Summary: Harnessing plant‐associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment and microbes, occurring both above and below ground, drive recognition, recruitment and colonization of plant‐associated microbes, resulting in activation of downstream host responses and functionality. Dissecting these complex interactions by integrating multiomic approaches, high‐throughput culturing, and computational and synthetic biology advances is providing deeper understanding of the structure and function of native microbial communities. Such insights are paving the way towards development of microbial products as well as microbiomes engineered with synthetic microbial communities capable of delivering agronomic solutions. While there is a growing market for microbial‐based solutions to improve crop productivity, challenges with commercialization of these products remain. The continued translation of plant‐associated microbiome knowledge into real‐world scenarios will require concerted transdisciplinary research, cross‐training of a next generation of scientists, and targeted educational efforts to prime growers and the general public for successful adoption of these innovative technologies.

Aerial imaging provides a landscape view of crop fields that can be utilized to monitor plant diseases. Phymatotrichopsis root rot (PRR) is a serious root rot disease affecting several dicotyledonous hosts, including the perennial forage crop alfalfa. PRR disease causes stand loss by spreading as circular to irregular diseased areas that increase over time, but disease progression in alfalfa fields is poorly understood. The objectives of this study were to develop a workflow to produce PRR disease maps from sets of high-resolution red, green and blue (RGB) images acquired from two different platforms and to assess the feasibility of using these PRR disease maps to monitor disease progression in alfalfa fields. Aerial RGB images, two from unmanned aircraft systems (UAS) and four images from a manned aircraft platform were acquired at different time points during the 2014–2015 growing seasons from a center-pivot irrigated, PRR-infested alfalfa field near Burneyville, OK. Supervised classification of images acquired from both platforms were performed using three spectral signatures: image-specific, UAS-platform-specific and manned-aircraft platform-specific. Our results showed that the UAS-platform-specific spectral signature was most efficient for classifying images acquired with the UAS, with accuracy ranging from 90 to 96%. In contrast, manned-aircraft-acquired images classified using image-specific spectral signatures yielded 95 to 100% accuracy. The effect of hue, saturation and value color space transformations (HSV and Hrot60SV) on classification accuracy was determined, but the accuracy estimates showed no improvement in their efficiency compared to the RGB color space. Finally, the data showed that the classification of the bare ground increased by 74% during the study period, indicating the extent of alfalfa stand loss caused by PRR disease. Thus, this study showed the utility of high-resolution RGB aerial images for monitoring PRR disease spread in alfalfa.

Venturia effusa (syn. Fusicladium effusum), causal agent of pecan scab, is the most prevalent pathogen of pecan (Carya illinoinensis), causing severe yield losses in the southeastern United States. V. effusa is currently known only by its asexual (conidial) stage. However, the degree and distribution of genetic diversity observed within and among populations of V. effusa are typical of a sexually reproducing fungal pathogen, and comparable with other dothideomycetes with a known sexual stage, including the closely related apple scab pathogen, V. inaequalis. Using the mating type (MAT) idiomorphs from V. inaequalis, we identified a single MAT gene, MAT1-1-1, in a draft genome of V. effusa. The MAT1-1-1 locus is flanked by two conserved genes encoding a DNA lyase (APN2) and a hypothetical protein. The MAT locus spanning the flanking genes was amplified and sequenced from a subset of 14 isolates, of which 7 contained MAT1-1-1 and the remaining samples contained MAT1-2-1. A multiplex polymerase chain reaction screen was developed to amplify MAT1-1-1, MAT1-2-1, and a conserved reference gene encoding β-tubulin, and used to screen 784 monoconidial isolates of V. effusa collected from 11 populations of pecan across the southeastern United States. A hierarchical sampling protocol representing region, orchard, and tree allowed for analysis of MAT structure at different spatial scales. Analysis of this collection revealed the frequency of the MAT idiomorphs is in a 1:1 equilibrium of MAT1-1:MAT1-2. The apparent equilibrium of the MAT idiomorphs provides impetus for a renewed effort to search for the sexual stage of V. effusa. [ ] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Root system architecture is critical for plant growth, which is influenced by several edaphic, environmental, genetic, and biotic factors including beneficial and pathogenic microbes. Studying root system architecture and the dynamic changes that occur during a plant’s lifespan, especially for perennial crops growing over multiple growing seasons, is still a challenge because of the nature of their growing environment. We describe the utility of an imaging platform called RhizoVision Crown to study root system architecture of alfalfa, a perennial forage crop threatened by Phymatotrichopsis root rot (PRR) disease. Phymatotrichopsis omnivora is the causal agent of PRR disease that reduces alfalfa stand longevity. During the lifetime of the stand, PRR disease rings enlarge and the field can be categorized into three zones based upon plant status: asymptomatic, disease front and survivor. To study root system architectural changes associated with PRR, a 4-year-old 25.6-ha alfalfa stand infested with PRR was selected at the Red River Farm, Burneyville, OK during October 2017. Line transect sampling was conducted from four actively growing PRR disease rings. At each disease ring, six line transects were positioned spanning 15 m on either side of the disease front with one alfalfa root crown sampled at every 3 m interval. Each alfalfa root crown was imaged with the RhizoVision Crown platform using a backlight and a high-resolution monochrome CMOS camera enabling preservation of the natural root system integrity. The platform’s image analysis software, RhizoVision Analyzer, automatically segmented images, skeletonized, and extracted a suite of features. Data indicated that the survivor plants compensated for damage or loss to the taproot through the development of more lateral and crown roots, and that a suite of multivariate features could be used to automatically classify roots as from survivor or asymptomatic zones. Root growth is a dynamic process adapting to ever changing interactions among various phytobiome components. By utilizing the low-cost, efficient, and high-throughput RhizoVision Crown platform, we quantified these changes in a mature perennial forage crop.

Grafting is effectively used worldwide to overcome abiotic and biotic factors impacting yield, including soil temperature. Field studies were conducted in 2020 and 2021 in a cool Mediterranean climate (average daily air temperature range of 12.8–17.1 °C) to identify suitable rootstock combinations for grafted cantaloupe (Cucumis melo var. reticulatus) and evaluate fruit yield and quality. Cantaloupe cultivars Sugar Rush (SR), Goddess (G), and Athena (A) were compatible with interspecific hybrid squash (Cucurbita maxima × C. moschata) rootstock cultivars Super Shintosa (SS) and Carnivor (CN) but were incompatible with ‘Carolina Strongback (CS)’ (Citrullus amarus) and ‘Pelop (P)’ (Lagenaria siceraria) rootstocks. Nongrafted cultivars exhibited vine decline at harvest in 2020 but not in 2021, and grafting tended to delay harvest by 15–18 days. Overall, while grafting with interspecific hybrid squash rootstocks may have delayed fruit harvest, fruit quality was not compromised. Further, yield was increased for ‘Goddess’ and ‘Athena’, but not ‘Sugar Rush’. ‘A/CN’ had the highest fruit yield/ha and number per plant. The grafted treatments of each cantaloupe cultivar with interspecific hybrid squash rootstocks met the U.S. fancy grade criteria.