Environmental DNA

@article{Taberlet2012EnvironmentalD,
  title={Environmental DNA},
  author={Pierre Taberlet and Eric Coissac and Mehrdad Hajibabaei and Loren H. Rieseberg},
  journal={Molecular Ecology},
  year={2012},
  volume={21}
}
PIERRE TABERLET,* ERIC COISSAC,* MEHRDAD HAJIBABAEI† and LOREN H. RIESEBERG,‡§ *Laboratoire d’Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France, †Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada, ‡Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada, §Department of Biology, Indiana University, Bloomington, IN 47405, USA 

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TLDR
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Integrating micro and macro-organism dispersal : modes , techniques and challenges with 1 particular focus on co-dispersal

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TLDR
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Book review: Environmental DNA: For Biodiversity Research and Monitoring by Pierre Taberlet, Aurélie Bonin, Lucie Zinger and Eric Coissac

TLDR
The authors of Environmental DNA aim to address the gap by focusing specifically on eDNA research and its applications, providing a vehicle which not only clearly articulates the basics to those unfamiliar with the field, but also provides an incredible amount of detail with regards to designing and performing metabarcoding studies.
...

References

SHOWING 1-10 OF 41 REFERENCES

Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation

TLDR
The genetic analyses on historical lake sediments revealed inter‐ and intra‐specific variation in diatoms, which is partially hidden behind single morphotypes.

Carnivore diet analysis based on next‐generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan

TLDR
The DNA‐based approach proposed here represents a valuable complement to current conventional methods and can be applied to other carnivore species with only a slight adjustment relating to the design of the blocking oligonucleotide specific to the predator sequence.

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

TLDR
Large variation in the level of detection among the groups and between modern and ancient samples is found, and the in silico approach offered a reliable estimate of the suitability of a marker.

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

TLDR
The power of applying next-generation pyrosequencing to identify and enumerate eukaryote species assemblages in the context of assessing the impacts of human activity on ecosystems is illustrated.

A DNA barcode for land plants

TLDR
The 2-locus combination of rbcL+matK will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

Tracking earthworm communities from soil DNA

TLDR
It is shown that combining DNA metabarcoding and next‐generation sequencing facilitates the identification of earthworm species from soil samples, and the potential of environmental DNA as a tool to assess the diversity of other soil‐dwelling animal taxa is illustrated.

Molecular detection of marine nematodes from environmental samples: overcoming eukaryotic interference

TLDR
This study demonstrates for the first time that PCR combined with DGGE can be used to explore the community composition of many meiofaunal groups, such as nematodes, from DNA extracted directly from marine and estuarine sediments.

Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms

TLDR
Phylogenetic analysis of 16S rRNA gene sequences recovered from one of the libraries indicates that the BAC libraries contain DNA from a wide diversity of microbial phyla, including sequences from diverse taxa such as the low-G+C, gram-positive Acidobacterium,Cytophagales, and Proteobacteria.

Species detection using environmental DNA from water samples

TLDR
A novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water, using specific primers that amplify short mitochondrial DNA sequences to track the existence of a frog in controlled environments and natural wetlands.

Meta‐barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

TLDR
It is found that DNA from the soil surface reflects overall taxonomic richness and relative biomass of individual species, however, one species that was recently introduced was not detected and animal behaviour was shown to influence DNA deposition rates.