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Tél. : +33 (0)4 50 26 78 60
Mail : agnes.bouchez[at]inrae.fr

Research interests

Microbial Ecology and quality of Aquatic Ecosystems – Environmental Biomonitoring – Metagenomics approaches.

Post Doc and PhD thesis

Sinziana Rivera (2018-2022) Biofilms aquatiques : capteurs de l’ADN environnemental et révélateurs de la biodiversité des milieux aquatiques / PhD University Savoie Mont- Blanc, co-supervision A. Bouchez - F. Rimet

Teofana Chonova (2015-2019) Pharmaceuticals in freshwater environments and their effect on microbial biofilm communities / PhD University of Innsbrück (Austria), co-supervision A. Bouchez - R. Kurmayer - P. Illmer  

Valentin Vasselon (2014-2017) Metabarcoding et bioindication : vers le biomonitoring moléculaire des diatomées / PhD University Savoie Mont- Blanc (funding ONEMA), co-supervision A. Bouchez - I. Domaizon

Kalman Tapolczaï (2014-2017) efficiency of alternative bioindicator metrics in tropical and temperate, adaptation of these metrics to next generation sequencing (NGS) data / PhD University Savoie Mont- Blanc (funding ONEMA), co-supervision A. Bouchez - F. Rimet

François Keck (2013-2016) Évaluation des liens entre phylogénie et traits écologiques, piste d’utilisation pour la bioindication des cours d’eau / PhD University Savoie Mont- Blanc (funding ONEMA), co-supervision A. Bouchez - A. Franc (INRA – BioGeCo Bordeaux)

Floriane Larras (2010-2013) Évaluation écotoxicologique de l'impact des pesticides sur les communautés microbiennes benthiques en zone côtière lacustre. co-supervision A. Bouchez – B. Montuelle

Lénaïg Kermarrec (2009-2012) Développement d'outils moléculaires pour l'utilisation des diatomées comme bioindicateurs de la qualité des écosystèmes aquatiques lotiques. co-supervision A. Bouchez – J.F. Humbert

Aurélie Villeneuve (2005-2008) : Fonctions et diversité des communautés microbiennes aquatiques soumises à des perturbations anthropiques : liens avec les structures physiques et chimiques du milieu.

Research projects

1. Leader of national and international projects to propose new metrics based on microbial communities for aquatic ecosystems biomonitoring, pollution impacts and risk assessment.

2. Vice-chair of the European COST Action DNAqua-Net (CA15219) 2016-2021 - www.DNAqua.Net

3. Organiser of the 1st DNAQUA International Conference, 9-11 March 2021 - https://symposium.inrae.fr/dnaqua-conference-evian2021 (1500 participants from 80 countries)

4. Head of a 6-year project on New generation biomonitoring with microalgae: developing new metrics and NGS approaches for biomonitoring in Mayotte - French tropical island (2013-2019).

5. Co-leader of INTERREG SYNAQUA (FR-CH) to develop DNA approaches on Lake Geneva (2017-2019) - https://internet6-national-synaqua.hub.inrae.fr/

6. Partner of INTERREG Eco-AlpsWater (Alpine Space) to develop DNA approaches in alpine aquatic ecosystems (2019-2022) - https://www.alpine-space.eu/project/eco-alpswater/

7. Impact of xenobiotics (pharmaceuticals, pesticides) on structure and functioning of aquatic microbial communities (ANR-CES: SENDEFO, POTOMAC; MEDLT: ECOMET, IMPALAC; ANSES: PERSIST-ENV, ANTIBIO-TOOLS).

Steering committees

ADN-O (2020-): French scientific network for the development of DNA-based methods for the knowledge and management of aquatic cosy stems (https://www6.inrae.fr/reseau-adn-o)

DNAqua-Net (2016-2021): Vice-chair (http://dnaqua.net/)

ZABR (2015-2020): Long Term Observatory on Rhône basin (https://www.zabr.assograie.org/). In charge of the scientific theme on “Pollutant fluxes and ecotoxicology “

Recent publications

1. VERDIER H., KONECNY-DUPRE L., MARQUETTE C., REVERON H., TADIER S., GRÉMILLARD L., BARTHES A., DATRY T., BOUCHEZ A., LEFEBURE T. (2022) Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers. Molecular Ecology Resources 00:1–13. https://doi.org/10.1111/1755-0998.13604

2. PAWLOWSKI J., BRUCE K., K PANKSEP; FI AGUIRRE; S AMALFITANO; L APOTHÉLOZ-PERRET-GENTIL; T BAUSSANT; A BOUCHEZ; L CARUGATI; K CERMAKOVA; T CORDIER; C CORINALDESI; FO COSTA; R DANOVARO; A DELL’ANNO; S DUARTE; U EISENDLE; BJD FERRARI; F FRONTALINI; L FRÜHE; A HAEGERBAEUMER; V KISAND; A KROLICKA; A LANZÉN; F LEESE; F LEJZEROWICZ; E LYAUTEY; I MAČEK; M SAGOVA-MAREČKOVÁ; JK PEARMAN; X POCHON; T STOECK; R VIVIEN; A WEIGAND; FAZI S. (2022) Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. STOTEN 818:151783. https://doi.org/10.1016/j.scitotenv.2021.151783

3. BERTRAND-KRAJEWSKI J.L., BOURNIQUE R., LECOMTE V., PERNIN N., WIEST L., BAZIN B., BOUCHEZ B., BRELOT E., COURNOYER B., CHONOVA T., DAGOT C., DI MAJO P., GONZALEZ-OSPINA A., KLEIN A., LABANOWSKI J., LEVI Y., PERRODIN Y., RABELLO-VARGAS S., REUILLY L., ROCH A., WAHL A. (2022) 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. Data in Brief 40:107726 https://doi.org/10.1016/j.dib.2021.107726

4. RIVERA S.F., VASSELON V., MARY N., MONNIER O., RIMET F., BOUCHEZ A. (2021) Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers. STOTEN 763:144208  https://doi.org/10.1016/j.scitotenv.2020.144208

5. TAPOLCZAI K., SELMECZY G., SZABÓ B., B.-BÉRES V., KECK F., BOUCHEZ A., RIMET F., PADISÁK J. (2021) The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding. Ecological Indicators 122:107322  https://doi.org/10.1016/j.ecolind.2020.107322

6. SAGOVA-MARECKOVA M., BOENIGK J ., BOUCHEZ A., CERMAKOVA K., CHONOVA T., CORDIER T., EISENDLE U.,  ELERSEK T., FAZI S., FLEITUCH T., FRÜHE L., GAJDOSOVA M., GRAUPNER N., HAEGERBAEUMER A., KELLY A-M., KOPECKY J., LEESE F., NÕGES P., ORLIC S., PANKSEP K., PAWLOWSKI J., PETRUSEK A., PIGGOTT J.J., RUSCH J.C., SALIS R., SCHENK J., SIMEK K., STOVICEK A., STRAND D.A., VASQUEZ M.I., VRÅLSTAD T., ZLATKOVIC S., ZUPANČIČ M., STOECK T. (2021) Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. Water Research 191:116767 https://doi.org/10.1016/j.watres.2020.116767

7. TARDY V., BONNINEAU C., BOUCHEZ A., MIÈGE C., MASSON M., JEANNIN P., PESCE S. (2021) An innovative pilot experiment to assess the efficiency of pharmaceutical plant wastewater treatment and the resulting decrease in effluent toxicity to periphytic microbial biofilms. Journal of Hazardous Material 411:125121  https://doi.org/10.1016/j.jhazmat.2021.125121

8. PISSARIDOU P., VASSELON., CHRISTOU A., CHONOVA T., LACROIX S., PAPATHEODOULOU A. DRAKOU K., TZIORTZIS I., DÖRFLINGER G., RIMET F., BOUCHEZ A., VASQUEZ M.I. (2021) Deciphering Cyprus’ diatom diversity and the effects of environmental and anthropogenic influences for ecological assessment of rivers using DNA metabarcoding. Chemosphere 272:129814 https://doi.org/10.1016/j.chemosphere.2021.129814

9. RIMET F., AYLAGAS E., BORJA A., BOUCHEZ A., CANINO A., CHAUVIN C., CHONOVA T., ČIAMPOR F.JR, COSTA F.O., FERRARI B.J.D, GASTINEAU R., GOULON C., GUGGER M., HOLZMAN M., JAHN R., KAHLERT M.,  KUSBER W.H., LAPLACE-TREYTURE C., LEESE F., LELIAERT F., MANN D.G., MARCHAND F., MÉLÉDER V., PAWLOWSKI J., RASCONI S., ROUGERIE R., SCHWEIZER M., TROBAJO R., VIVIEN R., WEIGAND A., WITKOWSKI A., ZIMMERMANN J., EKREM T. (2021) Metadata standards and practical guidelines for specimen and DNA curation when building DNA barcode reference libraries for aquatic life. MBMG 5: e58056. https://doi.org/10.3897/mbmg.5.58056

10. BLACKMAN R., ALTERMATT F., FOULQUIER A., LEFEBURE T., GAUTHIER M., BOUCHEZ A., STUBBINGTON R., WEIGAND A., LEESE F., DATRY, T. (2021) Unlocking our understanding of intermittent rivers and ephemeral streams with genomic tools. Frontiers in Ecology and the Environment 19(10):574–583 https://doi.org/10.1002/fee.2404

11. PISSARIDOU P., CANTONATI M., BOUCHEZ A., TZIORTZIS I., DÖRFLINGER G., VASQUEZ M.I. (2021) How can integrated morphotaxonomy- and metabarcoding-based diatom assemblage analyses best contribute to the ecological assessment of streams. MBMG 5: e68438 https://doi.org/10.3897/mbmg.5.68438

12. KONSCHAK M., ZUBROD J.Z., DUQUE ACOSTA T.S, BOUCHEZ A., KROLL A., FECKLER A., RÖDER N., BAUDY P., BUNDSCHUH M. (2021) Herbicide-induced shifts in the periphyton community composition indirectly affect feeding activity and physiology of the gastropod grazer Physella acuta. Environ. Sci. Technol. 55:14699–14709 https://doi.org/10.1021/acs.est.1c01819

13. RIVERA S.F., RIMET F., VASSELON V., VAUTIER M., DOMAIZON I., BOUCHEZ A. (2021) Fish eDNA metabarcoding from aquatic biofilm samples:methodological aspects. Molecular Ecology Resources 00:1-14 https://doi.org/10.1111/1755-0998.13568

14. CANINO A., BOUCHEZ A., LAPLACE-TREYTURE C., DOMAIZON I., RIMET F. (2021) Phytool, a ShinyApp to homogenise taxonomy of freshwater microalgae from DNA barcodes and microscopic observations. Metabarcoding and Metagenomics 5: 199–205 https://doi.org/10.3897/mbmg.5.74096