scholarly journals Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

2020 ◽  
Vol 10 (14) ◽  
pp. 7560-7584 ◽  
Author(s):  
Natalia Fraija‐Fernández ◽  
Marie‐Catherine Bouquieaux ◽  
Anaïs Rey ◽  
Iñaki Mendibil ◽  
Unai Cotano ◽  
...  
Keyword(s):  
Spatial Patterns ◽  
Environmental Dna ◽  
Marine Water ◽  
Fish Diversity ◽  
Oceanic Area ◽  
Diversity Assessment ◽  
Dna Metabarcoding

scholarly journals Fish diversity assessment in the headwaters of the Volga River using environmental DNA metabarcoding

2019 ◽  
Vol 29 (10) ◽  
pp. 1785-1800 ◽  
Author(s):  
Laurène A. Lecaudey ◽  
Martin Schletterer ◽  
Vyacheslav V. Kuzovlev ◽  
Christoph Hahn ◽  
Steven J. Weiss
Keyword(s):  
Environmental Dna ◽  
Fish Diversity ◽  
Volga River ◽  
Diversity Assessment ◽  
Dna Metabarcoding

scholarly journals FISH DIVERSITY DETECTION AT PORT AND URBAN CANAL AREA USING ENVIRONMENTAL DNA METABARCODING

2018 ◽  
Vol 74 (2) ◽  
pp. I_474-I_479 ◽  
Author(s):  
Satomi KAMIMURA ◽  
Yasunori KOZUKI ◽  
Sosuke OTANI ◽  
Rin HIRAKAWA ◽  
Kazuki IWAMI ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Fish Diversity ◽  
Canal Area ◽  
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.

scholarly journals Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

2019 ◽  
Author(s):  
Natalia Fraija-Fernández ◽  
Marie-Catherine Bouquieaux ◽  
Anaïs Rey ◽  
Iñaki Mendibil ◽  
Unai Cotano ◽  
...  
Keyword(s):  
Marine Fish ◽  
Environmental Dna ◽  
Distribution Patterns ◽  
Abundant Species ◽  
Fish Diversity ◽  
12S Rrna ◽  
Rrna Gene ◽  
Ecological Knowledge ◽  
Diversity Assessment ◽  
The Common

AbstractCurrent methods for monitoring marine fish diversity mostly rely on trawling surveys, which are invasive, costly and time-consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we explore the potential of environmental DNA (eDNA), the DNA present in the water column as part of shed cells, tissues or mucus, to provide comprehensive information about fish diversity in a large marine area. Further, eDNA results were compared to the fish diversity obtained in pelagic trawls. A total of 44 5L-water samples were collected onboard a wide-scale oceanographic survey covering about 120,000 square kilometres in Northeast Atlantic Ocean. A short region of the 12S rRNA gene was amplified and sequenced through metabarcoding generating almost 3.5 million quality-filtered reads. Trawl and eDNA samples resulted in the same most abundant species (European anchovy, European pilchard, Atlantic mackerel and blue whiting), but eDNA metabarcoding resulted in more detected fish and elasmobranch species (116) than trawling (16). Although an overall correlation between fish biomass and number of reads was observed, some species deviated from the common trend, which could be explained by inherent biases of each of the methods. Species distribution patterns inferred from eDNA metabarcoding data coincided with current ecological knowledge of the species, suggesting that eDNA has the potential to draw sound ecological conclusions that can contribute to fish surveillance programs. Our results support eDNA metabarcoding for broad scale marine fish diversity monitoring in the context of Directives such as the Common Fisheries Policy or the Marine Strategy Framework Directive.

scholarly journals Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

2020 ◽  
Author(s):  
C. Di Muri ◽  
L.L. Handley ◽  
C.W. Bean ◽  
J. Li ◽  
G. Peirson ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Quantitative Information ◽  
Fish Abundance ◽  
Fish Diversity ◽  
Natural Systems ◽  
Abundance Estimates ◽  
Dna Metabarcoding ◽  
Dna Capture ◽  
Cost Efficient ◽  
Number Of Individuals

AbstractThe sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the growth of DNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems remains a major challenge. Few studies have examined the association between eDNA metabarcoding data and biomass inferred by whole-organism sampling, mesocosms or mock communities, and the interpretation of sequencing reads as a measure of biomass or number of organisms is largely disputed.Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of fish abundance in holding ponds with known fish biomass and number of individuals.eDNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used.This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management.

COMPARATIVE STUDY BETWEEN FISH COLLECTION BY NATIONAL CENSUS ON RIVER ENVIRONMENT AND ENVIRONMENTAL DNA METABARCODING

2018 ◽  
Vol 74 (5) ◽  
pp. I_415-I_420 ◽  
Author(s):  
Yoshihisa AKAMATSU ◽  
Takayoshi TSUZUKI ◽  
Ryota YOKOYAMA ◽  
Yayoi FUNAHASHI ◽  
Munehiro OHTA ◽  
...  
Keyword(s):  
Comparative Study ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
Fish Collection

Environmental DNA for functional diversity

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Functional Groups ◽  
Functional Diversity ◽  
Environmental Dna ◽  
Soil Organisms ◽  
Meaningful Information ◽  
Dna Metabarcoding ◽  
Pros And Cons ◽  
Target Community

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.

Environmental DNA

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Graduate Students ◽  
Feeding Habits ◽  
Environmental Dna ◽  
Research Field ◽  
Background Information ◽  
Ecological Processes ◽  
Biodiversity Research ◽  
Dna Metabarcoding ◽  
Standard Information

Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.

Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests

2021 ◽  
Author(s):  
José Luis Mena ◽  
Hiromi Yagui ◽  
Vania Tejeda ◽  
Emilio Bonifaz ◽  
Eva Bellemain ◽  
...  
Keyword(s):  
Tropical Forests ◽  
Environmental Dna ◽  
Terrestrial Mammal ◽  
Dna Metabarcoding ◽  
Mammal Diversity
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