Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing

Marianne Potvin; Jeff Gauthier; Christophe Langevin; Vani Mohit; Naíla Barbosa da Costa; Thomas Deschênes; Maude Pomerleau; Irena Kukavica-Ibrulj; Daniel Verreault; Jérôme Comte; Roger C Levesque

doi:10.3389/fmicb.2023.1267652

Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing

Front Microbiol. 2023 Nov 1:14:1267652. doi: 10.3389/fmicb.2023.1267652. eCollection 2023.

Authors

Affiliations

¹ Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada.
² Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada.
³ Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, Canada.
⁴ Direction 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, Canada.

Abstract

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.

Keywords: Oxford Nanopore technologies; cyanobacteria; cyanobacteria genomic database; harmful algal blooms; on-site detection; whole genome sequencing.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. CL is supported by a Natural Science and Engineering Research Council of Canada (NSERC) studentship. The RL team is funded by Genome Canada, Génome Québec and by a CIHR-JPIAMR team grant. JC is funded by Genome Canada, Génome Québec, the Osmoz program and by NSERC. The RosHAB research is supported by a Genomic Applications Partnership Program funded by Genome Canada, Genome Quebec, and the Quebec Department of Environment, Climate Change, Forests and Parks.