Sampling

Sampling is crucial to any ecological study. Chapter 4 “Sampling” aims at proving keys for a successful sampling campaign when using DNA metabarcoding. It first describes the origin, fate, and transport of environmental DNA in various environments, from freshwater streams to soils, and discusses the implication of the DNA cycle in the environment for answering ecological questions. The chapter presents guidelines to appropriately sample the target DNA population and maximize the representativeness of the retrieved ecological signal. Different sampling strategies at the level of the sampling area and sampling units are proposed for different environmental matrices and ecological questions. Sample storage methods maximizing the preservation of environmental DNA are also discussed.

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

BMC Ecology and Evolution ◽

10.1186/s12862-021-01947-x ◽

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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Airborne Environmental DNA Metabarcoding Detects More Diversity, More Efficiently, Than a Traditional Plant Community Survey

10.21203/rs.3.rs-764264/v1 ◽

2021 ◽

Author(s):

Mark Johnson ◽

Robert D Cox ◽

Mohamed Fokar ◽

Matthew A Barnes

Keyword(s):

Plant Community ◽

Plant Communities ◽

Environmental Dna ◽

Single Species ◽

Community Survey ◽

Sampling Campaign ◽

Dna Metabarcoding ◽

Entire Plant ◽

Time Required ◽

First Time

Abstract BackgroundAirborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The study of airborne eDNA of plants has until now focused on single species detection, with no previous studies examining the entire plant community through metabarcoding. We therefore conducted airborne eDNA metabarcoding and compared the results to a traditional plant community survey.ResultsOver the course of a year, we conducted two traditional transect-based visual plant surveys alongside a yearlong 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 method to be more efficient in terms of the time required to conduct a survey and able to detect more invasive species than traditional methods.ConclusionsOverall, we have demonstrated for the first time 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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Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Scientific Reports ◽

10.1038/s41598-021-86396-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Miriam I. Brandt ◽

Florence Pradillon ◽

Blandine Trouche ◽

Nicolas Henry ◽

Cathy Liautard-Haag ◽

...

Keyword(s):

Deep Sea ◽

Sampling Methods ◽

Alpha Diversity ◽

Environmental Dna ◽

Size Class ◽

Sampling Strategies ◽

Water Sampling ◽

Dna Metabarcoding ◽

Genetic Assessment

AbstractDespite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1–V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.

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

Journal of Japan Society of Civil Engineers Ser B1 (Hydraulic Engineering) ◽

10.2208/jscejhe.74.5_i_415 ◽

2018 ◽

Vol 74 (5) ◽

pp. I_415-I_420 ◽

Cited By ~ 1

Author(s):

Yoshihisa AKAMATSU ◽

Takayoshi TSUZUKI ◽

Ryota YOKOYAMA ◽

Yayoi FUNAHASHI ◽

Munehiro OHTA ◽

...

Keyword(s):

Comparative Study ◽

Environmental Dna ◽

Dna Metabarcoding ◽

Fish Collection

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Environmental DNA for functional diversity

10.1093/oso/9780198767220.003.0010 ◽

2018 ◽

Cited By ~ 1

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.

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Environmental DNA

10.1093/oso/9780198767220.001.0001 ◽

2018 ◽

Cited By ~ 137

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.

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