Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring
DNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready for routine application. However, protocols and methods still vary between and within countries, limiting their transferability and the comparability...
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Pensoft Publishers
2025-01-01
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| Series: | Metabarcoding and Metagenomics |
| Online Access: | https://mbmg.pensoft.net/article/133264/download/pdf/ |
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| author | Valentin Vasselon Sinziana F. Rivera Éva Ács Salomé Baja Almeida Karl B. Andree Laure Apothéloz-Perret-Gentil Bonnie Bailet Ana Baričević Kevin K. Beentjes Juliane Bettig Agnès Bouchez Camilla Capelli Cécile Chardon Mónika Duleba Tina Elersek Clémence Genthon Maša Jablonska Louis Jacas Maria Kahlert Martyn G. Kelly Jan-Niklas Macher Federica Mauri Marina Moletta-Denat Andreia Mortágua Jan Pawlowski Javier Pérez-Burillo Martin Pfannkuchen Erik Pilgrim Panayiota Pissaridou Frédéric Rimet Karmen Stanic Kálmán Tapolczai Susanna Theroux Rosa Trobajo Berry Van der Hoorn Marlen I. Vasquez Marie Vidal David Wanless Jonathan Warren Jonas Zimmermann Benoît Paix |
| author_facet | Valentin Vasselon Sinziana F. Rivera Éva Ács Salomé Baja Almeida Karl B. Andree Laure Apothéloz-Perret-Gentil Bonnie Bailet Ana Baričević Kevin K. Beentjes Juliane Bettig Agnès Bouchez Camilla Capelli Cécile Chardon Mónika Duleba Tina Elersek Clémence Genthon Maša Jablonska Louis Jacas Maria Kahlert Martyn G. Kelly Jan-Niklas Macher Federica Mauri Marina Moletta-Denat Andreia Mortágua Jan Pawlowski Javier Pérez-Burillo Martin Pfannkuchen Erik Pilgrim Panayiota Pissaridou Frédéric Rimet Karmen Stanic Kálmán Tapolczai Susanna Theroux Rosa Trobajo Berry Van der Hoorn Marlen I. Vasquez Marie Vidal David Wanless Jonathan Warren Jonas Zimmermann Benoît Paix |
| author_sort | Valentin Vasselon |
| collection | DOAJ |
| description | DNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready for routine application. However, protocols and methods still vary between and within countries, limiting their transferability and the comparability of results. In order to overcome this, routine use of DNA metabarcoding for diatom biomonitoring requires knowledge of the sources of variability introduced by the different steps of the procedure. Here, we examine how elements of routine procedures contribute to variability between European laboratories. A set of four experiments were performed focusing on DNA extraction and PCR amplification steps to evaluate their reproducibility between different laboratories and the variability introduced by different protocols currently applied by the scientific community. Under the guidance of a reference laboratory, 17 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using the same fixed protocol and their own choice of protocol. Experiments were performed by each participant on a set of standardised DNA and biofilm samples (river, lake and mock community) to investigate potential systematic and random errors. Our results revealed the successful transferability of a protocol amongst labs and a highly similar and consistent ecological assessment outcome obtained regardless of the protocols used by each participant. We propose an “all for one but prove them all” strategy, suggesting that distinct protocols can be used within the scientific community, as long as their consistency is be proven by following minimum standard requirements. |
| format | Article |
| id | doaj-art-01b5f999523842bfb934ec8024b7e1bd |
| institution | Kabale University |
| issn | 2534-9708 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Pensoft Publishers |
| record_format | Article |
| series | Metabarcoding and Metagenomics |
| spelling | doaj-art-01b5f999523842bfb934ec8024b7e1bd2025-01-12T08:30:48ZengPensoft PublishersMetabarcoding and Metagenomics2534-97082025-01-019357010.3897/mbmg.9.133264133264Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoringValentin Vasselon0Sinziana F. Rivera1Éva Ács2Salomé Baja Almeida3Karl B. Andree4Laure Apothéloz-Perret-Gentil5Bonnie Bailet6Ana Baričević7Kevin K. Beentjes8Juliane Bettig9Agnès Bouchez10Camilla Capelli11Cécile Chardon12Mónika Duleba13Tina Elersek14Clémence Genthon15Maša Jablonska16Louis Jacas17Maria Kahlert18Martyn G. Kelly19Jan-Niklas Macher20Federica Mauri21Marina Moletta-Denat22Andreia Mortágua23Jan Pawlowski24Javier Pérez-Burillo25Martin Pfannkuchen26Erik Pilgrim27Panayiota Pissaridou28Frédéric Rimet29Karmen Stanic30Kálmán Tapolczai31Susanna Theroux32Rosa Trobajo33Berry Van der Hoorn34Marlen I. Vasquez35Marie Vidal36David Wanless37Jonathan Warren38Jonas Zimmermann39Benoît Paix40Scimabio-InterfaceSwiss Federal Research Institute WSL AgroscopeUniversity of Public ServiceUniversity of AveiroIRTAUnaffiliatedUMR DECOD, INRAERuder Boskovic InstituteNaturalis Biodiversity CenterFreie Universität BerlinUniversité de Savoie Mont-BlancSUPSI, Institute of Earth SciencesUniversité de Savoie Mont-BlancUniversity of Public ServiceNational Institute of BiologyINRAE Transfert - Metys- Service Génomique Plateforme GeT-PlaGeNational Institute of BiologyUniversité de Savoie Mont-BlancSwedish University of Agricultural SciencesUniversity of NottinghamNaturalis Biodiversity CenterSUPSI, Institute of MicrobiologyINRAE Transfert - Metys- LBE- Service GénomiqueUniversity of AveiroUniversity of GenevaIRTARuder Boskovic InstituteUS Environmental Protection AgencyCyprus University of TechnologyUniversité de Savoie Mont-BlancNational Institute of BiologyHUN-REN Balaton Limnological Research InstituteSCCWRPIRTANaturalis Biodiversity CenterCyprus University of TechnologyINRAE Transfert - Metys- Service Génomique Plateforme GeT-PlaGeSCCWRPEnvironment AgencyFreie Universität BerlinUniversité de Savoie Mont-BlancDNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready for routine application. However, protocols and methods still vary between and within countries, limiting their transferability and the comparability of results. In order to overcome this, routine use of DNA metabarcoding for diatom biomonitoring requires knowledge of the sources of variability introduced by the different steps of the procedure. Here, we examine how elements of routine procedures contribute to variability between European laboratories. A set of four experiments were performed focusing on DNA extraction and PCR amplification steps to evaluate their reproducibility between different laboratories and the variability introduced by different protocols currently applied by the scientific community. Under the guidance of a reference laboratory, 17 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using the same fixed protocol and their own choice of protocol. Experiments were performed by each participant on a set of standardised DNA and biofilm samples (river, lake and mock community) to investigate potential systematic and random errors. Our results revealed the successful transferability of a protocol amongst labs and a highly similar and consistent ecological assessment outcome obtained regardless of the protocols used by each participant. We propose an “all for one but prove them all” strategy, suggesting that distinct protocols can be used within the scientific community, as long as their consistency is be proven by following minimum standard requirements.https://mbmg.pensoft.net/article/133264/download/pdf/ |
| spellingShingle | Valentin Vasselon Sinziana F. Rivera Éva Ács Salomé Baja Almeida Karl B. Andree Laure Apothéloz-Perret-Gentil Bonnie Bailet Ana Baričević Kevin K. Beentjes Juliane Bettig Agnès Bouchez Camilla Capelli Cécile Chardon Mónika Duleba Tina Elersek Clémence Genthon Maša Jablonska Louis Jacas Maria Kahlert Martyn G. Kelly Jan-Niklas Macher Federica Mauri Marina Moletta-Denat Andreia Mortágua Jan Pawlowski Javier Pérez-Burillo Martin Pfannkuchen Erik Pilgrim Panayiota Pissaridou Frédéric Rimet Karmen Stanic Kálmán Tapolczai Susanna Theroux Rosa Trobajo Berry Van der Hoorn Marlen I. Vasquez Marie Vidal David Wanless Jonathan Warren Jonas Zimmermann Benoît Paix Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring Metabarcoding and Metagenomics |
| title | Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring |
| title_full | Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring |
| title_fullStr | Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring |
| title_full_unstemmed | Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring |
| title_short | Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring |
| title_sort | proficiency testing and cross laboratory method comparison to support standardisation of diatom dna metabarcoding for freshwater biomonitoring |
| url | https://mbmg.pensoft.net/article/133264/download/pdf/ |
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