Catching Spores: Linking Epidemiology, Pathogen Biology, and Physics to Ground-Based Airborne Inoculum Monitoring

Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes

The disease triangle is a structurally simple but conceptually rich model that is used in plant pathology and other fields of study to explain infectious disease as an outcome of the three-way relationship between a host, a pathogen, and their environment. It also serves as a guide for finding solutions to treat, predict, and prevent such diseases. With the omics-driven, evidence-based realization that the abundance and activity of a pathogen are impacted by proximity to and interaction with a diverse multitude of other microorganisms colonizing the same host, the disease triangle evolved into a tetrahedron shape, which features an added fourth dimension representing the host-associated microbiota. Another variant of the disease triangle emerged from the recently formulated pathobiome paradigm, which deviates from the classical "one pathogen" etiology of infectious disease in favor of a scenario in which disease represents a conditional outcome of complex interactions between and among a host, its microbiota (including microbes with pathogenic potential), and the environment. The result is a version of the original disease triangle where "pathogen" is substituted with "microbiota." Here, as part of a careful and concise review of the origin, history, and usage of the disease triangle, I propose a next step in its evolution, which is to replace the word "disease" in the center of the host-microbiota-environment triad with the word "health." This triangle highlights health as a desirable outcome (rather than disease as an unwanted state) and as an emergent property of host-microbiota-environment interactions. Applied to the discipline of plant pathology, the health triangle offers an expanded range of targets and approaches for the diagnosis, prediction, restoration, and maintenance of plant health outcomes. Its applications are not restricted to infectious diseases only, and its underlying framework is more inclusive of all microbial contributions to plant well-being, including those by mycorrhizal fungi and nitrogen-fixing bacteria, for which there never was a proper place in the plant disease triangle. The plant health triangle also may have an edge as an education and communication tool to convey and stress the importance of healthy plants and their associated microbiota to a broader public and stakeholdership.

Detection of Podosphaera macularis in Air Samples by Quantitative PCR

Detection and quantification of pathogen propagules in the air or other environmental samples is facilitated by culture-independent assays. We developed a quantitative PCR assay for the hop powdery mildew fungus, Podosphaera macularis, for detection of the organism from air samples. The assay uses primers and a TaqMan probe designed to target species-specific sequences in the 28S large subunit of the nuclear ribosomal DNA. Analytical sensitivity was not affected by the presence of an exogenous internal control or potential PCR inhibitors associated with DNA extracted from soil. The level of quantification of the assay was between 200 and 350 conidia when DNA was extracted from a fixed number of conidia. The assay amplified all isolates of P. macularis tested and had minimal cross-reactivity with other Podosphaera species when assayed with biologically relevant quantities of DNA. Standard curves generated independently in two other laboratories indicated that assay sensitivity was qualitatively similar and reproducible. All laboratories successfully detected eight unknown isolates of P. macularis and correctly discriminated Pseudoperonospora humuli and a water control. The usefulness of the assay for air sampling for late-season inoculum of P. macularis was demonstrated in field studies in 2019 and 2020. In both years, airborne populations of P. macularis in hop yards were detected consistently and increased during bloom and cone development.

From Detection to Protection: The Role of Optical Sensors, Robots, and Artificial Intelligence in Modern Plant Disease Management

In the past decade, there has been a recognized need for innovative methods to monitor and manage plant diseases, aiming to meet the precision demands of modern agriculture. Over the last 15 years, significant advances in the detection, monitoring, and management of plant diseases have been made, largely propelled by cutting-edge technologies. Recent advances in precision agriculture have been driven by sophisticated tools such as optical sensors, artificial intelligence, microsensor networks, and autonomous driving vehicles. These technologies have enabled the development of novel cropping systems, allowing for targeted management of crops, contrasting with the traditional, homogeneous treatment of large crop areas. The research in this field is usually a highly collaborative and interdisciplinary endeavor. It brings together experts from diverse fields such as plant pathology, computer science, statistics, engineering, and agronomy to forge comprehensive solutions. Despite the progress, translating the advancements in the precision of decision-making or automation into agricultural practice remains a challenge. The knowledge transfer to agricultural practice and extension has been particularly challenging. Enhancing the accuracy and timeliness of disease detection continues to be a priority, with data-driven artificial intelligence systems poised to play a pivotal role. This perspective article addresses critical questions and challenges faced in the implementation of digital technologies for plant disease management. It underscores the urgency of integrating innovative technological advances with traditional integrated pest management. It highlights unresolved issues regarding the establishment of control thresholds for site-specific treatments and the necessary alignment of digital technology use with regulatory frameworks. Importantly, the paper calls for intensified research efforts, widespread knowledge dissemination, and education to optimize the application of digital tools for plant disease management, recognizing the intersection of technology's potential with its current practical limitations.

It's a Trap! Part II: An Approachable Guide to Constructing and Using Rotating-Arm Air Samplers

An increasing number of researchers are looking to understand the factors affecting microbial dispersion but are often limited by the costs of commercially available air samplers. Some have reduced these costs by designing self-made versions; however, there are no published sampler designs, and there is limited information provided on the actual construction process. Lack of appropriate reference material limits the use of these self-made samplers by many researchers. This manuscript provides a guide to designing and constructing rotating-arm impaction air samplers by covering (i) environmental considerations, (ii) construction materials and equipment, (iii) the construction process, and (iv) air sampler deployment. Information regarding how to calculate rotational velocity, motor speed, and power supply requirements and to troubleshoot common issues is presented in an approachable format for individuals without experience in electronics or machining. Although many of the components discussed in this guide may change in their availability or be updated over time, this document is intended to serve as a "builder's guide" for future research into air sampling technology for phytopathology research.

It's a Trap! Part I: Exploring the Applications of Rotating-Arm Impaction Samplers in Plant Pathology

Although improved knowledge on the movement of airborne plant pathogens is likely to benefit plant health management, generating this knowledge is often far more complicated than anticipated. This complexity is driven by the dynamic nature of environmental variables, diversity among pathosystems that are targeted, and the unique needs of each research group. When using a rotating-arm impaction sampler, particle collection is dependent on the pathogen, environment, research objectives, and limitations (monetary, environmental, or labor). Consequently, no design will result in 100% collection efficiency. Fortunately, it is likely that multiple approaches can succeed despite these constraints. Choices made during design and implementation of samplers can influence the results, and recognizing this influence is crucial for researchers. This article is for beginners in the art and science of using rotating-arm impaction samplers; it provides a foundation for designing a project, from planning the experiment to processing samples. We present a relatively nontechnical discussion of the factors influencing pathogen dispersal and how placement of the rotating-arm air samplers alters propagule capture. We include a discussion of applications of rotating-arm air samplers to demonstrate their versatility and potential in plant pathology research as well as their limitations.

Sporulation and Dispersal of the Biological Control Agent Aspergillus flavus AF36 Under Field Conditions

Aflatoxins are carcinogens produced by the fungi Aspergillus flavus and A. parasiticus that contaminate pistachio crops. International markets reject pistachio when aflatoxins exceed permitted maximum levels. Releasing the atoxigenic strain AF36 of A. flavus is the leading aflatoxin pre-harvest control method. The product AF36 Prevail, sorghum grains coated with AF36 propagules, has been used in California since 2017. However, a high percentage of grains of the Prevail fail to sporulate in orchards. Here, the effect of soil moisture on the percentage of AF36 product grains sporulating (SG) and the quantity of spores per grain using a sporulation index (SI) was determined. Under controlled conditions, SG was higher than 85% when soil moisture was 13% or more, and SI increased with increasing soil moisture from 8.4 to 21%. The highest AF36 sporulation occurred near the micro-sprinklers when the grains were not impacted by the irrigation water drops. Arthropod predation was responsible for lost product grains, which was more pronounced in non-tilled soil than in tilled soil. Dispersal of the AF36 spores decreased markedly with the height and distance from the inoculum source, following a pattern of diffusion equations. However, AF36 spores easily reached canopies of pistachios located 10 m from the inoculum source. Our results indicate that AF36 Prevail should be applied close to the irrigation line in the moist soil area but avoiding the areas where excess irrigation causes water accumulation. The biocontrol of aflatoxins in California's pistachio production areas was optimized by improving the field realization of the biological control agent.

Quantifying water-use efficiency in plant canopies with varying leaf angle and density distribution

BACKGROUND AND AIMS

Variation in architectural traits related to the spatial and angular distribution of leaf area can have considerable impacts on canopy-scale fluxes contributing to water-use efficiency (WUE). These architectural traits are frequent targets for crop improvement and for improving the understanding and predictions of net ecosystem carbon and water fluxes.

METHODS

A three-dimensional, leaf-resolving model along with a range of virtually generated hypothetical canopies were used to quantify interactions between canopy structure and WUE by examining its response to variation of leaf inclination independent of leaf azimuth, canopy heterogeneity, vegetation density and physiological parameters.

KEY RESULTS

Overall, increasing leaf area index (LAI), increasing the daily-averaged fraction of leaf area projected in the sun direction (Gavg) via the leaf inclination or azimuth distribution and increasing homogeneity had a similar effect on canopy-scale daily fluxes contributing to WUE. Increasing any of these parameters tended to increase daily light interception, increase daily net photosynthesis at low LAI and decrease it at high LAI, increase daily transpiration and decrease WUE. Isolated spherical crowns could decrease photosynthesis by ~60 % but increase daily WUE ≤130 % relative to a homogeneous canopy with equivalent leaf area density. There was no observed optimum in daily canopy WUE as LAI, leaf angle distribution or heterogeneity was varied. However, when the canopy was dense, a more vertical leaf angle distribution could increase both photosynthesis and WUE simultaneously.

CONCLUSIONS

Variation in leaf angle and density distributions can have a substantial impact on canopy-level carbon and water fluxes, with potential trade-offs between the two. These traits might therefore be viable target traits for increasing or maintaining crop productivity while using less water, and for improvement of simplified models. Increasing canopy density or decreasing canopy heterogeneity increases the impact of leaf angle on WUE and its dependent processes.

Measuring the Distance and Effects of Weather Conditions on the Dispersal of Nothopassalora personata

Nothopassalora personata is one of the most economically severe pathogens of peanut in the United States. The fungus primarily relies on wind and rain for dispersal, which has been documented up to 10 m from an inoculum source. Spore traps have been used in a wide variety of pathosystems to study epidemiology, document detection, develop alert systems, and guide management programs. The objective of this study was to use spore traps and N. personata-specific qPCR primers to quantitatively evaluate dispersal of N. personata conidia at distances up to 70 m from an infected peanut field and to examine relationships between quantities captured and weather variables. Impaction spore samplers were placed at 4, 10, 30, 50, and 70 m from peanut fields at the Edisto Research and Education Center (six fields) and commercial peanut fields in Barnwell and Bamberg counties (one field each) from 2020 to 2022. Following initial detection, samples were collected at a 48-, 48-, 72-h interval until harvest. N. personata conidia were detected at all locations and distances, documenting dispersal up to 70 m from an inoculum source. This result is a reminder that volunteer management is crucial when rotating peanut in nearby fields. A model for predicting log spore quantities was developed using temperature and humidity variables. Temperature variables associated with observed sampling periods had a negative correlation with N. personata quantities, whereas parameters of relative humidity and mean windspeed were positively correlated.

A Rapid Glove-Based Inoculum Sampling Technique to Monitor Erysiphe necator in Commercial Vineyards

Information on the presence and severity of grape powdery mildew (GPM), caused by Erysiphe necator, has long been used to guide management decisions. While recent advances in the available molecular diagnostic assays and particle samplers have made monitoring easier, there is still a need for more efficient field collection of E. necator. The use of vineyard worker gloves worn during canopy manipulation as a sampler (glove swab) of E. necator was compared with samples identified by visual assessment with subsequent molecular confirmation (leaf swabs) and airborne spore samples collected by rotating-arm impaction traps (impaction traps). Samples from United States commercial vineyards in Oregon, Washington, and California were analyzed using two TaqMan qPCR assays targeting the internal transcribed spacer regions or cytochrome b gene of E. necator. Based on qPCR assays, visual disease assessments misidentified GPM up to 59% of the time with a higher frequency of misidentification occurring earlier in the growing season. Comparison of the aggregated leaf swab results for a row (n = 915) to the row's corresponding glove swab had 60% agreement. The latent class analysis (LCA) indicated that glove swabs were more sensitive than leaf swabs in detecting E. necator presence. The impaction trap results had 77% agreement to glove swabs (n = 206) taken from the same blocks. The LCAs estimated that the glove swabs and impaction trap samplers varied each year in which was more sensitive for detection. This likely indicates that these methods have similar levels of uncertainty and provide equivalent information. Additionally, all samplers, once E. necator was detected, were similarly sensitive and specific for detection of the A-143 resistance allele. Together, these results suggest that glove swabs are an effective sampling method for monitoring the presence of E. necator and, subsequently, the G143A amino acid substitution associated with resistance to quinone outside inhibitor fungicides in vineyards. Glove swabs could reduce sampling costs due to the lack of need for specialized equipment and time required for swab collection and processing.

Goldilocks mushrooms: How ballistospory has shaped basidiomycete evolution

Ballistospory has been a governing factor in mushroom diversification. Modifications to fruit body morphology are subject to a series of fundamental constraints imposed by this uniquely fungal mechanism. Gill spacing in lamellate mushrooms, tube width in poroid species, and other configurations of the hymenium must comply with the distance that spores shoot themselves from their basidia. This reciprocal relationship between the development of fruit bodies and spores may have been maintained by a form of evolutionary seesaw proposed in this article. The necessity of the accurate gravitropic orientation of gills and tubes is another constraint on mushroom development and physiology, along with the importance of evaporative cooling of the hymenium for successful spore discharge and the aerodynamic shaping of the fruit body to aid dispersal. Ballistospory has been lost in secotioid and gasteroid basidiomycetes whose spores are dispersed by animal vectors and has been replaced by alterative mechanisms of active spore discharge in some species. Partnered with the conclusions drawn from molecular phylogenetic research, the biomechanical themes discussed in this review afford new ways to think about the evolution of basidiomycetes.