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BACKGROUND: Coffee (Coffea arabica L.) is one of the most important commodities today, with a high economic value worldwide. Coffee leaf rust (Hemileia vastatrix Berk. et Br.) has been showing a high impact on Brazilian coffee trees among the various diseases that attack coffee. The climate has a great influence on the development of diseases, especially when fungi are the causal agents. This study aimed to carry out the zoning of climate favorability for coffee leaf rust in the traditional and main coffee‐producing regions of Brazil. The study was conducted in 13 locations in the states of Paraná, São Paulo, Rio de Janeiro, Espírito Santo, Minas Gerais, Goiás and Bahia. Air temperature and daily precipitation data for the current scenario were collected using the WorldClim version 2.1 platform for the last climatological normal and future climate change data. The ideal climate conditions for coffee leaf rust consist of a mean air temperature ranging from 21 to 25 °C and precipitation >30 mm per month. The Coupled Model Intercomparison Projects scenarios associated with the Intergovernmental Panel on Climate Change reports consisted of the Shared Socio‐Economic Pathways SSP‐1 2.6, SSP‐2 4.5, SSP‐3 7.0 and SSP‐5 8.5, the latter being considered one of the most catastrophic. All steps to carry out the suitability zoning were performed in a tool using the QGIS geographic information system software. RESULTS: Zoning for coffee leaf rust had three classes: favorable, relatively favorable and unfavorable. Currently, the largest coffee‐producing region in Brazil has 49.1% of its analyzed area classified as favorable, 39.2% as relatively favorable and 11.7% as unfavorable. In the current scenario, Patrocínio and Três Pontas are locations with high coffee production in which the favorable class is predominant. The state of Minas Gerais has an annual mean of 55.3% of its entire territory apt for the disease, with the highest occurrence between September and March. CONCLUSIONS: Climate change has a negative impact on the development of coffee leaf rust, mainly in the long term, as in the period of 2081–2100, in which the SSP‐5 8.5 scenario led to a decrease in the favorable and unfavorable areas and an increase in the relatively favorable areas of 9.8%, 18.6% and 71.5% for the Brazilian territory, respectively. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Summary: Ten years ago, (black) stem rust – the most damaging of wheat (Triticum aestivum) rusts – re‐emerged in western Europe. Disease incidences have since increased in scale and frequency. Here, we investigated the likely underlying causes and used those to propose urgently needed mitigating actions. We report that the first large‐scale UK outbreak of the wheat stem rust fungus, Puccinia graminis f. sp. tritici (Pgt), in 2022 may have been caused by timely arrival of airborne urediniospores from southwest Europe. The drive towards later‐maturing wheat varieties in the UK may be exacerbating Pgt incidences, which could have disastrous consequences. Indeed, infection assays showed that two UK Pgt isolates from 2022 could infect over 96% of current UK wheat varieties. We determined that the temperature response data in current disease risk simulation models are outdated. Analysis of germination rates for three current UK Pgt isolates showed substantial variation in temperature response functions, suggesting that the accuracy of disease risk simulations would be substantially enhanced by incorporating data from prevailing Pgt isolates. As Pgt incidences continue to accelerate in western Europe, we advocate for urgent action to curtail Pgt losses and help safeguard future wheat production across the region. [ABSTRACT FROM AUTHOR]

The anther‐smut host–pathogen system has provided extensive insights into the evolutionary ecology of disease resistance, transmission modes, host shifts, pathogen specialization, and disease evolution in metapopulations. It also has led to unexpected insights into sex ratio distorters, sex chromosome evolution, and transposable elements in fungi. In addition, anther‐smut disease played a major role in Linnaeus' germ theory and the correspondence on parasitic castration between Darwin and Becker, one of the first female botanists. Here, we explicitly highlight some of the realities in the process of science, using an unusual autobiographical approach to describe how we came to collaborate on this system in the 1980s. Using perspectives from our different career stages, we present a surprising narrative that could not be deduced from merely reading the published papers. While our work was grounded in previous ecological and evolutionary theory, it was the product as much of empirical failures and intellectual roadblocks, as the result of a progressive scientific method. Our experiences illustrate not only the "human dimension of science" but more importantly show that linear sequences of hypothesis testing do not necessarily lead to new study systems and new ideas. We suggest there is a need to re‐evaluate the scientific method in ecology and evolution, especially where the challenge is to engage in a productive dialog between natural history and theory. [ABSTRACT FROM AUTHOR]

Plant pathogens can decimate crops and render the local cultivation of a species unprofitable. In extreme cases this has caused famine and economic collapse. Timing is vital in treating crop diseases, and the use of computer vision for precise disease detection and timing of pesticide application is gaining popularity. Computer vision can reduce labour costs, prevent misdiagnosis of disease, and prevent misapplication of pesticides. Pesticide misapplication is both financially costly and can exacerbate pesticide resistance and pollution. Here, we review the application and development of computer vision and machine learning methods for the detection of plant disease. This review goes beyond the scope of previous works to discuss important technical concepts and considerations when applying computer vision to plant pathology. We present new case studies on adapting standard computer vision methods and review techniques for acquiring training data, the use of diagnostic tools from biology, and the inspection of informative features. In addition to an in‐depth discussion of convolutional neural networks (CNNs) and transformers, we also highlight the strengths of methods such as support vector machines and evolved neural networks. We discuss the benefits of carefully curating training data and consider situations where less computationally expensive techniques are advantageous. This includes a comparison of popular model architectures and a guide to their implementation. [ABSTRACT FROM AUTHOR]

Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI‐resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, shortly after the introduction of SDHIs. Two primary mutations in the SDH complex (SdhB‐H278Y and SdhC‐H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. For this project, we performed whole‐genome sequencing for 48 A. solani isolates from potato fields across Europe to better characterize the pathogen's genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. The isolates can be grouped into seven genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. We found clear evidence for recombination on the genome, and the observed admixtures might indicate a higher adaptive potential of the fungus than previously thought. Yet, we cannot link the observed recombination events to different Sdh mutations. The same Sdh mutations appear in different, non‐admixed genetic backgrounds; therefore, we conclude they arose independently. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes, apparent admixture in the populations, and evidence for recombination indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds. [ABSTRACT FROM AUTHOR]

The genus Colletotrichum comprises an important and diverse group of endophytes, saprophytes and plant pathogens, many of which cause a syndrome known as anthracnose, on a wide range of hosts, mainly in tropical and subtropical regions. Since most of the accumulated research on the genus focuses on cultivated plants of commercial interest, the aim of this review was to explore how the genus has been studied in native woody plants in natural ecosystems. Following the PRISMA protocol for systematic reviews, we identified 52 original scientific publications that recorded Colletotrichum species associated with native woody hosts in natural environments in a taxonomic, ecological or phytosanitary context. Here, we conclude that research in natural ecosystems is scarce, mostly carried out in tropical areas and mainly focused on aspects of community ecology. We also observed the cosmopolitan nature of the genus, associated with many hosts, mostly as endophytes. The species most frequently recorded were in the 'gloeosporioides' complex, although due to the limitations in identification methods used in the studies, a large proportion of records could not be identified or verified at the species level. [ABSTRACT FROM AUTHOR]

The global sustainability agenda is increasing the demand for reduction in inputs into agricultural production while maintaining profitable yield of quality products. Plant diseases are a major constraint for both yield and product quality, but often tools for their control are ineffective or lacking. Biological control using antagonistic microorganisms has long been a subject of research resulting in a wide range of products that are now available and marketed in specific territories around the world. These preparations are often niche products with narrow uses. The research effort is intense both to develop new biological control agents (BCAs) and to obtain knowledge of the mechanisms underlying biological disease control. The prospects for biological control are promising. As a minimum, BCAs supplement other sustainable disease management practices such as disease resistance, and present opportunities for controlling diseases for which other approaches are ineffective or unavailable. We can realistically expect increasing use of BCAs to control crop diseases in ways that will benefit the environment. This review paper arose from a webinar held by the British Society for Plant Pathology as part of the International Year of Plant Heath (IYPH2020), at which many of the 300 participants posed or discussed interesting questions. This review is based on that input and the panel members at the webinar are all included as co‐authors in this review. [ABSTRACT FROM AUTHOR]

Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), occurs in most wheat‐growing areas worldwide, and, in western Europe since 2013, has started to re‐emerge after many decades of absence. Following this trend across western Europe, in 2020, we also detected and recorded wheat stem rust for the first time in five decades in experimental plots across five locations in Ireland. To examine the potential origin of the Irish Pgt infection in 2020, we carried out transcriptome sequencing on 12 Pgt‐infected wheat samples collected across Ireland and compared these to 76 global P. graminis isolates. This analysis identified a close genetic relationship between the Irish Pgt isolates and those from Ethiopia collected in 2015 after a severe stem rust epidemic caused by the TKTTF Pgt race, and with the UK‐01 Pgt isolate that was previously assigned to the TKTTF race. Subsequent pathology‐based race profiling designated two Irish isolates and recent UK and French Pgt isolates to the TKTTF Pgt race group. This suggests that the Irish Pgt occurrence most probably originated from recent long‐distance windborne dispersal of Pgt urediniospores from neighbouring countries in Europe where we confirmed the Pgt TKTTF race continues to be prevalent. The identification of wheat stem rust in Ireland at multiple locations in 2020 illustrates that the disease can occur in Ireland and emphasizes the need to re‐initiate local monitoring for this re‐emergent threat to wheat production across western Europe. [ABSTRACT FROM AUTHOR]

Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), occurs in all major wheat‐growing regions worldwide and poses a constant threat to production. In South Africa, Pst first emerged in 1996 in the Western Cape and has since caused frequent epidemics with three further distinct races (pathotypes) recorded to date. Herein, we undertook detailed genomic‐based analyses of four Pst isolates that represent the four dominant Pst races in South Africa recorded between 1996 and 2005. This analysis identified a number of polymorphic genes with features of known effector proteins and provided additional support of the likely stepwise changes in virulence profile of these South African Pst isolates. Next, we carried out comparative genomic‐based analyses with 54 additional Pst isolates collected across wheat‐growing regions within South Africa between 1996 and 2017 and 58 Pst isolates from East Africa, Pakistan, the UK, and France. This revealed a close genetic relationship between Pst isolates in South Africa and a number from East Africa. Furthermore, we found the South African Pst isolates also grouped closely with isolates identified in the UK in 2013 that were specifically found on triticale, illustrating long‐distance transmission of Pst isolates either between these regions or from a common independent source area. This highlights the critical need for close monitoring of Pst. With wheat being the most planted winter cereal crop in South Africa, investment in continuous surveillance is essential to rapidly identify any future introductions that could quickly lead to rust epidemics. [ABSTRACT FROM AUTHOR]

The evolution of resistance has been seen across all major classes of xenobiotics, including antimicrobial drugs and agricultural pesticides. This repeated emergence of resistance is a case of phenotypic parallel evolution, but often the parallelism extends to the molecular level too, with multiple species gaining the same mutation in response to the same chemical treatment. We review the degree of repeatability in target‐site resistance mutations affecting different classes of site‐specific agricultural fungicides used in crop protection, comparing the extent to which resistance in different pathogen species has evolved via the same or different mutations. For all major fungicide target sites, substantial levels of molecular parallel evolution can be seen, with at least one mutation recurring in over 50% of species. Target‐site mutations appear to be most repeatable in cytochrome b, target site of quinone‐outside inhibitor fungicides, and least predictable for CYP51, target site of the azoles. Intermediate levels of repeatability are seen for the MBC target site β‐tubulin, and the SDHI target site succinate dehydrogenase. Repeatability may be lower where there are selective trade‐offs between resistance and pleiotropic fitness penalties, or differing levels of cross‐resistance across members of a fungicide class; or where single mutations confer only partial resistance, and epistatic interactions between multiple mutations result in a rugged fitness landscape. This affects the predictive power of in vitro mutation studies, and has practical implications for resistance monitoring strategies and diagnostic methods. [ABSTRACT FROM AUTHOR]

Cultivation of cannabis plants (Cannabis sativa L., marijuana) has taken place worldwide for centuries. In Canada, legalization of cannabis in October 2018 for the medicinal and recreational markets has spurned interest in large‐scale growing. This increased production has seen a rise in the incidence and severity of plant pathogens, causing a range of previously unreported diseases. The objective of this review is to highlight the important diseases currently affecting the cannabis and hemp industries in North America and to discuss various mitigation strategies. Progress in molecular diagnostics for pathogen identification and determining inoculum sources and methods of pathogen spread have provided useful insights. Sustainable disease management approaches include establishing clean planting stock, modifying environmental conditions to reduce pathogen development, implementing sanitation measures, and applying fungal and bacterial biological control agents. Fungicides are not currently registered for use and hence there are no published data on their efficacy. The greatest challenge remains in reducing microbial loads (colony‐forming units) on harvested inflorescences (buds). Contaminating microbes may be introduced during the cultivation and postharvest phases, or constitute resident endophytes. Failure to achieve a minimum threshold of microbes deemed to be safe for utilization of cannabis products can arise from conventional and organic cultivation methods, or following applications of beneficial biocontrol agents. The current regulatory process for approval of cannabis products presents a challenge to producers utilizing biological control agents for disease management. © 2021 The Author. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

BACKGROUND: Reliance on fungicides to manage disease creates selection pressure for the evolution of resistance in fungal and oomycete pathogens. Rust fungi (Pucciniales) are major pathogens of cereals and other crops and have been classified as low‐risk for developing resistance to fungicides; no case of field failure of fungicides in a cereal rust disease has yet been recorded. Recently, the Asian soybean rust pathogen, Phakopsora pachyrhizi evolved resistance to several fungicide classes, prompting us to screen a large sample of the globally widespread wheat yellow rust pathogen, Puccinia striiformis f. sp. tritici (Pst), for mutations associated with fungicide resistance. RESULTS: We evaluated 363 Pst isolates from Europe, the USA, Ethiopia, Chile, China and New Zealand for mutations in the target genes of demethylase inhibitor (DMI; Cyp51) and succinate dehydrogenase inhibitor (SDHI; SdhB, SdhC and SdhD) fungicides. A high proportion of Pst isolates carrying a Y134F DMI resistance‐associated substitution in the Cyp51 gene was found among those from China and New Zealand. A set of geographically diverse Pst isolates was also found to display a substitution in SdhC (I85V) that is homologous to that reported recently in P. pachyrhizi and linked to SDHI resistance. CONCLUSION: The identification of resistance‐associated alleles confirms that cereal rusts are not immune to fungicide resistance and that selection for resistance evolution is operating at high levels in certain locations. It highlights the need to adopt fungicide resistance management practices and to monitor cereal rust species for development of resistance. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Gray mold disease caused by the fungus Botrytis cinerea damages many crop hosts worldwide and is responsible for heavy economic losses. Early diagnosis and detection of the disease would allow for more effective crop management practices to prevent outbreaks in field or greenhouse settings. Furthermore, having a simple, non‐invasive way to quantify the extent of gray mold disease is important for plant pathologists interested in measuring infection rates. In this paper, we design and build a bispectral imaging system for discriminating between leaf regions infected with gray mold and those that remain unharmed on a lettuce (Lactuca spp.) host. First, we describe a method to select two optimal (high contrast) spectral bands from continuous hyperspectral imagery (450–800 nm). We then explain the process of building a system based on these two spectral bands, located at 540 and 670 nm. The resultant system uses two cameras, with a narrow band‐pass spectral filter mounted on each, to measure the bispectral reflectance of a lettuce leaf. The two resulting images are combined using a normalized difference calculation that produces a single image with high contrast between the leaves' infected and healthy regions. A classifier was then created based on the thresholding of single pixel values. We demonstrate that this simple classification produces a true‐positive rate of 95.25% with a false‐positive rate of 9.316% in laboratory conditions. [ABSTRACT FROM AUTHOR]

Since 1927, outbreaks of the leafy gall disease caused by Rhodococcus fascians on annual and perennial herbaceous plants have put the ornamental plant industry at risk. More recently, Pistachio Bushy top syndrome (PBTS), a serious disease emerging in the Western United States, has been declared as a natural disaster by the U.S. Department of Agriculture. Recent developments indicate that the taxonomic position of R. fascians should be re‐evaluated and circumscribed from other members of the genus. Due to the broad host range of this bacterium, economically important crops are in a vulnerable position especially with new members within the genus becoming able to interact synergistically with R. fascians to cause symptom development. The virulence strategies employed by R. fascians and the involvement of cytokinins (CKs) in its pathogenicity have been the subject of much controversy in the last years. Additionally, the detection of virulent strains of R. fascians from symptomatic tissues has been problematic for many researchers. This review focuses on plant–pathogen interaction in context with more recent findings on the association of CKs in virulence of R. fascians. Current knowledge on the worldwide distribution of the pathogen, a historical recap of its discovery and the economic impact of the disease caused by R. fascians are also described here. [ABSTRACT FROM AUTHOR]

Downy mildew, caused by the Oomycete Plasmopara viticola, is one of the most important diseases affecting the Eurasian grapevine, Vitis vinifera. The pathogen originated in Northern America and its presence was signalled for the first time into Europe in 1878. In this study, the genetic variability and structure of Italian P. viticola population was investigated by genotyping 106 P. viticola strains belonging to 12 different regions, at 31 microsatellite markers. As a result of the high percentage of missing data, 96 strains and 19 loci were retained for the data analysis. The overall Italian population presents absence of clones, evidence of sexual and asexual reproduction and a low genetic diversity, as expected for an introduced pathogen, but a slightly higher genetic diversity than that found in other European populations, based on allelic diversity at the investigated microsatellite loci. Out of 19 loci, half shows deviation from Hardy–Weinberg equilibrium and, indeed, structure analysis indicates the presence of two separate genetic clusters, with little but significantly different distribution according to geography (west–east gradient) and climatic conditions. Overall, the analysis of the P. viticola population, 140 years after its appearance in Italy, provides indication on the pathogen adaptability. This should be taken into consideration in the future for preserving the durability of disease resistant varieties in open field. In this view, all the disease control methods available should be integrated in order to reduce the selection of pathogen strains able to overcome plant resistance. [ABSTRACT FROM AUTHOR]

Summary: In recent years, the number of emergent plant pathogens (EPPs) has grown substantially, threatening agroecosystem stability and native biodiversity. Contributing factors include, among others, shifts in biogeography, with EPP spread facilitated by the global unification of monocultures in modern agriculture, high volumes of trade in plants and plant products and an increase in sexual recombination within pathogen populations. The unpredictable nature of EPPs as they move into new territories is a situation that has led to sudden and widespread epidemics. Understanding the underlying causes of pathogen emergence is key to managing the impact of EPPs. Here, we review some factors specifically influencing the emergence of oomycete and fungal EPPs, including new introductions through anthropogenic movement, natural dispersal and weather events, as well as genetic factors linked to shifts in host range. [ABSTRACT FROM AUTHOR]

Tree declines have been recorded across forests and woodlands on most continents, causing tree mortality over thousands of square kilometres, yet the impact of tree declines upon mammals have only rarely been quantified. Once the dominant tree over the western parts of the Swan Coastal Plain in Western Australia, tuart (Eucalyptus gomphocephala) forest has been reduced to less than a third of its former range through clearing for agriculture and urban development. Additionally, over the last 30 years, the remnant population has been heavily impacted by a decline that has an unknown cause, but is likely related to a root pathogen coupled with abiotic factors (reduced rainfall, increased salinity and elevated temperatures). Tuart decline is evident as marked canopy dieback, replacement with epicormic growth and increasing bare branches, while leaf litter is lost from the tree surrounds. We examined the effect of tuart decline and other vegetation measures upon bat activity using auditory monitoring. Vegetation structure was correlated with Vespertilionidae bat activity. Falsistrellus mackenziei were more likely to forage around healthy canopies (activity positively correlated with tuart crown density and negatively correlated with tuart crown dieback). By contrast, the other three taxa were more often encountered in declining rather than healthy tuart sites. Chalinolobus gouldii was positively associated with tuart crown dieback. Activity of Vespadelus regulus and Nyctophilus spp. (species not distinguishable from their calls) were significantly positively correlated with an open tall canopy (positively with cover of plants >10 m tall and negatively with overall canopy cover density). There were no vegetation measurements that were strong predictors of activity of two Molossidae species (Ozimops kitcheneri and Austronomus australis), which intercept insects above the forest canopy. This study clearly reveals different factors influencing the activity of bat taxa, which are likely related to where they feed and their manoeuvrability around tree canopies. [ABSTRACT FROM AUTHOR]

Accurate management practices in crop health and food safety are critical, especially regarding the detection of plant pathogens in the early stages of a disease. To date, specific, fast and sensitive technologies for point‐of‐care diagnosis and simple or grower‐friendly devices are very valuable, as no specialized staff are required for diagnosing a disease in the field. This is especially the case today, when factors such as climate change may cause the appearance of pathogens in areas where years ago they were unexpected. The aim of this research is to review some of the promising techniques that can be applied to in‐field molecular detection of plant pathogens and how these techniques can change the way farmers and pathologists are diagnosing plant diseases. Some of them, like loop‐mediated isothermal amplification and recombinase polymerase amplification, are already being successfully used for routine diagnosis. However, most technologies still need validation in the plant pathology field, where they have a promising future for in‐field diagnosis when combined with simple DNA extraction methods, reagent stabilization techniques and their integration into portable devices. [ABSTRACT FROM AUTHOR]

Fungal taxonomy and classification, and fungal identification tools, are increasingly based on DNA sequencing technologies. In contrast, many historical records of fungi are based on morphologically identified specimens. Scientific collections of specimens or living cultures provide a resource to enable these early records to be genetically validated using modern techniques. This project uses a set of cultures deposited prior to 2008 in the International Collection of Microorganisms from Plants ( ICMP) culture collection as Phoma, a genus of high biosecurity importance that is notoriously difficult to identify accurately using morphological characters. Of the 265 cultures sequenced, 23% had been misidentified. These misidentifications mean that six species previously thought to be present in New Zealand probably do not occur there. Fifty specimens had not previously been identified to species level; amongst these were eight species newly reported from New Zealand. Genetic validation projects such as this, using existing scientific collections, are essential for maintaining a robust global biosecurity system. [ABSTRACT FROM AUTHOR]

Togninia minima is the main fungal species associated with grapevine leaf stripe disease worldwide. This species is mainly known from its asexual state in nature; nevertheless, a biallelic heterothallic mating strategy has been confirmed for this species based on in vitro crossing studies. There are no data available on the incidence of an active sexual cycle within the populations of this species in many grapevine-producing countries as well as Iran. The possibility of a clandestine sexual cycle within the Iranian isolates of T. minima was evaluated by analysing the distribution and frequency of the mating-type alleles on a microspatial and a macrogeographical scales. Towards this aim, a total of 90 T. minima isolates were recovered from grapevines with esca disease from the vineyards in north and north-western Iran. A multiplex PCR method previously designed by authors was applied for simultaneous identification and determination of the mating-type alleles in T. minima populations. The results on the screening of mating-type alleles using multiplex PCR method revealed the mating-type identity of 77 isolates as Mat1-2 and 23 isolates as Mat1-1. Our results showed that both Mat1-1 and Mat1-2 isolates are present in a single vineyard and even on single vines. The distribution of mating-type alleles in the sampled area skewed from the 1 : 1 ratio (77 : 23); however, co-occurrence of both mating types in a single vineyard and even on single vines is suggestive for the presence of an active sexual cycle for T. minima in north-western Iran. [ABSTRACT FROM AUTHOR]

ABSTRACT Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases in rice worldwide. We aimed to develop an integrated approach for convenient collection, quantification and characterisation of M. oryzae spores (airborne inoculum) in the field. We developed an easy-to-use cyclone-based spore trap (the AirSampler) and a standard procedure for handling a small amount of airborne spores. Using a specific primer pair or a probe designed for the single-copy gene mif23, SYBR Green and TaqMan assays could quantify 10 and 4 copy numbers, respectively, of M. oryzae DNA. During 2012 and 2013, the AirSampler and SYBR Green quantitative real-time polymerase chain reaction were used to monitor temporal dynamics of M. oryzae spores in nursery fields of rice showing symptoms of blast disease. During four cropping seasons, the new techniques could detect M. oryzae spores before the appearance of rice blast symptoms. The amount of spores was low in the early season, then increased, with high fluctuations during the mid-season and decreased to low levels at the heading stage in the late season. To improve the handling and storage of spore samples, we tested the effect of different treatments on the preservation of spore DNA. DNA loss was reduced with samples protected from ultraviolet B radiation, suspended in CTAB buffer, kept at room temperature or 4°C and used for DNA extraction in 2 weeks. Finally, we demonstrated that the high resolution melting analysis could be used for rapid determination of A, D, A + D and C alleles of the avirulence gene pex31 ( Avr-Pik/kp/km) in M. oryzae. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Weather affects the severity of many plant diseases, and climate change is likely to alter the patterns of crop disease severity. Evaluating possible future patterns can help focus crop breeding and disease management research. We examined the global effect of climate change on potato late blight, the disease that caused the Irish potato famine and still is a common potato disease around the world. We used a metamodel and considered three global climate models for the A2 greenhouse gas emission scenario for three 20-year time-slices: 2000-2019, 2040-2059 and 2080-2099. In addition to global analyses, five regions were evaluated where potato is an important crop: the Andean Highlands, Indo-Gangetic Plain and Himalayan Highlands, Southeast Asian Highlands, Ethiopian Highlands, and Lake Kivu Highlands in Sub-Saharan Africa. We found that the average global risk of potato late blight increases initially, when compared with historic climate data, and then declines as planting dates shift to cooler seasons. Risk in the agro-ecosystems analyzed, varied from a large increase in risk in the Lake Kivu Highlands in Rwanda to decreases in the Southeast Asian Highlands of Indonesia. [ABSTRACT FROM AUTHOR]

Crop pests and pathogens pose a significant and growing threat to food security, but their geographical distributions are poorly understood. We present a global analysis of pest and pathogen distributions, to determine the roles of socioeconomic and biophysical factors in determining pest diversity, controlling for variation in observational capacity among countries., Known distributions of 1901 pests and pathogens were obtained from CABI. Linear models were used to partition the variation in pest species per country amongst predictors., Reported pest numbers increased with per capita gross domestic product ( GDP), research expenditure and research capacity, and the influence of economics was greater in micro-organisms than in arthropods. Total crop production and crop diversity were the strongest physical predictors of pest numbers per country, but trade and tourism were insignificant once other factors were controlled. Islands reported more pests than mainland countries, but no latitudinal gradient in species richness was evident., Country wealth is likely to be a strong indicator of observational capacity, not just trade flow, as has been interpreted in invasive species studies. If every country had US levels of per capita GDP, then 205 ± 9 additional pests per country would be reported, suggesting that enhanced investment in pest observations will reveal the hidden threat of crop pests and pathogens. [ABSTRACT FROM AUTHOR]

The article focuses on viroids and their relation to plant's lncRNA-directed regulatory networks. It states that viroids are sub-viral plant-pathogenic long noncoding RNAs that have a circular single-stranded molecule. It notes that viroid research could provide alternative concepts on lncRNA metabolism in plants.

The ubiquity, high diversity and often-cryptic manifestations of fungi and oomycetes frequently necessitate molecular tools for detecting and identifying them in the environment. In applications including DNA barcoding, pathogen detection from plant samples, and genotyping for population genetics and epidemiology, rapid and dependable DNA extraction methods scalable from one to hundreds of samples are desirable. We evaluated several rapid extraction methods ( Na OH, Rapid one-step extraction ( ROSE), Chelex 100, proteinase K) for their ability to obtain DNA of quantity and quality suitable for the following applications: PCR amplification of the multicopy barcoding locus ITS1/5.8 S/ ITS2 from various fungal cultures and sporocarps; single-copy microsatellite amplification from cultures of the phytopathogenic oomycete Phytophthora ramorum; probe-based P. ramorum detection from leaves. Several methods were effective for most of the applications, with Na OH extraction favored in terms of success rate, cost, speed and simplicity. Frozen dilutions of ROSE and Na OH extracts maintained PCR viability for over 32 months. DNA from rapid extractions performed poorly compared to CTAB/phenol-chloroform extracts for Taq Man diagnostics from tanoak leaves, suggesting that incomplete removal of PCR inhibitors is an issue for sensitive diagnostic procedures, especially from plants with recalcitrant leaf chemistry. Na OH extracts exhibited lower yield and size than CTAB/phenol-chloroform extracts; however, Na OH extraction facilitated obtaining clean sequence data from sporocarps contaminated by other fungi, perhaps due to dilution resulting from low DNA yield. We conclude that conventional extractions are often unnecessary for routine DNA sequencing or genotyping of fungi and oomycetes, and recommend simpler strategies where source materials and intended applications warrant such use. [ABSTRACT FROM AUTHOR]

Quarantined phytopathogens such as Pepino mosaic virus (PepMV) and Clavibacter michiganensis subsp. michiganensis can be introduced into tomato transplant houses and fields on infested seed and thereby cause significant economic losses. Hence, specific and sensitive seed health assays are required to exclude these organisms. Currently, separate assays must be conducted on seed samples for each pathogen, making the process time-consuming and expensive. One approach to improve the efficiency of seed health testing is multiplex real-time PCR; however, PCR can be inhibited by compounds co-extracted from seed tissues with nucleic acids. To address this concern, we explored the use of magnetic capture hybridization (MCH) to concentrate and purify target nucleic acids prior to real-time PCR. The combination of MCH with multiplex real-time PCR resulted in a 102-103-fold increase in detection sensitivity for both pathogens compared to DNA extraction and direct multiplex real-time PCR. The detection threshold observed for the MCH multiplex real-time PCR assay was a combination of 105 C. michiganensis subsp. michiganensis CFU/ml plus a 10−4-fold dilution of total RNA extracted from PepMV-infected tomato leaf tissue. These observations provide proof for the concept that MCH can facilitate the simultaneous detection of Clavibacter michiganensis subsp. michiganensis and PepMV by multiplex real-time PCR. [ABSTRACT FROM AUTHOR]

The article presents a study on the role of intraspecific genetic diversity on disease management of agricultural crops using the potato late blight in Peru. The study intends to develop a simple model pertaining to the effects of host diversity that can provide a better understanding on the effects of host diversity. It provides a comparison on the impact of host diversity on potato late blight diversity between the shorter and longer season region.

Arabidopsis thaliana is known to produce the phytoalexin camalexin in response to abiotic and biotic stress. Here we studied the mechanisms of tolerance to camalexin in the fungus Botrytis cinerea, a necrotrophic pathogen of A. thaliana. Exposure of B. cinerea to camalexin induces expression of BcatrB, an ABC transporter that functions in the efflux of fungitoxic compounds. B. cinerea inoculated on wild-type A. thaliana plants yields smaller lesions than on camalexin-deficient A. thaliana mutants. A B. cinerea strain lacking functional BcatrB is more sensitive to camalexin in vitro and less virulent on wild-type plants, but is still fully virulent on camalexin-deficient mutants. Pre-treatment of A. thaliana with UV-C leads to increased camalexin accumulation and substantial resistance to B. cinerea. UV-C-induced resistance was not seen in the camalexin-deficient mutants cyp79B2/B3, cyp71A13, pad3 or pad2, and was strongly reduced in ups1. Here we demonstrate that an ABC transporter is a virulence factor that increases tolerance of the pathogen towards a phytoalexin, and the complete restoration of virulence on host plants lacking this phytoalexin. [ABSTRACT FROM AUTHOR]

The article discusses the highlights of the International Conference on Biotic Plant Interactions (ICBPI) in Brisbane, Queensland in March 2008. Among the topics that were discussed at the conference were harmful biotic plant interactions and the interactions of plants with beneficial microbial communities. Several speakers at the conference claimed that identifying the defense mechanisms against pathogen and herbivore attack will reveal new insights into plant function.

A rapid spectroscopic approach for whole-organism fingerprinting of Fourier transform infrared (FT-IR) spectroscopy was used to analyse 16 isolates from five closely related species of Fusarium: F. graminearum, F. moniliforme, F. nivale, F. semitectum and F. oxysporum. Principal components analysis and hierarchical cluster analysis were used to study the clusters in the data. On visual inspection of the clusters from both methods, the spectra were not differentiated into five separate clusters corresponding to species and these unsupervised methods failed to identify these fungal strains. When the data were trained by back propagation algorithm of artificial neural networks (ANNs) with principal components scores of spectra used as input modes, the strains were accurately predicted and recognized. The results in this study show that FT-IR spectroscopy in combination with principal component artificial neural networks (PC-ANNs) is well suited for identifying Fusarium spp. It would be advantageous to establish a comprehensive database of taxonomically well-defined Fusarium species to aid the identification of unknown strains. [ABSTRACT FROM AUTHOR]

A real-time polymerase chain reaction (PCR) assay using a TaqMan® probe was developed to detect the causal agent of wilt and crown rot of basil from infected plants and seed in Italy. The aim of the study was to diminish testing time, previously performed using nested-PCR, and to create the conditions for future automation. The sensitivity of the assay was shown to be similar to the detection limit of the available nested-PCR procedure. The advantages of real-time PCR system include halving of the testing time, as well as the ability to identify both internally and externally infected seed to the sensitivity of 1 pg of genomic DNA. The assay was able to detect the presence of the pathogen in infected seed up to a sensitivity of 24 (SD: ± 10) CFU per 100 seeds. [ABSTRACT FROM AUTHOR]

Dutch elm disease is a phytopathogenic fungal disease transmitted bybark beetles, and it has eradicated elms from large parts of Europe and North America. I investigated phenotypic differences between diseased and healthy trees before and during infection, with special emphasis on measures of developmental instability of leaves (fluctuating asymmetry, frequency of phenodeviants) that may reflect adverse environmental and genetic conditions during foliar growth. I investigated whether stressed broad-leaved elm, Ulmus glabra, trees, as estimated from their leaf asymmetry and frequency of foliar phenodeviants, weremore susceptible to the disease than trees with less asymmetric leaves. Trees that became diseased had larger leaf asymmetry than the nearest healthy neighbouring tree before acquisition of the disease. Foliar asymmetry was also caused by the disease since the degree of asymmetry increased from the first to the second year of infection. The frequency of elm leaves with abnormal morphology increased considerably from trees that were healthy to those that became diseased and particularly to the second year of the infection. Furthermore, the relative frequency of foliar side veins that joined veins from the other half of the leaf at the central vein decreased from healthy trees over susceptible trees that became infected to diseased trees. These results suggest that measures of developmental instability of elm leaves reflected susceptibility to Dutch elm disease as well as the negative effects of the disease on phenotypic development. [ABSTRACT FROM AUTHOR]

Fifth leaves of the barley cultivar 'Osiris' with adult plant resistance against powdery mildew were inoculated with Erysiphe gramims f. sp. hordei. Samples were taken at 32 hours after inoculation for cytochemical treatments and electron microscopy. Deposition of gold-labelled wheat germ lectin was detected in the wall of the haustorial neck of the fungus and in an outer layer of a papilla, indicating the presence of oligomers of N-acetylglucosamine. Con A binding was detected mainly in a middle layer of a papilla, demonstrating the presence of a-bound glucose and/or mannose. Treatment with PA-TSH-SP revealed glycosubstances with vicinal hydroxyl groups present mainly in an outer layer of another type of papilla. Pretreatment with protease before PA-TSH-SP staining resulted in a positive Thiery reaction in spherical structures of a papilla, indicating that vicinal hydroxyl groups were exposed to staining after removal of protein from these structures. [ABSTRACT FROM AUTHOR]

Young leaves of two rose cultivars, one susceptible (rose Cardinal) and the other moderately resistant (rose Q. Elizabeth) to mildew infection, were either inoculated with Sphaerotheca pannosa or wounded with glass or metal needles. At different times after these treatments the presence of callose, lignin and phenolics in the infected or wounded cells was revealed by histochemical reactions. After either treatment no difference was found between the cultivars in the amount or earliness of deposition of callose or lignin, while phenolics were present in far larger amounts in the resistant cultivar. It is therefore suggested that one of the factors of rose resistance to powdery mildew might be the capacity to synthesize large amounts of phenolic compounds, also in view of the fact that the vacuoles of healthy epidermal cells are strongly electron opaque in rose Q. Elizabeth, while they are much more transparent in rose Cardinal. [ABSTRACT FROM AUTHOR]

In leaves of Hevea sp. the production of a blue fluorescing phytoalexin is induced by various fungi. This compound is shown by chromatographic and spectrophotometric means to be scopoletin. [ABSTRACT FROM AUTHOR]

The witches' broom disease has been recently observed on poplars in Paris and its suburbs. The incidence of the disease appeared to be considerably high along main roads. The electron microscopic examination of 350 nm thick sieve tube sections revealed the presence of wall-less mycoplasmalike organisms (MLOs) in diseased samples of Populus alba var. nivea Wesm. They could not be found in their healthy counterparts. [ABSTRACT FROM AUTHOR]

A little leaf disease has been observed in several plants of Eucalyptus microtheca Muell. grown in Wad Medani area, Sudan. The disease is characterized by general plant stunting, reduction in diameter and height of trunks of affected trees, yellowing and reduction in leaf size, shortening of internodes together with excessive proliferation of axillary shoots. Electron microscope observations on ultrathin sections have revealed the presence of pleomorphic bodies in the sieve elements of diseased but not of healthy plants. These bodies possess DNA strands, ribosome-like granules and a three-layered unit membrane well defined at high magnifications (>100,000) suggesting a mollicute nature of these bodies. Studies using semi-thin sections revealed the absence of helical forms. Thus, a mycoplasma-like organism (MLO) is suspected to be the agent responsible for the disease. The results are discussed with reference to the economic and environmental importance of this tree species in the Sudan and the possible threat of the disease to its cultivation. [ABSTRACT FROM AUTHOR]

During the systemic development of Plasmopara helianthi Novot. var. helianthi Novot. the hyphae in the stem advance especially through the intercellular spaces of loose parenchyma forming haustoria in adjacent cells. The hyphae which reach leaf blades through petioles continue their growth along the main veins intercellularly in non-vascular tissues enclosing the vascular bundles. At the same time, the hyphae spread to intercellular spaces of spongy parenchyma where the growth is limited by the veinlets resulting in angular chlorotic lesions. Under humid conditions the sporangiophores arising from the aggregated hyphae in a sub- stomatal cavity emerge through the stomatal pore on the lower side of the leaf and zoosporangia are borne terminally on sporangiophores. Soon after biflagellated zoospores are liberated into distilled water from the zoosporangia, they retract their flagellae and then lyse. [ABSTRACT FROM AUTHOR]

A strain of Guignardia citricarpa Kiely was isolated from infected mango (Mangifera indica L.) leaves. The morphological and physiological characteristics of perithecia and ascospores were identical with those described for G. citricarpa. Inoculated leaves developed lesions 7 to 10 days after ascospore germination. Young lesions appeared as minute, sunken, blackish depressions on upper and lower leaf surfaces. Mature lesions were roughly circular ranging from 1 to 2 mm in diameter. The fungus was consistently reisolated from the lesions which appeared on the leaves, arising from inoculation. Benomyl at 1.7 g/1 provided control of black spot. [ABSTRACT FROM AUTHOR]

On naturally with Botrytis cinerea Pers. infected and artificially inoculated outdoor- and greenhouse-plants of Fuchsia hybrida the extra- and intramatrical formation of the B. cinerea- chlamydospores was investigated. The chlamydospores served 1. as structures of survival, which were tested with regard to their tolerance of drought, nutrient- and oxygen-deficiency, attack by bacteria and pH-requirements. 2. The chlamydospores represented dispersal units, which were capable of germination. 3. The chlamydospores could function as structures of infection, because after chlamydospore germination the outgrowing mycelium -- either directly or after production of macroconidia -- could serve as secondary inoculum and start new infections. [ABSTRACT FROM AUTHOR]

Young leaves of rice bean produced relatively more fungitoxic compound(s) than the older leaves. Epicotyls, roots, mature leaves and pods, but not cotyledon and cotyledonary leaves, synthesized the antifungal compound(s) following inoculation with a non-pathogen of this plant. Epicotyl segments when chopped or pinpricked produced the phytoalexin. Treatment of epicotyls with a dilute concentration of various chemicals caused induction of the fungitoxic compound(s). Induction by inoculation, injury and chemicals suggest a phytoalexin nature of the compound. Presence of phaseollin in the extracts of inoculated, injured or chemical-treated epicotyls has been demonstrated. [ABSTRACT FROM AUTHOR]

The elicitation of pathogenesis on potato tuber slices by 6 strains of Erwinia carotovora ssp. atroseptica was investigated by neutral red vital staining and has been compared with bacterial growth rate, penetration ability, enzyme production and enzyme spectrum. The induction of enzyme synthesis (particularly, of the extracellular polygalacturonase) elicites the rot attack on tuber tissue and this requires a sufficient bacterial density. Due to wound healing, the inductors of enzyme production are removed, and after 48 h enzymes do not attack tuber tissue any more. Therefore, growth rate and penetration ability (to get the necessary bacterial density and inductor substances) may limit virulence. A similar influence of enzyme production and enzyme spectrum of the strains on the virulence was not detected. [ABSTRACT FROM AUTHOR]

Two cultivars of Cymbidium orchid were mechanically inoculated with Odontoglossum ring- spot virus (ORSV) and Cymbidium mosaic virus (CyMV), individually and in combination. ORSV was found to have an infection rate of 70% (as determined by ELISA), but seldom induced easily discernable leaf symptoms. CyMV had an infection rate of only 20%, but infected plants invariably produced a pronounced leaf mosaic either with or without necrotic streaks. Both viruses were found to reduce plant growth, the effects of CyMV being more severe than those of ORSV. [ABSTRACT FROM AUTHOR]

Toxic protein-lipopolysaccharide complexes (PLPC) were isolated from culture filtrates of Verticillium albo-atrum (isolate WCS 800) and V. dabliae (WCS 070) isolates, both virulent to tomato and potato cultivars, and from an isolate of V. albo-atrum (V22W) which was non-virulent to these hosts. The virulent isolates each produced one major PLPC in culture and the non-virulent isolate produced two (fractions 1 and 2, characterized by their elution pattern after gel filtration). Virulence in these three isolates was not related to quantity of PLPC produced in culture. However, PLPC from the virulent isolates were toxic to tomato in a leaf bioassay at 4 μg ml-1 (WCS 800) and 20 μg ml-1(WCS 070) but the two PLPC from the non-virulent isolate required concentrations of 100 and 1000 jug ml"1 for toxicity. Production of a modified, less toxic PLPC in V22W may partly account for its non-virulence. Gel filtration of PLPC from the three isolates on a calibrated Sephacryl S-400 column, eluted in phosphate buffer plus NaCl, indicated a compound of heterogeneous molecular mass with an average of 126,000 daltons for the PLPC of WCS 800, WCS 070 and fraction 1 of V22W, and 25,000 daltons for fraction 2 of V22W. Attempts to extract a low molecular weight toxin from the PLPC by extended dialysis were unsuccessful. The susceptibility of 12 tomato and 19 potato cultivars to the Verticillium isolates was compared with their sensitivity to PLPC. Susceptibility was not correlated with toxin sensitivity and the PLPC were concluded to be non-specific toxins in these hosts. [ABSTRACT FROM AUTHOR]

Six fungicides were used either alone or in binary combination to control Fusarium solani f. sp. phaseoli. Of the three methods of application used, seed treatments and soil drenches were the best, although phytotoxicity was evident in some instances. Application as a seed soak for 1 h proved to be the worst method with most treatments showing signs of phytotoxicity. The results are discussed with reference to the use of fungicide mixtures to control foot rot of beans. [ABSTRACT FROM AUTHOR]

Fusarium oxysporum, F. moniliforme and F. semitectum isolated from Brassica campestris var. dichotoma seeds were grown on autoclaved seeds and after several weeks of incubation the oil was analysed. All the three Fusarium species reduced oil content and altered its colour. The infested oil emitted mouldy odour and the refractive index increased. The free fatty acid content increased progressively. The saponification value increased but the iodine value decreased. [ABSTRACT FROM AUTHOR]

The accumulation of pisatin was induced non-specifically by elicitors prepared from the high molecular weight fraction (molecular weight: more than 10,000 daltons) of the spore germination fluid of three species of Mycosphaerella-phnt pathogens in pea leaves with epidermis removed, regardless of the pathogenicity of the fungi to pea. Before the elicitation of pisatin synthesis, local resistance to infection by Mycosphaerella pinodes was induced by elicitors again non-specifically in pea leaves in which wax had been removed from the leaf surface. The substance responsible for local resistance could be extracted with ethylacetate from the elicitor-containing drop diffusate which was placed on pea leaves. The substance prevented the penetration of M. pinodes through heat-killed pea epidermis, but did not affect spore germination. The suppressor prepared from the low molecular weight fraction (molecular weight: less than 10,000 daltons) of the spore germination fluid of M. pinodes counteracted the ability of elicitors to induce both phases of resistance mechanisms. [ABSTRACT FROM AUTHOR]

The changes of hydroxyproline (Hyp) content in cell wall after inoculation with Corynebacterium michiganense pv. insidiosum or Verticillium albo-atrum in 8 cultivars of alfalfa (Medicago sativa) were studied. In our experiments cultivars 'Trek' and 'Vernal'--resistant, 'Du Puits' and 'Verms'--susceptible to C. michiganense; 'Vela' and 'Maris Kabul'--resistant to V. albo-atrum, 'Sabilt' and 'Lahontan'--susceptible to V. albo-atrum were used. In resistant plants inoculated with C. michiganense none or a small increase of Hyp content in comparison with control plants was registered. On the other hand, inoculated susceptible plants showed markedly increase of Hyp content in comparison with the control plants. The differences in Hyp content between control and inoculated resistant and susceptible plants with V. albo-atrum were not markedly expressed in comparison with the alfalfa--C. michiganense pair. The changes had similar tendency both in C. michiganense and V. albo-atrum.--alfalfa pairs. [ABSTRACT FROM AUTHOR]

An enzyme-linked antigen distribution assay (MAKLER et at. 1981) was used to detect and to visualize the location of the lentil strain of pea seed-borne mosaic virus, a non-persistently transmitted potyvirus, on dissected vector stylets. [ABSTRACT FROM AUTHOR]