|
Passive sampling of environmental DNA in aquatic environments using 3D‐printed hydroxyapatite samplers
Héloïse Verdier
,
Lara Konecny‐dupre
,
Christophe Marquette
,
Helen Reveron
,
Solène Tadier
et al.
Journal articles
hal-03601922v1
|
|
SIPIBEL observatory: Data on usual pollutants (solids, organic matter, nutrients, ions) and micropollutants (pharmaceuticals, surfactants, metals), biological and ecotoxicity indicators in hospital and urban wastewater, in treated effluent and sludge from wastewater treatment plant, and in surface and groundwater
Jean-Luc Bertrand-Krajewski
,
Rémy Bournique
,
Vivien Lecomte
,
Noémie Pernin
,
Laure Wiest
et al.
Journal articles
hal-03511662v1
|
|
Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods
J. Pawlowski
,
K. Bruce
,
K. Panksep
,
F.I. Aguirre
,
S. Amalfitano
et al.
Journal articles
hal-03977006v1
|
|
A strategy for successful integration of DNA-based methods in aquatic monitoring
Philippe Blancher
,
Estelle Lefrançois
,
Frédéric Rimet
,
Valentin Vasselon
,
Christine Argillier
et al.
Journal articles
hal-03976834v1
|
|
Environmental filtering and mass effect are two important processes driving lake benthic diatoms: Results of a DNA metabarcoding study in a large lake
Frédéric Rimet
,
Alexis Canino
,
Teofana Chonova
,
Julie Guéguen
,
Agnes Bouchez
et al.
Journal articles
hal-03881952v1
|
|
Recommendations for the preservation of environmental samples in diatom metabarcoding studies
Ana Baricevic
,
Cécile Chardon
,
Maria Kahlert
,
Satu Maaria Karjalainen
,
Daniela Maric Pfannkuchen
et al.
Journal articles
hal-03976810v1
|
|
Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring
M. Sagova-Mareckova
,
J. Boenigk
,
Agnes Bouchez
,
K. Cermakova
,
T. Chonova
et al.
Journal articles
hal-03487093v1
|
|
How can integrated morphotaxonomy- and metabarcoding-based diatom assemblage analyses best contribute to the ecological assessment of streams?
Panayiota Pissaridou
,
Marco Cantonati
,
Agnes Bouchez
,
Iakovos Tziortzis
,
Gerald Dörflinger
et al.
Journal articles
hal-03528828v1
|
|
Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers
Sinziana Rivera
,
Valentin Vasselon
,
Nathalie Mary
,
Olivier Monnier
,
Fréderic Rimet
et al.
Journal articles
hal-03103971v1
|
|
The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding
Kálmán Tapolczai
,
Géza Selmeczy
,
Beáta Szabó
,
Viktória B-Béres
,
François Keck
et al.
Journal articles
hal-03238653v1
|
|
Unlocking our understanding of intermittent rivers and ephemeral streams with genomic tools
Rosetta C Blackman
,
Florian Altermatt
,
Arnaud Foulquier
,
Tristan Lefébure
,
Maïlys Gauthier
et al.
Journal articles
hal-03369170v1
|
|
A pilot experiment to assess the efficiency of pharmaceutical plant wastewater treatment and the decreasing effluent toxicity to periphytic biofilms
Vincent Tardy
,
Chloé Bonnineau
,
Agnes Bouchez
,
Cécile Miège
,
Matthieu Masson
et al.
Journal articles
hal-03238813v1
|
|
Phytool, a ShinyApp to homogenise taxonomy of freshwater microalgae from DNA barcodes and microscopic observations
Alexis Canino
,
Agnes Bouchez
,
Christophe Laplace-Treyture
,
Isabelle Domaizon
,
Frédéric Rimet
et al.
Journal articles
hal-03484541v1
|
|
Herbicide-Induced Shifts in the Periphyton Community Composition Indirectly Affect Feeding Activity and Physiology of the Gastropod Grazer Physella acuta
Marco Konschak
,
Jochen Zubrod
,
Tomás Duque Acosta
,
Agnes Bouchez
,
Alexandra Kroll
et al.
Journal articles
hal-03510646v1
|
|
Monitoring the ecological status of rivers with diatom eDNA metabarcoding: a comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index
Laure Apothéloz‐perret‐gentil
,
Agnes Bouchez
,
Tristan Cordier
,
Arielle Cordonier
,
Julie Guéguen
et al.
Journal articles
hal-02955898v1
|
|
Unlocking our understanding of intermittent rivers and ephemeral streams with genomic tools
Rosetta C Blackman
,
Florian Altermatt
,
Arnaud Foulquier
,
Tristan Lefébure
,
Maïlys Gauthier
et al.
Journal articles
hal-03977024v1
|
|
Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap
Tristan Cordier
,
Laura Alonso‐sáez
,
Laure Apothéloz‐perret‐gentil
,
Eva Aylagas
,
David Bohan
et al.
Journal articles
hal-02860583v1
|
|
Cyprus’ diatom diversity and the association of environmental and anthropogenic influences for ecological assessment of rivers using DNA metabarcoding
Panayiota Pissaridou
,
Valentin Vasselon
,
Andreas Christou
,
Teofana Chonova
,
Athina Papatheodoulou
et al.
Journal articles
hal-03303887v1
|
|
The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding
Kálmán Tapolczai
,
Géza Selmeczy
,
Beáta Szabó
,
Viktória B-Béres
,
François Keck
et al.
Journal articles
hal-03977040v1
|
|
Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life
Frédéric Rimet
,
Eva Aylagas
,
Ángel Borja
,
Agnes Bouchez
,
Alexis Canino
et al.
Journal articles
pasteur-03159791v1
|
|
Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects
Sinziana Rivera
,
Frédéric Rimet
,
Valentin Vasselon
,
Marine Vautier
,
Isabelle Domaizon
et al.
Journal articles
hal-03510613v1
|
|
The vertical distribution of tetA and intI1 in a deep lake is rather due to sedimentation than to resuspension
Andrea Di cesare
,
Ester Eckert
,
Camille Cottin
,
Agnes Bouchez
,
Cristiana Callieri
et al.
Journal articles
hal-02569099v1
|
|
Key questions for next-generation biomonitoring
Andreas Makiola
,
Zacchaeus G. Compson
,
Donald J Baird
,
Matthew A. Barnes
,
Sam Philip Boerlijst
et al.
Journal articles
hal-02402296v1
|
|
Environmental filtering and limiting similarity as main forces driving diatom community structure in Mediterranean and continental temporary and perennial streams
Gábor Várbíró
,
Gabor Borics
,
Maria Helena Novais
,
Maria Manuela Morais
,
Frédéric Rimet
et al.
Journal articles
hal-02901285v1
|
|
Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software
Sinziana Rivera
,
Valentin Vasselon
,
Agnes Bouchez
,
Frédéric Rimet
Journal articles
hal-02518194v1
|
|
A taxonomy-free approach based on machine learning to assess the quality of rivers with diatoms
Maria João Feio
,
Sonia R.Q. Serra
,
Andreia Mortágua
,
Agnes Bouchez
,
Frédéric Rimet
et al.
Journal articles
hal-02520169v1
|
|
Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers
Javier Pérez-Burillo
,
Rosa Trobajo
,
Valentin Vasselon
,
Frédéric Rimet
,
Agnes Bouchez
et al.
Journal articles
hal-02557859v1
|
|
Benthic diatom community dynamics in Mediterranean intermittent streams: Effects of water availability and their potential as indicators of dry-phase ecological status
Maria Helena Novais
,
Eduardo F Morales
,
Alexandra Marchã Penha
,
Miguel Potes
,
Agnes Bouchez
et al.
Journal articles
hal-02520259v1
|
|
Autumn drought drives functional diversity of benthic diatom assemblages of continental intermittent streams
Viktória B-Béres
,
Béla Tóthmérész
,
István Bácsi
,
Gabor Borics
,
András Abonyi
et al.
Journal articles
hal-02619814v1
|
|
Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)
Maria Kahlert
,
Martyn G. Kelly
,
David G. Mann
,
Frédéric Rimet
,
Shinya Sato
et al.
Journal articles
hal-02628803v1
|
|
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status
Bonnie Bailet
,
Agnes Bouchez
,
Alain Franc
,
Jean-Marc Frigerio
,
François Keck
et al.
Journal articles
hal-02432989v1
|
|
DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work
Hannah Weigand
,
Arne J. Beermann
,
Filipe O. Costa
,
Zoltán Csabai
,
Sofia Duarte
et al.
Journal articles
hal-02626077v1
|
|
Diatom DNA metabarcoding for biomonitoring: strategies to avoid major taxonomical and bioinformatical biases Llmiting molecular indices capacities
Kálmán Tapolczai
,
François Keck
,
Agnes Bouchez
,
Frédéric Rimet
,
Maria Kahlert
et al.
Journal articles
hal-02624302v1
|
|
Diat.barcode, an open-access curated barcode library for diatoms
Frédéric Rimet
,
Evgenuy Gusev
,
Maria Kahlert
,
Martyn G. Kelly
,
Maxim Kulikovskiy
et al.
Journal articles
hal-02619171v1
|
|
Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding
Teofana Chonova
,
Rainer Kurmayer
,
Frédéric Rimet
,
Jérôme Labanowski
,
Valentin Vasselon
et al.
Journal articles
hal-02381793v1
|
|
Assessing pollution of aquatic environments with diatoms' DNA metabarcoding: experience and developments from France Water Framework Directive networks
Valentin Vasselon
,
Frédéric Rimet
,
Isabelle Domaizon
,
Olivier Monnier
,
Yorick Reyjol
et al.
Journal articles
hal-03148548v1
|
|
Factors influencing the heterogeneity of benthic diatom communities along the shoreline of natural alpine lakes
Frédéric Rimet
,
Léa Féret
,
Agnes Bouchez
,
Jean Marcel Dorioz
,
Etienne Dambrine
et al.
Journal articles
hal-02618767v1
|
|
The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)
Kalman Tapolczai
,
Valentin Vasselon
,
Agnes Bouchez
,
Csilla Stenger-Kovács
,
Judit Padisák
et al.
Journal articles
hal-02619428v1
|
|
A comparison of biotic groups as dry-phase indicators of ecological quality in intermittent rivers and ephemeral streams
R. Stubbington
,
A. Paillex
,
J. England
,
A. Barthes
,
Agnes Bouchez
et al.
Journal articles
hal-02608198v1
|
|
Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms
Andreia Mortágua
,
Valentin Vasselon
,
Ricardo Oliveira
,
Carmen Elias
,
Cécile Chardon
et al.
Journal articles
hal-02623986v1
|
|
Recommandations d'un collectif franco-suisse d'experts pour une meilleure évaluation de la qualité écotoxicologique des sédiments par l'étude des communautés benthiques
Stéphane Pesce
,
J.D. Ferrari
,
C. Bonnineau
,
C. Casado
,
L. Apotheloz Perret Gentil
et al.
Sciences Eaux & Territoires, 2019, 55 (HS), pp.9
Journal articles
hal-02609267v1
|
|
Sensitivities of seven algal species to triclosan, fluoxetine and their mixtures
Ran Bi
,
Xiangfeng Zeng
,
Lei Mu
,
Liping Hou
,
Wenhua Liu
et al.
Journal articles
hal-02621712v1
|
|
Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes
Frédéric Rimet
,
Valentin Vasselon
,
Barbara A.-Keszte
,
Agnes Bouchez
Journal articles
hal-02625205v1
|
|
ECOTOX, new questions for terrestrial and aquatic ecotoxicology
Christian Mougin
,
Agnes Bouchez
,
Laurence Denaix
,
Jeanne Garric
,
Fabrice Martin-Laurent
et al.
Journal articles
hal-01878281v1
|
|
The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes
Frédéric Rimet
,
Nelida Abarca
,
Agnes Bouchez
,
Wolf-Henning Kusber
,
Regine Jahn
et al.
Journal articles
hal-02624468v1
|
|
Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment
S. F. Rivera
,
Valentin Vasselon
,
Stéphan Jacquet
,
Agnes Bouchez
,
D. Ariztegui
et al.
Journal articles
hal-02621047v1
|
|
DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior
Sinziana Rivera
,
Valentin Vasselon
,
Katia Ballorain
,
Alice Carpentier
,
Carlos E. Wetzel
et al.
Journal articles
hal-02624564v1
|
|
Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of OTUs' ecological profiles
F Keck
,
Valentin Vasselon
,
Frédéric Rimet
,
Agnes Bouchez
,
M Kahlert
et al.
Journal articles
hal-02625977v1
|
|
SIPIBEL : un site pilote pour l’étude des effluents hospitaliers et urbains. Les grands enseignements après cinq ans de suivi et de recherche
Vivien Lecomte
,
Jean-Luc Bertrand-Krajewski
,
Agnes Bouchez
,
Benoit Cournoyer
,
Christophe Dagot
et al.
Journal articles
hal-01825316v1
|
|
Implementation options for DNA-based identification into ecological status assessment under the european water framework directive
Daniel Hering
,
Angel Borja
,
J.Iwan Jones
,
Didier Pont
,
Pieter Boets
et al.
Journal articles
hal-02626478v1
|
|
Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program
Estelle Lefrancois
,
Laure Apothéloz-Perret-Gentil
,
Philippe Blancher
,
Samuel Botreau
,
Cécile Chardon
et al.
Journal articles
hal-02916342v1
|
|
The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems
Jan Pawlowski
,
Mary Kelly-Quinn
,
Florian Altermatt
,
Laure Apothéloz-Perret-Gentil
,
Pedro Beja
et al.
Journal articles
hal-02629210v1
|
|
River biofilm community changes related to pharmaceutical loads emitted by a wastewater treatment plant
Teofana Chonova
,
Jérôme Labanowski
,
Benoit Cournoyer
,
Cècile Chardon
,
François Keck
et al.
Journal articles
hal-01859406v1
|
|
Sensitive vs. tolerant Nitzschia palea (Kützing) W. Smith strains to atrazine: a biochemical perspective
S M Esteves
,
S F P Almeida
,
S Gonçalves
,
Frédéric Rimet
,
Agnes Bouchez
et al.
Journal articles
hal-02623950v1
|
|
The SIPIBEL project: treatment of hospital and urban wastewater in a conventional urban wastewater treatment plant.
Teofana Chonova
,
Vivien Lecomte
,
Jean-Luc Bertrand-Krajewski
,
Agnes Bouchez
,
Jérôme Labanowski
et al.
Journal articles
hal-01606931v1
|
|
Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?
Valentin Vasselon
,
|