scholarly journals Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding

2021 ◽  
Author(s):  
Sabrina Shirazi ◽  
Rachel S. Meyer ◽  
Beth Shapiro
Keyword(s):  
Environmental Dna ◽  
Sequencing Depth ◽  
Dna Metabarcoding

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

scholarly journals Corrigendum to: PEMA: a flexible pipeline for environmental DNA metabarcoding analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Haris Zafeiropoulos ◽  
Ha Quoc Viet ◽  
Katerina Vasileiadou ◽  
Antonis Potirakis ◽  
Christos Arvanitidis ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Environmental Dna ◽  
Marker Genes ◽  
18S Ribosomal Rna ◽  
Dna Metabarcoding

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 Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mark D. Johnson ◽  
Mohamed Fokar ◽  
Robert D. Cox ◽  
Matthew A. Barnes
Keyword(s):  
Plant Community ◽  
Plant Communities ◽  
Traditional Method ◽  
Environmental Dna ◽  
Single Species ◽  
Community Survey ◽  
Sampling Effort ◽  
Sampling Campaign ◽  
Dna Metabarcoding ◽  
Human Health Impacts

Abstract Background Airborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The majority of studies into airborne eDNA of plants has until now either focused on single species detection, specifically only pollen, or human health impacts, with no previous studies surveying an entire plant community through metabarcoding. We therefore conducted an airborne eDNA metabarcoding survey and compared the results to a traditional plant community survey. Results Over the course of a year, we conducted two traditional transect-based visual plant surveys alongside an airborne eDNA sampling campaign on a short-grass rangeland. We found that airborne eDNA detected more species than the traditional surveying method, although the types of species detected varied based on the method used. Airborne eDNA detected more grasses and forbs with less showy flowers, while the traditional method detected fewer grasses but also detected rarer forbs with large showy flowers. Additionally, we found the airborne eDNA metabarcoding survey required less sampling effort in terms of the time needed to conduct a survey and was able to detect more invasive species than the traditional method. Conclusions Overall, we have demonstrated that airborne eDNA can act as a sensitive and efficient plant community surveying method. Airborne eDNA surveillance has the potential to revolutionize the way plant communities are monitored in general, track changes in plant communities due to climate change and disturbances, and assist with the monitoring of invasive and endangered species.

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