Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing
With the increasing occurrence and severity of cyanobacterial harmful algal blooms (cHAB) at the global scale, there is an urgent need for rapid, accurate, accessible, and cost-effective detection tools. Here, we detail the RosHAB workflow, an innovative, in-the-field applicable genomics approach fo...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1267652/full |
| _version_ | 1797643280307978240 |
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| author | Marianne Potvin Jeff Gauthier Christophe Langevin Christophe Langevin Vani Mohit Naíla Barbosa da Costa Naíla Barbosa da Costa Thomas Deschênes Maude Pomerleau Irena Kukavica-Ibrulj Daniel Verreault Jérôme Comte Jérôme Comte Roger C. Levesque |
| author_facet | Marianne Potvin Jeff Gauthier Christophe Langevin Christophe Langevin Vani Mohit Naíla Barbosa da Costa Naíla Barbosa da Costa Thomas Deschênes Maude Pomerleau Irena Kukavica-Ibrulj Daniel Verreault Jérôme Comte Jérôme Comte Roger C. Levesque |
| author_sort | Marianne Potvin |
| collection | DOAJ |
| description | With the increasing occurrence and severity of cyanobacterial harmful algal blooms (cHAB) at the global scale, there is an urgent need for rapid, accurate, accessible, and cost-effective detection tools. Here, we detail the RosHAB workflow, an innovative, in-the-field applicable genomics approach for real-time, early detection of cHAB outbreaks. We present how the proposed workflow offers consistent taxonomic identification of water samples in comparison to traditional microscopic analyses in a few hours and discuss how the generated data can be used to deepen our understanding on cyanobacteria ecology and forecast HABs events. In parallel, processed water samples will be used to iteratively build the International cyanobacterial toxin database (ICYATOX; http://icyatox.ibis.ulaval.ca) containing the analysis of novel cyanobacterial genomes, including phenomics and genomics metadata. Ultimately, RosHAB will (1) improve the accuracy of on-site rapid diagnostics, (2) standardize genomic procedures in the field, (3) facilitate these genomics procedures for non-scientific personnel, and (4) identify prognostic markers for evidence-based decisions in HABs surveillance. |
| first_indexed | 2024-03-11T14:12:27Z |
| format | Article |
| id | doaj.art-ac12be1e0c5140ee82cdfcdfdc655d47 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-11T14:12:27Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-ac12be1e0c5140ee82cdfcdfdc655d472023-11-01T17:53:00ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-11-011410.3389/fmicb.2023.12676521267652Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencingMarianne Potvin0Jeff Gauthier1Christophe Langevin2Christophe Langevin3Vani Mohit4Naíla Barbosa da Costa5Naíla Barbosa da Costa6Thomas Deschênes7Maude Pomerleau8Irena Kukavica-Ibrulj9Daniel Verreault10Jérôme Comte11Jérôme Comte12Roger C. Levesque13Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, CanadaInstitut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, CanadaCentre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, CanadaGroupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, CanadaDirection générale de la coordination scientifique et du Centre d’expertise en analyse environnementale du Québec (CEAEQ), Ministère de l’Environnement et de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, QC, CanadaCentre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, CanadaGroupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, CanadaCentre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, CanadaCentre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, CanadaInstitut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, CanadaDirection générale de la coordination scientifique et du Centre d’expertise en analyse environnementale du Québec (CEAEQ), Ministère de l’Environnement et de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, QC, CanadaCentre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, CanadaGroupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, CanadaInstitut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, CanadaWith the increasing occurrence and severity of cyanobacterial harmful algal blooms (cHAB) at the global scale, there is an urgent need for rapid, accurate, accessible, and cost-effective detection tools. Here, we detail the RosHAB workflow, an innovative, in-the-field applicable genomics approach for real-time, early detection of cHAB outbreaks. We present how the proposed workflow offers consistent taxonomic identification of water samples in comparison to traditional microscopic analyses in a few hours and discuss how the generated data can be used to deepen our understanding on cyanobacteria ecology and forecast HABs events. In parallel, processed water samples will be used to iteratively build the International cyanobacterial toxin database (ICYATOX; http://icyatox.ibis.ulaval.ca) containing the analysis of novel cyanobacterial genomes, including phenomics and genomics metadata. Ultimately, RosHAB will (1) improve the accuracy of on-site rapid diagnostics, (2) standardize genomic procedures in the field, (3) facilitate these genomics procedures for non-scientific personnel, and (4) identify prognostic markers for evidence-based decisions in HABs surveillance.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1267652/fullcyanobacteriaharmful algal bloomson-site detectionOxford Nanopore technologieswhole genome sequencingcyanobacteria genomic database |
| spellingShingle | Marianne Potvin Jeff Gauthier Christophe Langevin Christophe Langevin Vani Mohit Naíla Barbosa da Costa Naíla Barbosa da Costa Thomas Deschênes Maude Pomerleau Irena Kukavica-Ibrulj Daniel Verreault Jérôme Comte Jérôme Comte Roger C. Levesque Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing Frontiers in Microbiology cyanobacteria harmful algal blooms on-site detection Oxford Nanopore technologies whole genome sequencing cyanobacteria genomic database |
| title | Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing |
| title_full | Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing |
| title_fullStr | Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing |
| title_full_unstemmed | Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing |
| title_short | Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing |
| title_sort | rapid on site detection of harmful algal blooms real time cyanobacteria identification using oxford nanopore sequencing |
| topic | cyanobacteria harmful algal blooms on-site detection Oxford Nanopore technologies whole genome sequencing cyanobacteria genomic database |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1267652/full |
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