Valentin Vasselon
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View article: Metabarcoding outperforms traditional electrofishing in decapod and fish inventories, paving the way for enhanced biodiversity monitoring in the Caribbean
Metabarcoding outperforms traditional electrofishing in decapod and fish inventories, paving the way for enhanced biodiversity monitoring in the Caribbean Open
Environmental DNA (eDNA) metabarcoding revolutionized the biodiversity monitoring in aquatic ecosystems, giving access to taxonomic lists in a non-disruptive way. Although the method has limits, such as reduced taxonomic resolution for cer…
View article: Omics to Study and Manage Aquatic Environments: A Snapshot From the <scp>A</scp>qua<scp>E</scp>c<scp>O</scp>mics Meeting (Evian‐les‐Bains, 2025)
Omics to Study and Manage Aquatic Environments: A Snapshot From the <span>A</span>qua<span>E</span>c<span>O</span>mics Meeting (Evian‐les‐Bains, 2025) Open
The AquaEcOmics meeting brought together 280 scientists applying omics tools to aquatic research in March 2025 (Evian‐les‐Bains, France). We synthesised here the main outcomes from the 167 presentations which were given. A similar number o…
View article: Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring
Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring Open
DNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready for routine application. However, protocols and methods still vary between and within co…
View article: AquaEcOmics meeting: exploring aquatic ecology through omics. March 17-20, 2025. Program and abstracts booklet
AquaEcOmics meeting: exploring aquatic ecology through omics. March 17-20, 2025. Program and abstracts booklet Open
A meeting to explore aquatic ecosystems biodiversity, functionning and monitoring with eDNA and multi-Omics methods
View article: When Methodological Innovation Changes the Game: A 10‐Year Review of Environmental DNA (eDNA) Applied to Crayfish
When Methodological Innovation Changes the Game: A 10‐Year Review of Environmental DNA (eDNA) Applied to Crayfish Open
The use of environmental DNA (eDNA) as a tool for monitoring represents a major innovative advance in environmental science, one that enables the detection of species without the need to observe or capture them. This article assesses the s…
View article: Influence of distance from source population and seasonality in <scp>eDNA</scp> detection of white‐clawed crayfish, through <scp>qPCR</scp> and <scp>ddPCR</scp> assays
Influence of distance from source population and seasonality in <span>eDNA</span> detection of white‐clawed crayfish, through <span>qPCR</span> and <span>ddPCR</span> assays Open
The white‐clawed crayfish ( Austropotamobius pallipes ) is an emblematic taxon of European rivers, found mainly in oxygenated streams, known to be an excellent indicator of river quality. Since several decades, the population of A. pallipe…
View article: Data from Meta-IBD Project, metabarcoding for the diatom trophic indices evaluation, South West France
Data from Meta-IBD Project, metabarcoding for the diatom trophic indices evaluation, South West France Open
These data were generated within the framework of the Meta-IBD project, led by the Laboratoires des Pyrénées et des Landes and financially supported by the Adour Garonne Water Agency, including two scientific partners, Scimabio Interface a…
View article: Data from Meta-IBD Project, metabarcoding for the diatom trophic indices evaluation, South West France
Data from Meta-IBD Project, metabarcoding for the diatom trophic indices evaluation, South West France Open
These data were generated within the framework of the Meta-IBD project, led by the Laboratoires des Pyrénées et des Landes and financially supported by the Adour Garonne Water Agency, including two scientific partners, Scimabio Interface a…
View article: <scp>eDNA</scp> metabarcoding from aquatic biofilms allows studying spatial and temporal fluctuations of fish communities from Lake Geneva
<span>eDNA</span> metabarcoding from aquatic biofilms allows studying spatial and temporal fluctuations of fish communities from Lake Geneva Open
Fish communities are now studied non‐invasively using environmental DNA (eDNA) recovered from water samples. The objective of this study is to evaluate the possibility of surveying these communities using fish eDNA passively “captured” by …
View article: Filling reference libraries with diatom environmental sequences: strengths and weaknesses
Filling reference libraries with diatom environmental sequences: strengths and weaknesses Open
International audience
View article: Filling reference libraries with diatom environmental sequences: strengths and weaknesses
Filling reference libraries with diatom environmental sequences: strengths and weaknesses Open
Diatom species identification with DNA metabarcoding is an economical, fast and reliable alternative to identification via light microscopy for river quality monitoring. Using a short DNA sequence of the rbcL gene and ‘Diat.barcode’, a ref…
View article: Recommendations for the preservation of environmental samples in diatom metabarcoding studies
Recommendations for the preservation of environmental samples in diatom metabarcoding studies Open
Implementation of DNA metabarcoding for diatoms for environmental monitoring is now moving from a research to an operational phase, requiring rigorous guidelines and standards. In particular, the first steps of the diatom metabarcoding pro…
View article: A strategy for successful integration of DNA-based methods in aquatic monitoring
A strategy for successful integration of DNA-based methods in aquatic monitoring Open
Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicat…
View article: Alpine freshwater fish biodiversity assessment: an inter-calibration test for metabarcoding method set up
Alpine freshwater fish biodiversity assessment: an inter-calibration test for metabarcoding method set up Open
The analysis of environmental DNA (eDNA) by high throughput sequencing (HTS) is proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC), especially for lar…
View article: Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples
Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples Open
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 gen…
View article: DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region
DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region Open
This dataset has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers, https:…
View article: DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region
DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region Open
This dataset has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers, https:…
View article: Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects
Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects Open
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 …
View article: Changes in Ciliate Communities Reveal Modification of Lake Functioning Over the Last Century
Changes in Ciliate Communities Reveal Modification of Lake Functioning Over the Last Century Open
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 co…
View article: A practical guide to DNA-based methods for biodiversity assessment
A practical guide to DNA-based methods for biodiversity assessment Open
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 collabora…
View article: Data supplementing the article "Paleoreconstructions of ciliate communities reveal long‑term ecological changes in temperate lakes" C. Barouillet, V. Vasselon, F. Keck, L. Millet, D. Etienne, D. Galop, D. Rius & I. Domaizon published in "Scientific reports"
Data supplementing the article "Paleoreconstructions of ciliate communities reveal long‑term ecological changes in temperate lakes" C. Barouillet, V. Vasselon, F. Keck, L. Millet, D. Etienne, D. Galop, D. Rius & I. Domaizon published in "Scientific reports" Open
These data supplement the article "Changes in ciliate communities reveal modification of lake ecosystem functioning over the last century" C. Barouillet, V. Vasselon, F. Keck, L. Millet, D. Etienne, D. Galop, D. Rius & I. Domaizon submitte…
View article: Data supplementing the article "Paleoreconstructions of ciliate communities reveal long‑term ecological changes in temperate lakes" C. Barouillet, V. Vasselon, F. Keck, L. Millet, D. Etienne, D. Galop, D. Rius & I. Domaizon published in "Scientific reports"
Data supplementing the article "Paleoreconstructions of ciliate communities reveal long‑term ecological changes in temperate lakes" C. Barouillet, V. Vasselon, F. Keck, L. Millet, D. Etienne, D. Galop, D. Rius & I. Domaizon published in "Scientific reports" Open
These data supplement the article "Changes in ciliate communities reveal modification of lake ecosystem functioning over the last century" C. Barouillet, V. Vasselon, F. Keck, L. Millet, D. Etienne, D. Galop, D. Rius & I. Domaizon submitte…
View article: Strategies for the bioinformatic treatment of high-throughput sequencing data for diatom studies and bioassessment
Strategies for the bioinformatic treatment of high-throughput sequencing data for diatom studies and bioassessment Open
Diatom biomonitoring and ecological studies can greatly benefit from DNA metabarcoding compared to conventional microscopical analysis by potentially providing more reliable and accurate data in a cost- and time-efficient way. A convention…
View article: Diat.barcode: a DNA tool to decipher diatom communities for the evaluation environmental pressures
Diat.barcode: a DNA tool to decipher diatom communities for the evaluation environmental pressures Open
Diatoms (Bacillariophyta) are ubiquitous microalgae, which present a huge taxonomic diversity, changing in correlation with differing environmental conditions. This makes them excellent ecological indicators for various ecosystems and ecol…
View article: The Wild Rivers Program: Development of a “Wild Rivers” Conservation Label to be used by River Management
The Wild Rivers Program: Development of a “Wild Rivers” Conservation Label to be used by River Management Open
A wild river is a living river, which is at baseline, well-preserved, and which runs freely and is home to a rich biodiversity in its high quality waters and on its banks. In Europe there are very few rivers which could be considered “wild…
View article: Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up
Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up Open
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 cur…
View article: Aquatic biofilms can act as natural environmental DNA samplers
Aquatic biofilms can act as natural environmental DNA samplers Open
Diatoms, macroinvertebrates and fish communities are widely used for the assessment of the ecological status of rivers and lakes. Metabarcoding studies of these communities are usually performed from “bulk” samples in the case of diatoms a…
View article: Morphotaxonomy- and metabarcoding-based ecological assessment of Cyprus streams’ diatom communities and correlation with environmental and anthropogenic influences
Morphotaxonomy- and metabarcoding-based ecological assessment of Cyprus streams’ diatom communities and correlation with environmental and anthropogenic influences Open
In freshwater ecosystems, periphytic biofilms include diatom assemblages that depend on environmental conditions (e.g., nutrient concentrations, salinity, temperature etc.). These assemblages respond rapidly to environmental changes, which…