SPYGEN

Le Bourget-du-Lac, France
Le Bourget-du-Lac, France
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Treguier A.,French National Institute for Agricultural Research | Treguier A.,Agrocampus Ouest | Treguier A.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Paillisson J.-M.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | And 6 more authors.
Journal of Applied Ecology | Year: 2014

Summary: The introduction of non-native species is a major threat to biodiversity. While eradication programs of well-established invaders are costly and hazardous for non-target species, the early detection of a non-native species at low density is critical for preventing biological invasions in recipient ecosystems. Recent studies reveal that environmental DNA (eDNA) is a powerful tool for detecting target species in aquatic ecosystems, but these studies focus mostly on fish and amphibians. We examine the reliability of using eDNA to detect the presence of an invasive freshwater crustacean species, the red swamp crayfish Procambarus clarkii. Species-specific primers and probes were designed; their specificity was tested using in silico PCR simulations and against tissues of other crayfish species. Limits of detection and quantification were specified for the target DNA sequence by means of quantitative PCR amplifications on dilution series of known amount of P. clarkii DNA. The method was applied to water samples collected in 158 ponds in a French Nature Park, and results were compared to a traditional method using food-baited funnel traps. Environmental DNA had a better detection efficiency but predominantly led to divergent results compared with the trapping method. While habitat features partly explained the failure of crayfish detection by trapping, detection by eDNA was problematic at low crayfish abundances. When P. clarkii was detected, the estimated concentrations of crayfish DNA in water samples were always below the limit of quantification for the target DNA sequence. Synthesis and applications. The combination of environmental DNA (eDNA) and conventional trapping methods is recommended to monitor the invasion by P. clarkii in small waterbodies such as ponds. However, the risk of mortality for non-target species, notably amphibians, has to be carefully evaluated before large-scale deployment of traps. Contrary to fish and amphibians, a low amount of extracellular DNA in water is suspected to be the major limitation for crayfish detection by molecular approaches. Current advancements in PCR technology, together with optimization of the water sampling method, promise upcoming developments of eDNA detection for aquatic invertebrate species. © 2014 British Ecological Society.


PubMed | Agence Center Ouest, IRSTEA, Copenhagen University, Rhone Alpes Regional Direction and 8 more.
Type: Journal Article | Journal: Molecular ecology | Year: 2016

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, invitro and insitu. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI=0.90-0.99) vs. 0.58 (CI=0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.


PubMed | University of Lorraine, SPYGEN, French National Center for Scientific Research, University of Strasbourg and University of Duisburg - Essen
Type: | Journal: PeerJ | Year: 2016

Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.


PubMed | University of Lausanne, University Grenoble Alpes, SPYGEN, Viale dellUniversita 10 and Museum of Zoology
Type: Journal Article | Journal: PloS one | Year: 2016

Repeated introductions and spread of invasive mosquito species (IMS) have been recorded on a large scale these last decades worldwide. In this context, members of the mosquito genus Aedes can present serious risks to public health as they have or may develop vector competence for various viral diseases. While the Tiger mosquito (Aedes albopictus) is a well-known vector for e.g. dengue and chikungunya viruses, the Asian bush mosquito (Ae. j. japonicus) and Ae. koreicus have shown vector competence in the field and the laboratory for a number of viruses including dengue, West Nile fever and Japanese encephalitis. Early detection and identification is therefore crucial for successful eradication or control strategies. Traditional specific identification and monitoring of different and/or cryptic life stages of the invasive Aedes species based on morphological grounds may lead to misidentifications, and are problematic when extensive surveillance is needed. In this study, we developed, tested and applied an environmental DNA (eDNA) approach for the detection of three IMS, based on water samples collected in the field in several European countries. We compared real-time quantitative PCR (qPCR) assays specific for these three species and an eDNA metabarcoding approach with traditional sampling, and discussed the advantages and limitations of these methods. Detection probabilities for eDNA-based approaches were in most of the specific comparisons higher than for traditional survey and the results were congruent between both molecular methods, confirming the reliability and efficiency of alternative eDNA-based techniques for the early and unambiguous detection and surveillance of invasive mosquito vectors. The ease of water sampling procedures in the eDNA approach tested here allows the development of large-scale monitoring and surveillance programs of IMS, especially using citizen science projects.


PubMed | Cornell University, British Petroleum, São Paulo State University and University of Sao Paulo
Type: | Journal: Molecular ecology resources | Year: 2016

Understanding the geographical distribution and community composition of species is crucial to monitor species persistence and define effective conservation strategies. Environmental DNA (eDNA) has emerged as a powerful noninvasive tool for species detection. However, most eDNA survey methods have been developed and applied in temperate zones. We tested the feasibility of using eDNA to survey anurans in tropical streams in the Brazilian Atlantic forest and compared the results with short-term visual and audio surveys. We detected all nine species known to inhabit our focal streams with one single visit for eDNA sampling. We found a higher proportion of sequence reads and larger number of positive PCR replicates for more common species and for those with life cycles closely associated with the streams, factors that may contribute to increased release of DNA in the water. However, less common species were also detected in eDNA samples, demonstrating the detection power of this method. Filtering larger volumes of water resulted in a higher probability of detection. Our data also show it is important to sample multiple sites along streams, particularly for detection of target species with lower population densities. For the three focal species in our study, the eDNA metabarcoding method had a greater capacity of detection per sampling event than our rapid field surveys, and thus, has the potential to circumvent some of the challenges associated with traditional approaches. Our results underscore the utility of eDNA metabarcoding as an efficient method to survey anuran species in tropical streams of the highly biodiverse Brazilian Atlantic forest.


Dejean T.,SPYGEN | Dejean T.,CNRS Alpine Ecology Laboratory | Valentini A.,SPYGEN | Valentini A.,CNRS Alpine Ecology Laboratory | And 5 more authors.
PLoS ONE | Year: 2011

The precise knowledge of species distribution is a key step in conservation biology. However, species detection can be extremely difficult in many environments, specific life stages and in populations at very low density. The aim of this study was to improve the knowledge on DNA persistence in water in order to confirm the presence of the focus species in freshwater ecosystems. Aquatic vertebrates (fish: Siberian sturgeon and amphibian: Bullfrog tadpoles) were used as target species. In control conditions (tanks) and in the field (ponds), the DNA detectability decreases with time after the removal of the species source of DNA. DNA was detectable for less than one month in both conditions. The density of individuals also influences the dynamics of DNA detectability in water samples. The dynamics of detectability reflects the persistence of DNA fragments in freshwater ecosystems. The short time persistence of detectable amounts of DNA opens perspectives in conservation biology, by allowing access to the presence or absence of species e.g. rare, secretive, potentially invasive, or at low density. This knowledge of DNA persistence will greatly influence planning of biodiversity inventories and biosecurity surveys. © 2011 Dejean et al.


Dejean T.,SPYGEN | Dejean T.,CNRS Alpine Ecology Laboratory | Valentini A.,SPYGEN | Miquel C.,CNRS Alpine Ecology Laboratory | And 4 more authors.
Journal of Applied Ecology | Year: 2012

1.Alien invasive species (AIS) are one of the major causes of biodiversity loss and global homogenization. Once an AIS becomes established, costs of control can be extremely high and complete eradication is not always achieved. The ability to detect a species at a low density greatly improves the success of eradication and decreases both the costs of control and the impact on ecosystems. 2.In this study, we compare the sensitivity of traditional field methods, based on auditory and visual encounter surveys, with an environmental DNA (eDNA) survey for the detection of the American bullfrog Rana catesbeiana=Lithobates catesbeianus, which is invasive in south-western France. 3.We demonstrate that the eDNA method is valuable for species detection and surpasses traditional amphibian survey methods in terms of sensitivity and sampling effort. The bullfrog was detected in 38 sites using the molecular method, compared with seven sites using the diurnal and nocturnal surveys, suggesting that traditional field surveys have strongly underestimated the distribution of the American bullfrog. 4.Synthesis and applications. The environmental DNA approach permits the early detection of alien invasive species (AIS), at very low densities and at any life stage, which is particularly important for the detection of rare and/or secretive aquatic species. This method can also be used to confirm the sensitivity of control operations and to better identify the distributions of vulnerable species, making this a very relevant tool for species inventory and management. The environmental DNA approach permits the early detection of alien invasive species (AIS), at very low densities and at any life stage, which is particularly important for the detection of rare and/or secretive aquatic species. This method can also be used to confirm the sensitivity of control operations and to better identify the distributions of vulnerable species, making this a very relevant tool for species inventory and management. © 2012 The Authors. Journal of Applied Ecology © 2012 British Ecological Society.


Biggs J.,Freshwater Habitats Trust | Ewald N.,Freshwater Habitats Trust | Valentini A.,Spygen | Gaboriaud C.,Spygen | And 8 more authors.
Biological Conservation | Year: 2014

The use of environmental DNA (eDNA) is rapidly emerging as a potentially valuable survey technique for rare or hard to survey freshwater organisms. For the great crested newt (Triturus cristatus) in the UK, the substantial cost and manpower requirements of traditional survey methods have hampered attempts to assess the status of the species. We tested whether eDNA could provide the basis for a national citizen science-based monitoring programme for great crested newts by (i) comparing the effectiveness of eDNA monitoring with torch counts, bottle trapping and egg searches and (ii) assessing the ability of volunteers to collect eDNA samples throughout the newt's UK range. In 35 ponds visited four times through the breeding season, eDNA detected newts on 139 out of 140 visits, a 99.3% detection rate. Bottle traps, torch counts and egg searches were significantly less effective, detecting newts 76%, 75% and 44% of the time. eDNA was less successful at predicting newt abundance being positively, but weakly, correlated with counts of the number of newts. Volunteers successfully collected eDNA samples across the UK with 219 of 239 sites (91.3%) correctly identified as supporting newts. 8.7% of sites generated false negatives, either because of very small newt populations or practical difficulties in sample collection. There were no false positives. Overall, we conclude that eDNA is a highly effective survey method and could be used as the basis for a national great crested newt monitoring programme. © 2014 Elsevier Ltd.


Giampaoli S.,Foro Italico University of Rome | Berti A.,Carabinieri | Di Maggio R.M.,Geoscienze Forensi Italia | Pilli E.,University of Florence | And 7 more authors.
Forensic Science International | Year: 2014

The identification of the source of a specific soil sample is a crucial step in forensic investigations. Rapid advances in next generation sequencing (NGS) technology and the strong reduction of the cost of sequencing have recently opened new perspectives. In the present work a metabarcoding approach has been successfully applied to forensic and environmental soil samples, allowing the accurate and sensitive analysis of microflora (mfDNA), plants, metazoa, and protozoa DNA. The identification of the biological component by DNA metabarcoding is a strong element for the discrimination of samples geologically very similar but coming for distinct environments. © 2014 Elsevier Ireland Ltd.


Patent
Spygen | Date: 2013-11-22

The invention relates to a floating vessel for taking liquid samples, comprising a shell (2) that has a hull (3) to be submerged in a liquid medium below the water line and a superstructure (4) arranged above the water line; the vessel also comprises air propulsion means, means for taking and storing samples, and means for remotely controlling the air propulsion means and the sampling means; and the vessel further comprises a secondary detachable shell (32) provided with means for fixing to the shell (2) of the vessel, covering at least the hull of the vessel.

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