Global demand for pesticide-free food products is increasing rapidly. Crops of all types are, however, under constant threat from various plant pathogens. To achieve adequate control with minimal pesticide use, close monitoring is imperative. Many plant pathogens spread through the air, so the atmosphere is composed of a wide variety of plant pathogenic and non-plant pathogenic organisms, in particular in agricultural environments. Aerobiology is the science that studies airborne microorganisms and their distribution, especially as agents of infection. Although this discipline has existed for decades, the development of new molecular technologies is contributing to an increase in the use of aerobiological data for several purposes, from day-to-day monitoring to improving our understanding of pathosystems. Although the importance of knowing the size and composition of plant pathogen populations present in the air is recognized, technical constraints hinder the development of agricultural aerobiology. Here we review the application of spore sampling systems in agriculture and discuss the main considerations underlying the implementation of airborne inoculum monitoring. The results of this literature review confirm that the use of aerobiological data to study the escape of inoculum from a source and its role in the development of diseases is well mastered, but point at a lack of knowledge to proceed with the deployment of these systems at the landscape scale. Thus, we conclude that airborne inoculum surveillance networks are still in their early stages and although more and more initiatives are emerging, research must be conducted primarily to integrate evolving technologies and improve the access, analysis, interpretation and sharing of data. These tools are needed to estimate short- and medium-term risks, identify the most appropriate control measures with the lowest environmental risk, develop indicators to document the effects of climate change, and monitor the evolution of new genotypes at multiple scales.

Real-time loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) assays were developed targeting the internal transcribed spacer 2 region of the ribosomal DNA of Phytophthora infestans, the potato late blight causal agent. A rapid crude plant extract (CPE) preparation method from infected potato leaves was developed for on-site testing. The assay’s specificity was tested using several species of Phytophthora and other potato fungal and oomycete pathogens. Both LAMP and RPA assays showed specificity to P. infestans but also to the closely related species P. andina, P. mirabilis, P. phaseoli, and P. ipomoeae, although the latter are not reported as potato pathogen species. No cross-reaction occurred with P. capsici or with the potato pathogens tested, including P. nicotianae and P. erythroseptica. The sensitivity was determined using P. infestans pure genomic DNA added into healthy CPE samples. Both LAMP and RPA assays detected DNA at 50 fg/μl and were insensitive to CPE inhibition. The isothermal assays were tested with artificially inoculated and naturally infected potato plants using a Smart-DART platform. The LAMP assay effectively detected P. infestans in symptomless potato leaves as soon as 24 h postinoculation. A rapid and accurate on-site detection of P. infestans in plant material using the LAMP assay will contribute to improved late blight diagnosis and early detection of infections and facilitate prompt management decisions.

More than 80% of Canadian lettuce production is located in the province of Quebec. Yet most of our knowledge on the epidemiology of lettuce downy mildew (Bremia lactucae) is derived from controlled-condition experiments or field experiments conducted in subtropical climates and, thus, cannot readily be applied to Quebec lettuce production. The influence of temperature and leaf wetness duration on the infection efficiency (IE) of B. lactucae was studied for 4 years (2003, 2004, 2012, and 2013) under field and growth-chamber conditions. IE was defined as the ratio of the number of lesions/leaf to the airborne conidia concentration (ACC). B. lactucae ACC was measured with rotating-arm samplers three times/week. In addition, 72 lettuce trap plants/sampling day were exposed to the potential airborne B. lactucae inoculum and disease intensity was assessed after 7 days of incubation in greenhouse. Under growth-chamber conditions, an ACC of 1 conidium/m³ was sufficient to cause 1 lesion/leaf, and IE ranged from 0.25 to 1.00. Under field conditions, an ACC of 10 to 14 conidia/m³ was required to cause 1 lesion/leaf, and IE ranged from 0.02 to 0.10, except in 2004, when IE ranged from 0.03 to 1.00. IE increased with increasing leaf wetness duration but decreased with increasing temperature. Also, considering an observed average temperature range from 10 to 20°C in the area of Quebec, 2 h of leaf wetness was sufficient for infection by B. lactucae. Therefore, under Quebec lettuce production conditions, a leaf wetness period of 2 h and an ACC of 10 to 14 conidia/m³ can be used as risk indicators to facilitate disease management decisions. Also, under typical Quebec weather conditions, measuring both morning and evening leaf wetness events could be used to improve the reliability of leaf wetness duration as a downy mildew risk indicator. Further research is needed to validate these risk indicators for integration into management strategies.

The presence and abundance of pathogen inoculum is with host resistance and environmental conditions a key factor in epidemic development. Therefore, several spore-sampling devices have been proposed to monitor pathogen inoculum above fields. However, to make spore sampling more reliable as a management tool and to facilitate its adoption, information on infection efficiency and molecular tools for estimating airborne sporangia concentration are needed. Experiments were thus undertaken in a growth chamber to study the infection efficiency of four clonal lineages of P. infestans (US-8, US-11, US-23, and US-24) by measuring the airborne sporangia concentration and resulting disease intensity. The relationship between the airborne sporangia concentration and the number of lesions per leaf was exponential. For the same concentration, the sporangia of US-23 caused significantly more lesions than the sporangia of the other clonal lineages did. Under optimal conditions, an airborne sporangia concentration of 10 sporangia m⁻³ for US-23 was sufficient to cause one lesion per leaf, whereas for the other clonal lineages, it took 15 to 25 sporangia m⁻³ to reach the same disease intensity. However, in terms of diseased leaf area, there was no difference between clonal lineages US-8, US-23 and US-24. Also, a sensitive quantitative real-time polymerase chain reaction (qPCR) tool was developed to quantify P. infestans airborne sporangia with detection sensitivity of one sporangium. The specificity of the qPCR assay was rigorously tested for airborne inoculum and was either similar to, or an improvement on, other published PCR assays. This assay allows rapid and reliable detection and quantification of P. infestans airborne sporangia and thereby, facilitates the implementation of spores-sampling network.

In the muck soil region of southwestern Quebec, vegetable growers are threatened by several soilborne diseases, particularly the bottom rot of lettuce caused by the fungus Rhizoctonia solani. The particularly warm temperature of the few last seasons was marked by an increase in disease severity, and the associated yield losses were significant for Quebec lettuce growers. In the absence of registered fungicides and resistant cultivars, the management of Rhizoctonia solani-induced diseases in lettuce is based on good agricultural practices, which require detailed knowledge of the pathogen. In this study, Rhizoctonia solani fungal strains were isolated from infected field-grown lettuce plants presenting bottom rot symptoms to determine the anastomotic groups (AGs) of these isolates by internal transcribed spacer region (ITS) sequencing. Rhizoctonia solani AG 1-IB was identified as the main anastomotic group causing bottom rot lettuce in field-grown lettuce in organic soils in the Montérégie region. Two specific and sensitive quantitative PCR assays were then developed for R. solani AG1-IB and R. solani. The AG 1-IB qPCR assay amplified all strains of R. solani AG 1-IB tested, and no PCR product was obtained for any non-target strains. The R. solani qPCR assay amplified all strains of R. solani and did not amplify non-target strains, except for two strains of binucleate Rhizoctonia AG-E. In artificially inoculated soils, the sensitivity of both qPCR assays was set to 1 μg of sclerotia g⁻¹ of dry soil. In the growth chamber experiment, a minimum concentration between 14 and 42 μg sclerotia g⁻¹ of dry soil was required to induce the development of symptoms on the lettuce. Indeed, the AG 1-IB qPCR assay was sensitive enough to detect the lowest soil concentration of AG1-IB capable of inducing symptoms in head lettuce. In addition, the qPCR assays successfully detected R. solani and R. solani AG 1-IB from infected plant tissue samples and soil samples from lettuce fields. The qPCR assays developed in this study will be useful tools in lettuce bottom rot management.