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Agnès BOUCHEZ

209
Documents

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Ecologie microbienne aquatique

Publications

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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 et al.
Molecular Ecology Resources, In press, ⟨10.1111/1755-0998.13604⟩
Journal articles hal-03601922v1
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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 et al.
Data in Brief, 2022, 40, pp.107726. ⟨10.1016/j.dib.2021.107726⟩
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.
Science of the Total Environment, 2022, 818, pp.151783. ⟨10.1016/j.scitotenv.2021.151783⟩
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.
Metabarcoding and Metagenomics, 2022, 6 (e85652), ⟨10.3897/mbmg.6.85652⟩
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.
Molecular Ecology, 2022, ⟨10.1111/mec.16737⟩
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.
Metabarcoding and Metagenomics, 2022, 6 (e85844), ⟨10.3897/mbmg.6.85844⟩
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.
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 et al.
Metabarcoding and Metagenomics, 2021, 5, pp.111-120. ⟨10.3897/MBMG.5.68438⟩
Journal articles hal-03528828v1
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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 et al.
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 et al.
Ecological Indicators, 2021, 122, pp.107322. ⟨10.1016/j.ecolind.2020.107322⟩
Journal articles hal-03238653v1
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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 et al.
Frontiers in Ecology and the Environment, 2021, 19 (10), pp.574-583. ⟨10.1002/fee.2404⟩
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 of Hazardous Materials, 2021, 411, pp.125121. ⟨10.1016/j.jhazmat.2021.125121⟩
Journal articles hal-03238813v1
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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 et al.
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 et al.
Environmental Science and Technology, 2021, 55 (21), pp.14699-14709. ⟨10.1021/acs.est.1c01819⟩
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.
Molecular Ecology, 2021, 30 (13), pp.2959-2968. ⟨10.1111/mec.15646⟩
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.
Frontiers in Ecology and the Environment, 2021, 19 (10), pp.574-583. ⟨10.1002/fee.2404⟩
Journal articles hal-03977024v1
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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 et al.
Molecular Ecology, 2021, 30 (13), pp.2937-2958. ⟨10.1111/mec.15472⟩
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.
Chemosphere, 2021, 272, pp.129814. ⟨10.1016/j.chemosphere.2021.129814⟩
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.
Ecological Indicators, 2021, 122, pp.107322. ⟨10.1016/j.ecolind.2020.107322⟩
Journal articles hal-03977040v1
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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 et al.
Metabarcoding and Metagenomics, 2021, 5, pp.e58056. ⟨10.3897/mbmg.5.58056⟩
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.
Molecular Ecology Resources, 2021, ⟨10.1111/1755-0998.13568⟩
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.
FEMS Microbiology Ecology, 2020, 96 (2), ⟨10.1093/femsec/fiaa002⟩
Journal articles hal-02569099v1
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Key questions for next-generation biomonitoring

Andreas Makiola , Zacchaeus G. Compson , Donald J Baird , Matthew A. Barnes , Sam Philip Boerlijst et al.
Frontiers in Environmental Science, inPress, 7, ⟨10.3389/fenvs.2019.00197⟩
Journal articles hal-02402296v1
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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 et al.
Science of the Total Environment, 2020, 741, pp.140459. ⟨10.1016/j.scitotenv.2020.140459⟩
Journal articles hal-02901285v1
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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 et al.
Science of the Total Environment, 2020, 722, ⟨10.1016/j.scitotenv.2020.137900⟩
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.
Science of the Total Environment, 2020, 727, ⟨10.1016/j.scitotenv.2020.138445⟩
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.
Science of the Total Environment, 2020, 719, pp.137462. ⟨10.1016/j.scitotenv.2020.137462⟩
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.
Advances in Water Resources, 2019, 126, pp.129-136. ⟨10.1016/j.advwatres.2019.02.010⟩
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 of Phycology, 2019, 55 (4), pp.948-970. ⟨10.1111/jpy.12886⟩
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.
Metabarcoding and Metagenomics, 2019, 3, ⟨10.3897/mbmg.3.34002⟩
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.
Science of the Total Environment, 2019, 678, pp.499-524. ⟨10.1016/j.scitotenv.2019.04.247⟩
Journal articles hal-02626077v1
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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 et al.
Frontiers in Ecology and Evolution, 2019, 7, ⟨10.3389/fevo.2019.00409⟩
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.
Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-51500-6⟩
Journal articles hal-02619171v1
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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 et al.
Frontiers in Microbiology, 2019, 10, ⟨10.3389/fmicb.2019.00653⟩
Journal articles hal-02381793v1
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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 et al.
Metabarcoding and Metagenomics, 2019, 3, ⟨10.3897/mbmg.3.39646⟩
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.
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 et al.
Ecology and Evolution, 2019, 9 (1), pp.166-179. ⟨10.1002/ece3.4701⟩
Journal articles hal-02619428v1
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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 et al.
Ecological Indicators, 2019, 97, pp.165-174. ⟨10.1016/j.ecolind.2018.09.061⟩
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.
Ecological Indicators, 2019, 106, pp.105470. ⟨10.1016/j.ecolind.2019.105470⟩
Journal articles hal-02623986v1
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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 et al.
Sciences Eaux & Territoires, 2019, 55 (HS), pp.9
Journal articles hal-02609267v1
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Sensitivities of seven algal species to triclosan, fluoxetine and their mixtures

Ran Bi , Xiangfeng Zeng , Lei Mu , Liping Hou , Wenhua Liu et al.
Scientific Reports, 2018, 8 (1), ⟨10.1038/s41598-018-33785-1⟩
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
Organisms Diversity and Evolution, 2018, 18 (1), pp.51-62. ⟨10.1007/s13127-018-0359-5⟩
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.
Environmental Science and Pollution Research, 2018, 25 (34), ⟨10.1007/s11356-018-3179-4⟩
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.
Fottea (Praha), 2018, 18 (1), pp.37-54. ⟨10.5507/fot.2017.013⟩
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.
Hydrobiologia, 2018, 807 (1), pp.37-51. ⟨10.1007/s10750-017-3381-2⟩
Journal articles hal-02621047v1
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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.
PLoS ONE, 2018, 13 (4), pp.e0195770. ⟨10.1371/journal.pone.0195770⟩
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.
Molecular Ecology Resources, 2018, 18 (6), pp.1299-1309. ⟨10.1111/1755-0998.12919⟩
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.
Environnement, Risques & Santé, 2018, 17 (S1), pp.59-74. ⟨10.1684/ers.2017.1074⟩
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.
Water Research, 2018, 138, pp.192-205. ⟨10.1016/j.watres.2018.03.003⟩
Journal articles hal-02626478v1
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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.
Environmental Science and Pollution Research, 2018, 25 (34), pp.33858-33866. ⟨10.1007/s11356-018-2172-2⟩
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.
Science of the Total Environment, 2018, 637-638, pp.1295-1310. ⟨10.1016/j.scitotenv.2018.05.002⟩
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.
Environmental Science and Pollution Research, 2018, 25 (10), pp.9254-9264. ⟨10.1007/s11356-017-0024-0⟩
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.
Ecotoxicology, 2018, 27 (7), pp.860-870. ⟨10.1007/s10646-018-1953-1⟩
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.
Environmental Science and Pollution Research, 2018, 25 (10), pp.9197-9206. ⟨10.1007/s11356-017-9302-0⟩
Journal articles hal-01606931v1
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Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?

Valentin Vasselon ,