Assessing performance of spore samplers in monitoring and forecasting aeromycobiota diversity and fungal plant pathogen distribution patterns

Chen W, Hambleton S, Seifert KA, Lévesque CA, Carisse O, Moussa SD, Peters RD, Lowe C, Chapados JT. 2017. Assessing performance of spore samplers in monitoring and forecasting aeromycobiota diversity and fungal plant pathogen distribution patterns. Applied and Environmental Microbiology Submitted, under peer review.

Abstract

Spore samplers are used widely in pathogen-surveillance but the performance of different operating models for collecting a broad taxonomic and ecological spectrum has not been studied. Air and rain samples collected by three different spore samplers during the summers of 2010 and 2011 were analyzed using Internal Transcribed Spacer (ITS) metabarcodes generated by High-Throughput Sequencing (HTS). Diverse spatial and temporal distribution patterns in the aeromycobiota were characterized at the west and east coasts of Canada. Spore samplers showed collection biases to fungal genera containing plant pathogens, e.g. Cladosprium and Fusarium. CART models suggested that fungal spores were transported northward and that the diversity was higher during the cooler, wetter summer. Classification of metabarcodes at the species-level must be critically evaluated for each taxonomic group, because of low interspecific ITS sequence variation in some groups, especially Ascomycetes, and the existence of large gaps in taxonomic coverage in reference databases for many fungal groups. Results suggest that the combination of HTS, spore-sampling networks and well-designed sampling strategies allow simultaneous detection of multiple pathogenic microorganisms, especially when accurate species / subspecies level classification for metabarcodes can be achieved using species-specific oligonucleotides. Importance This is the first study to compare the performance of spore samplers for collecting broad-spectrum air/rain-borne fungal pathogens using high-throughput sequencing (HTS). This is also the first study to thoroughly characterize the aeromycobiota in the coastal regions of Canada under the influence of climatic factors. This study provides science-based guidance on pest surveillance to farmers and regulators.

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