Survival Analysis as a Basis for Testing Hypotheses when Using Quantitative Ordinal Scale Disease Severity Data.

Disease severity in plant pathology is often measured by the amount of a plant or plant part that exhibits disease symptoms. This is typically assessed using a numerical scale, which allows a standardized, convenient, and quick method of rating. These scales, known as quantitative ordinal scales (QOS), divide the percentage scale into a predetermined number of intervals. There are various ways to analyze these ordinal data, with traditional methods involving the use of midpoint conversion to represent the interval. However, this may not be precise enough, as it is only an estimate of the true value. In this case, the data may be considered interval-censored, meaning that we have some knowledge of the value but not an exact measurement. This type of uncertainty is known as censoring, and techniques that address censoring, such as survival analysis (SA), use all available information and account for this uncertainty. To investigate the pros and cons of using SA with QOS measurements, we conducted a simulation based on three pathosystems. The results showed that SA almost always outperformed midpoint conversion with data analyzed using a t test, particularly when data were not normally distributed. Midpoint conversion is currently a standard procedure. In certain cases, the midpoint approach required a 400% increase in sample size to achieve the same power as the SA method. However, as the mean severity increases, fewer additional samples are needed (approximately an additional 100%), regardless of the assessment method used. Based on these findings, we conclude that SA is a valuable method for enhancing the power of hypothesis testing when analyzing QOS severity data. Future research should investigate the wider use of survival analysis techniques in plant pathology and their potential applications in the discipline.

Key Challenges in Plant Pathology in the Next Decade.

Plant diseases significantly impact food security and food safety. It was estimated that food production needs to increase by 50% to feed the projected 9.3 billion people by 2050. Yet, plant pathogens and pests are documented to cause up to 40% yield losses in major crops, including maize, rice, and wheat, resulting in annual worldwide economic losses of approximately US$220 billion. Yield losses due to plant diseases and pests are estimated to be 21.5% (10.1 to 28.1%) in wheat, 30.3% (24.6 to 40.9%) in rice, and 22.6% (19.5 to 41.4%) in maize. In March 2023, The American Phytopathological Society (APS) conducted a survey to identify and rank key challenges in plant pathology in the next decade. Phytopathology subsequently invited papers that address those key challenges in plant pathology, and these were published as a special issue. The key challenges identified include climate change effect on the disease triangle and outbreaks, plant disease resistance mechanisms and its applications, and specific diseases including those caused by Candidatus Liberibacter spp. and Xylella fastidiosa. Additionally, disease detection, natural and man-made disasters, and plant disease control strategies were explored in issue articles. Finally, aspects of open access and how to publish articles to maximize the Findability, Accessibility, Interoperability, and Reuse of digital assets in plant pathology were described. Only by identifying the challenges and tracking progress in developing solutions for them will we be able to resolve the issues in plant pathology and ultimately ensure plant health, food security, and food safety.

Disaster Plant Pathology: Smart Solutions for Threats to Global Plant Health from Natural and Human-Driven Disasters.

Disaster plant pathology addresses how natural and human-driven disasters impact plant diseases and the requirements for smart management solutions. Local to global drivers of plant disease change in response to disasters, often creating environments more conducive to plant disease. Most disasters have indirect effects on plant health through factors such as disrupted supply chains and damaged infrastructure. There is also the potential for direct effects from disasters, such as pathogen or vector dispersal due to floods, hurricanes, and human migration driven by war. Pulse stressors such as hurricanes and war require rapid responses, whereas press stressors such as climate change leave more time for management adaptation but may ultimately cause broader challenges. Smart solutions for the effects of disasters can be deployed through digital agriculture and decision support systems supporting disaster preparedness and optimized humanitarian aid across scales. Here, we use the disaster plant pathology framework to synthesize the effects of disasters in plant pathology and outline solutions to maintain food security and plant health in catastrophic scenarios. We recommend actions for improving food security before and following disasters, including (i) strengthening regional and global cooperation, (ii) capacity building for rapid implementation of new technologies, (iii) effective clean seed systems that can act quickly to replace seed lost in disasters, (iv) resilient biosecurity infrastructure and risk assessment ready for rapid implementation, and (v) decision support systems that can adapt rapidly to unexpected scenarios. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices.

The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.

Transcriptomics is essential but not sufficient to unravel complex plant-pathogen interactions.

KEY MESSAGE: A group of genes that were upregulated in a resistant cultivar while downregulated in a susceptible cultivar in a transcriptomics analysis of potato challenged by Spongospora subterranea infection, did not show the same expression pattern at the protein level.

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

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

Plant virology in the 21st century in China: Recent advances and future directions.

Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.

Machine learning for phytopathology: from the molecular scale towards the network scale.

With the increasing volume of high-throughput sequencing data from a variety of omics techniques in the field of plant-pathogen interactions, sorting, retrieving, processing and visualizing biological information have become a great challenge. Within the explosion of data, machine learning offers powerful tools to process these complex omics data by various algorithms, such as Bayesian reasoning, support vector machine and random forest. Here, we introduce the basic frameworks of machine learning in dissecting plant-pathogen interactions and discuss the applications and advances of machine learning in plant-pathogen interactions from molecular to network biology, including the prediction of pathogen effectors, plant disease resistance protein monitoring and the discovery of protein-protein networks. The aim of this review is to provide a summary of advances in plant defense and pathogen infection and to indicate the important developments of machine learning in phytopathology.

Key Discoveries in Plant Pathology During the Past Half Century: Impacts on the Life Sciences and on Plant Disease Management.

Plant pathology plays a critical role in safeguarding plant health, food security, and food safety through science-based solutions to protect plants against recurring and emerging diseases. In addition, plant pathology contributed significantly to basic discoveries that have had broad impacts on the life sciences beyond plant pathology. In December 2021, The American Phytopathological Society (APS) conducted a survey among its members and among the readership of its journals to identify and rank key discoveries in plant pathology that have had broad impacts on science and/or practical disease management during the past half century. Based on the responses received, key discoveries that have broadly impacted the life sciences during that period include the Agrobacterium Ti plasmid and its mechanism in T-DNA transfer, bacterial ice nucleation, cloning of resistance genes, discovery of viroids, effectors and their mechanisms, pattern-triggered immunity and effector-triggered immunity, RNA interference and gene silencing, structure and function of R genes, transcription activator-like effectors, and type-III secretion system and hrp/hrc. Major advances that significantly impacted practical disease management include the deployment and management of host resistance genes; the application of disease models and forecasting systems; the introduction of modern systemic fungicides and host resistance inducers, along with a better understanding of fungicide resistance mechanisms and management; and the utilization of biological controls and suppressive soils, including the implementation of methyl-bromide alternatives. In this special issue, experts from the pertinent fields review the discovery process, recent progress, and impacts of some of the highest ranked discoveries in each category while also pointing out future directions for new discoveries in fundamental and applied plant pathology.

Using Brainwave Patterns Recorded from Plant Pathology Experts to Increase the Reliability of AI-Based Plant Disease Recognition System.

One of the most challenging problems associated with the development of accurate and reliable application of computer vision and artificial intelligence in agriculture is that, not only are massive amounts of training data usually required, but also, in most cases, the images have to be properly labeled before models can be trained. Such a labeling process tends to be time consuming, tiresome, and expensive, often making the creation of large labeled datasets impractical. This problem is largely associated with the many steps involved in the labeling process, requiring the human expert rater to perform different cognitive and motor tasks in order to correctly label each image, thus diverting brain resources that should be focused on pattern recognition itself. One possible way to tackle this challenge is by exploring the phenomena in which highly trained experts can almost reflexively recognize and accurately classify objects of interest in a fraction of a second. As techniques for recording and decoding brain activity have evolved, it has become possible to directly tap into this ability and to accurately assess the expert's level of confidence and attention during the process. As a result, the labeling time can be reduced dramatically while effectively incorporating the expert's knowledge into artificial intelligence models. This study investigates how the use of electroencephalograms from plant pathology experts can improve the accuracy and robustness of image-based artificial intelligence models dedicated to plant disease recognition. Experiments have demonstrated the viability of the approach, with accuracies improving from 96% with the baseline model to 99% using brain generated labels and active learning approach.

How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape?

KEY MESSAGE: Long-read sequencing technologies are revolutionizing the sequencing and analysis of plant and pathogen genomes and transcriptomes, as well as contributing to emerging areas of interest in plant-pathogen interactions, disease management techniques, and the introduction of new plant varieties or cultivars. Long-read sequencing (LRS) technologies are progressively being implemented to study plants and pathogens of agricultural importance, which have substantial economic effects. The variability and complexity of the genome and transcriptome affect plant growth, development and pathogen responses. Overcoming the limitations of second-generation sequencing, LRS technology has significantly increased the length of a single contiguous read from a few hundred to millions of base pairs. Because of the longer read lengths, new analysis methods and tools have been developed for plant and pathogen genomics and transcriptomics. LRS technologies enable faster, more efficient, and high-throughput ultralong reads, allowing direct sequencing of genomes that would be impossible or difficult to investigate using short-read sequencing approaches. These benefits include genome assembly in repetitive areas, creating more comprehensive and exact genome determinations, assembling full-length transcripts, and detecting DNA and RNA alterations. Furthermore, these technologies allow for the identification of transcriptome diversity, significant structural variation analysis, and direct epigenetic mark detection in plant and pathogen genomic regions. LRS in plant pathology is found efficient for identifying and characterization of effectors in plants as well as known and unknown plant pathogens. In this review, we investigate how these technologies are transforming the landscape of determination and characterization of plant and pathogen genomes and transcriptomes efficiently and accurately. Moreover, we highlight potential areas of interest offered by LRS technologies for future study into plant-pathogen interactions, disease control strategies, and the development of new plant varieties or cultivars.

Engineered nanomaterials in plant diseases: can we combat phytopathogens?

Engineered nanomaterials (ENM) have a high potential for use in several areas of agriculture including plant pathology. Nanoparticles (NPs) alone can be applied for disease management due to their antimicrobial properties. Moreover, nanobiosensors allow a rapid and sensitive diagnosis of pathogens because NPs can be conjugated with nucleic acids, proteins and other biomolecules. The use of ENM in diagnosis, delivery of fungicides and therapy is an eco-friendly and economically viable alternative. This review focuses on different promising studies concerning ENM used for plant disease management including viruses, fungi, oomycetes and bacteria; diagnosis and delivery of antimicrobials and factors affecting the efficacy of nanomaterials, entry, translocation and toxicity. Although much research is required on metallic NPs due to the possible risks to the final consumer, ENMs are undoubtedly very useful tools to achieve food security in the world. KEY POINTS: • Increasing global population and fungicides have necessitated alternative technologies. • Nanomaterials can be used for detection, delivery and therapy of plant diseases. • The toxicity issues and safety should be considered before the use of nanomaterials.

Adjustment and quantification of UV-visible spectrophotometry analysis: an accurate and rapid method for estimating Cladosporium spp. spore concentration in a water suspension.

Cladosporium spp. are among the most important plant pathogens, plant endophytes, insect parasites and human pathogens in nature. The aim of this study was to increase the speed and accuracy of Cladosporium spp. spore counting using UV-visible spectrophotometry based on the regression model in a water suspension. Spores of C. ramotenellum AM55, C. limoniforme Br15, C. tenuissimum K15 and C. cladosporioides Ld13 fungi were diluted in sterile distilled water several times. Spore concentration/ml (SC) was counted with a hemocytometer. The spectrophotometer visible light absorption (ABS) was measured under 14 wavelengths from 300 to 950 nm for each dilution. The results showed that the morphological variation of the spores greatly affect the determination of the suitable wavelength. 650, 750, 500 and 400 nm wavelengths had the highest coefficient of determination (R2) values respectively for C. ramotenellum AM55, C. limoniforme Br15, C. tenuissimum K15 and C. cladosporioides Ld13 on the linear regression model. R2 values were 0.9874, 0.9647, 0.8856 and 0.9711 respectively, for the 650, 750, 500 and 400 nm wavelengths. The linear equation of SC = 107 × ABS-133,040 with the highest R2 value of 0.9532 had the best fit under a combinatorial regression model where SC and ABS of all Cladosporium spp. were presented. The proposed linear regression models can be used under in vivo and in vitro conditions for medicine or plant pathology studies which certainly increase the accuracy and speed of the future experiments compared to the hemocytometer method.

Versatile Applications of the CRISPR/Cas Toolkit in Plant Pathology and Disease Management.

New tools and advanced technologies have played key roles in facilitating basic research in plant pathology and practical approaches for disease management and crop health. Recently, the CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR-associated) system has emerged as a powerful and versatile tool for genome editing and other molecular applications. This review aims to introduce and highlight the CRISPR/Cas toolkit and its current and future impact on plant pathology and disease management. We will cover the rapidly expanding horizon of various CRISPR/Cas applications in the basic study of plant-pathogen interactions, genome engineering of plant disease resistance, and molecular diagnosis of diverse pathogens. Using the citrus greening disease as an example, various CRISPR/Cas-enabled strategies are presented to precisely edit the host genome for disease resistance, to rapidly detect the pathogen for disease management, and to potentially use gene drive for insect population control. At the cutting edge of nucleic acid manipulation and detection, the CRISPR/Cas toolkit will accelerate plant breeding and reshape crop production and disease management as we face the challenges of 21st century agriculture.

Screening of Marine Bioactive Antimicrobial Compounds for Plant Pathogens.

Plant diseases have been threatening food production. Controlling plant pathogens has become an important strategy to ensure food security. Although chemical control is an effective disease control strategy, its application is limited by many problems, such as environmental impact and pathogen resistance. In order to overcome these problems, it is necessary to develop more chemical reagents with new functional mechanisms. Due to their special living environment, marine organisms have produced a variety of bioactive compounds with novel structures, which have the potential to develop new fungicides. In the past two decades, screening marine bioactive compounds to inhibit plant pathogens has been a hot topic. In this review, we summarize the screening methods of marine active substances from plant pathogens, the identification of marine active substances from different sources, and the structure and antibacterial mechanism of marine active natural products. Finally, the application prospect of marine bioactive substances in plant disease control was prospected.

Advances in the biological control of phytoparasitic nematodes via the use of nematophagous fungi.

Agricultural production is one of most important activities for food supply and demand, that provides a source of raw materials, and generates commercial opportunities for other industries around the world. It may be both positively and negatively affected by climatic and biological factors. Negative biological factors are those caused by viruses, bacteria, or parasites. Given the serious problems posed by phytoparasitic nematodes for farmers, causing crop losses globally every year, the agrochemical industry has developed compounds with the capacity to inhibit their development; however, they can cause the death of other beneficial organisms and their lixiviation can contaminate the water table. On the other hand, the positive biological factors are found in biotechnology, the scientific discipline that develops products, such as nematophagous fungi (of which Purpureocillium lilacinum and Pochonia chlamydosporia have the greatest potential), for the control of pests and/or diseases. The present review focuses on the importance of nematophagous fungi, particularly sedentary endoparasitic nematodes, their research on the development of biological control agents, the mass production of fungi Purpureocillium lilacinum and Pochonia chlamydosporia, and their limited commercialization due to the lack of rigorous methods that enable the anticipation of complex interactions between plant and phytopathogenic agents.

Medicinal potentialities and pathogenic profile of Lasiodiplodia genus.

Considering that current biotechnological advances have been contributing towards improving the well-being of humanity, endophytic fungi, such as Lasiodiplodia, are promising sources of new substances to be used in chemical, pharmaceutical and agrochemical processes. Bioactive secondary metabolites are examples of such substances, although it is widely known that Lasiodiplodia inflicts irreparable damage to several crops of major economic importance. They are often produced as a response against biotic and abiotic factors, thus revealing that they play different roles, such as in signaling and defense mechanisms. Therefore, this review presents a few subtle differences between pathogenicity and mutualistic endophyte-host interactions. Moreover, the main secondary metabolites produced by Lasiodiplodia endophytes have been described with respect to their relevant antimicrobial and cytotoxic activities.

Advances in the control of phytopathogenic fungi that infect crops through their root system.

Productivity and economic sustainability of many herbaceous and woody crops are seriously threatened by numerous phytopathogenic fungi. While symptoms associated with phytopathogenic fungal infections of aerial parts (leaves, stems and fruits) are easily observable and therefore recognizable, allowing rapid or preventive action to control this type of infection, the effects produced by soil-borne fungi that infect plants through their root system are more difficult to detect. The fact that these fungi initiate infection and damage underground implies that the first symptoms are not as easily noticeable, and therefore both crop yield and plant survival are frequently severely compromised by the time the infection is found. In this paper we will review and discuss recent insights into plant-microbiota interactions in the root system crucial to understanding the beginning of the infectious process. We will also review different methods for diminishing and controlling the infection rate by phytopathogenic fungi penetrating through the root system including both the traditional use of biocontrol agents such as antifungal compounds as well as some new strategies that could be used because of their effective application, such as nanoparticles, virus-based nanopesticides, or inoculation of plant material with selected endophytes. We will also review the possibility of modeling and influencing the composition of the microbial population in the rhizosphere environment as a strategy for nudging the plant-microbiome interactions toward enhanced beneficial outcomes for the plant, such as controlling the infectious process.

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.

International Plant Pathology: Past and Future Contributions to Global Food Security.

The challenge of feeding the current and future world population is widely recognized, and the management of plant diseases has an important role in overcoming this. This paper explores the ways in which international plant pathology has contributed and continues to support efforts to secure adequate, safe and culturally appropriate nourishment and livelihoods for present and future generations. For the purposes of this paper, "international plant pathology" refers to the work that plant pathologists do when they work across international borders, with a focus on enhancing food security in tropical regions. Significant efforts involve public and philanthropic resources from the global North for addressing plant disease concerns in the global South, where food security is a legitimate and pressing concern. International disease management efforts are also aimed at protecting domestic food security, for example when pathogens of major staples migrate across national borders. In addition, some important crops are largely produced in tropical countries and consumed globally, including in industrialized countries; the diseases of these crops are of international interest, and they are largely managed by the private sector. Finally, host-microbe interactions are fascinating biological systems, and basic research on plant diseases of international relevance has often yielded insights and technologies with both scientific and practical implications.