Sampling and analysis methods for detecting and monitoring airborne plant pathogens and fungal diversity

Many important plant diseases are caused by airborne spores. This review explains the aerobiology of plant pathogens, sampling methods for collection of airborne spores, merits of different post-capture diagnostic methods (microscopy, immunology and DNA-based diagnostics) and non-capture (optical or imaging) methods to classify airborne particles. Different sampling, downstream processing and diagnostic methods can affect the efficiency of detection of certain species due to differences in traits such as spore size, adhesive surfaces, electrostatic charge, hydrophobicity, physical toughness and copy number of target DNA sequences. These considerations and an understanding of dispersal must be understood by all engaged in practical or academic measurement of bioaerosols, whether for plant pathology, fungal ecology or to measure biodiversity. In addition to surveillance of changes in pathogen populations, for example, for antimicrobial resistance or pathotype, the review describes how air sampling can provide accurate and cost-effective forecasting of imminent plant disease. The scale of spore dispersal processes and impacts on sampling strategies (e.g. spatial density of spore traps and sampling height above ground) for broad-acre or small-scale but high-value crops is also discussed. The fundamental concept behind these processes is the aerobiology pathway, which describes the production, release, dispersal, deposition and resulting effect, which, for air-dispersed plant pathogens, is plant disease. In addition to the seasonality to spore production for many fungi, each component of the aerobiology pathway is affected by the weather, which causes different types of spores to be released under different meteorological conditions or at different times of day and to disperse in different ways. Dispersal processes of fungal spores in air have been modelled and apply irrespective of pathogens or non-pathogenic fungi, or to spores of individuals that are insensitive to fungicides or not. Often, we do not know the location of spore sources or their relative source strength, which makes sampling strategies difficult to optimize initially, and the best strategy will vary from pathogen to pathogen and according to the rationale for monitoring and consequences of ‘missing’ a spore event.