Combining Air Sampling and DNA Metabarcoding to Monitor Plant Pathogens

Abstract

Monitoring the air for airborne plant pathogens is an increasingly common method for the management of economically important plant diseases. In Alberta, Canada, several commodity clusters, including dry bean, canola, potato, and wheat, currently support air monitoring research programs for airborne pathogens of interest. In this study, we assessed the feasibility of monitoring for these, and more, plant fungal pathogens simultaneously using two different sampler types (cyclone versus rotation impaction) and by metabarcoding the ITS1 region using the Illumina sequencing platform. We collected air samples from four geographically distant sites across Alberta and monitored four crop types in southern Alberta. Overall, we found weak, but statistically significant, effects of geographic location and crop type on the aeromycobiota community composition. A few common taxa, such as Ramularia, Alternaria, and Epicoccum, constituted the vast majority of reads across all samples. Nevertheless, in each sample, we identified many plant pathogens of interest and organisms that previous research has found antagonistic to those pathogens, highlighting the utility of these approaches in understanding the pathobiome. In assessing the real-world implications of read counts, we discovered that they were only weakly correlated with spore counts quantified by qPCR. The two types of samplers collected different community profiles, reinforcing the importance of carefully considering which sampler type to use in monitoring programs. Taken together, our results show promise for the future of monitoring the air pathobiome, although much more work is required to understand the relationship of airborne communities to their in-field impact on disease development. [Figure: see text] Copyright © 2023 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Keywords

• aerobiology
• air microbiome
• amplicon sequencing
• Illumina
• metabarcoding
• next-generation sequencing