Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France Water Framework Directive networks

Vasselon Valentin; Rimet Frédéric; Domaizon Isabelle; Monnier Olivier; Reyjol Yorick; Bouchez Agnès

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Maria Kahlert, Satu Maaria Karjalainen, Francois Keck, Martyn Kelly, Mathieu Ramon, Frederic Rimet, Susanne Schneider, Kálmán Tapolczai, Jonas Zimmermann (2022)
Co-occurrence, ecological profiles and geographical distribution based on unique molecular identifiers of the common freshwater diatoms Fragilaria and Ulnaria. Ecological Indicators 141: 109114.

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Ariel Levi Simons, Susanna Theroux, Melisa Osborne, Sergey Nuzhdin, Raphael Mazor, Joshua Steele (2023)
Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment. Ecological Applications 33: .

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Eric D. Stein, Christopher L. Jerde, Elizabeth Andruszkiewicz Allan, Adam J. Sepulveda, Cathryn L. Abbott, Melinda R. Baerwald, John Darling, Kelly D. Goodwin, Rachel S. Meyer, Molly A. Timmers, Peter M. Thielen (2023)
Critical considerations for communicating environmental DNA science. Environmental DNA : .

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Martyn G. Kelly, Tim Jones, Kerry Walsh (2021)
Potential for cross-contamination of diatom DNA samples when using toothbrushes. Metabarcoding and Metagenomics 5: .

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Frédéric Rimet, Alexis Canino, Teofana Chonova, Julie Guéguen, Agnès Bouchez (2023)
Environmental filtering and mass effect are two important processes driving lake benthic diatoms: Results of a DNA metabarcoding study in a large lake. Molecular Ecology 32: 124.

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Ana Baricevic, Cécile Chardon, Maria Kahlert, Satu Maaria Karjalainen, Daniela Maric Pfannkuchen, Martin Pfannkuchen, Frédéric Rimet, Mirta Smodlaka Tankovic, Rosa Trobajo, Valentin Vasselon, Jonas Zimmermann, Agnès Bouchez (2022)
Recommendations for the preservation of environmental samples in diatom metabarcoding studies. Metabarcoding and Metagenomics 6: .

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Javier Pérez-Burillo, Rosa Trobajo, Valentin Vasselon, Frédéric Rimet, Agnès Bouchez, David G. Mann (2020)
Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers. Science of The Total Environment 727: 138445.

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Nathan J. Smucker, Erik M. Pilgrim, Christopher T. Nietch, John A. Darling, Brent R. Johnson (2020)
DNA metabarcoding effectively quantifies diatom responses to nutrients in streams. Ecological Applications 30: .

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Sten Anslan, Vladimir Mikryukov, Kęstutis Armolaitis, Jelena Ankuda, Dagnija Lazdina, Kristaps Makovskis, Lars Vesterdal, Inger Kappel Schmidt, Leho Tedersoo (2021)
Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms. PeerJ 9: e12254.

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Marco Teixeira, Salomé Almeida, Maria Feio, Andreia Mortágua, Manuela Sales (2021)
Effects of anthropogenic pressures on diatom communities using morphological and molecular approaches. ARPHA Conference Abstracts 4: .

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Daeryul Kwon, Mirye Park, Hoil Lee, Jin-Young Lee, Sang Deuk Lee (2023)
New recorded diatoms in Holocene sediment cores from the Gonggeom-ji Wetland in Korea. Applied Microscopy 53: .

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Elena Kezlya, Natalia Tseplik, Maxim Kulikovskiy (2023)
Genetic Markers for Metabarcoding of Freshwater Microalgae: Review. Biology 12: 1038.

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Nicholas O. Schulte, Joseph M. Craine, Devin R. Leopold, Jessica K. Devitt, Noah Fierer (2023)
Diversity of freshwater algal assemblages across the United States as revealed by DNA metabarcoding. Environmental DNA : .

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Jorge Machuca-Sepúlveda, Javiera Miranda, Nicolás Lefin, Alejandro Pedroso, Jorge F. Beltrán, Jorge G. Farias (2023)
Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring. Biology 12: 923.

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María Borrego-Ramos, Eloy Bécares, Pedro García, Alejandro Nistal, Saúl Blanco (2021)
Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches. Water 13: 1351.

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Corinne Biderre‐Petit, Jean‐Christophe Charvy, Gisèle Bronner, Marina Chauvet, Didier Debroas, Hélène Gardon, Claire Hennequin, Isabelle Jouan‐Dufournel, Anne Moné, Arthur Monjot, Viviane Ravet, Agnès Vellet, Cécile Lepère (2023)
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes. Molecular Ecology Resources 23: 222.

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Fatemeh Parikhani, Ehsan Atazadeh, Jafar Razeghi, Mohammad Mosaferi, Maxim Kulikovskiy (2023)
Using Algal Indices to Assess the Ecological Condition of the Aras River, Northwestern Iran. Journal of Marine Science and Engineering 11: 1867.

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Paula C. Furey, Sylvia S. Lee, Daniel L. Clemans (2020)
Substratum‐associated microbiota. Water Environment Research 92: 1629.

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Panayiota Pissaridou, Marco Cantonati, Agnes Bouchez, Iakovos Tziortzis, Gerald Dörflinger, Marlen I. Vasquez (2021)
How can integrated morphotaxonomy- and metabarcoding-based diatom assemblage analyses best contribute to the ecological assessment of streams?. Metabarcoding and Metagenomics 5: .

DOI: 10.3897/mbmg.5.68438

Valentin Vasselon, Éva Ács, Salomé Almeida, Karl Andree, Laure Apothéloz-Perret-Gentil, Bonnie Bailet, Ana Baricevic, Kevin Beentjes, Juliane Bettig, Agnès Bouchez, Camilla Capelli, Cécile Chardon, Mónika Duleba, Tina Elersek, Clémence Genthon, Melanie Hurtz, Louis Jacas, Maria Kahlert, Martyn Kelly, Matthieu Lewis, Jan Macher, Federica Mauri, Marina Moletta-Denat, Andreia Mortágua, Jan Pawlowski, Javier Pérez Burillo, Martin Pfannkuchen, Erik Pilgrim, Panayiota Pissaridou, Jonathan Porter, Frederic Rimet, Karmen Stanic, Kálmán Tapolczai, Susanna Theroux, Rosa Trobajo, Berry van der Hoorn, Marlen Vasquez Hadjilyra, Kerry Walsh, David Wanless, Jonathan Warren, Jonas Zimmermann, Maša Zupančič (2021)
The Fellowship of the Ring Test: DNAqua-Net WG2 initiative to compare diatom metabarcoding protocols used in routine freshwater biomonitoring for standardisation. ARPHA Conference Abstracts 4: .

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James D. Hagy, Katelyn A. Houghton, David L. Beddick, Joseph B. James, Stephanie D. Friedman, Richard Devereux (2020)
Quantifying stream periphyton assemblage responses to nutrient amendments with a molecular approach. Freshwater Science 39: 292.

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Philippe Blancher, Estelle Lefrançois, Frédéric Rimet, Valentin Vasselon, Christine Argillier, Jens Arle, Pedro Beja, Pieter Boets, Jeanne Boughaba, Christian Chauvin, Michael Deacon, Willie Duncan, Gunilla Ejdung, Stefania Erba, Benoit Ferrari, Helmut Fischer, Bernd Hänfling, Michael Haldin, Daniel Hering, Nicolas Hette-Tronquart, Alice Hiley, Marko Järvinen, Benjamin Jeannot, Maria Kahlert, Martyn Kelly, Julia Kleinteich, Serdar Koyuncuoğlu, Sascha Krenek, Sidsel Langhein-Winther, Florian Leese, David Mann, Rémy Marcel, Stefania Marcheggiani, Kristian Meissner, Patricia Mergen, Olivier Monnier, Frank Narendja, Diane Neu, Veronica Onofre Pinto, Alina Pawlowska, Jan Pawlowski, Martin Petersen, Sandra Poikane, Didier Pont, Marie-Sophie Renevier, Steinar Sandoy, Jonas Svensson, Rosa Trobajo, Andrea Tünde Zagyva, Iakovos Tziortzis, Berry van der Hoorn, Marlen Ines Vasquez, Kerry Walsh, Alexander Weigand, Agnès Bouchez (2022)
A strategy for successful integration of DNA-based methods in aquatic monitoring. Metabarcoding and Metagenomics 6: .

DOI: 10.3897/mbmg.6.85652

Hristina Kochoska, Cécile Chardon, Teofana Chonova, François Keck, Lenaïg Kermarrec, Floriane Larras, Estelle Lefrancois, Sinziana F. Rivera, Kálmán Tapolczai, Valentin Vasselon, Zlatko Levkov, Frédéric Rimet (2023)
Filling reference libraries with diatom environmental sequences: strengths and weaknesses. Diatom Research 38: 103.

DOI: 10.1080/0269249X.2023.2237977

Sujatha Narayanan Kutty, Rebecca K. Loh, Wayne Bannister, David Taylor (2022)
Evaluation of a diatom eDNA-based technique for assessing water quality variations in tropical lakes and reservoirs. Ecological Indicators 141: 109108.

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Mathew Seymour (2022)
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