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Valentin Vasselon

Valentin Vasselon
Scimabio Interface

PhD

About

59
Publications
23,188
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Publications

Publications (59)
Article
In recent years, remarkable progress has been made in developing environmental DNA metabarcoding. However, its ability to quantify species relative abundance remains uncertain, limiting its application for biomonitoring. In diatoms, although the rbcL gene appears to be a suitable barcode for diatoms, providing relevant qualitative data to describe...
Article
Full-text available
Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identified using characteristics of their exoskeleton...
Article
Full-text available
Recent years provided intense progression in the implementation of molecular techniques in a wide variety of research fields in ecology. Biomonitoring and bioassessment can greatly benefit from DNA metabarcoding and High-Throughput Sequencing (HTS) methods that potentially provide reliable, high quantity and quality standardized data in a cost- and...
Article
Full-text available
Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In...
Article
Full-text available
Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate these bioindicators in paleoenvironmental reconstructions. In this study, we used the top–bottom paleolimnological approach and metabarcoding techniques...
Preprint
The development of DNA metabarcoding and High-Throughput Sequencing for diatoms is nowadays offering an interesting approach to assess their communities in freshwater and marine ecosystems. In the context of the implementation of these genomic methods to environmental monitoring, protocol constraints are moving from scientific to operational applic...
Article
Full-text available
The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and mic...
Book
Full-text available
This publication is an output from EU COST Action DNAqua-Net (CA 15219 - Developing new genetic tools for bioassessment of aquatic ecosystems in Europe) and would not have been possible without the opportunities for international collaboration provided by the network, supported by COST (European Cooperation in Science and Technology). Therefore, ou...
Article
Fish eDNA metabarcoding is usually performed from filtered water samples. The volume of filtered water depends on the study scope and can rapidly become time consuming according to the number of samples that have to be processed. To avoid time allocated to filtration, passive DNA samplers have been used to recover fish eDNA from marine environments...
Preprint
Full-text available
Ciliates are unicellular heterotrophic organisms that play a key role in the planktonic and benthic food webs of lakes, and represent a great potential as bioindicator. In this study, we used the top-bottom paleolimnological approach to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located a...
Presentation
Full-text available
Environmental DNA (eDNA) based methods are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Many freshwater fish are experiencing critical population decli...
Method
Full-text available
Grâce à un échantillonnage simple et un séquençage haut débit, l’identification des diatomées basée sur l’ADN est une nouvelle approche, complémentaire à la méthode classique d’identification morphologique des espèces, permettant d’obtenir des indices de qualité écologique des masses d’eau à plus haute fréquence.
Presentation
Full-text available
Many freshwater fish are experiencing critical population declines with risk of local or global extinction because of intense anthropogenic pressure and this can have serious consequences on freshwater ecosystem functioning and diversity. Current fish monitoring techniques for large rivers and lakes, however, have known shortcomings. Within the Wat...
Presentation
Full-text available
For the first time in Cyprus we consider the association of environmental and anthropogenic pressures to diatom assemblages using the rbcL 312 bp barcode, next-generation sequencing (MiSeq Illumina), and bioinformatic evaluation (Mothur Software). Statistical analysis was then applied to identify the environmental (i.e., river types, geo-morphologi...
Poster
Full-text available
Environmental DNA (eDNA) based methods (Fig.1) are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Freshwater fish are actively involved in aquatic ecosys...
Article
Full-text available
DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated wit...
Article
Human activities are the leading cause of environmental impairments. Appropriate biomonitoring of ecosystems is needed to assess these activities effectively. In freshwater ecosystems, periphytic and epilithic biofilms have diatom assemblages. These assemblages respond rapidly to environmental changes, making diatoms valuable bioindicators. For thi...
Article
Aquatic biofilms are heterogeneous assemblages of microorganisms surrounded by a matrix of extracellular polymeric substances (EPS). Recent studies suggest that aquatic biofilms can physically act as sorptive sponges of DNA. We took the opportunity from already available samples of stone biofilms and macroinvertebrates specimens collected in parall...
Technical Report
Full-text available
Detailed description of the main steps of the bio-informatics pipeline for the processing of high-throughput sequencing data for metabarcoding analysis.
Article
Full-text available
Recently, several studies demonstrated the usefulness of diatom eDNA metabarcoding as an alternative to assess the ecological quality of rivers and streams. However, the choice of the taxonomic marker as well as the methodology for data analysis differ between these studies, hampering the comparison of their results and effectiveness. The aim of th...
Article
Ecological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. H...
Article
Our study of 164 diatom samples from Catalonia (NE Spain) is the first to evaluate the applicability of DNA metabarcoding, based on high throughput sequencing (HTS) using a 312-bp rbcL marker, for biomonitoring Mediterranean rivers. For this, we compared the values of a biotic index (IPS) and the ecological status classes derived from them, between...
Article
Diatoms are a compulsory biological quality element in the ecological assessment of rivers according to the Water Framework Directive. The application of current official indices requires the identification of individuals to species or lower rank under a microscope based on the valve morphology. This is a highly time-consuming task, often susceptib...
Article
Benthic diatoms are routinely used as ecological indicators in rivers. A standardized methodology is based on biofilm sampling, species identification, and counting under microscope. DNA-metabarcoding is an alternative methodology that can identify species and assess their proportion based on high-throughput DNA sequencing. Sequence data is analyze...
Article
Full-text available
Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels—from genes to entire ecosystems. Here, we frame 10 key questions t...
Book
Full-text available
Guidance for the implementation of biological indicators in overseas territories - The diatom indices IDMsp and IDMtrait [in French]. The diatom indices IDMsp (Mayotte Species Diatom Index) and IDMtrait (Mayotte Trait Diatom Index) are tools based on the taxonomic composition of benthic diatom communities. They are designed for river quality assess...
Article
Full-text available
This report presents the outcome of the joint work of PhD students and senior researchers working with DNA-based biodiversity assessment approaches with the goal to facilitate others the access to definitions and explanations about novel DNA-based methods. The work was performed during a PhD course (SLU PNS0169) at the Swedish University of Agricul...
Article
Benthic diatom communities are used in the ecological assessment of Portuguese rivers through the calculation of an autecological index, the IPS (Indice de Polluosensibilite Specifique), officially adopted for Portugal. This index requires a high level of taxonomic expertise for morphological identification of individuals at species level. Advances...
Article
L’évaluation de l’état écologique des cours d’eau repose sur le calcul d’indices de qualité basés sur la sensibilité de certains groupes biologiques, dont les diatomées, à la pollution. La détermination et la quantification des espèces de diatomées reposent généralement sur des méthodes d’identification morphologique en microscopie qui peuvent para...
Article
Full-text available
Freshwater ecosystems are continuously affected by anthropogenic pressure. One of the main sources of contamination comes from wastewater treatment plant (WWTP) effluents that contain wide range of micro- and macropollutants. Chemical composition, toxicity levels and impact of treated effluents (TEs) on the recipient aquatic ecosystems may strongly...
Article
Full-text available
Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high-throughput sequencing (HTS) and meta-barcoding methods now used for bioassessment traditionally employ an arbitr...
Article
Full-text available
Current biomonitoring approaches are widely used but have some limitations. • DNA metabarcoding provides a new complementary tool for biomonitoring. • Metabarcoding allows extending the range of taxa used as bioindicators. • Metabarcoding data could be used to establish molecular metrics and indices. • Future work should standardise procedures and...
Article
DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices which are based o...
Article
Full-text available
Sea turtles are distributed in tropical and subtropical seas worldwide. They play several ecological roles and are considered important indicators of the health of marine ecosystems. Studying epibiotic diatoms living on turtle shells suggestively has great potential in the study of turtle behavior because diatoms are always there. However, diatom i...
Data
Spearman correlation coefficients calculated between the OTUs of Fig 7 and their abundances in the samples. (XLSX)
Data
rbcL alignment used for the constraint phylogeny in the Fig 6. (TXT)
Article
Full-text available
Wastewater treatment plants (WWTP) are the main sources of a broad spectrum of pharmaceuticals found in freshwater ecosystems. These pollutants raise environmental health concerns because of their highly bioactive nature and their chronic releases. Despite this, pharmaceuticals' effects on aquatic environments are poorly defined. Biofilms represent...
Article
Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High–Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barc...
Article
Full-text available
Stenotrophomonas maltophilia is found ubiquitously in the environment and is an important emerging nosocomial pathogen. S. maltophilia has been recently described as an Amoebae-Resistant Bacteria (ARB) that exists as part of the microbiome of various free-living amoebae (FLA) from waters. Co-culture approaches with Vermamoeba vermiformis demonstrat...
Article
Diatoms are a species-diverse phylum of microalgae often presenting high biomass in aquatic habitats. This makes them excellent ecological indicators in rivers and lakes. They are routinely used to assess ecological quality of rivers and lakes using microscopy, which is time consuming. An alternative is to determine species in samples based on shor...
Article
Full-text available
Benthic diatoms are relevant indicators of the ecological status of the littoral zone of lakes. Their use as bio-indicators is based on their morphological identification at species level using microscopy which is time consuming, requires taxonomic expertise, and is consequently expensive. To overcome these limitations, a molecular approach for dia...
Thesis
Les diatomées sont des algues unicellulaires microscopiques qui sont d’excellents indicateurs de l’état écologique du milieu dans lequel elles se trouvent. Dans le cadre de la Directive Cadre sur l’Eau (DCE), les communautés de diatomées sont utilisées pour évaluer la qualité des cours d’eau. Pour cela, des indices de qualité basés sur la sensibili...
Article
Diatoms are excellent ecological indicators of water quality because they are broadly distributed, they show high species diversity and they respond rapidly to human pressures. In Europe, the Water Framework Directive (WFD) gives the legal basis for the use of this indicator for water quality assessment and its management. Several quality indices,...
Article
Full-text available
Background Parkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobact...
Data
Mice infected by N. cyriacigeorgica GUH-2 presenting motor symptoms Behavioral disorders in two mice. One with the rhythmic and vertical movements of the head (mouse up) and the other with hemiparesis (mouse down).
Data
Number of nematodes affected in their movement using the touch response test Wild type response to the touch response test is characterised by backward movements of the nematode and then a leak forward. We compared this reaction on N2 and BY250 nematodes lineages that were not in contact with supernatant (control). Nematode affected had the same re...
Preprint
Full-text available
Background. Parkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobac...
Article
Freshwaters worldwide face serious threats, making their protection increasingly important. Freshwater monitoring has historically produced valuable data and continues to develop. Rapid improvements to biomolecular techniques are revolutionizing the way scientists describe biological communities and are bringing about major changes in biomonitoring...
Article
Current freshwater biomonitoring with diatoms is based on microscopic examination of the morphology of their silica skeleton. This standardized approach is time consuming and requires a high degree of taxonomic expertise. Metabarcoding combined with high-throughput sequencing (HTS) has great potential for next-generation biomonitoring applications...
Article
Full-text available
Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of...

Projects

Project (1)
Project
Diat.barcode is an open-access DNA barcode reference library for diatoms. Experts from several countries collaborate to complete and curate Diat.barcode. The database is accessible at https://www6.inrae.fr/carrtel-collection_eng/Barcoding-database.