Assessing performance of spore samplers in monitoring aeromycobiota and fungal plant pathogen diversity in Canada

Chen, Wen; Hambleton, Sarah; Seifert, Keith A.; Carisse, Odile; Diarra, Moussa S.; Peters, Rick D.; Lowe, Christine; Chapados, Julie T.; Lévesque, C. André

doi:https://open-science.canada.ca/handle/123456789/192

Assessing performance of spore samplers in monitoring aeromycobiota and fungal plant pathogen diversity in Canada

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dc.contributor.author: Chen, Wen; Hambleton, Sarah; Seifert, Keith A.; Carisse, Odile; Diarra, Moussa S.; Peters, Rick D.; Lowe, Christine; Chapados, Julie T.; Lévesque, C. André
dc.date.accessioned: 2023-04-17T17:42:02Z
dc.date.available: 2023-04-17T17:42:02Z
dc.date.issued: 2018-04-16
dc.description.abstract - en: Spore samplers are widely used in pathogen surveillance but not so much for monitoring the composition of aeromycobiota. In Canada, a nationwide spore-sampling network (AeroNet) was established as a pilot project to assess fungal community composition in air and rain samples collected using three different spore samplers in the summers of 2010 and 2011. Metabarcodes of the internal transcribed spacer (ITS) were exhaustively characterized for three of the network sites, in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI), to compare performance of the samplers. Sampler type accounted for ca. 20% of the total explainable variance in aeromycobiota compositional heterogeneity, with air samplers recovering more Ascomycota and rain samplers recovering more Basidiomycota. Spore samplers showed different abilities to collect 27 fungal genera that are plant pathogens. For instance, Cladosporium spp., Drechslera spp., and Entyloma spp. were collected mainly by air samplers, while Fusarium spp., Microdochium spp., and Ustilago spp. were recovered more frequently with rain samplers. The diversity and abundance of some fungi were significantly affected by sampling location and time (e.g., Alternaria and Bipolaris) and weather conditions (e.g., Mycocentrospora and Leptosphaeria), and depended on using ITS1 or ITS2 as the barcoding region (e.g., Epicoccum and Botrytis). The observation that Canada's aeromycobiota diversity correlates with cooler, wetter conditions and northward wind requires support from more long-term data sets. Our vision of the AeroNet network, combined with high-throughput sequencing (HTS) and well-designed sampling strategies, may contribute significantly to a national biovigilance network for protecting plants of agricultural and economic importance in Canada. IMPORTANCE The current study compared the performance of spore samplers for collecting broad-spectrum air- and rain-borne fungal pathogens using a metabarcoding approach. The results provided a thorough characterization of the aeromycobiota in the coastal regions of Canada in relation to the influence of climatic factors. This study lays the methodological basis to eventually develop knowledge-based guidance on pest surveillance by assisting in the selection of appropriate spore samplers.
dc.description.plainlanguage - en: Spore samplers are widely used to collect air/rain samples for monitoring plant pathogens. This paper reported how we established a nationwide spore-sampling network (AeroNet) to assess fungal community composition in air and rain collected in the summers of 2010 and 2011. We used a standard metabarcoding approach and compared the fungal spores recovered by three types of samplers at three agricultural sites in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI). We found that different types of samplers recovered more efficiently for different fungal genera containing plant pathogens. For example, Cladosporium spp., Drechslera spp., and Entyloma spp. were collected mainly by air samplers, while Fusarium spp., Microdochium spp., and Ustilago spp. were recovered more frequently with rain samplers. We also found that the diversity of the fungal community in Canada's air/rain was higher when the weather was cooler and wetter with a northward wind. We suggest that the spore trap network, combined with high-throughput sequencing (HTS) can be a platform for national biovigilance of pathogens that are of agricultural and economic importance in Canada.
dc.description.plainlanguage - fr: Les échantillonneurs de spores sont largement utilisés pour prélever des échantillons d’air et de pluie dans le cadre de la surveillance des phytopathogènes. Dans le présent article, nous relatons comment nous avons établi un réseau d’échantillonnage de spores à l’échelle nationale (AeroNet) pour évaluer la composition des communautés fongiques dans l’air et la pluie recueillis au cours des étés 2010 et 2011. Nous avons utilisé une approche de métacodage standard et comparé les spores fongiques récupérées par trois types d’échantillonneurs dans trois sites agricoles en Colombie-Britannique (C.-B.), au Québec (QC) et à l’Île-du-Prince-Édouard (Î.-P.-É.). Nous avons constaté que différents types d’échantillonneurs récupèrent plus efficacement différents genres de champignons dont font partie les phytopathogènes. Par exemple, Cladosporium spp., Drechslera spp. et Entyloma spp. ont été prélevés principalement au moyen d’échantillonneurs d’air, tandis que Fusarium spp., Microdochium spp. et Ustilago spp. ont été récupérés plus fréquemment avec des échantillonneurs de pluie. Nous avons également constaté que la diversité de la communauté fongique dans l’air et la pluie au Canada était plus élevée lorsque le temps était plus frais et plus humide, avec un vent vers le nord. Nous pensons que le réseau de pièges à spores, combiné au séquençage à haut débit (HTS), peut constituer une plateforme pour la biovigilance nationale des pathogènes d’importance agricole et économique au Canada.
dc.identifier.citation: Chen, W., Hambleton, S., Seifert, K. A., Carisse, O., Diarra, M. S., Peters, R. D., Lowe, C., Chapados, J. T., & Lévesque, C. A. (2018). Assessing performance of spore samplers in monitoring aeromycobiota and fungal plant pathogen diversity in Canada. Applied and Environmental Microbiology, 84(9). https://doi.org/10.1128/AEM.02601-17
dc.identifier.doi: https://doi.org/10.1128/AEM.02601-17
dc.identifier.issn: 1098-5336
dc.identifier.uri: https://open-science.canada.ca/handle/123456789/192
dc.language.iso: en
dc.publisher: American Society for Microbiology
dc.rights.openaccesslevel - en: Green
dc.rights.openaccesslevel - fr: Vert
dc.subject - en: Agriculture
dc.subject - fr: Agriculture
dc.subject.en - en: Agriculture
dc.subject.fr - fr: Agriculture
dc.title - en: Assessing performance of spore samplers in monitoring aeromycobiota and fungal plant pathogen diversity in Canada
dc.title.fosrctranslation - fr: Assessing performance of spore samplers in monitoring aeromycobiota and fungal plant pathogen diversity in Canada
dc.type - en: Article
dc.type - fr: Article
local.article.journalissue: 9
local.article.journaltitle: Applied and Environmental Microbiology
local.article.journalvolume: 84
local.peerreview - en: Yes
local.peerreview - fr: Oui

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