPCR) assays were established for the analysis of four salmon species inhabiting the Korean Peninsula. We designed four species-specific primer sets that showed high specificity and sensitivity in both tissue and environmental DNA (eDNA) samples collected from the Yangyangnamdae River. After normalization for PCR inhibition in each sample, the established qPCR assays produced standardized and realistic eDNA profiles for the four salmon species, suggesting that the newly developed qPCR assays are a useful tool for the management of Oncorhynchus resources in Korean waters. Abstract A species-specific quantitative PCR (qPCR) assay using environmental DNA (eDNA) is a promising tool for both qualitative and quantitative analyses of target species directly from water samples. Despite its reliability, an eDNA-based qPCR assay pipeline has not yet developed to monitor salmon species inhabiting Korean waters, which have been rapidly decreasing. We designed species-specific primers for four Oncorhynchus species inhabiting the eastern coastal waters along the Korean Peninsula. These include primers for two native species (Oncorhynchus keta and O. masou) and two that were introduced (O. mykiss and O. kisutch). The limit of detection and limit of quantification for the four qPCR assays ranged from 4.11 to 10.38 copies and from 30 to 81 copies, respectively, indicating a high sensitivity and specificity across all four species. Following optimization, the qPCR assays were used for the quantitative analyses of the four Oncorhynchus species in the Yangyangnamdae River during the spawning and non-spawning seasons in the year 2019–2020, one of the main rivers where salmon migrate during the spawning season in Korea. The raw copy numbers in all of the examined samples were normalized by PCR inhibition rates to standardize and compare with other studies. Among the four Oncorhynchus species examined, the eDNA concentration of O. keta increased significantly (63.60-fold, p < 0.0001) during the spawning season (November) compared with that in the non-spawning season (March), suggesting that O. keta is the main salmon species migrating through the Yangyangnamdae River. In contrast, we did not detect any differences in eDNA concentration for the other three Oncorhynchus species between the spawning and non-spawning seasons, indicating that their presence does not alter during the year. Their eDNA concentration is also relatively low compared to O. keta, which suggests that small numbers of these three species are present in the river. Overall, these newly developed qPCR assays represent useful monitoring tools for the management of four salmon species in Korean waters.
Collapse
|
5
|
Veilleux HD, Misutka MD, Glover CN. Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 782:146891. [PMID: 33848866 DOI: 10.1016/j.scitotenv.2021.146891] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/22/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Traditional environmental biomonitoring approaches have limitations in terms of species detectability and their capacity to account for spatial and temporal variation. Furthermore, as invasive techniques they can be harmful to individual organisms, populations and habitats. The application of non-invasive sampling methods that extract, isolate and identify nucleic acid sequences (i.e. DNA, RNA) from environmental matrices have significant potential for complementing, or even ultimately replacing, current methods of biological environmental assessment. These environmental DNA (eDNA) and environmental RNA (eRNA) techniques increase spatial and temporal acuity of monitoring, and in the case of the latter, may provide functional information regarding the health of individuals, and thus ecosystems. However, these assessments require robust analysis of factors such as the detectability and specificity of the developed assays. The presented work highlights the current and future uses of nucleic acid-based biomonitoring regimes, with a focus on fish and aquatic invertebrates and their utility for water quality, biodiversity and species-specific monitoring. These techniques are compared to traditional approaches, with a particular emphasis on the potential insights that could be provided by eRNA analysis, including the benefits of microRNAs as assay targets.
Collapse
Affiliation(s)
- Heather D Veilleux
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
| | - Melissa D Misutka
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Faculty of Science and Technology and Athabasca River Basin Research Institute, Athabasca University, Athabasca, Alberta, Canada
| | - Chris N Glover
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Faculty of Science and Technology and Athabasca River Basin Research Institute, Athabasca University, Athabasca, Alberta, Canada
| |
Collapse
|
6
|
Kasai A, Yamazaki A, Ahn H, Yamanaka H, Kameyama S, Masuda R, Azuma N, Kimura S, Karaki T, Kurokawa Y, Yamashita Y. Distribution of Japanese Eel Anguilla japonica Revealed by Environmental DNA. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.621461] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The abundance of Japanese eel Anguilla japonica has rapidly decreased in recent decades. Following a re-evaluation of the possibility of extinction, the Japanese Ministry of the Environment and the International Union for Conservation of Nature listed the Japanese eel as an endangered species in 2013 and 2014, respectively. However, their abundance and precise distribution have never been clarified owing to their nocturnality and difficulty in their capture. In this study, the distribution of Japanese eels was investigated by monitoring for environmental DNA (eDNA), a non-invasive and efficient detection method. A total of 365 water samples were collected from 265 rivers located throughout Japan. High concentrations of eDNA of Japanese eels were detected in rivers on the Pacific side, but were low in the Sea of Japan side. In particular, very little eDNA amplification was confirmed from Hokkaido and the north of the Sea of Japan. The eDNA distribution in Japanese rivers coincides with the transport of the larvae in the ocean, as estimated by numerical simulations. Generalized linear mixed models were developed to explain the distribution of eDNA concentrations. The total nitrogen concentration emerged as an important factor in the best model. These results indicate that the distribution of Japanese eel is mostly determined by the maritime larval transport, and their survival and growth depend on the abundance of food in the river. The findings of the present study are useful for the management of populations and in the conservation of Japanese eels.
Collapse
|
7
|
Muha TP, Rodriguez-Barreto D, O'Rorke R, Garcia de Leaniz C, Consuegra S. Using eDNA Metabarcoding to Monitor Changes in Fish Community Composition After Barrier Removal. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.629217] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Artificial instream barriers are a major cause of habitat fragmentation that reduce population connectivity and gene flow by limiting fish movements. To mitigate their impacts, obsolete barriers are increasingly been removed worldwide, but few barrier removal projects are monitored. We employed a powerful Before-After-Downstream-Upstream (BADU) approach using environmental DNA (eDNA) metabarcoding to examine the effects on fish community composition of removing a weir in the river Lugg (England) that had been suggested to have a detrimental effect on salmonid migration. We found no change in fish community diversity or relative abundance after the removal above or below the weir, but detected an important effect of sampling season, likely related to the species' life cycles. eDNA detected nine fish species that were also identified by electrofishing sampling and one additional species (Anguilla anguilla) that was missed by traditional surveys. Our results suggest that monitoring of barrier removal projects should be carried out to ensure that any ecological benefits are properly documented and that eDNA metabarcoding is a sensitive technique to monitor the effects of barrier removal.
Collapse
|
8
|
Mizumoto H, Mitsuzuka T, Araki H. An Environmental DNA Survey on Distribution of an Endangered Salmonid Species, Parahucho perryi, in Hokkaido, Japan. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.569425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
|
9
|
Yatsuyanagi T, Araki H. Understanding seasonal migration of Shishamo smelt in coastal regions using environmental DNA. PLoS One 2020; 15:e0239912. [PMID: 33002065 PMCID: PMC7529200 DOI: 10.1371/journal.pone.0239912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/15/2020] [Indexed: 11/18/2022] Open
Abstract
Migratory organisms have their own life histories that efficiently link multiple ecosystems. Therefore, comprehensive understanding of migration ecologies of these organisms is essential for both species conservation and ecosystem management. However, monitoring migration at fine spatiotemporal scales, especially in open marine systems, often requires huge costs and effort. Recently, environmental DNA (eDNA) techniques that utilize DNA released from living organisms into their environment became available for monitoring wild animals without direct handling. In this study, we conducted an eDNA survey for understanding marine migration of an endemic fish species, Shishamo smelt (Spirinchus lanceolatus). We examined 1) seasonal habitat changes in coastal regions and 2) environmental factors potentially driving the migration of this species. The eDNA concentrations along a 100 km-long coastline exhibited spatiotemporal variation, suggesting that this species shifts their habitat away from nearshore areas between spring and summer. We also found a significantly negative association between the eDNA concentration and sea surface temperature. That finding suggests that the offshore migration of this species is associated with increased sea surface temperature. This study reveals new aspects of S. lanceolatus life history in coastal regions. Together with our previous eDNA study on the freshwater migration of S. lanceolatus, this study illustrates the potential of eDNA techniques for understanding the whole life history of this migratory species.
Collapse
Affiliation(s)
- Tetsu Yatsuyanagi
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hitoshi Araki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail:
| |
Collapse
|
10
|
Aquatic suspended particulate matter as source of eDNA for fish metabarcoding. Sci Rep 2020; 10:14352. [PMID: 32873823 PMCID: PMC7463230 DOI: 10.1038/s41598-020-71238-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 07/31/2020] [Indexed: 11/17/2022] Open
Abstract
The use of environmental DNA (eDNA) for monitoring aquatic macrofauna allows the non-invasive species determination and measurement of their DNA abundance and typically involves the analysis of eDNA captured from water samples. In this proof-of-concept study, we focused on the novel use of eDNA extracted from archived suspended particulate matter (SPM) for identifying fish species using metabarcoding, which benefits from the prospect of retrospective monitoring and also analysis of fish communities through time. We used archived SPM samples of the German Environmental Specimen Bank (ESB), which were collected using sedimentation traps from different riverine points in Germany. Environmental DNA was extracted from nine SPM samples differing in location, organic content, and porosity (among other factors) using four different methods for the isolation of high-quality DNA. Application of the PowerSoil DNA Isolation Kit with an overnight incubation in lysis buffer, resulted in DNA extraction with the highest purity and eDNA metabarcoding of these eDNA fragments was used to detect a total of 29 fish taxa among the analyzed samples. Here we demonstrated for the first time that SPM is a promising source of eDNA for metabarcoding analysis, which could provide valuable retrospective information (when using archived SPM) for fish monitoring, complementing the currently used approaches.
Collapse
|