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Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring
Valentin Vasselon
,
Sinziana Rivera
,
Éva Ács
,
Salomé Baja Almeida
,
Karl Andree
Journal articles
hal-04930501v1
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eDNA metabarcoding from aquatic biofilms allows studying spatial and temporal fluctuations of fish communities from Lake Geneva
Sinziana F Rivera
,
Valentin Vasselon
,
Agnès Bouchez
,
Frédéric Rimet
Journal articles
hal-04213758v1
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Which barcode to decipher freshwater microalgal assemblages? Tests on mock communities
Alexis Canino
,
Clarisse Lemonnier
,
Benjamin Alric
,
Agnes Bouchez
,
Isabelle Domaizon
Journal articles
hal-04210529v1
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Diatom endemism and taxonomic turnover: Assessment in high-altitude alpine lakes covering a large geographical range
Frédéric Rimet
,
Eveline Pinseel
,
Agnes Bouchez
,
Bella Japoshvili
,
Levan Mumladze
Journal articles
hal-04247525v1
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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
Journal articles
hal-03881952v1
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Evidence of Bacterial Community Coalescence between Freshwater and Discharged tpm-Harboring Bacterial Taxa from Hospital and Domestic Wastewater Treatment Plants among Epilithic Biofilms
Rayan Bouchali
,
Laurence Marjolet
,
Leslie Mondamert
,
Teofana Chonova
,
Sébastien Ribun
Journal articles
hal-04154873v1
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Passive sampling of environmental DNA in aquatic environments using 3D‐printed hydroxyapatite samplers
Héloïse Verdier
,
Lara Konecny‐dupre
,
Christophe Marquette
,
Helen Reveron
,
Solène Tadier
Journal articles
hal-03601922v1
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A strategy for successful integration of DNA-based methods in aquatic monitoring
Philippe Blancher
,
Estelle Lefrançois
,
Frédéric Rimet
,
Valentin Vasselon
,
Christine Argillier
Journal articles
hal-03976834v1
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Recommendations for the preservation of environmental samples in diatom metabarcoding studies
Ana Baricevic
,
Cécile Chardon
,
Maria Kahlert
,
Satu Maaria Karjalainen
,
Daniela Maric Pfannkuchen
Journal articles
hal-03976810v1
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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
Journal articles
hal-03977006v1
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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
Journal articles
hal-03511662v1
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Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring
M. Sagova-Mareckova
,
J. Boenigk
,
Agnes Bouchez
,
K. Cermakova
,
T. Chonova
Journal articles
hal-03487093v1
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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
Journal articles
hal-03528828v1
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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
Journal articles
hal-02860583v1
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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
Journal articles
hal-03103971v1
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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
Journal articles
hal-03238653v1
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Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects
Sinziana Rivera
,
Frédéric Rimet
,
Valentin Vasselon
,
Marine Vautier
,
Isabelle Domaizon
Journal articles
hal-03510613v1
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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
Journal articles
pasteur-03159791v1
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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
Journal articles
hal-02955898v1
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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
Journal articles
hal-03484541v1
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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
Journal articles
hal-03510646v1
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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
Journal articles
hal-03303887v1
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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
Journal articles
hal-03238813v1
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Unlocking our understanding of intermittent rivers and ephemeral streams with genomic tools
Rosetta C Blackman
,
Florian Altermatt
,
Arnaud Foulquier
,
Tristan Lefébure
,
Maïlys Gauthier
Journal articles
hal-03369170v1
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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
Journal articles
hal-02901285v1
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Key questions for next-generation biomonitoring
Andreas Makiola
,
Zacchaeus G. Compson
,
Donald J Baird
,
Matthew A. Barnes
,
Sam Philip Boerlijst
Journal articles
hal-02402296v1
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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
Journal articles
hal-02520259v1
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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
Journal articles
hal-02569099v1
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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
Journal articles
hal-02557859v1
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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
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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
Journal articles
hal-02520169v1
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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
Journal articles
hal-02618767v1
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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
Journal articles
hal-02619428v1
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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
Journal articles
hal-03148548v1
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Autumn drought drives functional diversity of benthic diatom assemblages of continental intermittent streams
Viktória B-Béres
,
Béla Tóthmérész
,
István Bácsi
,
Gabor Borics
,
András Abonyi
Journal articles
hal-02619814v1
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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
Journal articles
hal-02609267v1
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Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms
Andreia Mortágua
,
Valentin Vasselon
,
Ricardo Oliveira
,
Carmen Elias
,
Cécile Chardon
Journal articles
hal-02623986v1
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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
Journal articles
hal-02381793v1
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Diat.barcode, an open-access curated barcode library for diatoms
Frédéric Rimet
,
Evgenuy Gusev
,
Maria Kahlert
,
Martyn G. Kelly
,
Maxim Kulikovskiy
Journal articles
hal-02619171v1
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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
Journal articles
hal-02624302v1
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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
Journal articles
hal-02608198v1
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Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)
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