Monitoring freshwater fish communities in large rivers using environmental DNA metabarcoding and a long‐term electrofishing survey

2020 ◽  
Vol 97 (2) ◽  
pp. 444-452 ◽  
Author(s):  
Aurélie Goutte ◽  
Noëlie Molbert ◽  
Sabrina Guérin ◽  
Robin Richoux ◽  
Vincent Rocher
Keyword(s):  
Freshwater Fish ◽  
Fish Communities ◽  
Environmental Dna ◽  
Large Rivers ◽  
Dna Metabarcoding

scholarly journals Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Hirotoshi Sato ◽  
Yuki Sogo ◽  
Hideyuki Doi ◽  
Hiroki Yamanaka
Keyword(s):  
Freshwater Fish ◽  
Fish Communities ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
Sample Pooling

scholarly journals Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods

2016 ◽  
Vol 25 (13) ◽  
pp. 3101-3119 ◽  
Author(s):  
Bernd Hänfling ◽  
Lori Lawson Handley ◽  
Daniel S. Read ◽  
Christoph Hahn ◽  
Jianlong Li ◽  
...  
Keyword(s):  
Survey Methods ◽  
Fish Communities ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
Lake Fish Communities ◽  
Term Data ◽  
Lake Fish

scholarly journals Environmental DNA metabarcoding uncovers environmental correlates of fish communities in spatially heterogeneous freshwater habitats

2021 ◽  
Vol 126 ◽  
pp. 107698
Author(s):  
Petr Blabolil ◽  
Lynsey R. Harper ◽  
Štěpánka Říčanová ◽  
Graham Sellers ◽  
Cristina Di Muri ◽  
...  
Keyword(s):  
Fish Communities ◽  
Environmental Dna ◽  
Environmental Correlates ◽  
Dna Metabarcoding ◽  
Freshwater Habitats

scholarly journals Environmental DNA metabarcoding uncovers environmental correlates of fish communities in spatially heterogeneous freshwater habitats

2020 ◽  
Author(s):  
Petr Blabolil ◽  
Lynsey Harper ◽  
Stepanka Ricanova ◽  
Graham Sellers ◽  
Cristina Di Muri ◽  
...  
Keyword(s):  
Fish Communities ◽  
Environmental Dna ◽  
Environmental Correlates ◽  
Dna Metabarcoding ◽  
Freshwater Habitats

scholarly journals A pilot for implementing environmental DNA (eDNA) based methods into environmental and biomonitoring

2021 ◽  
Vol 4 ◽  
Author(s):  
Tiina Laamanen ◽  
Veera Norros ◽  
Sanna Suikkanen ◽  
Mikko Tolkkinen ◽  
Kristiina Vuorio ◽  
...  
Keyword(s):  
Best Practices ◽  
Information Exchange ◽  
State Of The Art ◽  
Environmental Dna ◽  
Bulk Sample ◽  
The State ◽  
Molecular Techniques ◽  
Future Research ◽  
Dna Metabarcoding

Environmental DNA (eDNA) and other molecular based approaches are revolutionizing the field of biomonitoring. These approaches undergo rapid modifications, and it is crucial to develop the best practices by sharing the newest information and knowledge. In our ongoing project we: assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE; identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring; promote information exchange on eDNA methods and advance future research efforts both within SYKE and with our national and international partners. assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE; identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring; promote information exchange on eDNA methods and advance future research efforts both within SYKE and with our national and international partners. Scientific background Well-functioning and intact natural ecosystems are essential for human well-being, provide a variety of ecosystem services and contain a high diversity of organisms. However, human activities such as eutrophication, pollution, land-use or invasive species, are threatening the state and functioning of ecosystems from local to global scale (e.g. Benateau et al. 2019; Reid et al. 2018; Vörösmarty et al. 2010). New molecular techniques in the field and in the laboratory have enabled sampling and identification of much of terrestrial, marine and freshwater biodiversity. These include environmental DNA (eDNA, e.g. Valentini et al. 2016) and bulk-sample DNA metabarcoding approaches (e.g. Elbrecht et al. 2017) and targeted RNA-based methods (e.g. Mäki and Tiirola 2018). The eDNA technique uses DNA that is released from organisms into their environment, from which a signal of organisms’ presence in the system can be obtained. For example, in aquatic ecosystems, eDNA is typically extracted from sediment or filtered water samples (e.g. Deiner et al. 2016), and this approach is distinguished from bulk DNA metabarcoding, where organisms are directly identified from e.g. complete biological monitoring samples (e.g. Elbrecht et al. 2017). Despite the demonstrated potential of environmental and bulk-sample DNA metabarcoding approaches in recent years, there are still significant bottlenecks to their routine use that need to be addressed (e.g. Pawlowski et al. 2020). Methods and implementati on The project is divided into three work packages: WP1 Gathering existing knowledge, identifying knowledge gaps and proposing best practices, WP2 Roadmap to implementation and WP3 eDNA monitoring pilot. Please see more details in the Fig. 1

scholarly journals Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika

2019 ◽  
Vol 2 (1) ◽  
pp. 24-41 ◽  
Author(s):  
Christopher J. Doble ◽  
Helen Hipperson ◽  
Walter Salzburger ◽  
Gavin J. Horsburgh ◽  
Chacha Mwita ◽  
...  
Keyword(s):  
Lake Tanganyika ◽  
Fish Communities ◽  
Environmental Dna ◽  
Tropical Fish ◽  
Dna Metabarcoding

Estimation of biodiversity metrics by environmental DNA metabarcoding compared with visual and capture surveys of river fish communities

2021 ◽  
Author(s):  
Hideyuki Doi ◽  
Ryutei Inui ◽  
Shunsuke Matsuoka ◽  
Yoshihisa Akamatsu ◽  
Masuji Goto ◽  
...  
Keyword(s):  
Fish Communities ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
River Fish

scholarly journals Proper environmental DNA metabarcoding data transformation reveals temporal stability of fish communities in a dendritic river system

2021 ◽  
Author(s):  
Martin Laporte ◽  
Emilie Reny‐Nolin ◽  
Victoria Chouinard ◽  
Cécilia Hernandez ◽  
Eric Normandeau ◽  
...  
Keyword(s):  
Temporal Stability ◽  
Fish Communities ◽  
Environmental Dna ◽  
River System ◽  
Data Transformation ◽  
Dna Metabarcoding

scholarly journals Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giorgi Dal Pont ◽  
Camila Duarte Ritter ◽  
Andre Olivotto Agostinis ◽  
Paula Valeska Stica ◽  
Aline Horodesky ◽  
...  
Keyword(s):  
Fish Communities ◽  
Environmental Dna ◽  
Hydropower Plant ◽  
Southeastern Brazil ◽  
Fish Diversity ◽  
Pass System ◽  
Fish Pass ◽  
Dna Metabarcoding ◽  
The World ◽  
The Impact

AbstractThe Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of environmental DNA metabarcoding to monitor the impact of both the dam and associated fish pass system in the Paraná River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.

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