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Use of insecticides has been questioned due to their harmful effects on edible items. Biological control of insects along with other effective practices for checking spread of parasites on crops are discussed. (PS)

In the light of new knowledge about insecticides, future research should be conducted by plant and insect physiologists together. Plant physiologists should explain what characteristics in plants attract insects and insect physiologists should study adaptive patterns of insects and combine their knowledge to control insects. (PS)

Describes several simple and inexpensive experiments designed to facilitate the study of normal and abnormal morphogenesis in the biology laboratory. Seedlings of the common garden pea are used in the experiments, and abnormal morphogenesis (tumors) are induced by a virulent strain of the crown-gall organism, Agrobacterium tumefaciens. (JR)

Insect-transmitted plant pathogens threaten crop production and conservation of natural habitat. Despite decades of research aimed at controlling these pathogens in crops, our understanding of vector behavior and ecology and genetic diversity beyond the borders of agriculture is lacking, limiting the efficacy of disease management efforts. This dissertation explores these three factors with regard to the transmission of viruses and fastidious bacterial pathogens by phloem-feeding insects in the suborder Sternorrhyncha. In chapter 1, I report how treating cultivated melon with a synthetic plant hormone analog affects symptom induction by two phylogenetically distant viruses, and how this alteration in symptoms may influence vector behavior in ways that decrease pathogen spread. This work demonstrates the potential utility of disease management tools that mitigate symptom development and disrupt transmission-enhancing vector behaviors, rather than solely controlling vector populations or breeding host plants for resistance. In Chapter 2, I pivot to investigate the ecology and population genetics of the bacterial pathogen Candidatus Liberibacter solanacearum (CLso) and its vector, the potato psyllid (Bactericera cockerelli), in natural plant communities in southern California. I report that CLso and potato psyllids commonly associate with the native perennial Solanum umbelliferum, but these CLso and potato psyllid populations are both genetically distinct from and more diverse than their counterparts in agricultural fields. This suggests that multiple sympatric, but genetically isolated populations of potato psyllid may exist in California, with members of these psyllid populations, and CLso, only rarely moving between crop and wild habitats. In Chapter 3, I tested this hypothesis by sampling potato psyllids from both native and crop plant hosts throughout the state of California. I used restriction enzyme-associated DNA-sequencing (RADseq) to assess genetic connectivity between these psyllid populations and evaluated their CLso infection status, to better understand the importance of different potato psyllid genotypes in spreading CLso. Results of this study greatly improve our understanding of CLso and potato psyllid distribution and genetic diversity in an understudied portion of the country. They confirm that studying plant pathogens and their insect vectors in natural habitats could drastically enhance our ability to forecast and manage future outbreaks of plant disease.

Polyploidy or whole-genome duplication (WGD) is a ubiquitous phenomenon in the evolutionary history of land-plants. As WGD often induces many new novel, adaptive, or transgressive phenotypes, it can have cascading ecological effects on biotic interactions and potentially the microbiome. There is a growing body of research on the impact that the microbiome plays in plant ecology, but few studies have looked at the potential interactions between ploidy, microbiomes, and pathogens in shaping the ecology of newly established polyploids. This study uses synthetic auto-tetraploid Arabidopsis accessions and a synthetic microbiome representative of natural commensal bacteria in order to assay how these interactions impact host phenotype with respect to pathogen response. In Chapter 1, I describe how the induction of polyploidy does not change the beta diversity of the phyllosphere but does alter the selection of various taxa of the synthetic community. In Chapter 2, I describe a phenomenon whereby polyploids fare better than diploids when treated with a pathogen regardless of inoculation with a protective microbiome, but where diploids treated with a microbiome better arrest the growth of pathogens than the non-treated diploids. In Chapter 3, I perform an RNA-Seq experiment and find a pattern where defense-associated genes are expressed less in diploid accessions than in polyploids when treated with a microbiome. Together, these chapters for the first time demonstrate that a potential consequence of whole genome duplication may be a loss of control over the composition of the microbiome. Finally in chapter 4, I review and synthesize the literature on somatic polyploidy to assess whether endopolyploidy and whole-genome duplication have shared underlying evolutionary rules.

To efficiently protect themselves against pests and disease, plants surveil for attacking organisms and upon recognition, activate protective inducible defenses. Here, I present my work on the regulation and function of maize inducible defenses by integrating genetic, transcriptomic and physiological approaches. This work elucidated mechanisms underlying three layers of the maize immune response, including: (1) A novel genetic locus associated with sensitivity to exogenous herbivore-associated elicitors of the fatty-acid amino-acid conjugate (FAC) family, (2) regulatory function of phytocytokines from the Plant elicitor peptide (Pep) family, and (3) biosynthesis of antibiotic specialized metabolite defenses. Early maize signaling events triggered in the context of herbivory, were probed through comparative transcriptomic analyses upon treatment with ZmPeps and FACs, indicating a largely shared signaling pathway and identifying specific genes involved in antiherbivore defense. Genetic mapping using the Intermated B73 x Mo17 mapping population derived from B73, an FAC sensitive line, and Mo17, an FAC insensitive line, identified a single locus on chromosome 4 associated with FAC sensitivity that was further fine-mapped to a region containing 19 genes. A candidate gene within this region, FAC SENSITIVITY-ASSOCIATED (FACS), was expressed at significantly lower levels in the insensitive parent line, and heterologous expression of FACS increased FAC sensitivity in Nicotiana benthamiana, suggesting a role in regulation of FAC-induced responses. Work characterizing the maize ZmPep family led to several new insights into Pep signaling mechanisms: Maize Pep precursors (PROPEPs) were found to contain multiple nested active peptides, a phenomenon not previously observed for this family. Additionally, in contrast to Peps in Arabidopsis, individual maize Peps were found to have specific activities defined by the relative magnitude of elicited responses through rheostat-like tuning of phytohormone levels. Finally, peptide structure-function analysis and physiological assays identified ZmPep5a as a potential antagonist peptide. Finally, we report on the development of an R Shiny web-application that was developed to facilitate mutual rank-based coexpression analyses integrating user-provided supporting information. The utility of this user-friendly app was demonstrated through application to define two new biosynthetic pathways for maize terpenoid antibiotics.

Sudden Oak Death (SOD), caused by the oomycete pathogen, Phytophthora ramorum, is an introduced forest disease causing large-scale tree mortality in the oak woodlands of California. Pathogen dynamics are bound to be affected by site ecology, forest structure and composition and by interactions among sympatric pathogens. In the four chapters included in this dissertation I address various aspects of the both ecology and epidemiology of the Sudden Oak Death disease, including the competition between three sympatric species of Phytophthora, the population structure of the P.ramorum on its three main hosts, California bay laurel (Umbellularia californica), tanoak (Notholithocarpus densiflorus) and coast live oak (Quercus agrifolia), and at sites with different levels of disease incidence and the population structure of isolates found in two different substrates, soil and bay laurel leaves, in various weather conditions. Using molecular tools coupled with an intensive multi-year field sampling approach, all within a coastal California watershed with a relatively long and uniform history of disease presence, I determined the following: When in competition with other Phytophthora species, specifically P. nemorosa, P. ramorum prevalence increases to levels higher than those of the competing species when abundant rainfall triggers its sporulation. Despite P. nemorsa having a broader geographic range, it exhibits a narrower ecological amplitude and, in any given region, occupies fewer sites than P. ramorum. Results additionally suggest that, perhaps due to priority effects, P. nemorosa can persist at levels comparable to those of P. ramorum in ecologically suitable plots when climate favors P. ramorum dormancy.Shifts in weather, primarily levels of rainfall are accurate predictors in the likelihood of both bay laurel and oak infection as well as transitions between dormant and active infection of the pathogen itself. Additionally site specific factors such as aspect, bay laurel density and bay laurel basal area drive differences in levels of both disease incidence and prevalence on both bay laurel and oak hosts. For oaks specifically, infection rates are greater among larger trees, yet levels of mortality are greater among smaller trees. Neighborhood effects such as proximity to infected bay laurel foliage, and surrounding bay laurel density and basal area are important factors in predicting oak infection. Ten microsatellites were used for genetic analyses on cultures from successful isolations to determine differences in population structure between different substrates, namely populations isolated from soil versus aerial populations isolated from bay laurel leaves in various weather conditions. Migration of genotypes among sites was low and spatially limited during dry periods, but intensity and range of migration of genotypes significantly increased for leaf populations during wet periods. Only leaf genotypes persisted significantly between years, and genotypes present in different substrates were distributed differently in soil and leaves. It was concluded that epidemics start rapidly at the onset of favorable climatic conditions through highly transmissible leaf genotypes, and that soil populations are transient and may be less epidemiologically relevant than previously thought.Population structure of the pathogen in each of the three main hosts was examined to provide evidence of contagion pathways among hosts, as well as differences in population structure in wet vs. dry years and at sites with various levels of disease incidence and prevalence. The relationships among P. ramorum populations in bay laurels, oaks and tanoaks were analyzed and structure was found to exist among hosts. It was determined that bay laurel is the source population for both tanoak and oak infection, and that tanoak contributes minimally to oak infection. In spite of their common source of inoculum, oaks and tanoaks were found to be sinks that select for different pathogen genotypes, due to the variance in selection pressure in each host type. Additionally, different sites supported a dominance of different genotypes, more genotypes overall and more persistent genotypes, when compared to other sites, and these ‘hotspots’ are likely to play a more significant epidemiological and evolutionary role for the pathogen.Together these results help to advance the state of knowledge surrounding the ecology, epidemiology and population genetics of the Sudden Oak Death pathogen in California, add to the growing body of research on invasive plant pathogens, support theories of invasion biology and most importantly can be applied to regulatory and land management practices in attempt to mitigate the spread of this disease. Chair Date

Oomycetes, a class in the kingdom Stramenopila, are filamentous eukaryotic microorganisms that are known informally as water molds, but have adapted to many environmental niches. Phytophthora, an oomycete genus of approximately 100 plant-pathogenic species, has specifically adapted to several environmental niches. Environmental conditions play an influential role in the development of Phytophthora, particularly in sporangium formation. Sporangia, the main driver of Phytophthora epidemics, are especially susceptible to damage by environmental conditions, such as light-induced DNA lesions or desiccation by drying. Variable by species, light can stimulate (e.g. P. infestans) or repress (e.g. P. capsici) the production of sporangia. Light may have two developmental roles: an early pre-sporangiophore induction signal, and a later post-sporangiophore repression signal. In this work, I found that although many types of photoreceptors are described in eukaryotes, Phytophthora genomes encode only cryptochrome photoreceptors. The foliar-adapted species P. infestans encodes three cryptochromes, while the soilborne species P. capsici encodes two cryptochromes. Silencing of the P. infestans gene encoding cryptochrome PITG_01718, which lacks an ortholog in P. capsici, inhibits sporulation. While cryptochromes have traditionally been described in other organisms as blue light receptors, each red and blue light represses P. infestans sporulation. In contrast, P. capsici sporulation responds to blue light but not red light. This work also describes the use of RNA-seq to study the genetic control of sporulation by light and humidity. Constant light was found to repress the expression of genes induced in the post-sporangiophore stage by P. infestans, while constant darkness repressed the expression of genes in the pre-sporangiophore stage in P. capsici. Humidity also had a strong effect on repressing gene expression in the pre-sporangiophore stage of sporulation in P. infestans. This work also describes that specific types of nitrogen starvation induce sporulation. In addition to advancing our knowledge of sporulation control in oomycetes, this work also provides a better understanding of the homology-based gene silencing method. While this technique is an effective method for functional genomics in Phytophthora, work in this dissertation shows that the technique must be used with prudence due to the frequency of off-target effects.

Read it on medium (recommended). In the unending coevolutionary dance between plants and microbes, each player impacts the evolution of the other. This article provides an overview of the burgeoning field of Evolutionary Molecular Plant-Microbe Interactions (EVO-MPMI), tracing its progression from foundational science to practical implementation. It delves into central concepts and methodologies, and offers a snapshot of current research. Moreover, the review sheds light on the practical applications of EVO-MPMI, particularly within the realm of disease control. Looking ahead, we discuss potential future trajectories for EVO-MPMI research, spotlighting the innovative tools and technologies propelling the discipline forward.

The plant cuticle is a waxy, hydrophobic coating found on all aerial non-woody plant tissue and serves as a physical barrier protecting the plant from environmental stresses including pathogen infection, dehydration, and UV radiation. Studies on the plant cuticle in various plant model systems show differences in ultrastructure and chemical composition across different plant species, and even within a species, depending on many factors: organ identity, developmental stage and growth conditions. Little functional analysis has been performed to characterize the cuticle’s relationship to pathogen resistance in adult Zea mays, thus leaving the agronomic impact of the cuticle on the adult-stage plant health largely unknown. Maize glossy mutants have defects in cuticle production—examples include lines with impaired levels of lipid biosynthesis or wax transport proteins, making them effective tools to study the cuticle’s impact on pathogen resistance.In this study, we take a panel of glossy mutants and observe their differences in early stages of pathogen resistance to Cochliobolus heterostrophus and Colletotrichum graminicola, causal agents of Southern Leaf Blight and Anthracnose Stalk Rot, respectively. After establishing methods to observe and quantify GFP-labelled strains of these fungal infections on adult plants, which include fungal adhesion and long-term visual lesion formation, we detected differences in pathogenicity and cuticle wax profiles among our tested glossy mutants by utilizing epifluorescence microscopy, fungal quantification and gas chromatography/mass spectrophotometry. Combined with preliminary data on fungal penetration with confocal microscopy, these results will guide further investigation in elucidating the relationship between adult maize cuticle and pathogen resistance.

Keynote address at the13thArab Congress of Plant Protection, Hammamet, Tunisia, 17 October 2022. Plant health vision for the 21st century: new knowledge and approaches. Sophien Kamoun, The Sainsbury Laboratory, Norwich, United Kingdom. رؤية الصحة النباتية للقرنالحادي والعشرين: معرفة وأساليب جديدة.سفيان كمون، مختبر سانسبري، نورويتش، المملكة المتحدة Summary (rough outline): * Plants diseases increased in frequency due to a number of factors * Case study: blast diseases. First, wheat blast * Magnaporthe oryzaehas many host-specific lineages; two are pandemic * How wheat blast ermerged in the 1980s after a host jump from wild grass * Wheat blast has been pandemic since 2016 * Heightened risk as wheat blast is seed transmitted, many countries import wheat from Brazil and germplasm movement can be an issue * Wheat blast appearedin Zambia in 2017/18 (but was only reported in 2020, more on that later) * We rallied the community (again) with openwheatblast; all contributors published their reports on Zenodo * Then the reports were compiled into afull paper * Pandemic wheat blastlineage is a clonal lineageout of a diverse South American population; spread twice out of South America * We learned quite a few things from genomics, including mating type and risk of sexual recombination in Africa * Now to rice blast; 3 pandemic lineages that are centuries old * We wanted to sample in a well-studied region of the world; field trip from Germany to Italy * 950 samples collected; used fast cheap MonsterPlex; ~20% samples positive for blast fungus * blast was also found in Germany! * German isolates can infect barley and wheat in the lab * Blast ticks 3 boxes of the main causes of plant health outbreaks; may be 4th soon with the Ukraine war resaping trading routes * Take home messages * Now back to the start—plant health emergencies—are we well prepared? What are the challenges? * Too many outbreaks poorly diagnosed; unacceptable in the genomics era * We can’t wait, sequence now, as with nextstrain influenza, COVID etc. * GSS called for massive increase in genome sequencing few years ago but it’s not happening; and if it’s happening it’s not being shared with the community #FAIL * Blog post:enough excuses; two cases of failure: Sicily stem rust and Zambia wheat blast * ACTIONS that can be taken now * ISPP code of ethics to be voted next year in Lyon, I hope your society will sign up * A reminder that we are in a new world of scholarly publishing; open science doesn’t mean you don’t get credit for your work; good for ECRs * A plug for GetGenome to address inequity but also to educate about open science * A new publishing culture? YOU can make it happen

Accessible Science Talks 2022 Annual Science Meeting, Norwich Research Park Illustrating the world of plants and their biotic environment Lives on earth are living in a close association with other organisms, especially the plant holobiont is a complex system in balancing the beneficial and pathogenic interactions. In contrast to animals, the non-mobile property makes plants more resilient to the surrounding environment. While plants have developed multilayered immune system to protect themselves, as a counter-act, microbes evolved effectors and other strategies to regulate host performance for successful colonization. The crosstalk between host plants and microbes shaped today’s plant biology, ecology, and evolution. We all appreciate plants in our lives: they served as life essentials, as ornamentals, and as a factor in the changing seasons. However, people might never have had a glance into the micro-universe of plants and its associated microbes. With the aid of scientific illustration, the visual communication bridge the gap between technical and conceptual. Researchers could share knowledge and their findings in an accessible approach to a wide range of audiences. This talk introduces the fascinating world of molecular plant-microbe interactions in a pictorial way, plus a brief guide for developing graphical abstracts. About the speaker: Hsuan Pai Pai is a technician at The Sainsbury Laboratory. As a scientist, she helps the team to work on deciphering the plant immune networks. When off from academic, she enjoyed drawing and crafting, and is interested in communicating scientific concepts through illustrations., This is a Zenodo publish version of the slides used in 2022 RSSV Annual Science Meeting talk in Norwich Research Park. Please cite the DOI when using information/images from the slides. For the reference images used in this presentation, all rights reserved to the original authors.

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.

American ginseng (Panax quinquefolius) is a highly valued perennial crop grown for its roots during a four-year cultivation cycle. American ginseng is subject to ginseng replant disease (GRD) in which severe root rot develops in newly planted ginseng grown in a former ginseng garden. A common strategy to mitigating GRD is not available and techniques such as fumigation, fungicides, and biocontrol are ineffective, banned, or are slowly being phased out. Alternatively, soil solarization is a pre-plant technique used to treat soil to reduce disease inoculum and alter soil microbiomes. In summer 2019, a six-week soil solarization experiment was conducted in a former ginseng garden using 24 randomized-plot design comparing solarization duration (zero, two, four, six weeks). In this study, a microbiome analysis was conducted using DNA extracted from solarized ginseng garden soils to determine whether soil solarization altered the microbiome in a former ginseng garden.

The thorny politics of the global food trade are often an excuse against the application of open science principles to plant disease epidemics. But scientists have often themselves to blame for the slow release of information and data, and there are ways around some of the issues.

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.

Büyükada, İstanbul’un en önemli doğasal ve turistik merkezlerinden biridir. Adalar’da yeşil örtünün korunmaya çalışılmasına rağmen son yıllarda artan çevresel problemlerin yanında artan antropojenik baskılar ve etkilerden dolayı ağaçlarda da tahribat ve hastalıklar hızlı bir yükseliş göstermiştir. Bu hastalıklar Büyükada’ya peyzaj değeri katan canlı ağaçların kalite ve görünümlerini bozacağı gibi, çoğu tabii anıt olan bu ağaçları yok olma tehlikesiyle karşı karşıya getirmektedir. Hastalıkların artmasının diğer olumsuz yönü de bu hastalıkların Büyükada’da Avrupa’nın en büyük ahşap eseri olan yetimhanenin, birçok köşk, villa, yalı ve bazı devlet kurum binalarının ahşap kısımlarında yaptığı ve yapacağı tahribatlardır. Bu çalışmada Büyükada’daki canlı ağaçlarda tespit edilen “odun çürüklüğü” yapan mantarlar incelenmiştir. Çalışmada belirlenen odun çürüklüğü yapan mantarlar tespit edilip, beyaz çürüklük, esmer (kahverengi) çürüklük ve yumuşak çürüklük yapan mantarlar şeklinde sınıflandırılmıştır. Çalışmada Basidiomycota (26) ve az sayıda Ascomycota üyesi (2) mantar tespit edilmiştir. Büyükada’da çok sayıda ağaçta tespit edilen beyaz çürüklük mantarlarından, Stereum hirsutum, Schizophyllum commune, Ganoderma applanatum, Trametes versicolor ve Porodaedalea pini mantarlarının çok sayıda ve yaygın olduğu görülmüştür. Çalışmanın en önemli sonuçlarından biri de çok sayıda hastalıklardan dolayı tamamen kurumuş ve kesilmek zorunda kalınmış ağaçlar olduğunun görülmesidir. Bu sonuca göre Büyükada’da ciddi bir ağaç tedavisi ve restorasyonu yapılması, ahşap binaların ahşap kısımlarının emprenyelenmesi veya boyanmasının zorunlu olduğu tespit edilmiştir. Buyukada, is one of the most important natural and touristic centers of Istanbul. Despite the efforts to protect the vegetation on the islands, the damage and diseases in the trees have shown a rapid increase due to the increasing environmental problems as well as the increasing anthropogenic impact in recent years. These diseases will deteriorate the quality and appearance of trees that add landscape value to Buyukada, and bring these trees, most of which are natural monuments, in danger of death. Another negative aspect of the increase of diseases is the destructions on the wooden parts of the biggest wooden structure of Europe; the orphanage, mansions, villas, and government buildings. In this study, the fungi that cause "Wood decay" detected on living trees in Buyukada. Wood decay fungi were determined in the study and classified as white, brown and soft rot. Basidiomycota (26) and a small number of Ascomycota members (2) were found. Among the white rot fungi detected in many trees, white rot fungi such as, Stereum hirsutum, Schizophyllum commune, Ganoderma applanatum, Trametes versicolor and Porodaedalea pini fungi have been seen to be numerous and common. One of the most important results of the study is also that it is seen that there are many trees; these have completely dried up and had to be cut because of the diseases. Therefore, it was determined that a serious tree treatment and restorations should be carried out in Buyukada, and the wooden parts of wooden buildings should be impregnated or painted.

Digital Image Processing (DIP) applications in agriculture sector is becoming popular because of its fast, cost-effective and accurate solutions related to diseases and marketing. The hands-on solutions are being provided through various applications. Leaf Sopot disease has become the major constraint in the turmeric cultivation in India. Colletotrichum capsici is a fungal disease commonly known as leaf Spot. The brown spots of 4-5 cm length and 2-3 cm width with a grey centre are found on either surface of the leaves. If not treated timely, it causes the heavy loss in terms of quality and quantity. This paper proposes the methodology using Image Processing for measuring the severity of this disease in plant pathology. The image acquisition of infected leaves is done in the first stage then the images are pre-processed. Histogram is used for colour feature extraction The Edge detection methodology is used for infected area measurement and the results are fed to disease classifier to identify the stage of disease. This helps the plant pathologist in preparing consultative module to eradicate the disease completely.

Summary In this work, we found that tomato and guava plants infected with Meloidogyne enterolobii showed different Fourier-transformed infrared spectral patterns compared to non-infected plants. Additionally, by using two-dimensional correlation spectroscopy (2D-COS) we were able to track and explain those spectral differences according to the progression of the nematode infection in the plants. In general, 2D-COS reveals the same chain of changes in both tomatoes and guavas when under nematode infection. There is a decrease in bands representing amino acids and proteins, fatty acids and lipids are down-regulated, and sugars and total phenols increase in leaves of infected plants. The application of this technique provides useful information on the metabolic and biochemical changes in plant tissues when diseased in a rapid manner. This technique could be used in the future, combined with other methods, to improve field diagnosis, quality control, or to reduce analytical time for biochemical purposes.

The genus Gliocephalotrichum (Nectriaceae), originally described as a soil-borne fungus, has been associated with postharvest diseases, especially of tropical fruits. Taxonomic studies using both morphological and molecular phylogenetic analyses have contributed to recognition of novel species in several countries. However, in Brazil, only three isolates of Gliocephalotrichum have been collected from soil samples and roots since the late 1970s. Our study expands the sample range using many Gliocephalotrichum isolates obtained from rotting fruits of tropical plant species in different states of Brazil. Polyphasic taxonomy was assessed with phylogenetic analyses of DNA sequences from four nuclear loci, morphological comparisons, and pathogenicity tests. As a result, three known species (G. bulbilium, G. longibrachium, and G. simplex) were identified from new hosts and locations in Brazil. In addition, three new species are described—G. abrachium, G. brasiliense, and G. caryocaris. A key to all Gliocephalotrichum species worldwide is provided. Although species of Gliocephalotrichum have not been considered to be important plant pathogens, this study shows they may cause postharvest fruit rot in tropical fruits and therefore have an impact in communities that depend economically on the harvest and sale of these fruits. Coordenação de aperfeiçoamento de pessoal de nivel superior/[]/CAPES/Brasil Conselho Nacional de Pesquisa[]/CNPq/Brasil Fundação de Apoio a Pesquisa do Distrito Federal/[0193.000825/2015]/FAP-DF/Brasil Fundação de Apoio a Pesquisa do Distrito Federal/[193.000.512/2018-57]/FAP-DF/Brasil UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA) UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biología

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.

To better understand the evolution of virulence we are interested in identifying the genetic basis of this trait in pathogenic fungi and in developing tools for the rapid characterization of variation in virulence among populations associated with epidemics. Fusarium oxysporum f. sp. vasinfectum (FOV) is a haploid fungus that causes devastating outbreaks of Fusarium wilt of cotton wherever it is grown. In the United States, six nominal races and eleven genotypes of FOV have been characterized based on the translation elongation factor (EF-1α) gene and intergenic spacer region (IGS), but it is unclear how race or genotype based on these regions relates to population structure or virulence. We used genotyping-by-sequencing to identify SNPs and determine genetic diversity and population structure among 86 diverse FOV isolates. Six individuals of Fusarium oxysporum closely related to FOV were genotyped and included in some analyses. Between 193 and 354 SNPs were identified and included in the analyses depending on the pipeline and filtering criteria used. Phylogenetic trees, minimum spanning networks (MSNs), principal components analysis (PCA), and discriminant analysis of principal components (DAPC) demonstrated that races and genotypes of FOV are generally not structured by EF-1α genotype, nor are they monophyletic groups with the exception of race 4 isolates, which are distinct. Furthermore, DAPC identified between 11 and 14 genetically distinct clusters of FOV, whereas only eight EF-1α genotypes were represented among isolates; suggesting that FOV, especially isolates within the widely distributed and common race 1 genotype, is more genetically diverse than currently recognized.

During the Cold War, coffee became a strategically important crop in the global contest between the United States and the Soviet Union. The economies of many US allies in Latin America depended upon coffee. In the Cold War context, then, the coffee leaf rust ( Hemileia vastatrix) became a geopolitical problem. Coffee experts in Latin America, which produced most of the world's coffee, began to prepare for an outbreak. In the 1950s, they built a global network of coffee experts. This network was sustained by US-led Cold War programs that promoted technical collaboration across the Global South, such as Harry Truman's Point Four programs. We explore the network's growth and evolution through one of its central figures, the American plant pathologist Frederick L. Wellman. This network has survived the end of the Cold War and evolved to reflect the new geopolitical context.

Crop yield often varies within a field of a single genetically uniform crop plant, with the causes presumed to be a mix of both biotic and abiotic factors. Manipulating crop root mycobiomes could potentially increase yield by reducing pathogen impacts and improving access to soil water and nutrients. This study aimed to identify different fungal inoculation treatments that could increase the growth of corn seedlings sown in low productivity soils to that in high productivity soils and shift the root mycobiome composition. Fungal inoculation treatments did not have significantly different root mycobiome composition than seedlings grown in low yield control soils. However, indicator species varied across primary inoculation treatments and controls. Although corn grown in an autoclaved substrate showed growth promotion with the fungal inoculant Fusarium oxysporum, no fungal inoculant added to low productivity soils resulted in a similar yield to that of seedlings grown in high productivity soils.

Chloroplasts are essential semi-autonomous organelles that regulate energy production, metabolites synthesis, signal transduction, and stress response in plants and algae. They are responsible for photosynthesis, a process that converts carbon dioxide and water to sugars and oxygen, using light to support nearly all organisms on Earth. Despite their functional importance and their ability to perform transcription and translation within themselves, the chloroplast genome size is very small. Consequently, proper function of the chloroplasts largely relies on anterograde signaling from the nucleus. The mechanisms that regulate the import of nucleus-encoded proteins into chloroplasts have been extensively studied. However, much less is known about nucleus-encoded RNAs imported into chloroplasts, and it has been unclear whether chloroplast RNAs are modified for their proper function. In addition to their function in energy production, chloroplasts are also significant in plant defense. Retrograde signaling of the chloroplast can reprogram numerous nucleus-encoded genes which are involved in plant immunity. Chloroplasts are capable of modulating levels of defense-related molecules by controlling photosynthesis. This project had its beginnings in a study in which our lab discovered the target of a bacterial-induced small RNA: Arabidopsis thaliana protein containing an RNA-binding domain abundant in Apicomplexans (AtRAP). Two separate approaches were taken to further study the function of AtRAP: 1) AtRAP was characterized as the target protein of a siRNA induced by bacteria Pseudomonas syringae pv. tomato (Pst) (avrRpt2). We show that AtRAP acts as a negative regulator of plant defense by using loss-of-function and gain-of-function analysis. AtRAP functions through direct interaction with Low Sulfur Upregulated 2 (LSU2), a positive regulator of plant defense. AtRAP also regulates transcription factor GOLDEN2-LIKE 1 (GLK1) that is involved in plant biotic and abiotic stress responses. Thus, this approach aims to study the functional mechanism of AtRAP in plant immunity. 2) AtRAP was characterized as a chloroplast-localized RNA-binding protein. By characterizing AtRAP-associated RNAs, we discovered a group of nucleus-encoded RNAs, which are translocated into chloroplasts. Further structural analysis suggests that many of these AtRAP-bound chloroplast-localized nuclear RNAs are small nucleolar RNAs (snoRNAs). These nucleus-encoded snoRNAs are imported into chloroplasts, where they methylate chloroplast-encoded rRNAs and mRNAs. Thus, this approach aims to study the translocation and function of nucleus-encoded RNAs, mainly snoRNAs, inside chloroplasts.

Aphids are the primary vector of plant viruses. Transient aphids, which probe several plants per day, are considered to be the principal vectors of non-persistently transmitted (NPT) viruses. However, resident aphids, which can complete their life cycle on a single host and are affected by agronomic practices, can transmit NPT viruses as well. Moreover, they can interfere both directly and indirectly with transient aphids, eventually shaping plant disease dynamics. By means of an epidemiological model, originally accounting for ecological principles and agronomic practices, we explore the consequences of fertilization and irrigation, pesticide deployment and roguing of infected plants on the spread of viral diseases in crops. Our results indicate that the spread of NPT viruses can be i) both reduced or increased by fertilization and irrigation, depending on whether the interference is direct or indirect; ii) counter-intuitively increased by pesticide application and iii) reduced by roguing infected plants. We show that a better understanding of vectors’ interactions would enhance our understanding of disease transmission, supporting the development of disease management strategies., Author summary A range of both experimental and theoretical studies show that the behaviour and population dynamics of insects depend strongly upon interactions with other insect species. These interactions have the potential to greatly affect the dynamics of insect-vectored plant disease, as transmission of viruses is intimately dependent on the local density of vectors, as well as how they select and move between potential host plants. Surprisingly, the effects of interaction between vector species on epidemics remains little studied and even worse understood, probably because experimentation is costly and difficult. Here, we present a model which permits us to investigate the effect of interaction between a virus, two vector species and the host plant on the spread of viral disease in crops. In this study, our model is used to explore the consequences of common agronomic practices on epidemics. Our study highlights the importance of exploring vectors’ interactions to enhance the understanding of disease transmission, supporting the development of disease management strategies.