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.

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.

Plant virology: an RNA treasure trove

Key principles pertaining to RNA biology not infrequently have their origins in plant virology. Examples have arisen from studies on viral RNA-intrinsic properties and the infection process from gene expression, replication, movement, and defense evasion to biotechnological applications. Since RNA is at the core of the central dogma in molecular biology, how plant virology assisted in the reinforcement or adaptations of this concept, while at other instances shook up elements of the doctrine, is discussed. Moreover, despite the negative effects of viral diseases in agriculture worldwide, plant viruses can be considered a scientific treasure trove. Today they remain tools of discovery for biotechnology, studying evolution, cell biology, and host-microbe interactions.

Towards integrative plant pathology

The field of plant pathology has revealed many of the mechanisms underlying the arms race, providing crucial knowledge and genetic resources for improving plant health. Although the host-microbe interaction seemingly favors rapidly evolving pathogens, it has also generated a vast evolutionary history of largely unexplored plant immunodiversity. We review studies that characterize the scope and distribution of genetic and ecological diversity in model and non-model systems with specific reference to pathogen effector diversity, plant immunodiversity in both cultivated species and their wild relatives, and diversity in the plant-associated microbiota. We show how the study of evolutionary and ecological processes can reveal patterns of genetic convergence, conservation, and diversification, and that this diversity is increasingly tractable in both experimental and translational systems. Perhaps most importantly, these patterns of diversity provide largely untapped resources that can be deployed for the rational engineering of durable resistance for sustainable agriculture.

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

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.

Historical and Scientific Evidence for the Origin and Cultural Importance to Australia's First-Nations Peoples of the Laboratory Accession of Nicotiana benthamiana, a Model for Plant Virology

Nicotiana benthamiana is an indigenous plant species distributed across northern Australia. The laboratory accession (LAB) of N. benthamiana has become widely adopted as a model host for plant viruses, and it is distinct from other accessions morphologically, physiologically, and by having an attenuation-of-function mutation in the RNA-dependent RNA polymerase 1 (NbRdr1) gene, referred to as NbRdr1m. Recent historical evidence suggested LAB was derived from a 1936 collection by John Cleland at The Granites of the Northern Territory, although no scientific evidence was provided. We provide scientific evidence and further historical evidence supporting the origin of LAB as The Granites. Analysis of a herbarium specimen of N. benthamiana collected by Cleland in 1936 revealed that The Granites population contains plants heterozygous for the NbRdr1 locus, having both the functional NbRdr1 and the mutant NbRdr1m alleles. N. benthamiana was an important cultural asset actively utilised as the narcotic Pituri (chewing tobacco) by the Warlpiri Aboriginal people at the site, who prevented women of child-bearing age from consuming it. We propose that Aboriginal people selected some of the unique traits of LAB that have subsequently facilitated its adoption as a model plant, such as lack of seed dormancy, fast maturity, low nornicotine content, and gracility.

Computational Analysis of HTS Data and Its Application in Plant Pathology

High-throughput sequencing is a basic tool of biological research, and it is extensively used in plant pathology projects. Here, we describe how to handle data coming from a variety of sequencing experiments, focusing on the analysis of Illumina reads. We describe how to perform genome assembly and annotation with DNA reads, correctly analyze RNA-seq data to discover differentially expressed genes, handle amplicon sequencing data from microbial communities, and utilize small RNA sequencing data to predict miRNA sequences and their putative targets.

Transmission Electron Microscopic Methods for Plant Virology

Transmission electron microscopy (TEM) is an important tool for observing the ultrastructure of plant virions and their host cells. The two main applicable TEM technologies used in plant virology are negative staining and ultrathin section. Negative staining is mainly used to observe the high-resolution structure of virus particles under a transmission electron microscope. Sample preparation for negative staining is convenient and fast, making it suitable for studying the virions in crude sap or purified solution. A modification of negative staining, by combining immunological reaction, named as technique of immuno-negative staining, is used to enrich or identify viruses. Ultrathin section is used for ultrastructural cytopathological studies in the virus-infected host cells, including the morphology of virus particles, the structure of viral induced inclusion bodies, the subcellular distribution of virions and the structural alteration of the host cell induced by viral infection. Such information is valuable to analyze the behavior of virus in replication, assembly, and intercellular transportation, and thus to understand the viral infection cycle. The present chapter describes the operation details of negative staining and ultrathin section TEM.

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.

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.

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.

Plant Virology Delivers Diverse Toolsets for Biotechnology

Over a hundred years of research on plant viruses has led to a detailed understanding of viral replication, movement, and host-virus interactions. The functions of vast viral genes have also been annotated. With an increased understanding of plant viruses and plant-virus interactions, various viruses have been developed as vectors to modulate gene expressions for functional studies as well as for fulfilling the needs in biotechnology. These approaches are invaluable not only for molecular breeding and functional genomics studies related to pivotal agronomic traits, but also for the production of vaccines and health-promoting carotenoids. This review summarizes the latest progress in these forefronts as well as the available viral vectors for economically important crops and beyond.

First Inventory of Fungi in Symptomless and Symptomatic Chinese Mesona Indicates Phytopathological Threat

Chinese mesona (Platostoma palustre) plays an important role as special crop in Southeast Asia and Taiwan for the production of herbal tea, grass jelly, and further processed food. In order to assess the potential threat of fungi to Chinese mesona, we surveyed isolates from symptomless plants in the area of mesona production, as well as from leaf spots of potted plants in a garden shop and a plantation in a botanical garden in Taiwan. From leaves, stems, and roots of 15 symptomless plants sampled at five collection events over two years, 154 isolates from 810 surface-sterilized plant fragments were obtained and identified based on DNA sequence data of the internal transcribed spacer region, and partially of the β-tubulin and histone H3 genes. The most common species belonged to the genera Cercospora, Colletotrichum, and Fusarium and were considered to be potential plant pathogens. Latent pathogenicity was confirmed by an infection experiment with an endophytic strain of Corynespora cassiicola. Observation of leaf spot disease associated with Cercospora kikuchii suggested pathogenicity of this fungus, which was also isolated as an endophyte from symptomless leaves. We hypothesize that the most common endophytic fungi are latent pathogens in the host and may cause plant disease when the host becomes weakened by senescence or changed cultivation condition. Leaf spots of plants in the botanical garden were associated with a species of Pseudocercospora, which was not found among the endophytic isolates and is newly described based on morphology and analysis of translation elongation factor 1 alpha gene sequences.

Developing Public-Private Partnerships in Plant Pathology Extension: Case Studies and Opportunities in the United States

Public-private partnerships (PPPs) can be an effective and advantageous way to accomplish extension and outreach objectives in plant pathology. The greatest opportunities for extension-focused PPPs may be in response to large-scale or emerging disease management concerns or in addressing complex issues that impact agriculture, such as climate change, digital technology, and public perception of science. The most fertile ground for forming PPPs is where the needs and strengths of the public and private sectors are complementary. Developing PPPs depends as much on professional relationships as on technical skills or contracts. Defining and making room for the success of all partners, identifying and addressing barriers to success, and earning and maintaining trust are components that contribute to the effectiveness of PPPs. Case studies in plant pathology demonstrate the positive impact PPPs can have on partners and stakeholders and provide guidance on the formation of PPPs in the future.

Modeling the Impact of Crop Diseases on Global Food Security

Plant pathology must contribute to improving food security in a safe operating space, which is shrinking as a result of declining natural resources, climate change, and the growing world population. This review analyzes the position of plant pathology in a nexus of relationships, which is mapped and where the coupled dynamics of crop growth, disease, and yield losses are modeled. We derive a hierarchy of pathogens, whereby pathogens reducing radiation interception (RI), radiation use efficiency (RUE), and harvest index increasingly impact crop yields in the approximate proportions: 1:4.5:4,700. Since the dawn of agriculture, plant breeding has targeted the harvest index as a main objective for domesticated plants. Surprisingly, the literature suggests that pathogens that reduce yields by directly damaging harvestable plant tissues have received much less attention than those that reduce RI or RUE. Ecological disease management needs to target diverse production situations and therefore must consider variation in attainable yields; this can be achieved through the reengineering of agrosystems to incorporate built-in dynamic diversity of genes, plants, and crop stands.

An Arabidopsis DISEASE RELATED NONSPECIFIC LIPID TRANSFER PROTEIN 1 is required for resistance against various phytopathogens and tolerance to salt stress

Synchronous and timely regulation of multiple genes results in an effective defense response that decides the fate of the host when challenged with pathogens or unexpected changes in environmental conditions. One such gene, which is downregulated in response to multiple bacterial pathogens, is a putative nonspecific lipid transfer protein (nsLTP) of unknown function that we have named DISEASE RELATED NONSPECIFIC LIPID TRANSFER PROTEIN 1 (DRN1). We show that upon pathogen challenge, DRN1 is strongly downregulated, while a putative DRN1-targeting novel microRNA (miRNA) named DRN1 Regulating miRNA (DmiR) is reciprocally upregulated. Furthermore, we provide evidence that DRN1 is required for defense against bacterial and fungal pathogens as well as for normal seedling growth under salinity stress. Although nsLTP family members from different plant species are known to be a significant source of food allergens and are often associated with antimicrobial properties, our knowledge on the biological functions and regulation of this gene family is limited. Our current work not only sheds light on the mechanism of regulation but also helps in the functional characterization of DRN1, a putative nsLTP family member of hitherto unknown function.

Quantitative Ordinal Scale Estimates of Plant Disease Severity: Comparing Treatments Using a Proportional Odds Model

Studies in plant pathology, agronomy, and plant breeding requiring disease severity assessment often use quantitative ordinal scales (i.e., a special type of ordinal scale that uses defined numeric ranges); a frequently used example of such a scale is the Horsfall-Barratt scale. Parametric proportional odds models (POMs) may be used to analyze the ratings obtained from quantitative ordinal scales directly, without converting ratings to percent area affected using range midpoints of such scales (currently a standard procedure). Our aim was to evaluate the performance of the POM for comparing treatments using ordinal estimates of disease severity relative to two alternatives, the midpoint conversions (MCs) and nearest percent estimates (NPEs). A simulation method was implemented and the parameters of the simulation estimated using actual disease severity data from the field. The criterion for comparison of the three approaches was the power of the hypothesis test (the probability to reject the null hypothesis when it is false). Most often, NPEs had superior performance. The performance of the POM was never inferior to using the MC at severity <40%. Especially at low disease severity (≤10%), the POM was superior to using the MC method. Thus, for early onset of disease or for comparing treatments with severities <40%, the POM is preferable for analyzing disease severity data based on quantitative ordinal scales when comparing treatments and at severities >40% is equivalent to other methods.

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.

CRISPR Applications in Plant Virology: Virus Resistance and Beyond

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated genes (Cas) is a prokaryotic adaptive immune system which has been reprogrammed into a precise, simple, and efficient gene targeting technology. This emerging technology is revolutionizing various areas of life sciences, medicine, and biotechnology and has raised significant interest among plant biologists, both in basic science and in plant protection and breeding. In this review, we describe the basic principles of CRISPR/Cas systems, and how they can be deployed to model plants and crops for the control, monitoring, and study of the mechanistic aspects of plant virus infections. We discuss how Cas endonucleases can be used to engineer plant virus resistance by directly targeting viral DNA or RNA, as well as how they can inactivate host susceptibility genes. Additionally, other applications of CRISPR/Cas in plant virology such as virus diagnostics and imaging are reviewed. The review also provides a systemic comparison between CRISPR/Cas technology and RNA interference approaches, the latter of which has also been used for development of virus-resistant plants. Finally, we outline challenges to be solved before CRISPR/Cas can produce virus-resistant crop plants which can be marketed.

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.

Sciadopitys verticillata Resin: Volatile Components and Impact on Plant Pathogenic and Foodborne Bacteria

Sciadopitys verticillata (Sv) produces a white, sticky, latex-like resin with antimicrobial properties. The aims of this research were to evaluate the effects of this resin (Sv resin) on bacterial populations and to determine the impact of its primary volatile components on bioactivity. The impact of sample treatment on chemical composition of Sv resin was analyzed using Fourier transform infrared spectroscopy (FTIR) coupled with principal component analysis. The presence and concentration of volatiles in lyophilized resin were determined using gas chromatography/mass spectrometry (GC/MS). Changes in bacterial population counts due to treatment with resin or its primary volatile components were monitored. Autoclaving of the samples did not affect the FTIR spectra of Sv resin; however, lyophilization altered spectra, mainly in the CH and C=O regions. Three primary bioactive compounds that constituted >90% of volatiles (1R-α-pinene, tricyclene, and β-pinene) were identified in Sv resin. Autoclaved resin impacted bacterial growth. The resin was stimulatory for some plant and foodborne pathogens (Pseudomonas fluorescens, P. syringae, and Xanthomonas perforans) and antimicrobial for others (Escherichia coli, Bacillus cereus, Agrobacterium tumefaciens, and Erwinia amylovora). Treatment with either 1R-α-pinene or β-pinene reduced B. cereus population growth less than did autoclaved resin. The complex resin likely contains additional antimicrobial compounds that act synergistically to inhibit bacterial growth.

Molecular and morphological characterization of rice phylloplane fungi and determination of the antagonistic activity against rice pathogens

Cladosporium spp. is a cosmopolitan fungal genus. In the literature, it has been reported as a biological agent for controlling several plant diseases, but its mechanism of action has never been clarified. The present study aims to identify Cladosporium spp. based on the DNA phylogeny of nine isolates obtained from the phylloplane of rice and their potential antagonistic activity against the main fungal pathogens that affect rice crop. Nine isolates of Cladosporium spp. were identified based on DNA phylogeny, molecular and morphological characterization, and their antagonistic effects with the rice pathogens C. miyabeanus, M. oryzae, M. albescens and S. oryzae. Four isolates were selected to study lytic enzymes such as β-1,3-glucanase, chitinase and protease, and only one isolate was selected for a conidial germination and appressoria formation assay. The nine isolates were identified as C. cladosporioides, C. tenuissimum and C. subuliforme. Four isolates, identified as C. cladosporioides, inhibited the mycelial growth of rice pathogens such as C1H (68.59%) of S. oryzae, C5 G (74.32%) of C. miyabeanus, C11 G (75.97%) of M. oryzae and C24 G (77.39%) of M. albescens. C24 G showed a high activity of lytic enzymes, was tested against C. miyabeanus and M. oryzae, and inhibited conidial germination and appressorium formation by more than 59.36%. The characterization of C. cladosporioides suggested this species as a potential bioagent for the management of several rice diseases, especially rice blast. This is the first time that a potential biological agent from the genus Cladosporium identified at the species level was isolated from the rice phylloplane, and some of its mechanisms of action were demonstrated, such as increasing lytic enzyme activity against rice pathogens.

Evaluation of the Phytopathological Reaction of Wild and Cultivated Olives as a Means of Finding Promising New Sources of Genetic Diversity for Resistance to Root-Knot Nematodes

Olive (Olea europaea L.) is one of the most important fruit crops in the Mediterranean Basin, because it occupies significant acreage in these countries and often has important cultural heritage and landscape value. This crop can be infected by several Meloidogyne species (M. javanica, M. arenaria, and M. incognita, among others), and only a few cultivars with some level of resistance to these nematodes have been found. Innovations in intensive olive growing using high planting densities, irrigation, and substantial amounts of fertilizers could increase the nematode population to further damaging levels. To further understand the interactions involved between olive and pathogenic nematodes and in the hope of finding solutions to the agricultural risks, this research aimed to determine the reaction of important olive cultivars in Spain and wild olives to M. javanica infection, including genotypes of the same and other O. europaea subspecies. All olive cultivars tested were good hosts for M. javanica, but high levels of nematode reproduction found in three cultivars (Gordal Sevillana, Hojiblanca, and Manzanilla de Sevilla) were substantially different. In the wild accessions, O. europaea subsp. cerasiformis (genotype W147) and O. europaea subsp. europaea var. sylvestris (genotype W224) were resistant to M. javanica at different levels, with strong resistance in W147 (reproduction factor [Rf] = 0.0003) and moderate resistance in W224 (Rf = 0.79). The defense reaction of W147 to M. javanica showed a strong increase of phenolic compounds but no hypersensitive reaction.

Quantitative and qualitative phenotyping of disease resistance of crops by hyperspectral sensors: seamless interlocking of phytopathology, sensors, and machine learning is needed!

Determination and characterization of resistance reactions of crops against fungal pathogens are essential to select resistant genotypes. In plant breeding, phenotyping of genotypes is realized by time consuming and expensive visual plant ratings. During resistance reactions and during pathogenesis plants initiate different structural and biochemical defence mechanisms, which partly affect the optical properties of plant organs. Recently, intensive research has been conducted to develop innovative optical methods for an assessment of compatible and incompatible plant pathogen interaction. These approaches, combining classical phytopathology or microbiology with technology driven methods - such as sensors, robotics, machine learning, and artificial intelligence - are summarized by the term digital phenotyping. In contrast to common visual rating, detection and assessment methods, optical sensors in combination with advanced data analysis methods are able to retrieve pathogen induced changes in the physiology of susceptible or resistant plants non-invasively and objectively. Phenotyping disease resistance aims different tasks. In an early breeding step, a qualitative assessment and characterization of specific resistance action is aimed to link it, for example, to a genetic marker. Later, during greenhouse and field screening, the assessment of the level of susceptibility of different genotypes is relevant. Within this review, recent advances of digital phenotyping technologies for the detection of subtle resistance reactions and resistance breeding are highlighted and methodological requirements are critically discussed.

Factors in hybridization of local medical systems: Simultaneous use of medicinal plants and modern medicine in Northeast Brazil

The presence of mainstream medicine in local medical systems inserts a set of external treatments and concepts that generate adjustments in the local conceptions of health and disease. What points in the system are most receptive to change? Who are the residents most likely to adopt these external treatments to deal with diseases? To answer these questions, this work used a study model consisting of the simultaneous use of medicinal plants and modern medicine, testing whether diseases that require greater treatment efforts are the main targets of adherence to modern medicine and if socioeconomic characteristics of residents can cause intracultural variation in relation to simultaneous use. To obtain socioeconomic data on the knowledge of medicinal plants and simultaneous use of these resources with modern medicine, semistructured interviews were conducted in a rural community that has easy access to modern medicine. Participatory workshops were held to access the local perceptions about the frequency of occurrence and severity of illnesses. A multilevel logistic regression model was applied for data analysis. We found that chronic, severe and frequently occurring diseases in the community tended to show greater simultaneous use locally. Among the socioeconomic factors, we determined that high educational levels positively influenced the combined use of plants and modern medicine. The need to ensure the cure of frequent, severe and chronic diseases is a factor that leads residents to seek a greater number of possible treatments, stimulating the combined use of plants and modern medicine. Residents with higher educational levels were more likely to use a combination of treatments than those with lower educational levels, demonstrating that more participation in formal education may facilitate the combined use of medicinal plants and modern medicine.

The Future of Nanotechnology in Plant Pathology

Engineered nanoparticles are materials between 1 and 100 nm and exist as metalloids, metallic oxides, nonmetals, and carbon nanomaterials and as functionalized dendrimers, liposomes, and quantum dots. Their small size, large surface area, and high reactivity have enabled their use as bactericides/ fungicides and nanofertilizers. Nanoparticles can be designed as biosensors for plant disease diagnostics and as delivery vehicles for genetic material, probes, and agrichemicals. In the past decade, reports of nanotechnology in phytopathology have grown exponentially. Nanomaterials have been integrated into disease management strategies and diagnostics and as molecular tools. Most reports summarized herein are directed toward pathogen inhibition using metalloid/metallic oxide nanoparticles as bactericides/fungicides and as nanofertilizers to enhance health. The use of nanoparticles as biosensors in plant disease diagnostics is also reviewed. As global demand for food production escalates against a changing climate, nanotechnology could sustainably mitigate many challenges in disease management by reducing chemical inputs and promoting rapid detection of pathogens.

RNA Interference Mechanisms and Applications in Plant Pathology

The origin of RNA interference (RNAi), the cell sentinel system widely shared among eukaryotes that recognizes RNAs and specifically degrades or prevents their translation in cells, is suggested to predate the last eukaryote common ancestor ( 138 ). Of particular relevance to plant pathology is that in plants, but also in some fungi, insects, and lower eukaryotes, RNAi is a primary and effective antiviral defense, and recent studies have revealed that small RNAs (sRNAs) involved in RNAi play important roles in other plant diseases, including those caused by cellular plant pathogens. Because of this, and because RNAi can be manipulated to interfere with the expression of endogenous genes in an intra- or interspecific manner, RNAi has been used as a tool in studies of gene function but also for plant protection. Here, we review the discovery of RNAi, canonical mechanisms, experimental and translational applications, and new RNA-based technologies of importance to plant pathology.

The diagnosis of plant pathogenic bacteria: a state of art

Plant protection plays an important role in agriculture for the food quality and quantity. The diagnosis of plant diseases and the identification of the pathogens are essential prerequisites for their understanding and control. Among the plant pests, the bacterial pathogens have devastating effects on plant productivity and yield. Different techniques (microscopy, serology, biochemical, physiological, molecular tools and culture propagation) are currently used to detect and identify bacterial pathogens. Detection and identification are critical steps for the appropriate application of phytosanitary measures. The "harmonization of phytosanitary regulations and all other areas of official plant protection action" mean the good practices for plant protection and plant material certification. The prevention of diseases progression and spread by early detection are a valuable strategy for proper pest management and disease control. For this purpose, innovative methods aim achieving results within a shorter time and higher performance, to provide rapidly, accurately and reliably diagnosis. In this review, we focus on the techniques for plant bacterial diagnosis and on the regulations for harmonizing plant protection issue.

Environmental fate and behaviour of the biocontrol agent Bacillus amyloliquefaciens CPA-8 after preharvest application to stone fruit

BACKGROUND

Bacillus amyloliquefaciens strain CPA-8 has been described as an effective biocontrol agent to control brown rot in stone fruit for both preharvest and postharvest applications. However, no information about the environmental fate and behaviour of this strain under field conditions is available.

RESULTS

The dispersion of the CPA-8 application was evaluated using water-sensitive papers, and complete coverage was observed on the leaves of treated trees, while <1% of non-treated tree leaves had CPA-8. CPA-8 persisted on the fruit of treated trees during preharvest and postharvest conditions, while a significant decrease on leaves and weeds was observed 21 days after treatment. On non-treated trees, CPA-8 was detected on leaves until 180 days after treatment, and on weeds, the CPA-8 population was dependent on the distance from the treated trees. A high persistence of CPA-8 was detected on inert materials, such as clothes and gloves worn by handlers and plastic harvesting boxes. More than 99% of the samples with a CPA-8 phenotype were confirmed as CPA-8 using polymerase chain reaction (PCR).

CONCLUSION

This work demonstrated a good distribution, persistence and adaptation of the CPA-8 strain to field and postharvest conditions. Monitoring of dispersion and persistence is an excellent tool to determine the time of application and provides valuable information for registering issues. © 2017 Society of Chemical Industry.

Epidemiology: Past, Present, and Future Impacts on Understanding Disease Dynamics and Improving Plant Disease Management-A Summary of Focus Issue Articles

Epidemiology has made significant contributions to plant pathology by elucidating the general principles underlying the development of disease epidemics. This has resulted in a greatly improved theoretical and empirical understanding of the dynamics of disease epidemics in time and space, predictions of disease outbreaks or the need for disease control in real-time basis, and tactical and strategic solutions to disease problems. Availability of high-resolution experimental data at multiple temporal and spatial scales has now provided a platform to test and validate theories on the spread of diseases at a wide range of spatial scales ranging from the local to the landscape level. Relatively new approaches in plant disease epidemiology, ranging from network to information theory, coupled with the availability of large-scale datasets and the rapid development of computer technology, are leading to revolutionary thinking about epidemics that can result in considerable improvement of strategic and tactical decision making in the control and management of plant diseases. Methods that were previously restricted to topics such as population biology or evolution are now being employed in epidemiology to enable a better understanding of the forces that drive the development of plant disease epidemics in space and time. This Focus Issue of Phytopathology features research articles that address broad themes in epidemiology including social and political consequences of disease epidemics, decision theory and support, pathogen dispersal and disease spread, disease assessment and pathogen biology and disease resistance. It is important to emphasize that these articles are just a sample of the types of research projects that are relevant to epidemiology. Below, we provide a succinct summary of the articles that are published in this Focus Issue .

Application of Next Generation Sequencing for Diagnostic Testing of Tree Fruit Viruses and Viroids

Conventional detection of viruses and virus-like diseases of plants is accomplished using a combination of molecular, serological, and biological indexing. These are the primary tools used by plant virologists to monitor and ensure trees are free of known viral pathogens. The biological indexing assay, or bioassay, is considered to be the "gold standard" as it is the only method of the three that can detect new, uncharacterized, or poorly characterized viral disease agents. Unfortunately, this method is also the most labor intensive and can take up to three years to complete. Next generation sequencing (NGS) is a technology with rapidly expanding possibilities including potential applications for the detection of plant viruses. In this study, comparisons are made between tree fruit testing by conventional and NGS methods, to demonstrate the efficacy of NGS. A comparison of 178 infected trees, many infected with several viral pathogens, demonstrated that conventional and NGS were equally capable of detecting known viruses and viroids. Comparable results were obtained for 170 of 178 of the specimens. Of the remaining eight specimens, some discrepancies were observed between viruses detected by the two methods, representing less than 5% of the specimens. NGS was further demonstrated to be equal or superior for the detection of new or poorly characterized viruses when compared with a conventional bioassay. These results validated both the effectiveness of conventional virus testing methods and the use of NGS as an additional or alternative method for plant virus detection.

The Impact of "Coat Protein-Mediated Virus Resistance" in Applied Plant Pathology and Basic Research

Worldwide, plant viruses cause serious reductions in marketable crop yield and in some cases even plant death. In most cases, the most effective way to control virus diseases is through genetically controlled resistance. However, developing virus-resistant (VR) crops through traditional breeding can take many years, and in some cases is not even possible. Because of this, the demonstration of the first VR transgenic plants in 1985 generated much attention. This seminal report served as an inflection point for research in both basic and applied plant pathology, the results of which have dramatically changed both basic research and in a few cases, commercial crop production. The typical review article on this topic has focused on only basic or only applied research results stemming from this seminal discovery. This can make it difficult for the reader to appreciate the full impact of research on transgenic virus resistance, and the contributions from fundamental research that led to translational applications of this technology. In this review, we take a global view of this topic highlighting the significant changes to both basic and applied plant pathology research and commercial food production that have accumulated in the last 30 plus years. We present these milestones in the historical context of some of the scientific, economic, and environmental drivers for developing specific VR crops. The intent of this review is to provide a single document that adequately records the significant accomplishments of researchers in both basic and applied plant pathology research on this topic and how they relate to each other. We hope this review therefore serves as both an instructional tool for students new to the topic, as well as a source of conversation and discussion for how the technology of engineered virus resistance could be applied in the future.

Data processing of qualitative results from an interlaboratory comparison for the detection of "Flavescence dorée" phytoplasma: How the use of statistics can improve the reliability of the method validation process in plant pathology

A working group established in the framework of the EUPHRESCO European collaborative project aimed to compare and validate diagnostic protocols for the detection of "Flavescence dorée" (FD) phytoplasma in grapevines. Seven molecular protocols were compared in an interlaboratory test performance study where each laboratory had to analyze the same panel of samples consisting of DNA extracts prepared by the organizing laboratory. The tested molecular methods consisted of universal and group-specific real-time and end-point nested PCR tests. Different statistical approaches were applied to this collaborative study. Firstly, there was the standard statistical approach consisting in analyzing samples which are known to be positive and samples which are known to be negative and reporting the proportion of false-positive and false-negative results to respectively calculate diagnostic specificity and sensitivity. This approach was supplemented by the calculation of repeatability and reproducibility for qualitative methods based on the notions of accordance and concordance. Other new approaches were also implemented, based, on the one hand, on the probability of detection model, and, on the other hand, on Bayes' theorem. These various statistical approaches are complementary and give consistent results. Their combination, and in particular, the introduction of new statistical approaches give overall information on the performance and limitations of the different methods, and are particularly useful for selecting the most appropriate detection scheme with regards to the prevalence of the pathogen. Three real-time PCR protocols (methods M4, M5 and M6 respectively developed by Hren (2007), Pelletier (2009) and under patent oligonucleotides) achieved the highest levels of performance for FD phytoplasma detection. This paper also addresses the issue of indeterminate results and the identification of outlier results. The statistical tools presented in this paper and their combination can be applied to many other studies concerning plant pathogens and other disciplines that use qualitative detection methods.

Profiling the extended phenotype of plant pathogens: Challenges in Bacterial Molecular Plant Pathology

One of the most fundamental questions in plant pathology is what determines whether a pathogen grows within a plant? This question is frequently studied in terms of the role of elicitors and pathogenicity factors in the triggering or overcoming of host defences. However, this focus fails to address the basic question of how the environment in host tissues acts to support or restrict pathogen growth. Efforts to understand this aspect of host-pathogen interactions are commonly confounded by several issues, including the complexity of the plant environment, the artificial nature of many experimental infection systems and the fact that the physiological properties of a pathogen growing in association with a plant can be very different from the properties of the pathogen in culture. It is also important to recognize that the phenotype and evolution of pathogen and host are inextricably linked through their interactions, such that the environment experienced by a pathogen within a host, and its phenotype within the host, is a product of both its interaction with its host and its evolutionary history, including its co-evolution with host plants. As the phenotypic properties of a pathogen within a host cannot be defined in isolation from the host, it may be appropriate to think of pathogens as having an 'extended phenotype' that is the product of their genotype, host interactions and population structure within the host environment. This article reflects on the challenge of defining and studying this extended phenotype, in relation to the questions posed below, and considers how knowledge of the phenotype of pathogens in the host environment could be used to improve disease control. What determines whether a pathogen grows within a plant? What aspects of pathogen biology should be considered in describing the extended phenotype of a pathogen within a host? How can we study the extended phenotype in ways that provide insights into the phenotypic properties of pathogens during natural infections?

Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology

A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.

Phenomic Approaches and Tools for Phytopathologists

Plant phenomics approaches aim to measure traits such as growth, performance, and composition of plants using a suite of noninvasive technologies. The goal is to link phenotypic traits to the genetic information for particular genotypes, thus creating the bridge between the phenome and genome. Application of sensing technologies for detecting specific phenotypic reactions occurring during plant-pathogen interaction offers new opportunities for elucidating the physiological mechanisms that link pathogen infection and disease symptoms in the host, and also provides a faster approach in the selection of genetic material that is resistant to specific pathogens or strains. Appropriate phenomics methods and tools may also allow presymptomatic detection of disease-related changes in plants or to identify changes that are not visually apparent. This review focuses on the use of sensor-based phenomics tools in plant pathology such as those related to digital imaging, chlorophyll fluorescence imaging, spectral imaging, and thermal imaging. A brief introduction is provided for less used approaches like magnetic resonance, soft x-ray imaging, ultrasound, and detection of volatile compounds. We hope that this concise review will stimulate further development and use of tools for automatic, nondestructive, and high-throughput phenotyping of plant-pathogen interaction.

Bacterial disease management: challenges, experience, innovation and future prospects: Challenges in Bacterial Molecular Plant Pathology

Plant diseases caused by bacterial pathogens place major constraints on crop production and cause significant annual losses on a global scale. The attainment of consistent effective management of these diseases can be extremely difficult, and management potential is often affected by grower reliance on highly disease-susceptible cultivars because of consumer preferences, and by environmental conditions favouring pathogen development. New and emerging bacterial disease problems (e.g. zebra chip of potato) and established problems in new geographical regions (e.g. bacterial canker of kiwifruit in New Zealand) grab the headlines, but the list of bacterial disease problems with few effective management options is long. The ever-increasing global human population requires the continued stable production of a safe food supply with greater yields because of the shrinking areas of arable land. One major facet in the maintenance of the sustainability of crop production systems with predictable yields involves the identification and deployment of sustainable disease management solutions for bacterial diseases. In addition, the identification of novel management tactics has also come to the fore because of the increasing evolution of resistance to existing bactericides. A number of central research foci, involving basic research to identify critical pathogen targets for control, novel methodologies and methods of delivery, are emerging that will provide a strong basis for bacterial disease management into the future. Near-term solutions are desperately needed. Are there replacement materials for existing bactericides that can provide effective disease management under field conditions? Experience should inform the future. With prior knowledge of bactericide resistance issues evolving in pathogens, how will this affect the deployment of newer compounds and biological controls? Knowledge is critical. A comprehensive understanding of bacterial pathosystems is required to not only identify optimal targets in the pathogens, but also optimal seasonal timings for deployment. Host resistance to effectors must be exploited, carefully and correctly. Are there other candidate genes that could be targeted in transgenic approaches? How can new technologies (CRISPR, TALEN, etc.) be most effectively used to add sustainable disease resistance to existing commercially desirable plant cultivars? We need an insider's perspective on the management of systemic pathogens. In addition to host resistance or reduced sensitivity, are there other methods that can be used to target these pathogen groups? Biological systems are variable. Can biological control strategies be improved for bacterial disease management and be made more predictable in function? The answers to the research foci outlined above are not all available, as will become apparent in this article, but we are heading in the right direction. In this article, we summarize the contributions from past experiences in bacterial disease management, and also describe how advances in bacterial genetics, genomics and host-pathogen interactions are informing novel strategies in virulence inhibition and in host resistance. We also outline potential innovations that could be exploited as the pressures to maximize a safe and productive food supply continue to become more numerous and more complex.

Bacterial pathogenesis of plants: future challenges from a microbial perspective: Challenges in Bacterial Molecular Plant Pathology

Plant infection is a complicated process. On encountering a plant, pathogenic microorganisms must first adapt to life on the epiphytic surface, and survive long enough to initiate an infection. Responsiveness to the environment is critical throughout infection, with intracellular and community-level signal transduction pathways integrating environmental signals and triggering appropriate responses in the bacterial population. Ultimately, phytopathogens must migrate from the epiphytic surface into the plant tissue using motility and chemotaxis pathways. This migration is coupled with overcoming the physical and chemical barriers to entry into the plant apoplast. Once inside the plant, bacteria use an array of secretion systems to release phytotoxins and protein effectors that fulfil diverse pathogenic functions (Fig. ) (Melotto and Kunkel, ; Phan Tran et al., ). As our understanding of the pathways and mechanisms underpinning plant pathogenicity increases, a number of central research challenges are emerging that will profoundly shape the direction of research in the future. We need to understand the bacterial phenotypes that promote epiphytic survival and surface adaptation in pathogenic bacteria. How do these pathways function in the context of the plant-associated microbiome, and what impact does this complex microbial community have on the onset and severity of plant infections? The huge importance of bacterial signal transduction to every stage of plant infection is becoming increasingly clear. However, there is a great deal to learn about how these signalling pathways function in phytopathogenic bacteria, and the contribution they make to various aspects of plant pathogenicity. We are increasingly able to explore the structural and functional diversity of small-molecule natural products from plant pathogens. We need to acquire a much better understanding of the production, deployment, functional redundancy and physiological roles of these molecules. Type III secretion systems (T3SSs) are important and well-studied contributors to bacterial disease. Several key unanswered questions will shape future investigations of these systems. We need to define the mechanism of hierarchical and temporal control of effector secretion. For successful infection, effectors need to interact with host components to exert their function. Advanced biochemical, proteomic and cell biological techniques will enable us to study the function of effectors inside the host cell in more detail and on a broader scale. Population genomics analyses provide insight into evolutionary adaptation processes of phytopathogens. The determination of the diversity and distribution of type III effectors (T3Es) and other virulence genes within and across pathogenic species, pathovars and strains will allow us to understand how pathogens adapt to specific hosts, the evolutionary pathways available to them, and the possible future directions of the evolutionary arms race between effectors and molecular plant targets. Although pathogenic bacteria employ a host of different virulence and proliferation strategies, as a result of the space constraints, this review focuses mainly on the hemibiotrophic pathogens. We discuss the process of plant infection from the perspective of these important phytopathogens, and highlight new approaches to address the outstanding challenges in this important and fast-moving field.

The Ebb and Flow of Airborne Pathogens: Monitoring and Use in Disease Management Decisions

Perhaps the earliest form of monitoring the regional spread of plant disease was a group of growers gathering together at the market and discussing what they see in their crops. This type of reporting continues to this day through regional extension blogs, by crop consultants and more formal scouting of sentential plots in the IPM PIPE network (http://www.ipmpipe.org/). As our knowledge of plant disease epidemiology has increased, we have also increased our ability to detect and monitor the presence of pathogens and use this information to make management decisions in commercial production systems. The advent of phylogenetics, next-generation sequencing, and nucleic acid amplification technologies has allowed for development of sensitive and accurate assays for pathogen inoculum detection and quantification. The application of these tools is beginning to change how we manage diseases with airborne inoculum by allowing for the detection of pathogen movement instead of assuming it and by targeting management strategies to the early phases of the epidemic development when there is the greatest opportunity to reduce the rate of disease development. While there are numerous advantages to using data on inoculum presence to aid management decisions, there are limitations in what the data represent that are often unrecognized. In addition, our understanding of where and how to effectively monitor airborne inoculum is limited. There is a strong need to improve our knowledge of the mechanisms that influence inoculum dispersion across scales as particles move from leaf to leaf, and everything in between.

Transmission and Propagation of 'Candidatus Liberibacter asiaticus' by Grafting with Individual Citrus Leaves

Huanglongbing (HLB) is a chronic, progressive decline disease in citrus associated with a systemic infection by the bacterium 'Candidatus Liberibacter asiaticus'. Transmission of the bacterium in the field is by the Asian citrus psyllid, Diaphorina citri Kuwayama. Experimental propagation of 'Ca. L. asiaticus' is done primarily by grafting pieces of bud wood from an infected plant. To produce a small-scale model system for investigation of pathogen biology, we investigated grafting single leaves from infected citrus plants as sources of inoculum for propagation of the bacterium. In total, 162 plants ranging in age from 3 to 18 months were grafted. Grafting with intact asymptomatic and HLB-symptomatic leaves resulted in 61 of 78 (78%) and 35 of 41 (85%) of the plants infected with 'Ca. L. asiaticus', respectively. Inoculum consisting of the leaf petiole only or only an inoculum tissue remnant under the bark of the receptor tree resulted in 6 of 12 (50%) and 7 of 31 (23%) infected trees, respectively. Real-time polymerase chain reaction (qPCR) assays verified the infection in plants, a majority of which developed the foliar blotchy mottle symptom considered diagnostic for HLB, while some plants also displayed the stunted, chlorotic shoots for which the disease is named. The qPCR data together with the symptoms displayed demonstrated that individual leaves from infected trees can serve as effective inoculum sources for transmission and propagation of 'Ca. L. asiaticus' via grafting.

Powerful qPCR assays for the early detection of latent invaders: interdisciplinary approaches in clinical cancer research and plant pathology

Latent invaders represent the first step of disease before symptoms occur in the host. Based on recent findings, tumors are considered to be ecosystems in which cancer cells act as invasive species that interact with the native host cell species. Analogously, in plants latent fungal pathogens coevolve within symptomless host tissues. For these reasons, similar detection approaches can be used for an early diagnosis of the invasion process in both plants and humans to prevent or reduce the spread of the disease. Molecular tools based on the evaluation of nucleic acids have been developed for the specific, rapid, and early detection of human diseases. During the last decades, these techniques to assess and quantify the proliferation of latent invaders in host cells have been transferred from the medical field to different areas of scientific research, such as plant pathology. An improvement in molecular biology protocols (especially referring to qPCR assays) specifically designed and optimized for detection in host plants is therefore advisable. This work is a cross-disciplinary review discussing the use of a methodological approach that is employed within both medical and plant sciences. It provides an overview of the principal qPCR tools for the detection of latent invaders, focusing on comparisons between clinical cancer research and plant pathology, and recent advances in the early detection of latent invaders to improve prevention and control strategies.

Does the P Value Have a Future in Plant Pathology?

The P value (significance level) is possibly the mostly widely used, and also misused, quantity in data analysis. P has been heavily criticized on philosophical and theoretical grounds, especially from a Bayesian perspective. In contrast, a properly interpreted P has been strongly defended as a measure of evidence against the null hypothesis, H0. We discuss the meaning of P and null-hypothesis statistical testing, and present some key arguments concerning their use. P is the probability of observing data as extreme as, or more extreme than, the data actually observed, conditional on H0 being true. However, P is often mistakenly equated with the posterior probability that H0 is true conditional on the data, which can lead to exaggerated claims about the effect of a treatment, experimental factor or interaction. Fortunately, a lower bound for the posterior probability of H0 can be approximated using P and the prior probability that H0 is true. When one is completely uncertain about the truth of H0 before an experiment (i.e., when the prior probability of H0 is 0.5), the posterior probability of H0 is much higher than P, which means that one needs P values lower than typically accepted for statistical significance (e.g., P = 0.05) for strong evidence against H0. When properly interpreted, we support the continued use of P as one component of a data analysis that emphasizes data visualization and estimation of effect sizes (treatment effects).

Cyclic Lipopeptide Biosynthetic Genes and Products, and Inhibitory Activity of Plant-Associated Bacillus against Phytopathogenic Bacteria

The antibacterial activity against bacterial plant pathogens and its relationships with the presence of the cyclic lipopeptide (cLP) biosynthetic genes ituC (iturin), bmyB (bacillomycin), fenD (fengycin) and srfAA (surfactin), and their corresponding antimicrobial peptide products have been studied in a collection of 64 strains of Bacillus spp. isolated from plant environments. The most frequent antimicrobial peptide (AMP) genes were bmyB, srfAA and fenD (34-50% of isolates). Most isolates (98.4%) produced surfactin isoforms, 90.6% iturins and 79.7% fengycins. The antibacterial activity was very frequent and generally intense among the collection of strains because 75% of the isolates were active against at least 6 of the 8 bacterial plant pathogens tested. Hierarchical and correspondence analysis confirmed the presence of two clearly differentiated groups. One group consisted of Bacillus strains that showed a strong antibacterial activity, presented several cLPs genes and produced several isoforms of cLPs simultaneously, mainly composed of B. subtilis and B. amyloliquefaciens, although the last one was exclusive to this group. Another group was characterized by strains with very low or none antibacterial activity, that showed one or none of the cLP genes and produced a few or none of the corresponding cLPs, and was the most heterogenous group including B. subtilis, B. licheniformis, B. megaterium, B. pumilus, B. cereus and B. thuringiensis, although the last two were exclusive to this group. This work demonstrated that the antagonistic capacity of plant-associated Bacillus against plant pathogenic bacteria is related to the presence of cLP genes and to the production of the corresponding cLPs, and it is mainly associated to the species B. subtilis and B. amyloliquefaciens. Our findings would help to increase the yield and efficiency of screening methods to obtain candidate strains to biocontrol agents with a mechanism of action relaying on the production of antimicrobial cLPs.

Identifying and naming plant-pathogenic fungi: past, present, and future

Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk. Our understanding of fungal biodiversity and fungal systematics has undergone an exponential leap, incorporating genomics, web-based systems, and DNA data for rapid identification to link species to metadata. The impact of our ability to recognize hitherto unknown organisms on plant pathology and trade is enormous and continues to grow. Major challenges for phytomycology are intertwined with the Genera of Fungi project, which adds DNA barcodes to known biodiversity and corrects the application of old, established names via epi- or neotypification. Implementing the one fungus-one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication of names of plant pathogens will rest.

Hitchhiker's guide to multi-dimensional plant pathology

Filamentous pathogens pose a substantial threat to global food security. One central question in plant pathology is how pathogens cause infection and manage to evade or suppress plant immunity to promote disease. With many technological advances over the past decade, including DNA sequencing technology, an array of new tools has become embedded within the toolbox of next-generation plant pathologists. By employing a multidisciplinary approach plant pathologists can fully leverage these technical advances to answer key questions in plant pathology, aimed at achieving global food security. This review discusses the impact of: cell biology and genetics on progressing our understanding of infection structure formation on the leaf surface; biochemical and molecular analysis to study how pathogens subdue plant immunity and manipulate plant processes through effectors; genomics and DNA sequencing technologies on all areas of plant pathology; and new forms of collaboration on accelerating exploitation of big data. As we embark on the next phase in plant pathology, the integration of systems biology promises to provide a holistic perspective of plant–pathogen interactions from big data and only once we fully appreciate these complexities can we design truly sustainable solutions to preserve our resources.

Anti-inflammatory activity of animal oils from the Peruvian Amazon

ETHNOPHARMACOLOGICAL RELEVANCE

Animal oils and fats from the fishes Electrophorus electricus and Potamotrygon motoro, the reptiles Boa constrictor, Chelonoidis denticulata (Geochelone denticulata) and Melanosuchus niger and the riverine dolphin Inia geoffrensis are used as anti-inflammatory agents in the Peruvian Amazon. The aim of the study was to assess the topic anti-inflammatory effect of the oils/fats as well as to evaluate its antimicrobial activity and fatty acid composition.

MATERIALS AND METHODS

The oils/fats were purchased from a traditional store at the Iquitos market of Belen, Peru. The topic anti-inflammatory effect was evaluated by the mice ear edema induced by arachidonic acid (AA) and 12-O-tetradecanoylphorbol-13-acetate (TPA) at the dose of 3mg oil/ear. Indomethacine and nimesulide were used as reference anti-inflammatory drugs. The application resembles the traditional topical use of the oils. The antimicrobial effect of the oils/fats was assessed by the microdilution test against reference strains of Escherichia coli, Staphylococcus aureus and Salmonella enteritidis. The fatty acid composition of the oils/fats (as methyl esters) was determined by GC and GC-MS analysis after saponification.

RESULTS

All oils/fats showed topic anti-inflammatory activity, with better effect in the TPA-induced mice ear edema assay. The most active drugs were Potamotrygon motoro, Melanosuchus niger and Geochelone denticulata. In the AA-induced assay, the best activity was found for Potamotrygon motoro and Electrophorus electricus oil. The oil of Electrophorus electricus also showed a weak antimicrobial effect with MIC values of 250 µg/mL against Escherichia coli ATCC 25922 and Salmonella enteritidis-MI. The main fatty acids in the oils were oleic, palmitic and linoleic acids.

CONCLUSIONS

Topical application of all the oils/fats investigated showed anti-inflammatory activity in the mice ear edema assay. The effect can be related with the identity and composition of the fatty acids in the samples. This study gives support to the traditional use of animal oils/fats as ant-inflammatory agents in the Peruvian Amazon. However, new alternative should be encouraged due to the conservation status of several of the animal sources of the crude drugs.