scholarly journals Assessing environmental DNA metabarcoding and camera trap surveys as complementary tools for biomonitoring of remote desert water bodies

2021 ◽  
Author(s):  
Eduard Mas‐Carrió ◽  
Judith Schneider ◽  
Battogtokh Nasanbat ◽  
Samiya Ravchig ◽  
Mmabaledi Buxton ◽  
...  
Author(s):  
Yoshihisa AKAMATSU ◽  
Takayoshi TSUZUKI ◽  
Ryota YOKOYAMA ◽  
Yayoi FUNAHASHI ◽  
Munehiro OHTA ◽  
...  

Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac

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.


Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac

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.


2021 ◽  
Author(s):  
José Luis Mena ◽  
Hiromi Yagui ◽  
Vania Tejeda ◽  
Emilio Bonifaz ◽  
Eva Bellemain ◽  
...  

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Haris Zafeiropoulos ◽  
Ha Quoc Viet ◽  
Katerina Vasileiadou ◽  
Antonis Potirakis ◽  
Christos Arvanitidis ◽  
...  

2021 ◽  
Vol 126 ◽  
pp. 107698
Author(s):  
Petr Blabolil ◽  
Lynsey R. Harper ◽  
Štěpánka Říčanová ◽  
Graham Sellers ◽  
Cristina Di Muri ◽  
...  

Genome ◽  
2018 ◽  
Vol 61 (11) ◽  
pp. 807-814 ◽  
Author(s):  
Bastian Egeter ◽  
Sara Peixoto ◽  
José C. Brito ◽  
Simon Jarman ◽  
Pamela Puppo ◽  
...  

The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of difficulties with sampling eDNA from such turbid water-bodies and it is often not feasible to rely on electrical tools in remote desert environments. We trialled a manually powered filtering method in Mauritania, using pre-filtration to circumvent problems posed by turbid water in remote arid areas. From nine vertebrate species expected in the water-bodies, four were detected visually, two via metabarcoding, and one via both methods. Difficulties filtering turbid water led to severe constraints, limiting the sampling protocol to only one sampling point per study site, which alone may largely explain why many of the expected vertebrate species were not detected. The amplification of human DNA using general vertebrate primers is also likely to have contributed to the low number of taxa identified. Here we highlight a number of challenges that need to be overcome to successfully conduct metabarcoding eDNA studies for vertebrates in desert environments in Africa.


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