DNA from soil mirrors plant taxonomic and growth form diversity.

@article{Yoccoz2012DNAFS,
  title={DNA from soil mirrors plant taxonomic and growth form diversity.},
  author={Nigel Gilles Yoccoz and Kari Anne Br{\aa}then and Ludovic Gielly and James Haile and Mary E. Edwards and Tomasz Goslar and Henrik von Stedingk and Anne Krag Brysting and Eric Coissac and François Pompanon and J{\o}rn Henrik S{\o}nsteb{\o} and Christian Miquel and Alice Valentini and Francesco de Bello and J{\'e}r{\^o}me Chave and Wilfried Thuiller and Patrick Wincker and Corinne Cruaud and Frédérick Gavory and Magnus Rasmussen and M. Gilbert and Ludovic Orlando and Christian Brochmann and Eske Willerslev and Pierre Taberlet},
  journal={Molecular ecology},
  year={2012},
  volume={21 15},
  pages={
          3647-55
        }
}
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from… 

Figures and Tables from this paper

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers

The value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs is established and the collaborative development of DNA barcoding and metabarcoding is supported.

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys.

Short and informative DNA products to indirectly measure vascular plant biodiversity

The research examines the complexities associated with deriving biomass estimates from molecular data and the need to consider biomass turnover, and the use of soil‐derived meta‐barcodes extends beyond estimating vascular plant diversity, with the approach being suited to the range of ecological applications, especially scenarios where DNA may be degraded.

Evaluating a multigene environmental DNA approach for biodiversity assessment

It is demonstrated that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S, and the COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods.

Assessing Belowground Plant Diversity in Wetland Soil through DNA Metabarcoding: Impact of DNA Marker Selection and Analysis of Temporal Patterns

Based on the relative annotation, resolution and recovery ability of the DNA markers, rbcL and ITS2 were recommended for future biodiversity assessments and an interaction between DNA marker and observed community turnover was identified and positively correlated with length of DNA marker.

Towards next‐generation biodiversity assessment using DNA metabarcoding

The near‐term future of DNA metabarcoding has an enormous potential to boost data acquisition in biodiversity research as further developments associated with the impressive progress in DNA sequencing will eliminate the currently required DNA amplification step, and comprehensive taxonomic reference libraries can be built based on the well‐curated DNA extract collections maintained by standardized barcoding initiatives.

Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps)

The results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.

Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning

Soil DNA is explored at four forest types in Doi Suthep-Pui National Park in Northern Thailand with a strong congruence between the conventional morphology- and eDNA-based data of plant diversity in the studied areas, suggesting that the authors are now facing agricultural intensification leading to deforestation.

A multi-gene region targeted capture approach to detect plant DNA in environmental samples: A case study from coastal environments

A multi-gene targeted capture method that simultaneously targets 20 chloroplast gene regions in a single assay across all flowering plant species is developed, which confers an improved level of data on community composition, which can be used to better understand flowering plant assemblages in environmental samples.

Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost.

The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost by detecting 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered.
...

References

SHOWING 1-10 OF 44 REFERENCES

Spatial patterns of plant diversity below‐ground as revealed by DNA barcoding

Insight is provided into the role of environmental filtering and competitive interactions in the organization of plant diversity below‐ground, and the utility of barcoding for the identification of plant roots is demonstrated.

Using next‐generation sequencing for molecular reconstruction of past Arctic vegetation and climate

The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high‐throughput parallel pyrosequencing of permafrost‐preserved DNA and reconstruction of two plant communities from the last glacial period.

Identification of Amazonian Trees with DNA Barcodes

It is concluded that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

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.

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach

This work demonstrated that this new method for species identification using universal primers that amplify a very short but informative DNA fragment can be applied for diet analyses of a wide range of phytophagous species at large scales and is efficient for mammals, birds, insects and molluscs.

Evaluating high‐throughput sequencing as a method for metagenomic analysis of nematode diversity

Overall, results support the suitability of massively parallel sequencing for identification of nematodes and the frequency of reads representing individual species did not correlate with the number of individuals in the metagenomic samples, suggesting that further methodological work is necessary before it will be justified for inferring the relative abundances of species within a nematode community.

DNA barcoding for ecologists.

New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study

Analysis of diet from feces in a wild herbivore, the alpine chamois, shows that DNA-based diet analysis is faster and more taxonomically precise than studies based on microhistology, and opens new possibilities for analysing plant-herbivore interactions in the wild.

Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments

Genetic analyses of permafrost and temperate sediments reveal that plant and animal DNA may be preserved for long periods, even in the absence of obvious macrofossils, and may contain unique, and widespread, genetic records of paleoenvironments.

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

Novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method is compared, giving a detailed and relatively unbiased picture of food utilization of herbivores.