Article

Species detection using environmental DNA from water samples.

Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble Cedex 09, France.
Biology letters (Impact Factor: 3.43). 09/2008; 4(4):423-5. DOI: 10.1098/rsbl.2008.0118
Source: PubMed

ABSTRACT The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog (Rana catesbeiana) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.

1 Bookmark
 · 
170 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: DNA quantity can be a hindrance in ecological and evolutionary research programs due to a range of factors including endangered status of target organisms, available tissue type, and the impact of field conditions on preservation methods. A potential solution to low quantity DNA lies in whole genome amplification (WGA) techniques that can substantially increase DNA yield. To date, few studies have rigorously examined sequence bias that might result from WGA and next-generation sequencing of non-model taxa. To address this knowledge deficit, we use multiple displacement amplification (MDA) and double-digest RAD sequencing on the gray mouse lemur (Microcebus murinus) to quantify bias in genome coverage and SNP calls when compared to raw genomic DNA (gDNA). We focus our efforts in providing baseline estimates of potential bias by following manufacturer's recommendations for starting DNA quantities (>100 ng). Our results are strongly suggestive that MDA enrichment does not introduce systematic bias to genome characterization. SNP calling between samples when genotyping both de-novo and with a reference genome are highly congruent (>98%) when specifying a minimum threshold of 20X stack depth to call genotypes. Relative genome coverage is also similar between MDA and gDNA and allelic dropout is not observed. SNP concordance varies based on coverage threshold, with 95% concordance reached at ~12X coverage genotyping de-novo and ~7X coverage genotyping with the reference genome. These results suggest that MDA may be a suitable solution for next-generation molecular ecological studies when DNA quantity would otherwise be a limiting factor.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 01/2015; · 7.43 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Non-indigenous species (NIS) are recognized as a global threat to biodiversity and monitoring their presence and impacts is considered a prerequisite for marine environmental management and sustainable development. However, monitoring for NIS seldom takes place except for a few baseline surveys. With the goal of serving the requirements of the EU Marine Strategy Framework Directive and the EU Regulation on the prevention and management of the introduction and spread of invasive alien species, the paper highlights the importance of early detection of NIS in dispersal hubs for a rapid management response, and of long-term monitoring for tracking the effects of NIS within recipient ecosystems, including coastal systems especially vulnerable to introductions. The conceptual framework also demonstrates the need for port monitoring, which should serve the above mentioned requirements but also provide the required information for implementation of the International Convention for the Control and Management of Ships Ballast Water and Sediments. Large scale monitoring of native, cryptogenic and NIS in natural and man-made habitats will collectively lead to meeting international requirements. Cost-efficient rapid assessments of target species may provide timely information for managers and policy-advisers focusing on particular NIS at particular localities, but this cannot replace long-term monitoring. To support legislative requirements, collected data should be verified and stored in a publicly accessible and routinely updated database/information system. Public involvement should be encouraged as part of monitoring programs where feasible.
    Marine Policy 04/2015; 54:26-35. · 2.62 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Environmental DNA (eDNA) is used to detect biodiversity by the capture, extraction, and identification of DNA shed to the environment. However, eDNA capture and extraction protocols vary widely across studies. This use of different protocols potentially biases detection results and could significantly hinder a reliable use of eDNA to detect biodiversity. We tested whether choice of eDNA capture and extraction protocols significantly influenced biodiversity detection in aquatic systems. We sampled lake and river water, captured and extracted eDNA using six combinations of different protocols with replication, and tested for the detection of four macroinvertebrate species. Additionally, using the same lake water technical replicates, we compared the effect of capture and extraction protocols on metabarcode detections of biodiversity using 16S for eubacteria and cytochrome c oxidase I (COI) for eukaryotes. Protocol combinations for capture and extraction of eDNA significantly influenced DNA yield and number of sequences obtained from next generation sequencing. We found significantly different detection rates of species ranging from zero percent to thirty-three percent. Differences in which protocol combinations produced the highest metabarcoded biodiversity were detected and demonstrate that different protocols are required for different biodiversity targets. Our results highlight that the choice of molecular protocols used for capture and extraction of eDNA from water can strongly affect biodiversity detection. Consideration of biases caused by choice of protocols should lead to a more consistent and reliable molecular workflow for repeatable and increased detection of biodiversity in aquatic communities.
    Biological Conservation 12/2014; · 4.04 Impact Factor

Full-text

Download
79 Downloads
Available from
May 22, 2014

Gentile Francesco Ficetola