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Environmental Science and Pollution Research

, Volume 25, Issue 34, pp 33858–33866 | Cite as

Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

  • Estelle LefrançoisEmail author
  • Laure Apothéloz-Perret-Gentil
  • Philippe Blancher
  • Samuel Botreau
  • Cécile Chardon
  • Laura Crepin
  • Tristan Cordier
  • Arielle Cordonier
  • Isabelle Domaizon
  • Benoit J. D. Ferrari
  • Julie Guéguen
  • Jean-Christophe Hustache
  • Louis Jacas
  • Stephan Jacquet
  • Sonia Lacroix
  • Anne-Laurence Mazenq
  • Alina Pawlowska
  • Pascal Perney
  • Jan Pawlowski
  • Frédéric Rimet
  • Jean-François Rubin
  • Dominique Trevisan
  • Régis Vivien
  • Agnès Bouchez
ECOTOX, new questions for terrestrial and aquatic ecotoxicology

Abstract

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators’ communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017–2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration, and follow their evolution.

Keywords

Metabarcoding Bioindication Water quality assessment Diatoms Aquatic oligochaetes 

Notes

Funding information

The SYNAQUA project is supported by the European Cross-Border Cooperation Program (Interreg France-Switzerland 2014-2020) and has thus received a European (European Regional Development Fund) and a Swiss Federal grant covering respectively 60% of the French total cost and 29% of the Swiss total cost. Funding was also provided by Swiss cantons (Valais, Geneva, Vaud).

References

  1. AFNOR (2016) NF T 90-393 Qualité de l’eau – Echantillonnage, Traitement et Analyse Des Oligochètes Dans Les Sédiments Des Eaux de Surface Continentales. pp.1–14+ annexesGoogle Scholar
  2. Apothéloz-Perret-Gentil L, Cordonier A, Straub F, Iseli J, Esling P, Pawlowsk J (2017) Taxonomy-free molecular diatom index for high-throughput EDNA biomonitoring. Mol Ecol Resour 17(6):1231–1242.  https://doi.org/10.1111/1755-0998.1266 CrossRefGoogle Scholar
  3. Baird D, Hajibabei M (2012) Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol Ecol 21:2039–2044CrossRefGoogle Scholar
  4. Carpenter S, Stanley EH, Vander Zanden MF (2011) State of the world’s freshwater ecosystems: physical, chemical, and biological changes. Annu Rev Environ Resour 36:75–99CrossRefGoogle Scholar
  5. Cordier T, Esling P, Lejzerowicz F, Visco J, Ouadahi A, Martins C, Cedhagen T, Pawlowski P (2017) Predicting the ecological quality status of marine environments from EDNA metabarcoding data using supervised machine learning. Environ Sci Technol 51(16):9118–9126.  https://doi.org/10.1021/acs.est.7b01518 CrossRefGoogle Scholar
  6. Coste M, Boutry S, Tison-Rosebery J, Delmas F (2009) Improvements of the Biological Diatom Index (BDI): description and efficiency of the new version (BDI-2006). Ecol Indic 9:621–650.  https://doi.org/10.1016/j.ecolind.2008.06.003 CrossRefGoogle Scholar
  7. Creer S (2010) Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists. Mol Ecol 19:2829–2831CrossRefGoogle Scholar
  8. European Commission (2000) Directive 2000/60/EC of the European Parliament and of the council of 23rd October 2000 establishing a framework for community action in the field of water policy. Off J Eur Communities 327:1–72Google Scholar
  9. Holt EA, Miller SW (2011) Bioindicators: using organisms to measure environmental impacts. Nat Educ Knowl 3(10):8Google Scholar
  10. Hürlimann J, Niederhauser P (2007) Méthodes d’Analyse et d’Appreçiation Des Cours d’Eau. Diatoméés Niveau R (Region); Etat de l’environnement N° 0740. Office Fédéral de l’Environnement, Berne 132pGoogle Scholar
  11. Keck F, Vasselon V, Tapolczai K, Rimet F, Agnès Bouchez A (2017) Freshwater biomonitoring in the information age. Front Ecol Environ 15(5):266–274.  https://doi.org/10.1002/fee.1490 CrossRefGoogle Scholar
  12. Kermarrec L, Franc A, Rimet F (2014) A next-generation sequencing approach to river biomonitoring using benthic diatoms. Freshw Sci 33:349–363CrossRefGoogle Scholar
  13. Kermarrec L, Bouchez A, Rimet F, & Humbert JF (2012) First evidence of the existence of semi-cryptic species and of a phylogeographic structure in the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta). Protist 164:686–705CrossRefGoogle Scholar
  14. Kermarrec L, Franc A, Rimet F, Chaumeil P, Humbert JF, Bouchez A, (2013) Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Mol Ecol Resour 13(4):607–619CrossRefGoogle Scholar
  15. Kolkwitz R, Marson M (1908) Okologie Der Pflanzliche Saprobien. Berichte Der Deutsche Botanische Gesellschaften 26:505–519Google Scholar
  16. Lafont M (1989) Contribution à La Gestion Des Eaux Continentales: Utilisation Des Oligochètes Comme Descripteurs de l’état Biologique et Du Degré de Pollution Des Eaux et Des Sédiments. Thèse de Doctorat ès Sciences, Université de Lyon IGoogle Scholar
  17. Lafont M, Vivier A (2006) Oligochaete assemblages in the hyporheic zone and coarse surface sediments: their importance for understanding of ecological functioning of watercourses. Hydrobiologia 564:171–181CrossRefGoogle Scholar
  18. Lafont M, Jézéquel C, Vivier A, Breil P, Schmitt L, Bernoud S (2010) Refinement of biomonitoring of urban watercourses by combining descriptive and ecohydrological approaches. Ecohydrol Hydrobiol 10:3–11CrossRefGoogle Scholar
  19. Lafont M, Tixier G, Marsalek J, Jézéquel C, Breil P, Schmitt L (2012) From research to operational biomonitoring of freshwaters: a suggested conceptual framework and practical solutions. Ecohydrol Hydrobiol 12:9–20CrossRefGoogle Scholar
  20. Lang C (1997) Oligochaetes, organic sedimentation, and trophic state: how to assess the biological recovery of sediments in lakes? Aquat Sci 59:26–33CrossRefGoogle Scholar
  21. Lang C (2009) Indices Basé Sur Les Oligochètes et Les Chironomes Indiquant La Restauration Écologique Des Sédiments Du Léman. Bulletin de La Société Vaudoise Des Sciences Naturelles 91:283–300Google Scholar
  22. Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Björnsdóttir S, Boets P, Boggero A, Bones A, Borja Á, Bruce K, Bursić V, Carlsson J, Čiampor F, Čiamporová-Zatovičová Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls Á, Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot JF, Fonseca V, Fontaneto D, Grabowski M, Graf W, Guðbrandsson J, Hellström M, Hershkovitz Y, Hollingsworth P, Japoshvili B, Jones J, Kahlert M, Kalamujic Stroil B, Kasapidis P, Kelly M, Kelly-Quinn M, Keskin E, Kõljalg U, Ljubešić Z, Maček I, Mächler E, Mahon A, Marečková M, Mejdandzic M, Mircheva G, Montagna M, Moritz C, Mulk V, Naumoski A, Navodaru I, Padisák J, Pálsson S, Panksep K, Penev L, Petrusek A, Pfannkuchen M, Primmer C, Rinkevich B, Rotter A, Schmidt-Kloiber A, Segurado P, Speksnijder A, Stoev P, Strand M, Šulčius S, Sundberg P, Traugott M, Tsigenopoulos C, Turon X, Valentini A, van der Hoorn B, Várbíró G, Vasquez Hadjilyra M, Viguri J, Vitonytė I, Vogler A, Vrålstad T, Wägele W, Wenne R, Winding A, Woodward G, Zegura B, Zimmermann J (2016) DNAqua-Net: developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. Res Ideas Outcomes 2:e11321.  https://doi.org/10.3897/rio.2.e11321 CrossRefGoogle Scholar
  23. Lenoir A, Coste M (1996) Development of a practical diatom index of overall water quality applicable to the French National Water Board Network. Use of algae for monitoring rivers, Vol. II. In: Whitton BA, Rott E (Eds.) edition, sec. Studia Student, GmbHGoogle Scholar
  24. Liechti P, Sieber U, Bundi U, Frutiger A, Hütte M, Peter A, von Blücher U, Willi AP, Göldi C, Kupper U, Meier W, Niederhauser P, (1998) Méthodes d'analyse et d'appréciation des cours d'eau. Système Modulaire Gradué. Informations concernant la protection des eaux n°26. Office fédéral de l'environnement, Berne, p 43Google Scholar
  25. Prygiel J, Rosso-Darmet A, Lafont M, Durbec A, Ouddane B (2000) Use of oligochaete communities for assessment of ecotoxicological risk in fine sediment of rivers and canals of the Artois-Picardie Water Basin (France). Hydrobiologia 410:25–37CrossRefGoogle Scholar
  26. Rimet F (2012) Recent views on river pollution and diatoms. Hydrobiologia 683:1–24.  https://doi.org/10.1007/s10750-011-0949-0 CrossRefGoogle Scholar
  27. Rimet F, Chaumeil P, Keck F (2016) R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database 2016:Baw016CrossRefGoogle Scholar
  28. Rimet F, Vasselon V, Keszte B, Bouchez A (2018) Do We Similarly Assess Diversity with Microscopy and High-Throughput Sequencing? Case of Microalgae in Lakes. Org Divers Evol 18:51.  https://doi.org/10.1007/s13127-018-0359-5 CrossRefGoogle Scholar
  29. Rivera SF, Vasselon V, Jacquet S, Bouchez A, Ariztegui D, Rimet F (2018) Metabarcoding of Lake Benthic diatoms: from structure assemblages to ecological assessment. Hydrobiologia 807(1):37–51.  https://doi.org/10.1007/s10750-017-3381-2 CrossRefGoogle Scholar
  30. Rodriguez P, Reynoldson TB (2011) The Pollution Biology of Aquatic Oligochaetes. Springer Science+Business Media B.V. 2011.  https://doi.org/10.1007/978-94-007-1718-3_1 CrossRefGoogle Scholar
  31. Taberlet P, Croissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21(8):2045–2050CrossRefGoogle Scholar
  32. Vasselon V, Rimet F, Tapolczai K, Bouchez A (2017) Assessing ecological status with diatoms DNA metabarcoding: scaling-up on a WFD monitoring network (Mayotte Island, France). Ecol Indic 82(November):1–12.  https://doi.org/10.1016/j.ecolind.2017.06.024 CrossRefGoogle Scholar
  33. Vasselon V, Bouchez A, Rimet F, Jacquet S, Trobajo R, Corniquel M, Tapolczai K, Domaizon I (2018) Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring. Methods Ecol Evol 00:1–10.  https://doi.org/10.1111/2041-210X.12960 CrossRefGoogle Scholar
  34. Visco JA, Apothéloz-Perret-Gentil L, Cordonier A, Esling P, Pillet L, Pawlowski J (2015) Environmental monitoring: inferring the diatom index from next-generation sequencing data. Environ Sci Technol 49(13):7597–7605.  https://doi.org/10.1021/es506158m CrossRefGoogle Scholar
  35. Vivien R, Tixier G, Lafont M (2014) Use of oligochaete communities for assessing the quality of sediments in watercourses of the Geneva area (Switzerland) and Artois-Picardie Basin (France): proposition of heavy metal toxicity thresholds. Ecohydrology & Hydrobiology 14:142–151CrossRefGoogle Scholar
  36. Vivien R, Lafont M, Ferrari BJD (2015a) Utilisation Des Communautés d’oligochètes Pour l’évaluation de La Qualité Biologique et Du Fonctionnement Des Cours d’eau : Un Bilan à Partir de Données Genevoises (Suisse). Arch Des Sci 68:105–116Google Scholar
  37. Vivien R, Wyler S, Lafont M, Pawlowski J (2015b) Molecular Barcoding of Aquatic Oligochaetes: Implications for Biomonitoring. PLoS ONE 10(4):e0125485CrossRefGoogle Scholar
  38. Vivien R, Holzmann M, Werner I, Pawlowski J, Lafont M, Ferrari BJD (2017) Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database. PeerJ 5:e4122.  https://doi.org/10.7717/peerj.4122 CrossRefGoogle Scholar
  39. Vörösmarty CJ, Mcintyre PB, Gessner MO, Dudgeon D, Prusevitch A, Green P, Glidden S et al (2010) Global threats to human water security and river biodiversity. Nature 467:555–561CrossRefGoogle Scholar
  40. Wasson JG, Blanc L, Chandesris A, Pella H (2002) Définition Des Hydro-Écoregions de France Métroplolitaine. Approche Regionale de Typologie Des Eaux Courantes et Éléments Pour La Définition Des Peuplements de Référence d’invertébrés. Lyon BEA/LH: CemagrefGoogle Scholar
  41. WPO (1998) Water Protection Ordinance of 28 October 1998 (814.201). UNECE, Geneve.Google Scholar
  42. Zelinka M, Marvan P (1961) Zur Prazisierung Der Biologischen Klassifikation Des Reinheit Fliessender Gewasser. Arch Hydrobiol 57:389–407Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Estelle Lefrançois
    • 1
    • 2
    Email author
  • Laure Apothéloz-Perret-Gentil
    • 3
  • Philippe Blancher
    • 4
  • Samuel Botreau
    • 5
  • Cécile Chardon
    • 2
  • Laura Crepin
    • 2
  • Tristan Cordier
    • 3
  • Arielle Cordonier
    • 6
  • Isabelle Domaizon
    • 2
  • Benoit J. D. Ferrari
    • 7
  • Julie Guéguen
    • 2
  • Jean-Christophe Hustache
    • 2
  • Louis Jacas
    • 2
  • Stephan Jacquet
    • 2
  • Sonia Lacroix
    • 2
  • Anne-Laurence Mazenq
    • 5
  • Alina Pawlowska
    • 8
  • Pascal Perney
    • 2
  • Jan Pawlowski
    • 3
  • Frédéric Rimet
    • 2
  • Jean-François Rubin
    • 9
  • Dominique Trevisan
    • 2
  • Régis Vivien
    • 7
  • Agnès Bouchez
    • 2
  1. 1.Eco-in’EauMontferrier sur LezFrance
  2. 2.UMR CARRTEL, INRA, USMBThonon-les-BainsFrance
  3. 3.Département de Génétique et EvolutionUniversité de GenèveGenevaSwitzerland
  4. 4.Philippe BlancherSaint-Genis-LavalFrance
  5. 5.ASTERS Conservatoire D’Espaces Naturels De Haute-SavoiePringyFrance
  6. 6.Service de l’Ecologie de l’EauRépublique et Canton de GenèveGenevaSwitzerland
  7. 7.Swiss Centre for Applied Ecotocicology (Ecotox Centre) EAWAG-EPFLLausanneSwitzerland
  8. 8.ID-GENE EcodiagnosticsGenevaSwitzerland
  9. 9.Maison de la RivièreTolochenazSwitzerland

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