Seed Pathology Progress in Academia and Industry

Genetic Diversity and Pathogenicity of the Fusarium Species Complex on Soybean in Serbia

Using morphological and cultural characteristics for identification, 36 Fusarium isolates were recovered from diseased roots, stems, and seeds of soybean from several localities throughout Vojvodina Province, Serbia. Based on molecular characterization, 12 Fusarium species were identified: F. acuminatum, F. avenaceum, F. commune, F. equiseti, F. graminearum, F. incarnatum, F. oxysporum, F. proliferatum, F. solani, F. sporotrichioides, F. subglutinans, and F. tricinctum. The elongation factor 1-α-based phylogeny grouped the isolates into 12 well-supported clades, but polymorphisms among sequences in some clades suggested the use of the species complex concept: (i) F. incarnatum-equiseti species complex (FIESC)-F. incarnatum and F. equiseti; (ii) F. oxysporum species complex (FOSC)-F. oxysporum; (iii) F. solani species complex (FSSC)-F. solani; and (iv) F. acuminatum/F. avenaceum/F. tricinctum species complex (FAATSC)-F. acuminatum, F. avenaceum, and F. tricinctum. Pathogenicity tests showed that the most aggressive species causing soybean seed rot were F. sporotrichioides, F. graminearum, FIESC, and F. avenaceum. Furthermore, F. subglutinans, FSSC, and F. proliferatum showed a high percentage of pathogenicity on soybean seeds (80 to 100%), whereas variability in pathogenicity occurred within isolates of F. tricinctum. FOSC, F. commune, and F. acuminatum had the lowest pathogenicity. To our knowledge, this is the first study of the characterization of Fusarium species on soybean in Serbia. This study provides valuable information about the composition of Fusarium species and pathogenicity that will be used in further research on soybean resistance to Fusarium-based diseases.

Management of Soybean Cyst Nematode and Sudden Death Syndrome with Nematode-Protectant Seed Treatments Across Multiple Environments in Soybean

As soybean (Glycine max) production continues to expand in the United States and Canada, so do pathogens and pests that directly threaten soybean yield potential and economic returns for farmers. One such pathogen is the soybean cyst nematode (SCN; Heterodera glycines). SCN has traditionally been managed using SCN-resistant cultivars and rotation with nonhost crops, but the interaction of SCN with sudden death syndrome (SDS; caused by Fusarium virguliforme) in the field makes management more difficult. Nematode-protectant seed treatments have become options for SCN and SDS management. The objectives of this study were to evaluate nematode-protectant seed treatments for their effects on (i) early and full season SCN reproduction, (ii) foliar symptoms and root-rot caused by SDS, and (iii) soybean yield across environments accounting for the above factors. Using a standard protocol, field trials were implemented in 13 states and one Canadian province from 2019 to 2021 constituting 51 site-years. Six nematode-protectant seed treatment products were compared with a fungicide + insecticide base treatment and a nontreated check. Initial (at soybean planting) and final (at soybean harvest) SCN egg populations were enumerated, and SCN females were extracted from roots and counted at 30 to 35 days postplanting. Foliar disease index (FDX) and root rot caused by the SDS pathogen were evaluated, and yield data were collected for each plot. No seed treatment offered significant nematode control versus the nontreated check for in-season and full-season nematode response, no matter the initial SCN population or FDX level. Of all treatments, ILEVO (fluopyram) and Saltro (pydiflumetofen) provided more consistent increases in yield over the nontreated check in a broader range of SCN environments, even when FDX level was high.

The Impact of Climate Change on Vegetable Crop Diseases and Their Management: The Value of Phytotron Studies for the Agricultural Industry and Associated Stakeholders

Climate change is having a significant impact on global agriculture, particularly on vegetable crops, which play a critical role in global nutrition. Recently, increasing research has concentrated on the impact of climate change on vegetable crop diseases, with several studies being conducted in phytotrons, which have been used to explore the effects of increased temperatures and CO2 concentrations to simulate future scenarios. This review focuses on the combined effects of temperature and carbon dioxide increases on foliar and soilborne vegetable diseases, as evaluated under phytotron conditions. The influence of climate change on mycotoxin production and disease management strategies is also explored through case studies. The results offer valuable information that can be used to guide both seed and agrochemical industries, as well as to develop disease-resistant varieties and innovative control measures, including biocontrol agents, considering the diseases that are likely to become prevalent under future climatic scenarios. Recommendations on how to manage vegetable diseases under ongoing climate change are proposed to facilitate plants' adaptation to and enhanced against the changing conditions. A proactive and comprehensive response to climate-induced challenges in vegetable farming is imperative to ensure food security and sustainability.

Hyperspectral imaging for the detection of plant pathogens in seeds: recent developments and challenges

Food security, a critical concern amid global population growth, faces challenges in sustainable agricultural production due to significant yield losses caused by plant diseases, with a multitude of them caused by seedborne plant pathogen. With the expansion of the international seed market with global movement of this propagative plant material, and considering that about 90% of economically important crops grown from seeds, seed pathology emerged as an important discipline. Seed health testing is presently part of quality analysis and carried out by seed enterprises and governmental institutions looking forward to exclude a new pathogen in a country or site. The development of seedborne pathogens detection methods has been following the plant pathogen detection and diagnosis advances, from the use of cultivation on semi-selective media, to antibodies and DNA-based techniques. Hyperspectral imaging (HSI) associated with artificial intelligence can be considered the new frontier for seedborne pathogen detection with high accuracy in discriminating infected from healthy seeds. The development of the process consists of standardization of methods and protocols with the validation of spectral signatures for presence and incidence of contamined seeds. Concurrently, epidemiological studies correlating this information with disease outbreaks would help in determining the acceptable thresholds of seed contamination. Despite the high costs of equipment and the necessity for interdisciplinary collaboration, it is anticipated that health seed certifying programs and seed suppliers will benefit from the adoption of HSI techniques in the near future.

Room Temperature Phosphorescence from Natural, Organic Emitters and Their Application in Industrially Compostable Programmable Luminescent Tags

Organic semiconductors provide the potential of biodegradable technologies, but prototypes do only rarely exist. Transparent, ultrathin programmable luminescent tags (PLTs) are presented for minimalistic yet efficient information storage that are fully made from biodegradable or at least industrially compostable, ready-to-use materials (bioPLTs). As natural emitters, the quinoline alkaloids show sufficient room temperature phosphorescence when being embedded in polymer matrices with cinchonine exhibiting superior performance. Polylactic acid provides a solution for both the matrix material and the flexible substrate. Room temperature phosphorescence can be locally controlled by the oxygen concentration in the film by using Exceval as additional oxygen blocking layers. These bioPLTs exhibit all function-defining characteristics also found in their regular nonenvironmentally degradable analogs and, additionally, provide a simplified, high-contrast readout under continuous-wave illumination as a consequence of the unique luminescence properties of the natural emitter cinchonine. Limitations for flexible devices arise from limited thermal stability of the polylactic acid foil used as substrate allowing only for one writing cycle and preventing an annealing step during fabrication. Few-cycle reprogramming is possible when using the architecture of the bioPLTs on regular quartz substrates. This work realizes the versatile platform of PLTs with less harmful materials offering more sustainable use in future.

Fungicide Sensitivity of Fusarium oxysporum f. sp. lentis and Fusarium acuminatum Affecting Lentil in the Northern Great Plains

Fusarium oxysporum f. sp. lentis and F. acuminatum cause wilting and root rot in pulse crops including lentil. Fungicide seed treatments are widely used, but information about Fusarium spp. sensitivity in lentils is limited. Here, 30 F. oxysporum f. sp. lentis and 30 F. acuminatum isolates from Montana, southern Canada, North Dakota, and Washington were identified, tested for pathogenicity, and assayed for in vitro sensitivity to pyraclostrobin, prothioconazole, ipconazole, and thiophanate-methyl. F. oxysporum f. sp. lentis and F. acuminatum differed in their sensitivity to all fungicides. No resistant isolates were identified, but F. oxysporum f. sp. lentis had lower EC50 values in pyraclostrobin (averaging 0.47 μg a.i./ml) than F. acuminatum (averaging 0.89 μg a.i./ml) for mycelia assays. Both species had lower EC50 values in prothioconazole, averaging EC50 0.23 in F. oxysporum f. sp. lentis and 0.53 μg a.i./ml in F. acuminatum. F. oxysporum f. sp. lentis isolates had the lowest EC50 values on ipconazole compared to F. acuminatum (0.78 and 1.49 μg a.i./ml). The pathogens were least sensitive to thiophanate-methyl (1.74 μg a.i./ml for F. oxysporum f. sp. lentis and 1.91 μg a.i./ml for F. acuminatum). Overall sensitivity to the fungicides was higher in F. oxysporum f. sp. lentis than F. acuminatum. This study provides reference EC50 values while pointing to the possibility of differential fungicide efficacies on Fusarium spp. This will be helpful to monitor shifts in sensitivity of Fusarium spp. and devise robust root rot/wilt management approaches.

Effect of Infection Timing by Four Pythium spp. on Soybean Damping-Off Symptoms with and Without Cold Stress

Pythium spp. cause damping-off of soybean, especially when soil conditions at or shortly after planting are cool and wet. Soybean planting dates continue to shift to earlier dates, so germinating seed and seedlings are exposed to periods of cold stress at a time which favors infection by Pythium, and seedling disease occurs. The objective of this study was to assess infection timing and cold stress on soybean seedling disease severity caused by four Pythium spp. prevalent in Iowa, namely P. lutarium, P. oopapillum, P. sylvaticum, and P. torulosum. Each species was used individually to inoculate soybean cultivar 'Sloan' using a rolled towel assay. Two temperature treatments (continuous 18°C [C18]; a 48-h cold stress period at 10°C [CS]) were applied. Soybean seedling age was divided into five growth stages (GS1 to GS5). Root rot severity and root length were assessed at 2, 4, 7, and 10 days after inoculation (DAI). At C18, root rot was greatest when soybean was inoculated with P. lutarium or P. sylvaticum at GS1 (seed imbibes water) and with P. oopapillum or P. torulosum at GS1, GS2 (radicle elongation), and GS3 (hypocotyl emergence). After CS, soybean susceptibility to P. lutarium and P. sylvaticum was reduced compared to C18 for inoculation at all GSs except GS5 (unifoliate leaf emergence). Conversely, root rot by P. oopapillum and P. torulosum was greater after CS compared to C18. Data from this study demonstrate that greater root rot, and consequently more damping-off, is likely if infection occurs at early germination stages before seedling emergence.

Fungal Pathogens and Seed Storage in the Dry State

Seeds can harbor a wide range of microorganisms, especially fungi, which can cause different sanitary problems. Seed quality and seed longevity may be drastically reduced by fungi that invade seeds before or after harvest. Seed movement can be a pathway for the spread of diseases into new areas. Some seed-associated fungi can also produce mycotoxins that may cause serious negative effects on humans, animals and the seeds themselves. Seed storage is the most efficient and widely used method for conserving plant genetic resources. The seed storage conditions used in gene banks, low temperature and low seed moisture content, increase seed longevity and are usually favorable for the survival of seed-borne mycoflora. Early detection and identification of seed fungi are essential activities to conserve high-quality seeds and to prevent pathogen dissemination. This article provides an overview of the characteristics and detection methods of seed-borne fungi, with a special focus on their potential effects on gene bank seed conservation. The review includes the following aspects: types of seed-borne fungi, paths of infection and transmission, seed health methods, fungi longevity, risk of pathogen dissemination, the effect of fungi on seed longevity and procedures to reduce the harmful effects of fungi in gene banks.

Fluopyram activates systemic resistance in soybean

The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is a significant yield-limiting factor in soybean production in the Midwestern US. Several management practices are implemented to mitigate yield losses caused by SCN, including using SDHI (succinate dehydrogenase inhibitors) fungicides delivered as seed treatments. A set of studies was conducted to evaluate the effect of two seed-applied succinate dehydrogenase inhibitors (SDHI) compounds, fluopyram and pydiflumetofen, on SCN population densities, plant injury, and plant growth. Cyst counts in untreated control and pydiflumetofen treated plants were 3.44 and 3.59 times higher than fluopyram, respectively, while egg counts were 8.25 and 7.06 times higher in control and pydiflumetofen. Next-generation sequencing was later employed to identify transcriptomic shifts in gene expression profiles in fluopyram and pydiflumetofen -treated seedlings. RNA expression patterns of seed treatments clustered by sampling time (5 DAP vs. 10 DAP); therefore, downstream analysis was conducted by timepoint. At 5 DAP, 10,870 and 325 differentially expressed genes (DEG) were identified in fluopyram and pydiflumetofen, respectively. These same treatments generated 219 and 2 DEGs at 10 DAP. Multiple DEGs identified in soybean seedlings treated with fluopyram are linked to systemic resistance, suggesting a potential role of systemic resistance in the suppression of SCN by fluopyram, in addition to the known nematicidal activity. The non-target inhibition of soybean succinate dehydrogenase genes by fluopyram may be the origin of the phytotoxicity symptoms observed and potentially the source of the systemic resistance activation reported in the current study. This work helps to elucidate the mechanisms of suppression of SCN by fluopyram.

Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds

Seeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a "black box" of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination. IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.

A comprehensive review on recent advances in preparation, physicochemical characterization, and bioengineering applications of biopolymers

Biopolymers are mainly the polymers which are created or obtained from living creatures such as plants and bacteria rather than petroleum, which has traditionally been the source of polymers. Biopolymers are chain-like molecules composed of repeated chemical blocks derived from renewable resources that may decay in the environment. The usage of biomaterials is becoming more popular as a means of reducing the use of non-renewable resources and reducing environmental pollution produced by synthetic materials. Biopolymers' biodegradability and non-toxic nature help to maintain our environment clean and safe. This study discusses how to improve the mechanical and physical characteristics of biopolymers, particularly in the realm of bioengineering. The paper begins with a fundamental introduction and progresses to a detailed examination of synthesis and a unique investigation of several recent focused biopolymers with mechanical, physical, and biological characterization. Biopolymers' unique non-toxicity, biodegradability, biocompatibility, and eco-friendly features are boosting their applications, especially in bioengineering fields, including agriculture, pharmaceuticals, biomedical, ecological, industrial, aqua treatment, and food packaging, among others, at the end of this paper. The purpose of this paper is to provide an overview of the relevance of biopolymers in smart and novel bioengineering applications.

Graphical abstract

The Graphical abstract represents the biological sources and applications of biopolymers. Plants, bacteria, animals, agriculture wastes, and fossils are all biological sources for biopolymers, which are chemically manufactured from biological monomer units, including sugars, amino acids, natural fats and oils, and nucleotides. Biopolymer modification (chemical or physical) is recognized as a crucial technique for modifying physical and chemical characteristics, resulting in novel materials with improved capabilities and allowing them to be explored to their full potential in many fields of application such as tissue engineering, drug delivery, agriculture, biomedical, food industries, and industrial applications.

Soil Disinfestation: From Soil Treatment to Soil and Plant Health

This feature article tracks 100 years of soil disinfestation, from the goal of eradicating soilborne pathogens and pests to much milder approaches, aimed at establishing a healthier soil, by favoring or enhancing the beneficial soil microflora and introducing biological control agents. Restrictions on the use of many chemical fumigants is favoring the adoption of nonchemical strategies, from soilless cultivation to the use of physical or biological control measures, with more focus on maintaining soil microbial diversity, thus enhancing soil and plant health. Such approaches are described and discussed, with special focus on their integrated use.

Seedborne Cercospora beticola Can Initiate Cercospora Leaf Spot from Sugar Beet (Beta vulgaris) Fruit Tissue

Cercospora leaf spot (CLS) is a globally important disease of sugar beet (Beta vulgaris) caused by the fungus Cercospora beticola. Long-distance movement of C. beticola has been indirectly evidenced in recent population genetic studies, suggesting potential dispersal via seed. Commercial sugar beet "seed" consists of the reproductive fruit (true seed surrounded by maternal pericarp tissue) coated in artificial pellet material. In this study, we confirmed the presence of viable C. beticola in sugar beet fruit for 10 of 37 tested seed lots. All isolates harbored the G143A mutation associated with quinone outside inhibitor resistance, and 32 of 38 isolates had reduced demethylation inhibitor sensitivity (EC₅₀ > 1 µg/ml). Planting of commercial sugar beet seed demonstrated the ability of seedborne inoculum to initiate CLS in sugar beet. C. beticola DNA was detected in DNA isolated from xylem sap, suggesting the vascular system is used to systemically colonize the host. We established nuclear ribosomal internal transcribed spacer region amplicon sequencing using the MinION platform to detect fungi in sugar beet fruit. Fungal sequences from 19 different genera were identified from 11 different sugar beet seed lots, but Fusarium, Alternaria, and Cercospora were consistently the three most dominant taxa, comprising an average of 93% relative read abundance over 11 seed lots. We also present evidence that C. beticola resides in the pericarp of sugar beet fruit rather than the true seed. The presence of seedborne inoculum should be considered when implementing integrated disease management strategies for CLS of sugar beet in the future.

Natural Salicylaldehyde for Fungal and Pre- and Post-Emergent Weed Control

A sustainable, alternative weed control strategy is developed using salicylaldehyde (SA; 2-hydroxybenzaldehyde) as an active ingredient. SA is a natural, redox-active small molecule listed as a Generally Recognized As Safe food additive by the European Food Safety Authority and the United States Food and Drug Administration. The repurposing of SA determined that SA possesses both pre- and post-emergent herbicidal, fumigant activity, where the emitted SA from the source completely prevented the germination of plant seeds and/or the growth of the germinated plants. As a proof-of-concept, we developed agricultural byproducts (tree nutshell particles) as SA delivery vehicles to the soil, thus helping the growers’ sustainable byproduct recycling program, necessary for carbon sequestration. In plate assays, SA emitted from the nutshell vehicles (0.15 to 1.6 M) completely prevented the germination of six invasive or native weed seeds (monocots, dicots). In Magenta vessel assays, SA emitted from the nutshell vehicles (0.8 to 1.6 M) not only prevented the germination (pre-emergent) of Lagurus ovatus (Bunny Tails Grass) seeds but also inhibited the growth (post-emergent) of the germinated weeds. We determined further that soil covering (soil pasteurization) could be one of the practices to effectively deliver SA to the soil, whereby 1.6 M of SA emitted from the nutshell vehicles prevented the germination of the L. ovatus seeds maintained in soil trays covered with plastic tarp at 22 °C, while 0.8 M SA allowed partial (15%) germination of the weed seeds. Of note, SA also possesses an intrinsic antifungal activity that overcomes the tolerance of the stress signaling mutants of filamentous fungal pathogens (Aspergillus fumigatus, Penicillium expansum) to the phenylpyrrole fungicide fludioxonil. Environmental degradation data available in the public database indicate that, once released to the environment, SA will be broken down in the air by sunlight or microorganisms and, thus, is not built up in aquatic organisms. Altogether, SA can serve as a safe, potent pesticide (herbicidal, fungicidal) ingredient that promotes sustainable crop production by lowering the pesticide burden in fields.

Sterically Stabilized Diblock Copolymer Nanoparticles Enable Convenient Preparation of Suspension Concentrates Comprising Various Agrochemical Actives

It is well known that sterically stabilized diblock copolymer nanoparticles can be readily prepared using polymerization-induced self-assembly. Recently, we reported that such nanoparticles can be employed as a dispersant to prepare micron-sized particles of a widely used fungicide (azoxystrobin) via ball milling. In the present study, we examine the effect of varying the nature of the steric stabilizer block, the mean nanoparticle diameter, and the glass transition temperature (Tg) of the core-forming block on the particle size and colloidal stability of such azoxystrobin microparticles. In addition, the effect of crosslinking the nanoparticle cores is also investigated. Laser diffraction studies indicated the formation of azoxystrobin microparticles of approximately 2 μm diameter after milling for between 15 and 30 min at 6000 rpm. Diblock copolymer nanoparticles comprising a non-ionic steric stabilizer, rather than a cationic or anionic steric stabilizer, were determined to be more effective dispersants. Furthermore, nanoparticles of up to 51 nm diameter enabled efficient milling and ensured overall suspension concentrate stability. Moreover, crosslinking the nanoparticle cores and adjusting the Tg of the core-forming block had little effect on the milling of azoxystrobin. Finally, we show that this versatile approach is also applicable to five other organic crystalline agrochemicals, namely pinoxaden, cyproconazole, difenoconazole, isopyrazam and tebuconazole. TEM studies confirmed the adsorption of sterically stabilized nanoparticles at the surface of such agrochemical microparticles. The nanoparticles are characterized using TEM, DLS, aqueous electrophoresis and 1H NMR spectroscopy, while the final aqueous' suspension concentrates comprising microparticles of the above six agrochemical actives are characterized using optical microscopy, laser diffraction and electron microscopy.

The 'black box' of plant demography: how do seed type, climate and seed fungal communities affect grass seed germination?

Demographic studies measure drivers of plant fecundity including seed production and survival, but few address both abiotic and biotic drivers of germination such as variation in climate among sites, population density, maternal plants, seed type and fungal pathogen abundance. We examined germination and microbial communities of seeds of Danthonia californica, which are either chasmogamous (external, wind-pollinated) or cleistogamous (internal, self-fertilized) and Festuca roemeri, which are solely chasmogamous. Seed populations were sourced across environmental gradients. We tested germination and used high-throughput sequencing to characterize seed fungal community structure. For F. roemeri, maternal plants significantly influenced germination as did climate and pathogens; germination increased from wetter, cooler sites. For D. californica, the main drivers of germination were maternal plant, seed type and pathogens; on average, more chasmogamous seeds germinated. Fungal communities depended largely on seed type, with fewer fungi associated with cleistogamous seeds, but the communities also depended on site factors such as vapor pressure deficit, plant density and whether the seeds had germinated. Putative pathogens that were negatively correlated with germination were more abundant for both D. californica and F. roemeri chasmogamous seeds than D. californica cleistogamous seeds. In D. californica, cleistogamous and chasmogamous seeds contain vastly different fungal communities.

Everything Is Faster: How Do Land-Grant University-Based Plant Diagnostic Laboratories Keep Up with a Rapidly Changing World?

Plant diagnostic laboratories (PDLs) are at the heart of land-grant universities (LGUs) and their extension mission to connect citizens with research-based information. Although research and technological advances have led to many modern methods and technologies in plant pathology diagnostics, the pace of adopting those methods into services at PDLs has many complexities we aim to explore in this review. We seek to identify current challenges in plant disease diagnostics, as well as diagnosticians' and administrators'perceptions of PDLs' many roles. Surveys of diagnosticians and administrators were conducted to understand the current climate on these topics. We hope this article reaches researchers developing diagnostic methods with modern and new technologies to foster a better understanding of PDL diagnosticians' perspective on method implementation. Ultimately, increasing researchers' awareness of the factors influencing method adoption by PDLs encourages support, collaboration, and partnerships to advance plant diagnostics.

Sustainable Wheat Production and Food Security of Domestic Wheat in Tajikistan: Implications of Seed Health and Protein Quality

Staple crop yield, quality and sustainable production are critical for domestic food security in developing countries. In Tajikistan, both seed-borne diseases and protein quality impair the yield and the quality of the major staple crop, wheat. Here, we used a detailed two-year survey of fields on 21 wheat-producing farms in Tajikistan, combined with lab analyses on seed health and protein quality, to investigate the presence of seed-borne diseases and bread-making quality in Tajik wheat. Seed samples were collected for the analysis of: (i) the presence of common bunt (Tilletia spp.) using the centrifuge wash test, (ii) the major pathogenic fungi on/in the seed using the agar plate test and (iii) the protein amount and size distribution using size-exclusion high-performance liquid chromatography (SE-HPLC). Field occurrence of common bunt and loose smut was generally low (3 farms in year one (14%) showed common bunt occurrence), but the presence of fungi was observed microscopically on most seed samples (on seeds from 19 out of 21 farms = 91%). Tilletia laevis was the dominant agent in common bunt (present in 19 farms compared to T. tritici present in 6 farms). Altogether, 18 different fungi were identified from seed samples by microscopy. Protein composition, measured with high-performance liquid chromatography as protein amount and size distribution (known to correlate with bread-making quality), differed significantly between samples from different farms and years, although the farm type and land elevation of the farm were not the determinants of the protein composition. The presence of certain fungi on the seed correlated significantly with the protein quality and could then have an impact on the bread-making quality of the Tajik wheat. The presence of seed-borne diseases, a low protein content and weak gluten were the characteristics of the majority of the grain samples, mostly irrespective of farm type and farmer’s knowledge. For sustainable development of the Tajik farming systems, and to strengthen the food security of the country, the knowledge of Tajik farmers needs to be increased independently of farm type; in general, plant breeding is required and certified seeds need to be made available throughout the country.

Illumina Sequencing of 18S/16S rRNA Reveals Microbial Community Composition, Diversity, and Potential Pathogens in 17 Turfgrass Seeds

The increasing need for turfgrass seeds is coupled with the high risk of dangerous microbial pathogens being transmitted through the domestic and international trade of seeds. Concerns continue to be raised about seed safety and quality. Here, we show that next-generation sequencing (NGS) of DNA represents an effective and reliable tactic to monitor the microbial communities within turfgrass seeds. A comparison of DNA sequence data with reference databases revealed the presence of 26 different fungal orders. Among them, serious plant disease pathogens such as Bipolaris sorokiniana, Boeremia exigua, Claviceps purpurea, and Rhizoctonia zeae were detected. Seedborne bacteria, including Erwinia persicina and Acidovorax avenae, were identified from different bacterial orders. Our study indicated that the traditional culturing method and the NGS approach for pathogen identification complement each other. The reliability of culturing and NGS methods was further validated by PCR with specific primers. The combination of these different techniques ensures maximum sensitivity and specificity for turfgrass seed pathogen testing assay.

Bedding Plant Production and the Challenge of Fungal Diseases

Bedding plants are a major group of ornamentals produced in greenhouses or nurseries worldwide and planted outdoors. Their economic importance has increased continuously in the last four decades in both the United States and the European Union. These plants are subject to a broad number of diseases that can negatively impact their production and cultivation. The initial steps of production strongly influence the health status of these plants and, consequently, their aesthetic appeal, which is a strong requisite for consumers. Seeds, cuttings, and other forms of propagative material, along with production systems and growing media, can influence the phytosanitary status of the final product. In this article, case studies of soilborne and foliar diseases are presented together with preventive measures to achieve innovative disease management strategies. Quarantine restrictions and eradication measures are also discussed, in consideration of the high likelihood for ornamental plants to be long-distance vectors of new pathogens and pests.

Sympatric divergence of the ergot fungus, Claviceps purpurea, populations infecting agricultural and nonagricultural grasses in North America

The ergot diseases of agricultural and nonagricultural grasses are caused by the infection of Claviceps spp. (Hypocreales, Ascomycota) on florets, producing dark spur-like sclerotia on spikes that are toxic to humans and animals, leading to detrimental impacts on agriculture and economy due to the downgrading of cereal grains, import-export barriers, reduced yield, and ecological concerns. At least seven phylogenetic lineages (phylogenetic species) were identified within the premolecular concept of C. purpurea s.l. (sensu lato) in agricultural areas and vicinities in Canada and the Western United States. Claviceps purpurea s.s (sensu stricto) remained as the most prevalent species with a wide host range, including cereal crops, native, invasive, and weedy grasses. The knowledge on genetic diversity and distribution of C. purpurea s.s. in North America is lacking. The objective of the present study was to shed light on genetic differentiation and evolution of the natural populations of C. purpurea s.s. Multilocus DNA sequences of samples from Canada and the Western USA were analyzed using a phylogenetic network approach, and population demographic parameters were investigated. Results showed that three distinct genetically subdivided populations exist, and the subdivision is not correlated with geographic or host differentiations. Potential intrinsic mechanisms that might play roles in leading to the cessation of gene flows among the subpopulations, that is, mating and/or vegetative incompatibility, genomic adaptation, were discussed. The neutrality of two house-keeping genes that are widely used for DNA barcoding, that is, translation elongation factor 1-α (TEF1-α) and RNA polymerase II second largest subunit (RPB2), was challenged and discussed.

Modeling the relationship between estimated fungicide use and disease-associated yield losses of soybean in the United States II: Seed-applied fungicides vs seedling diseases

Use of seed-applied fungicides has become commonplace in the United States soybean production systems. Although fungicides have the potential to protect seed/seedlings from critical early stage diseases such as damping-off and root/stem rots, results from previous studies are not consistent in terms of seed-applied fungicide's ability to mitigate yield losses. In the current study, the relationship between estimated soybean production losses due to seedling diseases and estimated seed-applied fungicide use was investigated using annual data from 28 soybean growing states in the U.S. over the period of 2006 to 2014. National, regional (northern and southern U.S.), state, and temporal scale trends were explored using mixed effects version of the regression analysis. Mixed modeling allowed computing generalized R2 values for conditional (R2GLMM(c); contains fixed and random effects) and marginal (R2GLMM(m); contains only fixed effects) models. Similar analyses were conducted to investigate how soybean production was related to fungicide use. National and regional scale modeling revealed that R2GLMM(c) values were significantly larger compared to R2GLMM(m) values, meaning fungicide use had limited utility in explaining the national/regional scale variation of yield loss and production. The state scale analysis revealed the usefulness of seed-applied fungicides to mitigate seedling diseases-associated soybean yield losses in Illinois, Indiana, North Carolina, and Ohio. Further, fungicide use positively influenced the soybean production and yield in Illinois and South Dakota. Taken together, use of seed-applied fungicide did not appear to be beneficial to many of the states. Our findings corroborate the observations made by a number of scientists through field scale seed-applied fungicide trials across the U.S and reiterate the importance of need base-use of seed-applied fungicides rather than being a routine practice in soybean production systems.

Multiplex qPCR Assay for Direct Detection and Quantification of Colletotrichum truncatum, Corynespora cassiicola, and Sclerotinia sclerotiorum in Soybean Seeds

Precise diagnosis of plant diseases is one of the most effective tools to minimize yield losses. Colletotrichum truncatum, Corynespora cassiicola, and Sclerotinia sclerotiorum are common soilborne pathogens that affect soybeans all over the world. We developed a multiplex quantitative real-time polymerase chain reaction (qPCR) assay to simultaneously detect and quantify the three pathogens in soybean seeds and to survey their occurrence in the main soybean production areas in Brazil. Species-specific primers and probes for C. truncatum and C. cassiicola were designed based on GAPDH and TEF1 genes, respectively, to be combined with qPCR detection of S. sclerotiorum previously reported. The multiplex qPCR assay was successful in the simultaneous detection of C. truncatum, C. cassiicola, and S. sclerotiorum, along with a host internal control. The four pathogens were detected and quantified in artificially and naturally infested soybean seeds, even in the lowest incidence level tested of 0.0625% or 1 infected seed out of 1,599 healthy ones. From 81 seed samples tested, C. truncatum was the most frequently detected pathogen and with higher incidence levels (0.25 to 0.125%), followed by S. sclerotiorum and C. cassiicola, both with lower incidence levels (0.125 to 0.0625%). Together, the results evidenced the high sensitivity of the multiplex qPCR assay, indicating its usefulness for a quick and reliable diagnosis of soybean diseases in seeds.

Soybean seed treatment: how do fungicides translocate in plants?

BACKGROUND

Soybean seed treatment with fungicides is a well-established disease management strategy. However, the movement of these fungicides within seedlings is not always well characterized. Thus, the objectives of this study were to determine the pattern of translocation of three fungicides with different modes of action applied as a seed treatment, and the effect of soil type on translocation.

RESULTS

Most of the absorbed radioactivity was concentrated in the cotyledons and the maximum sum of the rates of absorption by roots, stems, and leaves of the plants was 15%. In most cases, absorption by roots, stems, and leaves were lower than 5% for 14 C-pyraclostrobin and 14 C-metalaxyl, and 1.6% for 14 C-carbendazim. Fungicides absorbed by the roots and the whole seedlings were higher when plants were grown in soil with lower organic matter content. Fungicides in the cotyledons are unlikely to be redistributed and are lost when cotyledons fall off the plants.

CONCLUSION

Cotyledons are the part of the plant where fungicides are most absorbed, regardless of the fungicide. Soil type affects the absorption of fungicides, and in this study it was most likely caused by soil organic matter. These data improve knowledge of the movement of seed treatment fungicides in soybean seedlings and may help the development of seed treatment chemistry to manage seed and soilborne pathogens.

Diversity of the Seedborne Fungi and Pathogenicity of Fusarium Species Associated with Intercropped Soybean

Maize/soybean relay strip intercropping has been widely practiced in Southwest China due to its high productivity and effective application of agricultural resources; however, several seedborne diseases such as seedling blight, pod and seed decay are frequently observed causing severe yield loss and low seed quality. So far, the population and pathogenicity of the seedborne fungi associated with intercropped soybean remain unexplored. In this study, seeds of 12 soybean cultivars screened for intercropping were collected from three growing regions in Sichuan Province of Southwest China, and the seedborne fungi were isolated from the surface-sterilized seeds. Based on sequence analysis of ribosomal DNA internal transcribed spacer (rDNA ITS), 148 isolates were identified into 13 fungal genera, among which Fusarium covered 55.0% as the biggest population followed by Colletotrichum. Furthermore, Fusarium isolates were classified into five distinct species comprising F. fujikuroi, F. proliferatum, F. verticillioides, F. asiaticum and F. incarnatum through sequence analysis of translation elongation factor 1 alpha (EF-1α) and DNA-directed RNA ploymerase II second largest subunit (RPB2). Among them, F. fujikuroi accounted for 51.22% (42/82) and was isolated from 91.7% (11/12) soybean varieties. Pathogenicity assay showed that five Fusarium species were able to infect the seeds of soybean cultivar “Nandou12” and caused water-soaked or rot symptoms, while F. fujikuroi and F. asiaticum had much higher aggressiveness than other species with significant reductions of seed fresh weight and germination percentage. Accordingly, this study indicates that Fusarium species are the dominant seedborne fungi in the intercropped soybean in Sichuan, China, and this provides some useful references for the effective management of seedborne fungal diseases as well as soybean resistance breeding in maize/soybean relay strip intercropping.

The Efficacy of Ethaboxam as a Soybean Seed Treatment Toward Phytophthora, Phytopythium, and Pythium in Ohio

Phytophthora, Phytopythium, and Pythium species that cause early-season seed decay and pre-emergence and post-emergence damping off of soybean are most commonly managed with seed treatments. The phenylamide fungicides metalaxyl and mefenoxam, and ethaboxam are effective toward some but not all species. The primary objective of this study was to evaluate the efficacy of ethaboxam in fungicide mixtures and compare those with other fungicides as seed treatments to protect soybean against Pythium, Phytopythium, and Phytophthora species in both high-disease field environments and laboratory seed plate assays. The second objective was to evaluate these seed treatment mixtures on cultivars that have varying levels and combinations of resistance to these soilborne pathogens. Five of eight environments received adequate precipitation in the 14 days after planting for high levels of seedling disease development and treatment evaluations. Three environments had significantly greater stands, and three had significantly greater yield when ethaboxam was used in the seed treatment mixture compared with treatments containing metalaxyl or mefenoxam alone. Three fungicide formulations significantly reduced disease severity compared with nontreated in the seed plate assay for 17 species. However, the combination of ethaboxam plus metalaxyl in a mixture was more effective than either fungicide alone against some Pythium and Phytopythium species. Overall, our results indicate that the addition of ethaboxam to a fungicide seed treatment is effective in reducing seed rot caused by these pathogens commonly isolated from soybean in Ohio but that these effects can be masked when cultivars with resistance are planted.

Detection of Cercospora beticola and Phoma betae on Table Beet Seed using Quantitative PCR

Cercospora beticola and Phoma betae are important pathogens of table beet, sugar beet, and Swiss chard (Beta vulgaris subsp. vulgaris), causing Cercospora leaf spot (CLS) and Phoma leaf spot, root rot, and damping-off, respectively. Both pathogens may be seedborne; however, limited evidence is available for seed infestation by C. beticola. Due to the limitations of culture-based seed assessment methods, detection of these pathogens was investigated using PCR. A P. betae-specific quantitative PCR assay was developed and used in conjunction with a C. beticola-specific assay to assess the presence of pathogen DNA in 12 table beet seed lots. DNA of C. beticola and P. betae was detected in four and eight seed lots, respectively. Plate tests and BIO-PCR confirmed the viability of each pathogen; however, competitive growth of other microbes and low incidence limited the frequency and sensitivity of detection in some seed lots. The results for P. betae support previously described infestation of seed. Further investigation of C. beticola-infested seed lots indicated the ability of seedborne C. beticola to cause CLS on plants grown from infested seed. Detection of viable C. beticola on table beet seed demonstrates the potential for pathogen dispersal and disease initiation via infested seed, and provides valuable insight into the epidemiology of CLS. Surveys of commercial table beet seed are required to determine the frequency and source of C. beticola seed infestation and its role as primary inoculum for epidemics, and to evaluate the effectiveness of seed treatments.

Sowing Uncertainty: What We Do and Don’t Know about the Planting of Pesticide-Treated Seed

Farmers, regulators, and researchers rely on pesticide use data to assess the effects of pesticides on crop yield, farm economics, off-target organisms, and human health. The publicly available pesticide use data in the United States do not currently account for pesticides applied as seed treatments. We find that seed treatment use has increased in major field crops over the last several decades but that there is a high degree of uncertainty about the extent of acreage planted with treated seeds, the amount of regional variability, and the use of certain active ingredients. One reason for this uncertainty is that farmers are less likely to know what pesticides are on their seed than they are about what pesticides are applied conventionally to their crops. This lack of information affects the quality and availability of seed treatment data and also farmers’ ability to tailor pesticide use to production and environmental goals.

Evaluating the Sensitivities and Efficacies of Fungicides with Different Modes of Action Against Phomopsis asparagi

Asparagus stem blight caused by Phomopsis asparagi is a major hindrance to asparagus production worldwide. Currently, fungicides are used to manage the disease in commercial production, but resistance to common fungicides has emerged in the wild population. In the present study, 132 isolates of P. asparagi collected from different provinces in China were tested for sensitivities to pyraclostrobin, tebuconazole, and fluazinam. We also determined the efficacies of six fungicides against P. asparagi. The frequency distributions of EC₅₀ values of the isolates tested were unimodal, but the curves for pyraclostrobin and tebuconazole had long right-hand tails. The mean EC₅₀ values for pyraclostrobin, tebuconazole, and fluazinam were 0.0426 ± 0.0029, 0.6041 ± 0.0416, and 0.0314 ± 0.0013 μg/ml, respectively. In addition, the EC₅₀ values for pyraclostrobin were very similar with or without salicylhydroxamic acid (SHAM), 20 μg/ml, indicating that SHAM is not needed to determine the sensitivity of P. asparagi to pyraclostrobin when using the mycelial growth inhibition assay. In greenhouse assays, Merivon (42.4% fluxapyroxad plus pyraclostrobin SC), Frown-cide (500 g/liter fluazinam SC), Cabrio (250 g/liter pyraclostrobin EC), and Nativo (75% trifloxystrobin plus tebuconazole WG) showed excellent preventive efficacy against P. asparagi. And these fungicides were more effective before inoculation than when they were applied after inoculation (P < 0.05). Therefore, these fungicides should be applied prior to infection to control stem blight. In field trials, Frown-cide, Merivon, Nativo, and Cabrio also performed good control effects, ranging from 75.2 to 86.0% in 2017 and 75.4 to 87.1% in 2018. We demonstrated that Frown-cide, Merivon, Nativo, and Cabrio had considerable potential to manage asparagus stem blight. In addition, rotations of these fungicides are essential for precluding or delaying the development of resistance and for controlling the disease.

Fundamental Aspects of Plant Viruses-An Overview on Focus Issue Articles

Given the importance of and rapid research progress in plant virology in recent years, this Focus Issue broadly emphasizes advances in fundamental aspects of virus infection cycles and epidemiology. This Focus Issue comprises three review articles and 18 research articles. The research articles cover broad research areas on the identification of novel viruses, the development of detection methods, reverse genetics systems and functional genomics for plant viruses, vector and seed transmission studies, viral population studies, virus-virus interactions and their effect on vector transmission, and management strategies of viral diseases. The three review articles discuss recent developments in application of prokaryotic clustered regularly interspaced short palindromic repeats/CRISPR-associated genes (CRISPR/Cas) technology for plant virus resistance, mixed viral infections and their role in disease synergism and cross-protection, and viral transmission by whiteflies. The following briefly summarizes the articles appearing in this Focus Issue.

Multiple Introductions of Tomato Pathogen Clavibacter michiganensis subsp. michiganensis into Iran as Revealed by a Global-Scale Phylogeographic Analysis

Tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis is one of the most important seed-borne tomato diseases around the globe. The disease was initially reported in 1993 in Iran, and it became a rising threat for the multibillion dollar tomato industry of the country during the last decade. In this study, using phylogeographic analyses, we determined genetic diversity and geographic distribution of C. michiganensis subsp. michiganensis in Iran. Our field surveys showed that the pathogen is expanding into the southern and eastern areas of the country. Furthermore, multilocus sequence analysis and typing (MLSA/MLST) using the sequences of five housekeeping genes (atpD, gyrB, ppk, recA, and rpoB) revealed that 37 C. michiganensis subsp. michiganensis strains isolated in Iran had high genetic diversity and placed in 15 sequence types (STs), while all the available 184 worldwide C. michiganensis subsp. michiganensis sequences were placed in 43 STs. MLSA divided the worldwide C. michiganensis subsp. michiganensis strains into two phylogroups (I and II). Among the 37 strains isolated in Iran, 30 strains clustered in phylogroup I, while 7 strains clustered in phylogroup II. Phylogeographic data inferred from the allelic profile of the five housekeeping genes suggested multiple introductions of C. michiganensis subsp. michiganensis inoculum into Iran, while the geographic origin of the Iranian C. michiganensis subsp. michiganensis strains remains undetermined. Further analyses using higher numbers of strains are warranted to decipher the evolutionary history of C. michiganensis subsp. michiganensis in Iran. Additionally, stricter seed/transplant inspections are recommended to reduce the risk of pathogen expansion to areas with no history of the disease.IMPORTANCE Clavibacter michiganensis subsp. michiganensis, the causal agent of tomato bacterial canker disease, is one of the economically important pathogens of solanaceous crops (e.g., eggplant, pepper, and tomato) around the world. The disease occurs in many countries, with a particular importance in regions characterized by high precipitation and humid environmental conditions. As a seed-borne pathogen, C. michiganensis subsp. michiganensis is included in the A2 (high risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Bacterial canker disease was reported for the first time in 1993 in Iran, while the geographic distribution, genetic diversity, and phylogenetic position of the causal agent remain undetermined. In this study, using the multilocus sequence analysis and typing (MLSA/MLST) approach, we provided a phylogeographic scheme for the C. michiganensis subsp. michiganensis strains isolated in Iran. Furthermore, global-scale phylogenetic analyses led to determination of phylogenetic position of Iranian C. michiganensis subsp. michiganensis strains among worldwide population of the pathogen. Based on diversity parameters and population structure, we suggest relatively higher genetic diversity of the bacterial canker pathogen in Iran than has so far been observed in the other areas of the world. Results obtained in this study provide a novel insight into the genetic diversity and population structure of the bacterial canker pathogen on a global scale.

Variation in Streptomycin Resistance Mechanisms in Clavibacter michiganensis

Clavibacter michiganensis is the causal agent of bacterial canker of tomato, which causes significant economic losses because of the lack of resistant tomato varieties. Chemical control with streptomycin or cupric bactericides is the last defensive line in canker disease management. Streptomycin is an aminoglycoside antibiotic that inhibits protein synthesis and targets the 30S ribosomal protein RpsL. Streptomycin has been used to control multiple plant bacterial diseases. However, identification and characterization of streptomycin resistance in C. michiganensis have remained unexplored. In this study, a naturally occurring C. michiganensis strain TX-0702 exhibiting spontaneous streptomycin resistance was identified, with a minimum inhibitory concentration of 128 μg/ml. Additionally, an induced streptomycin-resistant strain BT-0505-R was generated by experimental evolution of the sensitive C. michiganensis strain BT-0505. Genome sequencing and functional analyses were used to identify the genes conferring resistance. A point mutation at the 128th nucleotide in the rpsL gene of strain BT-0505-R is responsible for conferring streptomycin resistance. However, in TX-0702, resistance is not attributed to mutation of rpsL, streptomycin inactivation enzymes, or multidrug efflux pumps. The mechanism of resistance in TX-0702 is independent of previously reported bacterial loci. Taken together, these data highlight diverse mechanisms used by a Gram-positive plant pathogenic bacterium to confer antibiotic resistance.

qPCR and loop mediated isothermal amplification for rapid detection of Ustilago tritici

Loose smut of wheat caused by the basidiomycete fungus Ustilago tritici, a seed-borne disease, is difficult to control because of the expanse of wheat planting area and difficulty in pathogen detection. In this study, real-time fluorescence quantitative PCR (qPCR) and loop-mediated isothermal amplification (LAMP) assays are used to rapidly amplify the DNA of U. tritici. Five pairs of primers for qPCR and two series primers for LAMP were designed. Primarily, the specificity of the primer was assessed by using genomic DNA of U. tritici, Fusarium graminearum, Blumeria graminis, Rhizoctonia cerealis, Puccinia striiformis, Bipolaris sorokiniana, and Alternaria solani as templates. Further, the amplification systems were optimized. Finally, the sensitivity of qPCR and LAMP assays were evaluated. The results showed that the primer Y-430 F/R, Y-307 F/R, Y-755 F/R, and Y-139 F/R for qPCR and primers L-139 and L-988 for LAMP could be used for U. tritici detection. In the sensitivity test, the detection limit of qPCR assay was identified as 10 pg μL⁻¹ of genomic DNA, the detection limit for LAMP assay was 100 fg μL⁻¹. We successfully performed qPCR and LAMP assays on wheat loose smut wheat samples. This paper establishes two methods for U. tritici detection, which can be used for diagnosis of wheat loose smut in the laboratory and in the field.

Cross-resistance of the pathogenic fungus Alternaria alternata to fungicides with different modes of action

BACKGROUND

Cross-resistance, a phenomenon that a pathogen resists to one antimicrobial compound also resists to one or several other compounds, is one of major threats to human health and sustainable food production. It usually occurs among antimicrobial compounds sharing the mode of action. In this study, we determined the sensitivity profiles of Alternaria alternata, a fungal pathogen which can cause diseases in many crops to two fungicides (mancozeb and difenoconazole) with different mode of action using a large number of isolates (234) collected from seven potato fields across China.

RESULTS

We found that pathogens could also develop cross resistance to fungicides with different modes of action as indicated by a strong positive correlation between mancozeb and difenoconazole tolerances to A. alternata. We also found a positive association between mancozeb tolerance and aggressiveness of A. alternata, suggesting no fitness penalty of developing mancozeb resistance in the pathogen and hypothesize that mechanisms such as antimicrobial compound efflux and detoxification that limit intercellular accumulation of natural/synthetic chemicals in pathogens might account for the cross-resistance and the positive association between pathogen aggressiveness and mancozeb tolerance.

CONCLUSIONS

The detection of cross-resistance among different classes of fungicides suggests that the mode of action alone may not be an adequate sole criterion to determine what components to use in the mixture and/or rotation of fungicides in agricultural and medical sects. Similarly, the observation of a positive association between the pathogen's aggressiveness and tolerance to mancozeb suggests that intensive application of site non-specific fungicides might simultaneously lead to reduced fungicide resistance and enhanced ability to cause diseases in pathogen populations, thereby posing a greater threat to agricultural production and human health. In this case, the use of evolutionary principles in closely monitoring populations and the use of appropriate fungicide applications are important for effective use of the fungicides and durable infectious disease management.

Ready-to-Eat Salad Crops: A Plant Pathogen's Heaven

The ready-to-eat salad sector, also called fresh-cut or bagged salads, is a fast-growing segment of the fresh-food industry. The dynamism and specialization of this sector, together with the lack of adequate crop rotation, the globalization of the seed market, and climate change, are the main causes of the development of many new diseases that cause severe production losses. Newly detected diseases of the most important crops grown (lettuce, wild and cultivated rocket, lamb's lettuce, chicory, endive, basil, spinach, and Swiss chard) are critically discussed. The management of these diseases represents a formidable challenge, since few fungicides are registered on these minor-use crops. An interesting feature of the ready-to-eat salad sector is that most crops are grown under protection, often in soilless systems, which provide an environment helpful to the implementation of innovative control methods. Current trends in disease management are discussed, with special focus on the most sustainable practices.

Variation in the Resistance of Japanese Soybean Cultivars to Phytophthora Root and Stem Rot during the Early Plant Growth Stages and the Effects of a Fungicide Seed Treatment

Soybean cultivars susceptible to Phytophthora root and stem rot are vulnerable to seed rot and damping-off of seedlings and young plants following an infection by Phytophthora sojae. In this study, the disease responses of Japanese soybean cultivars including currently grown main cultivars during the early growth stages were investigated following infections by multiple P. sojae isolates from Japanese fields. The extent of the resistance to 17 P. sojae isolates after inoculations at 14, 21, and 28 days after seeding varied significantly among 18 Japanese and two US soybean cultivars. Moreover, the disease responses of each cultivar differed significantly depending on the P. sojae isolate and the plant age at inoculation. Additionally, the treatment of 'Nattosyo-ryu' seeds with three fungicidal agrochemicals provided significant protection from P. sojae when plants were inoculated at 14-28 days after seeding. These results indicate that none of the Japanese soybean cultivars are completely resistant to all tested P. sojae isolates during the first month after sowing. However, the severity of the disease was limited when plants were inoculated during the later growth stages. Furthermore, the protective effects of the tested agrochemicals were maintained for at least 28 days after the seed treatment. Japanese soybean cultivars susceptible to Phytophthora root and stem rot that are grown under environmental conditions favorable for P. sojae infections require the implementation of certain practices, such as seed treatments with appropriate agrochemicals, to ensure they are protected from P. sojae during the early part of the soybean growing season.

Avicta and Clariva Affect the Biology of the Soybean Cyst Nematode, Heterodera glycines

Nematicidal seed treatments are a relatively new strategy for managing plant-parasitic nematodes in row crops. Two such seed treatments, Avicta (abamectin) and Clariva (Pasteuria nishizawae), are marketed by Syngenta for use against Heterodera glycines in soybean production in the upper Midwest. The specific effects of these seed treatments on the biology of the nematode have not been previously reported. The effects of Avicta and Clariva on H. glycines hatching, movement, attraction, penetration, development, and reproduction were determined in controlled-environment experiments. Avicta inhibited juvenile movement and penetration at the seed depth and 3 cm below the seed. Clariva inhibited juvenile movement and penetration 3 and 5 cm below the seed and nematode development within the roots of young plants. Both seed treatments affected nematodes in 10- and 20-day-old plants, but effects were not detected on nematodes developing in older plants (30 and 60 days) with larger root systems. These results provide details of the specific mechanisms of early-season protection provided by Avicta and Clariva seed treatments.

Isolate-Cultivar Interactions, In Vitro Growth, and Fungicide Sensitivity of Fusarium oxysporum Isolates Causing Seedling Disease on Soybean

Fusarium oxysporum is frequently associated with soybean root rot in the United States. Information about pathogenicity and other phenotypic characteristics of F. oxysporum populations is limited. The objective of the research described herein was to assess phenotypic characteristics of F. oxysporum isolates from soybean, including the interaction between isolates and soybean cultivars, fungal growth characteristics in culture, and sensitivity to fungicides commonly used as seed treatment products. The pathogenicity of 14 isolates was evaluated in rolled-towel and Petri-dish assays using 11 soybean cultivars. In the rolled-towel assay, seed were inoculated with a conidial suspension and disease severity was observed. In the Petri-dish assay, F. oxysporum isolates were grown on 2% water agar and seed were placed on the F. oxysporum colony to observe the symptoms that developed. Cultivars differed in susceptibility to F. oxysporum, and significant (P = 0.0140) isolate-cultivar interactions were observed. F. oxysporum isolates differed in radial growth on potato dextrose agar at 25°C. Pyraclostrobin and trifloxystrobin reduced conidial germination with average 50% effective concentration (EC50) of 0.15 and 0.20 µg active ingredient (a.i.)/ml, respectively. Ipconazole reduced fungal growth with average EC50 of 0.23 µg a.i./ml, whereas fludioxonil was ineffective. Our results illustrate soybean F. oxysporum isolate variability and the potential for their management through cultivar selection or seed treatment.

Effect of potassium and manganese phosphites in the control of Pythium damping-off in soybean: a feasible alternative to fungicide seed treatments

BACKGROUND

Use of fungicide seed treatments for control of soybean soilborne diseases such as Pythium damping-off has increased worldwide. However, emergence of Pythium strains resistant to metalaxyl-M has prompted the need for alternative technologies to fungicides for damping-off control. The use of phosphites (Phis) has been proposed as a method to control oomycetes, but their use as seed treatments in soybean is limited by the lack of information on their efficacy. The effect of potassium (K) and manganese (Mn) Phis (as seed treatments) in the control of Pythium damping-off in soybean was evaluated in vitro and in vivo. In vitro, treated seeds and a control were placed on potato dextrose agar and the damping-off severity caused by Pythium aphanidermatum (Edson) Fitzpatrick, Pythium irregulare Buisman, and Pythium ultimum Trow was assessed 5 days after incubation using an ordinal scale. In vivo, treated seeds and a control were planted in polystyrene pots and emergence was evaluated 21 days after planting.

RESULTS

Analysis of the in vitro data using a multinomial generalized linear model showed that the probabilities of non-germinated, dead seeds ranged from 0.64 to 1.00 in the control and from 0 to 0.13 in the Phi treatments in each of the Pythium species. Probabilities of seed germination without or with damping-off symptoms were significantly higher for seeds treated with the Phi products than for the control. In the in vivo experiment, the Phi-based products increased seedling emergence by up to 29% on average compared with the untreated control.

CONCLUSION

Mn and K Phis are feasible alternatives as seed treatments to control Pythium damping-off in soybean. This study is the first, worldwide, to document the efficacy of K and Mn Phis in the control of soybean Pythium damping-off. © 2017 Society of Chemical Industry.

Advanced DNA-Based Point-of-Care Diagnostic Methods for Plant Diseases Detection

Diagnostic technologies for the detection of plant pathogens with point-of-care capability and high multiplexing ability are an essential tool in the fight to reduce the large agricultural production losses caused by plant diseases. The main desirable characteristics for such diagnostic assays are high specificity, sensitivity, reproducibility, quickness, cost efficiency and high-throughput multiplex detection capability. This article describes and discusses various DNA-based point-of care diagnostic methods for applications in plant disease detection. Polymerase chain reaction (PCR) is the most common DNA amplification technology used for detecting various plant and animal pathogens. However, subsequent to PCR based assays, several types of nucleic acid amplification technologies have been developed to achieve higher sensitivity, rapid detection as well as suitable for field applications such as loop-mediated isothermal amplification, helicase-dependent amplification, rolling circle amplification, recombinase polymerase amplification, and molecular inversion probe. The principle behind these technologies has been thoroughly discussed in several review papers; herein we emphasize the application of these technologies to detect plant pathogens by outlining the advantages and disadvantages of each technology in detail.

A Framework for Optimizing Phytosanitary Thresholds in Seed Systems

Seedborne pathogens and pests limit production in many agricultural systems. Quarantine programs help prevent the introduction of exotic pathogens into a country, but few regulations directly apply to reducing the reintroduction and spread of endemic pathogens. Use of phytosanitary thresholds helps limit the movement of pathogen inoculum through seed, but the costs associated with rejected seed lots can be prohibitive for voluntary implementation of phytosanitary thresholds. In this paper, we outline a framework to optimize thresholds for seedborne pathogens, balancing the cost of rejected seed lots and benefit of reduced inoculum levels. The method requires relatively small amounts of data, and the accuracy and robustness of the analysis improves over time as data accumulate from seed testing. We demonstrate the method first and illustrate it with a case study of seedborne oospores of Peronospora effusa, the causal agent of spinach downy mildew. A seed lot threshold of 0.23 oospores per seed could reduce the overall number of oospores entering the production system by 90% while removing 8% of seed lots destined for distribution. Alternative mitigation strategies may result in lower economic losses to seed producers, but have uncertain efficacy. We discuss future challenges and prospects for implementing this approach.

Development and Validation of a TaqMan Real-Time PCR Assay for the Specific Detection and Quantification of Fusarium fujikuroi in Rice Plants and Seeds

Bakanae disease, which is caused by the seedborne pathogen Fusarium fujikuroi, is found throughout the world on rice. A TaqMan real-time PCR has been developed on the TEF 1-α gene to detect F. fujikuroi in different rice tissues. Three primer/probe sets were tested. The selected set produced an amplicon of 84 bp and was specific for F. fujikuroi with respect to eight Fusarium species of rice and six other rice common pathogens. The assay was validated for specificity, selectivity, sensitivity, repeatability, and reproducibility. The detection limit was set at 27.5 fg of DNA, which is approximately equivalent to one haploid genome of F. fujikuroi. The developed TaqMan real-time assay was able to efficiently detect and quantify F. fujikuroi from rice culms, leaves, roots, and seeds. At 1 week post-germination (wpg), the pathogen was more diffused in the green tissues, while at 3 wpg it was uniformly spread also in the roots. The highest concentration of F. fujikuroi was measured in the M6 cultivar, which showed around 1,450 fungal cells/g. The assay was sufficiently sensitive to detect a few genomic equivalents in the rice seeds, corresponding to 9.89 F. fujikuroi cells/g. The assay permitted bakanae disease to be detected in asymptomatic tissues at the early rice development stages.

Ecological patterns of seed microbiome diversity, transmission, and assembly

Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transmission (vertical vs horizontal) of the microbial entities composing the seed microbiota as well as the potential connections existing between seed and other plant habitats such as the anthosphere and the spermosphere is discussed. Finally the governing processes (niche vs neutral) involved in the assembly and the dynamics of the seed microbiota are examined.

Baseline Sensitivity of Fusarium virguliforme to Fluopyram Fungicide

Fluopyram, a succinate dehydrogenase inhibitor (SDHI) fungicide, was recently registered for use as a soybean seed treatment for management of sudden death syndrome (SDS) caused by Fusarium virguliforme. Although registered and now used commercially, in vitro baseline fungicide sensitivity of F. virguliforme to fluopyram has not yet been established. In this study, the baseline sensitivity of F. virguliforme to fluopyram was determined using in vitro growth of mycelium and germination of conidia assays with two collections of F. virguliforme isolates. A total of 130 and 75 F. virguliforme isolates were tested using the mycelial growth and conidia germination assays, respectively, including a core set of isolates that were tested with both assays. In the mycelial growth inhibition assay, 113 out of 130 isolates (86.9%) were inhibited 50% by effective concentrations (EC₅₀) less than 5 µg/ml with a mean EC₅₀ of 3.35 µg/ml. For the conidia germination assay, 73 out of 75 isolates (97%) were determined to have an estimated EC₅₀ of less than 5 µg/ml with a mean EC₅₀ value of 2.28 µg/ml. In a subset of 20 common isolates that were phenotyped with both assays, conidia germination of F. virguliforme was determined to be more sensitive to fluopyram (mean EC₅₀ = 2.28 µg/ml) than mycelial growth (mean EC₅₀ = 3.35 µg/ml). Hormetic effects were observed in the mycelial growth inhibition assay as 22% of the isolates demonstrated more growth on medium amended with the lowest fluopyram concentration (1 µg/ml), as compared with the nonfluopyram amended control. It was not possible to determine EC₅₀ values for nine out of 185 isolates (4.8%), as those isolates were not inhibited by 50% even at the highest fluopyram concentrations of 100 µg/ml for mycelial growth and 20 µg/ml for conidia germination inhibition assays. On the whole, the F. virguliforme population appears to be sensitive to fluopyram, and this study enables future monitoring of fungicide sensitivity.

Efficacy of Difenoconazole Emulsifiable Concentrate with Ionic Liquids against Cucumbers Powdery Mildew

Among eight ionic liquids (ILs) examined, 1-n-butyl-4-methyl-pyridinium bromide (BMPyBr,  5) was used in this study as an appropriate alternative to benzene homologs and derivatives to be used in 10 wt% water-insoluble difenoconazole emulsifiable concentrate (EC). Moreover, 10 wt% difenoconazole EC with BMPyBr (5) exhibited the same efficacy as 10 wt% difenoconazole wettable powder (WP) against powdery mildew on cucumbers under field conditions. The results revealed that difenoconazole EC with BMPyBr (5) had excellent stability at 268 K and 327 K after 14 days through high-performance liquid chromatography (HPLC). Therefore, ILs can be considered as promising environment-friendly adjuvants for pesticides that are commercially processed as EC formulation.

Assessing pigmented pericarp of maize kernels as possible source of resistance to fusarium ear rot, Fusarium spp. infection and fumonisin accumulation

One of the purposes of maize genetic improvement is the research of genotypes resistant to fusarium ear rot (FER) and fumonisin accumulation. Flavonoids in the pericarp of the kernels are considered particularly able to reduce the fumonisin accumulation (FUM). The aim of this field study was to assess the effect of flavonoids, associated with anti-insect protection and Fusarium verticillioides inoculation, on FER symptoms and fumonisin contamination in maize kernels. Two isogenic hybrids, one having pigmentation in the pericarp (P1-rr) and the other without it (P1-wr), were compared. P1-rr showed lower values of FER symptoms and FUM contamination than P1-wr only if the anti-insect protection and the F. verticillioides inoculations were applied in combination. Fusarium spp. kernel infection was not influenced by the presence of flavonoids in the pericarp. Artificial F. verticillioides inoculation was more effective than anti-insect protection in enhancing the inhibition activity of flavonoids toward FUM contamination. The interactions between FUM contamination levels and FER ratings were better modeled in the pigmented hybrid than in the unpigmented one. The variable role that the pigment played in kernel defense against FER and FUM indicates that flavonoids alone may not be completely effective in the resistance of fumonisin contamination in maize.

Differential Inactivation of Fungal Spores in Water and on Seeds by Ozone and Arc Discharge Plasma

Seed sterilization is essential for preventing seed borne fungal diseases. Sterilization tools based on physical technologies have recently received much attention. However, available information is very limited in terms of efficiency, safety, and mode of action. In this study, we have examined antifungal activity of ozone and arc discharge plasma, potential tools for seed sterilization. In our results, ozone and arc discharge plasma have shown differential antifungal effects, depending on the environment associated with fungal spores (freely submerged in water or infected seeds). Ozone inactivates Fusarium fujikuroi (fungus causing rice bakanae disease) spores submerged in water more efficiently than arc discharge plasma. However, fungal spores associated with or infecting rice seeds are more effectively deactivated by arc discharge plasma. ROS generated in water by ozone may function as a powerful fungicidal factor. On the other hand, shockwave generated from arc discharge plasma may have greatly contributed to antifungal effects on fungus associated with rice seeds. In support of this notion, addition of ultrasonic wave in ozone generating water has greatly increased the efficiency of seed disinfection.

Quantitative Molecular Detection of Xanthomonas hortorum pv. carotae in Carrot Seed Before and After Hot-Water Treatment

Molecular assays to detect and quantify DNA from viable cells of the seedborne pathogen Xanthomonas hortorum pv. carotae in carrot seed were developed and evaluated for use on nontreated and hot-water-treated seed lots. Both a TaqMan real-time polymerase chain reaction (PCR) assay and a loop-mediated isothermal amplification (LAMP) dilution endpoint assay detected and quantified DNA from viable pathogen cells after treatment of carrot seed washes with the live-dead discriminating dye propidium monoazide (PMA). The detection limits of the assays were approximately 10¹ CFU for pure cultures of X. hortorum pv. carotae, and 10² to 10³ CFU/g seed from naturally infested carrot seed lots. X. hortorum pv. carotae in and on carrot seed was killed by soaking the seed in hot water (52°C for 25 min), and a subsequent PMA treatment of these hot-water-treated seed washes suppressed detection of the pathogen with both the real-time PCR and LAMP assays. For 36 commercial seed lots treated with PMA but not hot water, regression of colony counts of X. hortorum pv. carotae measured by dilution plating on a semiselective agar medium versus estimates of pathogen CFU determined by the molecular assays resulted in significant (P ≤ 0.05) linear relationships (R² = 0.68 for the real-time PCR assay and 0.79 for the LAMP assay). The molecular assays provided quantitative estimates of X. hortorum pv. carotae infestations in carrot seed lots in <24 h, which is a significant improvement over the 7 to 14 days required to obtain results from the traditional dilution-plating assay.