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Agnès BOUCHEZ

214
Documents

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Ecologie microbienne aquatique

Publications

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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
Metabarcoding and Metagenomics, 2025, 9, pp.e133264. ⟨10.3897/mbmg.9.133264⟩
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
Environmental DNA, 2023, 5 (3), pp.570-581. ⟨10.1002/edn3.413⟩
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
International Journal of Limnology, 2023, 59, pp.8. ⟨10.1051/limn/2023008⟩
Journal articles hal-04210529v1

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
Science of the Total Environment, 2023, 871, pp.161970. ⟨10.1016/j.scitotenv.2023.161970⟩
Journal articles hal-04247525v1

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
Molecular Ecology, 2023, 32 (1), pp.124-137. ⟨10.1111/mec.16737⟩
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
Microorganisms, 2023, 11 (4), pp.922. ⟨10.3390/microorganisms11040922⟩
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
Molecular Ecology Resources, 2022, 22, pp.2158-2170. ⟨10.1111/1755-0998.13604⟩
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
Metabarcoding and Metagenomics, 2022, 6 (e85652), ⟨10.3897/mbmg.6.85652⟩
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
Metabarcoding and Metagenomics, 2022, 6 (e85844), ⟨10.3897/mbmg.6.85844⟩
Journal articles hal-03976810v1

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
Science of the Total Environment, 2022, 818, pp.151783. ⟨10.1016/j.scitotenv.2021.151783⟩
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
Data in Brief, 2022, 40, pp.107726. ⟨10.1016/j.dib.2021.107726⟩
Journal articles hal-03511662v1

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

M. Sagova-Mareckova , J. Boenigk , Agnes Bouchez , K. Cermakova , T. Chonova
Water Research, 2021, 191, pp.116767. ⟨10.1016/j.watres.2020.116767⟩
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
Metabarcoding and Metagenomics, 2021, 5, pp.111-120. ⟨10.3897/MBMG.5.68438⟩
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
Molecular Ecology, 2021, 30 (13), pp.2937-2958. ⟨10.1111/mec.15472⟩
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
Science of the Total Environment, 2021, 763, pp.144208. ⟨10.1016/j.scitotenv.2020.144208⟩
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
Ecological Indicators, 2021, 122, pp.107322. ⟨10.1016/j.ecolind.2020.107322⟩
Journal articles hal-03238653v1

Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects

Sinziana Rivera , Frédéric Rimet , Valentin Vasselon , Marine Vautier , Isabelle Domaizon
Molecular Ecology Resources, 2021, ⟨10.1111/1755-0998.13568⟩
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
Metabarcoding and Metagenomics, 2021, 5, pp.e58056. ⟨10.3897/mbmg.5.58056⟩
Journal articles pasteur-03159791v1

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
Molecular Ecology, 2021, 30 (13), pp.2959-2968. ⟨10.1111/mec.15646⟩
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
Metabarcoding and Metagenomics, 2021, 5, pp.199-205. ⟨10.3897/mbmg.5.74096⟩
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
Environmental Science and Technology, 2021, 55 (21), pp.14699-14709. ⟨10.1021/acs.est.1c01819⟩
Journal articles hal-03510646v1

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
Chemosphere, 2021, 272, pp.129814. ⟨10.1016/j.chemosphere.2021.129814⟩
Journal articles hal-03303887v1

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 of Hazardous Materials, 2021, 411, pp.125121. ⟨10.1016/j.jhazmat.2021.125121⟩
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
Frontiers in Ecology and the Environment, 2021, 19 (10), pp.574-583. ⟨10.1002/fee.2404⟩
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
Science of the Total Environment, 2020, 741, pp.140459. ⟨10.1016/j.scitotenv.2020.140459⟩
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
Frontiers in Environmental Science, In press, 7, ⟨10.3389/fenvs.2019.00197⟩
Journal articles hal-02402296v1

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
Science of the Total Environment, 2020, 719, pp.137462. ⟨10.1016/j.scitotenv.2020.137462⟩
Journal articles hal-02520259v1

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
FEMS Microbiology Ecology, 2020, 96 (2), ⟨10.1093/femsec/fiaa002⟩
Journal articles hal-02569099v1

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
Science of the Total Environment, 2020, 727, ⟨10.1016/j.scitotenv.2020.138445⟩
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
Ecological Indicators, 2020, 109, ⟨10.1016/j.ecolind.2019.105775⟩
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
Science of the Total Environment, 2020, 722, ⟨10.1016/j.scitotenv.2020.137900⟩
Journal articles hal-02520169v1

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
Hydrobiologia, 2019, 839 (1), pp.103-118. ⟨10.1007/s10750-019-03999-z⟩
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
Ecology and Evolution, 2019, 9 (1), pp.166-179. ⟨10.1002/ece3.4701⟩
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
Metabarcoding and Metagenomics, 2019, 3, ⟨10.3897/mbmg.3.39646⟩
Journal articles hal-03148548v1

Autumn drought drives functional diversity of benthic diatom assemblages of continental intermittent streams

Viktória B-Béres , Béla Tóthmérész , István Bácsi , Gabor Borics , András Abonyi
Advances in Water Resources, 2019, 126, pp.129-136. ⟨10.1016/j.advwatres.2019.02.010⟩
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
Sciences Eaux & Territoires, 2019, HS, pp.9. ⟨10.14758/SET-REVUE.2019.hs.04⟩
Journal articles hal-02609267v1

Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms

Andreia Mortágua , Valentin Vasselon , Ricardo Oliveira , Carmen Elias , Cécile Chardon
Ecological Indicators, 2019, 106, pp.105470. ⟨10.1016/j.ecolind.2019.105470⟩
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
Frontiers in Microbiology, 2019, 10, ⟨10.3389/fmicb.2019.00653⟩
Journal articles hal-02381793v1

Diat.barcode, an open-access curated barcode library for diatoms

Frédéric Rimet , Evgenuy Gusev , Maria Kahlert , Martyn G. Kelly , Maxim Kulikovskiy
Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-51500-6⟩
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
Frontiers in Ecology and Evolution, 2019, 7, ⟨10.3389/fevo.2019.00409⟩
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
Ecological Indicators, 2019, 97, pp.165-174. ⟨10.1016/j.ecolind.2018.09.061⟩
Journal articles hal-02608198v1

Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)