Rapid measurement of the three-dimensional distribution of leaf orientation and the leaf angle probability density function using terrestrial LiDAR scanning

At the plant or stand level, leaf orientation is often highly anisotropic and heterogeneous, yet most analyses neglect such complexity. In many cases, this is due to the difficulty in measuring the spatial variation of the leaf angle distribution function. There is a critical need for a technique that can rapidly measure the leaf angle distribution function at any point in space and time. A new method was developed and tested that uses terrestrial LiDAR scanning data to rapidly measure the three-dimensional distribution of leaf orientation for an arbitrary volume of leaves. The method triangulates laser-leaf intersection points recorded by the LiDAR scan, which allows for easy calculation of normal vectors. As a byproduct, the triangulation also yields continuous surfaces that reconstruct individual leaves. In order to produce a probability density function for leaf orientation from triangle normal vectors, it is critical that the proper weighting be applied to each triangle. Otherwise, results will heavily bias toward normal vectors pointed toward the the LiDAR scanner. The method was validated using artificially generated LiDAR data where the exact leaf angle distributions were known, and in the field for an isolated tree and a grapevine canopy by comparing LiDAR-generated distribution functions to manual measurements. The artificial test cases demonstrated the consistency of the method, and quantitatively showed that errors in the predicted leaf angle distribution functions decreased as scan resolution was increased or as the density of leaves was increased. The isolated tree field validation showed qualitatively similar trends between manual and LiDAR measurements of distribution functions. Manual measurements of leaf orientation in the vineyard were shown to have large errors due to high leaf curvature, which illustrated the benefits of the more detailed LiDAR measurement method

Development of a quantitative loop-mediated isothermal amplification assay for the field detection of Erysiphe necator

Plant pathogen detection systems have been useful tools to monitor inoculum presence and initiate management schedules. More recently, a loop-mediated isothermal amplification (LAMP) assay was successfully designed for field use in the grape powdery mildew pathosystem; however, false negatives or false positives were prevalent in grower-conducted assays due to the difficulty in perceiving the magnesium pyrophosphate precipitate at low DNA concentrations. A quantitative LAMP (qLAMP) assay using a fluorescence resonance energy transfer-based probe was assessed by grape growers in the Willamette Valley of Oregon. Custom impaction spore samplers were placed at a research vineyard and six commercial vineyard locations, and were tested bi-weekly by the lab and by growers. Grower-conducted qLAMP assays used a beta-version of the Smart-DART handheld LAMP reaction devices (Diagenetix, Inc., Honolulu, HI, USA), connected to Android 4.4 enabled, Bluetooth-capable Nexus 7 tablets for output. Quantification by a quantitative PCR assay was assumed correct to compare the lab and grower qLAMP assay quantification. Growers were able to conduct and interpret qLAMP results; however, the Erysiphe necator inoculum quantification was unreliable using the beta-Smart-DART devices. The qLAMP assay developed was sensitive to one spore in early testing of the assay, but decreased to >20 spores by the end of the trial. The qLAMP assay is not likely a suitable management tool for grape powdery mildew due to losses in sensitivity and decreasing costs and portability for other, more reliable molecular tools

Phyllosphere, Front and Center: Focus on a Formerly ‘Ecologically Neglected’ Microbial Milieu

The phyllosphere encompasses leaves and other aerial tissues of plants, which together provide diverse habitats for micro- and macro-organisms. In this editorial for the Phytobiomes Journal Focus Issue on the Phyllosphere, we celebrate the tremendous growth and impact of phyllosphere science as a discipline by introducing and providing context for 14 articles by nearly 100 authors from over 40 institutions. These articles collectively highlight the current status of the field and offer ideas for future directions. They explore topics related to phyllosphere biodiversity, community assembly and dynamics, and the adaptive capacity of species, populations, and communities on leaf surfaces and other phyllosphere compartments. The articles also delve into the multipartite relationships that phyllosphere colonizers have with each other and with their host, and issues of global concern such as food security, food safety, and climate change. This collection of work illustrates the international, transdisciplinary and collaborative nature of phyllosphere science, the challenges that the discipline faces, and the importance of recruiting and training the next generation of phyllosphere scientists.This editorial is published as Leveau, Johan HJ, Gwyn A. Beattie, Steven E. Lindow, and Walter F. Mahaffee. "Phyllosphere, Front and Center: Focus on a Formerly ‘Ecologically Neglected’Microbial Milieu." Phytobiomes Journal 7 (2023): 140-144. doi:10.1094/PBIOMES-08-23-0088-E.Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted

Phyllosphere, Front and Center: Focus on a Formerly ‘Ecologically Neglected’ Microbial Milieu

The phyllosphere encompasses leaves and other aerial tissues of plants, which together provide diverse habitats for micro- and macro-organisms. In this editorial for the Phytobiomes Journal Focus Issue on the Phyllosphere, we celebrate the tremendous growth and impact of phyllosphere science as a discipline by introducing and providing context for 14 articles by nearly 100 authors from over 40 institutions. These articles collectively highlight the current status of the field and offer ideas for future directions. They explore topics related to phyllosphere biodiversity, community assembly and dynamics, and the adaptive capacity of species, populations, and communities on leaf surfaces and other phyllosphere compartments. The articles also delve into the multipartite relationships that phyllosphere colonizers have with each other and with their host, and issues of global concern such as food security, food safety, and climate change. This collection of work illustrates the international, transdisciplinary and collaborative nature of phyllosphere science, the challenges that the discipline faces, and the importance of recruiting and training the next generation of phyllosphere scientists

Association of Spring Pruning Practices with Severity of Powdery Mildew and Downy Mildew on Hop

Downy mildew (caused by Pseudoperonospora humuli) and powdery mildew (caused by Podosphaera macularis) are important diseases of hop in the Pacific Northwest United States, and cultural practices may affect the severity of both diseases. The association of spring pruning quality and timing with severity of downy mildew and powdery mildew was assessed through analysis of survey data collected from commercial hop yards in Oregon and Washington. Among 149 hop yards surveyed, the most common pruning method was chemical desiccation (48% of yards), mechanical pruning (23%), or a combination of these practices (15%). The quality of pruning was assessed using a three-category ordinal scale (“excellent”, “moderate”, or “poor”) based on the amount of foliage remaining on plants following pruning. Excellent pruning quality was attained more often in yards pruned twice (74.6 to 82.1% of yards) versus once (33.8% of yards), independent of pruning method. Seasonal severity of downy mildew in Oregon increased approximately twofold with reduction in pruning quality from excellent to moderate to poor. Pruning quality was not significantly related to levels of powdery mildew on leaves or cones in Oregon. Under more severe disease pressure in Washington, however, seasonal severity of powdery mildew on leaves and the incidence of cones with powdery mildew were significantly greater in yards that had poor pruning compared with excellent pruning. Moreover, yards that had excellent pruning quality received, on average, 1.1 to 1.5 fewer fungicide applications per season for downy mildew or powdery mildew compared with yards that had moderate or poor pruning quality. This savings was associated with delayed initiation of the first application by 7.5 to 14.2 days in yards with excellent pruning quality. Replicated experiments in commercial yards in Oregon quantified the effect of delaying pruning timing 5 to 21 days compared with growers' standard practices on the diseases and yield. Downy mildew suppression by delayed pruning was dependent on cultivar and year of sampling, being significantly reduced fivefold only in ‘Willamette’ in 2007. Severity of powdery mildew and cone yield was similar between plots that received the delayed or standard pruning timing treatments. Collectively, these studies emphasize that early spring sanitation measures are associated with reduced primary inoculum and are critically important for managing both downy mildew and powdery mildew. A savings of at least one fungicide application per year appears achievable when spring pruning is conducted thoroughly and slightly delayed compared with growers' current practices